diff --git a/mappings/scdo-sssom-xrefs-rename.tsv b/mappings/scdo-sssom-xrefs-rename.tsv index f1a8aeb..fc1ce69 100644 --- a/mappings/scdo-sssom-xrefs-rename.tsv +++ b/mappings/scdo-sssom-xrefs-rename.tsv @@ -1,687 +1,687 @@ subject_id object_id -SCDO:0007198 DOID:2326 -SCDO:0008484 DOID:1826 -SCDO:0008927 NCIT:C35152 -SCDO:0000654 HP:0002170 -SCDO:1000438 HP:0010876 -SCDO:0001233 NCIT:C3439 -SCDO:1000672 GSSO:000109 -SCDO:0000207 HP:0002181 -SCDO:0001038 HP:0000763 -SCDO:0001116 NCIT:C93407 SCDO:1000666 HP:0004379 -SCDO:0004437 HP:0030248 -SCDO:1000011 NCIT:C84980 -SCDO:1000665 HP:0012379 -SCDO:0008348 HP:0000951 -SCDO:0009818 HP:0000118 -SCDO:0005758 HP:0012330 -SCDO:0000210 HP:0005318 -SCDO:1000404 OBI:0002557 -SCDO:0001259 NCIT:C519 -SCDO:0003119 ARO:0000006 -SCDO:0004183 NCIT:C3890 -SCDO:0001347 HP:0000079 -SCDO:0005061 NCIT:C99042 -SCDO:0000200 DOID:9220 -SCDO:1000618 HP:0001894 -SCDO:1000810 MP:0002329 -SCDO:0009334 HP:0001875 -SCDO:0000214 HP:0002341 -SCDO:1000634 MP:0005561 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HP:0002204 +SCDO:0001026 HP:0002650 +SCDO:0001038 HP:0000763 +SCDO:0001042 CMO:0000057 +SCDO:0001874 NCIT:C74096 SCDO:0000686 HP:0007340 -SCDO:1000644 UO:0000187 -SCDO:0007326 HP:0001433 -SCDO:0004802 NCIT:C3833 -SCDO:0000848 CMO:0001324 -SCDO:1000278 HP:0000820 -SCDO:0000499 CMO:0000665 -SCDO:1000473 NCIT:C91106 -SCDO:0000100 NCIT:C2890 -SCDO:0000982 HP:0001920 -SCDO:0001096 OBI:0400115 -SCDO:0007371 HP:0001931 -SCDO:0000816 HP:0001513 -SCDO:0003024 HP:0000271 +SCDO:1000382 NCIT:C115224 +SCDO:1000414 DUO:0000027 +SCDO:0001078 NCIT:C75583 +SCDO:0001103 HP:0005268 +SCDO:1000557 NCIT:C164339 +SCDO:1000881 NCIT:C40978 +SCDO:1000608 HP:0020058 +SCDO:0000446 NCIT:C92803 SCDO:0003929 NCIT:C116161 +SCDO:0000209 HP:0001342 +SCDO:1000811 MP:0005376 SCDO:1000283 HP:0011014 -SCDO:1000420 NCIT:C142494 -SCDO:1000169 NCIT:C107564 -SCDO:0004047 NCIT:C17004 -SCDO:0000795 HP:0000112 -SCDO:1000859 NCIT:C25191 -SCDO:1000358 NCIT:C84983 -SCDO:0003672 NCIT:C82909 -SCDO:0000450 STATO:0000091 -SCDO:0000707 HP:0002665 -SCDO:1000770 NCIT:C48660 -SCDO:1000168 NCIT:C114300 -SCDO:0000143 CMO:0000035 -SCDO:0000549 NCIT:C131682 -SCDO:1000275 NCIT:C126120 -SCDO:0000039 NBO:0000131 +SCDO:1000540 NCIT:C83031 +SCDO:1000359 NCIT:C16612 +SCDO:0000884 HP:0009830 +SCDO:1000411 DUO:0000022 +SCDO:0006790 NCIT:C51993 +SCDO:1000249 CMO:0000507 +SCDO:0000837 NCIT:C19228 +SCDO:0002133 HP:0000077 +SCDO:0000655 HP:0002516 SCDO:1000451 NCIT:C34887 -SCDO:1000656 MP:0011470 -SCDO:0007438 NCIT:C2905 -SCDO:0009817 HP:0012243 -SCDO:0004069 HP:0012735 -SCDO:1000752 OBI:0002140 -SCDO:1000653 MP:0011468 -SCDO:1000676 NCIT:C51776 -SCDO:1000368 HP:0011025 -SCDO:0005335 CHEBI:35493 -SCDO:1000899 NCIT:C64387 -SCDO:1000658 NCIT:C67376 -SCDO:1000491 UO:0000051 -SCDO:1000636 HP:0025548 -SCDO:0000439 OGMS:0000046 -SCDO:0001163 CMO:0000365 -SCDO:1000006 NCIT:C15900 -SCDO:0000014 CMO:0000210 +SCDO:0000095 HP:0003418 +SCDO:0005287 HP:0001744 +SCDO:0001343 NCIT:C26548 +SCDO:0001074 HP:0200042 +SCDO:0000040 NCIT:C81229 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-SCDO:0005773 NCIT:C103270 -SCDO:1000562 OPMI:0000025 -SCDO:1000246 HP:0030058 -SCDO:0000790 HP:0030050 -SCDO:1000640 MP:0010068 -SCDO:0001314 HP:0001999 -SCDO:0000477 NCIT:C28516 -SCDO:1000664 HP:0003155 -SCDO:1000642 UO:0000186 -SCDO:0001042 CMO:0000057 -SCDO:1000269 HP:0025142 -SCDO:0001024 HP:0011868 -SCDO:0000445 OGMS:0000047 -SCDO:0001072 MP:0001212 +SCDO:0005660 HP:0001903 +SCDO:1000473 NCIT:C91106 +SCDO:0007371 HP:0001931 SCDO:0000281 NCIT:C123446 -SCDO:0006790 NCIT:C51993 -SCDO:1000385 NCIT:C78254 -SCDO:1000655 MP:0011471 -SCDO:0000800 HP:0012759 -SCDO:0000933 CMO:0000211 -SCDO:1000628 UO:0000002 -SCDO:0000622 MP:0001792 -SCDO:1000382 NCIT:C115224 -SCDO:0004314 NCIT:C18133 -SCDO:0002067 DOID:813 -SCDO:0000672 HP:0001382 -SCDO:0000264 CHMO:0002580 -SCDO:0000137 CMO:0000204 -SCDO:0000512 NCIT:C84481 -SCDO:0007386 HP:0000829 -SCDO:1000311 CMO:0002079 +SCDO:1000674 NCIT:C51773 +SCDO:0000428 HP:0003457 +SCDO:0000671 HP:0000952 SCDO:0000821 ExO:0000034 -SCDO:0008043 HP:0002014 -SCDO:1000410 DUO:0000021 -SCDO:0000646 NCIT:C120254 -SCDO:0000880 ARO:0000054 -SCDO:1000564 OPMI:0000024 -SCDO:0000638 OBI:0000925 -SCDO:0000150 CMO:0000021 -SCDO:0008115 ICO:0000179 -SCDO:1000447 HP:0011897 -SCDO:0000590 HP:0003077 -SCDO:0000090 HP:0007018 -SCDO:0007437 HP:0000834 -SCDO:0000089 HP:0012444 -SCDO:0000837 NCIT:C19228 -SCDO:0005364 NCIT:C16779 -SCDO:1000200 CHEBI:23888 -SCDO:1000416 DUO:0000019 -SCDO:0005864 HP:0001889 -SCDO:0002710 HP:0005162 -SCDO:0000395 MP:0001762 -SCDO:0000015 DOID:1584 -SCDO:1000478 UO:0000000 -SCDO:0000939 NCIT:C17873 +SCDO:1000185 OGMS:0000028 +SCDO:0000075 HP:0001369 +SCDO:0000891 NCIT:C18772 +SCDO:1000652 HP:0025435 +SCDO:0002780 HP:0000818 +SCDO:0000137 CMO:0000204 +SCDO:0001233 NCIT:C3439 +SCDO:0000180 OBI:1110053 +SCDO:1000500 CMO:0000376 +SCDO:0000622 MP:0001792 +SCDO:0000467 CMO:0002520 +SCDO:0001347 HP:0000079 +SCDO:0009334 HP:0001875 +SCDO:1000567 NCIT:C168823 +SCDO:0009619 HP:0011675 +SCDO:1000265 HP:0004312 +SCDO:1000453 ICO:0000304 +SCDO:1000454 ICO:0000305 SCDO:0003789 NCIT:C62198 -SCDO:1000334 NCIT:C155932 -SCDO:0000658 HP:0001511 -SCDO:0001060 NCIT:C155310 -SCDO:0000043 NCIT:C95536 -SCDO:0000279 OGMS:0000051 -SCDO:0001673 HP:0030243 -SCDO:1000616 HP:0001872 -SCDO:0000203 HP:0002059 -SCDO:0000099 HP:0006689 -SCDO:0000308 HP:0000953 -SCDO:0008538 HP:0001935 -SCDO:0001012 NCIT:C80411 -SCDO:1000294 HP:0000478 +SCDO:1000200 CHEBI:23888 +SCDO:0000159 HP:0030049 +SCDO:0000695 NCIT:C74954 +SCDO:0007493 CHEBI:42797 +SCDO:0005809 CHEBI:35475 +SCDO:1000267 HP:0003116 +SCDO:0000439 OGMS:0000046 +SCDO:0001096 OBI:0400115 +SCDO:0000830 HP:0002164 +SCDO:0000707 HP:0002665 SCDO:0001030 HP:0001250 -SCDO:0000907 CMO:0000921 -SCDO:0001202 OBI:0001098 -SCDO:0000534 NCIT:C95504 -SCDO:0001370 IDOMAL:50000026 -SCDO:0004899 HP:0002086 -SCDO:1000567 NCIT:C168823 -SCDO:0000870 NCIT:C103526 -SCDO:1000648 HP:0012101 -SCDO:0000721 CMO:0000291 -SCDO:0002784 NCIT:C96239 -SCDO:0001109 VO:0000675 -SCDO:0006934 NCIT:C41129 -SCDO:1000622 UO:0000095 -SCDO:0004249 OBI:0000626 -SCDO:0001488 HP:0001394 -SCDO:0000013 NCIT:C98805 -SCDO:1000646 NCIT:C67015 -SCDO:0000159 HP:0030049 -SCDO:0000914 HP:0001271 +SCDO:0000673 HP:0001343 +SCDO:1000718 CMO:0000225 +SCDO:1000442 CMO:0000030 +SCDO:1000006 NCIT:C15900 +SCDO:1000367 NCIT:C16632 +SCDO:0000949 NCIT:C17047 +SCDO:0000617 NCIT:C16723 +SCDO:0000186 CMO:0000001 +SCDO:0000270 CMO:0000364 SCDO:1000195 OBI:0002146 -SCDO:0001058 NCIT:C98835 -SCDO:1000434 HP:0031368 -SCDO:0002912 CHEBI:6909 -SCDO:1000273 HP:0002715 -SCDO:0000723 CMO:0000038 -SCDO:1000284 MP:0002118 -SCDO:0007716 NCIT:C63547 -SCDO:1000263 HP:0000078 -SCDO:0005287 HP:0001744 -SCDO:0005490 HP:0011950 -SCDO:0001341 NCIT:C17357 -SCDO:0001078 NCIT:C75583 -SCDO:1000715 UO:0000280 -SCDO:1000412 DUO:0000028 -SCDO:0000154 HP:0002653 -SCDO:1000415 DUO:0000024 -SCDO:0000040 NCIT:C81229 -SCDO:0000784 HP:0003198 -SCDO:1000440 HP:0001874 +SCDO:0000014 CMO:0000210 +SCDO:1000676 NCIT:C51776 +SCDO:1000675 NCIT:C51775 +SCDO:0000043 NCIT:C95536 +SCDO:1000446 HP:0011991 +SCDO:0001028 HP:0008245 +SCDO:0001238 HP:0007902 SCDO:1000388 NCIT:C78638 -SCDO:0000847 CHEBI:7852 -SCDO:0000209 HP:0001342 -SCDO:0001324 HP:0001371 -SCDO:0000434 HP:0000805 -SCDO:0001367 HP:0000005 -SCDO:0300001 NCIT:C39796 -SCDO:0000831 HP:0012203 -SCDO:0006222 NCIT:C124059 -SCDO:1000391 NCIT:C116081 -SCDO:0002870 DOID:0060181 -SCDO:0000770 HP:0012282 -SCDO:1000287 HP:0001977 -SCDO:1000626 HP:0005518 -SCDO:0000543 CMO:0000508 -SCDO:0000612 OBI:0000185 -SCDO:0000428 HP:0003457 -SCDO:1000185 OGMS:0000028 -SCDO:0000027 NCIT:C154481 -SCDO:0000503 CMO:0000037 -SCDO:0000758 NCIT:C124475 -SCDO:1000544 NCIT:C68615 -SCDO:1000405 OBI:0002556 -SCDO:1000761 MP:0005533 -SCDO:1000563 OPMI:0000023 -SCDO:0007493 CHEBI:42797 -SCDO:0000105 HP:0000708 +SCDO:0005490 HP:0011950 +SCDO:0001100 NCIT:C85397 +SCDO:0005864 HP:0001889 +SCDO:1000511 NCIT:C67244 +SCDO:1000443 PR:000001318 +SCDO:0001344 NCIT:C15238 +SCDO:0008079 NCIT:C128326 +SCDO:0000629 HP:0011001 +SCDO:1000646 NCIT:C67015 +SCDO:0000005 NCIT:C71375 +SCDO:0000087 NCIT:C26702 +SCDO:1000169 NCIT:C107564 +SCDO:1000720 UO:0000109 +SCDO:1000506 UO:0000180 +SCDO:0000795 HP:0000112 +SCDO:0000836 CHEBI:35482 +SCDO:0000100 NCIT:C2890 +SCDO:0000451 GAZ:00000448 +SCDO:0008272 HP:0001269 SCDO:0000555 NCIT:C124065 -SCDO:0000695 NCIT:C74954 -SCDO:0001028 HP:0008245 -SCDO:0000820 HP:0002870 -SCDO:0006481 HP:0012574 -SCDO:0000270 CMO:0000364 -SCDO:1000096 NCIT:C70817 -SCDO:0000212 HP:0012229 -SCDO:0009453 NCIT:C16676 -SCDO:0001057 NCIT:C95539 -SCDO:0000367 HP:0000819 -SCDO:1000852 NCIT:C103165 -SCDO:0008766 NCIT:C35372 -SCDO:0000779 SYMP:0019161 -SCDO:1000765 HP:0012638 -SCDO:1000384 NCIT:C2959 -SCDO:0001101 IDOMAL:0000592 -SCDO:1000359 NCIT:C16612 -SCDO:0005439 NCIT:C20629 -SCDO:0008454 NCIT:C64625 -SCDO:0004832 NCIT:C118385 -SCDO:0000597 HP:0011886 -SCDO:0001137 HP:0002725 +SCDO:0000802 MP:0003224 +SCDO:0005758 HP:0012330 SCDO:1000381 NCIT:C152089 -SCDO:1000293 NCIT:C50474 -SCDO:0005660 HP:0001903 -SCDO:0000629 HP:0011001 -SCDO:1000629 UO:0000025 +SCDO:0001102 HP:0003302 +SCDO:0001313 NCIT:C38060 +SCDO:0000134 CMO:0000123 SCDO:0001039 HP:0100806 -SCDO:0000075 HP:0001369 -SCDO:1000468 NCIT:C16495 -SCDO:0000647 NCIT:C120256 -SCDO:0000092 HP:0000027 -SCDO:0000865 HP:0003470 -SCDO:0000842 NCIT:C35447 -SCDO:0000648 NCIT:C120255 -SCDO:1000249 CMO:0000507 -SCDO:0001308 HP:0009045 -SCDO:0004190 NCIT:C62005 -SCDO:0001221 VO:0000001 -SCDO:0000204 NCIT:C154865 -SCDO:1000262 HP:0001197 -SCDO:0000059 NCIT:C258 -SCDO:0000918 HP:0100602 -SCDO:0000591 HP:0100774 +SCDO:0001988 HP:0100749 +SCDO:1000656 MP:0011470 +SCDO:0009838 HP:0002090 +SCDO:0003118 NCIT:C27088 +SCDO:1000435 NCIT:C3671 +SCDO:0006222 NCIT:C124059 +SCDO:0000459 HP:0100820 +SCDO:0001046 NCIT:C155312 +SCDO:1000654 MP:0011469 +SCDO:1000653 MP:0011468 +SCDO:0000445 OGMS:0000047 +SCDO:1000167 NCIT:C86008 +SCDO:0001272 HP:0001923 +SCDO:0000914 HP:0001271 SCDO:0000118 HP:0004586 -SCDO:1000674 NCIT:C51773 -SCDO:0000844 HP:0000939 -SCDO:0008272 HP:0001269 +SCDO:1000610 HP:0020059 SCDO:1000264 HP:0001871 -SCDO:1000762 MP:0005534 -SCDO:1000511 NCIT:C67244 -SCDO:1000414 DUO:0000027 -SCDO:0000180 OBI:1110053 -SCDO:1000651 HP:0003110 -SCDO:1000272 HP:0001392 +SCDO:0001057 NCIT:C95539 +SCDO:0000630 HP:0045048 +SCDO:0001072 MP:0001212 +SCDO:0001216 NCIT:C17241 +SCDO:0000635 IDO:0000586 +SCDO:0000153 HP:0002659 +SCDO:0000722 CMO:0000290 +SCDO:1000852 NCIT:C103165 +SCDO:1000507 UO:0000316 +SCDO:0001466 NCIT:C25460 +SCDO:1000499 VT:0000202 +SCDO:0000205 NCIT:C173396 +SCDO:1000617 HP:0011873 +SCDO:1000450 NCIT:C61797 +SCDO:0000550 NCIT:C95534 +SCDO:0006670 NCIT:C25474 +SCDO:1000275 NCIT:C126120 +SCDO:0001341 NCIT:C17357 +SCDO:0000962 NCIT:C17049 +SCDO:0000099 HP:0006689 +SCDO:0000639 HP:0000789 +SCDO:0000203 HP:0002059 +SCDO:1000681 HP:0003573 +SCDO:0000674 HP:0000084 +SCDO:1000384 NCIT:C2959 SCDO:1000503 UO:0000200 -SCDO:1000373 HP:0002597 -SCDO:1000335 NCIT:C123667 -SCDO:1000267 HP:0003116 -SCDO:0009619 HP:0011675 -SCDO:1000456 ICO:0000278 -SCDO:0000769 DOID:1188 -SCDO:1000441 CMO:0000111 -SCDO:0000142 CMO:0000195 -SCDO:0000158 HP:0002067 -SCDO:1000893 NCIT:C25299 -SCDO:1000647 HP:0004364 -SCDO:1000811 MP:0005376 +SCDO:0004899 HP:0002086 SCDO:0000793 HP:0000123 -SCDO:0002771 NCIT:C38698 -SCDO:1000271 HP:0001507 -SCDO:0001238 HP:0007902 -SCDO:0007856 NCIT:C34465 -SCDO:0000103 NCIT:C40438 -SCDO:1000265 HP:0004312 +SCDO:0001447 NCIT:C113340 +SCDO:1000168 NCIT:C114300 +SCDO:0000223 NCIT:C92755 +SCDO:0001243 CMO:0000027 +SCDO:0000512 NCIT:C84481 +SCDO:0000602 HP:0001265 +SCDO:0000534 NCIT:C95504 +SCDO:1000447 HP:0011897 +SCDO:0000827 HP:0000798 +SCDO:0003672 NCIT:C82909 +SCDO:1000562 OPMI:0000025 +SCDO:0000366 HP:0000873 SCDO:0006404 HP:0011907 -SCDO:1000417 DUO:0000029 -SCDO:1000661 HP:0031956 -SCDO:1000277 MP:0009568 -SCDO:0000655 HP:0002516 -SCDO:0000752 CHEBI:6807 -SCDO:1000380 NCIT:C133543 -SCDO:1000617 HP:0011873 -SCDO:0000168 HP:0011410 -SCDO:1000560 NCIT:C16576 -SCDO:1000652 HP:0025435 -SCDO:0000560 NCIT:C129072 -SCDO:0005115 NCIT:C95437 -SCDO:0008273 HP:0001640 +SCDO:0000135 CMO:0000036 SCDO:0000788 HP:0008404 -SCDO:1000505 NCIT:C64572 -SCDO:0004740 NCIT:C49131 -SCDO:0008046 HP:0003158 -SCDO:0000144 CMO:0000003 -SCDO:0001251 OBI:0001138 -SCDO:0000614 NCIT:C17230 -SCDO:1000499 VT:0000202 -SCDO:0000890 NCIT:C19332 -SCDO:1000865 UO:0000015 +SCDO:1000661 HP:0031956 +SCDO:1000658 NCIT:C67376 +SCDO:1000389 NCIT:C71746 +SCDO:1000631 HP:0025546 +SCDO:0003769 HP:0004756 +SCDO:0000912 ENVO:02500036 +SCDO:0000786 CMO:0002876 +SCDO:0003901 CHEBI:50858 +SCDO:1000531 ICO:0000036 +SCDO:1000410 DUO:0000021 +SCDO:1000387 NCIT:C114714 SCDO:1000378 HP:0020063 -SCDO:1000625 HP:0025066 -SCDO:0007991 HP:0001658 +SCDO:1000368 HP:0011025 +SCDO:0000770 HP:0012282 +SCDO:1000416 DUO:0000019 +SCDO:0001202 OBI:0001098 +SCDO:0000893 OGMS:0000023 +SCDO:0007744 NCIT:C50791 +SCDO:0008915 NCIT:C79903 +SCDO:0000779 SYMP:0019161 +SCDO:1000405 OBI:0002556 +SCDO:1000644 UO:0000187 +SCDO:1000279 HP:0000828 SCDO:0002381 ARO:0000064 -SCDO:1000418 DUO:0000025 -SCDO:0000792 NCIT:C28407 -SCDO:0002903 HP:0000044 -SCDO:0000802 MP:0003224 -SCDO:0002803 HP:0001712 -SCDO:0003263 HP:0002019 -SCDO:0000036 HP:0001022 -SCDO:1000559 NCIT:C20197 -SCDO:1000411 DUO:0000022 -SCDO:0000755 IDO:0000515 -SCDO:0000202 NCIT:C27222 -SCDO:1000347 NCIT:C50767 -SCDO:0008079 NCIT:C128326 -SCDO:0003913 HP:0011007 -SCDO:1000186 HP:0020061 -SCDO:0006467 NCIT:65495 -SCDO:0000915 NCIT:C1643 -SCDO:1000450 NCIT:C61797 -SCDO:0000429 HP:0001298 -SCDO:1000375 HP:0011122 -SCDO:0008895 HP:0002060 -SCDO:0000335 HP:0025031 -SCDO:0000266 NCIT:C16453 -SCDO:1000603 EUPATH:0021227 -SCDO:0000592 HP:0000843 -SCDO:1000365 NCIT:C75434 SCDO:0006120 NCIT:C96391 -SCDO:1000454 ICO:0000305 -SCDO:0001298 NCIT:C16564 -SCDO:1000809 MP:0009642 -SCDO:0003158 HP:0000876 +SCDO:0000136 CMO:0000023 +SCDO:0000783 HP:0002913 +SCDO:0000596 HP:0002149 +SCDO:1000648 HP:0012101 +SCDO:0006934 NCIT:C41129 +SCDO:1000269 HP:0025142 +SCDO:1000848 EUPATH:0000050 +SCDO:0001248 HP:0004870 +SCDO:0300001 NCIT:C39796 +SCDO:0000939 NCIT:C17873 +SCDO:0003035 HP:0011106 +SCDO:0004047 NCIT:C17004 +SCDO:0002700 HP:0001873 +SCDO:1000469 NCIT:C69256 +SCDO:0009748 NCIT:C142541 +SCDO:1000375 HP:0011122 +SCDO:0000890 NCIT:C19332 +SCDO:0000092 HP:0000027 +SCDO:0002245 HP:0001626 +SCDO:1000399 NCIT:C34941 +SCDO:0000693 NCIT:C51677 +SCDO:0001337 HP:0002007 +SCDO:1000248 HP:0004825 +SCDO:0000154 HP:0002653 +SCDO:0000652 HP:0001970 +SCDO:1000560 NCIT:C16576 +SCDO:0000911 NCIT:C38141 +SCDO:1000428 ICO:0000255 +SCDO:0000918 HP:0100602 +SCDO:0001381 NCIT:C84979 SCDO:0001365 DOID:4 -SCDO:0000205 NCIT:C173396 -SCDO:1000002 NCIT:C70731 -SCDO:1000624 HP:0025065 -SCDO:0004140 NCIT:C25464 -SCDO:0000679 HP:0002808 -SCDO:1000608 HP:0020058 -SCDO:0000708 NCIT:C16809 -SCDO:1000623 UO:0000104 +SCDO:0000586 HP:0000815 +SCDO:0000560 NCIT:C129072 +SCDO:1000186 HP:0020061 +SCDO:0000871 NCIT:C102988 +SCDO:0000266 NCIT:C16453 +SCDO:0000342 HP:0000823 +SCDO:1000156 NCIT:C39547 SCDO:0000785 HP:0100614 -SCDO:0007242 NCIT:C71754 -SCDO:0000843 HP:0000938 -SCDO:0000891 NCIT:C18772 -SCDO:1000504 NCIT:C67251 -SCDO:0009968 HP:0000097 +SCDO:0001081 NCIT:C29719 +SCDO:0000214 HP:0002341 +SCDO:0002067 DOID:813 +SCDO:0000059 NCIT:C258 +SCDO:1000011 NCIT:C84980 +SCDO:1000564 OPMI:0000024 +SCDO:0000403 HP:0001260 +SCDO:0001109 VO:0000675 +SCDO:1000434 HP:0031368 +SCDO:0000792 NCIT:C28407 +SCDO:0007437 HP:0000834 +SCDO:1000643 UO:0000190 +SCDO:1000417 DUO:0000029 +SCDO:1000404 OBI:0002557 +SCDO:0000800 HP:0012759 +SCDO:1000762 MP:0005534 +SCDO:0004832 NCIT:C118385 +SCDO:0007198 DOID:2326 +SCDO:0000606 NCIT:C561 +SCDO:1000478 UO:0000000 +SCDO:0000434 HP:0000805 +SCDO:1000865 UO:0000015 +SCDO:1000002 NCIT:C70731 +SCDO:0000875 NCIT:C78652 +SCDO:1000393 NCIT:C20711 +SCDO:0001324 HP:0001371 +SCDO:0002803 HP:0001712 +SCDO:0009698 HP:0000707 +SCDO:0000872 OGMS:0000088 +SCDO:0000308 HP:0000953 +SCDO:0001011 HP:0001370 +SCDO:0000030 NCIT:C25150 +SCDO:1000347 NCIT:C50767 +SCDO:0001138 OBI:0200198 +SCDO:1000633 MP:0005562 +SCDO:1000270 HP:0000080 +SCDO:1000380 NCIT:C133543 +SCDO:0001244 CMO:0002341 +SCDO:0000769 DOID:1188 +SCDO:0000995 CMO:0000094 +SCDO:0001115 NCIT:C15320 +SCDO:1000456 ICO:0000278 +SCDO:0007326 HP:0001433 +SCDO:0000612 OBI:0000185 +SCDO:0000848 CMO:0001324 +SCDO:0000936 HP:0003765 +SCDO:0003844 HP:0001878 +SCDO:0000460 HP:0000096 +SCDO:0000888 HP:0011904 +SCDO:0001137 HP:0002725 +SCDO:1000418 DUO:0000025 +SCDO:1000641 MP:0010067 +SCDO:0008115 ICO:0000179 +SCDO:1000764 HP:0012639 +SCDO:0000503 CMO:0000037 +SCDO:0000752 CHEBI:6807 +SCDO:1000293 NCIT:C50474 +SCDO:1000770 NCIT:C48660 +SCDO:1000370 HP:0001743 +SCDO:0000870 NCIT:C103526 +SCDO:0003024 HP:0000271 +SCDO:0000017 HP:0001919 +SCDO:1000440 HP:0001874 +SCDO:0000642 VO:0000642 +SCDO:0000450 STATO:0000091 +SCDO:0000200 DOID:9220 +SCDO:0009656 HP:0002098 +SCDO:1000505 NCIT:C64572 +SCDO:1000667 HP:0003282 SCDO:0000432 HP:0030127 -SCDO:0001493 HP:0001395 -SCDO:1000613 HP:0011893 -SCDO:1000659 HP:0031964 -SCDO:0000745 HP:0000132 -SCDO:1000428 ICO:0000255 +SCDO:1000407 ICO:0000293 +SCDO:0008538 HP:0001935 +SCDO:1000678 NCIT:C51774 +SCDO:1000859 NCIT:C25191 +SCDO:0000757 OBI:0400169 +SCDO:0000658 HP:0001511 +SCDO:0004203 HP:0012819 +SCDO:0004183 NCIT:C3890 +SCDO:0009818 HP:0000118 +SCDO:0000595 HP:0000836 +SCDO:1000311 CMO:0002079 SCDO:1000312 CMO:0001321 -SCDO:1000500 CMO:0000376 -SCDO:0000446 NCIT:C92803 -SCDO:0000652 HP:0001970 -SCDO:0001074 HP:0200042 -SCDO:0002133 HP:0000077 +SCDO:0000425 HP:0012465 +SCDO:0000756 SBO:0000316 +SCDO:0000449 NCIT:C15709 +SCDO:1000677 NCIT:C156541 +SCDO:1000867 UO:0000009 +SCDO:1000672 GSSO:000109 +SCDO:1000659 HP:0031964 +SCDO:0008801 HP:0000822 +SCDO:0005061 NCIT:C99042 +SCDO:1000022 HP:0000505 +SCDO:0008553 HP:0001279 +SCDO:0001371 NCIT:C19296 +SCDO:0000458 HP:0000099 +SCDO:0000538 NCIT:C141366 +SCDO:0000784 HP:0003198 +SCDO:0000143 CMO:0000035 +SCDO:0000599 HP:0001943 +SCDO:0009586 ICO:0000228 +SCDO:0001245 CMO:0000011 +SCDO:0000648 NCIT:C120255 +SCDO:0005247 NCIT:C29107 +SCDO:0004802 NCIT:C3833 +SCDO:1000412 DUO:0000028 +SCDO:0009774 HP:0001406 +SCDO:1000541 HP:0012100 +SCDO:0005031 NCIT:C43646 +SCDO:0001709 HP:0011906 +SCDO:1000581 HP:0032224 +SCDO:1000623 UO:0000104 +SCDO:0003765 HP:0001701 +SCDO:1000266 HP:0500015 +SCDO:1000245 HP:0004447 +SCDO:0001071 HP:0011123 +SCDO:0000543 CMO:0000508 +SCDO:1000544 NCIT:C68615 +SCDO:0008484 DOID:1826 +SCDO:0000554 HP:0003641 +SCDO:0000883 MP:0002081 +SCDO:0001118 HP:0002138 +SCDO:1000760 MP:0005535 +SCDO:0001221 VO:0000001 +SCDO:1000761 MP:0005533 +SCDO:1000334 NCIT:C155932 +SCDO:0000150 CMO:0000021 +SCDO:0001298 NCIT:C16564 +SCDO:0000644 HP:0000855 +SCDO:0007856 NCIT:C34465 +SCDO:0009293 ICO:0000157 +SCDO:0000577 CHEBI:5790 +SCDO:0005566 HP:0002240 +SCDO:0001314 HP:0001999 +SCDO:0000020 HP:0008682 +SCDO:1000372 HP:0001787 +SCDO:1000504 NCIT:C67251 +SCDO:0000614 NCIT:C17230 +SCDO:0000909 NCIT:C97120 +SCDO:0001196 HP:0003126 +SCDO:0000910 NCIT:C97121 +SCDO:0000920 HP:0001622 +SCDO:0000916 NCIT:C92853 +SCDO:0003119 ARO:0000006 +SCDO:0005364 NCIT:C16779 +SCDO:0000578 HP:0001789 +SCDO:0001423 HP:0001896 +SCDO:0001012 NCIT:C80411 +SCDO:0008273 HP:0001640 +SCDO:0000759 HP:0002076 +SCDO:0000395 MP:0001762 +SCDO:0005773 NCIT:C103270 +SCDO:0000632 MP:0002412 +SCDO:0001009 NCIT:C101217 +SCDO:1000096 NCIT:C70817 +SCDO:0003776 HP:0003265 +SCDO:0000721 CMO:0000291 +SCDO:0001024 HP:0011868 +SCDO:0000816 HP:0001513 +SCDO:0000647 NCIT:C120256 +SCDO:1000021 HP:0000618 +SCDO:1000286 HP:0020054 +SCDO:0000422 OBI:0000990 +SCDO:0000604 HP:0012418 +SCDO:0001493 HP:0001395 +SCDO:0009017 MP:0010163 +SCDO:0004877 HP:0001635 +SCDO:0000672 HP:0001382 +SCDO:1000899 NCIT:C64387 SCDO:1000140 HP:0000006 -SCDO:0000673 HP:0001343 +SCDO:0000844 HP:0000939 +SCDO:1000851 EUPATH:0000310 SCDO:1000377 HP:0020062 +SCDO:0001673 HP:0030243 +SCDO:0005335 CHEBI:35493 +SCDO:1000263 HP:0000078 +SCDO:0001259 NCIT:C519 +SCDO:0000654 HP:0002170 +SCDO:0000027 NCIT:C154481 +SCDO:1000246 HP:0030058 +SCDO:1000415 DUO:0000024 +SCDO:0000430 HP:0003774 +SCDO:0008348 HP:0000951 +SCDO:1000613 HP:0011893 +SCDO:0008454 NCIT:C64625 +SCDO:1000719 CMO:0000283 +SCDO:0000167 ExO:0000048 +SCDO:0000842 NCIT:C35447 +SCDO:1000603 EUPATH:0021227 +SCDO:0005115 NCIT:C95437 +SCDO:0000974 CMO:0001356 +SCDO:0007716 NCIT:C63547 +SCDO:0000523 CMO:0000506 +SCDO:0000549 NCIT:C131682 +SCDO:1000491 UO:0000051 +SCDO:0008927 NCIT:C35152 SCDO:0001231 HP:0001714 -SCDO:0000671 HP:0000952 -SCDO:0005566 HP:0002240 -SCDO:0000827 HP:0000798 -SCDO:0001383 HP:0005560 -SCDO:0000642 VO:0000642 -SCDO:1000675 NCIT:C51775 -SCDO:1000632 MP:0001589 -SCDO:0000087 NCIT:C26702 -SCDO:1000167 NCIT:C86008 -SCDO:0000904 HP:0011856 -SCDO:0000074 HP:0002829 -SCDO:0000645 NCIT:C122920 -SCDO:0005809 CHEBI:35475 -SCDO:0001423 HP:0001896 -SCDO:0001874 NCIT:C74096 -SCDO:0000136 CMO:0000023 -SCDO:0001415 HP:0012532 -SCDO:0000604 HP:0012418 -SCDO:1000614 HP:0001882 -SCDO:0000599 HP:0001943 -SCDO:0000687 HP:0001909 -SCDO:0001988 HP:0100749 -SCDO:1000156 NCIT:C39547 -SCDO:0000893 OGMS:0000023 -SCDO:0006670 NCIT:C25474 -SCDO:0007836 NCIT:C78598 -SCDO:1000633 MP:0005562 -SCDO:1000476 NCIT:C91105 -SCDO:0001045 HP:0011413 -SCDO:0001371 NCIT:C19296 +SCDO:0001311 HP:0002071 +SCDO:1000273 HP:0002715 +SCDO:1000287 HP:0001977 +SCDO:0000048 NCIT:C52009 +SCDO:0000151 CMO:0000015 +SCDO:0000823 HP:0000969 +SCDO:1000712 UO:0000005 +SCDO:1000671 NCIT:C28421 +SCDO:0003263 HP:0002019 +SCDO:1000413 DUO:0000018 SCDO:0001214 CMO:0000256 -SCDO:1000720 UO:0000109 -SCDO:0003844 HP:0001878 +SCDO:0000591 HP:0100774 +SCDO:1000400 NCIT:C142664 +SCDO:0000589 HP:0000962 +SCDO:1000752 OBI:0002140 +SCDO:0000264 CHMO:0002580 SCDO:0000275 NCIT:C97123 -SCDO:0000005 NCIT:C71375 -SCDO:1000386 NCIT:C114717 -SCDO:0005226 NCIT:C99063 +SCDO:0000646 NCIT:C120254 +SCDO:0000140 CMO:0000366 +SCDO:0001116 NCIT:C93407 +SCDO:0000103 NCIT:C40438 +SCDO:0000025 CHEBI:60809 +SCDO:0008766 NCIT:C35372 +SCDO:1000713 NCIT:C42559 +SCDO:0000367 HP:0000819 +SCDO:1000565 OPMI:0000028 +SCDO:0001488 HP:0001394 +SCDO:1000810 MP:0002329 +SCDO:0000335 HP:0025031 +SCDO:0000089 HP:0012444 +SCDO:1000278 HP:0000820 +SCDO:0000778 HP:0003394 SCDO:0000413 HP:0031456 -SCDO:1000443 PR:000001318 +SCDO:0000036 HP:0001022 +SCDO:1000715 UO:0000280 +SCDO:0005226 NCIT:C99063 +SCDO:0007242 NCIT:C71754 +SCDO:1000640 MP:0010068 +SCDO:0009453 NCIT:C16676 +SCDO:1000335 NCIT:C123667 +SCDO:0001254 DRON:00017565 +SCDO:0000279 OGMS:0000051 +SCDO:0001368 HP:0000007 +SCDO:1000665 HP:0012379 +SCDO:0000667 MP:0013305 +SCDO:0004833 HP:0002907 +SCDO:1000636 HP:0025548 +SCDO:1000853 NCIT:C81262 +SCDO:0000687 HP:0001909 +SCDO:0000613 NCIT:C122931 +SCDO:0000207 HP:0002181 +SCDO:1000057 NCIT:C126121 +SCDO:0007384 HsapDv:0000000 +SCDO:0002784 NCIT:C96239 +SCDO:0005733 DOID:0050731 +SCDO:0001045 HP:0011413 +SCDO:0000168 HP:0011410 +SCDO:0004314 NCIT:C18133 +SCDO:1000272 HP:0001392 +SCDO:1000628 UO:0000002 +SCDO:0001367 HP:0000005 +SCDO:0000273 HP:0001289 SCDO:0000093 HP:0002157 -SCDO:1000216 EUPATH:0000034 -SCDO:0009656 HP:0002098 -SCDO:0001305 NCIT:C16567 -SCDO:0001118 HP:0002138 +SCDO:1000437 HP:0032180 +SCDO:0001101 IDOMAL:0000592 +SCDO:0001293 NCIT:C116942 +SCDO:0000768 NCIT:C19771 SCDO:0000906 CMO:0000029 -SCDO:0005247 NCIT:C29107 +SCDO:0000563 CHMO:0001009 +SCDO:1000476 NCIT:C91105 +SCDO:1000369 HP:0030680 SCDO:0000773 HP:0002427 -SCDO:0000841 HP:0010885 -SCDO:0000912 ENVO:02500036 -SCDO:0000783 HP:0002913 -SCDO:1000019 IDO:0000560 -SCDO:0001447 NCIT:C113340 -SCDO:0001081 NCIT:C29719 +SCDO:0002771 NCIT:C38698 +SCDO:0001251 OBI:0001138 +SCDO:0001060 NCIT:C155310 +SCDO:0000433 HP:0025636 +SCDO:1000634 MP:0005561 +SCDO:0008043 HP:0002014 +SCDO:1000618 HP:0001894 +SCDO:0000820 HP:0002870 +SCDO:0000982 HP:0001920 +SCDO:0000880 ARO:0000054 +SCDO:0001415 HP:0012532 +SCDO:0000703 HP:0003563 +SCDO:1000374 HP:0011121 +SCDO:0000832 NCIT:C115319 +SCDO:0004740 NCIT:C49131 +SCDO:1000419 DUO:0000026 +SCDO:0005790 HP:0001974 +SCDO:0000013 NCIT:C98805 +SCDO:0000105 HP:0000708 +SCDO:1000420 NCIT:C142494 +SCDO:1000358 NCIT:C84983 +SCDO:1000349 NCIT:C3245 +SCDO:1000385 NCIT:C78254 +SCDO:1000386 NCIT:C114717 +SCDO:0000892 HP:0000967 +SCDO:0008046 HP:0003158 +SCDO:0000404 HP:0003611 +SCDO:0000144 CMO:0000003 +SCDO:0000074 HP:0002829 +SCDO:1000403 APOLLO_SV:00000241 +SCDO:0000755 IDO:0000515 +SCDO:1000271 HP:0001507 +SCDO:0004069 HP:0012735 +SCDO:0000452 HP:0000225 +SCDO:1000892 NCIT:C25298 SCDO:1000864 UO:0000001 -SCDO:0000974 CMO:0001356 -SCDO:0000756 SBO:0000316 -SCDO:1000400 NCIT:C142664 -SCDO:0000962 NCIT:C17049 -SCDO:0000603 HP:0000821 -SCDO:0003776 HP:0003265 -SCDO:0000459 HP:0100820 -SCDO:0001313 NCIT:C38060 -SCDO:0000458 HP:0000099 -SCDO:0000135 CMO:0000036 +SCDO:1000655 MP:0011471 +SCDO:1000625 HP:0025066 +SCDO:0000210 HP:0005318 +SCDO:0000758 NCIT:C124475 +SCDO:0001058 NCIT:C98835 +SCDO:0009817 HP:0012243 +SCDO:0004249 OBI:0000626 +SCDO:1000216 EUPATH:0000034 +SCDO:0001370 IDOMAL:50000026 +SCDO:1000809 MP:0009642 +SCDO:1000365 NCIT:C75434 +SCDO:0004437 HP:0030248 +SCDO:0000946 HP:0000999 +SCDO:1000614 HP:0001882 +SCDO:0002710 HP:0005162 +SCDO:1000642 UO:0000186 +SCDO:1000427 GSSO:003239 +SCDO:1000373 HP:0002597 +SCDO:1000438 HP:0010876 +SCDO:0000645 NCIT:C122920 +SCDO:1000277 MP:0009568 +SCDO:0000723 CMO:0000038 SCDO:1000055 EUPATH:0000215 -SCDO:0000875 NCIT:C78652 -SCDO:1000565 OPMI:0000028 +SCDO:1000284 MP:0002118 +SCDO:0000841 HP:0010885 +SCDO:0003913 HP:0011007 +SCDO:0000044 NCIT:C95535 +SCDO:1000390 NCIT:C115199 +SCDO:0001219 HP:0001025 +SCDO:0000601 HP:0001010 +SCDO:0007091 HP:0001081 +SCDO:1000561 OPMI:0000027 +SCDO:0000211 HP:0005305 +SCDO:0008895 HP:0002060 +SCDO:1000626 HP:0005518 +SCDO:0005439 NCIT:C20629 +SCDO:0000847 CHEBI:7852 +SCDO:0000345 HP:0000726 +SCDO:1000391 NCIT:C116081 +SCDO:0007386 HP:0000829 +SCDO:1000683 HP:0045040 +SCDO:1000765 HP:0012638 +SCDO:1000668 IDOMAL:0000122 +SCDO:0000708 NCIT:C16809 +SCDO:0001308 HP:0009045 +SCDO:1000346 NCIT:C17655 +SCDO:0001163 CMO:0000365 +SCDO:1000632 MP:0001589 +SCDO:0007991 HP:0001658 +SCDO:0000904 HP:0011856 +SCDO:1000019 IDO:0000560 +SCDO:1000620 NCIT:C64783 +SCDO:0008218 HP:0000824 +SCDO:0000745 HP:0000132 +SCDO:0000212 HP:0012229 +SCDO:0001383 HP:0005560 +SCDO:0006467 NCIT:65495 +SCDO:0000464 HP:0002955 +SCDO:0000933 CMO:0000211 +SCDO:1000635 HP:0025547 diff --git a/mappings/scdo-sssom-xrefs.tsv b/mappings/scdo-sssom-xrefs.tsv index f4e9cca..52c29cb 100644 --- a/mappings/scdo-sssom-xrefs.tsv +++ b/mappings/scdo-sssom-xrefs.tsv @@ -1,1022 +1,1022 @@ subject_id subject_label predicate_id predicate_label object_id object_label match_type mapping_provider -SCDO:0007198 Gastroenteritis oio:hasDbXref database cross reference DOID:2326 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001140 Tertiary Healthcare oio:hasDbXref database cross reference MESH:D063128 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0008484 Epilepsy oio:hasDbXref database cross reference DOID:1826 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000452 Cancer Pain oio:hasDbXref database cross reference MESH:D000072716 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000869 Patient Compliance oio:hasDbXref database cross reference MESH:D010349 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0008927 Acute Cholecystitis oio:hasDbXref database cross reference NCIT:C35152 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000397 Drug Clearance Decreased AE oio:hasDbXref database cross reference OAE:0000887 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000113 Beta Thalassemia Major oio:hasDbXref database cross reference ORPHA:231214 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000654 Intracranial Hemorrhage oio:hasDbXref database cross reference HP:0002170 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000438 Abnormal Circulating Protein Level oio:hasDbXref database cross reference HP:0010876 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001233 Viral Infection oio:hasDbXref database cross reference NCIT:C3439 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000672 Intersex oio:hasDbXref database cross reference GSSO:000109 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000207 Cerebral Edema oio:hasDbXref database cross reference HP:0002181 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000012 Beta-Globin Family Members oio:hasDbXref database cross reference MESH:D055544 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001038 Sensory Neuropathy oio:hasDbXref database cross reference HP:0000763 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000822 Occupational Therapy oio:hasDbXref database cross reference MESH:D009788 HumanCurated 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-SCDO:0008348 Abnormality of the Skin oio:hasDbXref database cross reference HP:0000951 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0009818 Abnormal Phenotype oio:hasDbXref database cross reference HP:0000118 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0005758 Pyelonephritis oio:hasDbXref database cross reference HP:0012330 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000210 Cerebral Vasculitis oio:hasDbXref database cross reference HP:0005318 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000404 Maximum Age Value Specification oio:hasDbXref database cross reference OBI:0002557 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000944 Pulse Oximeter oio:hasDbXref database cross reference ERO:0000876 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001259 Gentamicin oio:hasDbXref database cross reference NCIT:C519 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0003119 Erythromycin oio:hasDbXref database cross reference ARO:0000006 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0004183 Hypoxia oio:hasDbXref database cross reference NCIT:C3890 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0004598 Anticodon oio:hasDbXref database cross reference MESH:D000926 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001347 Abnormality of the Urinary System oio:hasDbXref database cross reference HP:0000079 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000902 Physiological Assay oio:hasDbXref database cross reference ERO:0001292 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0005061 Renal Vein Thrombosis oio:hasDbXref database cross reference NCIT:C99042 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000316 D57.2 Sickle-cell/Hb-C disease oio:hasDbXref database cross reference ICD10CM:D57.2 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000305 Pulse Oximetry (Exercise) oio:hasDbXref database cross reference phenX:91001 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001296 Erythrocyte Transfusion oio:hasDbXref database cross reference MESH:D017707 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000200 Central Sleep Apnea oio:hasDbXref database cross reference DOID:9220 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000424 Electrophoresis oio:hasDbXref database cross reference MESH:D004586 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000618 Thrombocytosis oio:hasDbXref database cross reference HP:0001894 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000810 Abnormal Blood Gas Level oio:hasDbXref database cross reference MP:0002329 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0009334 Neutropenia oio:hasDbXref database cross reference HP:0001875 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000214 Cervical Cord Compression oio:hasDbXref database cross reference HP:0002341 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001027 Secondary Healthcare oio:hasDbXref database cross reference MESH:D063127 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000634 Increased Mean Corpuscular Hemoglobin oio:hasDbXref database cross reference MP:0005561 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000830 Nail Dysplasia oio:hasDbXref database cross reference HP:0002164 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001046 Sickle Cell Chronic Lung Disease oio:hasDbXref database cross reference NCIT:C155312 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000420 Electroencephalography oio:hasDbXref database cross reference 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database cross reference HP:0000836 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0007091 Cholelithiasis oio:hasDbXref database cross reference HP:0001081 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000617 Immunological Assay oio:hasDbXref database cross reference NCIT:C16723 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000372 Abnormal Delivery oio:hasDbXref database cross reference HP:0001787 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000506 Hematopoietic Stem Cell Transplantation oio:hasDbXref database cross reference MESH:D018380 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001293 Developmental Delay oio:hasDbXref database cross reference NCIT:C116942 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000382 Diet, Food, and Nutrition oio:hasDbXref database cross reference MESH:D000066888 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001337 Frontal Bossing oio:hasDbXref database cross reference HP:0002007 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001254 Xylometazoline oio:hasDbXref database cross reference DRON:00017565 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001091 Socioeconomic Status oio:hasDbXref database cross reference APAONTO:Socioeconomic_Status HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000835 Ophthalmoscopy oio:hasDbXref database cross reference MESH:D009887 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000746 Mental Health oio:hasDbXref database cross reference MESH:D008603 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0007912 Pulmonary Embolism oio:hasDbXref database cross reference HP:0002204 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000367 Geographic Area oio:hasDbXref database cross reference NCIT:C16632 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000843 Hypercapnia oio:hasDbXref database cross reference MESH:D006935 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000388 Disaster oio:hasDbXref database cross reference MESH:D004190 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0003769 Ventricular Tachycardia oio:hasDbXref database cross reference HP:0004756 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000550 Hemoglobin Trait oio:hasDbXref database cross reference NCIT:C95534 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000435 Injury oio:hasDbXref database cross reference NCIT:C3671 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0003089 Lethargy oio:hasDbXref database cross reference HP:0001254 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000888 Increased Hemoglobin F oio:hasDbXref database cross reference HP:0011904 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000422 Electron Microscope oio:hasDbXref database cross reference OBI:0000990 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000419 User Specific Restriction oio:hasDbXref database cross reference DUO:0000026 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000531 Date of Signing Consent oio:hasDbXref database cross reference ICO:0000036 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000606 Ibuprofen oio:hasDbXref database cross reference NCIT:C561 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000057 Deoxygenated Hemoglobin oio:hasDbXref database cross reference NCIT:C126121 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000881 Telephone Number oio:hasDbXref database cross reference NCIT:C40978 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000066 Antihistamine oio:hasDbXref database cross reference MESH:D006633 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:1000250 deprecated Abnormal Molecular Function oio:hasDbXref database cross reference FYPO:0000707 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000057 Anti-Inflammatory Agent oio:hasDbXref database cross reference MESH:D000893 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0002106 Splenic Infarction oio:hasDbXref database cross reference EFO:1001190 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001234 Virus oio:hasDbXref database cross reference MESH:D014780 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001009 Retinal Examination oio:hasDbXref database cross reference NCIT:C101217 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001144 Thalassemia oio:hasDbXref database cross reference NCIT:C35069 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001115 Study Design oio:hasDbXref database cross reference NCIT:C15320 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0003118 Hyperbilirubinemia oio:hasDbXref database cross reference NCIT:C27088 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001344 Gene Therapy oio:hasDbXref database cross reference NCIT:C15238 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0009838 Pneumonia oio:hasDbXref database cross reference HP:0002090 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0000744 Meningitis oio:hasDbXref database cross reference HP:0001287 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0005464 Myocardial Ischemia oio:hasDbXref database cross reference EFO:1001375 HumanCurated http://scdontology.h3abionet.org/ontology/scdo.owl -SCDO:0001026 Scoliosis oio:hasDbXref database cross reference HP:0002650 HumanCurated 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+SCDO:0005439 Silent Mutation oio:hasDbXref database cross reference NCIT:C20629 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0000847 Oxycodone oio:hasDbXref database cross reference CHEBI:7852 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0000345 Dementia oio:hasDbXref database cross reference HP:0000726 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:1000391 Dialysis Access Complication oio:hasDbXref database cross reference NCIT:C116081 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0007386 Hypoparathyroidism oio:hasDbXref database cross reference HP:0000829 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:1000683 Abnormal Lactate Dehydrogenase Level oio:hasDbXref database cross reference HP:0045040 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:1000765 Abnormal Nervous System Physiology oio:hasDbXref database cross reference HP:0012638 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:1000668 Malaria Chemoprophylaxis oio:hasDbXref database cross reference IDOMAL:0000122 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0000708 Magnetic Resonance Imaging oio:hasDbXref database cross reference NCIT:C16809 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0001308 Exercise-Induced Rhabdomyolysis oio:hasDbXref database cross reference HP:0009045 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:1000346 Reproductive History oio:hasDbXref database cross reference NCIT:C17655 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0001163 Total White Blood Cell Count oio:hasDbXref database cross reference CMO:0000365 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:1000632 Abnormal Mean Corpuscular Hemoglobin oio:hasDbXref database cross reference MP:0001589 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0007991 Myocardial Infarction oio:hasDbXref database cross reference HP:0001658 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0000904 Pica oio:hasDbXref database cross reference HP:0011856 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0001027 Secondary Healthcare oio:hasDbXref database cross reference MESH:D063127 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:1000019 Antifungal oio:hasDbXref database cross reference IDO:0000560 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:1000620 g/dL oio:hasDbXref database cross reference NCIT:C64783 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0008218 Growth Hormone Deficiency oio:hasDbXref database cross reference HP:0000824 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0001234 Virus oio:hasDbXref database cross reference MESH:D014780 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0000745 Menorrhagia oio:hasDbXref database cross reference HP:0000132 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0000212 Cerebrospinal Fluid Pleocytosis oio:hasDbXref database cross reference HP:0012229 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0001383 Imbalanced Hemoglobin Synthesis oio:hasDbXref database cross reference HP:0005560 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0006467 Duloxetine oio:hasDbXref database cross reference NCIT:65495 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0000944 Pulse Oximeter oio:hasDbXref database cross reference ERO:0000876 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0000464 Granulomatosis oio:hasDbXref database cross reference HP:0002955 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:0000933 Prothrombin Time oio:hasDbXref database cross reference CMO:0000211 HumanCurated http://purl.obolibrary.org/obo/scdo.owl +SCDO:1000635 Decreased Mean Corpuscular Hemoglobin Concentration oio:hasDbXref database cross reference HP:0025547 HumanCurated http://purl.obolibrary.org/obo/scdo.owl diff --git a/scdo.obo b/scdo.obo index 7903c30..f8c3782 100644 --- a/scdo.obo +++ b/scdo.obo @@ -1,10 +1,10 @@ format-version: 1.2 -data-version: scdo/releases/2021-04-09/scdo.owl +data-version: releases/2021-04-15 synonymtypedef: abbreviation "abbreviation" synonymtypedef: layperson "layperson term" synonymtypedef: obsolete_synonym "discarded/obsoleted synonym" synonymtypedef: plural_form "plural form" -ontology: http://scdontology.h3abionet.org/ontology/scdo.owl +ontology: scdo property_value: http://purl.org/dc/elements/1.1/abstract "Sickle cell disease (SCD) is one of the most common monogenic diseases in humans with multiple phenotypic expressions that can manifest as both acute and chronic complications. Although described more than a century ago, challenges in comprehensive disease management and collaborative research on this disease are compounded by the complex molecular and clinical phenotypes of SCD, environmental and psychosocial factors, limited therapeutic options and ambiguous terminology. This ambiguous terminology has hampered the integration and interoperability of existing SCD knowledge, and SCD research translation. The SCD Ontology (SCDO), which is a community-driven integrative and universal knowledge representation system for SCD, overcomes this issue by providing a controlled vocabulary developed by a group of experts in both SCD and ontology design. SCDO is the first and most comprehensive standardized human- and machine-readable resource that unambiguously represents terminology and concepts about SCD for researchers, patients and clinicians. It is built around the central concept ‘hemoglobinopathy’, allowing inclusion of non-SCD haemoglobinopathies, such as thalassaemias, which may interfere with or influence SCD phenotypic manifestations. This collaboratively developed ontology constitutes a comprehensive knowledge management system and standardized terminology of various SCD-related factors. The SCDO will promote interoperability of different research datasets, facilitate seamless data sharing and collaborations, including meta-analyses within the SCD community, and support the development and curation of data-basing and clinical informatics in SCD." xsd:string property_value: http://purl.org/dc/elements/1.1/accessRights "Anyone can access the resource." xsd:string property_value: http://purl.org/dc/elements/1.1/accrualMethod "Manually, based on terms in existing ontologies and in collaboration with sickle cell disease (SCD) experts where necessary." xsd:string @@ -5730,20 +5730,6 @@ property_value: SCDO:0000340 http://purl.obolibrary.org/obo/IDOMAL_50000026 xsd: property_value: SCDO:1000288 "Sufficient" xsd:string property_value: SCDO:1000910 SCDO:0001370 xsd:string -[Term] -id: LNC:LP16433-2 -name: Hemoglobin G-Philadelphia -def: "Hemoglobin G Philadelphia (HbG Phil) is a structural variant of the hemoglobin molecule that involves the alpha chain rather than the beta chain. It has a frequency of about 1 in 5,000 African Americans, but has been reported in other ethnic groups in the Mediterranean region as well, HbG Phil itself has no clinical consequences. The only finding of clinical interest is the mild microcytosis. While this molecule has no clinical consequences, the presence helps to distinguish HbG from HbD that shares its electrophoretic migration on HPLC and gel electrophoresis and which does have consequences when it occurs with sickle trait." [] -synonym: "Hb G-Phil" EXACT [] -synonym: "Hb G-Philadelphia" EXACT [] -synonym: "HbG Phil" EXACT [] -synonym: "Hemoglobin G Philadelphia" EXACT [] -xref: LNC:LP16433-2 -is_a: SCDO:0006921 ! Hemoglobin Variant -property_value: SCDO:0000340 https://loinc.org/80655-4/ -property_value: SCDO:1000288 "Sufficient" xsd:string -property_value: SCDO:1000910 SCDO:1000689 xsd:string - [Term] id: MP:0001212 name: Skin Lesions @@ -25931,7 +25917,6 @@ name: SickleInAfrica CDE - Hb Assay Results Recorded Question def: "The Sickle in Africa core data element that records the hemoglobins for which assay results were recorded." [] is_a: SCDO:1000509 ! SickleInAfrica Core Data Element relationship: SCDO:1000525 SCDO:1000495 ! is question type Multiple Choice Multiple Selection Question -relationship: SCDO:1000526 LNC:LP16433-2 ! has answer option Hemoglobin G-Philadelphia relationship: SCDO:1000526 SCDO:0000513 ! has answer option Hemoglobin C relationship: SCDO:1000526 SCDO:0000514 ! has answer option Hemoglobin S relationship: SCDO:1000526 SCDO:0000528 ! has answer option Hemoglobin D-Punjab @@ -25940,6 +25925,7 @@ relationship: SCDO:1000526 SCDO:0005446 ! has answer option Fetal Hemoglobin relationship: SCDO:1000526 SCDO:1000009 ! has answer option Hemoglobin E relationship: SCDO:1000526 SCDO:1000016 ! has answer option Hemoglobin O-Arab relationship: SCDO:1000526 SCDO:1000364 ! has answer option Hemoglobin A2 +relationship: SCDO:1000526 SCDO:1000689 ! has answer option Hemoglobin G-Philadelphia relationship: SCDO:1000528 SCDO:1000688 ! collects Hemoglobin Assay Results Recorded property_value: SCDO:1000517 "1, Hb A\n2, Hb F\n3, Hb S\n4, Hb C\n5, Hb E\n6, Hb A2\n7, Hb D-Punjab\n8, Hb G-Philadelphia\n9, Hb O-Arab" xsd:string property_value: SCDO:1000518 "For which hemoglobins were assay results recorded?" xsd:string @@ -25958,6 +25944,20 @@ is_a: SCDO:1000576 ! Diagnostic Measurement Descriptor property_value: http://purl.org/dc/elements/1.1/creator "SCDO (Jade Hotchkiss)" xsd:string property_value: SCDO:1000288 "None" xsd:string +[Term] +id: SCDO:1000689 +name: Hemoglobin G-Philadelphia +def: "Hemoglobin G Philadelphia (HbG Phil) is a structural variant of the hemoglobin molecule that involves the alpha chain rather than the beta chain. It has a frequency of about 1 in 5,000 African Americans, but has been reported in other ethnic groups in the Mediterranean region as well, HbG Phil itself has no clinical consequences. The only finding of clinical interest is the mild microcytosis. While this molecule has no clinical consequences, the presence helps to distinguish HbG from HbD that shares its electrophoretic migration on HPLC and gel electrophoresis and which does have consequences when it occurs with sickle trait." [] +synonym: "Hb G-Phil" EXACT [] +synonym: "Hb G-Philadelphia" EXACT [] +synonym: "HbG Phil" EXACT [] +synonym: "Hemoglobin G Philadelphia" EXACT [] +xref: LNC:LP16433-2 +is_a: SCDO:0006921 ! Hemoglobin Variant +property_value: SCDO:0000340 https://loinc.org/80655-4/ +property_value: SCDO:1000288 "Sufficient" xsd:string +property_value: SCDO:1000910 SCDO:1000689 xsd:string + [Term] id: SCDO:1000690 name: Hemoglobin A Level diff --git a/scdo.owl b/scdo.owl index 682f1c5..9d63900 100644 --- a/scdo.owl +++ b/scdo.owl @@ -1,6 +1,6 @@ - - - + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + + Sickle cell disease (SCD) is one of the most common monogenic diseases in humans with multiple phenotypic expressions that can manifest as both acute and chronic complications. Although described more than a century ago, challenges in comprehensive disease management and collaborative research on this disease are compounded by the complex molecular and clinical phenotypes of SCD, environmental and psychosocial factors, limited therapeutic options and ambiguous terminology. This ambiguous terminology has hampered the integration and interoperability of existing SCD knowledge, and SCD research translation. The SCD Ontology (SCDO), which is a community-driven integrative and universal knowledge representation system for SCD, overcomes this issue by providing a controlled vocabulary developed by a group of experts in both SCD and ontology design. SCDO is the first and most comprehensive standardized human- and machine-readable resource that unambiguously represents terminology and concepts about SCD for researchers, patients and clinicians. It is built around the central concept ‘hemoglobinopathy’, allowing inclusion of non-SCD haemoglobinopathies, such as thalassaemias, which may interfere with or influence SCD phenotypic manifestations. This collaboratively developed ontology constitutes a comprehensive knowledge management system and standardized terminology of various SCD-related factors. The SCDO will promote interoperability of different research datasets, facilitate seamless data sharing and collaborations, including meta-analyses within the SCD community, and support the development and curation of data-basing and clinical informatics in SCD. Anyone can access the resource. @@ -51,8 +50,8 @@ The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - - no + + no definition @@ -62,8 +61,8 @@ For external terms/classes, the ontology from which the term was imported. - no - metadata complete - requires restrictions and relationships + no + metadata complete - requires restrictions and relationships IAO:0000412 imported from @@ -74,268 +73,20 @@ Use on obsolete terms, relating the term to another term that can be used as a substitute. - + IAO:0100001 term replaced by - - - - A shortened form of a word or phrase, in this case a class/term. It consists of a group of letters taken from the word or phrase. - - yes - metadata complete - requires restrictions and relationships - abbreviation - - - - - - - - - discarded/obsoleted synonym - - - - - - - - - plural form - - - - - - - - - layperson term - - - - - - - - - A legal document giving official permission to do something with a Resource. - - no - ontology annotation property - dc:LicenseDocument - License Document - - - - - - - - A summary of the resource. - - no - ontology annotation property - dc:abstract - Abstract - - - - - - - - Information about who can access the resource or an indication of its security status. - - no - ontology annotation property - dc:accessRights - Access Rights - - - - - - - - The method by which items are added to a collection. - - no - ontology annotation property - dc:accrualMethod - Accrual Method - - - - - - - - The frequency with which items are added to a collection. - - no - ontology annotation property - dc:accrualPeriodicity - Accrual Periodicity - - - - - - - - The policy governing the addition of items to a collection. - - no - ontology annotation property - dc:accrualPolicy - Accrual Policy - - - - - - - - A class of entity for whom the resource is intended or useful. - - no - ontology annotation property - dc:audience - Audience - - - + - - - - Date (often a range) that the resource became or will become available. - - no - ontology annotation property - dc:available - Date Available - - - - - - - - An established standard to which the described resource conforms. - - no - ontology annotation property - dc:conformsTo - Conforms To - - - - - - - - The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant. - - no - ontology annotation property - dc:coverage - Coverage - - - - - - - - An entity primarily responsible for making the resource. (This property is used in the SCDO when a term was created by the SCDO Working Group or a curator.) The SCDO uses this especially to apply to term descriptions. - - no - ready for release - dc:creator - Creator - - - - - - - - A related resource that references, cites, or otherwise points to the described resource. - - no - ontology annotation property - dc:isReferencedBy - Is Referenced By - - - - - - - - Date of formal issuance (e.g., publication) of the resource. - - no - ontology annotation property - dc:issued - Date Issued - - - - - - - - A language of the resource. - - no - ontology annotation property - Recommended best practice is to use a controlled vocabulary such as RFC 4646 [RFC4646]. - dc:language - Language - - - - - - - - A legal document giving official permission to do something with the resource. - - no - ontology annotation property - dc:license - License - - - - - - - - A related resource from which the described class/term's annotations are derived. - - yes - pending vetting by the SCDO developers - dc:source - - - - - - - + An administrative note of use for a curator but of no use for a user. - - no - organizational term + + no + organizational term IAO:0000232 editor_notes curator note @@ -343,13 +94,13 @@ - + - + A source from where the formal description was derived. This can be in the form of a link to a relevant webpage, the IRI of a term in an existing ontology, a reference to specific literature, etc. - - yes - metadata complete - requires restrictions and relationships + + yes + metadata complete - requires restrictions and relationships IAO:0000119 definition source description source @@ -357,13 +108,13 @@ - + - + An assertion of whether or not the term/class description is an adaptation of the description in the description source. + Requested inclusion of this property into RO. Check details here again after inclusion. + metadata complete - requires restrictions and relationships SCDO - Requested inclusion of this property into RO. Check details here again after inclusion. - metadata complete - requires restrictions and relationships 'yes' indicates that only the description has been adaptation from the source. 'no' indicates that neither the label nor the description have been adapted from the source. 'only label adapted' indicates that only the label has been adapted from the source but the description is the same as that provided by the source. @@ -376,159 +127,159 @@ - + - + A relation between a disease and the age, developmental stage, or period of life at which the disease or the initial symptoms or manifestations of the disease usually appear in individuals. - SCDO - Requested inclusion of this property into RO. Check details here again after inclusion. + Requested inclusion of this property into RO. Check details here again after inclusion. -This property might be better suited as a data property? If as a data property, perhaps there should be a standardised way of inputting age of onset? - metadata complete - requires restrictions and relationships +This property might be better suited as a data property? If as a data property, perhaps there should be a standardised way of inputting age of onset? + metadata complete - requires restrictions and relationships + SCDO has age of onset - + - + A relation between a measure (e.g. a survey) and how the measure has been adapted cross-culturally. - SCDO - Requested inclusion of this property into RO. Check details here again after inclusion. + Requested inclusion of this property into RO. Check details here again after inclusion. -Should be restricted to all measure/questionnaire classes. - metadata complete - requires restrictions and relationships +Should be restricted to all measure/questionnaire classes. + metadata complete - requires restrictions and relationships + SCDO has cross-cultural adaptation - + - + A relationship between a condition/disease and a description of how the condition/disease is staged/graded. + Requested inclusion of this property into RO. Check details here again after inclusion. + metadata complete - requires restrictions and relationships SCDO - Requested inclusion of this property into RO. Check details here again after inclusion. - metadata complete - requires restrictions and relationships Staging provided is disease/phenotype specific. has disease stage - + - + A relation between a measurement and a plan specification for obtaining the measurement that has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. - SCDO - Requested inclusion of this property into RO. Check details here again after inclusion. + Requested inclusion of this property into RO. Check details here again after inclusion. -To be applied to "Measurement", "Test, Method or Assay", "Therapeutics" - metadata complete - requires restrictions and relationships +To be applied to "Measurement", "Test, Method or Assay", "Therapeutics" + metadata complete - requires restrictions and relationships + SCDO has protocol - + - + A relation between a measure or measurement and the recommended procedure used by the measure or used to obtain the measurement. + Requested inclusion of this property into RO. Check details here again after inclusion. + metadata complete - requires restrictions and relationships SCDO - Requested inclusion of this property into RO. Check details here again after inclusion. - metadata complete - requires restrictions and relationships has recommended procedure - + - + A relation between a measure (e.g. a survey) and the measure's respondents (people who respond). Respondents can be types or groups of people or people with a specific relationship to the main person of interest in the measure. - SCDO - Requested inclusion of this property into RO. Check details here again after inclusion. + Requested inclusion of this property into RO. Check details here again after inclusion. -Should be restricted to all measure/questionnaire classes. - no - metadata complete - requires restrictions and relationships +Should be restricted to all measure/questionnaire classes. + no + metadata complete - requires restrictions and relationships + SCDO If the main person of interest responds, "Self" is indicated. If a person other than the main person of interest can respond, "Proxy" is indicated. If the proxy responder has a specific relationship (Family Members; Health Care Provider or Care-giver) to the main person of interest, that relationship should be indicated in brackets after "Proxy", e.g. Proxy (Health Care Provider or Care-giver). If more than one type of proxy responder is relevant, these should be listed and separated by ";", e.g. Proxy (Family Members; Health Care Provider or Care-giver) has respondents - + - + A relation between a measure (e.g. a survey) and the population that the measure was designed to target. - SCDO - Requested inclusion of this property into RO. Check details here again after inclusion. + Requested inclusion of this property into RO. Check details here again after inclusion. -Should be restricted to all measure/questionnaire classes. - metadata complete - requires restrictions and relationships +Should be restricted to all measure/questionnaire classes. + metadata complete - requires restrictions and relationships + SCDO Possible values used in the SCDO: Healthy Population; Clinic Patients (Children and/or Adults with SCD); Family Members; and/or Health Care Provider has target population - + - + An account of known translations of a measure into other languages (other than English). - SCDO - Requested inclusion of this property into RO. Check details here again after inclusion. + Requested inclusion of this property into RO. Check details here again after inclusion. -Should be restricted to all measure/questionnaire classes. - metadata complete - requires restrictions and relationships +Should be restricted to all measure/questionnaire classes. + metadata complete - requires restrictions and relationships + SCDO has translations - + - + A relation between a planned process and an objective it can be used to achieve. - Requested inclusion of this property into RO. Check details here again after inclusion. - This property is originally an object property. - - metadata complete - requires restrictions and relationships + Requested inclusion of this property into RO. Check details here again after inclusion. + This property is originally an object property. + + metadata complete - requires restrictions and relationships has_application_toward - + - - Eventually to be replaced by "is caused by" object property - metadata incomplete + + Eventually to be replaced by "is caused by" object property + metadata incomplete is caused by - + - + A relationship between a condition (a phenotype or disease) and a description of distinctive characteristics or essential features. + Requested inclusion of this property into RO. Check details here again after inclusion. + metadata complete - requires restrictions and relationships SCDO - Requested inclusion of this property into RO. Check details here again after inclusion. - metadata complete - requires restrictions and relationships is characterised by - + - + Description inherent in name (not provided by source) - Only label adapted - organizational term + Only label adapted + organizational term Used for properties, not classes. For classes, use "has curation status" object property. @@ -537,52 +288,52 @@ For classes, use "has curation status" object property. - + - + A relation between a selected entity and the predefined criteria that were met by the entity and that made it eligible for selection. - SCDO - Requested inclusion of this property into RO. Check details here again after inclusion. + Requested inclusion of this property into RO. Check details here again after inclusion. -Should be restricted to all measure/questionnaire classes. - metadata complete - requires restrictions and relationships +Should be restricted to all measure/questionnaire classes. + metadata complete - requires restrictions and relationships + SCDO selection criteria met - + - + A relation between a measure and the age ranges for which the measure has been validated. - SCDO - Requested inclusion of this property into RO. Check details here again after inclusion. + Requested inclusion of this property into RO. Check details here again after inclusion. -Should be restricted to all measure/questionnaire classes. - metadata complete - requires restrictions and relationships +Should be restricted to all measure/questionnaire classes. + metadata complete - requires restrictions and relationships + SCDO validated for age ranges - + - + A relation between a measure (e.g. a survey) and an indication of whether the measure is freely available. - SCDO - Requested inclusion of this property into RO. Check details here again after inclusion. + Requested inclusion of this property into RO. Check details here again after inclusion. -Should be restricted to all measure/questionnaire classes. - metadata complete - requires restrictions and relationships +Should be restricted to all measure/questionnaire classes. + metadata complete - requires restrictions and relationships + SCDO 'yes' indicates that the measure is freely available. 'no' indicates that the measure is not freely available. freely available - + - + Records the slider label used by REDCap for a data element that uses a slider to collect data. SCDO (Jade Hotchkiss) has slider label @@ -590,36 +341,36 @@ Should be restricted to all measure/questionnaire classes. + - + curation status - complete - + - + curation status - incomplete - + - + An indication of whether or not a clinical code requires an additional code to be specified with it. Annotation is either "yes", "no" or "if applicable, X", where X is the name of a diagnosis for which a code should be provided if it is applicable. SCDO (Jade Hotchkiss) requires additional code - + - + - + An indication of whether a term/class already exists in other ontologies. Only used for term (descriptions) that were not taken directly from an existing ontology. SCDO (Jade Hotchkiss) Annotation options: @@ -634,97 +385,97 @@ None - + - + Records the answer options text for input in Redcap for a data element that provides answer options. SCDO (Jade Hotchkiss) has answer options text - + - + - + Records the field label of a data element. SCDO (Jade Hotchkiss) has field label - + - + - + Records the variable of the associated data element from a REDCap data capture instrument. SCDO (Jade Hotchkiss) has redcap variable - + - + - + Records the section of a CRF in which a data element occurs. SCDO (Jade Hotchkiss) in CRF section - + - + - + Records the calculation used to automatically calculate the value for a data element in REDCap. SCDO (Jade Hotchkiss) has calculation equation - + - + - + Records a data element's field note (a note provided below the answer field). SCDO (Jade Hotchkiss) has field note - + - + - + Records the order in which a data element appears in a specific section of a specific CRF/questionnaire/instrument. This is provided in the form of a number which is relative to the order numbers of other data elements of the section. SCDO (Jade Hotchkiss) order in CRF section - + - + - + Used to provide a list of sections present in a questionnaire/instrument. SCDO (Jade Hotchkiss) has sections - + - + - + Records the type of validation used for a data element in REDCap. SCDO (Jade Hotchkiss) has redcap validation @@ -732,75 +483,75 @@ None - + - + Records the branching logic applied to a data element in REDCap. SCDO (Jade Hotchkiss) has branching logic - + - + - + Records the mainimum value that is accepted for a data element that has validation applied to it in REDCap. SCDO (Jade Hotchkiss) has redcap min number validation - + - + - + Records the maximum value that is accepted for a data element that has validation applied to it in REDCap. SCDO (Jade Hotchkiss) has redcap max number validation - + - + - + Records the field annotations of a data element in REDCap. SCDO (Jade Hotchkiss) has redcap field annotation - + - + - + Used to show if a data element is considered an "identifier" (meaning it contains identifying information). SCDO (Jade Hotchkiss) is identifier - + - + - + Used to show if a data element is a required field. "y" is assigned to it if the data element is a required field. SCDO (Jade Hotchkiss) required field - + - + - + Records the custom alignment of a data element in REDCap. SCDO (Jade Hotchkiss) custom alignment @@ -808,31 +559,31 @@ None - + - + Records a data element's field type, as per REDCap. SCDO (Jade Hotchkiss) has field type - + - + - + Used to record the matrix group that a data element occurs in. SCDO (Jade Hotchkiss) in matrix group - + - + - + An indication of whether or not a data element with a dropdown field should be autocompleted. Annotation is either "yes" or "no". SCDO (Jade Hotchkiss) autocomplete @@ -840,9 +591,9 @@ None - + - + An indication of whether or not a data element with a slider field should display the slider's number values. Annotation is either "yes" or "no". SCDO (Jade Hotchkiss) show slider @@ -850,9 +601,9 @@ None - + - + Used to record the identifier that had been used previously but is no longer in use. SCDO (Jade Hotchkiss) previous identifier @@ -860,6 +611,254 @@ None + + + + A shortened form of a word or phrase, in this case a class/term. It consists of a group of letters taken from the word or phrase. + + yes + metadata complete - requires restrictions and relationships + abbreviation + + + + + + + + + discarded/obsoleted synonym + + + + + + + + + plural form + + + + + + + + + layperson term + + + + + + + + + A legal document giving official permission to do something with a Resource. + + no + ontology annotation property + dc:LicenseDocument + License Document + + + + + + + + A summary of the resource. + + no + ontology annotation property + dc:abstract + Abstract + + + + + + + + Information about who can access the resource or an indication of its security status. + + no + ontology annotation property + dc:accessRights + Access Rights + + + + + + + + The method by which items are added to a collection. + + no + ontology annotation property + dc:accrualMethod + Accrual Method + + + + + + + + The frequency with which items are added to a collection. + + no + ontology annotation property + dc:accrualPeriodicity + Accrual Periodicity + + + + + + + + The policy governing the addition of items to a collection. + + no + ontology annotation property + dc:accrualPolicy + Accrual Policy + + + + + + + + A class of entity for whom the resource is intended or useful. + + no + ontology annotation property + dc:audience + Audience + + + + + + + + Date (often a range) that the resource became or will become available. + + no + ontology annotation property + dc:available + Date Available + + + + + + + + An established standard to which the described resource conforms. + + no + ontology annotation property + dc:conformsTo + Conforms To + + + + + + + + The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant. + + no + ontology annotation property + dc:coverage + Coverage + + + + + + + + An entity primarily responsible for making the resource. (This property is used in the SCDO when a term was created by the SCDO Working Group or a curator.) The SCDO uses this especially to apply to term descriptions. + + no + ready for release + dc:creator + Creator + + + + + + + + A related resource that references, cites, or otherwise points to the described resource. + + no + ontology annotation property + dc:isReferencedBy + Is Referenced By + + + + + + + + Date of formal issuance (e.g., publication) of the resource. + + no + ontology annotation property + dc:issued + Date Issued + + + + + + + + A language of the resource. + + no + ontology annotation property + Recommended best practice is to use a controlled vocabulary such as RFC 4646 [RFC4646]. + dc:language + Language + + + + + + + + A legal document giving official permission to do something with the resource. + + no + ontology annotation property + dc:license + License + + + + + + + + A related resource from which the described class/term's annotations are derived. + + yes + pending vetting by the SCDO developers + dc:source + + + + @@ -872,9 +871,9 @@ None An alias in which the alias is broader than the primary class name. Example: cell division is a broad synonym of cytokinesis. - - no - pending vetting by the SCDO developers + + no + pending vetting by the SCDO developers hasBroadSynonym @@ -884,8 +883,8 @@ None A database cross-reference. An annotation which directs one to information contained within a database. - - metadata complete - requires restrictions and relationships + + metadata complete - requires restrictions and relationships SBO:0000554 DbXref Xref @@ -902,9 +901,9 @@ None An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle. - - no - pending vetting by the SCDO developers + + no + pending vetting by the SCDO developers hasExactSynonym @@ -914,9 +913,9 @@ None An alias in which the alias is narrower than the primary class name. Example: pyrimidine-dimer repair by photolyase is a narrow synonym of photoreactive repair. - - no - pending vetting by the SCDO developers + + no + pending vetting by the SCDO developers hasNarrowSynonym @@ -926,9 +925,9 @@ None An alias in which the alias is related to the primary class name, but not necessarily broader or narrower. Example: cytochrome bc1 complex is a related synonym of ubiquinol-cytochrome-c reductase activity; virulence is a related synonym of pathogenesis. - - no - pending vetting by the SCDO developers + + no + pending vetting by the SCDO developers hasRelatedSynonym @@ -947,8 +946,8 @@ None Additional information describing the class/term. - - yes + + yes rdfs:comment @@ -958,8 +957,8 @@ None A human-readable name for the class/term. - - yes + + yes rdfs:label @@ -969,8 +968,8 @@ None Further information about the class/term. - - yes + + yes rdfs:seeAlso @@ -989,9 +988,9 @@ None A preferred label. - - yes - pending vetting by the SCDO developers + + yes + pending vetting by the SCDO developers skos:prefLabel @@ -1012,9 +1011,9 @@ None A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - - no - metadata complete - requires restrictions and relationships + + no + metadata complete - requires restrictions and relationships RO:0002200 has phenotype @@ -1025,10 +1024,10 @@ None Inverse of "has phenotype" object property. - If required later, specify as inverse of "has phenotype" in Protege. - - no - metadata complete - requires restrictions and relationships + If required later, specify as inverse of "has phenotype" in Protege. + + no + metadata complete - requires restrictions and relationships phenotype of @@ -1039,8 +1038,8 @@ None A relation that holds between a disease or an organism and a phenotype that is a symptom (subjective evidence of disease perceived by the patient). - Description adapted from RO. Suggest this description be updated in RO. - + Description adapted from RO. Suggest this description be updated in RO. + RO:0002452 has symptom @@ -1050,9 +1049,9 @@ None - + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. - + RO:0003302 causes or contributes to condition @@ -1062,9 +1061,9 @@ None - + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. - + RO:0003303 results_in causes condition @@ -1075,9 +1074,9 @@ None - + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. - + RO:0003306 contributes to frequency of condition @@ -1087,9 +1086,9 @@ None - + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. - + RO:0003307 ameliorates condition @@ -1099,9 +1098,9 @@ None - + A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. - + RO:0003309 exacerbates condition @@ -1111,9 +1110,9 @@ None - + A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. - + RO:0003310 condition ameliorated by @@ -1123,30 +1122,19 @@ None - + A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. - + RO:0003311 condition exacerbated by - - - - - - so:associated_with - associated with - - - - - + - - + + A relationship between a phenotype and a disease modifier, where the disease modifier modifies the age of onset of the phenotype. Age of onset is defined as "The age group in which disease manifestations appear." (HPO) SCDO (Jade Hotchkiss) age of onset modified by @@ -1154,20 +1142,20 @@ None - + - + A relationship between a condition (phenotype or disease) and a relevant ICD-10-CM Diagnosis Code. + None SCDO (Jade Hotchkiss) - None has clinical code - + - + A relation between a device (diagnostic device) and the recording of the output (diagnostic measurement) of the device. SCDO (Jade Hotchkiss) @@ -1176,9 +1164,9 @@ None - + - + A relation between a process (e.g. a form of therapy) and a medical device, where the medical device is used in the process. SCDO (Jade Hotchkiss) @@ -1187,9 +1175,9 @@ None - + - + A relationship between a condition (a phenotype or disease) and an entity (a genotype or genetic variation) where the entity has a causal role for the condition. SCDO (Jade Hotchkiss) @@ -1198,9 +1186,9 @@ None - + - + A relation between a phenotype that is a diagnosis and a diagnostic tool used in making the diagnosis. SCDO (Jade Hotchkiss) diagnosed using tool @@ -1208,21 +1196,21 @@ None - + - + A relation between a condition (phenotype or disease) and a type of treatment or a specific treatment, where the condition can be treated with the treatment. + If required later, specify as inverse of "treats". SCDO (Jade Hotchkiss) - If required later, specify as inverse of "treats". treated with - + - - + + A relationship between a phenotype and a disease modifier, where the disease modifier modifies the mortality (due to the phenotype) of the SCD sufferer. SCDO (Jade Hotchkiss) mortality modified by @@ -1230,10 +1218,10 @@ None - + - - + + A relationship between a phenotype and a disease modifier, where the disease modifier modifies the temporal pattern of the phenotype. Temporal pattern is defined as "The speed at which disease manifestations appear and develop." (HPO) SCDO (Jade Hotchkiss) temporal pattern modified by @@ -1241,9 +1229,9 @@ None - + - + A measure that is critical to the collection of the measure at hand or is necessary for the interpretation of results for the measure at hand. Without such information, the data collected would be incomplete or misleading. SCDO (Jade Hotchkiss) Essential measures have been attributed according to information in PhenX. @@ -1252,9 +1240,9 @@ None - + - + A relation between a particular genotype or disorder and the pattern in which the particular genotype or disorder is passed from one generation to the next. SCDO (Jade Hotchkiss) has mode of inheritance @@ -1262,9 +1250,9 @@ None - + - + A relationship between a condition (phenotype or disease), entity (aspect of quality of life) or process (therapy) and a disease modifier, where the condition, entity or process is modified by the disease modifier in some way. SCDO (Jade Hotchkiss) @@ -1273,9 +1261,9 @@ None - + - + A relationship between a disease modifier and a condition (phenotype or disease), entity (aspect of quality of life) or process (therapy), where the disease modifier modifies the condition, entity or process in some way. SCDO (Jade Hotchkiss) @@ -1284,20 +1272,20 @@ None - + - + A relation between a type of treatment or a specific treatment and a condition (phenotype or disease), where the type of treatment or specific treatment treat the condition. + If required later, specify as inverse of "treated with". SCDO (Jade Hotchkiss) - If required later, specify as inverse of "treated with". treats - + - + A relation between a Diagnostic Tool (test, method, assay, etc.) or the Diagnostic Measurement obtained from such a tool and a specific Diagnostic Device, where the Diagnostic Device is used in the application of the Diagnostic Tool or to obtain the Diagnostic Measurement. SCDO (Jade Hotchkiss) @@ -1306,10 +1294,10 @@ None - + - - + + A relation between a condition (hemoglobinopathy) and the genotype that causes the condition. SCDO (Jade Hotchkiss) has causal genotype @@ -1317,12 +1305,12 @@ None - + - + - - + + An object property that specifies the type of an ICD-10-CM code, whether Billable or Non-Billable. SCDO (Jade Hotchkiss) is ICD-10-CM code type @@ -1330,9 +1318,9 @@ None - + - + A relationship that holds between a phenotype (i.e. manifestation) and a condition such as a disease (hemoglobinopathy), wherein the phenotype is evidence of the condition. SCDO (Jade Hotchkiss) @@ -1341,9 +1329,9 @@ None - + - + A relation between a phenotype that is a symptom (subjective evidence of disease perceived by the patient) and a disease. SCDO (Jade Hotchkiss) @@ -1352,9 +1340,9 @@ None - + - + A relationship between 'a' and 'b', where 'a' has some causal role for 'b'. SCDO (Jade Hotchkiss) @@ -1363,10 +1351,10 @@ None - + - - + + A relationship between an entity (e.g. genetic variation such as mutation or specific allele) and a genotype, where the entity contributes to the genotype. SCDO (Jade Hotchkiss) contributes to genotype @@ -1374,9 +1362,9 @@ None - + - + A relation between a condition (Hemoglobinopathy) and a form of research (type of study) that the condition was studied in. SCDO (Jade Hotchkiss) @@ -1385,9 +1373,9 @@ None - + - + A relation between a condition (disease or phenotype) and a type of linking association (e.g. age of onset association). SCDO (Jade Hotchkiss) associated via @@ -1395,9 +1383,9 @@ None - + - + A relationship between a diagnostic measurement and the diagnostic tool used to produce the measurement. SCDO (Jade Hotchkiss) @@ -1406,9 +1394,9 @@ None - + - + A relationship between a diagnostic device and the diagnostic tool by which the device is used. SCDO (Jade Hotchkiss) @@ -1417,9 +1405,9 @@ None - + - + A relation between a diagnostic tool (test, method, assay, etc.) and a diagnostic device, where the diagnostic device is used in the application of the diagnostic tool. SCDO (Jade Hotchkiss) @@ -1428,9 +1416,9 @@ None - + - + A relation between a diagnostic measurement and a diagnostic device, where the diagnostic measurement is the output of the diagnostic device. SCDO (Jade Hotchkiss) @@ -1439,9 +1427,9 @@ None - + - + A relation between a diagnostic tool and the diagnostic measurement that it measures. SCDO (Jade Hotchkiss) @@ -1450,10 +1438,10 @@ None - + - - + + A relation between a genotype and a genetic variation (e.g. mutation or genetic recombination), where the genetic variation contributes to the genotype. SCDO (Jade Hotchkiss) has contributing genetic variation @@ -1461,22 +1449,22 @@ None - + - + A condition (phenotype or disease) or event (adverse event) induced by an entity (e.g. a drug) or activity (e.g. exercise). + The "developmentally induced by" object property in RO has the alternative term "induced by". SCDO (Jade Hotchkiss) - The "developmentally induced by" object property in RO has the alternative term "induced by". induced by - + - - + + A relationship between a condition (a phenotype or disease) and an entity (e.g. environment) or condition (phenotype or disease) which could be an existing condition or an event, where the entity or second condition has a causal role for the condition being described. SCDO (Jade Hotchkiss) caused by @@ -1484,9 +1472,9 @@ None - + - + A relation between a condition (disease or phenotype) and an aspect of an individual's life (personal attribute), behavior, an environmental exposure, or an inborn or inherited characteristic that increases the likelihood of the condition. SCDO (Jade Hotchkiss) @@ -1495,9 +1483,9 @@ None - + - + A relation between an aspect of an individual's life (personal attribute), behavior, an environmental exposure, or an inborn or inherited characteristic that increases the likelihood of a condition and the condition (disease or phenotype) that it increases the likelihood of. SCDO (Jade Hotchkiss) @@ -1506,10 +1494,10 @@ None - + - - + + A relation between a condition (disease or phenotype) or an entity (molecular phenotype) and a genetic variation (e.g. mutation or genetic recombination), where the genetic variation has some causal or contributing role that influences the condition or entity. SCDO (Jade Hotchkiss) has causal or contributing genetic variation @@ -1517,10 +1505,10 @@ None - + - - + + A relation between an entity (genotype) and a molecular phenotype, where the entity has some causal or contributing role that influences the molecular phenotype. SCDO (Jade Hotchkiss) causes or contributes to molecular phenotype @@ -1528,9 +1516,9 @@ None - + - + A relationship that holds between a condition such as a disease (hemoglobinopathy) and a phenotype (i.e. manifestation), where the phenotype is evidence of the condition. SCDO (Jade Hotchkiss) @@ -1539,9 +1527,9 @@ None - + - + A relation between a condition that is a diagnosis and a phenotype used in making the diagnosis. diagnosed by @@ -1549,9 +1537,9 @@ None - + - + A relation between an Abnormal Phenotype that is a diagnosis and a Diagnostic Measurement or Diagnostic Device Visual Output used in making the diagnosis. SCDO (Jade Hotchkiss) @@ -1560,10 +1548,10 @@ None - + - - + + A relation between a genotype and a molecular phenotype, where the genotype has a causal role for the molecular phenotype. SCDO (Jade Hotchkiss) causes molecular phenotype @@ -1571,10 +1559,10 @@ None - + - - + + A relation between a condition (disease such as a Hemoglobinopathy) and a molecular phenotype, where the molecular phenotype is evidence of the condition. SCDO (Jade Hotchkiss) has causal molecular phenotype @@ -1582,64 +1570,64 @@ None - + - - - + + + A relationship between a Clinical or Research Assessment Data Element and a Clinical or Research Assessment Question Type. + None SCDO (Jade Hotchkiss) - None is question type - + - + - + A relationship between a multiple choice data element and an answer option or a group of answer options that are provided to the respondent by the data element. + None SCDO (Jade Hotchkiss) - None has answer option - + - + - + A relationship between a data element and the type of information that is collected by that data element. + None SCDO (Jade Hotchkiss) - None collects - + - + - + A relationship between a data element and the unit of measurement used, as a standard, for the information that is collected by the data element. + None SCDO (Jade Hotchkiss) - None has answer standard unit - + - + - + A relationship between a Diagnostic Measurement and a Phenotype, where the Phenotype is a possible finding of the Diagnostic Measurement, depending on the value recorded for the Diagnostic Measurement. SCDO (Jade Hotchkiss) @@ -1648,9 +1636,9 @@ None - + - + A relationship between an Abnormal Phenotype that is a diagnosis of a condition and a Phenotype that is a finding from a Diagnostic Measurement, where the Phenotype that is a finding is used as evidence to diagnose patients with the Abnormal Phenotype that is a diagnosis. @@ -1660,22 +1648,22 @@ None - + - - + + A relationship between a Diagnostic Measurement and the Unit of Measurement used for the values provided by the data properties that specify upper (ULN) or lower (LLN) limit of normal for the Diagnostic Measurement. + None SCDO (Jade Hotchkiss) - None has reference range standard unit - + - + A relationship between a clinical code (such as ICD10 code) and a Phenotype, where the code can only be applied in instances where the phenotype is present. SCDO (Jade Hotchkiss) @@ -1684,9 +1672,9 @@ None - + - + A relation between an entity (phenotypic, therapeutic or diagnostic concept) and a guideline or directive. SCDO (Jade Hotchkiss) in guideline @@ -1694,10 +1682,21 @@ None + + + + + + so:associated_with + associated with + + + + - Add properties that link diagnostic tools or measurements back to phenotypes..."diagnoses" when linked to a diagnosis? "detects" when linked to a phenotype that is a deviation from normal (e.g. an increased level of something). + Add properties that link diagnostic tools or measurements back to phenotypes..."diagnoses" when linked to a diagnosis? "detects" when linked to a phenotype that is a deviation from normal (e.g. an increased level of something). @@ -1713,16 +1712,16 @@ None - + - + - + Used to record the lowest value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for particular laboratory result or other quantitative parameter. + None - None has lower limit of normal has lower reference limit has LLN @@ -1730,16 +1729,16 @@ None - + - + - + Used to record the top value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for particular laboratory result or other quantitative parameter. + None - None has upper limit of normal has upper reference limit has ULN @@ -1747,9 +1746,9 @@ None - + - + Records the minimum number of selections that a respondent is allowed to make from a list of multiple answer options provided for a data element. @@ -1759,9 +1758,9 @@ None - + - + Records the maximum number of selections that a respondent is allowed to make from a list of multiple answer options provided for a data element. @@ -1771,96 +1770,96 @@ None - + - + - + Used to record the lowest value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for males for a particular laboratory result or other quantitative parameter. + None - None has lower limit of normal for males has LLN male - + - + - + Used to record the lowest value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for females for a particular laboratory result or other quantitative parameter. + None - None has lower limit of normal for females has LLN female - + - + - + Used to record the lowest value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for children for a particular laboratory result or other quantitative parameter. + None - None has lower limit of normal for children has LLN pediatric - + - + - + Used to record the top value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for males for a particular laboratory result or other quantitative parameter. + None - None has upper limit of normal for males has ULN male - + - + - + Used to record the top value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for females for a particular laboratory result or other quantitative parameter. + None - None has upper limit of normal for females has ULN female - + - + - + Used to record the top value of the range of statistical characteristics that are supposed to represent accepted standard, non-pathological pattern for children for a particular laboratory result or other quantitative parameter. + None - None has upper limit of normal for children has ULN pediatric @@ -1883,10 +1882,10 @@ None A spatiotemporal region encompassing some part of the life cycle of an organism. - See specific stages in the "Human Developmental Stages Ontology" - http://purl.obolibrary.org/obo/HsapDv_0000000 - Sufficient - SCDO:0007384 + See specific stages in the "Human Developmental Stages Ontology" + http://purl.obolibrary.org/obo/HsapDv_0000000 + Sufficient + SCDO:0007384 HsapDv:0000000 Developmental Stage Human Life Cycle Stage @@ -1897,11 +1896,11 @@ None - + An information content entity specifying the upper and lower limit of a range of ages of continuants. - - Sufficient - SCDO:1000403 + + Sufficient + SCDO:1000403 APOLLO_SV:00000241 Age Range Category @@ -1912,59 +1911,59 @@ None - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Erythromycin is a macrolide antibiotic with a 14-carbon ring that has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people that have an allergy to penicillins. Erythromycin may possess bacteriocidal activity, particularly at higher concentrations by binding to the 50S subunit of the bacterial 70S rRNA complex, inhibiting peptidyl-tRNA translocation. Thus, protein synthesis and subsequently structure/function processes critical for life or replication are inhibited. - http://purl.obolibrary.org/obo/ARO_0000006 - Sufficient - SCDO:0003119 + http://purl.obolibrary.org/obo/ARO_0000006 + Sufficient + SCDO:0003119 ARO:0000006 Abomacetin Emgel @@ -1984,77 +1983,77 @@ None - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Penicillin (sometimes abbreviated PCN) is a beta-lactam antibiotic used in the treatment of bacterial infections caused by susceptible, usually Gram-positive, organisms. It works by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. - - Sufficient - SCDO:0000880 + + Sufficient + SCDO:0000880 ARO:0000054 PCN Penicillins @@ -2069,20 +2068,20 @@ None - + - - + + Amoxicillin is a moderate-spectrum, bacteriolytic, beta-lactam antibiotic used to treat bacterial infections caused by susceptible microorganisms. A derivative of penicillin, it has a wider range of treatment but remains relatively ineffective against Gram-negative bacteria. It is commonly taken with clavulanic acid, a beta-lactamase inhibitor. Like other beta-lactams, amoxicillin interferes with the synthesis of peptidoglycan. - http://purl.obolibrary.org/obo/ARO_0000064 - Sufficient - SCDO:0002381 + http://purl.obolibrary.org/obo/ARO_0000064 + Sufficient + SCDO:0002381 ARO:0000064 AMX Amolin @@ -2101,13 +2100,13 @@ None - + Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances. - Add sub-class "Iron Chelator" with sub-classes "Deferoxamine" and "Deferiprone" (see wikipedia page for "Beta Thalassemia"...mentions how they're used to treat beta thalassemia major). -Also add "Deferoxamine" and "Deferiprone" below "Iron Chelation Therapy". - - Sufficient - SCDO:1000200 + Add sub-class "Iron Chelator" with sub-classes "Deferoxamine" and "Deferiprone" (see wikipedia page for "Beta Thalassemia"...mentions how they're used to treat beta thalassemia major). +Also add "Deferoxamine" and "Deferiprone" below "Iron Chelation Therapy". + + Sufficient + SCDO:1000200 CHEBI:23888 Drug @@ -2117,59 +2116,59 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An anti-inflammatory drug that is not a steroid. In addition to anti-inflammatory actions, non-steroidal anti-inflammatory drugs have analgesic, antipyretic, and platelet-inhibitory actions. They act by blocking the synthesis of prostaglandins by inhibiting cyclooxygenase, which converts arachidonic acid to cyclic endoperoxides, precursors of prostaglandins. - http://purl.obolibrary.org/obo/CHEBI_35475 - Sufficient - SCDO:0005809 + http://purl.obolibrary.org/obo/CHEBI_35475 + Sufficient + SCDO:0005809 CHEBI:35475 Non-Steroidal Anti-Inflammatory Agent Non-Steroidal Anti-Inflammatory Drug @@ -2180,59 +2179,59 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood. - http://purl.obolibrary.org/obo/CHEBI_35482 - Sufficient - SCDO:0000836 + http://purl.obolibrary.org/obo/CHEBI_35482 + Sufficient + SCDO:0000836 CHEBI:35482 Opioid Analgesic Opioid @@ -2244,35 +2243,35 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + - - + + - - + + - - + + - - + + A drug that prevents or reduces fever by lowering the body temperature from a raised state. An antipyretic will not affect the normal body temperature if one does not have fever. Antipyretics cause the hypothalamus to override an interleukin-induced increase in temperature. The body will then work to lower the temperature and the result is a reduction in fever. - http://purl.obolibrary.org/obo/CHEBI_35493 - Sufficient - SCDO:0005335 + http://purl.obolibrary.org/obo/CHEBI_35493 + Sufficient + SCDO:0005335 CHEBI:35493 Anti-Pyretic Antipyretic @@ -2284,23 +2283,23 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + - - + + - - + + A gamma-amino acid that is cyclohexane substituted at position 1 by aminomethyl and carboxymethyl groups. Used for treatment of neuropathic pain and restless legs syndrome. - http://purl.obolibrary.org/obo/CHEBI_42797 - Sufficient - SCDO:0007493 + http://purl.obolibrary.org/obo/CHEBI_42797 + Sufficient + SCDO:0007493 CHEBI:42797 1-(Aminomethyl)cyclohexaneacetic acid Neurontin @@ -2312,11 +2311,11 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + A natural or synthetic analogue of the hormones secreted by the adrenal gland. - - Sufficient - SCDO:0003901 + + Sufficient + SCDO:0003901 CHEBI:50858 Corticoides Corticosteroides @@ -2331,9 +2330,9 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C An opioid analgesic derived from morphine and used mainly as an analgesic. It has a shorter duration of action and is more potent than morphine. - http://www.drugbank.ca/drugs/DB00327 - Sufficient - SCDO:0000577 + http://www.drugbank.ca/drugs/DB00327 + Sufficient + SCDO:0000577 CHEBI:5790 3-hydroxy-17-methyl-4,5alpha-epoxymorphinan-6-one Hydromorphone @@ -2344,17 +2343,17 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + - + Any pharmacological or immunological agent that modifies the effect of other agents such as drugs or vaccines while having few if any direct effects when given by itself. - http://purl.obolibrary.org/obo/CHEBI_60809 - Sufficient - SCDO:0000025 + http://purl.obolibrary.org/obo/CHEBI_60809 + Sufficient + SCDO:0000025 CHEBI:60809 Adjuvant Medicine Adjuvant @@ -2368,20 +2367,20 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - - + + - - + + A synthetic opioid that is used as the hydrochloride. It is an opioid analgesic that is primarily a mu-opioid agonist. It has actions and uses similar to those of morphine. It also has a depressant action on the cough center and may be given to control intractable cough associated with terminal lung cancer. Methadone is also used as part of the treatment of dependence on opioid drugs, although prolonged use of methadone itself may result in dependence. - http://www.drugbank.ca/drugs/DB00333 - Sufficient - SCDO:0000752 + http://www.drugbank.ca/drugs/DB00333 + Sufficient + SCDO:0000752 CHEBI:6807 6-(dimethylamino)-4,4-diphenylheptan-3-one Physeptone @@ -2394,29 +2393,29 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + - + - - + + - - + + A member of the class of imidazoles substituted at C-1, -2 and -5 with 2-hydroxyethyl, nitro and methyl groups respectively. It has activity against anaerobic bacteria and protozoa, and has a radiosensitising effect on hypoxic tumour cells. It may be given by mouth in tablets, or as the benzoate in an oral suspension. The hydrochloride salt can be used in intravenous infusions. Metronidazole is a prodrug and is selective for anaerobic bacteria due to their ability to intracellularly reduce the nitro group of metronidazole to give nitroso-containing intermediates. These can covalently bind to DNA, disrupting its helical structure, inducing DNA strand breaks and inhibiting bacterial nucleic acid synthesis, ultimately resulting in bacterial cell death. - http://purl.obolibrary.org/obo/CHEBI_6909 - Sufficient - SCDO:0002912 + http://purl.obolibrary.org/obo/CHEBI_6909 + Sufficient + SCDO:0002912 CHEBI:6909 Satric Trichazol @@ -2431,38 +2430,38 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - - + + - - + + - - + + - - + + - - + + A semisynthetic derivative of codeine that acts as a narcotic analgesic more potent and addicting than codeine. - http://www.drugbank.ca/drugs/DB00497 - Sufficient - SCDO:0000847 + http://www.drugbank.ca/drugs/DB00497 + Sufficient + SCDO:0000847 CHEBI:7852 14-hydroxy-3-methoxy-17-methyl-4,5alpha-epoxymorphinan-6-one Dihydrone @@ -2475,14 +2474,14 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - - + + Column chromatography where the mobile phase is a liquid, the stationary phase consists of very small particles and the inlet pressure is relatively high. + Perhaps change label to "Hemoglobin by High Performance Liquid Chromatography"? See dc:source provided. + http://purl.obolibrary.org/obo/CHMO_0001009 + Sufficient + SCDO:0000563 - Perhaps change label to "Hemoglobin by High Performance Liquid Chromatography"? See dc:source provided. - http://purl.obolibrary.org/obo/CHMO_0001009 - Sufficient - SCDO:0000563 CHMO:0001009 HPLC High Performance Liquid Chromatography @@ -2496,11 +2495,11 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + A test which produces colour change in the sample. - http://purl.obolibrary.org/obo/CHMO_0002580 - Sufficient - SCDO:0000264 + http://purl.obolibrary.org/obo/CHMO_0002580 + Sufficient + SCDO:0000264 CHMO:0002580 Colorimetric Test @@ -2510,11 +2509,11 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart and/or blood vessels. - http://purl.obolibrary.org/obo/CMO_0000001 - Sufficient - SCDO:0000186 + http://purl.obolibrary.org/obo/CMO_0000001 + Sufficient + SCDO:0000186 CMO:0000001 Cardiovascular Measurement @@ -2527,15 +2526,15 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - - + + Measurement of the pressure, or force per area, exerted by circulating blood against the walls of the blood vessels. The pressure is dependent on the energy of the heart action, elasticity of the vessel walls and volume and viscosity of the blood. - There are many more specific sub-classes in the CMO. Are there any we want to include here? - http://purl.obolibrary.org/obo/CMO_0000003 - Sufficient - SCDO:0000144 + There are many more specific sub-classes in the CMO. Are there any we want to include here? + http://purl.obolibrary.org/obo/CMO_0000003 + Sufficient + SCDO:0000144 CMO:0000003 Blood Pressure Measurement @@ -2547,9 +2546,9 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C Morphological measurement involving the entire body of an organism. - http://purl.obolibrary.org/obo/CMO_0000011 - Sufficient - SCDO:0001245 + http://purl.obolibrary.org/obo/CMO_0000011 + Sufficient + SCDO:0001245 CMO:0000011 Whole Body Morphological Measurement @@ -2559,41 +2558,41 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + - + - - + + - + - + - + The level of heat in an organism. - - Sufficient - SCDO:0000151 + + Sufficient + SCDO:0000151 CMO:0000015 Body Temperature @@ -2603,12 +2602,12 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + Measurement of the structure or forms of the entire body or parts of the body of an organism. - Include the term "Body Composition" from PhenX? -- -- Any other relevant terms missing as sub-classes here? - http://purl.obolibrary.org/obo/CMO_0000021 - Sufficient - SCDO:0000150 + Include the term "Body Composition" from PhenX? -- -- Any other relevant terms missing as sub-classes here? + http://purl.obolibrary.org/obo/CMO_0000021 + Sufficient + SCDO:0000150 CMO:0000021 Anthropometric Measurement Anthropometrics @@ -2623,9 +2622,9 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C A quantification of a parameter of the chemical composition of blood. - http://purl.obolibrary.org/obo/CMO_0000023 - Sufficient - SCDO:0000136 + http://purl.obolibrary.org/obo/CMO_0000023 + Sufficient + SCDO:0000136 CMO:0000023 Blood Chemistry Measurement @@ -2638,38 +2637,38 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + - - + + - + - + - - + + The number of red blood cells in a specified volume of blood most commonly 1 cubic millimeter (i.e. 1 microliter) of peripheral venous blood. - http://purl.obolibrary.org/obo/CMO_0000025 - Sufficient - SCDO:0000973 + http://purl.obolibrary.org/obo/CMO_0000025 + Sufficient + SCDO:0000973 CMO:0000025 Erythrocyte Count Erythrocyte Number @@ -2686,44 +2685,44 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + - - + + - + - + - - + + - - + + The number of white blood cells in a specified volume of blood. - http://purl.obolibrary.org/obo/CMO_0000027 - Sufficient - SCDO:0001243 + http://purl.obolibrary.org/obo/CMO_0000027 + Sufficient + SCDO:0001243 CMO:0000027 Leukocyte Count White Corpuscle Count @@ -2738,38 +2737,38 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + - - + + - + - + - - + + The number of platelets (thrombocytes) in a specified volume of blood, usually expressed as platelets per cubic millimeter of whole blood. - http://purl.obolibrary.org/obo/CMO_0000029 - Sufficient - SCDO:0000906 + http://purl.obolibrary.org/obo/CMO_0000029 + Sufficient + SCDO:0000906 CMO:0000029 Blood Platelet Number Blood Platelet count @@ -2784,9 +2783,9 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C The number of granulocytes categorized as neutrophils in a specified volume of blood. A neutrophil is, or is in the process of becoming, a granular leucocyte having a nucleus with three to five lobes connected by threads of chromatin, cytoplasm containing very fine granules, and which is readily stainable with neutral dyes. - - Sufficient - SCDO:1000442 + + Sufficient + SCDO:1000442 CMO:0000030 Neutrophil Granulocyte Count Blood Neutrophil Count @@ -2797,11 +2796,11 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + A measurement of the blood, it's contents, cells or other factors contained within the blood. - http://purl.obolibrary.org/obo/CMO_0000035 - Sufficient - SCDO:0000143 + http://purl.obolibrary.org/obo/CMO_0000035 + Sufficient + SCDO:0000143 CMO:0000035 Blood Measurement @@ -2813,10 +2812,10 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C A value resulting from the quantification of a morphological or physiological parameter of blood cells, i.e. cells native to the circulation, including those of erythroid, lymphoid, myeloid and monocytic lineages. A cell is a membrane-enclosed protoplasmic mass constituting the smallest structural unit of an organism that is capable of independent functioning. - Perhaps include missing sub-classes of "Blood Cell Measurement" from the Clinical Measurement Ontology? - http://purl.obolibrary.org/obo/CMO_0000036 - Sufficient - SCDO:0000135 + Perhaps include missing sub-classes of "Blood Cell Measurement" from the Clinical Measurement Ontology? + http://purl.obolibrary.org/obo/CMO_0000036 + Sufficient + SCDO:0000135 CMO:0000036 Blood Cell Measurement @@ -2829,44 +2828,44 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - - + + - - + + - - + + - - + + - - + + - - + + Percentage of total blood volume that is made up of red blood cells. - http://purl.obolibrary.org/obo/CMO_0000037 - Sufficient - SCDO:0000503 + http://purl.obolibrary.org/obo/CMO_0000037 + Sufficient + SCDO:0000503 CMO:0000037 Hct Packed Cell Volume @@ -2882,32 +2881,32 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + - + - + - - + + A measure of the average volume or size of a single red blood cell. It is derived by dividing the total volume of packed red blood cells by the total red blood cell count. - http://purl.obolibrary.org/obo/CMO_0000038 - Sufficient - SCDO:0000723 + http://purl.obolibrary.org/obo/CMO_0000038 + Sufficient + SCDO:0000723 CMO:0000038 MCV Mean Cell Volume @@ -2922,63 +2921,63 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + - + - - + + - - + + - - + + - - + + - + - - + + - - + + The amount of creatinine, a catabolic product of creatine phosphate used in skeletal muscle contraction found in a specified volume of serum. - Link to "Glomerular Filtration Rate"... which object property? Create a new one and suggest to RO? "used to calculate"? - - Sufficient - SCDO:0001042 + Link to "Glomerular Filtration Rate"... which object property? Create a new one and suggest to RO? "used to calculate"? + + Sufficient + SCDO:0001042 CMO:0000057 Creatinine Level Serum Creatinine Level @@ -2989,11 +2988,11 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + A measurement to assess the morphological or physiological state of the respiratory system or portion of the respiratory system. - http://purl.obolibrary.org/obo/CMO_0000094 - Sufficient - SCDO:0000995 + http://purl.obolibrary.org/obo/CMO_0000094 + Sufficient + SCDO:0000995 CMO:0000094 Respiratory System Measurement @@ -3005,9 +3004,9 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C The number of granulocytes (polymorphonuclear leukocytes) in a specified volume of blood, usually 1 cubic millimeter. - - Sufficient - SCDO:1000441 + + Sufficient + SCDO:1000441 CMO:0000111 Blood Granulocyte Count @@ -3020,68 +3019,68 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + The amount of bilirubin found in a specific volume of blood. - http://purl.obolibrary.org/obo/CMO_0000123 - Sufficient - SCDO:0000134 + http://purl.obolibrary.org/obo/CMO_0000123 + Sufficient + SCDO:0000134 CMO:0000123 Bilirubin Level Blood Bilirubin Level @@ -3094,12 +3093,12 @@ Also add "Deferoxamine" and "Deferiprone" below "Iron C Any measurement of the movement of blood through the heart and blood vessels. - Add any more from below "circulation measurement" in the CMO? + Add any more from below "circulation measurement" in the CMO? Suggest to CMO "Blood Flow Measurement" be an exact synonym of "Circulation Measurement", as we have made it here. -Suggest to CRISP that their "blood flow measurement" instead be "Blood Flow Test". - - Sufficient - SCDO:0000142 +Suggest to CRISP that their "blood flow measurement" instead be "Blood Flow Test". + + Sufficient + SCDO:0000142 CMO:0000195 Circulation Measurement Blood Flow Measurement @@ -3112,15 +3111,15 @@ Suggest to CRISP that their "blood flow measurement" instead be " Measurement to assess the sequential process through which multiple factors of the blood interact to form an insoluble fibrin clot. - Add other sub-classes of "Blood Coagulation Measurement" from the CMO? + Add other sub-classes of "Blood Coagulation Measurement" from the CMO? blood fibrinogen level? thrombin time? activated clotting time (ACT)? platelet aggregation measurement? -bleeding time (BT)? - http://purl.obolibrary.org/obo/CMO_0000204 - Sufficient - SCDO:0000137 +bleeding time (BT)? + http://purl.obolibrary.org/obo/CMO_0000204 + Sufficient + SCDO:0000137 CMO:0000204 Blood Coagulation Measurement @@ -3132,9 +3131,9 @@ bleeding time (BT)? The time needed for plasma to form a fibrin clot after the addition of calcium and a phospholipid reagent. It is used to evaluate the intrinsic clotting system. - - Sufficient - SCDO:0000014 + + Sufficient + SCDO:0000014 CMO:0000210 APTT; Quick Activated Partial Thromboplastin Time @@ -3147,9 +3146,9 @@ bleeding time (BT)? Measurement of the clotting ability of fibrinogen, prothrombin, proaccelerin, proconvertin and Stuart factor, usually given in seconds to formation of clot after the addition of a tissue factor or thromboplastin. - - Sufficient - SCDO:0000933 + + Sufficient + SCDO:0000933 CMO:0000211 PTT Prothrombin Time @@ -3162,9 +3161,9 @@ bleeding time (BT)? Any measurement of a gas or gases dissolved in arterial blood, that is, blood which has absorbed oxygen in the lungs, including oxygen, nitrogen carbon dioxide and/or hydrogen. - - Sufficient - SCDO:1000718 + + Sufficient + SCDO:1000718 CMO:0000225 Arterial Blood Gas Measurement @@ -3174,11 +3173,11 @@ bleeding time (BT)? - + Any measurement of urine, the fluid waste product excreted by the kidneys, or its components. - http://purl.obolibrary.org/obo/CMO_0000256 - Sufficient - SCDO:0001214 + http://purl.obolibrary.org/obo/CMO_0000256 + Sufficient + SCDO:0001214 CMO:0000256 Urine Measurement @@ -3191,32 +3190,32 @@ bleeding time (BT)? - - + + - - + + - - + + - - + + The force per unit area attributable to the carbon dioxide, a colorless, odorless, incombustible gas formed during respiration and composed of one atom of carbon and two atoms of oxygen, dissolved in a specified volume of blood, defined as the force per unit area exerted by carbon dioxide in a mixture of gases in equilibrium with such a sample of blood at the same temperature. - - Sufficient - SCDO:1000719 + + Sufficient + SCDO:1000719 CMO:0000283 PaCO2 Partial Pressure of Blood Carbon Dioxide @@ -3234,32 +3233,32 @@ bleeding time (BT)? - + - + - + - - + + The average amount of hemoglobin per red blood cell calculated by dividing the total mass of hemoglobin by the number of red blood cells in a volume of blood. - http://purl.obolibrary.org/obo/CMO_0000290 - Sufficient - SCDO:0000722 + http://purl.obolibrary.org/obo/CMO_0000290 + Sufficient + SCDO:0000722 CMO:0000290 MCH Mean Cell Hemoglobin @@ -3278,33 +3277,33 @@ bleeding time (BT)? - + - + - + - - + + The amount of hemoglobin in a given volume of packed red blood cells and is often calculated by dividing the hemoglobin concentration by the hematocrit. - Add the sub-class "mean corpuscular sickle hemoglobin concentration (MCSHC)"? (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC290884/pdf/jcinvest00309-0076.pdf) - http://purl.obolibrary.org/obo/CMO_0000291 - Sufficient - SCDO:0000721 + Add the sub-class "mean corpuscular sickle hemoglobin concentration (MCSHC)"? (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC290884/pdf/jcinvest00309-0076.pdf) + http://purl.obolibrary.org/obo/CMO_0000291 + Sufficient + SCDO:0000721 CMO:0000291 MCHC Mean Cell Hemoglobin Concentration @@ -3317,67 +3316,67 @@ bleeding time (BT)? - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + The calculation of the cellular elements of the blood, usually including cell counts for white and red blood cells and platelets. - http://purl.obolibrary.org/obo/CMO_0000364 - - PhenX protocol: Complete Blood Count #220501 - Sufficient - SCDO:0000270 + http://purl.obolibrary.org/obo/CMO_0000364 + + PhenX protocol: Complete Blood Count #220501 + Sufficient + SCDO:0000270 CMO:0000364 Blood Cell Count Blood Cell Number @@ -3395,14 +3394,14 @@ bleeding time (BT)? - - + + The total number of leukocytes in 1 cubic millimeter of peripheral venous blood. - http://purl.obolibrary.org/obo/CMO_0000365 - Sufficient - SCDO:0001163 + http://purl.obolibrary.org/obo/CMO_0000365 + Sufficient + SCDO:0001163 CMO:0000365 Total White Blood Cell Count @@ -3414,10 +3413,10 @@ bleeding time (BT)? The number of each type of leukocyte present in a specific volume of blood, usually 1 cubic millimeter. - Perhaps add sub-classes from "Clinical Measurement Ontology"? - http://purl.obolibrary.org/obo/CMO_0000366 - Sufficient - SCDO:0000140 + Perhaps add sub-classes from "Clinical Measurement Ontology"? + http://purl.obolibrary.org/obo/CMO_0000366 + Sufficient + SCDO:0000140 CMO:0000366 Blood Differential Leukocyte Count Blood Differential WBC Count @@ -3433,26 +3432,26 @@ bleeding time (BT)? - - + + - + - - + + The complete or entire amount of bilirubin in a specified volume of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. Bilirubin is the bile pigment produced by breakdown of heme and reduction of biliverdin. - - Sufficient - SCDO:1000500 + + Sufficient + SCDO:1000500 CMO:0000376 Total Serum Bilirubin Level @@ -3465,38 +3464,38 @@ bleeding time (BT)? - + - - + + - + - + - - + + The amount of hemoglobin, the red oxygen-carrying pigment of erythrocytes, in a specified volume of blood, as calculated from the optical density of a solution of lysed red cells in which hemoglobin has been converted to cyanomethemoglobin and measured with a spectrophotometer. - - Sufficient - SCDO:0000523 + + Sufficient + SCDO:0000523 CMO:0000506 Hbtotal Hemoglobin Level @@ -3513,9 +3512,9 @@ bleeding time (BT)? The optical density as calculated from the intensity of light at a specified wavelength as it passes through a solution of lysed red blood cells. - - Sufficient - SCDO:1000249 + + Sufficient + SCDO:1000249 CMO:0000507 Hemoglobin Absorbance @@ -3527,9 +3526,9 @@ bleeding time (BT)? A measure of the oxygen carrying pigment of erythrocytes. - http://purl.obolibrary.org/obo/CMO_0000508 - Sufficient - SCDO:0000543 + http://purl.obolibrary.org/obo/CMO_0000508 + Sufficient + SCDO:0000543 CMO:0000508 Hemoglobin Measurement @@ -3539,11 +3538,11 @@ bleeding time (BT)? - + Pressure exerted by the heart muscle in its maximally contracted state. - http://purl.obolibrary.org/obo/CMO_0000665 - Sufficient - SCDO:0000499 + http://purl.obolibrary.org/obo/CMO_0000665 + Sufficient + SCDO:0000499 CMO:0000665 Heart Contraction Pressure @@ -3555,9 +3554,9 @@ bleeding time (BT)? Any measurement of platelets, the disk-shaped structures found in the blood of mammals which play a vital role in blood coagulation. Platelets lack nuclei and DNA but contain active enzymes and mitochondria. - http://purl.obolibrary.org/obo/CMO_0000921 - Sufficient - SCDO:0000907 + http://purl.obolibrary.org/obo/CMO_0000921 + Sufficient + SCDO:0000907 CMO:0000921 Platelet Measurement @@ -3569,9 +3568,9 @@ bleeding time (BT)? Any measurement of a gas or gases dissolved in the blood, including oxygen, nitrogen carbon dioxide and/or hydrogen. - - Sufficient - SCDO:1000312 + + Sufficient + SCDO:1000312 CMO:0001321 Blood Gas Measurement @@ -3583,9 +3582,9 @@ bleeding time (BT)? The amount of oxygen bound to hemoglobin in the blood expressed as a percentage of the maximal binding capacity. - - Sufficient - SCDO:0000848 + + Sufficient + SCDO:0000848 CMO:0001324 HbO2 Oxyhemoglobin Saturation @@ -3603,9 +3602,9 @@ bleeding time (BT)? Any measurement of a single red blood cell, one of the hemoglobin-containing blood cells that transport oxygen and carbon dioxide to and from the tissues, or of all of the red blood cells in a sample of blood. - http://purl.obolibrary.org/obo/CMO_0001356 - Sufficient - SCDO:0000974 + http://purl.obolibrary.org/obo/CMO_0001356 + Sufficient + SCDO:0000974 CMO:0001356 Erythrocyte Measurement Red Blood Cell Measurement @@ -3616,11 +3615,11 @@ bleeding time (BT)? - + The heaviness or degree to which the entire body of an organism at the point of or shortly after birth is drawn to the earth by gravity. - - Sufficient - SCDO:1000311 + + Sufficient + SCDO:1000311 CMO:0002079 Body Weight of Neonate Neonatal Body Weight @@ -3634,9 +3633,9 @@ bleeding time (BT)? Any value resulting from the quantification of a morphological or physiological parameter of leukocytes, largely colorless blood corpuscles capable of ameboid movement, whose chief function is to protect the body against microorganisms and other disease-causing entities. - http://purl.obolibrary.org/obo/CMO_0002341 - Sufficient - SCDO:0001244 + http://purl.obolibrary.org/obo/CMO_0002341 + Sufficient + SCDO:0001244 CMO:0002341 White Blood Cell Measurement @@ -3649,32 +3648,32 @@ bleeding time (BT)? - + - + - - + + - - + + Measurement of the amount of haptoglobin in a specified sample of serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. Haptoglobin is a serum alpha2 globulin glycoprotein, produced by the liver, that functions to bind free plasma hemoglobin, which allows degradative enzymes to gain access to the hemoglobin, while at the same time preventing loss of iron through the kidneys and protecting the kidneys from damage by hemoglobin. - - Sufficient - SCDO:0000467 + + Sufficient + SCDO:0000467 CMO:0002520 Haptoglobin Level Haptoglobin Levels @@ -3689,41 +3688,41 @@ bleeding time (BT)? - + - + - + - - + + - - + + The amount of N-terminal (NT)-pro hormone BNP (Nppb) in a specified volume of blood. - Value given as 1 Decimal Place Nanogram per Liter (according to PhenX https://www.phenxtoolkit.org/protocols/view/810501) + Value given as 1 Decimal Place Nanogram per Liter (according to PhenX https://www.phenxtoolkit.org/protocols/view/810501) -associated with acute congestive heart failure (http://www.ebi.ac.uk/efo/EFO_0004745) - - Sufficient - SCDO:0000786 +associated with acute congestive heart failure (http://www.ebi.ac.uk/efo/EFO_0004745) + + Sufficient + SCDO:0000786 CMO:0002876 BNPT Level Blood NH2-Terminal pro-B-Type Natriuretic Peptide Level @@ -3738,11 +3737,11 @@ associated with acute congestive heart failure (http://www.ebi.ac.uk/efo/EFO_000 - + A vitamin metabolic disorder that results from low blood levels of vitamin B12. - - Sufficient - SCDO:0005733 + + Sufficient + SCDO:0005733 DOID:0050731 Cobalamin Deficiency Hypocobalaminemia @@ -3757,15 +3756,15 @@ associated with acute congestive heart failure (http://www.ebi.ac.uk/efo/EFO_000 - - + + A colitis caused by inadequate blood supply to the colon. - Is diagnosed by: abdominal computed tomography scan - http://purl.obolibrary.org/obo/DOID_0060181 - Sufficient - SCDO:0002870 + Is diagnosed by: abdominal computed tomography scan + http://purl.obolibrary.org/obo/DOID_0060181 + Sufficient + SCDO:0002870 DOID:0060181 Ischemic Cholitis @@ -3775,11 +3774,11 @@ associated with acute congestive heart failure (http://www.ebi.ac.uk/efo/EFO_000 - + A hemochromatosis characterized by a predisposition to iron loading that is exacerbated by excessive intake of dietary iron, commonly related to consumption of tradition beer brewed in non-galvanized steel drums. - - Sufficient - SCDO:1000282 + + Sufficient + SCDO:1000282 DOID:0111033 Bantu Siderosis Iron Overload in Africa @@ -3794,50 +3793,50 @@ associated with acute congestive heart failure (http://www.ebi.ac.uk/efo/EFO_000 - + - + - - + + - - + + - - + + - - + + - - + + A neuropathy that is characterized by damage to a single nerve, which results in loss of movement, sensation, or other function of that nerve. - - Sufficient - SCDO:0000769 + + Sufficient + SCDO:0000769 DOID:1188 Single Damaged Nerve Mononeuropathy @@ -3849,139 +3848,139 @@ associated with acute congestive heart failure (http://www.ebi.ac.uk/efo/EFO_000 - + - + - - + + - - + + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A lung disease that involves a vasoocclusive crisis of the pulmonary vasculature seen in patients with sickle cell anemia. The crisis is initiated by a lung infection, and the resulting inflammation and loss of oxygen tension leads to sickling of red cells and further vasoocclusion. - This definition was given by the WG: 'Acute onset of respiratory symptoms and/or signs and an X-ray consistent with alveolar consolidation but not atelectasis, involving at least one complete lung segment." With this definition source:The acute chest syndrome in sickle cell disease: incidence and risk factors. The Cooperative Study of Sickle Cell Disease. O. Castro, D. J. Brambilla, B. Thorington, C. A. Reindorf, R. B. Scott, P. Gillette, J. C. Vera, P. S. Levy Blood. 1994 Jul 15; 84(2): 643–649. -However, the definition did not seem to come from this source, so the DO term was used instead. - - Sufficient - SCDO:0000015 + This definition was given by the WG: 'Acute onset of respiratory symptoms and/or signs and an X-ray consistent with alveolar consolidation but not atelectasis, involving at least one complete lung segment." With this definition source:The acute chest syndrome in sickle cell disease: incidence and risk factors. The Cooperative Study of Sickle Cell Disease. O. Castro, D. J. Brambilla, B. Thorington, C. A. Reindorf, R. B. Scott, P. Gillette, J. C. Vera, P. S. Levy Blood. 1994 Jul 15; 84(2): 643–649. +However, the definition did not seem to come from this source, so the DO term was used instead. + + Sufficient + SCDO:0000015 DOID:1584 Acute Chest Syndrome in Sickle Cell Disease From the DO: The disease has_symptom fever, has_symptom pleuritic chest pain, has_symptom tachypnea, has_symptom cough, has_symptom hypoxemia, has_symptom marked leukocytosis, has_symptom marked leukocytosis, and has_symptom diffuse infiltrates on chest radiograph. @@ -3996,26 +3995,26 @@ However, the definition did not seem to come from this source, so the DO term wa - - + + - - + + - - + + A brain disease that is characterized by the occurrance of at least two unprovoked seizures resulting from a persistent epileptogenic abnormality of the brain that is able to spontaneously generate paroxysmal activity and typically manifested by sudden brief episodes of altered or diminished consciousness, involuntary movements, or convulsions. - http://purl.obolibrary.org/obo/DOID_1826 - Sufficient - SCDO:0008484 + http://purl.obolibrary.org/obo/DOID_1826 + Sufficient + SCDO:0008484 DOID:1826 Epilepsy @@ -4028,20 +4027,20 @@ However, the definition did not seem to come from this source, so the DO term wa - - + + - - + + A gastrointestinal system infectious disease that involves inflammation of the lining of the stomach and small and large intestines, which is caused by viruses, bacteria, or parasites. Chemicals and drugs also cause gastroenteritis. The symptoms include diarrhea, loss of appetite, nausea, vomiting, cramps, and discomfort in the abdomen. - http://purl.obolibrary.org/obo/DOID_2326 - Sufficient - SCDO:0007198 + http://purl.obolibrary.org/obo/DOID_2326 + Sufficient + SCDO:0007198 DOID:2326 Gastroenteritis @@ -4051,17 +4050,17 @@ However, the definition did not seem to come from this source, so the DO term wa - + - + A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. - http://purl.obolibrary.org/obo/DOID_4 - Sufficient - SCDO:0001365 + http://purl.obolibrary.org/obo/DOID_4 + Sufficient + SCDO:0001365 DOID:4 Disease @@ -4075,32 +4074,32 @@ However, the definition did not seem to come from this source, so the DO term wa - - + + - - + + - - + + - - + + An arthritis that involves infection by a pathogen located in a joint. - http://purl.obolibrary.org/obo/DOID_813 - Sufficient - SCDO:0002067 + http://purl.obolibrary.org/obo/DOID_813 + Sufficient + SCDO:0002067 DOID:813 Infected Joint Infectious Arthritis @@ -4114,9 +4113,9 @@ However, the definition did not seem to come from this source, so the DO term wa A sleep apnea that is characterized by a malfunction of the basic neurological controls for breathing rate and the failure to give the signal to inhale, causing the individual to miss one or more cycles of breathing. - http://purl.obolibrary.org/obo/DOID_9220 - Sufficient - SCDO:0000200 + http://purl.obolibrary.org/obo/DOID_9220 + Sufficient + SCDO:0000200 DOID:9220 Primary Central Sleep Apnea Central Sleep Apnea @@ -4127,11 +4126,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + A nasal vasoconstricting decongestant drug which acts by binding to the same receptors as adrenaline. It is applied as a spray or as drops into the nose to ease inflammation and congestion of the nasal passageways. It binds alpha-adrenergic receptors to activate the adrenal system which causes systemic vasoconstriction, thereby easing nasal congestion. - http://www.drugbank.ca/drugs/DB06694 - Sufficient - SCDO:0001254 + http://www.drugbank.ca/drugs/DB06694 + Sufficient + SCDO:0001254 DRON:00017565 Balminil Otrivin @@ -4144,11 +4143,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + This requirement indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use. - - Sufficient - SCDO:1000413 + + Sufficient + SCDO:1000413 DUO:0000018 Not for Profit Use Only @@ -4158,11 +4157,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + This requirement indicates that requestor agrees to make results of studies using the data available to the larger scientific community. - - Sufficient - SCDO:1000416 + + Sufficient + SCDO:1000416 DUO:0000019 Publication Required @@ -4172,11 +4171,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + This could be coupled with a string describing the primary study investigator(s). - - Sufficient - SCDO:1000409 + + Sufficient + SCDO:1000409 DUO:0000020 Collaboration Required @@ -4186,11 +4185,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + This requirement indicates that the requestor must provide documentation of local IRB/ERB approval. - - Sufficient - SCDO:1000410 + + Sufficient + SCDO:1000410 DUO:0000021 Ethics Approval Required @@ -4200,11 +4199,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + This should be coupled with an ontology term describing the geographical location the restriction applies to. - - Sufficient - SCDO:1000411 + + Sufficient + SCDO:1000411 DUO:0000022 Geographical Restriction @@ -4214,11 +4213,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + This should be coupled with a date specified as ISO8601 - - Sufficient - SCDO:1000415 + + Sufficient + SCDO:1000415 DUO:0000024 Publication Moratorium @@ -4228,11 +4227,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + This should be coupled with an integer value indicating the number of months. - - Sufficient - SCDO:1000418 + + Sufficient + SCDO:1000418 DUO:0000025 Time Limit on Use @@ -4242,11 +4241,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + This requirement indicates that use is limited to use by approved users. - - Sufficient - SCDO:1000419 + + Sufficient + SCDO:1000419 DUO:0000026 User Specific Restriction @@ -4256,11 +4255,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + This requirement indicates that use is limited to use within an approved project. - - Sufficient - SCDO:1000414 + + Sufficient + SCDO:1000414 DUO:0000027 Project Specific Restriction @@ -4270,11 +4269,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + This requirement indicates that use is limited to use within an approved institution. - - Sufficient - SCDO:1000412 + + Sufficient + SCDO:1000412 DUO:0000028 Institution Specific Restriction @@ -4284,11 +4283,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + This requirement indicates that the requestor must return derived/enriched data to the database/resource. - - Sufficient - SCDO:1000417 + + Sufficient + SCDO:1000417 DUO:0000029 Return to Database or Resource @@ -4298,11 +4297,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + An environmental system process that results in the introduction of contaminants into an environment. - http://purl.obolibrary.org/obo/ENVO_02500036 - Sufficient - SCDO:0000912 + http://purl.obolibrary.org/obo/ENVO_02500036 + Sufficient + SCDO:0000912 ENVO:02500036 Environmental Pollution Pollution @@ -4313,7 +4312,7 @@ However, the definition did not seem to come from this source, so the DO term wa - + @@ -4329,19 +4328,19 @@ However, the definition did not seem to come from this source, so the DO term wa - + - - + + A genotype information which is about the presence and degree of alpha-thalassemia, a form of thalassemia involving the number of functional HBA1 and HBA2 genes. - - Sufficient - SCDO:1000216 + + Sufficient + SCDO:1000216 EUPATH:0000034 Alpha Thalassemia Genotype @@ -4353,9 +4352,9 @@ However, the definition did not seem to come from this source, so the DO term wa A clinical visit that is primarily for a regular examination. - - Sufficient - SCDO:1000848 + + Sufficient + SCDO:1000848 EUPATH:0000050 Routine Clinical Visit @@ -4368,56 +4367,56 @@ However, the definition did not seem to come from this source, so the DO term wa - + - + - - + + - - + + - - + + - - + + - - + + - - + + An anemia with hemoglobin levels less than 5 gm/dL. - http://purl.obolibrary.org/obo/EUPATH_0000215 - Sufficient - SCDO:1000055 + http://purl.obolibrary.org/obo/EUPATH_0000215 + Sufficient + SCDO:1000055 EUPATH:0000215 Severe Anemia @@ -4427,11 +4426,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + An information content entity that is about a clinical visit. - - Sufficient - SCDO:1000851 + + Sufficient + SCDO:1000851 EUPATH:0000310 Information on Observation Details @@ -4444,14 +4443,14 @@ However, the definition did not seem to come from this source, so the DO term wa - - + + A scalar measurement datum of the concentration of urea in blood that is a specified output of a blood test. - - Sufficient - SCDO:1000603 + + Sufficient + SCDO:1000603 EUPATH:0021227 Serum Urea Concentration Blood Urea Concentration @@ -4463,12 +4462,12 @@ However, the definition did not seem to come from this source, so the DO term wa - - + + An individual attribute that is the usual or principal work or business of an individual. - http://purl.obolibrary.org/obo/ExO_0000034 - Sufficient - SCDO:0000821 + http://purl.obolibrary.org/obo/ExO_0000034 + Sufficient + SCDO:0000821 ExO:0000034 Career Employment @@ -4482,11 +4481,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + Human-made surroundings that provide the setting for human activity, ranging in scale from personal shelter and buildings to neighborhoods and cite, and can often include their supporting infrastructure, such as water supply or energy networks. - - Sufficient - SCDO:0000167 + + Sufficient + SCDO:0000167 ExO:0000048 Built Environment @@ -4496,11 +4495,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + A reference to a place on the Earth, by its name or by its geographical location. - http://purl.obolibrary.org/obo/GAZ_00000448 - Sufficient - SCDO:0000451 + http://purl.obolibrary.org/obo/GAZ_00000448 + Sufficient + SCDO:0000451 GAZ:00000448 Geographic Region Geographic Location @@ -4513,9 +4512,9 @@ However, the definition did not seem to come from this source, so the DO term wa Intersex is an umbrella term with a complex history. It is usually used to refer to persons with congenital conditions which involve differences in the many intertwined processes of sexual development. - - Sufficient - SCDO:1000672 + + Sufficient + SCDO:1000672 GSSO:000109 Intersex @@ -4525,11 +4524,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + Principles which provide a framework within which ethical dilemmas and other problems may be analyzed. - - Sufficient - SCDO:1000427 + + Sufficient + SCDO:1000427 GSSO:003239 Ethical Principle @@ -4539,11 +4538,11 @@ However, the definition did not seem to come from this source, so the DO term wa - + The pattern in which a particular genetic trait or disorder is passed from one generation to the next. - http://purl.obolibrary.org/obo/HP_0000005 - Sufficient - SCDO:0001367 + http://purl.obolibrary.org/obo/HP_0000005 + Sufficient + SCDO:0001367 HP:0000005 Inheritance Mode of Inheritance @@ -4556,9 +4555,9 @@ However, the definition did not seem to come from this source, so the DO term wa A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele. - - Sufficient - SCDO:1000140 + + Sufficient + SCDO:1000140 HP:0000006 Autosomal Dominant Form Autosomal Dominant Inheritance @@ -4573,9 +4572,9 @@ However, the definition did not seem to come from this source, so the DO term wa A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in individuals with two pathogenic alleles, either homozygous (two copies of the same mutant allele) or compound heterozygous (whereby each copy of a gene has a distinct mutant allele). - http://purl.obolibrary.org/obo/HP_0000007 - Sufficient - SCDO:0001368 + http://purl.obolibrary.org/obo/HP_0000007 + Sufficient + SCDO:0001368 HP:0000007 Autosomal Recessive Form Autosomal Recessive Inheritance @@ -4590,9 +4589,9 @@ However, the definition did not seem to come from this source, so the DO term wa Absence of any measurable level of sperm in a male's semen. - - Sufficient - SCDO:0000092 + + Sufficient + SCDO:0000092 HP:0000027 Absent Sperm in Semen Azoospermia @@ -4605,9 +4604,9 @@ However, the definition did not seem to come from this source, so the DO term wa Hypogonadotropic hypogonadism is characterized by reduced function of the gonads (testes in males or ovaries in females) and results from the absence of the gonadal stimulating pituitary hormones: follicle stimulating hormone (FSH) and luteinizing hormone (LH). - - Sufficient - SCDO:0002903 + + Sufficient + SCDO:0002903 HP:0000044 Hypogonadotropic Hypogonadism Secondary Hypogonadism @@ -4621,9 +4620,9 @@ However, the definition did not seem to come from this source, so the DO term wa An abnormality of the kidney. - http://purl.obolibrary.org/obo/HP_0000077 - Sufficient - SCDO:0002133 + http://purl.obolibrary.org/obo/HP_0000077 + Sufficient + SCDO:0002133 HP:0000077 Abnormal Kidney Anomaly of the Kidney @@ -4638,9 +4637,9 @@ However, the definition did not seem to come from this source, so the DO term wa An abnormality of the genital system. - - Sufficient - SCDO:1000263 + + Sufficient + SCDO:1000263 HP:0000078 Genital Abnormalities Genital Abnormality @@ -4656,9 +4655,9 @@ However, the definition did not seem to come from this source, so the DO term wa An abnormality of the urinary system. - - Sufficient - SCDO:0001347 + + Sufficient + SCDO:0001347 HP:0000079 Anomaly of the Urinary System Urinary Tract Abnormalities @@ -4675,9 +4674,9 @@ However, the definition did not seem to come from this source, so the DO term wa An abnormal functionality of the genital system. - - Sufficient - SCDO:1000270 + + Sufficient + SCDO:1000270 HP:0000080 Abnormality of Genital Physiology Abnormality of Reproductive System Physiology @@ -4689,92 +4688,92 @@ However, the definition did not seem to come from this source, so the DO term wa - + - + - - + + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Failure of the kidneys to adequately filter toxins and waste products from the blood; classified as acute (as in acute kidney injury) or chronic (as in chronic kidney disease); a number of other diseases or health problems may cause either form of renal failure to occur. - http://purl.obolibrary.org/obo/MP_0003606 - Variable - May be Acute (acute kidney injury) or chronic (chronic kidney disease). - Has a variety of causes - dependent upon acuity - see definitions for acute kidney injury (acute renal failure) and chronic kidney disease. - Sufficient - SCDO:0000674 + http://purl.obolibrary.org/obo/MP_0003606 + Variable + May be Acute (acute kidney injury) or chronic (chronic kidney disease). + Has a variety of causes - dependent upon acuity - see definitions for acute kidney injury (acute renal failure) and chronic kidney disease. + Sufficient + SCDO:0000674 HP:0000084 Renal Failure Renal Insufficiency @@ -4790,29 +4789,29 @@ However, the definition did not seem to come from this source, so the DO term wa - - + + - - + + - - + + Scarring and fibrosis within the glomerulus. + + Any form of injury to the kidney can lead to glomerulosclerosis. + Histologically noted by scarring and fibrosis in the glomerulus. + Sufficient + SCDO:0000460 NHLBI 2014 Guidelines - - Any form of injury to the kidney can lead to glomerulosclerosis. - Histologically noted by scarring and fibrosis in the glomerulus. - Sufficient - SCDO:0000460 HP:0000096 Glomerular Sclerosis Renal Glomerular Fibrosis @@ -4826,9 +4825,9 @@ However, the definition did not seem to come from this source, so the DO term wa Segmental accumulation of scar tissue in individual (but not all) glomeruli. - - Sufficient - SCDO:0009968 + + Sufficient + SCDO:0009968 HP:0000097 Focal Glomerulosclerosis Focal and Segmental Glomerular Sclerosis @@ -4844,48 +4843,48 @@ However, the definition did not seem to come from this source, so the DO term wa - - + + - - + + - - + + - - + + - - + + - - + + Inflammation of the renal glomeruli. - Provide source for additional info. - - May occur at any age. - Variety of causes - in sickle cell disease, most common lesion is focal segmental glomerulosclerosis (FSGS) but also reported Membranoproliferative glomerulonephritis and other forms of glomerulonephritis. - Patients with hematuria may have dark-colored urine. Glomerulonephritis may lead to the proteinuria and "foamy" appearance of the urine. If the latter is substantial, patients may develop clinically evident edema. - Sufficient - SCDO:0000458 + Provide source for additional info. + + May occur at any age. + Variety of causes - in sickle cell disease, most common lesion is focal segmental glomerulosclerosis (FSGS) but also reported Membranoproliferative glomerulonephritis and other forms of glomerulonephritis. + Patients with hematuria may have dark-colored urine. Glomerulonephritis may lead to the proteinuria and "foamy" appearance of the urine. If the latter is substantial, patients may develop clinically evident edema. + Sufficient + SCDO:0000458 HP:0000099 GN Glomerular Nephritis @@ -4900,98 +4899,98 @@ However, the definition did not seem to come from this source, so the DO term wa - + - - + + - - + + - - + + - - + + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A nonspecific term referring to disease or damage of the kidneys. - - Sufficient - SCDO:0000795 + + Sufficient + SCDO:0000795 HP:0000112 Kidney Damage Kidney Disease @@ -5005,9 +5004,9 @@ However, the definition did not seem to come from this source, so the DO term wa A phenotype that shows detectable differences from normal. - http://purl.obolibrary.org/obo/FYPO_0001985 - Sufficient - SCDO:0009818 + http://purl.obolibrary.org/obo/FYPO_0001985 + Sufficient + SCDO:0009818 HP:0000118 Phenotypic Abnormality Abnormal Phenotype @@ -5020,26 +5019,26 @@ However, the definition did not seem to come from this source, so the DO term wa - + - + - - + + The presence of inflammation affecting the kidney. - Provide source for additional info. - - May be caused by autoimmune disease, allergic responses, toxic injury, infectious causes. - May be associated with loss of kidney function, pyuria or hematuria, and proteinuria dependent upon cause. - Sufficient - SCDO:0000793 + Provide source for additional info. + + May be caused by autoimmune disease, allergic responses, toxic injury, infectious causes. + May be associated with loss of kidney function, pyuria or hematuria, and proteinuria dependent upon cause. + Sufficient + SCDO:0000793 HP:0000123 Kidney Inflammation Nephritis @@ -5053,27 +5052,27 @@ However, the definition did not seem to come from this source, so the DO term wa - + - - + + - - + + Prolonged and/or excessive menses at regular intervals in excess of 80 ml or lasting longer than 7 days. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0000132 - Sufficient - SCDO:0000745 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0000132 + Sufficient + SCDO:0000745 HP:0000132 Abnormally Heavy Bleeding During Menstruation Hypermenorrhea @@ -5087,9 +5086,9 @@ However, the definition did not seem to come from this source, so the DO term wa Hemorrhage affecting the gingiva. - http://purl.obolibrary.org/obo/HP_0000225 - Sufficient - SCDO:0000452 + http://purl.obolibrary.org/obo/HP_0000225 + Sufficient + SCDO:0000452 HP:0000225 Bleeding Gums Gingival Hemorrhage @@ -5104,9 +5103,9 @@ However, the definition did not seem to come from this source, so the DO term wa An abnormality of the face. - http://purl.obolibrary.org/obo/HP_0000271 - Sufficient - SCDO:0003024 + http://purl.obolibrary.org/obo/HP_0000271 + Sufficient + SCDO:0003024 HP:0000271 Facial Abnormality Abnormality of the Face @@ -5121,39 +5120,39 @@ However, the definition did not seem to come from this source, so the DO term wa - + - + - - + + - - + + - - + + Inflammation or infection of the middle ear. - Source needed for additional information. - http://purl.obolibrary.org/obo/HP_0000388 - Sufficient - SCDO:0000846 + Source needed for additional information. + http://purl.obolibrary.org/obo/HP_0000388 + Sufficient + SCDO:0000846 HP:0000388 is caused by: Usually bacterial but can be caused by fungus or virus infection. @@ -5168,9 +5167,9 @@ is characterised by: Pain or discharge from one or both ears Any abnormality of the eye, including location, spacing, and intraocular abnormalities. - - Sufficient - SCDO:1000294 + + Sufficient + SCDO:1000294 HP:0000478 Abnormality of the Eye @@ -5183,9 +5182,9 @@ is characterised by: Pain or discharge from one or both ears Visual impairment (or vision impairment) is vision loss (of a person) to such a degree as to qualify as an additional support need through a significant limitation of visual capability resulting from either disease, trauma, or congenital or degenerative conditions that cannot be corrected by conventional means, such as refractive correction, medication, or surgery. - - Sufficient - SCDO:1000022 + + Sufficient + SCDO:1000022 HP:0000505 Impaired Vision Impaired Visual Function @@ -5202,32 +5201,32 @@ is characterised by: Pain or discharge from one or both ears - - + + - - + + - - + + - - + + Blindness is the condition of lacking visual perception defined as visual perception below 3/60 and/or a visual field of no greater than 10 degress in radius around central fixation. - - Sufficient - SCDO:1000021 + + Sufficient + SCDO:1000021 HP:0000618 Total Vision Loss Blindness @@ -5240,9 +5239,9 @@ is characterised by: Pain or discharge from one or both ears Any abnormality of the nervous system. - http://purl.obolibrary.org/obo/HP_0000707 - Sufficient - SCDO:0009698 + http://purl.obolibrary.org/obo/HP_0000707 + Sufficient + SCDO:0009698 HP:0000707 Brain and/or Spinal Cord Issue Neurologic Abnormalities @@ -5257,10 +5256,10 @@ is characterised by: Pain or discharge from one or both ears An abnormality of mental functioning including various affective, behavioural, cognitive and perceptual abnormalities. - Include "Poor School Performance" as a sub-class. - http://purl.obolibrary.org/obo/HP_0000708 - Sufficient - SCDO:0000105 + Include "Poor School Performance" as a sub-class. + http://purl.obolibrary.org/obo/HP_0000708 + Sufficient + SCDO:0000105 HP:0000708 Behavioral Abnormality Behavioural Abnormality @@ -5284,21 +5283,21 @@ is characterised by: Pain or discharge from one or both ears - + - - + + A loss of global cognitive ability of sufficient amount to interfere with normal social or occupational function. Dementia represents a loss of previously present cognitive abilities, generally in adults, and can affect memory, thinking, language, judgment, and behavior. - Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info. - - Sufficient - SCDO:0000345 + Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info. + + Sufficient + SCDO:0000345 HP:0000726 Dementia, Progressive Progressive Dementia @@ -5312,9 +5311,9 @@ is characterised by: Pain or discharge from one or both ears Peripheral neuropathy affecting the sensory nerves. - http://purl.obolibrary.org/obo/HP_0000763 - Sufficient - SCDO:0001038 + http://purl.obolibrary.org/obo/HP_0000763 + Sufficient + SCDO:0001038 HP:0000763 Peripheral Sensory Neuropathy Sensory Neuropathy @@ -5328,26 +5327,26 @@ is characterised by: Pain or discharge from one or both ears - - + + - - + + - - + + Inability to produce live offspring. - - Sufficient - SCDO:0000639 + + Sufficient + SCDO:0000639 HP:0000789 Sterility Infertility @@ -5360,9 +5359,9 @@ is characterised by: Pain or discharge from one or both ears Reduced count of spermatozoa in the semen, defined as a sperm count below 20 million per milliliter semen. - - Sufficient - SCDO:0000827 + + Sufficient + SCDO:0000827 HP:0000798 Low Sperm Count Oligospermia @@ -5374,71 +5373,71 @@ is characterised by: Pain or discharge from one or both ears - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Lack of the ability to control the urinary bladder leading to involuntary urination at an age where control of the bladder should already be possible. - http://purl.obolibrary.org/obo/HP_0000805 - Sufficient - SCDO:0000434 + http://purl.obolibrary.org/obo/HP_0000805 + Sufficient + SCDO:0000434 HP:0000805 Enuresis @@ -5451,21 +5450,21 @@ is characterised by: Pain or discharge from one or both ears - - + + - - + + Reduced function of the gonads (testes in males or ovaries in females) associated with excess pituitary gonadotropin secretion and resulting in delayed sexual development and growth delay. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0000815 - Sufficient - SCDO:0000586 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0000815 + Sufficient + SCDO:0000586 HP:0000815 Hypergonadotrophic Hypogonadism Primary Hypogonadism @@ -5479,9 +5478,9 @@ is characterised by: Pain or discharge from one or both ears An abnormality of the endocrine system. - - Sufficient - SCDO:0002780 + + Sufficient + SCDO:0002780 HP:0000818 Abnormality of the Endocrine System @@ -5493,41 +5492,41 @@ is characterised by: Pain or discharge from one or both ears - + - + - - + + - - + + - - + + - - + + A group of abnormalities characterized by hyperglycemia and glucose intolerance. - http://purl.obolibrary.org/obo/HP_0000819 - Sufficient - SCDO:0000367 + http://purl.obolibrary.org/obo/HP_0000819 + Sufficient + SCDO:0000367 HP:0000819 Diabetes Mellitus @@ -5539,9 +5538,9 @@ is characterised by: Pain or discharge from one or both ears An abnormality of the thyroid gland. - - Sufficient - SCDO:1000278 + + Sufficient + SCDO:1000278 HP:0000820 Thyroid Abnormality Abnormality of the Thyroid Gland @@ -5555,27 +5554,27 @@ is characterised by: Pain or discharge from one or both ears - - + + - - + + - - + + Deficiency of thyroid hormone. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0000821 - Sufficient - SCDO:0000603 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0000821 + Sufficient + SCDO:0000603 HP:0000821 Low T4 Underactive Thyroid @@ -5589,9 +5588,9 @@ is characterised by: Pain or discharge from one or both ears The presence of chronic increased pressure in the systemic arterial system. - - Sufficient - SCDO:0008801 + + Sufficient + SCDO:0008801 HP:0000822 Hypertension @@ -5603,35 +5602,35 @@ is characterised by: Pain or discharge from one or both ears - + - - + + - - + + - - + + - - + + Passing the age when puberty normally occurs with no physical or hormonal signs of the onset of puberty. - - Sufficient - SCDO:0000342 + + Sufficient + SCDO:0000342 HP:0000823 Delayed Development of Secondary Sex Characteristics Delayed Onset of Sexual Maturity @@ -5650,9 +5649,9 @@ is characterised by: Pain or discharge from one or both ears Insufficient production of growth hormone, which is produced by the anterior pituitary gland. Growth hormone is a major participant in control of growth and metabolism. - - Sufficient - SCDO:0008218 + + Sufficient + SCDO:0008218 HP:0000824 Growth Hormone Deficiency @@ -5664,9 +5663,9 @@ is characterised by: Pain or discharge from one or both ears An abnormality of the parathyroid gland. - - Sufficient - SCDO:1000279 + + Sufficient + SCDO:1000279 HP:0000828 Abnormality of the Parathyroid Gland @@ -5678,9 +5677,9 @@ is characterised by: Pain or discharge from one or both ears A condition caused by a deficiency of parathyroid hormone characterized by hypocalcemia and hyperphosphatemia. - - Sufficient - SCDO:0007386 + + Sufficient + SCDO:0007386 HP:0000829 Decreased Parathyroid Hormone Secretion Low Parathyroid Hormone @@ -5694,9 +5693,9 @@ is characterised by: Pain or discharge from one or both ears Abnormality of the adrenal glands, i.e., of the endocrine glands located at the top of the kidneys. - - Sufficient - SCDO:0007437 + + Sufficient + SCDO:0007437 HP:0000834 Adrenal Abnormalities Adrenal Abnormality @@ -5710,10 +5709,10 @@ is characterised by: Pain or discharge from one or both ears An abnormality of thyroid physiology characterized by excessive secretion of the thyroid hormones thyroxine (i.e., T4) and/or 3,3',5-triiodo-L-thyronine zwitterion (i.e., triiodothyronine or T3). - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0000836 - Sufficient - SCDO:0000595 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0000836 + Sufficient + SCDO:0000595 HP:0000836 Overactive Thyroid Hyperthyroidism @@ -5728,15 +5727,15 @@ is characterised by: Pain or discharge from one or both ears - + An increased concentration of insulin in the blood. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0000842 - Sufficient - SCDO:0000587 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0000842 + Sufficient + SCDO:0000587 HP:0000842 Elevated Insulin Level Hyperinsulinemia @@ -5750,21 +5749,21 @@ is characterised by: Pain or discharge from one or both ears - - + + - - + + Excessive production of parathyroid hormone (PTH) by the parathyroid glands. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0000843 - Sufficient - SCDO:0000592 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0000843 + Sufficient + SCDO:0000592 HP:0000843 Elevated Blood Parathyroid Hormone Level Hyperparathyroidism @@ -5778,26 +5777,26 @@ is characterised by: Pain or discharge from one or both ears - + - - + + - - + + Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels. - http://purl.obolibrary.org/obo/HP_0000855 - Sufficient - SCDO:0000644 + http://purl.obolibrary.org/obo/HP_0000855 + Sufficient + SCDO:0000644 HP:0000855 Body Fails to Respond to Insulin Insulin Resistance @@ -5810,9 +5809,9 @@ is characterised by: Pain or discharge from one or both ears A state of excessive water excretion and hypotonic (dilute) polyuria. Diabetes insipidus may be due to failure of vasopressin (AVP) release (central or neurogenic diabetes insipidus) or to a failure of the kidney to respond to AVP (nephrogenic diabetes insipidus). - http://purl.obolibrary.org/obo/HP_0000873 - Sufficient - SCDO:0000366 + http://purl.obolibrary.org/obo/HP_0000873 + Sufficient + SCDO:0000366 HP:0000873 Diabetes Insipidus @@ -5824,9 +5823,9 @@ is characterised by: Pain or discharge from one or both ears Infrequent menses (less than 6 per year or more than 35 days between cycles). - - Sufficient - SCDO:0003158 + + Sufficient + SCDO:0003158 HP:0000876 Light or Infrequent Menstrual Periods Oligomenorrhea @@ -5839,9 +5838,9 @@ is characterised by: Pain or discharge from one or both ears An abnormality of the skeletal system. - - Sufficient - SCDO:0006301 + + Sufficient + SCDO:0006301 HP:0000924 Skeletal Abnormalities Skeletal Anomalies @@ -5856,33 +5855,33 @@ is characterised by: Pain or discharge from one or both ears - + - - + + - - + + - - + + Osteopenia is a term to define bone density that is not normal but also not as low as osteoporosis. By definition from the World Health Organization osteopenia is defined by bone densitometry as a T score -1 to -2.5. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0000938 - Sufficient - SCDO:0000843 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0000938 + Sufficient + SCDO:0000843 HP:0000938 Decreased Bone Mineral Density Generalized Osteopenia @@ -5897,29 +5896,29 @@ is characterised by: Pain or discharge from one or both ears - + - - + + - - + + Osteoporosis is a systemic skeletal disease characterized by low bone density and microarchitectural deterioration of bone tissue with a consequent increase in bone fragility. According to the WHO criteria, osteoporosis is defined as a BMD that lies 2.5 standard deviations or more below the average value for young healthy adults (a T-score below -2.5 SD). - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0000939 - Genetic predisposition, low calcium diet, getting little exercise, smoking, decrease in estrogen at the menopause, steroid medicine use for a long time, Vitamin D insufficiency. - Bone pain, backache, gradual loss of height, stooped posture, fractures. - Sufficient - SCDO:0000844 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0000939 + Genetic predisposition, low calcium diet, getting little exercise, smoking, decrease in estrogen at the menopause, steroid medicine use for a long time, Vitamin D insufficiency. + Bone pain, backache, gradual loss of height, stooped posture, fractures. + Sufficient + SCDO:0000844 HP:0000939 Osteoporosis @@ -5931,9 +5930,9 @@ is characterised by: Pain or discharge from one or both ears An abnormality of the skin. - http://purl.obolibrary.org/obo/HP_0000951 - Sufficient - SCDO:0008348 + http://purl.obolibrary.org/obo/HP_0000951 + Sufficient + SCDO:0008348 HP:0000951 Abnormal skin morphology Abnormal skin structure @@ -5949,65 +5948,65 @@ is characterised by: Pain or discharge from one or both ears - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Yellow pigmentation of the skin or sclera due to bilirubin, which in turn is the result of increased bilirubin concentration in the bloodstream. - http://purl.obolibrary.org/obo/HP_0000952 - Sufficient - SCDO:0000671 + http://purl.obolibrary.org/obo/HP_0000952 + Sufficient + SCDO:0000671 HP:0000952 Icterus Yellow Skin @@ -6022,9 +6021,9 @@ is characterised by: Pain or discharge from one or both ears A darkening of the skin related to an increase in melanin production and deposition. - http://purl.obolibrary.org/obo/HP_0000953 - Sufficient - SCDO:0000308 + http://purl.obolibrary.org/obo/HP_0000953 + Sufficient + SCDO:0000308 HP:0000953 Hyperpigmentation of the Skin Increased Skin Pigmentation @@ -6042,14 +6041,14 @@ is characterised by: Pain or discharge from one or both ears - - + + Bluish discoloration of the skin and mucosa due to poor circulation or inadequate oxygenation of arterial or capillary blood. - - Sufficient - SCDO:0000309 + + Sufficient + SCDO:0000309 HP:0000961 Blue Discoloration of the Skin Cyanotic @@ -6064,14 +6063,14 @@ is characterised by: Pain or discharge from one or both ears - - + + Hyperkeratosis is thickening of the outer layer of the skin, the stratum corneum, which is composed of large, polyhedral, plate-like envelopes filled with keratin which are the dead cells that have migrated up from the stratum granulosum. - - Sufficient - SCDO:0000589 + + Sufficient + SCDO:0000589 HP:0000962 Hyperkeratosis @@ -6084,14 +6083,14 @@ is characterised by: Pain or discharge from one or both ears - - + + Petechiae are pinpoint-sized reddish/purple spots, resembling a rash, that appear just under the skin or a mucous membrane when capillaries have ruptured and some superficial bleeding into the skin has happened. This term refers to an abnormally increased susceptibility to developing petechiae. - - Sufficient - SCDO:0000892 + + Sufficient + SCDO:0000892 HP:0000967 Petechiae @@ -6101,53 +6100,53 @@ is characterised by: Pain or discharge from one or both ears - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An abnormal accumulation of fluid beneath the skin, or in one or more cavities of the body. - http://purl.obolibrary.org/obo/HP_0000969 - Sufficient - SCDO:0000823 + http://purl.obolibrary.org/obo/HP_0000969 + Sufficient + SCDO:0000823 HP:0000969 Dropsy Fluid Retention @@ -6165,50 +6164,50 @@ is characterised by: Pain or discharge from one or both ears - - + + - - + + - - + + - - + + - - + + - - + + - - + + Abnormally pale skin. - - Sufficient - SCDO:0000863 + + Sufficient + SCDO:0000863 HP:0000980 Pallor @@ -6222,14 +6221,14 @@ is characterised by: Pain or discharge from one or both ears - + Any manifestation of a skin disease associated with the production of pus. - - Sufficient - SCDO:0000946 + + Sufficient + SCDO:0000946 HP:0000999 Pus-Filled Lesion Pyoderma @@ -6242,9 +6241,9 @@ is characterised by: Pain or discharge from one or both ears A reduction of skin color related to a decrease in melanin production and deposition. - - Sufficient - SCDO:0000601 + + Sufficient + SCDO:0000601 HP:0001010 Hypopigmentation of the Skin Hypopigmented Skin @@ -6259,9 +6258,9 @@ is characterised by: Pain or discharge from one or both ears An abnormal reduction in the amount of pigmentation (reduced or absent) of skin, hair and eye (iris and retina). - - Sufficient - SCDO:0000036 + + Sufficient + SCDO:0000036 HP:0001022 Achromasia Albinism @@ -6274,9 +6273,9 @@ is characterised by: Pain or discharge from one or both ears Raised, well-circumscribed areas of erythema and edema involving the dermis and epidermis. Urticaria is intensely pruritic, and blanches completely with pressure. - - Sufficient - SCDO:0001219 + + Sufficient + SCDO:0001219 HP:0001025 Hives Urticaria @@ -6290,20 +6289,20 @@ is characterised by: Pain or discharge from one or both ears - + - - + + A skin condition in which there is an increase in sebum secretion by the pilosebaceous apparatus associated with open comedones (blackheads), closed comedones (whiteheads), and pustular nodules (papules, pustules, and cysts). - - Sufficient - SCDO:0000012 + + Sufficient + SCDO:0000012 HP:0001061 Break Out Breaking Out @@ -6318,63 +6317,63 @@ is characterised by: Pain or discharge from one or both ears - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + Hard, pebble-like deposits that form within the gallbladder. - Add here "bilirubin gallstones" (see paper "Liver involvement in sickle cell disease" by Emel GÜRKAN et al.). in HP these are called "Pigment Gallstones". - http://purl.obolibrary.org/obo/HP_0001081 - Sufficient - SCDO:0007091 + Add here "bilirubin gallstones" (see paper "Liver involvement in sickle cell disease" by Emel GÜRKAN et al.). in HP these are called "Pigment Gallstones". + http://purl.obolibrary.org/obo/HP_0001081 + Sufficient + SCDO:0007091 HP:0001081 Gallstones Cholelithiasis @@ -6387,9 +6386,9 @@ is characterised by: Pain or discharge from one or both ears An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities. - - Sufficient - SCDO:1000262 + + Sufficient + SCDO:1000262 HP:0001197 Abnormality of Prenatal Development or Birth @@ -6402,57 +6401,57 @@ is characterised by: Pain or discharge from one or both ears - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Seizures are an intermittent abnormality of the central nervous system due to a sudden, excessive, disorderly discharge of cerebral neurons and characterized clinically by some combination of disturbance of sensation, loss of consciousness, impairment of psychic function, or convulsive movements. The term epilepsy is used to describe chronic, recurrent seizures. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0001250 - Sufficient - SCDO:0001030 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0001250 + Sufficient + SCDO:0001030 HP:0001250 Seizures Seizure @@ -6465,9 +6464,9 @@ is characterised by: Pain or discharge from one or both ears A state of disinterestedness, listlessness, and indifference, resulting in difficulty performing simple tasks or concentrating. - - Sufficient - SCDO:0003089 + + Sufficient + SCDO:0003089 HP:0001254 Lethargy @@ -6480,45 +6479,45 @@ is characterised by: Pain or discharge from one or both ears - + - + - - + + - - + + - - + + - - + + Dysarthric speech is a general description referring to a neurological speech disorder characterized by poor articulation. Depending on the involved neurological structures, dysarthria may be further classified as spastic, flaccid, ataxic, hyperkinetic and hypokinetic, or mixed. - - Use description to add sub-classes of types of Dysarthria? -- Use text in comments to add relevant terms regarding disease progression? And link to these terms with relevant object property - - Sufficient - SCDO:0000403 + - Use description to add sub-classes of types of Dysarthria? -- Use text in comments to add relevant terms regarding disease progression? And link to these terms with relevant object property + + Sufficient + SCDO:0000403 HP:0001260 Difficulty Articulating Speech Dysarthric Speech @@ -6532,9 +6531,9 @@ is characterised by: Pain or discharge from one or both ears Reduction of neurologic reflexes such as the knee-jerk reaction. - - Sufficient - SCDO:0000602 + + Sufficient + SCDO:0000602 HP:0001265 Decreased Reflex Response Decreased Reflexes @@ -6549,32 +6548,32 @@ is characterised by: Pain or discharge from one or both ears - - + + - - + + - - + + - - + + Loss of strength in the arm, leg, and sometimes face on one side of the body. Hemiplegia refers to a complete loss of strength, whereas hemiparesis refers to an incomplete loss of strength. - http://purl.obolibrary.org/obo/HP_0001269 - Sufficient - SCDO:0008272 + http://purl.obolibrary.org/obo/HP_0001269 + Sufficient + SCDO:0008272 HP:0001269 Weakness of One Side of Body Hemiparesis @@ -6588,55 +6587,55 @@ is characterised by: Pain or discharge from one or both ears - + - + - - + + - - + + - - + + - - + + - - + + A generalized disorder of peripheral nerves. + http://purl.obolibrary.org/obo/HP_0001271 + Acute polyneuropathy has many causes: Infections involving a toxin produced by bacteria, as occurs in diphtheria,An autoimmune reaction (when the body attacks its own tissues), as occurs in Guillain-Barré syndrome (see Guillain-Barré Syndrome), Drugs, including the anticonvulsant phenytoin, some antibiotics (such as chloramphenicol, nitrofurantoin, and sulfonamides), some chemotherapy drugs (such as vinblastine and vincristine), and some sedatives (such as barbital and hexobarbital), Cancer (such as multiple myeloma), which damages nerves by directly invading or putting pressure on them or by triggering an autoimmune reaction, Certain toxins, such as organophosphate insecticides, triorthocresyl phosphate (TOCP), and thallium +The cause of chronic polyneuropathy is often unknown. Known causes include the following: Diabetes Mellitus, Excessive use of alcohol, Nutritional deficiencies (such as thiamin deficiency), an uncommon cause in the United States, except among alcoholics who are malnourished, Vitamin B12 deficiency, which causes subacute combined degeneration of the spinal cord (see Subacute Combined Degeneration) and often pernicious anemia (see Inadequate absorption), An underactive thyroid gland (hypothyroidism), Toxic substances, including heavy metals such as lead and mercury, Kidney failure, Certain cancers, such as lung cancer, Rarely, vitamin B6 (pyridoxine) taken in excessive amounts. + Acute polyneuropathy (as occurs in Guillain-Barré syndrome) begins suddenly in both legs and progresses rapidly upward to the arms. Symptoms include weakness and a pins-and-needles sensation or loss of sensation. The muscles that control breathing may be affected, resulting in respiratory failure.In the most common form of chronic polyneuropathy, only sensation is affected. Usually, the feet are affected first, but sometimes the hands are. A pins-and-needles sensation, numbness, burning pain, and loss of vibration sense and position sense (knowing where the arms and legs are) are prominent symptoms. Because position sense is lost, walking and even standing become unsteady. Consequently, muscles may not be used. Eventually, they may weaken and waste away. Then, muscles may become stiff and permanently shortened (called contractures). Diabetic neuropathy commonly causes painful tingling or burning sensations in the hands and feet-a condition called distal polyneuropathy. Pain is often worse at night and may be aggravated by touch or by a change in temperature. People may lose the senses of temperature and pain, so they often burn themselves and may have open sores caused by prolonged pressure or other injuries. Without pain as a warning of too much stress, joints are susceptible to injuries. This type of injury is called neurogenic arthropathy (Charcot joints) Polyneuropathy often affects the nerves of the autonomic nervous system, which controls involuntary functions in the body (such as blood pressure, heart rate, digestion, salivation, and urination). Typical symptoms are constipation, sexual dysfunction, and fluctuating blood pressure-most notably a sudden fall in blood pressure when a person stands up (orthostatic hypotension). The skin may become pale and dry, and sweating may be reduced. Much less often, control of bowel movements or urination is lost, leading to fecal or urinary incontinence. + Sufficient + SCDO:0000914 - http://purl.obolibrary.org/obo/HP_0001271 - Acute polyneuropathy has many causes: Infections involving a toxin produced by bacteria, as occurs in diphtheria,An autoimmune reaction (when the body attacks its own tissues), as occurs in Guillain-Barré syndrome (see Guillain-Barré Syndrome), Drugs, including the anticonvulsant phenytoin, some antibiotics (such as chloramphenicol, nitrofurantoin, and sulfonamides), some chemotherapy drugs (such as vinblastine and vincristine), and some sedatives (such as barbital and hexobarbital), Cancer (such as multiple myeloma), which damages nerves by directly invading or putting pressure on them or by triggering an autoimmune reaction, Certain toxins, such as organophosphate insecticides, triorthocresyl phosphate (TOCP), and thallium -The cause of chronic polyneuropathy is often unknown. Known causes include the following: Diabetes Mellitus, Excessive use of alcohol, Nutritional deficiencies (such as thiamin deficiency), an uncommon cause in the United States, except among alcoholics who are malnourished, Vitamin B12 deficiency, which causes subacute combined degeneration of the spinal cord (see Subacute Combined Degeneration) and often pernicious anemia (see Inadequate absorption), An underactive thyroid gland (hypothyroidism), Toxic substances, including heavy metals such as lead and mercury, Kidney failure, Certain cancers, such as lung cancer, Rarely, vitamin B6 (pyridoxine) taken in excessive amounts. - Acute polyneuropathy (as occurs in Guillain-Barré syndrome) begins suddenly in both legs and progresses rapidly upward to the arms. Symptoms include weakness and a pins-and-needles sensation or loss of sensation. The muscles that control breathing may be affected, resulting in respiratory failure.In the most common form of chronic polyneuropathy, only sensation is affected. Usually, the feet are affected first, but sometimes the hands are. A pins-and-needles sensation, numbness, burning pain, and loss of vibration sense and position sense (knowing where the arms and legs are) are prominent symptoms. Because position sense is lost, walking and even standing become unsteady. Consequently, muscles may not be used. Eventually, they may weaken and waste away. Then, muscles may become stiff and permanently shortened (called contractures). Diabetic neuropathy commonly causes painful tingling or burning sensations in the hands and feet-a condition called distal polyneuropathy. Pain is often worse at night and may be aggravated by touch or by a change in temperature. People may lose the senses of temperature and pain, so they often burn themselves and may have open sores caused by prolonged pressure or other injuries. Without pain as a warning of too much stress, joints are susceptible to injuries. This type of injury is called neurogenic arthropathy (Charcot joints) Polyneuropathy often affects the nerves of the autonomic nervous system, which controls involuntary functions in the body (such as blood pressure, heart rate, digestion, salivation, and urination). Typical symptoms are constipation, sexual dysfunction, and fluctuating blood pressure-most notably a sudden fall in blood pressure when a person stands up (orthostatic hypotension). The skin may become pale and dry, and sweating may be reduced. Much less often, control of bowel movements or urination is lost, leading to fecal or urinary incontinence. - Sufficient - SCDO:0000914 HP:0001271 Peripheral Nerve Disease Polyneuropathy @@ -6650,32 +6649,32 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + - - + + Syncope refers to a generalized weakness of muscles with loss of postural tone, inability to stand upright, and loss of consciousness. Once the patient is in a horizontal position, blood flow to the brain is no longer hindered by gravitation and consciousness is regained. Unconsciousness usually lasts for seconds to minutes. Headache and drowsiness (which usually follow seizures) do not follow a syncopal attack. Syncope results from a sudden impairment of brain metabolism usually due to a reduction in cerebral blood flow. - http://purl.obolibrary.org/obo/HP_0001279 - Sufficient - SCDO:0008553 + http://purl.obolibrary.org/obo/HP_0001279 + Sufficient + SCDO:0008553 HP:0001279 Fainting Spell Syncope @@ -6690,80 +6689,80 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Inflammation of the meninges. - - Sufficient - SCDO:0000744 + + Sufficient + SCDO:0000744 HP:0001287 Meningitis @@ -6775,10 +6774,10 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Lack of clarity and coherence of thought, perception, understanding, or action. - -- Perhaps move below "Behavioral Abnormality"? - - Sufficient - SCDO:0000273 + -- Perhaps move below "Behavioral Abnormality"? + + Sufficient + SCDO:0000273 HP:0001289 Confusion @@ -6791,45 +6790,45 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - + - - + + - - + + - - + + - - + + - - + + A term that means brain disease, damage, or malfunction. In general, it is manifested by an altered mental state. - -- Provide source for additional info. -- -- Specify which Blood Tests and Which Imaging Tests are used to diagnose. - - Sufficient - SCDO:0000429 + -- Provide source for additional info. -- -- Specify which Blood Tests and Which Imaging Tests are used to diagnose. + + Sufficient + SCDO:0000429 HP:0001298 Encephalopathy @@ -6842,80 +6841,80 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Hemorrhage into the parenchyma of the brain. - http://purl.obolibrary.org/obo/HP_0001342 - Sufficient - SCDO:0000209 + http://purl.obolibrary.org/obo/HP_0001342 + Sufficient + SCDO:0000209 HP:0001342 Bleeding in Brain Hemorrhagic Stroke @@ -6931,9 +6930,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Damage to cerebral nuclei caused in infants by highly increased levels of unconjugated bilirubin. The basal ganglia and brainstem nuclei could be shown to have a yellow staining historically in infants who died of kernicterus, that is, kernicterus is strictly speaking a pathological diagnosis. The presence of kernicterus may be inferred in infants with characteristic acute or chronic bilirubin-induced neurological dysfunction. - - Sufficient - SCDO:0000673 + + Sufficient + SCDO:0000673 HP:0001343 Kernicterus @@ -6946,29 +6945,29 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + Inflammation of a joint. - http://purl.obolibrary.org/obo/HP_0001369 - Any age - Infection (bacteria), ischemia, joint injury (trauma, surgery), degeneration. - Joint pain, joint swelling, stiffness, lack of function. - Sufficient - SCDO:0000075 + http://purl.obolibrary.org/obo/HP_0001369 + Any age + Infection (bacteria), ischemia, joint injury (trauma, surgery), degeneration. + Joint pain, joint swelling, stiffness, lack of function. + Sufficient + SCDO:0000075 HP:0001369 Joint Inflammation Arthritis @@ -6983,27 +6982,27 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + An autoimmune response that primarily affects connective tissue; it also results in chronic inflammation of the joints, especially of the hands and feet and may also cause inflammation of the tissue around the joints, as well as other organs in the body. - Provide source for additional info. - http://purl.obolibrary.org/obo/MP_0003561 - Sufficient - SCDO:0001011 + Provide source for additional info. + http://purl.obolibrary.org/obo/MP_0003561 + Sufficient + SCDO:0001011 HP:0001370 Osteoarthrosis Deformans RA @@ -7017,9 +7016,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f A flexion contracture is a bent (flexed) joint that cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement of joints. - http://purl.obolibrary.org/obo/HP_0001371 - Sufficient - SCDO:0001324 + http://purl.obolibrary.org/obo/HP_0001371 + Sufficient + SCDO:0001324 HP:0001371 Flexion Contractures Flexion Contractures of Joints @@ -7036,27 +7035,27 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - + - - + + - - + + The ability of a joint to move beyond its normal range of motion. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0001382 - Sufficient - SCDO:0000672 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0001382 + Sufficient + SCDO:0000672 HP:0001382 Double-Jointed Hyperextensible Joints @@ -7072,9 +7071,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f An abnormality of the liver. - - Sufficient - SCDO:1000272 + + Sufficient + SCDO:1000272 HP:0001392 Complication of the Liver Liver Abnormality @@ -7089,9 +7088,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f A chronic disorder of the liver in which liver tissue becomes scarred and is partially replaced by regenerative nodules and fibrotic tissue resulting in loss of liver function. - - Sufficient - SCDO:0001488 + + Sufficient + SCDO:0001488 HP:0001394 Hepatic Cirrhosis Scar Tissue Replaces Healthy Tissue in the Liver @@ -7105,9 +7104,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f The presence of excessive fibrous connective tissue in the liver. Fibrosis is a reparative or reactive process. - - Sufficient - SCDO:0001493 + + Sufficient + SCDO:0001493 HP:0001395 Hepatic Fibrosis @@ -7120,39 +7119,39 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + - - + + - - + + Impairment of bile flow due to obstruction in the small bile ducts within the liver. - Is managed by: analgesia, hydration, antibiotics, and in severe cases exchange transfusion may be needed. - http://purl.obolibrary.org/obo/HP_0001406 - Sufficient - SCDO:0009774 + Is managed by: analgesia, hydration, antibiotics, and in severe cases exchange transfusion may be needed. + http://purl.obolibrary.org/obo/HP_0001406 + Sufficient + SCDO:0009774 HP:0001406 Intrahepatic Cholestasis @@ -7166,9 +7165,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Simultaneous enlargement of the liver and spleen. - - Sufficient - SCDO:0007326 + + Sufficient + SCDO:0007326 HP:0001433 Hepatosplenomegaly @@ -7180,9 +7179,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Abnormality of growth. - - Sufficient - SCDO:1000271 + + Sufficient + SCDO:1000271 HP:0001507 Abnormal Growth Growth Issue @@ -7196,9 +7195,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Failure to thrive (FTT) refers to a child whose physical growth is substantially below the norm. - - Sufficient - SCDO:0002729 + + Sufficient + SCDO:0002729 HP:0001508 FTT Faltering Weight @@ -7218,51 +7217,51 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + - - + + - - + + - - + + - - + + An abnormal restriction of fetal growth with fetal weight below the tenth percentile for gestational age. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0001511 - Sufficient - SCDO:0000658 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0001511 + Sufficient + SCDO:0000658 HP:0001511 IUGR Intrauterine Growth Retardation @@ -7280,44 +7279,44 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + - - + + - - + + - - + + Body weight that is grossly above the acceptable or desirable weight, usually due to accumulation of excess fats in the body. The standards may vary with age, sex, genetic or cultural background. In the body mass index (BMI), a BMI greater than 30.0 kg/m2 is considered obese, and a BMI greater than 40.0 kg/m2 is considered morbidly obese. - http://purl.obolibrary.org/obo/HP_0001513 - Sufficient - SCDO:0000816 + http://purl.obolibrary.org/obo/HP_0001513 + Sufficient + SCDO:0000816 HP:0001513 Having too much body fat Obesity @@ -7330,9 +7329,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f An abnormality of the integument, which consists of the skin and the superficial fascia. - - Sufficient - SCDO:1000274 + + Sufficient + SCDO:1000274 HP:0001574 Abnormality of the Integument @@ -7345,27 +7344,27 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + The birth of a baby of less than 37 weeks of gestational age. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0001622 - Sufficient - SCDO:0000920 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0001622 + Sufficient + SCDO:0000920 HP:0001622 Premature Birth Premature Delivery @@ -7381,9 +7380,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Any abnormality of the cardiovascular system. - http://purl.obolibrary.org/obo/HP_0001626 - Sufficient - SCDO:0002245 + http://purl.obolibrary.org/obo/HP_0001626 + Sufficient + SCDO:0002245 HP:0001626 Abnormality of the Cardiovascular System Cardiovascular Abnormality @@ -7397,9 +7396,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f The presence of an abnormality of cardiac function that is responsible for the failure of the heart to pump blood at a rate that is commensurate with the needs of the tissues or a state in which abnormally elevated filling pressures are required for the heart to do so. Heart failure is frequently related to a defect in myocardial contraction. - - Sufficient - SCDO:0004877 + + Sufficient + SCDO:0004877 HP:0001635 CHF Cardiac Insufficiency, @@ -7416,20 +7415,20 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + Increased size of the heart. - http://purl.obolibrary.org/obo/HP_0001640 - Sufficient - SCDO:0008273 + http://purl.obolibrary.org/obo/HP_0001640 + Sufficient + SCDO:0008273 HP:0001640 Enlarged Heart Increased Heart Size @@ -7444,26 +7443,26 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + Necrosis of the myocardium caused by an obstruction of the blood supply to the heart and often associated with chest pain, shortness of breath, palpitations, and anxiety as well as characteristic EKG findings and elevation of serum markers including creatine kinase-MB fraction and troponin. - http://purl.obolibrary.org/obo/HP_0001658 - Sufficient - SCDO:0007991 + http://purl.obolibrary.org/obo/HP_0001658 + Sufficient + SCDO:0007991 HP:0001658 Myocardial Infarction @@ -7475,9 +7474,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Inflammation of the sac-like covering around the heart (pericardium). - - Sufficient - SCDO:0003765 + + Sufficient + SCDO:0003765 HP:0001701 Pericarditis @@ -7489,9 +7488,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Enlargement or increased size of the heart left ventricle. - - Sufficient - SCDO:0002803 + + Sufficient + SCDO:0002803 HP:0001712 Heart Left Ventricle Hypertrophy Left Ventricular Wall Hypertrophy @@ -7506,38 +7505,38 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + - - + + - - + + Enlargement of the cardiovascular ventricular muscle tissue with increase in the width of the wall of the ventricle and loss of elasticity. Ventricular hypertrophy is clinically differentiated into left and right ventricular hypertrophy. - http://purl.obolibrary.org/obo/HP_0001714 - Sufficient - SCDO:0001231 + http://purl.obolibrary.org/obo/HP_0001714 + Sufficient + SCDO:0001231 HP:0001714 Ventricular Hypertrophy @@ -7550,9 +7549,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f An abnormality of the spleen. - - Sufficient - SCDO:1000370 + + Sufficient + SCDO:1000370 HP:0001743 Abnormality of the Spleen @@ -7565,44 +7564,44 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + - - + + - - + + - - + + Abnormal increased size of the spleen. - http://purl.obolibrary.org/obo/HP_0001744 - Sufficient - SCDO:0005287 + http://purl.obolibrary.org/obo/HP_0001744 + Sufficient + SCDO:0005287 HP:0001744 Increased Spleen Size Results from splenic sequestration @@ -7616,9 +7615,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f An abnormality of the birth process. - - Sufficient - SCDO:1000372 + + Sufficient + SCDO:1000372 HP:0001787 Abnormal Delivery @@ -7632,32 +7631,32 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + - - + + The abnormal accumulation of fluid in two or more fetal compartments, including ascites, pleural effusion, pericardial effusion, and skin edema. - http://purl.obolibrary.org/obo/HP_0001789 - Sufficient - SCDO:0000578 + http://purl.obolibrary.org/obo/HP_0001789 + Sufficient + SCDO:0000578 HP:0001789 Hydrops Fetalis @@ -7668,11 +7667,11 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - + An abnormality of the hematopoietic system. - - Sufficient - SCDO:1000264 + + Sufficient + SCDO:1000264 HP:0001871 Abnormality of the Hematopoietic System Hematological Abnormality @@ -7687,9 +7686,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f An abnormality of platelets. Platelets, also known as thrombocytes, are non-nucleated disk-shaped cells mainly involved in blood coagulation. - - Sufficient - SCDO:1000616 + + Sufficient + SCDO:1000616 HP:0001872 Platelet Abnormalities Abnormal Thrombocyte Morphology @@ -7702,9 +7701,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f A reduction in the number of circulating thrombocytes. - - Sufficient - SCDO:0002700 + + Sufficient + SCDO:0002700 HP:0001873 Thrombocytopenia @@ -7716,9 +7715,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f A neutrophil abnormality. - - Sufficient - SCDO:1000440 + + Sufficient + SCDO:1000440 HP:0001874 Neutrophils are the most abundant leukocytes in blood and are considered to be the first line of defense during inflammation and infections. They are myeloid granulocytes and their names is derived from the fact that their cytoplasm contains granules that stain with acidic dye as well as granules that stain with basic dye. Their nuclei consist of three to five lobes connected by slender threads of chromatin. Mature neutrophils live for approximately one day. Abnormality of Neutrophils @@ -7731,9 +7730,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f An abnormally low number of neutrophils in the peripheral blood. - - Sufficient - SCDO:0009334 + + Sufficient + SCDO:0009334 HP:0001875 Decreased Neutrophil Count Low Blood Neutrophil Count @@ -7749,9 +7748,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Any structural abnormality of erythrocytes (red-blood cells). - - Sufficient - SCDO:1000285 + + Sufficient + SCDO:1000285 HP:0001877 Abnormal Erythrocyte Morphology @@ -7764,68 +7763,68 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A type of anemia caused by premature destruction of red blood cells (hemolysis). - http://purl.obolibrary.org/obo/HP_0001878 - Sufficient - SCDO:0003844 + http://purl.obolibrary.org/obo/HP_0001878 + Sufficient + SCDO:0003844 HP:0001878 Hemolytic Anemia @@ -7837,9 +7836,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f An abnormal decreased number of leukocytes in the blood. - - Sufficient - SCDO:1000614 + + Sufficient + SCDO:1000614 HP:0001882 Decreased Blood Leukocyte Number Low White Blood Cell Count @@ -7854,32 +7853,32 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + - - + + Anemia characterized by the presence of erythroblasts that are larger than normal (megaloblasts). - http://purl.obolibrary.org/obo/HP_0001889 - Sufficient - SCDO:0005864 + http://purl.obolibrary.org/obo/HP_0001889 + Sufficient + SCDO:0005864 HP:0001889 Megaloblastic Anemia @@ -7891,9 +7890,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Thrombocythemia and thrombocytosis are conditions with a higher than normal number of platelets. The term "thrombocythemia" is preferred when the cause of a high platelet count isn't known. The condition sometimes is called primary or essential thrombocythemia. Increased numbers of platelets in the peripheral blood. - - Sufficient - SCDO:1000618 + + Sufficient + SCDO:1000618 HP:0001894 Increased Number of Platelets in Blood Increased Platelet Count @@ -7908,14 +7907,14 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + A reduced number of reticulocytes in the peripheral blood. - - Sufficient - SCDO:0001423 + + Sufficient + SCDO:0001423 HP:0001896 Low Reticulocyte Count Reduced Number of Reticulocytes @@ -7931,74 +7930,74 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A reduction in erythrocytes volume or hemoglobin concentration. - http://purl.obolibrary.org/obo/HP_0001903 - Sufficient - SCDO:0005660 + http://purl.obolibrary.org/obo/HP_0001903 + Sufficient + SCDO:0005660 HP:0001903 Anemia @@ -8011,26 +8010,26 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + A cancer of the blood and bone marrow characterized by an abnormal proliferation of leukocytes. - http://purl.obolibrary.org/obo/HP_0001909 - Sufficient - SCDO:0000687 + http://purl.obolibrary.org/obo/HP_0001909 + Sufficient + SCDO:0000687 HP:0001909 Blood Cancer Leukaemia @@ -8044,107 +8043,107 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Sudden loss of renal function, as manifested by decreased urine production, and a rise in serum creatinine or blood urea nitrogen concentration (azotemia). - Further work - Provide source for additional info. - There is conflicting positioning of this term in different ontologies. Need an expert to decide descriptions and positioning of this and related terms. - http://purl.obolibrary.org/obo/HP_0001919 - Sufficient - SCDO:0000017 + Further work + Provide source for additional info. + There is conflicting positioning of this term in different ontologies. Need an expert to decide descriptions and positioning of this and related terms. + http://purl.obolibrary.org/obo/HP_0001919 + Sufficient + SCDO:0000017 HP:0001919 Acute Kidney Failure Acute Renal Failure @@ -8160,18 +8159,18 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + The presence of stenosis of the renal artery. - Provide source for additional info. - - If due to FMD, presents at younger age, typically between 25-50 (and more common in women); if related to atherosclerotic disase, more likely to present after age 50. - May be caused by atherosclerotic disease, fibromuscular dysplasia. - Reduced blood flow through the renal arteries, large and branching vessels. - Sufficient - SCDO:0000982 + Provide source for additional info. + + If due to FMD, presents at younger age, typically between 25-50 (and more common in women); if related to atherosclerotic disase, more likely to present after age 50. + May be caused by atherosclerotic disease, fibromuscular dysplasia. + Reduced blood flow through the renal arteries, large and branching vessels. + Sufficient + SCDO:0000982 HP:0001920 Narrowing of Kidney Artery RAS @@ -8186,26 +8185,26 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + An elevation in the number of reticulocytes (immature erythrocytes) in the peripheral blood circulation. - - Sufficient - SCDO:0001272 + + Sufficient + SCDO:0001272 HP:0001923 High Reticulocyte Count Increased Immature Red Blood Cells @@ -8222,9 +8221,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f A type of anemia characterized by an abnormally low concentration of hemoglobin in the erythrocytes. - - Sufficient - SCDO:0007371 + + Sufficient + SCDO:0007371 HP:0001931 Hypochromic Anemia @@ -8236,10 +8235,10 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f A kind of anemia in which the volume of the red blood cells is reduced. + + Sufficient + SCDO:0008538 - - Sufficient - SCDO:0008538 HP:0001935 In normocytic anemia, the mean corpuscular volume (MCV) is below normal limits (>80 fl in adults). Microcytic Anemia @@ -8252,10 +8251,10 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f A decreased concentration of glucose in the blood. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0001943 - Sufficient - SCDO:0000599 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0001943 + Sufficient + SCDO:0000599 HP:0001943 Low Blood Sugar Hypoglycemia @@ -8269,14 +8268,14 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + A type of diabetic metabolic abnormality with an accumulation of ketone bodies. - http://purl.obolibrary.org/obo/HP_0001953 - Sufficient - SCDO:0000369 + http://purl.obolibrary.org/obo/HP_0001953 + Sufficient + SCDO:0000369 HP:0001953 Diabetic Ketosis Diabetic Ketoacidosis @@ -8290,26 +8289,26 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - + - + - - + + A form of inflammation of the kidney affecting the interstitium of the kidneys surrounding the tubules. - - Sufficient - SCDO:0000652 + + Sufficient + SCDO:0000652 HP:0001970 Tubulointerstitial Nephritis Interstitial Nephritis @@ -8322,9 +8321,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f An abnormal increase in the number of leukocytes in the blood. - - Sufficient - SCDO:0005790 + + Sufficient + SCDO:0005790 HP:0001974 Elevated White Blood Count High White Blood Count @@ -8339,9 +8338,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Venous or arterial thrombosis (formation of blood clots) of spontaneous nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis). - - Sufficient - SCDO:1000287 + + Sufficient + SCDO:1000287 HP:0001977 Abnormal Thrombosis @@ -8353,10 +8352,10 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f An abnormal morphology (form) of the face or its components. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0001999 - Sufficient - SCDO:0001314 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0001999 + Sufficient + SCDO:0001314 HP:0001999 Abnormal Morphology of the Face Abnormal facial shape @@ -8373,14 +8372,14 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + Bilateral bulging of the lateral frontal bone prominences with relative sparing of the midline. - http://purl.obolibrary.org/obo/HP_0002007 - Sufficient - SCDO:0001337 + http://purl.obolibrary.org/obo/HP_0002007 + Sufficient + SCDO:0001337 HP:0002007 Frontal Protruberance Skull Bossing @@ -8394,9 +8393,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Abnormally increased frequency of loose or watery bowel movements. - - Sufficient - SCDO:0008043 + + Sufficient + SCDO:0008043 HP:0002014 Diarrhoea Watery stool @@ -8411,50 +8410,50 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + - - + + - - + + - - + + - - + + Infrequent or difficult evacuation of feces. - http://purl.obolibrary.org/obo/HP_0002019 - Sufficient - SCDO:0003263 + http://purl.obolibrary.org/obo/HP_0002019 + Sufficient + SCDO:0003263 HP:0002019 Constipation Costiveness @@ -8469,9 +8468,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Atrophy (wasting, decrease in size of cells or tissue) affecting the cerebrum. - http://purl.obolibrary.org/obo/HP_0002059 - Sufficient - SCDO:0000203 + http://purl.obolibrary.org/obo/HP_0002059 + Sufficient + SCDO:0000203 HP:0002059 Cortical Atrophy Degeneration of Cerebrum @@ -8487,9 +8486,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f An abnormality of the telencephalon, which is also known as the cerebrum. - http://purl.obolibrary.org/obo/HP_0002060 - Sufficient - SCDO:0008895 + http://purl.obolibrary.org/obo/HP_0002060 + Sufficient + SCDO:0008895 HP:0002060 Abnormal Cerebral Morphology Abnormality of the Telencephalon @@ -8503,9 +8502,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Bradykinesia literally means slow movement, and is used clinically to denote a slowness in the execution of movement (in contrast to hypokinesia, which is used to refer to slowness in the initiation of movement). - http://purl.obolibrary.org/obo/HP_0002067 - Sufficient - SCDO:0000158 + http://purl.obolibrary.org/obo/HP_0002067 + Sufficient + SCDO:0000158 HP:0002067 Slow Movements Slowness of Movements @@ -8520,38 +8519,38 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - + - + - + - - + + - - + + A neurological condition related to lesions of the basal ganglia leading to typical abnormalities including akinesia (inability to initiate changes in activity and perform volitional movements rapidly and easily), muscular rigidity (continuous contraction of muscles with constant resistance to passive movement), chorea (widespread arrhythmic movements of a forcible, rapid, jerky, and restless nature), athetosis (inability to sustain the muscles of the fingers, toes, or other group of muscles in a fixed position), and akathisia (inability to remain motionless). - - Sufficient - SCDO:0001311 + + Sufficient + SCDO:0001311 HP:0002071 Abnormality of Extrapyramidal Motor Function Extrapyramidal Dysfunction @@ -8569,44 +8568,44 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - + - + - - + + - - + + - - + + - - + + Migraine is a chronic neurological disorder characterized by episodic attacks of headache and associated symptoms. - - Sufficient - SCDO:0000759 + + Sufficient + SCDO:0000759 HP:0002076 Intermittent Migraine Headaches Migraine Headache @@ -8621,10 +8620,10 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles. - Curation completed by the SCDO curator team: Amy and Khuthala. - http://purl.obolibrary.org/obo/HP_0002086 - Sufficient - SCDO:0004899 + Curation completed by the SCDO curator team: Amy and Khuthala. + http://purl.obolibrary.org/obo/HP_0002086 + Sufficient + SCDO:0004899 HP:0002086 Respiratory Abnormality Abnormality of the Respiratory System @@ -8638,9 +8637,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Inflammation of any part of the lung parenchyma. - - Sufficient - SCDO:0009838 + + Sufficient + SCDO:0009838 HP:0002090 Pneumonia @@ -8653,51 +8652,51 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + - - + + - - + + - - + + - - + + Difficulty in breathing. The physical presentation of respiratory distress is generally referred to as labored breathing, while the sensation of respiratory distress is called shortness of breath or dyspnea. - Is a symptom of acute chest syndrome - http://purl.obolibrary.org/obo/HP_0002098 - Sufficient - SCDO:0009656 + Is a symptom of acute chest syndrome + http://purl.obolibrary.org/obo/HP_0002098 + Sufficient + SCDO:0009656 HP:0002098 Breathing Difficulties Difficulty Breathing @@ -8713,38 +8712,38 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - + - - + + - - + + - - + + - - + + Hemorrhage occurring between the arachnoid mater and the pia mater. - - Sufficient - SCDO:0001118 + + Sufficient + SCDO:0001118 HP:0002138 Subarachnoid Haemorrhage Subarachnoid hemorrhage may occur spontaneously, usually from a ruptured cerebral aneurysm, or may result from head injury. @@ -8759,14 +8758,14 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + An abnormally high level of uric acid in the blood. - - Sufficient - SCDO:0000596 + + Sufficient + SCDO:0000596 HP:0002149 High Blood Uric Acid Level Hyperuricaemia @@ -8781,21 +8780,21 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + An increased concentration of nitrogen compounds in the blood. - Perhaps move to below "Endocrine and Metabolic"? -- -- Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info. - - Sufficient - SCDO:0000093 + Perhaps move to below "Endocrine and Metabolic"? -- -- Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info. + + Sufficient + SCDO:0000093 HP:0002157 Azotemia Azotaemia @@ -8809,14 +8808,14 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + The presence of developmental dysplasia of the nail. - - Sufficient - SCDO:0000830 + + Sufficient + SCDO:0000830 HP:0002164 Dysplastic Nails Onychodysplasia @@ -8828,71 +8827,71 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Hemorrhage occurring within the skull. - - Sufficient - SCDO:0000654 + + Sufficient + SCDO:0000654 HP:0002170 Intracranial Hemorrhage @@ -8905,15 +8904,15 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + Abnormal accumulation of fluid in the brain. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0002181 - Sufficient - SCDO:0000207 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0002181 + Sufficient + SCDO:0000207 HP:0002181 Brain Edema Brain Oedema @@ -8928,9 +8927,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f An embolus (that is, an abnormal particle circulating in the blood) located in the pulmonary artery and thereby blocking blood circulation to the lung. Usually the embolus is a blood clot that has developed in an extremity (for instance, a deep venous thrombosis), detached, and traveled through the circulation before becoming trapped in the pulmonary artery. - - Sufficient - SCDO:0007912 + + Sufficient + SCDO:0007912 HP:0002204 Blood Clot in Artery of Lung Pulmonary Embolism @@ -8944,9 +8943,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Abnormally increased size of the liver. - - Sufficient - SCDO:0005566 + + Sufficient + SCDO:0005566 HP:0002240 Hepatomegaly @@ -8959,44 +8958,44 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - + - - + + - + - - + + - - + + - - + + Compression of the spinal cord in the cervical region, generally manifested by paresthesias and numbness, weakness, difficulty walking, abnormalities of coordination, and neck pain or stiffness. - http://purl.obolibrary.org/obo/HP_0002341 - Sufficient - SCDO:0000214 + http://purl.obolibrary.org/obo/HP_0002341 + Sufficient + SCDO:0000214 HP:0002341 Cervical Cord Compression Myelopathy Cervical Spondylotic Myelopathy @@ -9011,12 +9010,12 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f Impairment of expressive language and relative preservation of receptive language abilities. That is, the patient understands language (speech, writing) but cannot express it. - - Aphasia is one of the most common communication disorders to affect the brain. Although there are no official figures, the Stroke Association estimates more than 376,000 stroke survivors in the UK are living with aphasia. Aphasia can affect people of all ages, including children. It's most common in people over 65 years old as stroke and common progressive neurological conditions tend to affect older adults - Aphasia is caused by damage to parts of the brain responsible for understanding and using language. Common causes include:stroke, thought to be the most common cause, around one in three people experience some degree of aphasia after having a stroke.severe head injury. brain tumour.progressive neurological conditions (conditions that over time cause progressive brain and nervous system damage). - Experience difficulties with understanding or expressing language. - Sufficient - SCDO:0000773 + + Aphasia is one of the most common communication disorders to affect the brain. Although there are no official figures, the Stroke Association estimates more than 376,000 stroke survivors in the UK are living with aphasia. Aphasia can affect people of all ages, including children. It's most common in people over 65 years old as stroke and common progressive neurological conditions tend to affect older adults + Aphasia is caused by damage to parts of the brain responsible for understanding and using language. Common causes include:stroke, thought to be the most common cause, around one in three people experience some degree of aphasia after having a stroke.severe head injury. brain tumour.progressive neurological conditions (conditions that over time cause progressive brain and nervous system damage). + Experience difficulties with understanding or expressing language. + Sufficient + SCDO:0000773 HP:0002427 Broca's Aphasia Expressive Aphasia @@ -9033,14 +9032,14 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + An increase of the pressure inside the cranium (skull) and thereby in the brain tissue and cerebrospinal fluid. - http://purl.obolibrary.org/obo/HP_0002516 - Sufficient - SCDO:0000655 + http://purl.obolibrary.org/obo/HP_0002516 + Sufficient + SCDO:0000655 HP:0002516 Increased Intracranial Pressure Intracranial Pressure Elevation @@ -9055,9 +9054,9 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f An abnormality of the vasculature. - - Sufficient - SCDO:1000373 + + Sufficient + SCDO:1000373 HP:0002597 Abnormality of the Vasculature @@ -9070,29 +9069,29 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + - - + + The presence of an abnormal lateral curvature of the spine. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0002650 - Congenital vertebral anomalies, idiopathic, result of a neuromuscular condition. - Spinal tortuosity. - Sufficient - SCDO:0001026 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0002650 + Congenital vertebral anomalies, idiopathic, result of a neuromuscular condition. + Spinal tortuosity. + Sufficient + SCDO:0001026 HP:0002650 Abnormal Curving of the Spine Scoliosis @@ -9103,92 +9102,92 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to bone. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0002653 - A number of diseases may cause bone pain including osteoarthritis, Paget's disease, sickle cell anemia, and bone cancer. Acute leukemia;Acute rheumatic fever, a very dangerous disease that can cause permanent cardiac damage. Bursitis;Fibromyalgia like disease has been studied as a cause of joint pain in the child.Hypermobility syndrome can present with knee or ankle pain;Injury such as a fracture. Juvenile rheumatoid arthritis;Lupus;Lyme disease, which is transmitted by ticks and is characterized by debilatating polyarthritis, neurologic symptoms, and erythema migrans.;Osteomyelitis;Osteosarcoma.Septic arthritis, a severe infection of the joint that can lead to permanent joint damage.Synovitis;Viral diseases, including the measles, influenza, mononucleosis, chickenpox, and mumps. - Stimulation of specialized pain-sensitive nerve fibers (nociceptors) that innervate bone tissue leads to the sensation of bone pain. Bone pain originates from both the periosteum and the bone marrow which relay nociceptive signals to the brain creating the sensation of pain. Bone tissue is innervated by both myelinated (A beta and A delta fiber) and unmyelinated (C fiber) sensory neurons. In combination, they can provide an initial burst of pain, initiated by the faster myelinated fibers, followed by a slower and longer lasting dull pain initiated by unmyelinated fibers - Sufficient - SCDO:0000154 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0002653 + A number of diseases may cause bone pain including osteoarthritis, Paget's disease, sickle cell anemia, and bone cancer. Acute leukemia;Acute rheumatic fever, a very dangerous disease that can cause permanent cardiac damage. Bursitis;Fibromyalgia like disease has been studied as a cause of joint pain in the child.Hypermobility syndrome can present with knee or ankle pain;Injury such as a fracture. Juvenile rheumatoid arthritis;Lupus;Lyme disease, which is transmitted by ticks and is characterized by debilatating polyarthritis, neurologic symptoms, and erythema migrans.;Osteomyelitis;Osteosarcoma.Septic arthritis, a severe infection of the joint that can lead to permanent joint damage.Synovitis;Viral diseases, including the measles, influenza, mononucleosis, chickenpox, and mumps. + Stimulation of specialized pain-sensitive nerve fibers (nociceptors) that innervate bone tissue leads to the sensation of bone pain. Bone pain originates from both the periosteum and the bone marrow which relay nociceptive signals to the brain creating the sensation of pain. Bone tissue is innervated by both myelinated (A beta and A delta fiber) and unmyelinated (C fiber) sensory neurons. In combination, they can provide an initial burst of pain, initiated by the faster myelinated fibers, followed by a slower and longer lasting dull pain initiated by unmyelinated fibers + Sufficient + SCDO:0000154 HP:0002653 Bone Pain @@ -9200,10 +9199,10 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f An abnormally increased tendency to fractures of bones caused by an abnormal reduction in bone strength that is generally associated with an increased risk of fracture. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0002659 - Sufficient - SCDO:0000153 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0002659 + Sufficient + SCDO:0000153 HP:0002659 Abnormal Susceptibility to Fractures Frequent Broken Bones @@ -9221,20 +9220,20 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f - - + + - - + + A cancer originating in lymphocytes and presenting as a solid tumor of lymphoid cells. - http://purl.obolibrary.org/obo/HP_0002665 - Sufficient - SCDO:0000707 + http://purl.obolibrary.org/obo/HP_0002665 + Sufficient + SCDO:0000707 HP:0002665 Cancer of Lymphatic System Lymphoma @@ -9247,11 +9246,11 @@ The cause of chronic polyneuropathy is often unknown. Known causes include the f An abnormality of the immune system. - Include as sub-class: -Acquired Immunodeficiency Syndrome (term in NCIT) - - Sufficient - SCDO:1000273 + Include as sub-class: +Acquired Immunodeficiency Syndrome (term in NCIT) + + Sufficient + SCDO:1000273 HP:0002715 Abnormality of the Immune System @@ -9261,41 +9260,41 @@ Acquired Immunodeficiency Syndrome (term in NCIT) - + - + - + - - + + - - + + - - + + A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys, and serosal membranes. - http://purl.obolibrary.org/obo/HP_0002725 - Sufficient - SCDO:0001137 + http://purl.obolibrary.org/obo/HP_0002725 + Sufficient + SCDO:0001137 HP:0002725 Systemic Lupus Erythematosus @@ -9308,20 +9307,20 @@ Acquired Immunodeficiency Syndrome (term in NCIT) - + - - + + Exaggerated anterior convexity of the thoracic vertebral column. - http://purl.obolibrary.org/obo/HP_0002808 - Sufficient - SCDO:0000679 + http://purl.obolibrary.org/obo/HP_0002808 + Sufficient + SCDO:0000679 HP:0002808 Gibbus Deformity Hunched Back @@ -9335,36 +9334,36 @@ Acquired Immunodeficiency Syndrome (term in NCIT) - + - - + + - - + + - - + + - - + + Joint pain. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0002829 - Sufficient - SCDO:0000074 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0002829 + Sufficient + SCDO:0000074 HP:0002829 Arthralgias Joint pain @@ -9379,68 +9378,68 @@ Acquired Immunodeficiency Syndrome (term in NCIT) - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A condition characterized by obstruction of the airway and by pauses in breathing during sleep occurring many times during the night. Obstructive sleep apnea is related to a relaxation of muscle tone (which normally occurs during sleep) leading to partial collapse of the soft tissues in the airway with resultant obstruction of the air flow. - http://purl.obolibrary.org/obo/HP_0002870 - Sufficient - SCDO:0000820 + http://purl.obolibrary.org/obo/HP_0002870 + Sufficient + SCDO:0000820 HP:0002870 Obstructive Sleep Apnoea Obstructive Sleep Apnea @@ -9451,23 +9450,23 @@ Acquired Immunodeficiency Syndrome (term in NCIT) - + - - + + - - + + Microscopic hematuria detected by dipstick or microscopic examination of the urine. - http://purl.obolibrary.org/obo/HP_0002907 - Sufficient - SCDO:0004833 + http://purl.obolibrary.org/obo/HP_0002907 + Sufficient + SCDO:0004833 HP:0002907 Microhematuria Occult Hematuria @@ -9483,20 +9482,20 @@ Acquired Immunodeficiency Syndrome (term in NCIT) - - + + - - + + Presence of myoglobin in the urine. - - Sufficient - SCDO:0000783 + + Sufficient + SCDO:0000783 HP:0002913 Increased Urine Myoglobin Level Myoglobinuria @@ -9510,15 +9509,15 @@ Acquired Immunodeficiency Syndrome (term in NCIT) - - + + Any disease characterized by the formation of numerous granulomas. - Source needed for additional information. - http://purl.obolibrary.org/obo/HP_0002955 - Sufficient - SCDO:0000464 + Source needed for additional information. + http://purl.obolibrary.org/obo/HP_0002955 + Sufficient + SCDO:0000464 HP:0002955 Has disease stages: Allergic (Churg-strauss syndrome), eosinophilic (langerhan cell histiocytosis), langerhans (langerhan cell histiocytosis), lymphomatoid, siderotica, wegeners. @@ -9533,9 +9532,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation An elevated lipid concentration in the blood. - http://purl.obolibrary.org/obo/HP_0003077 - Sufficient - SCDO:0000590 + http://purl.obolibrary.org/obo/HP_0003077 + Sufficient + SCDO:0000590 HP:0003077 Elevated Lipids in Blood Hyperlipidemia @@ -9547,11 +9546,11 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + An abnormality of the composition of urine or the levels of its components. - - Sufficient - SCDO:1000651 + + Sufficient + SCDO:1000651 HP:0003110 Abnormal Urine Chemistry Abnormality of Urine Homeostasis @@ -9565,9 +9564,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation An abnormality detectable by sonography of the heart (echocardiography). - - Sufficient - SCDO:1000267 + + Sufficient + SCDO:1000267 HP:0003116 Abnormal ECG Abnormal Echocardiography @@ -9579,17 +9578,17 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - - + + Excretion in urine of proteins of a size smaller than albumin (molecular weight 69 kD). - http://purl.obolibrary.org/obo/HP_0003126 - Sufficient - SCDO:0001196 + http://purl.obolibrary.org/obo/HP_0003126 + Sufficient + SCDO:0001196 HP:0003126 Low-Molecular-Weight Proteinuria Tubular Proteinuria @@ -9602,9 +9601,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation Abnormally increased serum levels of alkaline phosphatase activity. - - Sufficient - SCDO:1000664 + + Sufficient + SCDO:1000664 HP:0003155 Blood Alkaline Phosphatase Increased Decreased Circulating Alkaline Phosphatase Level @@ -9624,51 +9623,51 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - - + + - - + + - - + + - - + + - - + + - - + + - - + + An abnormally low urinary specific gravity, i.e., reduced concentration of solutes in the urine. - Could this be a synonym for 'Impaired Urinary Concentration' (SCDO:0000621)? - http://purl.obolibrary.org/obo/HP_0003158 - Sufficient - SCDO:0008046 + Could this be a synonym for 'Impaired Urinary Concentration' (SCDO:0000621)? + http://purl.obolibrary.org/obo/HP_0003158 + Sufficient + SCDO:0008046 HP:0003158 Urine specific gravity is lower than that of plasma < 1.008. Hyposthenuria @@ -9679,36 +9678,36 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - - + + - - + + - - + + - - + + A disorder of muscle unrelated to impairment of innervation or neuromuscular junction. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0003198 - Sufficient - SCDO:0000784 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0003198 + Sufficient + SCDO:0000784 HP:0003198 Muscle Tissue Disease Myopathic Changes @@ -9723,9 +9722,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation A type of hyperbilirubinemia with neonatal onset. - - Sufficient - SCDO:0003776 + + Sufficient + SCDO:0003776 HP:0003265 High Blood Bilirubin Levels in Neonate Neonatal Hyperbilirubinemia @@ -9738,9 +9737,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation Abnormally reduced serum levels of alkaline phosphatase. - - Sufficient - SCDO:1000667 + + Sufficient + SCDO:1000667 HP:0003282 Low ALP Low Alkaline Phosphatase @@ -9756,34 +9755,34 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - - + + - - + + - - + + - - + + Complete bilateral fractures of the pars interarticularis resulting in the anterior slippage of the vertebra. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0003302 - Spondylolysis, arthritis, degeneration, trauma, metastases or metabolic bone disease, congenital. - Sufficient - SCDO:0001102 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0003302 + Spondylolysis, arthritis, degeneration, trauma, metastases or metabolic bone disease, congenital. + Sufficient + SCDO:0001102 HP:0003302 Displacement of One Backbone Compared to Another Slipped Backbone @@ -9796,17 +9795,17 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - - + + Sudden and involuntary contractions of one or more muscles. - - Sufficient - SCDO:0000778 + + Sufficient + SCDO:0000778 HP:0003394 Muscle Spasm Muscle Cramps @@ -9817,86 +9816,86 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the back. - Provide source for additional info. - - muscle strain, trauma, surgery, fracture, osteoporosis, fibromialgia, spinal disc herniation. - Pain in the lower back. - Sufficient - SCDO:0000095 + Provide source for additional info. + + muscle strain, trauma, surgery, fracture, osteoporosis, fibromialgia, spinal disc herniation. + Pain in the lower back. + Sufficient + SCDO:0000095 HP:0003418 Back Pain @@ -9906,11 +9905,11 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + Abnormal results of investigations using electromyography (EMG). - - Sufficient - SCDO:0000428 + + Sufficient + SCDO:0000428 HP:0003457 Abnormal EMG Abnormal Electromyography (EMG). @@ -9928,17 +9927,17 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - - + + Paralysis of voluntary muscles means loss of contraction due to interruption of one or more motor pathways from the brain to the muscle fibers. Motor paralysis is often accompanied by an impairment in the facility of movement. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0003470 - Most paralysis is due to strokes or injuries such as spinal cord injury or a broken neck. Other causes of paralysis include: Nerve diseases such as amyotrophic lateral sclerosis, Autoimmune diseases such as Guillain-Barre syndrome, Bell's palsy, which affects muscles in the face, Polio used to be a cause of paralysis, but polio no longer occurs in the U.S. - Paralysis can be complete or partial. It can occur on one or both sides of your body. It can also occur in just one area, or it can be widespread. Paralysis of the lower half of your body, including both legs, is called paraplegia. Paralysis of the arms and legs is quadriplegia. - Sufficient - SCDO:0000865 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0003470 + Most paralysis is due to strokes or injuries such as spinal cord injury or a broken neck. Other causes of paralysis include: Nerve diseases such as amyotrophic lateral sclerosis, Autoimmune diseases such as Guillain-Barre syndrome, Bell's palsy, which affects muscles in the face, Polio used to be a cause of paralysis, but polio no longer occurs in the U.S. + Paralysis can be complete or partial. It can occur on one or both sides of your body. It can also occur in just one area, or it can be widespread. Paralysis of the lower half of your body, including both legs, is called paraplegia. Paralysis of the arms and legs is quadriplegia. + Sufficient + SCDO:0000865 HP:0003470 Inability to Move Paralysis @@ -9951,9 +9950,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation Reduced amount in the blood of the lipoprotein:cholesterol complex that transports cholesterol out of the arteries and around the body, for use by various tissues in normal bodily functions. - - Sufficient - SCDO:0000703 + + Sufficient + SCDO:0000703 HP:0003563 Decreased Circulating Low-Density Lipoprotein Levels Decreased LDL @@ -9973,9 +9972,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation Increased concentration of total (conjugated and unconjugated) bilirubin in the blood. - - Sufficient - SCDO:1000681 + + Sufficient + SCDO:1000681 HP:0003573 High Bili Total High Total Bilirubin @@ -9991,27 +9990,27 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - - + + - - + + Anomalous concentrations of fat-soluble substances (molecules composed of carbon and hydrogen and are characteristically insoluble in water) in the blood. - Provide source for additional info. - http://purl.obolibrary.org/obo/MP_0003949 - Sufficient - SCDO:0000404 + Provide source for additional info. + http://purl.obolibrary.org/obo/MP_0003949 + Sufficient + SCDO:0000404 HP:0003611 Abnormal Circulating Lipid Concentration Abnormal Circulating Lipid Level @@ -10025,29 +10024,29 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - + - - + + - - + + The presence of free hemoglobin in the urine. - - Sufficient - SCDO:0000554 + + Sufficient + SCDO:0000554 HP:0003641 Increased Urine Hemoglobin Level If, following hemolysis, haptoglobins (hemoglobin-binding proteins) are saturated, then free hemoglobin appears in the urine. @@ -10061,9 +10060,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation A skin abnormality characterized by redness and irritation, with thick, red skin that displays flaky, silver-white patches (scales). - - Sufficient - SCDO:0000936 + + Sufficient + SCDO:0000936 HP:0003765 Psoriasiform Dermatitis Psoriasis @@ -10074,75 +10073,75 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - - + + - - + + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + A degree of kidney failure severe enough to require dialysis or kidney transplantation for survival characterized by a severe reduction in glomerular filtration rate (less than 15 ml/min/1.73 m2) and other manifestations including increased serum creatinine, greater than 3 months. - Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info. - - Variable - Final outcome of any form of kidney disease ; may be caused by diabetes, hypertension, glomerular disease, polycystic kidney disease, sickle cell disease, chronic toxic injury. - Elevated serum creatinine, uremia, acidosis, hyperkalemia, hyperphosphatemia, secondary hyperpararthyroidism, anemia, hypertension, fluid retention. - Sufficient - SCDO:0000430 + Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info. + + Variable + Final outcome of any form of kidney disease ; may be caused by diabetes, hypertension, glomerular disease, polycystic kidney disease, sickle cell disease, chronic toxic injury. + Elevated serum creatinine, uremia, acidosis, hyperkalemia, hyperphosphatemia, secondary hyperpararthyroidism, anemia, hypertension, fluid retention. + Sufficient + SCDO:0000430 HP:0003774 ESKD ESRD @@ -10162,9 +10161,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation A reticulocyte abnormality. - - Sufficient - SCDO:1000265 + + Sufficient + SCDO:1000265 HP:0004312 Abnormality of Reticulocytes @@ -10176,9 +10175,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation Any deviation from the normal concentration of a nitrogen compound in the blood circulation. - - Sufficient - SCDO:1000647 + + Sufficient + SCDO:1000647 HP:0004364 Abnormal Circulating Nitrogen Compound Concentration @@ -10190,9 +10189,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation An abnormality of alkaline phosphatase level. - - Sufficient - SCDO:1000666 + + Sufficient + SCDO:1000666 HP:0004379 Abnormality Alkaline Phosphatase Level Abnormality of ALP Level @@ -10209,9 +10208,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation The presence of abnormally shaped erythrocytes. - - Sufficient - SCDO:1000245 + + Sufficient + SCDO:1000245 HP:0004447 Poikilocytosis @@ -10224,14 +10223,14 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - - + + Exaggerated concavity of the anterior or posterior surface of the vertebral body, i.e., the upper and lower vertebral endplates are hollowed inward. - - Sufficient - SCDO:0000118 + + Sufficient + SCDO:0000118 HP:0004586 Biconcave Vertebrae Fish Mouth Deformity @@ -10248,16 +10247,16 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - - + + A defect in the ability to concentrate the urine. - http://purl.obolibrary.org/obo/HP_0004727 - Notable within the first decade of life. - Can be caused by tubular damage in the kidney; can be seen in sickle cell disease and sickle cell trait. - Sufficient - SCDO:0000621 + http://purl.obolibrary.org/obo/HP_0004727 + Notable within the first decade of life. + Can be caused by tubular damage in the kidney; can be seen in sickle cell disease and sickle cell trait. + Sufficient + SCDO:0000621 HP:0004727 UCD Urine Concentrating Defect @@ -10270,12 +10269,12 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + A tachycardia originating in the ventricles characterized by rapid heart rate (over 100 beats per minute) and broad QRS complexes (over 120 ms). + + Sufficient + SCDO:0003769 - - Sufficient - SCDO:0003769 HP:0004756 VT Ventricular tachycardia (VT) is a potentially life-threatening ventricular arrhythmia that presents as a wide QRS complex tachycardia, and is defined as three or more consecutive QRS complexes with a duration longer than 120 milliseconds (ms) and a rate of 100 beats per minute or more, whereby the complexes have a ventricular origin. VT can be subdivided as follows: (i) sustained VT persists for 30 seconds or more; (ii) non-sustained VT lasts less than 30 seconds; (iii) monomorphic VT displays a uniform QRS morphology; and (iv) polymorphic VT displays QRS morphologies that variy from beat to beat. VT is observed most commonly in individuals with structural heart disease or acute myocardial infarction (MI). VT may also be observed in in the setting of drug toxicity or electrolyte abnormalities or in individuals with Mendelian disease. @@ -10289,9 +10288,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation An abnormal increase in the binding affinity of hemoglobin for oxygen. - - Sufficient - SCDO:1000248 + + Sufficient + SCDO:1000248 HP:0004825 Increased Haemoglobin Oxygen Affinity Increased Hemoglobin Oxygen Affinity @@ -10303,47 +10302,47 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - - + + - - + + - - + + - - + + - - + + - - + + A chronic form of hemolytic anemia. - http://purl.obolibrary.org/obo/HP_0004870 - Sufficient - SCDO:0001248 + http://purl.obolibrary.org/obo/HP_0004870 + Sufficient + SCDO:0001248 HP:0004870 Chronic Hemolytic Anemia @@ -10356,32 +10355,32 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - - + + - - + + - - + + - - + + Inability of the left ventricle to perform its normal physiologic function. Failure is either due to an inability to contract the left ventricle or the inability to relax completely and fill with blood during diastole. - http://purl.obolibrary.org/obo/HP_0005162 - Sufficient - SCDO:0002710 + http://purl.obolibrary.org/obo/HP_0005162 + Sufficient + SCDO:0002710 HP:0005162 Impaired Left Ventricular Function Left Ventricular Failure @@ -10399,50 +10398,50 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - - + + - - + + - - + + - - + + - - + + - - + + - - + + A pregnancy that ends at a stage in which the fetus is incapable of surviving on its own, defined as the spontaneous loss of a fetus before the 20th week of pregnancy. - - Sufficient - SCDO:0001103 + + Sufficient + SCDO:0001103 HP:0005268 Miscarriage Spontaneous Abortion @@ -10457,45 +10456,45 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - + - - + + - - + + - - + + - - + + Formation of a blood clot (thrombus) inside a cerebral vein, causing the obstruction of blood flow. - Add "Cerebral Venous Sinus Thrombosis" (in the Stroke Ontology) as a sub-class - http://purl.obolibrary.org/obo/HP_0005305 - Sufficient - SCDO:0000211 + Add "Cerebral Venous Sinus Thrombosis" (in the Stroke Ontology) as a sub-class + http://purl.obolibrary.org/obo/HP_0005305 + Sufficient + SCDO:0000211 HP:0005305 Blood Clot in Cerebral Vein Cerebral Thrombosis @@ -10511,14 +10510,14 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + Inflammation of the blood vessels within the brain. - http://purl.obolibrary.org/obo/HP_0005318 - Sufficient - SCDO:0000210 + http://purl.obolibrary.org/obo/HP_0005318 + Sufficient + SCDO:0000210 HP:0005318 Cerebral Vasculitis @@ -10530,9 +10529,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation Larger than normal size of erythrocytes. Macrocytosis refers to a mean cell volume (MCV) greater than 100 fL. If macrocytosis is an isolated abnormality, the amount of hemoglobin in the cell increases proportionately, so the mean cell hemoglobin concentration (MCHC) remains within normal limits. - - Sufficient - SCDO:1000626 + + Sufficient + SCDO:1000626 HP:0005518 Erythrocyte Macrocytosis High MCV @@ -10546,23 +10545,23 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - - + + - - + + Normal hemoglobin synthesis is characterized by production of equal amounts of alpha and beta globins. This term refers to a deviation from this pattern and is the main characteristic of the various forms of thalassemia. - http://purl.obolibrary.org/obo/HP_0005560 - Sufficient - SCDO:0001383 + http://purl.obolibrary.org/obo/HP_0005560 + Sufficient + SCDO:0001383 HP:0005560 Imbalanced Hemoglobin Synthesis @@ -10575,21 +10574,21 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - + A bacterial infection of the endocardium, the inner layer of the heart, which usually involves the heart valves. + Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info. + Sufficient + SCDO:0000099 - Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info. - Sufficient - SCDO:0000099 HP:0006689 Infective Endocarditis Bacterial Endocarditis @@ -10602,9 +10601,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation Attention deficit hyperactivity disorder (ADHD) manifests at age 2-3 years or by first grade at the latest. The main symptoms are distractibility, impulsivity, hyperactivity, and often trouble organizing tasks and projects, difficulty going to sleep, and social problems from being aggressive, loud, or impatient. - http://purl.obolibrary.org/obo/HP_0007018 - Sufficient - SCDO:0000090 + http://purl.obolibrary.org/obo/HP_0007018 + Sufficient + SCDO:0000090 HP:0007018 ADHD Attention Deficit @@ -10621,17 +10620,17 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - - + + Weakness of the muscles of the legs. - - Sufficient - SCDO:0000686 + + Sufficient + SCDO:0000686 HP:0007340 Hind Limb Weakness Hindlimb Weakness @@ -10653,56 +10652,56 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Bleeding within the vitreous compartment of the eye. - - Sufficient - SCDO:0001238 + + Sufficient + SCDO:0001238 HP:0007902 Hemorrage Within the Vitreous Humor Vitreous Haemorrhage @@ -10716,10 +10715,10 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation A type of hypothyroidism that results from a defect in thyroid-stimulating hormone secretion. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0008245 - Sufficient - SCDO:0001028 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0008245 + Sufficient + SCDO:0001028 HP:0008245 TSH Deficient Hypothyroidism Thyroid Stimulating Hormone Deficiency @@ -10735,20 +10734,20 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - + Onychodystrophy (nail dystrophy) refers to nail changes apart from changes of the color (nail dyschromia) and involves partial or complete disruption of the various keratinous layers of the nail plate. - - Sufficient - SCDO:0000788 + + Sufficient + SCDO:0000788 HP:0008404 Dystrophic Nails Onychodystrophy @@ -10761,40 +10760,40 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - - + + - - + + - + - - + + Acute death of renal tubular cells that usually results from prolonged renal ischemia, nephrotoxins, or sepsis. - Provide source for additional info. - - Can occur at any age. - The clinical course of acute tubular necrosis may be divided into initiation, maintenance, and recovery phases. - Renal ischemia (which can occur due to prolonged prerenal states), nephrotoxins, or sepsis. In sickle cell disease, may occur due to renal ischemia related to sickle crisis. - Loss of kidney function, reduced urine output, elevated serum creatinine. - Sufficient - SCDO:0000020 + Provide source for additional info. + + Can occur at any age. + The clinical course of acute tubular necrosis may be divided into initiation, maintenance, and recovery phases. + Renal ischemia (which can occur due to prolonged prerenal states), nephrotoxins, or sepsis. In sickle cell disease, may occur due to renal ischemia related to sickle crisis. + Loss of kidney function, reduced urine output, elevated serum creatinine. + Sufficient + SCDO:0000020 HP:0008682 ATN Renal Tubular Necrosis @@ -10806,29 +10805,29 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - - + + - - + + - + Rhabdomyolysis induced by exercise. - http://purl.obolibrary.org/obo/HP_0009045 - Sufficient - SCDO:0001308 + http://purl.obolibrary.org/obo/HP_0009045 + Sufficient + SCDO:0001308 HP:0009045 Rhabdomyolysis with Exercise Exercise-Induced Rhabdomyolysis @@ -10842,52 +10841,52 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - + - - + + - - + + - - + + - - + + - - + + Peripheral neuropathy is a general term for any disorder of the peripheral nervous system. + http://purl.obolibrary.org/obo/HP_0009830 + Symptoms depend on which nerve is damaged, and whether the damage affects one nerve, several nerves, or the whole body. Pain and numbness: Tingling or burning in the arms and legs may be an early sign of nerve damage. These feelings often start in your toes and feet. You may have deep pain. This often happens in the feet and legs. You may lose feeling in your legs and arms. Because of this, you may not notice when you step on something sharp. You may not notice when you touch something that is too hot or cold, like the water in a bathtub. You may not know when you have a small blister or sore on your feet. Numbness may make it harder to tell where your feet are moving and can cause a loss of balance. Muscle problems: Damage to the nerves can make it harder to control muscles. It can also cause weakness. You may notice problems moving a part of your body. You may fall because your legs buckle. You may trip over your toes. Doing tasks such as buttoning a shirt may be harder. You may also notice that your muscles twitch or cramp. Your muscles may become smaller. Problems with body organs: People with nerve damage may have problems digesting food. You may feel full or bloated and have heartburn after eating only a little food. Sometimes you may vomit food that has not been digested well. You may have either loose stools or hard stools. Some people have problems swallowing. Damage to the nerves to your heart may cause you to feel light-headed, or faint, when you stand up. Angina is the warning chest pain for heart disease and heart attack. Nerve damage may "hide" this warning sign. You should learn other warning signs of a heart attack. They are sudden fatigue, sweating, shortness of breath, nausea, and vomiting. + Sufficient + SCDO:0000884 - http://purl.obolibrary.org/obo/HP_0009830 - Symptoms depend on which nerve is damaged, and whether the damage affects one nerve, several nerves, or the whole body. Pain and numbness: Tingling or burning in the arms and legs may be an early sign of nerve damage. These feelings often start in your toes and feet. You may have deep pain. This often happens in the feet and legs. You may lose feeling in your legs and arms. Because of this, you may not notice when you step on something sharp. You may not notice when you touch something that is too hot or cold, like the water in a bathtub. You may not know when you have a small blister or sore on your feet. Numbness may make it harder to tell where your feet are moving and can cause a loss of balance. Muscle problems: Damage to the nerves can make it harder to control muscles. It can also cause weakness. You may notice problems moving a part of your body. You may fall because your legs buckle. You may trip over your toes. Doing tasks such as buttoning a shirt may be harder. You may also notice that your muscles twitch or cramp. Your muscles may become smaller. Problems with body organs: People with nerve damage may have problems digesting food. You may feel full or bloated and have heartburn after eating only a little food. Sometimes you may vomit food that has not been digested well. You may have either loose stools or hard stools. Some people have problems swallowing. Damage to the nerves to your heart may cause you to feel light-headed, or faint, when you stand up. Angina is the warning chest pain for heart disease and heart attack. Nerve damage may "hide" this warning sign. You should learn other warning signs of a heart attack. They are sudden fatigue, sweating, shortness of breath, nausea, and vomiting. - Sufficient - SCDO:0000884 HP:0009830 Peripheral Nerve Damage Peripheral Neuritis @@ -10902,75 +10901,75 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - + Facial nerve palsy is a dysfunction of cranial nerve VII (the facial nerve) that results in inability to control facial muscles on the affected side with weakness of the muscles of facial expression and eye closure. This can either be present in unilateral or bilateral form. - - Provide source for additional info. - - Sufficient - SCDO:0001315 + - Provide source for additional info. + + Sufficient + SCDO:0001315 HP:0010628 Bell's Palsy Cranial Nerve VII Palsy @@ -10990,9 +10989,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation An abnormal level of a circulating protein in the blood. - - Sufficient - SCDO:1000438 + + Sufficient + SCDO:1000438 HP:0010876 Abnormality of Circulating Protein Level Blood Protein Disease @@ -11006,80 +11005,80 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A disease where there is cellular death (necrosis) of bone components due to interruption of the blood supply. + No one is sure what causes the disease. Risk factors include: -- -- Long-term steroid treatment -- Alcohol abuse -- Joint injuries -- Having certain diseases, including arthritis and cancer -- Doctors use imaging tests and other tests to diagnose osteonecrosis. -- -- Treatments include medicines, using crutches, limiting activities that put weight on the affected joints, electrical stimulation and surgery. + + Sufficient + SCDO:0000841 http://purl.bioontology.org/ontology/MEDLINEPLUS/C0029445 - No one is sure what causes the disease. Risk factors include: -- -- Long-term steroid treatment -- Alcohol abuse -- Joint injuries -- Having certain diseases, including arthritis and cancer -- Doctors use imaging tests and other tests to diagnose osteonecrosis. -- -- Treatments include medicines, using crutches, limiting activities that put weight on the affected joints, electrical stimulation and surgery. - - Sufficient - SCDO:0000841 HP:0010885 AVN Aseptic Bone Necrosis @@ -11104,35 +11103,35 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - - + + - - + + - - + + - - + + An abnormal increase of bone mineral density, that is, of the amount of matter per cubic centimeter of bones which is often refered to as osteosclerosis. Osteosclerosis can be detected on radiological examination as an increased whiteness (density) of affected bones. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0011001 - Ischemia, chronic infection, and tumor formation, osteoarthritis, osteoma, hepatitis C, . May be caused by faulty bone resorption as a result of some abnormality involving osteoclasts. - An increased whiteness (density) of affected bones. - Sufficient - SCDO:0000629 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0011001 + Ischemia, chronic infection, and tumor formation, osteoarthritis, osteoma, hepatitis C, . May be caused by faulty bone resorption as a result of some abnormality involving osteoclasts. + An increased whiteness (density) of affected bones. + Sufficient + SCDO:0000629 HP:0011001 Bone Sclerosis Increased Bone Density @@ -11148,9 +11147,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation The age group in which disease manifestations appear. - http://purl.obolibrary.org/obo/HP_0011007 - Sufficient - SCDO:0003913 + http://purl.obolibrary.org/obo/HP_0011007 + Sufficient + SCDO:0003913 HP:0011007 Age of Onset @@ -11160,11 +11159,11 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + Abnormality of glucose homeostasis. - - Sufficient - SCDO:1000283 + + Sufficient + SCDO:1000283 HP:0011014 Abnormal Glucose Homeostasis @@ -11176,9 +11175,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation Abnormal functionality of the cardiovascular system. - - Sufficient - SCDO:1000368 + + Sufficient + SCDO:1000368 HP:0011025 Abnormal Cardiovascular System Physiology @@ -11190,9 +11189,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation A decrease in the amount of intravascular fluid, particularly in the volume of the circulating blood. - - Sufficient - SCDO:0003035 + + Sufficient + SCDO:0003035 HP:0011106 Depleted Blood Volume Hypovolemia @@ -11205,9 +11204,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation Any morphological abnormality of the skin. - - Sufficient - SCDO:1000374 + + Sufficient + SCDO:1000374 HP:0011121 Abnormality of Skin Morphology @@ -11219,9 +11218,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation Any abnormality of the physiological function of the skin. - - Sufficient - SCDO:1000375 + + Sufficient + SCDO:1000375 HP:0011122 Abnormality of Skin Physiology @@ -11233,9 +11232,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation The presence of inflammation of the skin. That is, an abnormality of the skin resulting from the local accumulation of fluid, plasma proteins, and leukocytes. - - Sufficient - SCDO:0001071 + + Sufficient + SCDO:0001071 HP:0011123 Abnormal Tendency to Infections of the Skin Dermatitis @@ -11253,20 +11252,20 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - - + + - - + + Delivery of a fetus through surgical incisions made through the abdominal wall (laparotomy) and the uterine wall (hysterotomy). - http://purl.obolibrary.org/obo/HP_0011410 - Sufficient - SCDO:0000168 + http://purl.obolibrary.org/obo/HP_0011410 + Sufficient + SCDO:0000168 HP:0011410 Caesarian Section @@ -11278,9 +11277,9 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation Shoulder dystocia occurs when the fetal anterior shoulder impacts against the maternal symphysis following delivery of the vertex. - - Sufficient - SCDO:0001045 + + Sufficient + SCDO:0001045 HP:0011413 Shoulder Dystocia @@ -11293,32 +11292,32 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - - + + - - + + - - + + - - + + Any cardiac rhythm other than the normal sinus rhythm. Such a rhythm may be either of sinus or ectopic origin and either regular or irregular. An arrhythmia may be due to a disturbance in impulse formation or conduction or both. - http://purl.obolibrary.org/obo/HP_0011675 - Sufficient - SCDO:0009619 + http://purl.obolibrary.org/obo/HP_0011675 + Sufficient + SCDO:0009619 HP:0011675 Abnormal Heart Rate Abnormality of Cardiac Conduction @@ -11341,10 +11340,10 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation Hemorrhage into the parenchyma of the cerebellum. - Need to include this term mentioned here to the SCDO: -- obstructive hydrocephalus - - Sufficient - SCDO:0000201 + Need to include this term mentioned here to the SCDO: -- obstructive hydrocephalus + + Sufficient + SCDO:0000201 HP:0011695 Cerebellar Hemorrhage @@ -11355,23 +11354,23 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - + - - + + - - + + An appetite for and the persistent ingestion of non-food substances such as clay. In order to diagnose pica, this behavior must have persisted over a period of at least one month. - http://purl.obolibrary.org/obo/HP_0011856 - Sufficient - SCDO:0000904 + http://purl.obolibrary.org/obo/HP_0011856 + Sufficient + SCDO:0000904 HP:0011856 Pica @@ -11384,36 +11383,36 @@ Is caused by: Genetic predispositions, autoimmune mediated, chronic inflammation - - + + - - + + - - + + - - + + Pain in the lower back and hip radiating in the distribution of the sciatic nerve. - Provide source for additional info. + Provide source for additional info. -Terms to add to therapeutics for linking via "is treated with" obj property: Local heat, acupuncture, physical therapy, surgery - http://purl.obolibrary.org/obo/HP_0011868 - Compression of a spinal nerve root by disc or arthritic spur, degenerative changes involvind main structures, disc protrusion, congenital abnormalities of the bony spinal column, infection, inflammation, neoplasm, vascular diseases. - Sufficient - SCDO:0001024 +Terms to add to therapeutics for linking via "is treated with" obj property: Local heat, acupuncture, physical therapy, surgery + http://purl.obolibrary.org/obo/HP_0011868 + Compression of a spinal nerve root by disc or arthritic spur, degenerative changes involvind main structures, disc protrusion, congenital abnormalities of the bony spinal column, infection, inflammation, neoplasm, vascular diseases. + Sufficient + SCDO:0001024 HP:0011868 Sciatica @@ -11425,9 +11424,9 @@ Terms to add to therapeutics for linking via "is treated with" obj pro Abnormal number of platelets per volume of blood. In a healthy adult, a normal platelet count is between 150,000 and 450,000 per microliter of blood. - - Sufficient - SCDO:1000617 + + Sufficient + SCDO:1000617 HP:0011873 Abnormal Platelet Count @@ -11442,44 +11441,44 @@ Terms to add to therapeutics for linking via "is treated with" obj pro - + - - + + - - + + - - + + - - + + - - + + Bleeding in the anterior chamber of the eye. - http://purl.obolibrary.org/obo/HP_0011886 - Sufficient - SCDO:0000597 + http://purl.obolibrary.org/obo/HP_0011886 + Sufficient + SCDO:0000597 HP:0011886 Hyphema @@ -11489,11 +11488,11 @@ Terms to add to therapeutics for linking via "is treated with" obj pro - + Number of leukocytes per volume of blood beyond normal limits. - - Sufficient - SCDO:1000613 + + Sufficient + SCDO:1000613 HP:0011893 Abnormal White Blood Cell Count Abnormal Leukocyte Count @@ -11506,9 +11505,9 @@ Terms to add to therapeutics for linking via "is treated with" obj pro Increased number of neutrophils circulating in blood. - - Sufficient - SCDO:1000447 + + Sufficient + SCDO:1000447 HP:0011897 Neutrophilia @@ -11519,23 +11518,23 @@ Terms to add to therapeutics for linking via "is treated with" obj pro - + - - + + - - + + Hemoglobin F (HbF) contains two globin alpha chains and two globin gamma chains. It is the main form of hemoglobin in the fetus during the last seven months of intrauterine development and in the half year of postnatal life. In adults it normally makes up less than one percent of all hemoglobiin. This term refers to an increase in HbF above this limit. In beta thalassemia major, it may represent over 90 percent of all hemoglobin, and in beta thalassemia minor it may make up between 0.5 to 4 percent. - http://purl.obolibrary.org/obo/HP_0011904 - Sufficient - SCDO:0000888 + http://purl.obolibrary.org/obo/HP_0011904 + Sufficient + SCDO:0000888 HP:0011904 Increased Haemoglobin F Persistence of Hemoglobin F @@ -11551,14 +11550,14 @@ Terms to add to therapeutics for linking via "is treated with" obj pro - - + + A reduction in the ratio of production of beta globin to that of alpha globin. This is the major abnormality in the various forms of beta thalassemia. - http://purl.obolibrary.org/obo/HP_0011906 - Sufficient - SCDO:0001709 + http://purl.obolibrary.org/obo/HP_0011906 + Sufficient + SCDO:0001709 HP:0011906 Increased Alpha/Beta Synthesis Ratio Reduced Beta/Alpha Synthesis Ratio @@ -11572,14 +11571,14 @@ Terms to add to therapeutics for linking via "is treated with" obj pro - - + + A reduction in the ratio of production of alpha globin to that of beta globin. This is the major abnormality in the various forms of alpha thalassemia. - http://purl.obolibrary.org/obo/HP_0011907 - Sufficient - SCDO:0006404 + http://purl.obolibrary.org/obo/HP_0011907 + Sufficient + SCDO:0006404 HP:0011907 Increased Beta/Alpha Synthesis Ratio Reduced Alpha/Beta Synthesis Ratio @@ -11593,14 +11592,14 @@ Terms to add to therapeutics for linking via "is treated with" obj pro - - + + Inflammation of the bronchioles. - http://purl.obolibrary.org/obo/HP_0011950 - Sufficient - SCDO:0005490 + http://purl.obolibrary.org/obo/HP_0011950 + Sufficient + SCDO:0005490 HP:0011950 Bronchiolitis @@ -11613,9 +11612,9 @@ Terms to add to therapeutics for linking via "is treated with" obj pro A deviation from the normal range of neutrophil cell counts in the circulation. - - Sufficient - SCDO:1000446 + + Sufficient + SCDO:1000446 HP:0011991 Abnormal Neutrophil Cell Number Abnormal Neutrophil Count @@ -11628,9 +11627,9 @@ Terms to add to therapeutics for linking via "is treated with" obj pro An abnormal concentration of creatinine in the blood. - - Sufficient - SCDO:1000541 + + Sufficient + SCDO:1000541 HP:0012100 Abnormal Blood Creatinine Level Abnormal Serum Creatinine Level @@ -11645,9 +11644,9 @@ Terms to add to therapeutics for linking via "is treated with" obj pro An abnormally reduced amount of creatinine in the blood. - - Sufficient - SCDO:1000648 + + Sufficient + SCDO:1000648 HP:0012101 Low Blood Creatinine Low Serum Creatinine @@ -11663,21 +11662,21 @@ Terms to add to therapeutics for linking via "is treated with" obj pro - + - - + + A fungal infection of the toenails or fingernails that tends to cause the nails to thicken, discolor, disfigure, and split. + + Sufficient + SCDO:0000831 Medscape: Onychomycosis: Author: Antonella Tosti, MD; Chief Editor: Dirk M Elston, MD et al.. - - Sufficient - SCDO:0000831 HP:0012203 has disease stage: Distal lateral subungual onychomycosis (DLSO), White superficial onychomycosis (WSO), Proximal subungual onychomycosis (PSO), Endonyx onychomycosis (EO), Candidal onychomycosis. @@ -11692,9 +11691,9 @@ Is characterised by: Disfigured nails, pain, paraesthesia, loss of dexterity, di An increased white blood cell count in the cerebrospinal fluid. - http://purl.obolibrary.org/obo/HP_0012229 - Sufficient - SCDO:0000212 + http://purl.obolibrary.org/obo/HP_0012229 + Sufficient + SCDO:0000212 HP:0012229 CSF Pleocytosis Increased Leukocyte Count in CSF @@ -11708,9 +11707,9 @@ Is characterised by: Disfigured nails, pain, paraesthesia, loss of dexterity, di A structural or developmental anomaly of any of the tissues involved in the genital system. - - Sufficient - SCDO:0009817 + + Sufficient + SCDO:0009817 HP:0012243 Abnormal Genital System Morphology Abnormal Reproductive System Morphology @@ -11724,14 +11723,14 @@ Is characterised by: Disfigured nails, pain, paraesthesia, loss of dexterity, di - - + + An exanthema consisting of widespread pink-to-red macules (flat spots of 2-10 mm in diameter) or papules (red bumps) that blanch with pressure. The macules and papules may cluster and merge to form sheets over several days. - - Sufficient - SCDO:0000770 + + Sufficient + SCDO:0000770 HP:0012282 A morbilliform rash is said to resemble the rash of measles, rubella or scarlet fever, thus mimicking viral and bacterial exanthemas. Morbilliform Rash @@ -11745,20 +11744,20 @@ Is characterised by: Disfigured nails, pain, paraesthesia, loss of dexterity, di - - + + - - + + An inflammation of the kidney involving the parenchyma of kidney, the renal pelvis and the kidney calices. - http://purl.obolibrary.org/obo/HP_0012330 - Sufficient - SCDO:0005758 + http://purl.obolibrary.org/obo/HP_0012330 + Sufficient + SCDO:0005758 HP:0012330 Pyelonephritis @@ -11768,11 +11767,11 @@ Is characterised by: Disfigured nails, pain, paraesthesia, loss of dexterity, di - + An altered ability of any enzyme or their cofactors to act as catalysts. This term includes changes due to altered levels of an enzyme. - - Sufficient - SCDO:1000665 + + Sufficient + SCDO:1000665 HP:0012379 Abnormal Enzyme/Coenzyme Activity @@ -11785,38 +11784,38 @@ Is characterised by: Disfigured nails, pain, paraesthesia, loss of dexterity, di - - + + - - + + - - + + - - + + - - + + An abnormally low level of blood oxygen. - http://purl.obolibrary.org/obo/HP_0012418 - Sufficient - SCDO:0000604 + http://purl.obolibrary.org/obo/HP_0012418 + Sufficient + SCDO:0000604 HP:0012418 Decreased Partial Pressure of Oxygen Low Blood Oxygen Level @@ -11830,9 +11829,9 @@ Is characterised by: Disfigured nails, pain, paraesthesia, loss of dexterity, di Partial or complete wasting (loss) of brain tissue that was once present. - - Sufficient - SCDO:0000089 + + Sufficient + SCDO:0000089 HP:0012444 Brain Atrophy Brain Degeneration @@ -11848,9 +11847,9 @@ Is characterised by: Disfigured nails, pain, paraesthesia, loss of dexterity, di An increased level of iron in liver tissues. - http://purl.obolibrary.org/obo/HP_0012465 - Sufficient - SCDO:0000425 + http://purl.obolibrary.org/obo/HP_0012465 + Sufficient + SCDO:0000425 HP:0012465 Increased Iron Concentration in Liver Increased Liver Iron Level @@ -11864,60 +11863,60 @@ Equivalents - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Persistent pain, usually defined as pain that has lasted longer than 3 to 6 months. - - Sufficient - SCDO:0001415 + + Sufficient + SCDO:0001415 HP:0012532 Long-Lasting Pain Chronic Pain @@ -11930,9 +11929,9 @@ Equivalents Increased numbers of mesangial cells per glomerulus, defined as four or more nuclei in a peripheral mesangial segment. - - Sufficient - SCDO:0006481 + + Sufficient + SCDO:0006481 HP:0012574 Mesangial Proliferation Mesangial Hypercellularity @@ -11943,23 +11942,23 @@ Equivalents - + - - + + - - + + Hematuria that is visible upon inspection of the urine. - http://purl.obolibrary.org/obo/HP_0012587 - Sufficient - SCDO:0008145 + http://purl.obolibrary.org/obo/HP_0012587 + Sufficient + SCDO:0008145 HP:0012587 Bloody Urine Gross Hematuria @@ -11971,32 +11970,32 @@ Equivalents - + - - + + - - + + - - + + The presence of mildly increased concentrations of albumin in the urine (in adults, 30-150 mg per day). + + + http://patient.info/doctor/microalbuminuria + Sufficient + SCDO:0000764 Chronic kidney disease: early identification and management of chronic kidney disease in adults in primary and secondary care; NICE Clinical Guidelines (July 2014) - - - http://patient.info/doctor/microalbuminuria - Sufficient - SCDO:0000764 HP:0012594 Micro-albuminuria Microalbuminuria @@ -12013,9 +12012,9 @@ Equivalents A functional anomaly of the nervous system. - - Sufficient - SCDO:1000765 + + Sufficient + SCDO:1000765 HP:0012638 Abnormality of Nervous System Physiology Abnormal Nervous System Physiology @@ -12028,9 +12027,9 @@ Equivalents A structural anomaly of the nervous system. - - Sufficient - SCDO:1000764 + + Sufficient + SCDO:1000764 HP:0012639 Abnormal Shape of Nervous System Abnormality of Nervous System Morphology @@ -12044,9 +12043,9 @@ Equivalents A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation. - - Sufficient - SCDO:0004069 + + Sufficient + SCDO:0004069 HP:0012735 Cough @@ -12058,9 +12057,9 @@ Equivalents A deviation from normal of the neurological development of a child, which may include any or all of the aspects of the development of personal, social, gross or fine motor, and cognitive abilities. This term should be used to describe abnormalities with onset in the developmental period. - http://purl.obolibrary.org/obo/HP_0012759 - Sufficient - SCDO:0000800 + http://purl.obolibrary.org/obo/HP_0012759 + Sufficient + SCDO:0000800 HP:0012759 Neurodevelopmental Abnormality @@ -12072,10 +12071,10 @@ Equivalents Inflammation of the myocardium. + + Sufficient + SCDO:0004203 - - Sufficient - SCDO:0004203 HP:0012819 Myocarditis can be caused by a variety of bacterial and viral infections. Enteroviruses, especially coxsackievirus B, are often associated with acute myocarditis. However, with the advent of genetic analysis, adenovirus and parvovirus B19 have also been found to be frequent causes of myocarditis. Exposure to drug treatment, physical stimuli such as radiation and heat, metabolic disorders, immune disorders, and pregnancy are also causes of myocarditis. Many cases of myocarditis are idiopathic. Myocarditis presents with non-specific symptoms including chest pain, dyspnoea, and palpitations, and thus often mimics more common disorders such as coronary artery disease. In some patients, cardiac MRI and endomyocardial biopsy can help identify myocarditis, predict risk of cardiovascular events, and guide treatment. Myocarditis @@ -12088,9 +12087,9 @@ Equivalents Any functional abnormality of erythrocytes (red-blood cells). - - Sufficient - SCDO:1000286 + + Sufficient + SCDO:1000286 HP:0020054 Abnormal Erythrocyte Physiology @@ -12102,9 +12101,9 @@ Equivalents Any deviation from the normal number of red blood cells per volume in the circulation. - - Sufficient - SCDO:1000608 + + Sufficient + SCDO:1000608 HP:0020058 Abnormal RBC Count Abnormal Red Blood Cell Count @@ -12117,9 +12116,9 @@ Equivalents An abnormal elevation above the normal number of red blood cells per volume in the circulation. - - Sufficient - SCDO:1000610 + + Sufficient + SCDO:1000610 HP:0020059 Increased RBC Count Increased Red Blood Cell Count @@ -12132,9 +12131,9 @@ Equivalents An abnormal reduction below the normal number of red blood cells per volume in the circulation. - - Sufficient - SCDO:1000609 + + Sufficient + SCDO:1000609 HP:0020060 Decreased RBC Count Decreased Red Blood Cell Count @@ -12146,15 +12145,15 @@ Equivalents - + Any deviation from the normal concentration of hemoglobin in the blood. - SCDO (Jade Hotchkiss) - It might seem wrong to place this class here, but note that a change in hemoglobin concentration affects the size/volume and hence morphology of erythrocytes. + It might seem wrong to place this class here, but note that a change in hemoglobin concentration affects the size/volume and hence morphology of erythrocytes. -Perhaps add sub-classes "Increased hemoglobin concentration" and "Decreased hemoglobin concentration" from HPO...their descriptions don't seem quite right though (should it not rather be "in the erythrocytes", not "in the circulation"? - - Sufficient - SCDO:1000186 +Perhaps add sub-classes "Increased hemoglobin concentration" and "Decreased hemoglobin concentration" from HPO...their descriptions don't seem quite right though (should it not rather be "in the erythrocytes", not "in the circulation"? + + Sufficient + SCDO:1000186 + SCDO (Jade Hotchkiss) HP:0020061 Abnormal Hemoglobin Concentration @@ -12166,9 +12165,9 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " An abnormal reduction below normal hemoglobin concentration in the circulation. - - Sufficient - SCDO:1000377 + + Sufficient + SCDO:1000377 HP:0020062 Decreased Hemoglobin Concentration @@ -12180,9 +12179,9 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " An abnormal elevation above normal hemoglobin concentration in the circulation. - - Sufficient - SCDO:1000378 + + Sufficient + SCDO:1000378 HP:0020063 Increased Hemoglobin Concentration @@ -12194,10 +12193,10 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " Any anomaly of the digestive system, a collection of organs that is made up of the gastrointestinal tract and the liver, pancreas, and gallbladder. The gastrointestinal tract is a series of hollow organs joined in a long, twisting tube from the mouth to the anus, including the mouth, esophagus, stomach, small intestine, large intestine and anus. - Kaeda JS, Roper D, Srivastava P, et al. Severe hemolytic anemia associated with the homozygous state for an unstable hemoglobin variant (Hb Bushwick). Blood 1995; 86:1977. - http://purl.obolibrary.org/obo/HP_0025031 - Sufficient - SCDO:0000335 + Kaeda JS, Roper D, Srivastava P, et al. Severe hemolytic anemia associated with the homozygous state for an unstable hemoglobin variant (Hb Bushwick). Blood 1995; 86:1977. + http://purl.obolibrary.org/obo/HP_0025031 + Sufficient + SCDO:0000335 HP:0025031 Abnormality of the Digestive System @@ -12209,9 +12208,9 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " A deviation from normal of the mean corpuscular volume, or mean cell volume (MCV) of red blood cells, usually taken to be 80 to 100 femtoliters. - - Sufficient - SCDO:1000624 + + Sufficient + SCDO:1000624 HP:0025065 Abnormal Erythrocyte Volume Abnormal MCV @@ -12225,9 +12224,9 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " A reduction from normal of the mean corpuscular volume, or mean cell volume (MCV) of red blood cells (usually defined as an MCV below 80 femtoliters). - - Sufficient - SCDO:1000625 + + Sufficient + SCDO:1000625 HP:0025066 Decreased MCV Low MCV @@ -12243,9 +12242,9 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " A symptom or manifestation indicating a systemic or general effect of a disease and that may affect the general well-being or status of an individual. - - Sufficient - SCDO:1000269 + + Sufficient + SCDO:1000269 HP:0025142 Systemic Symptom Constitutional Symptom @@ -12258,9 +12257,9 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " An elevated level of the enzyme lactate dehydrogenase in serum. - - Sufficient - SCDO:1000652 + + Sufficient + SCDO:1000652 HP:0025435 High Lactate Dehydrogenase Level Increased Lactate Dehydrogenase Level @@ -12273,9 +12272,9 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " Deviation from the normal Hgb/Hct; the average hemoglobin concentration in a given volume of packed red cells, calculated from the hemoglobin therein and the hematocrit, in erythrocyte indices. - - Sufficient - SCDO:1000631 + + Sufficient + SCDO:1000631 HP:0025546 Abnormal MCHC Abnormal Mean Cell Haemoglobin Concentration @@ -12293,9 +12292,9 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " Less than the normal Hgb/Hct; the average hemoglobin concentration in a given volume of packed red cells, calculated from the hemoglobin therein and the hematocrit, in erythrocyte indices. - - Sufficient - SCDO:1000635 + + Sufficient + SCDO:1000635 HP:0025547 Decreased MCHC Decreased Mean Corpuscular Haemoglobin Concentration @@ -12314,9 +12313,9 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " Greater than the normal Hgb/Hct; the average hemoglobin concentration in a given volume of packed red cells, calculated from the hemoglobin therein and the hematocrit, in erythrocyte indices. - - Sufficient - SCDO:1000636 + + Sufficient + SCDO:1000636 HP:0025548 High MCHC High Mean Corpuscular Haemoglobin Concentration @@ -12334,10 +12333,10 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " Inflammation of the inner lining of the uterus Local accumulation of fluid, plasma proteins, and leukocytes in the endometrium. - Provide source for additional info. - http://purl.obolibrary.org/obo/MP_0009360 - Sufficient - SCDO:0000433 + Provide source for additional info. + http://purl.obolibrary.org/obo/MP_0009360 + Sufficient + SCDO:0000433 HP:0025636 Endometrial Inflammation Endometrium Inflammation @@ -12353,62 +12352,62 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " - + - + - - + + - - + + - - + + - - + + - + - + - - + + A collection of pus, immune cells, and other material in the brain. - http://purl.obolibrary.org/obo/HP_0030049 - Sufficient - SCDO:0000159 + http://purl.obolibrary.org/obo/HP_0030049 + Sufficient + SCDO:0000159 HP:0030049 Brain abscess usually results from a bacterial or fungal infection. Brain Abscess @@ -12422,20 +12421,20 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " - + - - + + An abnormal phenomenon characterized by a classic tetrad of excessive daytime sleepiness with irresistible sleep attacks, cataplexy (sudden bilateral loss of muscle tone), hypnagogic hallucination, and sleep paralysis. - - Sufficient - SCDO:0000790 + + Sufficient + SCDO:0000790 HP:0030050 Narcolepsy @@ -12447,9 +12446,9 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " An irreversible distortion of the morphology of an erythrocyte such that the cells are elongated and curved, resembling the blade of a sickle (the hand-held agricultural tool traditionally used to harvest grains). - - Sufficient - SCDO:1000246 + + Sufficient + SCDO:1000246 HP:0030058 Banana Cell Drepanocyte @@ -12467,27 +12466,27 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " - + - - + + - - + + The growth of endometrial tissue outside the uterus. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0030127 - Sufficient - SCDO:0000432 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0030127 + Sufficient + SCDO:0000432 HP:0030127 Endometriosis @@ -12500,14 +12499,14 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " - - + + An obstruction in the veins of the liver caused by a blood clot (thrombosis). - http://purl.obolibrary.org/obo/HP_0030243 - Sufficient - SCDO:0001673 + http://purl.obolibrary.org/obo/HP_0030243 + Sufficient + SCDO:0001673 HP:0030243 Blood Clot in Liver Vein Hepatic Vein Thrombosis @@ -12516,7 +12515,7 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " Blood Clot in Liver Vein - + @@ -12526,9 +12525,9 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " A clot that obstructs blood flow in a mesenteric vein (the superior and the inferior mesenteric vein drain blood from the small and large intestine). - - Sufficient - SCDO:0004437 + + Sufficient + SCDO:0004437 HP:0030248 Blood Clot in Mesenteric Vein Mesenteric Venous Thrombosis @@ -12541,9 +12540,9 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " Any structural anomaly of the heart and great vessels. - - Sufficient - SCDO:1000369 + + Sufficient + SCDO:1000369 HP:0030680 Abnormal Cardiovascular System Morphology @@ -12553,11 +12552,11 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " - + A hole (perforation) in the wall of the intestine. - - Sufficient - SCDO:1000434 + + Sufficient + SCDO:1000434 HP:0031368 Intestinal Perforation @@ -12568,11 +12567,11 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " - + A pregnancy in which the fertilized egg inserts in a location outside of the main cavity of the uterus (usually in the Fallopian tube). - - Sufficient - SCDO:0000413 + + Sufficient + SCDO:0000413 HP:0031456 Ectopic Pregnancy @@ -12584,9 +12583,9 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " An abnormally high concentration in the circulation of aspartate aminotransferase (AST). - - Sufficient - SCDO:1000661 + + Sufficient + SCDO:1000661 HP:0031956 Aspartate Aminotransferase Increased Elevated Serum AST @@ -12602,9 +12601,9 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " An abnormally high concentration in the circulation of alanine aminotransferase (ALT), which is an enzyme that catalyzes the transfer of amino groups to form the hepatic metabolite oxaloacetate. ALT is found abundantly in the cytosol of the hepatocyte. ALT activity in the liver is about 3000 times that of serum activity. Thus, in the case of hepatocellular injury or death, release of ALT from damaged liver cells increases measured ALT activity in the serum. Although it is generally thought to be specific to the liver, it is also found in the kidney, and, in much smaller quantities, in heart and skeletal muscle cells. - - Sufficient - SCDO:1000659 + + Sufficient + SCDO:1000659 HP:0031964 Alanine Aminotransferase Increased Elevated Serum Glutamic-Pyruvic Transaminase @@ -12619,9 +12618,9 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " An abnormal level of an analyte measured in the blood. - - Sufficient - SCDO:1000437 + + Sufficient + SCDO:1000437 HP:0032180 Abnormal Circulating Metabolite Concentration @@ -12631,11 +12630,11 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " - + The ABO histo-blood group consists of two antigens (A and B antigens) and four blood types (types A, B, AB, and O). The A and B antigens are the product of the ABO gene and are autosomal codominant. The group O phenotype is an autosomal-recessive phenotype due to the homozygous inheritance of two null ABO alleles. Group O individuals express the H antigen, the biosynthetic precursor to A and B antigens. ABO, therefore, is the blood type, whereas A, B, and H refer to the antigens. The ABO system consists of A and B antigens and antibodies against these antigens. - - Sufficient - SCDO:1000581 + + Sufficient + SCDO:1000581 HP:0032224 ABO Blood Group @@ -12647,9 +12646,9 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " A deviation from the normal serum concentration/activity of lactate dehydrogenase (LDH), which catalyzes the reduction of pyruvate to form lactate. - - Sufficient - SCDO:1000683 + + Sufficient + SCDO:1000683 HP:0045040 Abnormal Lactate Dehydrogenase Level @@ -12660,11 +12659,11 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " - + An elevated concentration in the blood of hemoglobin A2 (HbA2), which is a normal variant of hemoglobin A that consists of two alpha and two delta chains and is normally present at low levels in adults but may be increased in beta thalassemia. - http://purl.obolibrary.org/obo/HP_0045048 - Sufficient - SCDO:0000630 + http://purl.obolibrary.org/obo/HP_0045048 + Sufficient + SCDO:0000630 HP:0045048 Increased HbA2 Hemoglobin Increased Hemoglobin A2 @@ -12676,35 +12675,35 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " - + - - + + - + - - + + - - + + An acute and life-threatening complication of pregnancy, which is characterized by the appearance of tonic-clonic seizures, usually in a patient who had developed pre-eclampsia. Eclampsia includes seizures and coma that happen during pregnancy but are not due to preexisting or organic brain disorders. - - Sufficient - SCDO:0000411 + + Sufficient + SCDO:0000411 HP:0100601 Eclampsia @@ -12715,24 +12714,24 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " - - + + - - + + - - + + Pregnancy-induced hypertension in association with significant amounts of protein in the urine. - http://purl.obolibrary.org/obo/HP_0100602 - Sufficient - SCDO:0000918 + http://purl.obolibrary.org/obo/HP_0100602 + Sufficient + SCDO:0000918 HP:0100602 Pre-Eclampsia Preeclampsia @@ -12744,18 +12743,18 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " - + - - + + A general term for inflammation of the muscles without respect to the underlying cause. - Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0100614 - Sufficient - SCDO:0000785 + Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0100614 + Sufficient + SCDO:0000785 HP:0100614 Muscle Inflammation Myositis @@ -12766,11 +12765,11 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " - + An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the chest. - - Sufficient - SCDO:0001988 + + Sufficient + SCDO:0001988 HP:0100749 Thoracic Pain Chest Pain @@ -12784,32 +12783,32 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " - - + + - - + + - - + + - - + + Excessive growth or abnormal thickening of bone tissue. - http://purl.obolibrary.org/obo/HP_0100774 - Sufficient - SCDO:0000591 + http://purl.obolibrary.org/obo/HP_0100774 + Sufficient + SCDO:0000591 HP:0100774 Bone Hypertrophy Bone Overgrowth @@ -12825,83 +12824,83 @@ Perhaps add sub-classes "Increased hemoglobin concentration" and " - - + + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Severe systemic inflammatory response to infection. - Perhaps remove here and only keep below "Abnormality of the Immune System"? + Perhaps remove here and only keep below "Abnormality of the Immune System"? Source needed for additional information. -Perhaps include different types of sepsis (see under D018805 in MESH)? - http://purl.obolibrary.org/obo/HP_0100806 - Sufficient - SCDO:0001039 +Perhaps include different types of sepsis (see under D018805 in MESH)? + http://purl.obolibrary.org/obo/HP_0100806 + Sufficient + SCDO:0001039 HP:0100806 caused by: Bacteria and fungus mainly @@ -12919,26 +12918,26 @@ has disease stage: Mild, moderate, severe - - + + - - + + - - + + Inflammatory or noninflammatory diseases affecting the glomeruli of the nephron. - http://purl.obolibrary.org/obo/HP_0100820 - Sufficient - SCDO:0000459 + http://purl.obolibrary.org/obo/HP_0100820 + Sufficient + SCDO:0000459 HP:0100820 Diseased Glomeruli Glomerulopathies @@ -12951,36 +12950,36 @@ has disease stage: Mild, moderate, severe - + - - + + - - + + - - + + - - + + A discontinuity of the skin exhibiting loss of the epidermis and often portions of the dermis and subcutaneous fat. - Find source for additional info - http://purl.obolibrary.org/obo/HP_0200042 - Sufficient - SCDO:0001074 + Find source for additional info + http://purl.obolibrary.org/obo/HP_0200042 + Sufficient + SCDO:0001074 HP:0200042 Open Skin Sore Skin Ulcers @@ -12994,9 +12993,9 @@ has disease stage: Mild, moderate, severe Abnormal test result of cardiovascular physiology. - - Sufficient - SCDO:1000266 + + Sufficient + SCDO:1000266 HP:0500015 Abnormal Cardiac Test @@ -13006,11 +13005,11 @@ has disease stage: Mild, moderate, severe - + A date specification that designates when an informed consent form was signed. - - Sufficient - SCDO:1000531 + + Sufficient + SCDO:1000531 ICO:0000036 Date Subject Signed Consent Informed Consent Form Signing Date @@ -13022,12 +13021,12 @@ has disease stage: Mild, moderate, severe - - + + An informed consent by the parent/guardian of a child or a minor to consent to give permission for the child/minor to be included in research. - - Sufficient - SCDO:0009293 + + Sufficient + SCDO:0009293 ICO:0000157 Parental Informed Consent Process Parental Permission @@ -13040,11 +13039,11 @@ has disease stage: Mild, moderate, severe - + An informed consent for an unspecified range of future research subject to a few content and/or process restrictions. - - Sufficient - SCDO:0008115 + + Sufficient + SCDO:0008115 ICO:0000179 Broad Consent @@ -13054,11 +13053,11 @@ has disease stage: Mild, moderate, severe - + A planned process in which data possessed by one person or organization is shared with one or more other persons or organizations. - - Sufficient - SCDO:0009586 + + Sufficient + SCDO:0009586 ICO:0000228 Act of Data Sharing Data Sharing @@ -13069,11 +13068,11 @@ has disease stage: Mild, moderate, severe - + A directive information entity that prescribes some process for withdraw from another planned process. - - Sufficient - SCDO:1000428 + + Sufficient + SCDO:1000428 ICO:0000255 Withdrawal from Participation Directive Participant Withdrawal Process @@ -13086,9 +13085,9 @@ has disease stage: Mild, moderate, severe A descriptive information content entity that describes how biospecimens will be used. - - Sufficient - SCDO:1000456 + + Sufficient + SCDO:1000456 ICO:0000278 Description of Future Biospecimen Use @@ -13098,11 +13097,11 @@ has disease stage: Mild, moderate, severe - + A directive information entity that prescribes the information that is permitted to be shared or the processes for sharing that information. - - Sufficient - SCDO:1000407 + + Sufficient + SCDO:1000407 ICO:0000293 Data Sharing Directive Data Sharing Agreement @@ -13115,9 +13114,9 @@ has disease stage: Mild, moderate, severe A descriptive information content entity that describes how data will be used. - - Sufficient - SCDO:1000453 + + Sufficient + SCDO:1000453 ICO:0000304 Description of Future Data Use @@ -13127,11 +13126,11 @@ has disease stage: Mild, moderate, severe - + A descriptive information content entity that describes future use of material or information. - - Sufficient - SCDO:1000454 + + Sufficient + SCDO:1000454 ICO:0000305 Description of Future Use @@ -13141,11 +13140,11 @@ has disease stage: Mild, moderate, severe - + The use of antimalarial drugs for the prevention of infection. - - Sufficient - SCDO:1000668 + + Sufficient + SCDO:1000668 IDOMAL:0000122 Malaria Chemoprophylaxis @@ -13155,12 +13154,12 @@ has disease stage: Mild, moderate, severe - + Any process carried out to determine the condition of a patient's spleen. - Needs relating to Splenomegaly phenotype. - http://purl.obolibrary.org/obo/IDOMAL_0000592 - Sufficient - SCDO:0001101 + Needs relating to Splenomegaly phenotype. + http://purl.obolibrary.org/obo/IDOMAL_0000592 + Sufficient + SCDO:0001101 IDOMAL:0000592 Spleen Examination @@ -13170,18 +13169,18 @@ has disease stage: Mild, moderate, severe - + - + A permanent change in the DNA sequence of a gene that alters the genetic message carried by that gene. - Perhaps include here an "Alpha Thalassemia Mutation" sub-class? Could use the current description for "Alpha-Globin Locus Deletion" and instead give "Alpha-Globin Locus Deletion" a description similar to that of "Beta-Globin Locus Deletion" - http://purl.obolibrary.org/obo/IDOMAL_50000026 - Sufficient - SCDO:0001370 + Perhaps include here an "Alpha Thalassemia Mutation" sub-class? Could use the current description for "Alpha-Globin Locus Deletion" and instead give "Alpha-Globin Locus Deletion" a description similar to that of "Beta-Globin Locus Deletion" + http://purl.obolibrary.org/obo/IDOMAL_50000026 + Sufficient + SCDO:0001370 IDOMAL:50000026 Mutation @@ -13191,11 +13190,11 @@ has disease stage: Mild, moderate, severe - + An organism population whose members are particpating in non-parasitic symbiosis with a particular host. - http://purl.obolibrary.org/obo/IDO_0000515 - Sufficient - SCDO:0000755 + http://purl.obolibrary.org/obo/IDO_0000515 + Sufficient + SCDO:0000755 IDO:0000515 Normal Resident Microbiota Population Normal Resident Microflora Population @@ -13208,47 +13207,47 @@ has disease stage: Mild, moderate, severe - + - + - + - + - + - + - + A material entity bearing an antifungal disposition. - http://purl.obolibrary.org/obo/IDO_0000560 - Sufficient - SCDO:1000019 + http://purl.obolibrary.org/obo/IDO_0000560 + Sufficient + SCDO:1000019 IDO:0000560 Antifungal @@ -13261,71 +13260,71 @@ has disease stage: Mild, moderate, severe - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population. - Perhaps use Bacterial Infection and Viral Infection as modifiers? + Perhaps use Bacterial Infection and Viral Infection as modifiers? -Include here "transfusion-related hepatitis infections" and or "viral hepatitis" (See paper "Liver involvement in sickle cell disease" by Emel GÜRKAN et al.) - - Sufficient - SCDO:0000635 +Include here "transfusion-related hepatitis infections" and or "viral hepatitis" (See paper "Liver involvement in sickle cell disease" by Emel GÜRKAN et al.) + + Sufficient + SCDO:0000635 IDO:0000586 Infection @@ -13337,9 +13336,9 @@ Include here "transfusion-related hepatitis infections" and or "v Focal pathological and/or inflammatory changes characterized by alteration in the size, shape and organization of the cellular components of the skin. - - Sufficient - SCDO:0001072 + + Sufficient + SCDO:0001072 MP:0001212 Skin Lesions @@ -13351,9 +13350,9 @@ Include here "transfusion-related hepatitis infections" and or "v Anomalies in the average levels of hemoglobin contained in an erythrocyte. - - Sufficient - SCDO:1000632 + + Sufficient + SCDO:1000632 MP:0001589 Abnormal MCH Abnormal Mean Cell Hemoglobin @@ -13370,21 +13369,21 @@ Include here "transfusion-related hepatitis infections" and or "v - - + + - - + + Increased volume of urine produced and excreted. - Provide source for additional info. - http://purl.obolibrary.org/obo/MP_0001762 - Sufficient - SCDO:0000395 + Provide source for additional info. + http://purl.obolibrary.org/obo/MP_0001762 + Sufficient + SCDO:0000395 MP:0001762 Increased Urine Output Increased Urine Volume @@ -13398,29 +13397,29 @@ Include here "transfusion-related hepatitis infections" and or "v - + - - + + - - + + - - + + Reduced ability or inability to self-repair and close wounds. - - Sufficient - SCDO:0000622 + + Sufficient + SCDO:0000622 MP:0001792 Delayed Wound Healing Impaired Wound Repair @@ -13434,9 +13433,9 @@ Include here "transfusion-related hepatitis infections" and or "v Death anytime within the perinatal period. - - Sufficient - SCDO:0000883 + + Sufficient + SCDO:0000883 MP:0002081 Perinatal Lethality Perinatal Death @@ -13447,11 +13446,11 @@ Include here "transfusion-related hepatitis infections" and or "v - + Anomaly in the processes involved in the maintenance of an internal equilibrium of lipids in the fluids and tissues. - - Sufficient - SCDO:1000284 + + Sufficient + SCDO:1000284 MP:0002118 Abnormal Lipid Homeostasis @@ -13464,9 +13463,9 @@ Include here "transfusion-related hepatitis infections" and or "v Anomaly in the amount of oxygen and carbon dioxide in the blood. - - Sufficient - SCDO:1000810 + + Sufficient + SCDO:1000810 MP:0002329 Abnormal Blood Gas Level @@ -13479,68 +13478,68 @@ Include here "transfusion-related hepatitis infections" and or "v - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Greater likelihood that an organism will develop ill effects from a bacterial infection or from components of or toxins produced by bacteria. - http://purl.obolibrary.org/obo/MP_0002412 - Sufficient - SCDO:0000632 + http://purl.obolibrary.org/obo/MP_0002412 + Sufficient + SCDO:0000632 MP:0002412 Decreased Resistance to Bacterial infection Characterised by: Repeated/recurrent local or systemic bacterial infections. @@ -13556,14 +13555,14 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< A retrogressive impairment of function or destruction of the functional cells of the nervous system that receive, conduct, and transmit impulses. + Provide source for additional info. + + Usually in the elderly persons. Aging associated with most disorders + Multifactorial causes such as program cell death, genetic mutations, protein misfolding and intracellular mechanisms + Multiple disease entities such as alzhiemers disease, parkinsons disease , huntington's disease and amylotrophic lateral sclerosis + Sufficient + SCDO:0000802 http://www.neurodegenerationresearch.eu/about/what/ - Provide source for additional info. - - Usually in the elderly persons. Aging associated with most disorders - Multifactorial causes such as program cell death, genetic mutations, protein misfolding and intracellular mechanisms - Multiple disease entities such as alzhiemers disease, parkinsons disease , huntington's disease and amylotrophic lateral sclerosis - Sufficient - SCDO:0000802 MP:0003224 Nerve Degeneration Nerve Degenerations @@ -13578,9 +13577,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< The observable morphological and physiological characteristics related to a state of equilibrium in the body with respect to various functions and to chemical composition of the fluids and tissues or the processes that cause many of the chemical changes in living mammalian organisms that are manifested through development and lifespan. - - Sufficient - SCDO:1000811 + + Sufficient + SCDO:1000811 MP:0005376 Homeostasis Phenotype Homeostasis/Metabolism Phenotype @@ -13594,9 +13593,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Greater than the level of heat natural to a living being. - - Sufficient - SCDO:1000761 + + Sufficient + SCDO:1000761 MP:0005533 Raised Body Temperature Increased Body Temperature @@ -13609,9 +13608,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Less than the level of heat natural to a living being. - - Sufficient - SCDO:1000762 + + Sufficient + SCDO:1000762 MP:0005534 Reduced Body Temperature Decreased Body Temperature @@ -13622,11 +13621,11 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + Deviation in the level of heat natural to a living being. - - Sufficient - SCDO:1000760 + + Sufficient + SCDO:1000760 MP:0005535 Abnormal Body Temperature @@ -13638,9 +13637,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Greater than the average levels of hemoglobin contained in an erythrocyte. - - Sufficient - SCDO:1000634 + + Sufficient + SCDO:1000634 MP:0005561 High MCH High Mean Corpuscular Hemoglobin @@ -13656,9 +13655,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Less than the average levels of hemoglobin contained in an erythrocyte. - - Sufficient - SCDO:1000633 + + Sufficient + SCDO:1000633 MP:0005562 Decreased MCH Decreased Mean Cell Hemoglobin @@ -13674,9 +13673,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< A measure (DImax) related to cell surface area, of the changeability of the membrane of circulating oxygen transporting cells as a function of physiologically relevant osmolality at a constant applied shear stress. - - Sufficient - SCDO:1000277 + + Sufficient + SCDO:1000277 MP:0009568 Abnormal Red Blood Cell Deformability @@ -13687,11 +13686,11 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + Anomaly in the processes involved in the maintenance of an internal equilibrium of various functions or chemical or protein composition of the blood. - - Sufficient - SCDO:1000809 + + Sufficient + SCDO:1000809 MP:0009642 Abnormal Blood Chemistry Blood Chemistry Abnormalities @@ -13705,9 +13704,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< An anomaly in the coefficient of variance (reference range) of the red blood cell volume for an organism. - - Sufficient - SCDO:1000639 + + Sufficient + SCDO:1000639 MP:0010066 Abnormal Erythrocyte Distribution Width Abnormal RDW @@ -13721,9 +13720,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Higher than normal coefficient of variance (reference range) of the red blood cell volume for an organism. - - Sufficient - SCDO:1000641 + + Sufficient + SCDO:1000641 MP:0010067 High RCDW High RDW @@ -13741,9 +13740,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Lower than normal coefficient of variance (reference range) of the red blood cell volume for an organism. - - Sufficient - SCDO:1000640 + + Sufficient + SCDO:1000640 MP:0010068 Decreased Erythrocyte Distribution Width Decreased RCDW @@ -13764,9 +13763,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Destruction of erythrocytes such that hemoglobin is released from the cells; may occur by many different causal agents such as antibodies, bacteria, chemicals, temperature, and changes in tonicity. - - Sufficient - SCDO:0009017 + + Sufficient + SCDO:0009017 MP:0010163 Erythrocytolysis Erythrolysis @@ -13784,9 +13783,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Any anomaly in the amount in the urine of a carboxylic acid containing one or more amino groups (-NH2) and a carboxyl (-COOH) group. - - Sufficient - SCDO:1000653 + + Sufficient + SCDO:1000653 MP:0011468 Abnormal Urine Amino Acid Level @@ -13798,9 +13797,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Any change in the amount of creatinine in the urine - - Sufficient - SCDO:1000654 + + Sufficient + SCDO:1000654 MP:0011469 Abnormal Urine Creatinine Level @@ -13812,9 +13811,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< An increased amount of creatinine in the urine compared to the normal state. - - Sufficient - SCDO:1000656 + + Sufficient + SCDO:1000656 MP:0011470 Increased Urine Creatinine Level @@ -13826,9 +13825,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< a reduced amount of creatinine in the urine compared to the normal state - - Sufficient - SCDO:1000655 + + Sufficient + SCDO:1000655 MP:0011471 Low Urine Creatinine Level Reduced Urine Creatinine Level @@ -13842,9 +13841,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Inability of the kidneys to produce either a concentrated or a dilute urine; refers to a state in chronic renal disease in which the kidney cannot form urine with a higher or a lower specific gravity (concentration) than that of protein-free plasma; the specific gravity of the urine becomes fixed, irrespective of the fluid intake. - http://purl.obolibrary.org/obo/MP_0013305 - Sufficient - SCDO:0000667 + http://purl.obolibrary.org/obo/MP_0013305 + Sufficient + SCDO:0000667 MP:0013305 Impaired Urine-Concentrating Ability Urine Concentrating Defect @@ -13857,11 +13856,11 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + A drinking behavior associated with the intake of alcohol. - http://purl.obolibrary.org/obo/NBO_0000131 - Sufficient - SCDO:0000039 + http://purl.obolibrary.org/obo/NBO_0000131 + Sufficient + SCDO:0000039 NBO:0000131 Alcohol Consumption Alcohol Intake @@ -13873,18 +13872,18 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + - - + + A drug used to treat depression and peripheral neuropathy (pain, numbness, tingling, burning, or weakness in the hands or feet) that can occur with diabetes. + http://purl.obolibrary.org/obo/NCIT_C65495 + Sufficient + SCDO:0006467 - http://purl.obolibrary.org/obo/NCIT_C65495 - Sufficient - SCDO:0006467 NCIT:65495 Cymbalta Duloxetine HCl @@ -13897,11 +13896,11 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + An examination of the retina of the eye using an ophthalmoscope. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C101217 - Sufficient - SCDO:0001009 + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C101217 + Sufficient + SCDO:0001009 NCIT:C101217 Fundoscopy Retinal Examination @@ -13914,9 +13913,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< A finding indicating the presence of an inflammatory or neoplastic cellular infiltrate in the lung parenchyma. - - Sufficient - SCDO:0007383 + + Sufficient + SCDO:0007383 NCIT:C102531 Lung Infiltrate Pulmonary Infiltrate @@ -13927,15 +13926,15 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - - + + A project to develop standards for the collection and analysis of patient-reported health status data using a system of highly reliable, precise measures for physical, mental, and social well-being. Patients are asked a series of rigorously reviewed questions covering common domains and metrics across differing conditions and treatments. The questions can be administered in short forms or adaptively through computerized adaptive testing and reports can be generated to allow clinicians to better understand how treatments might affect the quality of life of their patients. + + Sufficient + SCDO:0000871 Bevans, M., Ross, A., & Cella, D. (2014). Patient-Reported Outcomes Measurement Information System (PROMIS): Efficient, standardized tools to measure self-reported health and quality of life. Nursing Outlook, 62, 339-345. Dampier C, Barry V, Gross HE, Lui Y, Thornburg CD, DeWalt DA, Reeve BB. (2016). Initial Evaluation of the Pediatric PROMIS® Health Domains in Children and Adolescents With Sickle Cell Disease. Pediatric Blood & Cancer. Feb 19. doi: 10.1002/pbc.25944. DeWitt, E. M., Barnett, K., Farrell, J., Revicki, D., Carle, A., Cook, K., Sherry, D. D. (2014). A164: Development of pediatric item banks to measure pain behavior in the Patient-Reported Outcomes Measurement Information System. Arthritis & Rheumatology, 66(Suppl. 11), S212-S2121. - - Sufficient - SCDO:0000871 NCIT:C102988 PROMIS Patient Reported Outcomes Measurement Information System @@ -13949,9 +13948,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< The kind of visit undertaken by the subject within a study, such as inpatient, outpatient, telephone, etc. - - Sufficient - SCDO:1000852 + + Sufficient + SCDO:1000852 NCIT:C103165 Subject Visit Type @@ -13961,12 +13960,12 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + The release from the requirement to obtain informed consent during a study that is granted by Human Subject Protection committee for a research institution for a protocol that is being reviewed by the Institutional Review Board. + + Sufficient + SCDO:0005773 International Ethical Guidelines for Health-related Research Involving Humans, Fourth Edition. Geneva. Council for International Organizations of Medical Sciences (CIOMS); 2016. - - Sufficient - SCDO:0005773 NCIT:C103270 Consent Waiver Waiver Of Informed Consent @@ -13979,13 +13978,13 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - - + + A 9-item scale using each of the 9 DSM-IV criteria with self-reported frequency of "0" (not at all) to "3" (nearly every day). One of the most widely used instruments to assess depression, PHQ-9 scores of 5, 10, 15, and 20 represent mild, moderate, moderately severe, and severe depression, respectively. + + Sufficient + SCDO:0000870 Kroenke K, Spitzer R, Williams W. The PHQ-9: Validity of a brief depression severity measure. Journal of General Internal Medicine. 2001; 16: 606-616. - - Sufficient - SCDO:0000870 NCIT:C103526 PHQ-9 PHQ01 @@ -14001,9 +14000,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Hemoglobin that has a nitric oxide bound to the cysteine at position 93 in the beta-globin chain. - - Sufficient - SCDO:1000169 + + Sufficient + SCDO:1000169 NCIT:C107564 S-Nitrosated Hemoglobin S-Nitrosohemoglobin @@ -14017,9 +14016,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< The cessation of menstruation for six months or more in a female that is not pregnant, breastfeeding or menopausal. - - Sufficient - SCDO:0001447 + + Sufficient + SCDO:0001447 NCIT:C113340 Secondary Amenorrhea @@ -14031,9 +14030,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Hemoglobin where the heme group has formed a stable complex with carbon monoxide (CO). This complex is produced after CO has been inhaled or as a byproduct of hemoglobin, protoporphyrin or dichloromethane catabolism. The heme-CO complex is approximately 200 times more stable than heme-oxygen complexes. Thus, high levels of carboxyhemoglobin in the circulation can lead to tissue hypoxia and death. - - Sufficient - SCDO:1000168 + + Sufficient + SCDO:1000168 NCIT:C114300 COHb Carboxyhemoglobin @@ -14052,9 +14051,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< A severe hypersensitivity-like reaction occurring during dialysis due to exposure to the dialysis membrane. - - Sufficient - SCDO:1000387 + + Sufficient + SCDO:1000387 NCIT:C114714 Dialyzer Reaction Dialysis Membrane Reaction @@ -14067,9 +14066,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< A crack or break in a dialysis catheter caused by material weakness or mechanical compression. - - Sufficient - SCDO:1000386 + + Sufficient + SCDO:1000386 NCIT:C114717 Dialysis Catheter Fracture @@ -14081,9 +14080,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Any heart or vascular disorder occurring as a consequence of injury to the cardiovascular system. - - Sufficient - SCDO:1000390 + + Sufficient + SCDO:1000390 NCIT:C115199 Cardiovascular Complication @@ -14095,9 +14094,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Any disorder of the liver occurring as a consequence of injury to the liver parenchyma. - - Sufficient - SCDO:1000382 + + Sufficient + SCDO:1000382 NCIT:C115224 Liver Complication Hepatic Complication @@ -14111,44 +14110,44 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - - + + - - + + - - + + - - + + - - + + - - + + Any eye disorder occurring as a consequence of injury to the eye. - - Sufficient - SCDO:0000832 + + Sufficient + SCDO:0000832 NCIT:C115319 Ophthalmologic Manifestations Ophthalmologic Complication @@ -14161,9 +14160,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Any issue that arises as a consequence of a problem with a patient's dialysis access. - - Sufficient - SCDO:1000391 + + Sufficient + SCDO:1000391 NCIT:C116081 Dialysis Access Complication @@ -14173,11 +14172,11 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + A type of high-throughput, multiplex PCR method used to determine abnormal DNA copy number changes of up to 50 genomic DNA or RNA sequences with a single pair of PCR primers. It is frequently used in the detection of genetic aberrations in tumors, and can distinguish sequences differing in only a single nucleotide. - - Sufficient - SCDO:0003929 + + Sufficient + SCDO:0003929 NCIT:C116161 MLPA Multiplex Ligation-Dependent Probe Amplification @@ -14191,22 +14190,22 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - - + + - - + + Failure to meet, or late achievement of developmental milestones. + + Can have many different causes, such as genetic causes (like Down syndrome), or complications of pregnancy and birth (like prematurity or infections). Often, however, the specific cause is unknown. Some causes can be easily reversed if caught early enough, such as hearing loss from chronic ear infections, or lead poisoning. + Sufficient + SCDO:0001293 http://www.med.umich.edu/yourchild/topics/devdel.htm - - Can have many different causes, such as genetic causes (like Down syndrome), or complications of pregnancy and birth (like prematurity or infections). Often, however, the specific cause is unknown. Some causes can be easily reversed if caught early enough, such as hearing loss from chronic ear infections, or lead poisoning. - Sufficient - SCDO:0001293 NCIT:C116942 Developmental Delay @@ -14216,13 +14215,13 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + Tissue death resulting from an interruption to the blood supply. - - This is a synonym for osteonecrosis in our ontology (SCDO:0000841), which is controversial between different literature. Please check with a clinician if these two terms refer to the same condition. - http://purl.obolibrary.org/obo/NCIT_C118385 - Sufficient - SCDO:0004832 + + This is a synonym for osteonecrosis in our ontology (SCDO:0000841), which is controversial between different literature. Please check with a clinician if these two terms refer to the same condition. + http://purl.obolibrary.org/obo/NCIT_C118385 + Sufficient + SCDO:0004832 NCIT:C118385 AVN deprecated-Avascular Necrosis @@ -14236,12 +14235,12 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< A standardized tool designed to assess an individual's cognitive abilities. It consists of a battery of tests that allow an investigator to conduct a comprehensive cognitive evaluation of IQ. - Life stage: Adolescent, Adult - The Sickle Cell Disease Neurology, Quality of Life, and Health Services Working Group recognizes that there is an age overlap between the WAIS-IV and the Wechsler Intelligence Scale for Children-Fifth Edition (WISC-V). The Working Group recommends providers use their clinical judgment, consider the purpose of testing participants, and refer to the frequently asked questions section of the Pearson website for the WAIS-IV and the WISC-V for guidance on selecting an age-appropriate test for individuals. - http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820501 - PhenX protocol: Intelligence Scale - 16 to 90 years #820501 - Sufficient - SCDO:0000646 + Life stage: Adolescent, Adult + The Sickle Cell Disease Neurology, Quality of Life, and Health Services Working Group recognizes that there is an age overlap between the WAIS-IV and the Wechsler Intelligence Scale for Children-Fifth Edition (WISC-V). The Working Group recommends providers use their clinical judgment, consider the purpose of testing participants, and refer to the frequently asked questions section of the Pearson website for the WAIS-IV and the WISC-V for guidance on selecting an age-appropriate test for individuals. + http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820501 + PhenX protocol: Intelligence Scale - 16 to 90 years #820501 + Sufficient + SCDO:0000646 NCIT:C120254 WAIS-IV Wechsler Adult Intelligence Scale - Fourth Edition @@ -14258,13 +14257,13 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< A battery of tests that allow an investigator to conduct a comprehensive evaluation of a child or adolescent's cognitive ability. - It consists of a core battery of subtests, which focus on five specific domains (verbal comprehension, processing speed, visual spatial, working memory, and fluid reasoning), as well as optional ancillary subtests. These ancillary subtests measure areas that are important to areas of academic achievement. - Life stage: Child, Adolescent - The Sickle Cell Disease Neurology, Quality of Life, and Health Services Working Group recognizes that there is an age overlap between the Wechsler Intelligence Scale for Children®-Fifth Edition (WISC-V) and Wechsler Preschool and Primary Scale of Intelligence-Fourth Edition (WPPSI-IV), as well as between the WISC-V and the Wechsler Adult Intelligence Scale, Fourth Edition (WAIS-IV). The Working Group recommends that providers use their clinical judgment, consider the purpose of testing participants, and refer to the frequently asked questions section of the Pearson website for WISC-V, WPPSI-IV, and WAIS-IV for guidance on selecting an age-appropriate test. - http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820503 - PhenX protocol: Intelligence Scale - 6 to 16 years 11 months #820503 - Sufficient - SCDO:0000648 + It consists of a core battery of subtests, which focus on five specific domains (verbal comprehension, processing speed, visual spatial, working memory, and fluid reasoning), as well as optional ancillary subtests. These ancillary subtests measure areas that are important to areas of academic achievement. + Life stage: Child, Adolescent + The Sickle Cell Disease Neurology, Quality of Life, and Health Services Working Group recognizes that there is an age overlap between the Wechsler Intelligence Scale for Children®-Fifth Edition (WISC-V) and Wechsler Preschool and Primary Scale of Intelligence-Fourth Edition (WPPSI-IV), as well as between the WISC-V and the Wechsler Adult Intelligence Scale, Fourth Edition (WAIS-IV). The Working Group recommends that providers use their clinical judgment, consider the purpose of testing participants, and refer to the frequently asked questions section of the Pearson website for WISC-V, WPPSI-IV, and WAIS-IV for guidance on selecting an age-appropriate test. + http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820503 + PhenX protocol: Intelligence Scale - 6 to 16 years 11 months #820503 + Sufficient + SCDO:0000648 NCIT:C120255 WISC-V Wechsler Intelligence Scale for Children-Fifth Edition @@ -14279,12 +14278,12 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< A standardized tool designed to assess the cognitive development in preschool and young children (up to age 7 years and 7 months). It consists of a battery of tests that allow an investigator to conduct a comprehensive evaluation of IQ. - Life stage: Toddler, Child - The Sickle Cell Disease Neurology, Quality of Life, and Health Services Working Group recognizes that there is an age overlap between the WPPSI-IV and the Bayley Scales of Infant and Toddler Development, Third Edition (Bayley-III) and between the WPPSI-IV and the Wechsler Intelligence Scale for Children-Fifth Edition (WISC-V). The Working Group recommends that providers use their clinical judgment, consider the purpose of testing participants, and refer to the frequently asked questions section of the Pearson website for the WPPSI-IV, Bayley-III, and the WISC-V for guidance on selecting an age-appropriate test. - http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820502 - PhenX protocol: Intelligence Scale - 2 years, 6 months to 7 years, 7 months #820502 - Sufficient - SCDO:0000647 + Life stage: Toddler, Child + The Sickle Cell Disease Neurology, Quality of Life, and Health Services Working Group recognizes that there is an age overlap between the WPPSI-IV and the Bayley Scales of Infant and Toddler Development, Third Edition (Bayley-III) and between the WPPSI-IV and the Wechsler Intelligence Scale for Children-Fifth Edition (WISC-V). The Working Group recommends that providers use their clinical judgment, consider the purpose of testing participants, and refer to the frequently asked questions section of the Pearson website for the WPPSI-IV, Bayley-III, and the WISC-V for guidance on selecting an age-appropriate test. + http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820502 + PhenX protocol: Intelligence Scale - 2 years, 6 months to 7 years, 7 months #820502 + Sufficient + SCDO:0000647 NCIT:C120256 WPPSI-IV Wechsler Preschool & Primary Scale of Intelligence 4th Edition @@ -14300,35 +14299,35 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + - + - + - + - - + + An assessment tool designed to measure an individual's cognitive capabilities. It may be general or it may assess abilities in more discrete cognitive domains. - - Sufficient - SCDO:0000645 + + Sufficient + SCDO:0000645 NCIT:C122920 Intelligence Test Intelligence Scale @@ -14342,9 +14341,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< A diagnostic technique that uses pulsed Doppler ultrasound to both identify blood vessels in the brain and measure the velocity of blood flow through those vessels. It allows a more accurate estimation of stroke risk because it allows outlining of parenchymal structures and visualization of the examined vessels. - http://purl.obolibrary.org/obo/NCIT_C122931 - Sufficient - SCDO:0000613 + http://purl.obolibrary.org/obo/NCIT_C122931 + Sufficient + SCDO:0000613 NCIT:C122931 TCDi Imaging Transcranial Doppler Ultrasonography @@ -14355,17 +14354,17 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + - - + + A continuous electrocardiographic (ECG) recording that utilizes one or more leads that both records and stores data directly to a device worn by the subject, such that the subject need not be restricted to a medical facility, and may be able to participate in their customary activities of daily living. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C123446 - Sufficient - SCDO:0000281 + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C123446 + Sufficient + SCDO:0000281 NCIT:C123446 Continuous Ambulatory ECG @@ -14375,13 +14374,13 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + A standardized rating scale developed by Ziad Nasreddine in 1996 to screen for mild cognitive dysfunction and impairment. This instrument assesses the following cognitive domains: attention and concentration, executive functions, memory, language, visuoconstructional skills, conceptual thinking, calculations, and orientation + + PhenX protocol: Global Mental Status Screener - Adult #130701 + Sufficient + SCDO:1000335 - - PhenX protocol: Global Mental Status Screener - Adult #130701 - Sufficient - SCDO:1000335 NCIT:C123667 MOCA MOCA01 @@ -14399,27 +14398,27 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - - + + - - + + - - + + A chest X-ray finding indicating the presence of a radio-opaque area in the lung. The opacification is caused by fluid or solid material within the airways or lung parenchyma. - Described in the Tanzania guidelines as 'reduced air entry, increased tactile vocal fremitus, and dull percussion at lung bases, usually bilateral'. - http://purl.obolibrary.org/obo/NCIT_C124059 - Sufficient - SCDO:0006222 + Described in the Tanzania guidelines as 'reduced air entry, increased tactile vocal fremitus, and dull percussion at lung bases, usually bilateral'. + http://purl.obolibrary.org/obo/NCIT_C124059 + Sufficient + SCDO:0006222 NCIT:C124059 Air Space Opacificatio Air-Space Shadowing @@ -14434,29 +14433,29 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + - + - + - - + + A measurement of the concentration of iron in the liver as an estimate of body iron load. - http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C124065 - Sufficient - SCDO:0000555 + http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C124065 + Sufficient + SCDO:0000555 NCIT:C124065 Hepatic Iron Liver Iron @@ -14471,9 +14470,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< A circumferential measurement of the largest part of the upper arm. - http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C124475 - Sufficient - SCDO:0000758 + http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C124475 + Sufficient + SCDO:0000758 NCIT:C124475 MUAC MUARMCIR @@ -14488,9 +14487,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Hemoglobin where the heme group has formed a reversible complex with oxygen (O2) in the lungs. This molecule is found in the systemic arteries and transports O2 from the lungs to the tissues where it is readily released. - - Sufficient - SCDO:1000275 + + Sufficient + SCDO:1000275 NCIT:C126120 HbO2 Oxyhemoglobin @@ -14504,9 +14503,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< Hemoglobin containing a heme group that is not bound to oxygen (O2). This molecule is normally found in the systemic veins following transit through capillaries and release of O2 into the tissues. Excess deoxyhemoglobin can be associated with hypoxia. - - Sufficient - SCDO:1000057 + + Sufficient + SCDO:1000057 NCIT:C126121 Deoxyhemoglobin Deoxygenated Hemoglobin @@ -14520,14 +14519,14 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - - + + An abscess within the abdomen. - http://purl.obolibrary.org/obo/NCIT_C128326 - Sufficient - SCDO:0008079 + http://purl.obolibrary.org/obo/NCIT_C128326 + Sufficient + SCDO:0008079 NCIT:C128326 Intra-Abdominal Abscess @@ -14537,53 +14536,53 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + - - + + - - + + - - + + - - + + - + - + - - + + The persistence of substantial fetal hemoglobin production into adulthood, usually associated with hemoglobinopathies due to mutations in the alpha and/or beta chain of hemoglobin. - - Sufficient - SCDO:0000560 + + Sufficient + SCDO:0000560 NCIT:C129072 HPFH Hereditary Persistence of Foetal Haemoglobin @@ -14596,642 +14595,642 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - - + + - + - + - - + + - - + + - - + + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A variant of sickle cell disease due to homozygosity of the E6V mutation, amino acid substitution of valine for glutamic acid in the sixth position of the beta chain, resulting in the production of hemoglobin S from both alleles. - - Sufficient - SCDO:0000549 + + Sufficient + SCDO:0000549 NCIT:C131682 Hb SS Disease Hb SS-Disease @@ -15253,13 +15252,13 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + A humanized monoclonal immunoglobulin G1 anti-P-selectin antibody with vaso-protective and anti-vaso-occlusive properties. Upon administration, crizanlizumab binds to P-selectin and blocks its interaction with P-selectin glycoprotein ligand-1 (PSGL-1; SELPLG) on neutrophils and monocytes. P-selectin, a glycoprotein that functions as a cell adhesion molecule (CAM), translocates to the surface of activated endothelial cells and platelets, upon stimulation, where it binds to its ligand and mediates the rolling of platelets and neutrophils on activated endothelial cells. Therefore, blockade of p-selectin may inhibit platelet aggregation, maintain blood flow and minimize sickle cell-related pain crises (SCPC). + + Sufficient + SCDO:1000380 - - Sufficient - SCDO:1000380 NCIT:C133543 Adakveo SEG101 @@ -15272,41 +15271,41 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + - + - + - - + + - + - - + + A rare autosomal recessive hemoglobinopathy, caused by the presence of two deltabeta globin fusion chains, which occurs due to a crossover between the delta (HBD) and beta globin (HBB) gene loci during meiosis. - http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome - Sufficient - SCDO:0000538 + http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome + Sufficient + SCDO:0000538 NCIT:C141366 Hb Lepore Hb Lepore Syndrome @@ -15320,11 +15319,11 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + To maintain data by placing the data, or a copy of the data, onto an electronically accessible device for preservation (either in plain-text or encrypted format). - - Sufficient - SCDO:1000420 + + Sufficient + SCDO:1000420 NCIT:C142494 Data Storage @@ -15334,11 +15333,11 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + An independent group that comprises medical, scientific, and non-scientific members, and is tasked with the continuing review and approval of research, including clinical trials, with respect to the protocols, methods, and informed consent process to ensure the protection of the rights, safety, and wellbeing of participants. - - Sufficient - SCDO:0009748 + + Sufficient + SCDO:0009748 NCIT:C142541 Ethics Committee Human Subject Protection Committee @@ -15352,11 +15351,11 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + The interval of time during which subjects are to be enrolled in a clinical study. - - Sufficient - SCDO:1000400 + + Sufficient + SCDO:1000400 NCIT:C142664 Recruitment Period @@ -15367,11 +15366,11 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + An orally bioavailable modulator and stabilizer of sickle cell hemoglobin (HbS), with potential use in the treatment of sickle cell disease (SCD). Upon administration, voxelotor targets and covalently binds to the N-terminal valine of the alpha chain of HbS. This stabilizes HbS, thereby improving oxygen binding affinity. The binding of voxelotor to HbS prevents HbS polymerization, reduces sickling, decreases red blood cell (RBC) damage and increases the half-life of RBCs. This improves blood flow and decreases hemolytic anemia. - - Sufficient - SCDO:1000381 + + Sufficient + SCDO:1000381 NCIT:C152089 GBT-440 GBT440 @@ -15385,41 +15384,41 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + - + - + - + - + - - + + Application of genetic material (usually DNA) into cells in order to permanently correct an inherited disease or acquired disease. - http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C15238 - Sufficient - SCDO:0001344 + http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C15238 + Sufficient + SCDO:0001344 NCIT:C15238 DNA Therapy Gene Therapy @@ -15430,12 +15429,12 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + A plan detailing how a study will be performed in order to represent the phenomenon under examination, to answer the research questions that have been asked, and defining the methods of data analysis. Study design is driven by research hypothesis being posed, study subject/population/sample available, logistics/resources: technology, support, networking, collaborative support, etc. - Review current sub-classes in light of and include relevant classes from "EDDA Study Designs Taxonomy" to be added as sub-classes. - - Sufficient - SCDO:0001115 + Review current sub-classes in light of and include relevant classes from "EDDA Study Designs Taxonomy" to be added as sub-classes. + + Sufficient + SCDO:0001115 NCIT:C15320 Experiment Design Experimental Design @@ -15449,34 +15448,34 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + - + - - + + A patient-reported outcome measurement system designed to evaluate and monitor the physical, mental, and social well-being of adults with sickle cell disease. + + Cross-cultural adaptation underway in Brazil. ASCQ-Me's development using modern measurement theory facilitates cross cultural adaptation. + PhenX protocol: Adult Sickle Cell Quality of Life Measurement Information System (ASCQ-Me) #820201 + Self + Clinic Patients (Adults with SCD) + Spanish; Portuguese + This measure can be used to track health status and treatment outcomes and understand the health care requirements of patients with chronic conditions, such as sickle cell disease (SCD). + Rigor in development, using modern measurement theory and aligned with PROMIS measurement development. + 18 years and older + no + Sufficient + SCDO:0000027 Keller SD, Yang M, Treadwell MJ, Werner EM, Hassell KL (2014).Patient reports of health outcome for adults living with sickle cell disease: development and testing of the ASCQ-Me item banks. Health and Quality of Life Outcomes,12,125. - - Cross-cultural adaptation underway in Brazil. ASCQ-Me's development using modern measurement theory facilitates cross cultural adaptation. - PhenX protocol: Adult Sickle Cell Quality of Life Measurement Information System (ASCQ-Me) #820201 - Self - Clinic Patients (Adults with SCD) - Spanish; Portuguese - This measure can be used to track health status and treatment outcomes and understand the health care requirements of patients with chronic conditions, such as sickle cell disease (SCD). - Rigor in development, using modern measurement theory and aligned with PROMIS measurement development. - 18 years and older - no - Sufficient - SCDO:0000027 NCIT:C154481 ASCQ-Me Adult Sickle Cell Quality of Life Measurement Information System @@ -15490,12 +15489,12 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - - + + An evaluation of the perfusion of blood through the brain. - - Sufficient - SCDO:0000204 + + Sufficient + SCDO:0000204 NCIT:C154865 Cerebral Blood Flow Assessment Cerebral Blood Flow Measurement @@ -15508,156 +15507,156 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - - + + - + - + - - + + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A variant of sickle cell disease due to heterozygosity for hemoglobin S and hemoglobin D mutations. Patients present with the symptoms of sickle cell disease but the symptoms are less frequent and severe compared to patients with hemoglobin SS disease. - - Sufficient - SCDO:0001060 + + Sufficient + SCDO:0001060 NCIT:C155310 Haemoglobin S-D Disease Hb SD-Disease @@ -15675,92 +15674,92 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A pulmonary complication of sickle cell disease characterized by radiographic interstitial abnormalities and impaired pulmonary function. In severe cases, pulmonary hypertension is present. + + Restricive lung disease often associated with chest pain and hypoxemia. May also be associated with pulmonary hypertension. + Sufficient + SCDO:0001046 Powars et al 1988 Medicine (Baltimore), Knight-Madden et al 2010 Lung. - - Restricive lung disease often associated with chest pain and hypoxemia. May also be associated with pulmonary hypertension. - Sufficient - SCDO:0001046 NCIT:C155312 Sickle Cell Chronic Restrictive Lung Disease Sickle Cell Chronic Lung Disease @@ -15771,13 +15770,13 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + A clinician-assessed rating of psychological and social functioning in children ages six to seventeen that was developed by Shaffer et al. in 1983. The numerical scale, which is an adaptation of the adult Global Assessment Scale (GAS) developed by Endicott et al in 1976, is scored from 0 to 100 based on behaviors and life situations that are applicable to children. + + PhenX protocol: Global Mental Status Screener - Older Children and Adolescents #130703 + Sufficient + SCDO:1000334 - - PhenX protocol: Global Mental Status Screener - Older Children and Adolescents #130703 - Sufficient - SCDO:1000334 NCIT:C155932 CGAS Children’s Global Assessment Scale @@ -15792,9 +15791,9 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< A person who is separated from their spouse, whether or not there is a legal arrangement. - - Sufficient - SCDO:1000677 + + Sufficient + SCDO:1000677 NCIT:C156541 Separated @@ -15804,14 +15803,14 @@ Caused by: Multifactorial generally factors ultimately cause impaired immunity.< - + The process of isolating and testing the DNA of an embryo or a person to detect the presence of genetic alterations or defects that may predispose to the future development of a disease or disorder. - Note: "Genetic Test" is a SNOMED CT term. + Note: "Genetic Test" is a SNOMED CT term. -Include NCIT's "Presymptomatic Testing" as a sub-class? - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C15709 - Sufficient - SCDO:0000449 +Include NCIT's "Presymptomatic Testing" as a sub-class? + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C15709 + Sufficient + SCDO:0000449 NCIT:C15709 Genetic Analysis Genetic Examination @@ -15824,23 +15823,23 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? - + - + - + Therapy dealing with lifestyle management and includes: behavioral and dietary modifications, exercise, stress management, and addiction control. This therapy must be used as major adjunct to 'standard care' or be applied as alternative treatment to conventional medicine practices. - - Sufficient - SCDO:1000006 + + Sufficient + SCDO:1000006 NCIT:C15900 Lifestyle Therapy @@ -15852,9 +15851,9 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? An polyvalent vaccine used to prevent infection by the bacterium Streptococcus pneumoniae. Pneumococcal polyvalent vaccine contains highly purified capsular antigens from the 23 most prevalent or invasive pneumococcal types of Streptococcus pneumoniae to ensure cross-protection. Following vaccination, protective capsular type-specific antibody levels typically develop by the third week; serotype-specific antibody levels generally decline after 5-10 years. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C1643&jump_to_nav=true - Sufficient - SCDO:0000915 + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C1643&jump_to_nav=true + Sufficient + SCDO:0000915 NCIT:C1643 PPSV Pneumococcal Polysaccharide Vaccine @@ -15867,11 +15866,11 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? - + The date on which a diagnosis of disease was made. - - Sufficient - SCDO:1000557 + + Sufficient + SCDO:1000557 NCIT:C164339 Date of Diagnosis @@ -15881,11 +15880,11 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? - + A set of people with some shared element. The substance of shared element varies widely, from geography to a situation to interest to lives and values. The term is widely used to evoke sense of collectivity. - - Sufficient - SCDO:0000266 + + Sufficient + SCDO:0000266 NCIT:C16453 Community @@ -15897,9 +15896,9 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? The statistical characterization of human populations or segments of human populations (e.g., characterization by age, sex, race, or income). - - Sufficient - SCDO:1000468 + + Sufficient + SCDO:1000468 NCIT:C16495 Demographic Factors Demographics @@ -15913,18 +15912,18 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? - + - + A social group characterized by a distinctive social and cultural tradition that is maintained from generation to generation. Members share a common history and origin and a sense of identification with the group. They have similar and distinctive features in their lifestyle habits and shared experiences. They often have a common genetic heritage which may be reflected in their experience of health and disease. - Include other Ethnic groups that are sub-classes of "Ethnic Group" in ERO. - http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C16564 - Sufficient - SCDO:0001298 + Include other Ethnic groups that are sub-classes of "Ethnic Group" in ERO. + http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C16564 + Sufficient + SCDO:0001298 NCIT:C16564 Ethnic Origin Ethnic Origins @@ -15938,65 +15937,65 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? - + - + - + - + - + - + - + - + - + - - + + Activity that requires physical or mental exertion, especially when performed to develop or maintain fitness. - - Sufficient - SCDO:0001305 + + Sufficient + SCDO:0001305 NCIT:C16567 Exercise @@ -16008,9 +16007,9 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? A person who belongs to the sex that normally produces ova. The term is used to indicate biological sex distinctions, or cultural gender role distinctions, or both. - - Sufficient - SCDO:1000560 + + Sufficient + SCDO:1000560 NCIT:C16576 Female @@ -16020,11 +16019,11 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? - + A functional unit of heredity which occupies a specific position on a particular chromosome and serves as the template for a product that contributes to a phenotype or a biological function. - - Sufficient - SCDO:1000359 + + Sufficient + SCDO:1000359 NCIT:C16612 Gene @@ -16036,9 +16035,9 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? Any demarcated area of the Earth; may be determined by both natural and human boundaries. - - Sufficient - SCDO:1000367 + + Sufficient + SCDO:1000367 NCIT:C16632 Geographic Location Geographic Region @@ -16052,9 +16051,9 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? The red respiratory protein of erythrocytes, consisting of approximately 3.8% heme and 96.2% globin (64.5 KD), which as oxyhemoglobin (HbO2) transports oxygen from the lungs to the tissues where the oxygen is readily released and HbO2 becomes Hb. - - Sufficient - SCDO:0009453 + + Sufficient + SCDO:0009453 NCIT:C16676 Hb Hgb @@ -16066,11 +16065,11 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? - + Laboratory test involving interaction of antigens with specific antibodies. - - Sufficient - SCDO:0000617 + + Sufficient + SCDO:0000617 NCIT:C16723 Immunoassay Immunological Laboratory Method @@ -16083,11 +16082,11 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? - + A systematic means of communicating by the use of sounds, symbols, or gestures. - http://purl.obolibrary.org/obo/NCIT_C16779 - Sufficient - SCDO:0005364 + http://purl.obolibrary.org/obo/NCIT_C16779 + Sufficient + SCDO:0005364 NCIT:C16779 Language @@ -16100,56 +16099,56 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Imaging that uses radiofrequency waves and a strong magnetic field rather than x-rays to provide amazingly clear and detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders. - http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C16809 - Sufficient - SCDO:0000708 + http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C16809 + Sufficient + SCDO:0000708 NCIT:C16809 MIR Scan MRI @@ -16167,11 +16166,11 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? - + The year when a diagnosis was assigned to an individual's condition. - - Sufficient - SCDO:1000567 + + Sufficient + SCDO:1000567 NCIT:C168823 Year of Diagnosis @@ -16181,11 +16180,11 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? - + The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site to large nucleotide sequences visible at a chromosomal level. - - Sufficient - SCDO:0004047 + + Sufficient + SCDO:0004047 NCIT:C17004 Genetic Polymorphism @@ -16195,35 +16194,35 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? - + - + - - + + - - + + - - + + The subjective measurement of an individual's sense of well-being and ability to enjoy life. The concept holds varying meanings for different people and may evolve over time. For some individuals it implies autonomy, empowerment, capability, and choice; for others, security, social integration, or freedom from stress or illness. - - Sufficient - SCDO:0000949 + + Sufficient + SCDO:0000949 NCIT:C17047 Health Related Quality of Life QOL @@ -16236,19 +16235,19 @@ Include NCIT's "Presymptomatic Testing" as a sub-class? - + - + An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. - Different relevant racial groups need to be recorded. Perhaps as sub-classes of this class? -The PhenX protocol is U.S. specific. Is there one relevant to the African setting? - http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17049 - Sufficient - SCDO:0000962 + Different relevant racial groups need to be recorded. Perhaps as sub-classes of this class? +The PhenX protocol is U.S. specific. Is there one relevant to the African setting? + http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17049 + Sufficient + SCDO:0000962 NCIT:C17049 Racial Group Race @@ -16262,14 +16261,14 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + A technique in which high-frequency sound waves are bounced off internal organs and the echo pattern is converted into a 2 dimensional picture of the structures beneath the transducer. - http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17230 - Sufficient - SCDO:0000614 + http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17230 + Sufficient + SCDO:0000614 NCIT:C17230 Immaging by Ultrasonography Ultrasonography @@ -16283,12 +16282,12 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + Laboratory analysis of urine, commonly used to aid in the diagnosis of disease or to detect the presence of a specific substance. It involves examination of the urine by physical or chemical means as well as microscopic examination that helps to screen for urinary tract infections, renal disease, and diseases of other organs, that result in abnormal metabolites (break-down products) appearing in the urine. - Other urine tests to be added as sub-classes? There are many in the NCIT. - - Sufficient - SCDO:0001216 + Other urine tests to be added as sub-classes? There are many in the NCIT. + + Sufficient + SCDO:0001216 NCIT:C17241 Urinalysis Urine Analysis @@ -16300,23 +16299,23 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + - - + + - - + + The rate of blood flow through the cerebral arteries. - - Sufficient - SCDO:0000205 + + Sufficient + SCDO:0000205 NCIT:C173396 CBF Velocity CBFV @@ -16331,9 +16330,9 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti The assemblage of properties that distinguish people on the basis of the societal roles expected for the two sexes. - - Sufficient - SCDO:0001341 + + Sufficient + SCDO:0001341 NCIT:C17357 Gender @@ -16345,9 +16344,9 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti An account of all reproductive events and problems a person has experienced. An important aggregate factor in epidemiological studies of women's health. The concept usually includes the number and timing of pregnancies and their outcomes, the incidence of breast feeding, and may include age of menarche and menopause, regularity of menstruation, fertility, gynecological or obstetric problems, or contraceptive usage. - - Sufficient - SCDO:1000346 + + Sufficient + SCDO:1000346 NCIT:C17655 Reproductive History @@ -16357,11 +16356,11 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + Having to do with the physical, psychological, cognitive, and social consequences of disease, including stigmatization of persons affected. - http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17873 - Sufficient - SCDO:0000939 + http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17873 + Sufficient + SCDO:0000939 NCIT:C17873 Psychosocial Effects Psychosocial Effects/Treatment @@ -16375,9 +16374,9 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti A single base pair substitution that alters the genetic code in a way that produces an amino acid that is different from the usual amino acid at that position. Some missense mutations will alter the function of the protein. - - Sufficient - SCDO:0004314 + + Sufficient + SCDO:0004314 NCIT:C18133 Missense Mutation @@ -16388,12 +16387,12 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + A record of a patient's background regarding health and the occurrence of disease events of the individual. In addition, personal medical history may be a variable in epidemiologic studies. - Sub-classes in NCIT to be added here. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C18772 - Sufficient - SCDO:0000891 + Sub-classes in NCIT to be added here. + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C18772 + Sufficient + SCDO:0000891 NCIT:C18772 General Medical History Medical History @@ -16409,9 +16408,9 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti An instrument used to measure an event involving emission, absorption, or refraction of light. - http://purl.obolibrary.org/obo/NCIT_C19228 - Sufficient - SCDO:0000837 + http://purl.obolibrary.org/obo/NCIT_C19228 + Sufficient + SCDO:0000837 NCIT:C19228 Optical Instrument @@ -16424,14 +16423,14 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + Any rearrangement to the genomic content that results in the loss of one or more nucleotides of DNA. Deletions are generally irreversible rearrangements. They may alter the reading frame of a gene, or may result in loss of large chromosomal regions. - http://purl.obolibrary.org/obo/NCIT_C19296 - Sufficient - SCDO:0001371 + http://purl.obolibrary.org/obo/NCIT_C19296 + Sufficient + SCDO:0001371 NCIT:C19296 Deletion Abnormality Deletion Mutation @@ -16442,12 +16441,12 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + The distinguishing qualities or prominent aspects of an individual person. - Populate this class with demographic terms from PhenX and elsewhere. Some terms will be duplicated in QoL. -- -- Add these from PhenX?: -- - Acculturation -- - Residential History -- -- Also look at other sub-classes in NCIT. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C19332 - Sufficient - SCDO:0000890 + Populate this class with demographic terms from PhenX and elsewhere. Some terms will be duplicated in QoL. -- -- Add these from PhenX?: -- - Acculturation -- - Residential History -- -- Also look at other sub-classes in NCIT. + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C19332 + Sufficient + SCDO:0000890 NCIT:C19332 Subject Characteristics Personal Attribute @@ -16458,11 +16457,11 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + Analysis of the RNA expression pattern in a tissue sample using molecular techniques. - - Sufficient - SCDO:0000768 + + Sufficient + SCDO:0000768 NCIT:C19771 Expression Profiling Molecular Fingerprinting @@ -16477,9 +16476,9 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti A person who belongs to the sex that normally produces sperm. The term is used to indicate biological sex distinctions, cultural gender role distinctions, or both. - - Sufficient - SCDO:1000559 + + Sufficient + SCDO:1000559 NCIT:C20197 Male @@ -16491,9 +16490,9 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti A point mutation occurring within the protein-coding region of a gene, and which codes for the same amino acid as expected. - - Sufficient - SCDO:0005439 + + Sufficient + SCDO:0005439 NCIT:C20629 Exon Synonymous Mutation Exonic Synonymous Mutation @@ -16508,9 +16507,9 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti This gene plays a role in transcriptional regulation and is involved in several signal transduction pathways. - - Sufficient - SCDO:1000393 + + Sufficient + SCDO:1000393 NCIT:C20711 SP1 Sp1 Transcription Factor Gene @@ -16523,12 +16522,12 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + How long something has existed; elapsed time since birth. - Could add many sub-classes of "Age" from NCIT. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25150 - Sufficient - SCDO:0000030 + Could add many sub-classes of "Age" from NCIT. + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25150 + Sufficient + SCDO:0000030 NCIT:C25150 Aged Chronological Age @@ -16543,9 +16542,9 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti A word or group of words indicating the identity of a person usually consisting of a first (personal) name and a last (family) name with an optional middle name. In some cultural traditions the family name comes first. - - Sufficient - SCDO:1000859 + + Sufficient + SCDO:1000859 NCIT:C25191 Contact Name Individual's Name @@ -16562,9 +16561,9 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti The maximum pressure exerted into the systemic arterial circulation during the contraction of the left ventricle of the heart. - - Sufficient - SCDO:1000892 + + Sufficient + SCDO:1000892 NCIT:C25298 SYSBP Systolic Pressure @@ -16579,11 +16578,11 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti The minimum pressure exerted into the systemic arterial circulation during cardiac ventricular relaxation and filling. - - Sufficient - Vital Signs - 6 - SCDO:1000893 + + Sufficient + Vital Signs + 6 + SCDO:1000893 NCIT:C25299 DIABP Diastolic Pressure @@ -16596,11 +16595,11 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + Permission to do something. - http://purl.obolibrary.org/obo/NCIT_C25460 - Sufficient - SCDO:0001466 + http://purl.obolibrary.org/obo/NCIT_C25460 + Sufficient + SCDO:0001466 NCIT:C25460 Consent @@ -16610,12 +16609,12 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + A collective generic term that refers here to a wide variety of dependencies, areas of special sovereignty, uninhabited islands, and other entities in addition to the traditional countries or independent states. - - http://purl.obolibrary.org/obo/NCIT_C25464 - Sufficient - SCDO:0004140 + + http://purl.obolibrary.org/obo/NCIT_C25464 + Sufficient + SCDO:0004140 NCIT:C25464 deprecated Country true @@ -16628,9 +16627,9 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti A collection or single item of factual or reported information, derived from measurement or research, from which conclusions may be drawn. - - Sufficient - SCDO:0006670 + + Sufficient + SCDO:0006670 NCIT:C25474 Data @@ -16641,191 +16640,191 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Substances naturally produced by microorganisms or their derivatives that selectively target microorganisms not humans. Antibiotics kill or inhibit the growth of microorganisms by targeting components of the microbial cell absent from human cells, including bacterial cell walls, cell membrane, and 30S or 50S ribosomal subunits. These substances are used in the treatment of bacterial and other microbial infections. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C258 - Sufficient - SCDO:0000059 + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C258 + Sufficient + SCDO:0000059 NCIT:C258 Antibiotic Agents Antibiotic Drug @@ -16841,30 +16840,30 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + - + - + - + A protein, RNA or a complex that contains proteins and/or RNA. - If additional gene products are included in the future, they can be categorised according to those below this term in the "National Cancer Institute Thesaurus" (NCIT) - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C26548 - Sufficient - SCDO:0001343 + If additional gene products are included in the future, they can be categorised according to those below this term in the "National Cancer Institute Thesaurus" (NCIT) + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C26548 + Sufficient + SCDO:0001343 NCIT:C26548 Genome Encoded Entity Gene Product @@ -16878,69 +16877,69 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + Lack of coordination of muscle movements resulting in the impairment or inability to perform voluntary activities. Causes include peripheral nerve disorders, posterior column injuries, cerebral and cerebellar disorders, basal ganglia disorders, and thalamic disorders. - Perhaps add "Cerebellar Ataxia" subclass? - - Sufficient - SCDO:0000087 + Perhaps add "Cerebellar Ataxia" subclass? + + Sufficient + SCDO:0000087 NCIT:C26702 Ataxia @@ -16952,9 +16951,9 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti Abnormally high level of bilirubin in the blood. Excess bilirubin is associated with jaundice. - - Sufficient - SCDO:0003118 + + Sufficient + SCDO:0003118 NCIT:C27088 High Blood Bilirubin Levels Hyperbilirubinemia @@ -16968,20 +16967,20 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + - - + + A balloon type pouch or bulge in the wall of a cerebral blood vessel. - - Sufficient - SCDO:0000202 + + Sufficient + SCDO:0000202 NCIT:C27222 Brain Aneurysm Cerebral Artery Aneurysm @@ -16996,12 +16995,12 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + System of classification based on nation from which a person originates, regardless of the nation in which he/she currently resides. - Include list of nations below. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C28407 - Sufficient - SCDO:0000792 + Include list of nations below. + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C28407 + Sufficient + SCDO:0000792 NCIT:C28407 Birth Country Country of Birth @@ -17015,11 +17014,11 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + The totality of characteristics of reproductive structure, functions, phenotype, and genotype, differentiating the male from the female organism. - - Sufficient - SCDO:1000671 + + Sufficient + SCDO:1000671 NCIT:C28421 Participant Sex Participant's Sex @@ -17034,77 +17033,77 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A severe acute inflammatory response affecting the hands and feet of individuals with sickle cell disease, sickle cell-hemoglobin C disease or sickle cell-beta-thalassemia. It is caused by vaso-occlusive episodes leading to ischemia and finally infarction of the distal portions of the extremities. Clinical signs of pain, swelling and tenderness of digits usually begin in early childhood and may be the initial manifestations of sickle cell anemia. Clinical course is self-limited with instances typically lasting a few weeks and occurring during sickling crises. An initial episode before the age of 1 strongly correlates with a more severe disease course. - http://purl.obolibrary.org/obo/NCIT_C28516 - Sufficient - SCDO:0000477 + http://purl.obolibrary.org/obo/NCIT_C28516 + Sufficient + SCDO:0000477 NCIT:C28516 Sickle Cell Dactylitis @@ -17117,57 +17116,57 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An acute infectious disorder caused by gram positive or gram negative bacteria. Representative examples include pneumococcal, streptococcal, salmonella and meningeal infections. - Perhaps use as Disease Modifier? - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C2890 - Sufficient - SCDO:0000100 + Perhaps use as Disease Modifier? + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C2890 + Sufficient + SCDO:0000100 NCIT:C2890 Bacterial Infection @@ -17180,14 +17179,14 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - - + + Increase in the number of hematopoietic cells in the bone marrow. It may involve all or individual hematopoietic cell lines. - http://purl.obolibrary.org/obo/NCIT_C2905 - Sufficient - SCDO:0007438 + http://purl.obolibrary.org/obo/NCIT_C2905 + Sufficient + SCDO:0007438 NCIT:C2905 Hyperplasia of Bone Marrow Marrow Hyperplasia @@ -17202,32 +17201,32 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - - + + - - + + - - + + - - + + A non-infectious mixture containing recombinant hepatitis B surface antigen (HBsAg) in a liquid vehicle. Immunization with the hepatitis B vaccine induces the formation of specific anti-hepatitis B antibodies and an active immunity against hepatitis B infection. - http://purl.obolibrary.org/obo/NCIT_C29091 - Sufficient - SCDO:0008062 + http://purl.obolibrary.org/obo/NCIT_C29091 + Sufficient + SCDO:0008062 NCIT:C29091 ENGERIX-B Hepatitis B Vaccine (Recombinant) @@ -17241,29 +17240,29 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + - - + + - - + + - - + + A sterile liquid preparation infused into a vein. IV fluid is prescribed as a replacement of fluid, electrolytes, calories, vitamins, and other nutritional substances. In addition, IV fluids are used to administer blood products and medications such as chemotherapy. Examples of IV fluids include Normal Saline, Ringers Solution, and Lactated Ringers Solution. - http://purl.obolibrary.org/obo/NCIT_C29107 - Sufficient - SCDO:0005247 + http://purl.obolibrary.org/obo/NCIT_C29107 + Sufficient + SCDO:0005247 NCIT:C29107 Intravenous Fluid IV fluids @@ -17276,9 +17275,9 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti Any disease or disorder that occurs during the course of, or because of, another disease, treatment, or procedure. - - Sufficient - SCDO:1000384 + + Sufficient + SCDO:1000384 NCIT:C2959 Complications Medical Complication @@ -17290,11 +17289,11 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - + A record of an individual's background in regard to smoking tobacco. This would include such factors as start date, end date (if applicable), number of cigarette smoked, attempts to quit, and others. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C29719 - Sufficient - SCDO:0001081 + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C29719 + Sufficient + SCDO:0001081 NCIT:C29719 Tobacco Smoking History Smoking History @@ -17307,9 +17306,9 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti An account of all experiences related to the receipt of blood, WBC, platelets, and/or other blood components. - - Sufficient - SCDO:0000569 + + Sufficient + SCDO:0000569 NCIT:C30142 Transfusion History History of Transfusion @@ -17322,9 +17321,9 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti An infection caused by a fungus. - - Sufficient - SCDO:1000349 + + Sufficient + SCDO:1000349 NCIT:C3245 Fungal Infection @@ -17337,62 +17336,62 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African setti - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Any disease caused by a virus. - Perhaps use as Disease Modifier? + Perhaps use as Disease Modifier? Add these sub-classes: Hepatitis C Infection (term in NCIT) Hepatitis B Infection (term in NCIT) -HIV Infection (term in NCIT) - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C3439 - Sufficient - SCDO:0001233 +HIV Infection (term in NCIT) + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C3439 + Sufficient + SCDO:0001233 NCIT:C3439 Viral Disease Virus Disease @@ -17407,56 +17406,56 @@ HIV Infection (term in NCIT) - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An acute or chronic inflammation involving the gallbladder wall. It may be associated with the presence of gallstones. - http://purl.obolibrary.org/obo/NCIT_C34465 - Sufficient - SCDO:0007856 + http://purl.obolibrary.org/obo/NCIT_C34465 + Sufficient + SCDO:0007856 NCIT:C34465 Cholecystitis @@ -17466,11 +17465,11 @@ HIV Infection (term in NCIT) - + A sensation of discomfort secondary to surgery. - - Sufficient - SCDO:1000451 + + Sufficient + SCDO:1000451 NCIT:C34887 Perioperative Pain Post Surgery Pain @@ -17486,9 +17485,9 @@ HIV Infection (term in NCIT) The co-occurrence of pregnancy and a disease. The disease may precede or follow conception and it may or may not have a deleterious effect on the pregnant woman or fetus. - - Sufficient - SCDO:1000399 + + Sufficient + SCDO:1000399 NCIT:C34941 Complication Related to Pregnancy Pregnancy Complication @@ -17499,77 +17498,77 @@ HIV Infection (term in NCIT) - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An inherited blood disorder characterized by a decreased synthesis of one of the polypeptide chains that form hemoglobin. Anemia results from this abnormal hemoglobin formation. - - Sufficient - SCDO:0001144 + + Sufficient + SCDO:0001144 NCIT:C35069 Thalassemia @@ -17580,23 +17579,23 @@ HIV Infection (term in NCIT) - + - - + + - - + + Cholecystitis that is persistent and long-standing. - http://purl.obolibrary.org/obo/NCIT_C35146 - Sufficient - SCDO:0009201 + http://purl.obolibrary.org/obo/NCIT_C35146 + Sufficient + SCDO:0009201 NCIT:C35146 Chronic Cholecystitis @@ -17607,41 +17606,41 @@ HIV Infection (term in NCIT) - + - - + + - - + + - - + + - - + + - - + + Acute inflammation of the gallbladder. - http://purl.obolibrary.org/obo/NCIT_C35152 - Sufficient - SCDO:0008927 + http://purl.obolibrary.org/obo/NCIT_C35152 + Sufficient + SCDO:0008927 NCIT:C35152 Acute Cholecystitis @@ -17654,20 +17653,20 @@ HIV Infection (term in NCIT) - - + + - - + + Acute infection of the bile ducts caused by bacteria ascending from the small intestine. - http://purl.obolibrary.org/obo/NCIT_C35372 - Sufficient - SCDO:0008766 + http://purl.obolibrary.org/obo/NCIT_C35372 + Sufficient + SCDO:0008766 NCIT:C35372 Ascending Cholangitis @@ -17680,51 +17679,51 @@ HIV Infection (term in NCIT) - - + + - - + + - - + + - - + + - - + + - - + + - - + + Necrotic changes in the bone tissue of the femoral head due to interruption of blood supply. - Add description. -- See HPO term "Avascular necrosis of the capital femoral epiphysis". -- -- Perhaps add "Bone decompression by drilling" to therapeutics and link to it with "is treated with - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C35447 - Sufficient - SCDO:0000842 + Add description. -- See HPO term "Avascular necrosis of the capital femoral epiphysis". -- -- Perhaps add "Bone decompression by drilling" to therapeutics and link to it with "is treated with + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C35447 + Sufficient + SCDO:0000842 NCIT:C35447 Avascular Necrosis of Femoral Head Avascular Necrosis of the Capital Femoral Epiphysis @@ -17741,9 +17740,9 @@ HIV Infection (term in NCIT) Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity. - - Sufficient - SCDO:1000435 + + Sufficient + SCDO:1000435 NCIT:C3671 Trauma Wound @@ -17755,11 +17754,11 @@ HIV Infection (term in NCIT) - + A test performed by an ophthalmologist or optometrist assessing vision and ability to focus on and discern objects, as well as other tests and examinations pertaining to the eyes. - http://purl.obolibrary.org/obo/NCIT_C38060 - Sufficient - SCDO:0001313 + http://purl.obolibrary.org/obo/NCIT_C38060 + Sufficient + SCDO:0001313 NCIT:C38060 Eye Exam Eye Examination @@ -17770,11 +17769,11 @@ HIV Infection (term in NCIT) - + A non-invasive method that provides estimates of arterial oxyhemoglobin saturation by utilizing selected wavelengths of light to determine the saturation of oxyhemoglobin. - - Sufficient - SCDO:1000351 + + Sufficient + SCDO:1000351 NCIT:C38085 Pulse Oximetry @@ -17786,9 +17785,9 @@ HIV Infection (term in NCIT) An active immunizing agent used to prevent infection by the bacterium Streptococcus pneumoniae. Pneumococcal 7-valent conjugate vaccine consists of a solution of saccharides of the capsular antigens of Streptococcus serotypes 4, 6B, 9V, 14, 18C, 19F, and 23F individually conjugated to diphtheria CRM 197 protein. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C38141 - Sufficient - SCDO:0000911 + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C38141 + Sufficient + SCDO:0000911 NCIT:C38141 7 Valent PncOMPC Vaccine 7-Valent PncOMPC Vaccine @@ -17810,9 +17809,9 @@ HIV Infection (term in NCIT) Without clinical signs or indications that raise the possibility of a particular disorder or dysfunction. - - Sufficient - SCDO:0004802 + + Sufficient + SCDO:0004802 NCIT:C3833 No Symptoms Asymptomatic @@ -17826,38 +17825,38 @@ HIV Infection (term in NCIT) - - + + - - + + - - + + - - + + - - + + An increase in the viscosity of blood resulting from an increase in the proportion of cellular elements of the blood, a change in the mechanical properties of the cellular elements of the blood, and/or an alteration in plasma viscosity. - http://purl.obolibrary.org/obo/NCIT_C38698 - Sufficient - SCDO:0002771 + http://purl.obolibrary.org/obo/NCIT_C38698 + Sufficient + SCDO:0002771 NCIT:C38698 Blood Hyperviscosity Hypercoagulability @@ -17873,72 +17872,72 @@ HIV Infection (term in NCIT) - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A decrease in the amount of oxygen in the body. Symptoms range from mild (impaired judgment, memory loss, impaired motor coordination) to severe (seizures and coma). In SCD patients, this is considered as saturated oxygen < 95% on air. - Have merged the definition of hypoxia from NCIT and the Tanzanian Management Guidelines. Not sure if the SaO2 value is specific to SCD patients - please get a clinician to review. + Have merged the definition of hypoxia from NCIT and the Tanzanian Management Guidelines. Not sure if the SaO2 value is specific to SCD patients - please get a clinician to review. -This is a symptom of acute chest syndrome. - - SCD Management guidelines - Tanzania - Sufficient - SCDO:0004183 +This is a symptom of acute chest syndrome. + + SCD Management guidelines - Tanzania + Sufficient + SCDO:0004183 NCIT:C3890 Hypoxia @@ -17950,9 +17949,9 @@ This is a symptom of acute chest syndrome. The probability of benefit to individuals in a defined population from a medical technology applied for a given medical problem under ideal conditions of use. Efficacy is a measure of effect of therapy among appropriate patients in whom treatment is tolerated and effectively administered, under the condition of sufficient patients' compliance, usually determined in randomized trials. - - Sufficient - SCDO:1000156 + + Sufficient + SCDO:1000156 NCIT:C39547 Clinical Efficacy Treatment Efficacy @@ -17963,12 +17962,12 @@ This is a symptom of acute chest syndrome. - + The philosophical study of moral values and rules. Ethics is a general term for what is often described as the "science of morality". The Western tradition of ethics is sometimes called moral philosophy. This is one of the three major branches of philosophy, alongside metaphysics and logic. - - http://purl.bioontology.org/ontology/MESH/D004989 - Sufficient - SCDO:0300001 + + http://purl.bioontology.org/ontology/MESH/D004989 + Sufficient + SCDO:0300001 NCIT:C39796 Moral Philosophy Natural Law @@ -17980,18 +17979,18 @@ This is a symptom of acute chest syndrome. - - + + The BDI-II is the most widely used instrument for measuring depression. It consists of 21 items to assess the intensity of depression in clinical and normal patients. Each item is a list of four statements arranged in increasing severity about a particular symptom of depression, and rated on a scale of 0 to 3. - Beck A.T., Ward C. H., Mendelson M., Mock J., & Erbaugh J. (1961) An inventory for measuring depression. Archives of General Psychiatry, 4, 561-571. - Multiple countries and cultural groups - Self - Clinic Patients - Spanish - 13 years and older - yes - Sufficient - SCDO:0000103 + Beck A.T., Ward C. H., Mendelson M., Mock J., & Erbaugh J. (1961) An inventory for measuring depression. Archives of General Psychiatry, 4, 561-571. + Multiple countries and cultural groups + Self + Clinic Patients + Spanish + 13 years and older + yes + Sufficient + SCDO:0000103 NCIT:C40438 BDI-II Beck Depression Inventory @@ -18006,9 +18005,9 @@ This is a symptom of acute chest syndrome. A sequence of decimal digits (0-9) that is used for identifying a destination telephone line or other device in a telephone network. - - Sufficient - SCDO:1000881 + + Sufficient + SCDO:1000881 NCIT:C40978 Phone Phone Number @@ -18021,13 +18020,13 @@ This is a symptom of acute chest syndrome. - + An area or portion of something with more or less definite boundaries designed or specified according to some established biological, administrative, economic, demographic, etc. criteria. - - It didn't have sense to have this term as a sub-class of "Major Area", which has also been deprecated. - http://purl.obolibrary.org/obo/NCIT_C41129 - Sufficient - SCDO:0006934 + + It didn't have sense to have this term as a sub-class of "Major Area", which has also been deprecated. + http://purl.obolibrary.org/obo/NCIT_C41129 + Sufficient + SCDO:0006934 NCIT:C41129 deprecated Region true @@ -18040,9 +18039,9 @@ This is a symptom of acute chest syndrome. A unit of temperature of the temperature scale designed so that the freezing point of water is 0 degrees and the boiling point is 100 degrees at standard atmospheric pressure. The current official definition of the Celsius sets 0.01 C to be at the triple point of water and a degree to be 1/273.16 of the difference in temperature between the triple point of water and absolute zero. One degree Celsius represents the same temperature difference as one Kelvin. - - Sufficient - SCDO:1000713 + + Sufficient + SCDO:1000713 NCIT:C42559 C Celsius @@ -18060,11 +18059,11 @@ This is a symptom of acute chest syndrome. - + An association is a non-hierarchical, named relationship between a source and target concept that does not affect classification and is not inherited by child concepts during classification. Associations are bidirectional and have a stated inverse. Unlike roles, associations do not have a domain or range. - - Sufficient - SCDO:0005031 + + Sufficient + SCDO:0005031 NCIT:C43646 Association @@ -18076,8 +18075,8 @@ This is a symptom of acute chest syndrome. Determination of a value is not relevant in the current context. - Sufficient - SCDO:1000770 + Sufficient + SCDO:1000770 NCIT:C48660 Not Applicable NA @@ -18088,11 +18087,11 @@ This is a symptom of acute chest syndrome. - + A diagnostic test used to examine and define microscopic tissue structure, composition, or etiology. The test results are often used by a clinician to diagnose disease or disordered function. - - Sufficient - SCDO:0004740 + + Sufficient + SCDO:0004740 NCIT:C49131 Histologic Test Diagnostic Histology Test @@ -18105,9 +18104,9 @@ This is a symptom of acute chest syndrome. The number of breaths (inhalation and exhalation) taken per minute time. - - Sufficient - SCDO:1000716 + + Sufficient + SCDO:1000716 NCIT:C49674 Breaths/Minute bpm @@ -18124,9 +18123,9 @@ This is a symptom of acute chest syndrome. Abnormal decrease of rate of breathing. - - Sufficient - SCDO:1000293 + + Sufficient + SCDO:1000293 NCIT:C50474 Decreased Respiratory Rate Bradypnea @@ -18139,9 +18138,9 @@ This is a symptom of acute chest syndrome. Abnormal increase of rate of breathing. - - Sufficient - SCDO:1000347 + + Sufficient + SCDO:1000347 NCIT:C50767 Fast Breathing Increased Respiratory Rate @@ -18156,44 +18155,44 @@ This is a symptom of acute chest syndrome. - - + + - - + + - - + + - - + + - - + + - - + + A bacterial infectious process affecting any part of the urinary tract, most commonly the bladder and the urethra. Symptoms include urinary urgency and frequency, burning sensation during urination, lower abdominal discomfort, and cloudy urine. - http://purl.obolibrary.org/obo/NCIT_C50791 - Sufficient - SCDO:0007744 + http://purl.obolibrary.org/obo/NCIT_C50791 + Sufficient + SCDO:0007744 NCIT:C50791 Urinary Tract Infection @@ -18203,12 +18202,12 @@ This is a symptom of acute chest syndrome. - + Removal of tissue from the liver for microscopic examination. - Use relevant object property to link to "Elevated Hepatic Iron Concentration". - http://purl.obolibrary.org/obo/NCIT_C51677 - Sufficient - SCDO:0000693 + Use relevant object property to link to "Elevated Hepatic Iron Concentration". + http://purl.obolibrary.org/obo/NCIT_C51677 + Sufficient + SCDO:0000693 NCIT:C51677 Liver Biopsy @@ -18220,9 +18219,9 @@ This is a symptom of acute chest syndrome. Indicates a person currently joined in a legally binding matrimonial union. Classify common law marriage as married. Includes married couples living together and not living together. - - Sufficient - SCDO:1000674 + + Sufficient + SCDO:1000674 NCIT:C51773 Married Status Married @@ -18235,9 +18234,9 @@ This is a symptom of acute chest syndrome. Indicates a person who has never been married or whose marriages have been annulled. - - Sufficient - SCDO:1000678 + + Sufficient + SCDO:1000678 NCIT:C51774 Never Been Married/Annulled Never Married @@ -18252,9 +18251,9 @@ This is a symptom of acute chest syndrome. Indicates a person who is no longer married because of the death of his/her spouse and has not remarried. - - Sufficient - SCDO:1000675 + + Sufficient + SCDO:1000675 NCIT:C51775 Widowed Status Widowed @@ -18267,10 +18266,10 @@ This is a symptom of acute chest syndrome. Indicates a person whose marriage has been legally dissolved and has not remarried. + Sufficient + SCDO:1000676 SCDO (Jade Hotchkiss) - Sufficient - SCDO:1000676 NCIT:C51776 Divorced @@ -18283,20 +18282,20 @@ This is a symptom of acute chest syndrome. - + - - + + A broad-spectrum aminoglycoside antibiotic produced by fermentation of Micromonospora purpurea or M. echinospora. Gentamicin is an antibiotic complex consisting of four major (C1, C1a, C2, and C2a) and several minor components. This agent irreversibly binds to the bacterial 30S ribosomal subunit. Specifically, this antibiotic is lodged between 16S rRNA and S12 protein within the 30S subunit. This leads to interference with translational initiation complex, misreading of mRNA, thereby hampering protein synthesis and resulting in bactericidal effect. Aminoglycosides are mostly ineffective against anaerobic bacteria, fungi and viruses. - http://purl.obolibrary.org/obo/NCIT_C519 - Sufficient - SCDO:0001259 + http://purl.obolibrary.org/obo/NCIT_C519 + Sufficient + SCDO:0001259 NCIT:C519 Garamicin Garamycin @@ -18313,59 +18312,59 @@ This is a symptom of acute chest syndrome. - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Administration of antibiotics with the intent of preventing bacterial infection. - http://purl.obolibrary.org/obo/NCIT_C51993 - Sufficient - SCDO:0006790 + http://purl.obolibrary.org/obo/NCIT_C51993 + Sufficient + SCDO:0006790 NCIT:C51993 Is recommended, particularly up to the age of 5 years, to prevent bacterial infections in SCD patients. Antibiotic Prophylaxis @@ -18376,11 +18375,11 @@ This is a symptom of acute chest syndrome. - + A prenatal diagnostic procedure in which a small sample of amniotic fluid is removed from the uterus by a needle inserted into the abdomen. This procedure is used to detect various genetic abnormalities in the fetus and/or the sex of the fetus. - http://purl.obolibrary.org/obo/NCIT_C52009 - Sufficient - SCDO:0000048 + http://purl.obolibrary.org/obo/NCIT_C52009 + Sufficient + SCDO:0000048 NCIT:C52009 Amniotic Fluid Testing Amniocentesis @@ -18395,57 +18394,57 @@ This is a symptom of acute chest syndrome. - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A propionic acid derivate and nonsteroidal anti-inflammatory drug (NSAID) with anti-inflammatory, analgesic, and antipyretic effects. Ibuprofen inhibits the activity of cyclo-oxygenase I and II, resulting in a decreased formation of precursors of prostaglandins and thromboxanes. This leads to decreased prostaglandin synthesis, by prostaglandin synthase, the main physiologic effect of ibuprofen. Ibuprofen also causes a decrease in the formation of thromboxane A2 synthesis, by thromboxane synthase, thereby inhibiting platelet aggregation. + + Sufficient + SCDO:0000606 http://www.drugbank.ca/drugs/DB01050 - - Sufficient - SCDO:0000606 NCIT:C561 2-[4-(2-methylpropyl)phenyl]propanoic acid Advil @@ -18461,9 +18460,9 @@ This is a symptom of acute chest syndrome. A cyclohexanone derivative with analgesic and anesthetic properties. Although its mechanism of action is not well understood, ketamine appears exerts complex pharmacological actions including inhibition of biogenic amine uptake, binding to opioid receptors, and inhibition of N-methyl D-aspartate (NMDA) receptors. Because of the involvement of spinal NMDA receptors in the process of central sensitization, this agent may reduce pain perception and induce sedation. - - Sufficient - SCDO:1000450 + + Sufficient + SCDO:1000450 NCIT:C61797 Ketamine @@ -18474,30 +18473,30 @@ This is a symptom of acute chest syndrome. - + - - + + - - + + - - + + A derivative of dibenzocycloheptadiene and a tricyclic antidepressant. Amitriptyline inhibits the re-uptake of norepinephrine and serotonin by the presynaptic neuronal membrane in the central nervous system (CNS), thereby increasing the synaptic concentration of norepinephrine and serotonin. Due to constant stimulation to these receptors, amitriptyline may produce a downregulation of adrenergic and serotonin receptors, which may contribute to the antidepressant activity. - Used to treat neuropathic pain - http://purl.obolibrary.org/obo/NCIT_C62005 - Sufficient - SCDO:0004190 + Used to treat neuropathic pain + http://purl.obolibrary.org/obo/NCIT_C62005 + Sufficient + SCDO:0004190 NCIT:C62005 Amitriptyline @@ -18509,9 +18508,9 @@ This is a symptom of acute chest syndrome. A point mutation occurring within the protein-coding region of a gene, and which codes for a stop that can truncate the protein. - - Sufficient - SCDO:0003789 + + Sufficient + SCDO:0003789 NCIT:C62198 Premature Termination Abnormality Premature Termination Mutation @@ -18526,14 +18525,14 @@ This is a symptom of acute chest syndrome. - + A small scale mutation caused by the substitution of a single nucleotide for another nucleotide. - http://purl.obolibrary.org/obo/NCIT_C62200 - Sufficient - SCDO:0001372 + http://purl.obolibrary.org/obo/NCIT_C62200 + Sufficient + SCDO:0001372 NCIT:C62200 Point Mutation @@ -18543,11 +18542,11 @@ This is a symptom of acute chest syndrome. - + A way of denoting the collective genotype of a number of closely linked loci on a chromosome. - - Sufficient - SCDO:0007716 + + Sufficient + SCDO:0007716 NCIT:C63547 Haplotype @@ -18559,9 +18558,9 @@ This is a symptom of acute chest syndrome. A unit of concentration (molarity unit) equal to one millimole of solute per liter of solution. - - Sufficient - SCDO:1000899 + + Sufficient + SCDO:1000899 NCIT:C64387 Millimolar mM @@ -18576,9 +18575,9 @@ This is a symptom of acute chest syndrome. A metric unit of mass concentration defined as the concentration of one gram of a substance per unit volume of the mixture equal to one cubic meter. The concept also refers to the metric unit of mass density (volumic mass) defined as the density of a substance which mass equal to one gram occupies the volume of one cubic meter. - - Sufficient - SCDO:1000505 + + Sufficient + SCDO:1000505 NCIT:C64572 Gram per Cubic Meter Microgram per Milliliter @@ -18611,23 +18610,23 @@ This is a symptom of acute chest syndrome. - + - - + + - - + + A 3-isobutyl derivative of gamma-amino butyric acid (GABA) with anti-convulsant, anti-epileptic, anxiolytic, and analgesic activities. Although the exact mechanism of action is unknown, pregabalin selectively binds to alpha2delta (A2D) subunits of presynaptic voltage-dependent calcium channels (VDCCs) located in the central nervous system (CNS). Binding of pregabalin to VDCC A2D subunits prevents calcium influx and the subsequent calcium-dependent release of various neurotransmitters, including glutamate, norepinephrine, serotonin, dopamine, and substance P, from the presynaptic nerve terminals of hyperexcited neurons; synaptic transmission is inhibited and neuronal excitability is diminished. Pregabalin does not bind directly to GABA-A or GABA-B receptors and does not alter GABA uptake or degradation. - http://purl.obolibrary.org/obo/NCIT_C64625 - Sufficient - SCDO:0008454 + http://purl.obolibrary.org/obo/NCIT_C64625 + Sufficient + SCDO:0008454 NCIT:C64625 3-(Aminomethyl)-5-methyl-hexanoic Acid 3-Isobutyl GABA @@ -18644,9 +18643,9 @@ This is a symptom of acute chest syndrome. A unit of mass concentration defined as the concentration of one gram of a substance per unit volume of the mixture equal to one deciliter (100 milliliters). The concept also refers to the metric unit of mass density (volumic mass) defined as the density of substance which mass equal to one gram occupies the volume one deciliter. - - Sufficient - SCDO:1000620 + + Sufficient + SCDO:1000620 NCIT:C64783 Gram per Deciliter Gram/Deciliter @@ -18662,9 +18661,9 @@ This is a symptom of acute chest syndrome. A unit of mass concentration defined as the concentration of one milligram of a substance in unit volume of the mixture equal to one cubic deciliter or 100 cubic centimeters. It is also a unit of mass density (volumic mass) defined as the density of substance which mass equal to one milligram occupies the volume one cubic deciliter or 100 cubic centimeters. - - Sufficient - SCDO:1000646 + + Sufficient + SCDO:1000646 NCIT:C67015 Milligram per Deciliter Milligram/Deciliter @@ -18679,9 +18678,9 @@ This is a symptom of acute chest syndrome. A unit of cell concentration expressed as a number of cells in thousands per unit volume equal to one microliter. - - Sufficient - SCDO:1000511 + + Sufficient + SCDO:1000511 NCIT:C67244 1000 cells/µL 10E3 Cells/uL @@ -18702,9 +18701,9 @@ This is a symptom of acute chest syndrome. A unit of cell concentration expressed as a number of cells in millions per unit volume equal to one microliter. - - Sufficient - SCDO:1000504 + + Sufficient + SCDO:1000504 NCIT:C67251 10E6 cells/uL 10^6 Cells/uL @@ -18724,9 +18723,9 @@ This is a symptom of acute chest syndrome. Unit of arbitrary substance concentration (biologic activity concentration) defined as the concentration of one international unit per one liter of the system volume. - - Sufficient - SCDO:1000658 + + Sufficient + SCDO:1000658 NCIT:C67376 IE/L International Unit per Liter @@ -18744,11 +18743,11 @@ This is a symptom of acute chest syndrome. - + The calendar date on which a person was born. - - Sufficient - SCDO:1000544 + + Sufficient + SCDO:1000544 NCIT:C68615 BD DOB @@ -18762,12 +18761,12 @@ This is a symptom of acute chest syndrome. - - + + A unique identifier for a subject in a study. - - Sufficient - SCDO:1000469 + + Sufficient + SCDO:1000469 NCIT:C69256 Participant ID Participant Identifier @@ -18794,9 +18793,9 @@ This is a symptom of acute chest syndrome. A unique identifier assigned to each clinical trial subject to protect the subject's identity and used in lieu of the subject's name when the investigator reports adverse events and/or other trial-related data. - http://purl.obolibrary.org/obo/NCIT_C70731 - Sufficient - SCDO:1000002 + http://purl.obolibrary.org/obo/NCIT_C70731 + Sufficient + SCDO:1000002 NCIT:C70731 Clinical Study Subject Unique Identifier Clinical Trial Subject Unique Identifier @@ -18808,11 +18807,11 @@ This is a symptom of acute chest syndrome. - + The formal plan of an experiment or research activity, including the objective, rationale, design, materials and methods for the conduct of the study; intervention description, and method of data analysis. - - Sufficient - SCDO:1000096 + + Sufficient + SCDO:1000096 NCIT:C70817 Study Protocol @@ -18824,9 +18823,9 @@ This is a symptom of acute chest syndrome. A method of ultrasound imaging in which the ultrasound probe is pressed against the skin of the abdomen in order to create an image of the abdominal organs. - - Sufficient - SCDO:0000005 + + Sufficient + SCDO:0000005 NCIT:C71375 Abdominal Sonogram TUS @@ -18841,9 +18840,9 @@ This is a symptom of acute chest syndrome. Difficulties related to an apparatus used to gain access to arteries and veins. - - Sufficient - SCDO:1000389 + + Sufficient + SCDO:1000389 NCIT:C71746 Vascular Access Device Complications @@ -18853,11 +18852,11 @@ This is a symptom of acute chest syndrome. - + Having no known name or identity or known source. - - Sufficient - SCDO:0007242 + + Sufficient + SCDO:0007242 NCIT:C71754 Anonymous @@ -18867,11 +18866,11 @@ This is a symptom of acute chest syndrome. - + Of your own free will or design; not forced or compelled; controlled by individual volition. - - Sufficient - SCDO:0001874 + + Sufficient + SCDO:0001874 NCIT:C74096 Voluntary @@ -18881,13 +18880,13 @@ This is a symptom of acute chest syndrome. - + The quantitative measurement of liver enzymes in the blood, which is useful in assessing the functional state of a patient's liver. Liver function tests include the measurement of albumin, alanine transaminase, aspartate transaminase, alkaline phosphatase, bilirubin, and gamma glutamyl transferase. - Other LFTs to be added here? There are more in NCIT - - PhenX protocol: Liver Function - Assay #190801 - Sufficient - SCDO:0000695 + Other LFTs to be added here? There are more in NCIT + + PhenX protocol: Liver Function - Assay #190801 + Sufficient + SCDO:0000695 NCIT:C74954 LFT Liver Function Assay @@ -18901,11 +18900,11 @@ This is a symptom of acute chest syndrome. - + Hemoglobin subunit alpha (142 aa, ~15 kDa) is encoded by both the human HBA1 and human HBA2 genes. This protein plays a role in the distribution of oxygen from the lungs to other organs and tissues. - - Sufficient - SCDO:1000365 + + Sufficient + SCDO:1000365 NCIT:C75434 Alpha Globin Alpha-Globin @@ -18925,14 +18924,14 @@ This is a symptom of acute chest syndrome. - - + + Examination of the anterior segment of the eye using a medical instrument called a slit lamp. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C75583 - Sufficient - SCDO:0001078 + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C75583 + Sufficient + SCDO:0001078 NCIT:C75583 SLIT LAMP Slit-Lamp Biomicroscopy @@ -18947,9 +18946,9 @@ This is a symptom of acute chest syndrome. Any problem arising from the use of a medical device. - - Sufficient - SCDO:1000385 + + Sufficient + SCDO:1000385 NCIT:C78254 Device Complication @@ -18959,76 +18958,76 @@ This is a symptom of acute chest syndrome. - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Accumulation of iron in the tissues. It may be a manifestation of an inherited disorder (e.g., hemochromatosis) or acquired (in patients with repeated blood transfusions). Symptoms include hepatomegaly, arthritis, diabetes mellitus, and bronzed skin. If untreated it has a progressive course and may lead to death. - Perhaps suggest that NCIT merges this term with "Hemochromatosis", which they have as a separate term. + Perhaps suggest that NCIT merges this term with "Hemochromatosis", which they have as a separate term. Sub-classes need to be worked on further. Consider sub-classes of "hemochromatosis" in the DO. -Include Hemosiderosis as a sub-class? - http://purl.obolibrary.org/obo/NCIT_C78393 - Sufficient - SCDO:0001945 +Include Hemosiderosis as a sub-class? + http://purl.obolibrary.org/obo/NCIT_C78393 + Sufficient + SCDO:0001945 NCIT:C78393 Diabetes Bronze Haemochromatosis @@ -19045,14 +19044,14 @@ Include Hemosiderosis as a sub-class? - - + + An acute or subacute reversible condition characterized by headaches, mental status changes, visual disturbances, and seizures associated with imaging findings of posterior leukoencephalopathy. It has been observed in association with hypertensive encephalopathy, eclampsia, and immunosuppressive and cytotoxic drug treatment. - http://purl.obolibrary.org/obo/NCIT_C78598 - Sufficient - SCDO:0007836 + http://purl.obolibrary.org/obo/NCIT_C78598 + Sufficient + SCDO:0007836 NCIT:C78598 Reversible Posterior Leukoencephalopathy Syndrome Posterior Reversible Leukoencephalopathy @@ -19065,9 +19064,9 @@ Include Hemosiderosis as a sub-class? The development of a blood clot in a catheter. - - Sufficient - SCDO:1000388 + + Sufficient + SCDO:1000388 NCIT:C78638 Thrombus in Catheter @@ -19077,17 +19076,17 @@ Include Hemosiderosis as a sub-class? - + A parent report or patient self report for measuring health-related quality of life (HRQOL) in healthy children and adolescents and those with acute and chronic health conditions. The PedsQL Measurement Model uses a modular approach that integrates both generic core scales and disease-specific modules into one measurement system. (Copyright 1998-2008 James W. Varni, Ph.D.) + + Self; Proxy (Parent report) + Clinic patients + Many measures available in Spanish, French and Portuguese + Toddlers; Children; Adolescents + yes + Sufficient + SCDO:0000875 Varni, J. W., Seid, M., and Kurtin, P. S. (2001). PedsQL 4.0: Reliability and validity of the 86 pediatric quality of life inventory version 4.0 generic core scales in healthy and patient populations. Medical Care, 39, 800-812. - - Self; Proxy (Parent report) - Clinic patients - Many measures available in Spanish, French and Portuguese - Toddlers; Children; Adolescents - yes - Sufficient - SCDO:0000875 NCIT:C78652 Pediatric Quality of Life Inventory PedsQL @@ -19099,11 +19098,11 @@ Include Hemosiderosis as a sub-class? - + A sample of blood applied in a thin film to a microscope slide for study under a microscope. - - Sufficient - SCDO:0008915 + + Sufficient + SCDO:0008915 NCIT:C79903 Blood Smear @@ -19113,35 +19112,35 @@ Include Hemosiderosis as a sub-class? - + - - + + - - + + - - + + - - + + A diagnostic procedure in which a catheter is guided into the right heart, where pressures may be measured and radiocontrast material may be injected to visualize blood flow in and around the right heart. - http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C80411 - Sufficient - SCDO:0001012 + http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C80411 + Sufficient + SCDO:0001012 NCIT:C80411 Pulmonary Artery Catheterization Swan-Ganz Catheterization @@ -19153,12 +19152,12 @@ Include Hemosiderosis as a sub-class? - + A description of an individual's current and past experience with alcoholic beverage consumption. - Add other terms in the PhenX "Alcohol Use" collection? - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C81229 - Sufficient - SCDO:0000040 + Add other terms in the PhenX "Alcohol Use" collection? + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C81229 + Sufficient + SCDO:0000040 NCIT:C81229 Alcohol Use History @@ -19170,9 +19169,9 @@ Include Hemosiderosis as a sub-class? An identifying number within an institution that is used to reference a subject's medical information. - - Sufficient - SCDO:1000853 + + Sufficient + SCDO:1000853 NCIT:C81262 Medical Record Number @@ -19184,9 +19183,9 @@ Include Hemosiderosis as a sub-class? Anemia not associated with symptoms of fatigue, headaches, palpitations, or shortness of breath. In asymptomatic anemia the hematocrit levels usually range from 32 to 35%. - http://purl.obolibrary.org/obo/NCIT_C82909 - Sufficient - SCDO:0003672 + http://purl.obolibrary.org/obo/NCIT_C82909 + Sufficient + SCDO:0003672 NCIT:C82909 Mild Anemia @@ -19197,11 +19196,11 @@ Include Hemosiderosis as a sub-class? - + The date on which a visit occurred. - - Sufficient - SCDO:1000540 + + Sufficient + SCDO:1000540 NCIT:C83031 Clinical Visit Date Visit Date @@ -19214,9 +19213,9 @@ Include Hemosiderosis as a sub-class? An inherited metabolic disorder characterized by iron accumulation in the tissues. - - Sufficient - SCDO:0000512 + + Sufficient + SCDO:0000512 NCIT:C84481 Congenital Haemochromatosis Hereditary Haemochromatosis @@ -19230,11 +19229,11 @@ Include Hemosiderosis as a sub-class? - + Hemoglobin subunit epsilon (147 aa, ~16 kDa) is encoded by the human HBE1 gene. This protein plays a role in the transport of oxygen to tissues of the embryo. - http://purl.obolibrary.org/obo/NCIT_C84979 - Sufficient - SCDO:0001381 + http://purl.obolibrary.org/obo/NCIT_C84979 + Sufficient + SCDO:0001381 NCIT:C84979 Epsilon-Globin Haemoglobin Epsilon Chain @@ -19248,12 +19247,12 @@ Include Hemosiderosis as a sub-class? - + A type of polypeptide chain that when in combination with alpha globin polypeptide chains forms adult hemoglobin 2 (HbA2). HbA2 comprises around 3% of adult hemoglobin. Hemoglobin subunit delta (147 aa, ~16 kDa) is encoded by the human HBD gene. This protein plays a role in the transport of oxygen to tissues of the adult body. - http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C84980 - https://www.ncbi.nlm.nih.gov/gene/3045 - Sufficient - SCDO:1000011 + http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C84980 + https://www.ncbi.nlm.nih.gov/gene/3045 + Sufficient + SCDO:1000011 NCIT:C84980 Delta Globin Delta-Globin @@ -19268,11 +19267,11 @@ Include Hemosiderosis as a sub-class? - + Hemoglobin subunit beta (147 aa, ~16 kDa) is encoded by the human HBB gene. This protein plays a role in the transport of oxygen to tissues of the adult body. - - Sufficient - SCDO:1000358 + + Sufficient + SCDO:1000358 NCIT:C84983 Beta Globin Beta Globin Chain @@ -19290,71 +19289,71 @@ Include Hemosiderosis as a sub-class? - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Measurement of the breathing capacity of the lung by means of a spirometer. - - Sufficient - SCDO:0001100 + + Sufficient + SCDO:0001100 NCIT:C85397 Spirometry @@ -19366,9 +19365,9 @@ Include Hemosiderosis as a sub-class? A product of hemoglobin produced by oxidation of the iron atom from the ferrous to the ferric state. - - Sufficient - SCDO:1000167 + + Sufficient + SCDO:1000167 NCIT:C86008 MetHb Methemoglobin @@ -19379,11 +19378,11 @@ Include Hemosiderosis as a sub-class? - + An instrument consisting of a predetermined set of questions for a clinical or research assessment. - - Sufficient - SCDO:1000476 + + Sufficient + SCDO:1000476 NCIT:C91105 Clinical or Research Assessment Questionnaire @@ -19393,11 +19392,11 @@ Include Hemosiderosis as a sub-class? - + A statement (either spoken or written) that is made in reply to a clinical research assessment question. - - Sufficient - SCDO:1000473 + + Sufficient + SCDO:1000473 NCIT:C91106 Clinical or Research Assessment Response Clinical or Research Assessment Answer @@ -19408,11 +19407,11 @@ Include Hemosiderosis as a sub-class? - + The biopsy of placental tissue containing the chorionic villi from the maternal uterus in early pregnancy to diagnose fetal genetic defects. - http://purl.obolibrary.org/obo/NCIT_C92755 - Sufficient - SCDO:0000223 + http://purl.obolibrary.org/obo/NCIT_C92755 + Sufficient + SCDO:0000223 NCIT:C92755 CVS Chorionic Villus Sampling @@ -19425,9 +19424,9 @@ Include Hemosiderosis as a sub-class? Testing to determine if there is a predisposition or indication of a possible genetic or a chromosomal abnormality. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C92803 - Sufficient - SCDO:0000446 + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C92803 + Sufficient + SCDO:0000446 NCIT:C92803 Genetic Screening @@ -19442,20 +19441,20 @@ Include Hemosiderosis as a sub-class? - - + + - - + + Hemorrhage defined as a blood loss in excess of 500 mL after vaginal delivery or more than 1000 mL after a cesarean delivery. - - Sufficient - SCDO:0000916 + + Sufficient + SCDO:0000916 NCIT:C92853 Postpartum Hemorrhage @@ -19465,11 +19464,11 @@ Include Hemosiderosis as a sub-class? - + Specific key measurement(s) or observation(s) used to measure the effect of experimental variables on the subjects in a study, or for observational studies, to describe patterns of diseases or traits or associations with exposures, risk factors or treatment. The specific measure that receives the most emphasis in assessment. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C93407 - Sufficient - SCDO:0001116 + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C93407 + Sufficient + SCDO:0001116 NCIT:C93407 Study Outcome Measure Study Outcome Measurement @@ -19481,41 +19480,41 @@ Include Hemosiderosis as a sub-class? - + - - + + - - + + - - + + - - + + - - + + An acute inflammatory process that leads to necrosis of the pancreatic parenchyma. Signs and symptoms include severe abdominal pain, nausea, vomiting, diarrhea, fever, and shock. Causes include alcohol consumption, presence of gallstones, trauma, and drugs. - http://purl.obolibrary.org/obo/NCIT_C95437 - Sufficient - SCDO:0005115 + http://purl.obolibrary.org/obo/NCIT_C95437 + Sufficient + SCDO:0005115 NCIT:C95437 Acute Pancreatitis @@ -19525,71 +19524,71 @@ Include Hemosiderosis as a sub-class? - + - - + + - - + + - + - - + + - - + + - + - - + + - + - + - - + + A form of alpha thalassemia that results from reduced protein production from three of the four alpha-globin genes. Clinically it is characterized by chronic hemolytic anemia. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C95504 - Sufficient - SCDO:0000534 + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C95504 + Sufficient + SCDO:0000534 NCIT:C95504 Alpha-Thalassemia Intermedia Haemoglobin H Disease @@ -19602,12 +19601,12 @@ Include Hemosiderosis as a sub-class? - + A condition in which a person is heterozygous for a globin gene, with one normal allele and one defective allele. - NCIT includes this class below "Hemoglobinopathy", hence its inclusion here. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C95534 - Sufficient - SCDO:0000550 + NCIT includes this class below "Hemoglobinopathy", hence its inclusion here. + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C95534 + Sufficient + SCDO:0000550 NCIT:C95534 Heterozygous Hemoglobinopathy Hemoglobin Trait @@ -19618,42 +19617,42 @@ Include Hemosiderosis as a sub-class? - + - - + + - - + + - + - - + + - + A condition in which a person has reduced protein production from two of the four alpha-globin alleles. + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C95535 + Sufficient + SCDO:0000044 - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C95535 - Sufficient - SCDO:0000044 NCIT:C95535 Alpha-Thalassemia Trait -/- alpha/alpha or -/alpha -/alpha. It can exist in two forms: (1) alpha-thal-1 (alpha alpha/--), involves cis deletion of both alpha genes on the same chromosome; (2) alpha-thal-2 (alpha-/alpha-), involves trans deletion of alpha genes this occurs on different (homologous) chromosomes. @@ -19665,30 +19664,30 @@ Include Hemosiderosis as a sub-class? - + - + - - + + - + A condition in which a person has reduced protein production from one of the four alpha-globin alleles. + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C95536 + Sufficient + SCDO:0000043 - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C95536 - Sufficient - SCDO:0000043 NCIT:C95536 Alpha Thalassemia Silent Alpha-Thalassemia Silent Carrier @@ -19700,125 +19699,125 @@ Include Hemosiderosis as a sub-class? - + - + - + - - + + - - + + - - + + - - + + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A compound heterozygous state in which a person has a hemoglobin S allele along with a beta-thalassemia allele. The severity of the condition is determined to a large extent by the quantity of normal hemoglobin produced by the beta-thalassemia gene. - - Sufficient - SCDO:0001057 + + Sufficient + SCDO:0001057 NCIT:C95539 Hb S-Beta Thalassemia HbS-Beta-Thalassemia Syndrome @@ -19842,9 +19841,9 @@ Include Hemosiderosis as a sub-class? A morphologic finding indicating enlargement of the glomeruli in a kidney specimen. - - Sufficient - SCDO:0002784 + + Sufficient + SCDO:0002784 NCIT:C96239 Glomerular Hypertrophy @@ -19857,38 +19856,38 @@ Include Hemosiderosis as a sub-class? - - + + - - + + - - + + - - + + - - + + A conjugate vaccine of meningococcal polysaccharide used for active immunization against invasive meningococcal disease caused by Neisseria meningiditis serogroups A, C, Y, and W-135. - http://purl.obolibrary.org/obo/NCIT_C96391 - Sufficient - SCDO:0006120 + http://purl.obolibrary.org/obo/NCIT_C96391 + Sufficient + SCDO:0006120 NCIT:C96391 MCV4 Menactra @@ -19905,9 +19904,9 @@ Include Hemosiderosis as a sub-class? An active immunizing vaccine used to prevent infection by the bacterium Streptococcus pneumoniae. It is indicated for disease caused by serotypes 1, 5, 4, 6B, 7, 9V, 14, 18C, 19F, and 23F. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C97120 - Sufficient - SCDO:0000909 + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C97120 + Sufficient + SCDO:0000909 NCIT:C97120 PCV 10 Pneumococcal 10-Valent Conjugate Vaccine @@ -19921,38 +19920,38 @@ Include Hemosiderosis as a sub-class? - - + + - - + + - - + + - - + + - - + + A pneumococcal conjugate vaccine containing 13 different strains of the bacterium Streptococcus pneumoniae, used in children and studied in immunocompromised patients for the prevention of pneumococcal disease. The pneumococcal 13-valent conjugate vaccine contains capsular antigen polysaccharides derived from the S. pneumoniae serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F and 23F that are individually conjugated to a nontoxic diphtheria cross-reactive material (CRM) carrier protein (CRM197). Upon vaccination, pneumococcal 13-valent conjugate vaccine induces active immunization against 13 different serotypes of S. pneumoniae and protects against pneumococcal disease. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C97121 - Sufficient - SCDO:0000910 + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C97121 + Sufficient + SCDO:0000910 NCIT:C97121 PCV 13 PCV13 Vaccine @@ -19968,68 +19967,68 @@ Include Hemosiderosis as a sub-class? - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An active immunizing vaccine used to prevent infection by the bacterium Streptococcus pneumoniae. It consists of a solution of saccharides of the capsular antigens of Streptococcus serotypes individually conjugated to proteins. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C97123 - Sufficient - SCDO:0000275 + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C97123 + Sufficient + SCDO:0000275 NCIT:C97123 Pneumococcal Conjugate Vaccine Conjugate Pneumococcal Vaccine @@ -20040,11 +20039,11 @@ Include Hemosiderosis as a sub-class? - + Methemoglobinemia that is caused by exposure to certain drugs (xylocaine and benzene) and nitrate-rich foods. - - Sufficient - SCDO:0000013 + + Sufficient + SCDO:0000013 NCIT:C98805 Acquired Methemoglobinemia @@ -20057,123 +20056,123 @@ Include Hemosiderosis as a sub-class? - + - + - - + + - - + + - - + + - - + + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A form of sickle cell thalassemia characterized by the absence of hemoglobin A. Patients usually have severe anemia identical to that seen in sickle cell disease. - Requires further refinement. - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C98835 - Sufficient - SCDO:0001058 + Requires further refinement. + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C98835 + Sufficient + SCDO:0001058 NCIT:C98835 Hb S Beta 0 Thalassemia Hemoglobin S Beta 0 Thalassemia @@ -20195,14 +20194,14 @@ Include Hemosiderosis as a sub-class? - - + + The formation of a thrombus in the renal vein. - http://purl.obolibrary.org/obo/NCIT_C99042 - Sufficient - SCDO:0005061 + http://purl.obolibrary.org/obo/NCIT_C99042 + Sufficient + SCDO:0005061 NCIT:C99042 Renal Vein Thrombosis @@ -20215,21 +20214,21 @@ Include Hemosiderosis as a sub-class? - - + + - - + + Ischemic necrosis of the spinal cord caused by occlusion of the arteries that supply blood to the spinal cord. Signs and symptoms include intermittent back pain, pain in the legs, paralysis, and incontinence. - Can be treated with exchange transfusion (SCDO:0001303) - http://purl.obolibrary.org/obo/NCIT_C99063 - Sufficient - SCDO:0005226 + Can be treated with exchange transfusion (SCDO:0001303) + http://purl.obolibrary.org/obo/NCIT_C99063 + Sufficient + SCDO:0005226 NCIT:C99063 Spinal Cord Infarction @@ -20239,12 +20238,12 @@ Include Hemosiderosis as a sub-class? - + An assay that produces a picture of an entity. - Perhaps replace this term with "Diagnostic Imaging" from NCIT? - http://purl.obolibrary.org/obo/OBI_0000185 - Sufficient - SCDO:0000612 + Perhaps replace this term with "Diagnostic Imaging" from NCIT? + http://purl.obolibrary.org/obo/OBI_0000185 + Sufficient + SCDO:0000612 OBI:0000185 Imaging Assay @@ -20254,12 +20253,12 @@ Include Hemosiderosis as a sub-class? - + A sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument. - Add sub-class "beta-globin gene sequencing" as per the "Diagnostic Methods" section of the term "Dominant beta-thalassemia" in Orphanet. - - Sufficient - SCDO:0004249 + Add sub-class "beta-globin gene sequencing" as per the "Diagnostic Methods" section of the term "Dominant beta-thalassemia" in Orphanet. + + Sufficient + SCDO:0004249 OBI:0000626 DNA Sequencing @@ -20269,11 +20268,11 @@ Include Hemosiderosis as a sub-class? - + A material entity bearing the disposition to infect an organism - - Sufficient - SCDO:0000638 + + Sufficient + SCDO:0000638 OBI:0000925 Infectious Agent @@ -20285,9 +20284,9 @@ Include Hemosiderosis as a sub-class? A microscope that produces an image of an object by targeting it with an electron beam. - - Sufficient - SCDO:0000422 + + Sufficient + SCDO:0000422 OBI:0000990 It is capable of much higher magnifications and has a greater resolving power than a light microscope, allowing it to see much smaller objects in finer detail. Electron Microscope @@ -20298,17 +20297,17 @@ Include Hemosiderosis as a sub-class? - + - + A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs. - - Sufficient - SCDO:0001202 + + Sufficient + SCDO:0001202 OBI:0001098 Ultrasound Machine @@ -20318,23 +20317,23 @@ Include Hemosiderosis as a sub-class? - + - - + + - - + + A device that is used to generate X-rays. - http://purl.obolibrary.org/obo/OBI_0001138 - Sufficient - SCDO:0001251 + http://purl.obolibrary.org/obo/OBI_0001138 + Sufficient + SCDO:0001251 OBI:0001138 Radiographic Unit X-Ray Machine @@ -20345,11 +20344,11 @@ Include Hemosiderosis as a sub-class? - + An assay to determine the temperature of an evaluant. - - Sufficient - SCDO:1000752 + + Sufficient + SCDO:1000752 OBI:0002140 Temperature Measurement Assay @@ -20359,12 +20358,12 @@ Include Hemosiderosis as a sub-class? - + An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens. + + Sufficient + SCDO:1000195 - - Sufficient - SCDO:1000195 OBI:0002146 HIV Antibody Assay The window period for antibody tests in most people is somewhere between 3 to 12 weeks from the time of infection. @@ -20376,11 +20375,11 @@ Include Hemosiderosis as a sub-class? - + A value specifcation that specifies the youngest age when specifying an age range. - - Sufficient - SCDO:1000405 + + Sufficient + SCDO:1000405 OBI:0002556 Minimum Age Value Specification @@ -20390,11 +20389,11 @@ Include Hemosiderosis as a sub-class? - + A value specifcation that specifies the oldest age when specifying an age range. - - Sufficient - SCDO:1000404 + + Sufficient + SCDO:1000404 OBI:0002557 Maximum Age Value Specification @@ -20404,12 +20403,12 @@ Include Hemosiderosis as a sub-class? - + A data transformation that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules). + + Sufficient + SCDO:0001138 - - Sufficient - SCDO:0001138 OBI:0200198 MS/MS Tandem MS @@ -20422,11 +20421,11 @@ Include Hemosiderosis as a sub-class? - + A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance. - - Sufficient - SCDO:0001096 + + Sufficient + SCDO:0001096 OBI:0400115 Spectrophotometer @@ -20436,11 +20435,11 @@ Include Hemosiderosis as a sub-class? - + A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope). - - Sufficient - SCDO:0000757 + + Sufficient + SCDO:0000757 OBI:0400169 Microscope @@ -20450,47 +20449,47 @@ Include Hemosiderosis as a sub-class? - + - - + + - - + + - - + + - - + + - - + + - - + + A disease characterized by abnormal and uncontrolled cell division. - http://purl.obolibrary.org/obo/OBI_1110053 - Sufficient - SCDO:0000180 + http://purl.obolibrary.org/obo/OBI_1110053 + Sufficient + SCDO:0000180 OBI:1110053 Malignancy Malignant Neoplasia @@ -20505,13 +20504,13 @@ Include Hemosiderosis as a sub-class? - + A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. - Sub-classes to be added?: -- increased lactate dehydrogenase level (in Ontology of Adverse Events AOE) -- decreased lactate dehydrogenase level (Mammalian Phenotype Ontology) -- Splenomegaly (link this to Spleen Examination) -- Obstructive Hydrocephalus (see "Cerebellar Hemorrhage") -- Failure to Thrive (MeSH) -- Cardiac Output, Low (MeSH) -- Cardiac Output, High (MeSH) -- -Add the sub-class "Clinical Phenotype" from Ontology for General Medical Science - http://bioportal.bioontology.org/ontologies/OGMS?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000023 - Sufficient - SCDO:0000893 + Sub-classes to be added?: -- increased lactate dehydrogenase level (in Ontology of Adverse Events AOE) -- decreased lactate dehydrogenase level (Mammalian Phenotype Ontology) -- Splenomegaly (link this to Spleen Examination) -- Obstructive Hydrocephalus (see "Cerebellar Hemorrhage") -- Failure to Thrive (MeSH) -- Cardiac Output, Low (MeSH) -- Cardiac Output, High (MeSH) -- +Add the sub-class "Clinical Phenotype" from Ontology for General Medical Science + http://bioportal.bioontology.org/ontologies/OGMS?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000023 + Sufficient + SCDO:0000893 OGMS:0000023 Phenotype @@ -20523,9 +20522,9 @@ Add the sub-class "Clinical Phenotype" from Ontology for General Medic A clinically abnormal phenotype that is characteristic of a single disease. - - Sufficient - SCDO:1000185 + + Sufficient + SCDO:1000185 OGMS:0000028 Disease Phenotype @@ -20535,11 +20534,11 @@ Add the sub-class "Clinical Phenotype" from Ontology for General Medic - + A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence. - http://purl.obolibrary.org/obo/OGMS_0000046 - Sufficient - SCDO:0000439 + http://purl.obolibrary.org/obo/OGMS_0000046 + Sufficient + SCDO:0000439 OGMS:0000046 Epigenomic Disorder Epigenetic Disorder @@ -20551,11 +20550,11 @@ Add the sub-class "Clinical Phenotype" from Ontology for General Medic - + A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome. - http://purl.obolibrary.org/obo/OGMS_0000047 - Sufficient - SCDO:0000445 + http://purl.obolibrary.org/obo/OGMS_0000047 + Sufficient + SCDO:0000445 OGMS:0000047 Genetic Disorder @@ -20567,10 +20566,10 @@ Add the sub-class "Clinical Phenotype" from Ontology for General Medic A genetic disorder inherited during conception that is part of all cells in the organism. - Perhaps remove this class but keep sub-classes? Or include the class "Acquired Genetic Disorder" as a sibling of this class if terms are included that can be sub-classes of it? - http://purl.obolibrary.org/obo/OGMS_0000051 - Sufficient - SCDO:0000279 + Perhaps remove this class but keep sub-classes? Or include the class "Acquired Genetic Disorder" as a sibling of this class if terms are included that can be sub-classes of it? + http://purl.obolibrary.org/obo/OGMS_0000051 + Sufficient + SCDO:0000279 OGMS:0000051 Constitutional Genetic Disorder @@ -20580,11 +20579,11 @@ Add the sub-class "Clinical Phenotype" from Ontology for General Medic - + A communication from a patient about something they perceive as being abnormal about their body or life. - http://purl.obolibrary.org/obo/OGMS_0000088 - Sufficient - SCDO:0000872 + http://purl.obolibrary.org/obo/OGMS_0000088 + Sufficient + SCDO:0000872 OGMS:0000088 Patient Symptom Report @@ -20596,9 +20595,9 @@ Add the sub-class "Clinical Phenotype" from Ontology for General Medic An answer to question where the answer is Yes. - - Sufficient - SCDO:1000563 + + Sufficient + SCDO:1000563 OPMI:0000023 yes answer to question Yes @@ -20611,9 +20610,9 @@ Add the sub-class "Clinical Phenotype" from Ontology for General Medic An answer to question where the answer is No. - - Sufficient - SCDO:1000564 + + Sufficient + SCDO:1000564 OPMI:0000024 no answer to question No @@ -20626,9 +20625,9 @@ Add the sub-class "Clinical Phenotype" from Ontology for General Medic An answer to question that indicates the response to the specified question is unknown. - - Sufficient - SCDO:1000562 + + Sufficient + SCDO:1000562 OPMI:0000025 Don't know unknown answer to question @@ -20642,9 +20641,9 @@ Add the sub-class "Clinical Phenotype" from Ontology for General Medic An answer to question where one declines to answer the specified question. - - Sufficient - SCDO:1000561 + + Sufficient + SCDO:1000561 OPMI:0000027 Refuse to answer Refused to answer @@ -20660,9 +20659,9 @@ Add the sub-class "Clinical Phenotype" from Ontology for General Medic An answer to question that is not enumerated in the list and then may be entered with free text in a separate text box - - Sufficient - SCDO:1000565 + + Sufficient + SCDO:1000565 OPMI:0000028 other answer to question Other @@ -20675,10 +20674,10 @@ Add the sub-class "Clinical Phenotype" from Ontology for General Medic A protein that is a translation product of the human SELL gene or a 1:1 ortholog thereof. It is a leukocyte adhesion receptor that play an important role in regulating the inflammatory response by mediating leukocyte tethering and rolling on adherent leukocytes. + + Sufficient + SCDO:1000443 - - Sufficient - SCDO:1000443 PR:000001318 CD62 Antigen-Like Family Member L CD62L @@ -20694,9 +20693,9 @@ Add the sub-class "Clinical Phenotype" from Ontology for General Medic Single-stranded RNA molecules thought to regulate the expression of other genes. miRNAs are encoded by genes that are transcribed from DNA but not translated into protein (non-coding RNA). - - Sufficient - SCDO:0000756 + + Sufficient + SCDO:0000756 SBO:0000316 miRNA MicroRNA @@ -20704,877 +20703,313 @@ Add the sub-class "Clinical Phenotype" from Ontology for General Medic - + - - - Genome wide association study is a kind of study whose objective is to detect association between genetic markers (SNP or otherwise) accross the genome and a trait which may be a disease or another phenotype (e.g. trait of agronomic relevance in animal or plant studies). Genome wide association study compare the allele frequencies in 2 populations, one free of the trait used as control, the other one showing the trait use as 'case'. GWAS studies implement case-control design. - http://purl.obolibrary.org/obo/STATO_0000091 - Sufficient - SCDO:0000450 - STATO:0000091 - GWAS - Genome Wide Association Study + + + The performance of the basic activities of self care, such as dressing, ambulation, or eating. + http://purl.bioontology.org/ontology/MESH/D000203 + Sufficient + SCDO:0000006 + MESH:D000203 + ADL + Daily Living Activities + Daily Living Activity + Self Care (Rehabilitation) + Self-Care + Ability to Carry Out Activities of Daily Living - + - - - - - - - - - - + + + + A structurally abnormal hemoglobin that occurs in one or more forms of Sickle Cell Disease (SCD). + Probably too specific to SCD be included in other ontologies. + None + SCDO (Jade Hotchkiss) + Structurally Abnormal Hemoglobin Present in SCD + Abnormal Hemoglobin in SCD + + + + + + + + + Abnormality in structure and function of the Red Blood Cell. + Are there other relevant erythrocyte abnormalities that can be included as children here? If not, this class can be removed and just keep "Abnormal Hemoglobin". + http://purl.obolibrary.org/obo/HP_0001877 + Sufficient + Abnormality of Red Blood Cell + Abnormality of Red Blood Cells + deprecated Abnormality of Erythrocytes + true + + + + + + + + + - - + + - - + + - - + + - - + + - A neurological and physiological symptom characterized by a painful or apprehensive uneasiness of mind usually over an impending or anticipated ill. - http://www.apa.org/topics/anxiety/ - http://purl.obolibrary.org/obo/SYMP_0000412 - Sufficient - SCDO:0000068 - SYMP:0000412 - Anxiety Symptoms - Panic - Worry - Physical symptoms include increased blood pressure (rapid heartbeat), trembling or dizziness. - Anxiety - - - - - - - - - - + + - - + + - - + + - - + + - - + + - Muscle pain is a pain characterized by pain in one or more muscles. - Provide source for additional info - http://purl.obolibrary.org/obo/SYMP_0019161 - Over-stretching of one muscle or a group of muscles, trauma, infections ( influenza, Lyme, Ebola, Dengue fever, Chicungunya fever, Babesiosis, Malaria, Toxoplasmosis, Hemorrhage fever, polio, Rocky Mountain spotted fever, Trichinosis), vaccines, muscle hematoma, autoimmune disorders ( lupus, polymyalgia, polymyositis, nutricional deficiencies, chronic fatigue syndrome, acute rejection after heart transplant surgery, rhabdomyolysis, severe potassium deficiency, fibromialgia, muscle abscess , reaction to drugs ( statins, fibrates, ACE inhibitors, cocaine), repetitive strain injury,withdrawal syndrome of certain drugs ( corticosteroids, opioids, barbiturates, benzodiazepines, caffeine, alcohol). - Pain of a muscle or a group of muscles. - Sufficient - SCDO:0000779 - SYMP:0019161 - Myalgia - Muscle Pain - - - - - - - - - A standardized quantity of a physical quality. - - Sufficient - SCDO:1000478 - UO:0000000 - Unit - Unit of Measure - Units - Unit of Measurement - - - - - - - - - A unit which is a standard measure of the distance between two points. - - Sufficient - SCDO:1000864 - UO:0000001 - Length Unit - - - - - - - - - A unit which is a standard measure of the amount of matter/energy of a physical object. - - Sufficient - SCDO:1000628 - UO:0000002 - Mass Unit - - - - - - - - - A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. - - Sufficient - SCDO:1000712 - UO:0000005 - Temperature Unit - - - - - - - - - A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. - - Sufficient - SCDO:1000867 - UO:0000009 - Kilogram - - - - - - - - - A length unit which is equal to one hundredth of a meter or 10^[-2] m. - - Sufficient - SCDO:1000865 - UO:0000015 - Centimeter - - - - - - - - - A mass unit which is equal to 10^[-12] g. - - Sufficient - SCDO:1000629 - UO:0000025 - picogram - pg - - - - - - - - - A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. - - Sufficient - SCDO:1000491 - UO:0000051 - Concentration Unit - - - - - - - - - A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. - - Sufficient - SCDO:1000622 - UO:0000095 - Volume Unit - - - - - - - - - A volume unit which is equal to 10^[-15] L. - - Sufficient - SCDO:1000623 - UO:0000104 - cubic micrometre - femtoliter - femtolitre - μm^3 - fL - - - - - - - - - A unit which is a standard measure of the force applied to a given area. - - Sufficient - SCDO:1000720 - UO:0000109 - Pressure Unit - - - - - - - - - A concentration unit which is a standard measure of the mass of a substance in a given volume (density). - - Sufficient - SCDO:1000506 - UO:0000180 - Unit of Density - Definition from BioAssay Ontology - Mass Per Unit Volume - - - - - - - - - A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. - - Sufficient - SCDO:1000642 - UO:0000186 - Dimensionless Unit - - - - - - - - - A dimensionless ratio unit which denotes numbers as fractions of 100. - - Sufficient - SCDO:1000644 - UO:0000187 - % - Percent - - - - - - - - - A dimensionless unit which denotes an amount or magnitude of one quantity relative to another. - - Sufficient - SCDO:1000643 - UO:0000190 - Ratio + Analgesic antipyretic derivative of acetanilide. It has weak anti-inflammatory properties and is used as a common analgesic, but may cause liver, blood cell, and kidney damage. + + Sufficient + SCDO:0000010 + MESH:D000082 + Paracetamol + Tylenol + Acetaminophen - + - - - A concentration unit which denotes the average cell number in a given volume. - - Sufficient - SCDO:1000503 - UO:0000200 - Cell Concentration Unit + + + + A condition that co-exists or follows from sickle cell disease and that has a severe and rapid onset of symptoms with short duration. + Probably too specific to warrant inclusion into anther ontology. + None + SCDO + http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C14140 + http://purl.bioontology.org/ontology/MESH/Q000150 + Acute Complications of SCD + Acute Complications of Sickle Cell Disease - - - - - A unit of pressure equal to the amount of fluid pressure one millimeter deep in mercury at zero degrees centigrade on Earth. - - Sufficient - SCDO:1000721 - UO:0000272 - millimetres of mercury - mmHg - - - + - - - - - A unit which represents a standard measurement occurrence of a process per unit time. - - Sufficient - SCDO:1000715 - UO:0000280 - Rate Unit - - - - - + + + + + + + + + + + + + + + + + + + + + + An acute onset of wheezing in a person with SCD who has no co-morbid asthma. + Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info. + Cohen et al 2011 Am J Hematol., Glassberg et al 2014 Curr Opin Pediatr., Knight-Madden et al 2014 Ped Resp Rev + Etiology may be unclear. May be related to inflammation of SCD and/or viral lower respiratory tract infection. + Normal Chest X-ray + None + Cohen et al 2011 Am J Hematol., Glassberg et al 2014 Curr Opin Pediatr., Knight-Madden et al 2014 Ped Resp Rev + Too specific to SCD to be included in other ontologies? - - - A unit of cell concentration which is equal to one cell in a volume of 1 microliter. - - Sufficient - SCDO:1000507 - UO:0000316 - cells per microliter - cells/µL - cells per microliter +PFTs may be done to asses for airway hyper-responsiveness. + Acute Non-Specific Wheezing Episode - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - - - - A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine. - http://purl.obolibrary.org/obo/VO_0000001 - Sufficient - SCDO:0001221 - VO:0000001 - Vaccine - - - - - - - - - - - - - - - A viral vaccine that protects against infection with influenza virus. - http://purl.obolibrary.org/obo/VO_0000642 - Sufficient - SCDO:0000642 - VO:0000642 - Influenza Virus Vaccine - - - - - - - - - - - - - - - - - - - - - - - - - - - A Streptococcal vaccine that is used against S. pneumoniae infection, which causes pneumococcal diseases. - http://purl.obolibrary.org/obo/VO_0000675 - Sufficient - SCDO:0001109 - VO:0000675 - Pneumococcal Vaccine - Streptococcus Pneumoniae Vaccine - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The amount of alkaline phosphatase present in a specified volume of blood. - The proportion, quantity, or volume in whole blood, serum, or plasma of this enzyme, which hydrolyzes orthophosphoric monoesters. - - Sufficient - SCDO:1000499 - VT:0000202 - AP Level - Blood Alkaline Phosphatase Amount - Circulating ALP Level - Circulating Alkaline Phosphatase Level - Alkaline Phosphatase Level - - - - - - - - - The performance of the basic activities of self care, such as dressing, ambulation, or eating. - http://purl.bioontology.org/ontology/MESH/D000203 - Sufficient - SCDO:0000006 - MESH:D000203 - ADL - Daily Living Activities - Daily Living Activity - Self Care (Rehabilitation) - Self-Care - Ability to Carry Out Activities of Daily Living - - - - - - - - - - A structurally abnormal hemoglobin that occurs in one or more forms of Sickle Cell Disease (SCD). - SCDO (Jade Hotchkiss) - Probably too specific to SCD be included in other ontologies. - None - Structurally Abnormal Hemoglobin Present in SCD - Abnormal Hemoglobin in SCD - - - - - - - - - Abnormality in structure and function of the Red Blood Cell. - Are there other relevant erythrocyte abnormalities that can be included as children here? If not, this class can be removed and just keep "Abnormal Hemoglobin". - http://purl.obolibrary.org/obo/HP_0001877 - Sufficient - Abnormality of Red Blood Cell - Abnormality of Red Blood Cells - deprecated Abnormality of Erythrocytes - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Analgesic antipyretic derivative of acetanilide. It has weak anti-inflammatory properties and is used as a common analgesic, but may cause liver, blood cell, and kidney damage. - - Sufficient - SCDO:0000010 - MESH:D000082 - Paracetamol - Tylenol - Acetaminophen - - - - - - - - - - A condition that co-exists or follows from sickle cell disease and that has a severe and rapid onset of symptoms with short duration. - SCDO - http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C14140 - http://purl.bioontology.org/ontology/MESH/Q000150 - Probably too specific to warrant inclusion into anther ontology. - None - Acute Complications of SCD - Acute Complications of Sickle Cell Disease - - - - - - - - - - - - - - - - - - - - - - - - - - - - An acute onset of wheezing in a person with SCD who has no co-morbid asthma. - Cohen et al 2011 Am J Hematol., Glassberg et al 2014 Curr Opin Pediatr., Knight-Madden et al 2014 Ped Resp Rev - Check and show which source was used for the description and whether the description was adapted from the source. -- Provide source for additional info. - Cohen et al 2011 Am J Hematol., Glassberg et al 2014 Curr Opin Pediatr., Knight-Madden et al 2014 Ped Resp Rev - Etiology may be unclear. May be related to inflammation of SCD and/or viral lower respiratory tract infection. - Normal Chest X-ray - None - Too specific to SCD to be included in other ontologies? - -PFTs may be done to asses for airway hyper-responsiveness. - Acute Non-Specific Wheezing Episode - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Sickle cell pain management that aims to heal the acute process. + Request inclusion into MESH below "Pain Management" / "Sickle Cell Pain Management" (also to be suggested for inclusion) + + None SCDO - Request inclusion into MESH below "Pain Management" / "Sickle Cell Pain Management" (also to be suggested for inclusion) - - None Acute Sickle Cell Pain Treatment Acute Sickle Cell Pain Management - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + An acute respiratory illness with no lower respiratory tract signs or infiiltrate on chest radiograph. + Request inclusion into relevant ontology + Few but definitions not freely available SCDO - Request inclusion into relevant ontology - Few but definitions not freely available Acute Upper Respiratory Infection URI URTI @@ -21583,16 +21018,16 @@ PFTs may be done to asses for airway hyper-responsiveness. - + - - + + The extent to which a person's behaviour - taking medications, following a diet and/or executing life style changes, corresponds to agreed recommendations by a health care provider. - + + Suggest update to description for "Patient Compliance" in MESH. + + Suggest update to description - Suggest update to description for "Patient Compliance" in MESH. - - Suggest update to description MESH:D010349 Adherence to Long Term Therapy Patient Adherence @@ -21604,30 +21039,30 @@ PFTs may be done to asses for airway hyper-responsiveness. - + - - + + A 20-item questionnaire that assesses the frequency of severe headaches, the level of pain, whether the person is taking medications, and associated complications such as nausea. - Suggest update to label in PhenX (from "Migraine - Adult") as we have done. - - PhenX protocol: Migraine - Adult #130501 - Suggest update to label + Suggest update to label in PhenX (from "Migraine - Adult") as we have done. + + PhenX protocol: Migraine - Adult #130501 + Suggest update to label phenX:130501 Adult Migraine Questionnaire - + - - + + An adverse event that occurs after a drug administration. - Should this be a sub-class of "Environmental Disease Modifier"? - http://purl.obolibrary.org/obo/OAE_0000005 - Sufficient - SCDO:0000028 + Should this be a sub-class of "Environmental Disease Modifier"? + http://purl.obolibrary.org/obo/OAE_0000005 + Sufficient + SCDO:0000028 OAE:0000005 ADE ADR @@ -21638,14 +21073,14 @@ PFTs may be done to asses for airway hyper-responsiveness. - + - - + + Electrophoresis in which agar or agarose gel is used as the diffusion medium. - http://purl.bioontology.org/ontology/MESH/D004587 - Sufficient - SCDO:0000029 + http://purl.bioontology.org/ontology/MESH/D004587 + Sufficient + SCDO:0000029 MESH:D004587 Agar Gel Electrophoresis Agarose Gel Electrophoresis @@ -21653,53 +21088,53 @@ PFTs may be done to asses for airway hyper-responsiveness. - + - + - + - + - - + + - - + + - - + + - - + + A rare congenital disorder characterized by a partial or complete absence (agenesis) of an area of the brain that connects the two cerebral hemispheres. It can be the result of a failure in any one of the multiple steps of callosal development including cellular proliferation and migration, axonal growth or glial patterning at the midline. - Suggest update to description in HPO. + Suggest update to description in HPO. -Include links to relevant Therapeutics. - - http://rarediseases.org/rare-diseases/agenesis-of-corpus-callosum/ - Suggest update to description +Include links to relevant Therapeutics. + + http://rarediseases.org/rare-diseases/agenesis-of-corpus-callosum/ + Suggest update to description ACC Absence of Corpus Callosum Absent Corpus Callosum @@ -21712,22 +21147,22 @@ Include links to relevant Therapeutics. - + - + - + - - + + A quantitative measurement of alanine aminotransferase present in a blood sample. + Suggest update to description in NCIT (from "Alanine Aminotransferase Measurement") + + Suggest update to description - Suggest update to description in NCIT (from "Alanine Aminotransferase Measurement") - - Suggest update to description NCIT:C64433 ALT Blood Test Alanine Transaminase Blood Test @@ -21739,32 +21174,32 @@ Include links to relevant Therapeutics. - + - + - - + + - + - - + + The amount of alanine aminotransferase present in a specified volume of blood. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None ALT Level Alanine Aminotransferase Level Alanine Transaminase Level @@ -21777,82 +21212,82 @@ Include links to relevant Therapeutics. - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Increased concentration of albumin in the urine; more than 30mg in 24hours or urine albumin creatinine ratio (ACR) >3 mg/mmol. + Suggest update to description in HPO. + + http://www.nice.org.uk/guidance/CG182/chapter/introduction + Suggest update to description in HPO. - Suggest update to description in HPO. - - http://www.nice.org.uk/guidance/CG182/chapter/introduction - Suggest update to description in HPO. HP:0012592 Because albuminuria may be affected by non-pathological factors (exercise, menstruation contamination, biological variability, etc.), abnormal values should be confirmed within 1-2 months. Albuminuria @@ -21860,97 +21295,97 @@ Include links to relevant Therapeutics. - + - + - + - + - - + + - - + + An indication of whether the respondent has ever consumed any alcoholic beverage during his or her entire life. + Request inclusion into relevant ontology + Not relevant to context of sickle cell SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - Not relevant to context of sickle cell Alcohol - Lifetime Use - + - + - + - + - - + + - - + + - + - - + + - + - - + + A disorder characterized by reduced synthesis of the alpha chains of hemoglobin. The severity of this condition can vary from mild anemia to death, depending on the number of genes deleted. A hemoglobinopathy with two clinically significant forms: hemoglobin Bart hydrops fetalis (deletion of all 4 alpha-globin genes; --/--) which is severe and often results in neonatal death; and hemoglobin H disease (most commonly caused by deletion of 3 alpha-globin genes; --/-alpha) which results in hemolytic anemia, splenomegaly and bone changes. - Curation completed by the SCDO curator team: Clair. - Origa R, Moi P. Alpha-Thalassemia. 2005 Nov 1 [Updated 2016 Dec 29]. In: Adam MP, Ardinger HH, Pagon RA, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle 1993-2018. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1435/ - http://purl.bioontology.org/ontology/MESH/D017085 - Sufficient - SCDO:0000042 + Curation completed by the SCDO curator team: Clair. + Origa R, Moi P. Alpha-Thalassemia. 2005 Nov 1 [Updated 2016 Dec 29]. In: Adam MP, Ardinger HH, Pagon RA, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle 1993-2018. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1435/ + http://purl.bioontology.org/ontology/MESH/D017085 + Sufficient + SCDO:0000042 MESH:D017085 A-Thalassemia Alpha-Thalassemia @@ -21960,20 +21395,20 @@ Include links to relevant Therapeutics. - + - - + + - - + + Drugs that selectively bind to and activate alpha adrenergic receptors. - http://purl.bioontology.org/ontology/MESH/D000316 - Sufficient - SCDO:0000045 + http://purl.bioontology.org/ontology/MESH/D000316 + Sufficient + SCDO:0000045 MESH:D000316 Adrenergic Alpha Agonists Adrenergic Alpha-Agonists @@ -21983,90 +21418,90 @@ Include links to relevant Therapeutics. - + - - + + A region of chromosome 16 that includes five functional genes and two pseudogenes. The order of genes is: 5' - zeta - pseudozeta - mu - pseudoalpha-1 - alpha-2 -alpha-1 - theta1 - 3'. It is responsible for the creation of the alpha parts (roughly half) of the oxygen transport protein Hemoglobin. + Request inclusion into relevant ontology perhaps below "Genetic Locus"/"Globin Locus" (also to be included) in MESH. + + + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology perhaps below "Genetic Locus"/"Globin Locus" (also to be included) in MESH. - - - None Alpha-Globin Gene Cluster Alpha-Globin Locus - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Methods of pain relief that may be used with or in place of analgesics. - http://purl.bioontology.org/ontology/MESH/D000698 - Sufficient - SCDO:0000049 + http://purl.bioontology.org/ontology/MESH/D000698 + Sufficient + SCDO:0000049 MESH:D000698 Analgesias Analgesia @@ -22074,159 +21509,159 @@ Include links to relevant Therapeutics. - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A compound capable of relieving pain without the loss of consciousness. - http://purl.bioontology.org/ontology/MESH/D000700 - Sufficient - SCDO:0000050 + http://purl.bioontology.org/ontology/MESH/D000700 + Sufficient + SCDO:0000050 MESH:D000700 Analgesic Analgesic Agent @@ -22241,103 +21676,103 @@ Include links to relevant Therapeutics. - + - - + + An adverse drug event that results in unexpected and unwanted events due to anesthetic drug treatment. - http://purl.obolibrary.org/obo/OAE_0002348 - Sufficient - SCDO:0000053 + http://purl.obolibrary.org/obo/OAE_0002348 + Sufficient + SCDO:0000053 OAE:0002348 Anesthetic Complication AE - + - + - - + + Grayish, brown, or dark red streaks caused by cracks in Bruch's membrane that are histologically characterized by calcium deposition. Angioid streaks are most characteristic of sickle cell anemia and can occur to a lesser extent in other sickle cell syndromes, but not in sickle cell trait. - Suggest update to description in DO. Currently no description. - Ballas et al 2010 Am J Hematol - Suggest update to description + Suggest update to description in DO. Currently no description. + Ballas et al 2010 Am J Hematol + Suggest update to description DOID:13401 Angioid Streaks - + - - + + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A class of drugs whose main indications are the treatment of hypertension and heart failure. They exert their hemodynamic effect mainly by inhibiting the renin-angiotensin system. They also modulate sympathetic nervous system activity and increase prostaglandin synthesis. They cause mainly vasodilation and mild natriuresis without affecting heart rate and contractility. - http://purl.bioontology.org/ontology/MESH/D000806 - Sufficient - SCDO:0000055 + http://purl.bioontology.org/ontology/MESH/D000806 + Sufficient + SCDO:0000055 MESH:D000806 ACE ACE Inhibitors @@ -22348,147 +21783,147 @@ Include links to relevant Therapeutics. - + - + - - + + - - + + - - + + The respondent's total family income from the last calendar year. - Request inclusion into MESH below "Income". + Request inclusion into MESH below "Income". -The PhenX protocol is U.S. specific. Is there one relevant to the African setting? - - PhenX protocol: Annual Family Income #11101 - Negligable +The PhenX protocol is U.S. specific. Is there one relevant to the African setting? + + PhenX protocol: Annual Family Income #11101 + Negligable phenX:11100 Annual Family Income - + - - + + - + - + - + - + - + - + - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + Substance that reduces or suppresses inflammation. - http://purl.bioontology.org/ontology/MESH/D000893 - Sufficient - SCDO:0000057 + http://purl.bioontology.org/ontology/MESH/D000893 + Sufficient + SCDO:0000057 MESH:D000893 Anti Inflammatories Anti Inflammatory Agents @@ -22502,45 +21937,45 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African settin - + - + - + - - + + - - + + - - + + - - + + - - + + Drugs that bind to but do not activate histamine receptors, thereby blocking the actions of histamine or histamine agonists. Classical antihistaminics block the histamine H1 receptors only. - http://purl.bioontology.org/ontology/MESH/D006633 - Sufficient - SCDO:0000066 + http://purl.bioontology.org/ontology/MESH/D006633 + Sufficient + SCDO:0000066 MESH:D006633 Antihistamines Histamine Antagonist @@ -22550,39 +21985,39 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African settin - + - + - + - + - + - + - - + + Used in the treatment of acute or chronic vascular hypertension regardless of pharmacological mechanism. Among the antihypertensive agents are diuretics; (especially diuretics, thiazide); adrenergic aeta-antagonists; adrenergic alpha-antagonistics; angiotensin-converting enzyme inhibitors; calcium channel blockers; ganglionic blockers; and vasodilator agents. - http://purl.bioontology.org/ontology/MESH/D000959 - Sufficient - SCDO:0000067 + http://purl.bioontology.org/ontology/MESH/D000959 + Sufficient + SCDO:0000067 MESH:D000959 Agents, Antihypertensive Anti Hypertensive Agent @@ -22595,14 +22030,14 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African settin - + - - + + This gene encodes a secreted high density lipoprotein which binds to apolipoprotein A-I. Variants in the APOL1 gene can influence susceptibility to end-stage renal disease and Trypanosomiasis (African Sleeping Sickness). - Exists in other ontologies but we have provided a description more relevant to its relationship with SCD. - http://www.ncbi.nlm.nih.gov/gene/8542 - Not relevant to context of sickle cell + Exists in other ontologies but we have provided a description more relevant to its relationship with SCD. + http://www.ncbi.nlm.nih.gov/gene/8542 + Not relevant to context of sickle cell APO-L APOL APOL1 Gene @@ -22612,14 +22047,14 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African settin - + - - + + Exercises performed in or underwater for conditioning or rehabilitation (e.g., in injured athletes or patients with joint diseases). - Request inclusion into relevant ontology - http://medical-dictionary.thefreedictionary.com/aquatic+therapy - None + Request inclusion into relevant ontology + http://medical-dictionary.thefreedictionary.com/aquatic+therapy + None Aqua Therapy Hydrotherapy Aquatic Rehabilitation @@ -22627,20 +22062,20 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African settin - + - - + + - - + + A hematology assay that measures the acidity (pH) and the levels of oxygen and carbon dioxide in the blood from an artery. This test is used to check how well the lungs are able to move oxygen into the blood and remove carbon dioxide from the blood. - - Sufficient - SCDO:0000071 + + Sufficient + SCDO:0000071 ERO:0000533 ABG Test Arterial Blood Gas Test @@ -22648,14 +22083,14 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African settin - + - + Abnormal formation of blood vessels that shunt arterial blood directly into veins without passing through the CAPILLARIES. They usually are crooked, dilated, and with thick vessel walls. A common type is the congenital arteriovenous fistula. The lack of blood flow and oxygen in the capillaries can lead to tissue damage in the affected areas. - http://purl.bioontology.org/ontology/MESH/D001165 - Sufficient - SCDO:0000072 + http://purl.bioontology.org/ontology/MESH/D001165 + Sufficient + SCDO:0000072 MESH:D001165 Arteriovenous Malformations Arteriovenous Malformation @@ -22663,15 +22098,15 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African settin - + - + - + A water-soluble, semi-synthetic derivative of the sesquiterpene lactone artemisinin with anti-malarial, anti-schistosomiasis, antiviral, and potential anti-neoplastic activities. - - Sufficient - SCDO:0000073 + + Sufficient + SCDO:0000073 MESH:D000077332 Artesunic Acid Dihydroartemisinine 12 Alpha Succinate @@ -22680,17 +22115,17 @@ The PhenX protocol is U.S. specific. Is there one relevant to the African settin - + - - + + The score obtained from the Adult Sickle Cell Quality-of-Life Measurement Information System (ASCQ-Me). - + + Is this term acceptable? +If so, request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820201 - Is this term acceptable? -If so, request inclusion into relevant ontology - None ASCQ-Me - Quality of Life in SCD Sickle Cell Disease Adult Quality of Life Questionnaire Assessment Score deprecated ASCQ-Me Score @@ -22699,22 +22134,22 @@ If so, request inclusion into relevant ontology - + - + - - + + - - + + A bioassay to measure levels of aspartate aminotransferase (AST), which is released into the blood following tissue damage. - Suggest update to PhenX label ("Aspartate Aminotransferase Level") also to NCIT label (from "Aspartate Aminotransferase Measurement") - - Suggest update to label + Suggest update to PhenX label ("Aspartate Aminotransferase Level") also to NCIT label (from "Aspartate Aminotransferase Measurement") + + Suggest update to label phenX:811201 AST Blood Test Aspartate Transaminase Blood Test @@ -22724,50 +22159,50 @@ If so, request inclusion into relevant ontology - + - + - + - + - - + + - - + + - + - - + + The amount of aspartate aminotransferase present in a specified volume of blood. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None AST Level Aspartate Transaminase Level Blood Aspartate Transaminase Amount @@ -22776,37 +22211,37 @@ If so, request inclusion into relevant ontology - + - - + + A set of 27 questions administered to adults with sickle cell disease (SCD) to determine the quality of care that they have received from health care providers. + Suggest update to label in PhenX (from "Quality of Care") + http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820101 + PhenX protocol: Quality of Care - Adults #820101 + Self + Clinic Patients (Adults with SCD) + These questions are used to assess the patient-reported health care needs and quality of service from health care providers for individuals with chronic conditions such as sickle cell disease (SCD). + 18 and older + Suggest update to label SCDO Keller, S. D., Yang, M., Treadwell, M. J., Werner, E. M., & Hassell, K. L. (2014). Patient reports of health outcome for adults living with sickle cell disease: Development and testing of the ASCQ-Me item banks. Health and Quality of Life Outcomes, 12(1), 125. doi:10.1186/s12955-014-0125-0 - Suggest update to label in PhenX (from "Quality of Care") - http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820101 - PhenX protocol: Quality of Care - Adults #820101 - Self - Clinic Patients (Adults with SCD) - These questions are used to assess the patient-reported health care needs and quality of service from health care providers for individuals with chronic conditions such as sickle cell disease (SCD). - 18 and older - Suggest update to label ASCQ-Me Quality of Care Module ASCQ-Me - Quality of Care in SCD - + - - + + A planned process with the objective of producing diagnostic information about the material entity that is the evaluant, by physically examining it or its proxies. + Possibly too specifiic to this ontology to be included in another ontology? +Use structuring of sub-classes within MESH's "Diagnostic Techniques and Procedures" and NCIT's "Diagnostic Procedure" to inform structuring of terms in this class. + None SCDO (Jade Hotchkiss) http://purl.obolibrary.org/obo/OBI_0000070 - Possibly too specifiic to this ontology to be included in another ontology? -Use structuring of sub-classes within MESH's "Diagnostic Techniques and Procedures" and NCIT's "Diagnostic Procedure" to inform structuring of terms in this class. - None Diagnostic Assay Diagnostic Method Diagnostic Technique @@ -22816,93 +22251,93 @@ Use structuring of sub-classes within MESH's "Diagnostic Techniques an - + - + - + This measure is a magnetic resonance imaging (MRI) method of capturing an individual's heart performance, and is considered the gold standard for capturing ventricular volumes and mass. It is used to detect cardiac abnormalities, such as cardiomyopathies, myocardial fibrosis, and infarction. - Request inclusion into relevant ontology. Perhaps in the CPT. - http://www.phenxtoolkit.org/toolkit_content/supplemental_info/scd_cardio_pulm_renal/measures/Short_Axis_Function_20May2015.doc - None + Request inclusion into relevant ontology. Perhaps in the CPT. + http://www.phenxtoolkit.org/toolkit_content/supplemental_info/scd_cardio_pulm_renal/measures/Short_Axis_Function_20May2015.doc + None MRI of Short-Axis Cardiac Function Assessment of Short-Axis Cardiac Function by MRI - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + A form of bronchial disorder with three distinct components: airway hyper-responsiveness, airway inflammation, and intermittent airway obstruction. It is characterized by spasmodic contraction of airway smooth muscle, wheezing and dyspnea. - Further work: -is caused by links to be moved to object property links - Include a copy of this term below "Comorbid Disease" and/or below "Respiratory System". - http://purl.bioontology.org/ontology/MESH/D001249 - Airway hyper-responsiveness - Airway inflammation - Intermittent airway obstruction - It is characterized by spasmodic contraction of airway smooth muscle, wheezing and dyspnea. - Sufficient - SCDO:0000086 + Further work: +is caused by links to be moved to object property links + Include a copy of this term below "Comorbid Disease" and/or below "Respiratory System". + http://purl.bioontology.org/ontology/MESH/D001249 + Airway hyper-responsiveness + Airway inflammation + Intermittent airway obstruction + It is characterized by spasmodic contraction of airway smooth muscle, wheezing and dyspnea. + Sufficient + SCDO:0000086 MESH:D001249 Asthma - + - + - + A chronic inflammatory genetically determined disease of the skin marked by increased ability to form reagin (IgE), with increased susceptibility to allergic rhinitis and asthma, and hereditary disposition to a lowered threshold for pruritus. It is manifested by lichenification, excoriation, and crusting, mainly on the flexural surfaces of the elbow and knee. In infants it is known as infantile eczema. - - Sufficient - SCDO:0000088 + + Sufficient + SCDO:0000088 MESH:D003876 Atopic Eczema Baby Eczema @@ -22912,21 +22347,21 @@ is caused by links to be moved to object property links - + - - + + - - + + This gene encodes a C2H2 type zinc-finger protein by its similarity to the mouse Bcl11a/Evi9 protein. During hematopoietic cell differentiation, this gene is down-regulated. It is possibly involved in lymphoma pathogenesis since translocations associated with B-cell malignancies also deregulates its expression. Multiple transcript variants encoding several different isoforms have been found for this gene. - Link to "Hereditary Persistence of fetal hemoglobin". - Request inclusion into relevant ontology - http://www.ncbi.nlm.nih.gov/gene/53335 - Not relevant to context of sickle cell + Link to "Hereditary Persistence of fetal hemoglobin". + Request inclusion into relevant ontology + http://www.ncbi.nlm.nih.gov/gene/53335 + Not relevant to context of sickle cell B-Cell CLL/Lymphoma 11A Gene B-cell CLL/lymphoma 11A (zinc finger protein) B-cell CLL/lymphoma 11A Gene @@ -22940,35 +22375,35 @@ is caused by links to be moved to object property links - + - + One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to oxygen: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or phototrophy (via light reaction); for chemotrophs by their source of chemical energy: chemolithotrophy (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for carbon; nitrogen; etc.; heterotrophy (from organic sources) or autotrophy (from carbon dioxide). They can also be classified by whether or not they stain (based on the structure of their cell walls) with crystal violet dye: gram-negative or gram-positive. - http://purl.bioontology.org/ontology/MESH/D001419 - Sufficient - SCDO:0000098 + http://purl.bioontology.org/ontology/MESH/D001419 + Sufficient + SCDO:0000098 MESH:D001419 Bacteria - + - - - + + + The BAI is the most widely used instument for measuring anxiety. It consists of 21 items to assess how bothersome a symptom of anxiety has been for the subject over the past month. Scoring the BAI is based on a 0-3 point scale with higher scores indicating severity. - Request inclusion into relevant ontology. Could be as a child of "Symptom Specific Assessment Tool" in the NCIT. - Beck, A. T., Epstein, N., Brown, G., & Steer, R. A. (1988). An inventory for measuring clinical anxiety: psychometric properties. Journal of Consulting and Clinical Psychology, 56, 893-897. - Multiple countries and cultural groups - Self - Clinic Patients - Spanish - 17 years and older - yes - Few but definitions not freely available + Request inclusion into relevant ontology. Could be as a child of "Symptom Specific Assessment Tool" in the NCIT. + Beck, A. T., Epstein, N., Brown, G., & Steer, R. A. (1988). An inventory for measuring clinical anxiety: psychometric properties. Journal of Consulting and Clinical Psychology, 56, 893-897. + Multiple countries and cultural groups + Self + Clinic Patients + Spanish + 17 years and older + yes + Few but definitions not freely available BAI Beck Anxiety Inventory Beck Anxiety Inventory (BAI) @@ -22976,15 +22411,15 @@ is caused by links to be moved to object property links - + - - + + The Behavior Rating Inventory of Executive Function (BRIEF) is a detailed questionnaire designed to assess executive function behaviors of children and adolescents in the school and home environments. The BRIEF is completed by parents and teachers. - Suggest update to label in PhenX. - - PhenX protocol: #131102 - Suggest update to label + Suggest update to label in PhenX. + + PhenX protocol: #131102 + Suggest update to label phenX:131102 BRIEF Executive Function - Child @@ -22993,27 +22428,27 @@ is caused by links to be moved to object property links - + - - + + The actions or reactions of a person in response to a situation or stimuli. + Few but definitions not specific enough SCDO - Few but definitions not specific enough Behaviour - + - - + + Personal or collective understanding of what the causes (could be predisposing factors, enabling factors, precipitating factors, reinforcing factors, and/or risk factors) are of a certain illness. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) http://purl.bioontology.org/ontology/MESH/D015984 - Request inclusion into relevant ontology - None Beliefs about Causality Cultural beliefs, such as re-incarnation and witchcraft, may influence notions on causality of sickle cell disease. Beliefs About Causes of Illness @@ -23021,64 +22456,64 @@ is caused by links to be moved to object property links - + - - + + Personal or collective understanding of what can remedy or treat illness. + Request inclusion into relevant ontology, perhaps MESH. + none SCDO http://www.ncbi.nlm.nih.gov/mesh/68003469 - Request inclusion into relevant ontology, perhaps MESH. - none Beliefs About Remedies and Treatment - + - - + + - + - + - - + + - + - - + + - - + + A beta-thalassemia caused by the reduced (beta-) synthesis of the beta globin chains of the hemoglobin (Hb) tetramer. - Request inclusion into relevant ontology, perhaps DOID. - A. Cao and R. Galanello, "Beta Thalassemia", Genetics in Medicine, Vol. 12, No. 2, 2010, pp. 61 76. doi:10.1097/GIM.0b013e3181cd68ed - None + Request inclusion into relevant ontology, perhaps DOID. + A. Cao and R. Galanello, "Beta Thalassemia", Genetics in Medicine, Vol. 12, No. 2, 2010, pp. 61 76. doi:10.1097/GIM.0b013e3181cd68ed + None Beta - Thalassemia Beta Minus-Thalassemia Beta- Thalassemia @@ -23088,98 +22523,98 @@ is caused by links to be moved to object property links - + - + - + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A hemoglobinopathy characterized by the reduced (beta plus) or absent (beta zero) synthesis of the beta globin chains of hemoglobin, resulting in variable outcomes ranging from severe anemia to clinically asymptomatic individuals. - Suggest update to description in DOID. - -Include a "Dominant Beta-Thalassemia" sub-class? (see Orphanet) - A. Cao and R. Galanello, "Beta Thalassemia", Genetics in Medicine, Vol. 12, No. 2, 2010, pp. 61 76. doi:10.1097/GIM.0b013e3181cd68ed - Origa R. Beta-Thalassemia. 2000 Sep 28 [Updated 2018 Jan 25]. In: Adam MP, Ardinger HH, Pagon RA, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle 1993-2018. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1426/ - http://en.wikipedia.org/wiki/Beta_thalassemia - http://purl.obolibrary.org/obo/DOID_12241 - Suggest update to description + Suggest update to description in DOID. + +Include a "Dominant Beta-Thalassemia" sub-class? (see Orphanet) + A. Cao and R. Galanello, "Beta Thalassemia", Genetics in Medicine, Vol. 12, No. 2, 2010, pp. 61 76. doi:10.1097/GIM.0b013e3181cd68ed + Origa R. Beta-Thalassemia. 2000 Sep 28 [Updated 2018 Jan 25]. In: Adam MP, Ardinger HH, Pagon RA, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle 1993-2018. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1426/ + http://en.wikipedia.org/wiki/Beta_thalassemia + http://purl.obolibrary.org/obo/DOID_12241 + Suggest update to description DOID:12241 Beta Thalassemias Beta Type Thalassemia @@ -23192,86 +22627,86 @@ Include a "Dominant Beta-Thalassemia" sub-class? (see Orphanet) + - - + + - + - + - - + + - + - + - + - + - + - + - + - - + + - - + + A homozygous (B+/B+) or compound heterozygous (B0/B+) form of beta-thalassemia characterized by mild to moderate anemia which does not or only occasionally requires transfusion. - - Sufficient - SCDO:0000112 + + Sufficient + SCDO:0000112 ORPHA:231222 B+/B+ B0/B+ @@ -23282,146 +22717,146 @@ Include a "Dominant Beta-Thalassemia" sub-class? (see Orphanet) + - - + + - + - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + A severe early-onset form of beta thalassemia characterized by severe anemia requiring regular red blood cell transfusions. - - Sufficient - SCDO:0000113 + + Sufficient + SCDO:0000113 ORPHA:231214 B0/B0 BT Major @@ -23435,29 +22870,29 @@ Include a "Dominant Beta-Thalassemia" sub-class? (see Orphanet) + - - - + + + - + - - + + The inheritance of only one mutated beta-globin allele (beta+ or beta0). - Request inclusion into relevant ontology. Perhaps below "clinical subtype" in Orphanet. + Request inclusion into relevant ontology. Perhaps below "clinical subtype" in Orphanet. -The exact synonym "B+/B" has been changed to "B-/B", as per the change in convention from "Beta Plus Thalassemia" to "Beta Minus Thalassemia". - http://en.wikipedia.org/wiki/Beta_thalassemia - Few but definitions not freely available +The exact synonym "B+/B" has been changed to "B-/B", as per the change in convention from "Beta Plus Thalassemia" to "Beta Minus Thalassemia". + http://en.wikipedia.org/wiki/Beta_thalassemia + Few but definitions not freely available B-/B B0/B Beta Thalassemia Minor @@ -23469,62 +22904,62 @@ The exact synonym "B+/B" has been changed to "B-/B", as per - + - - + + - + - + - - + + - - + + - - + + - + - - + + - - + + Beta-zero thalassemia is a form of beta-thalassemia in which beta-globin chain synthesis is absent. The clinical phenotype is often that of transfusion-dependant beta thalassemia major, however modifying factors may ameliorate the symptoms of severe anemia (Cao & Gallanelo, 2010). - Request inclusion into relevant ontology, perhaps DOID. - A. Cao and R. Galanello, "Beta Thalassemia", Genetics in Medicine, Vol. 12, No. 2, 2010, pp. 61 76. doi:10.1097/GIM.0b013e3181cd68ed - None + Request inclusion into relevant ontology, perhaps DOID. + A. Cao and R. Galanello, "Beta Thalassemia", Genetics in Medicine, Vol. 12, No. 2, 2010, pp. 61 76. doi:10.1097/GIM.0b013e3181cd68ed + None Beta 0 Thalassemia Beta Zero-Thalassemia Beta-Zero-Thalassemia @@ -23536,16 +22971,16 @@ The exact synonym "B+/B" has been changed to "B-/B", as per - + - - + + A globin locus composed of five genes located on a short 45 kb region of chromosome 11. The order of genes in this cluster is: 5' - epsilon - gamma-G - gamma-A - delta - beta - 3'. It is responsible for the creation of the beta parts (roughly half) of the oxygen transport protein Hemoglobin. + Request inclusion into relevant ontology perhaps below "Genetic Locus"/"Globin Locus" (also to be included) in MESH. + + + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology perhaps below "Genetic Locus"/"Globin Locus" (also to be included) in MESH. - - - None Beta-Globin Cluster Beta-Globin Gene Cluster HBB Locus @@ -23554,27 +22989,27 @@ The exact synonym "B+/B" has been changed to "B-/B", as per - + - + - - + + - - + + Defined arrays of polymorphic gene sites that are inherited together across the genetic vicinity of the beta-globin gene or gene cluster on chromosome 11. + Request inclusion into relevant ontology + Nagel, et. al. NEngl J Med. 1985 Apr 4;312(14):880-4 + None SCDO - Request inclusion into relevant ontology - Nagel, et. al. NEngl J Med. 1985 Apr 4;312(14):880-4 - None Beta-Globin Haplotypes Beta-Haplotypes Beta-S Haplotype @@ -23584,283 +23019,283 @@ The exact synonym "B+/B" has been changed to "B-/B", as per - + - + - + - + - + - - + + - + A bioassay to measure levels of bilirubin, a yellow substance found in bile produced when the liver breaks down old red blood cells. - Suggest update to label in PhenX (from "Bilirubin Level"). - - Suggest update to label + Suggest update to label in PhenX (from "Bilirubin Level"). + + Suggest update to label phenX:810901 Bilirubin Blood Test - + - - + + An analytical in vitro procedure used to detect, quantify and/or study the binding or activity of a biological molecule, such as an enzyme. - Request inclusion into relevant ontology. - http://www.nature.com/subjects/biochemical-assays - Negligable + Request inclusion into relevant ontology. + http://www.nature.com/subjects/biochemical-assays + Negligable Biochemical Assay - + - - + + A biological factor that modifies one or more aspects of a disease, such as sickle cell disease (SCD) (e.g. aspects such as temporal pattern, age of onset and mortality), for specific phenotype(s) of the disease. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Biological Disease Modifier - + - + The country in which the respondent was born. - Request inclusion into relevant ontology - http://www.phenxtoolkit.org/index.php?pageLink=browse.protocols&id=010200 - Negligable + Request inclusion into relevant ontology + http://www.phenxtoolkit.org/index.php?pageLink=browse.protocols&id=010200 + Negligable Place of Birth Birthplace - + - - + + The country in which the respondent's biological father was born. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Birthplace of Biological Father - + - - + + The country in which the respondent's biological mother was born. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Birthplace of Biological Mother - + - + The country or countires in which the respondent's biological grandparents were born. + Request inclusion into relevant ontology + +There is a protocol in PhenX but it is US specific. + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - -There is a protocol in PhenX but it is US specific. - Negligable Birthplace of Grandparents - + - - + + The country in which the respondent's biological maternal (on the mother's side of the family) grandfather was born. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Birthplace of Maternal Grandfather - + - - + + The country in which the respondent's biological maternal (on the mother's side of the family) grandmother was born. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Birthplace of Maternal Grandmother - + - + The country or countires in which the respondent's biological parents were born. + Request inclusion into relevant ontology + +There is a protocol in PhenX but it is US specific. + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - -There is a protocol in PhenX but it is US specific. - Negligable Birthplace of Parents - + - - + + The country in which the respondent's biological paternal (on the father's side of the family) grandfather was born. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Birthplace of Paternal Grandfather - + - - + + The country in which the respondent's biological paternal (on the father's side of the family) grandmother was born. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Birthplace of Paternal Grandmother - + - + - + - - + + Black lesions in the retina that form at the border of perfused and nonperfused retina that are caused by the migration of hyperplastic retinal pigment epithelial cells into sensory retina. The sensory retina surrounding the lesion is atrophic. - Request inclusion into relevant ontology. - Ballas et al 2010 Am J Hematol - None + Request inclusion into relevant ontology. + Ballas et al 2010 Am J Hematol + None Black Sunburst Lesion - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Test used in the analysis of the hemic system. - http://purl.bioontology.org/ontology/MESH/D006403 - Sufficient - SCDO:0000133 + http://purl.bioontology.org/ontology/MESH/D006403 + Sufficient + SCDO:0000133 MESH:D006403 Blood Assay Blood Tests @@ -23873,28 +23308,28 @@ There is a protocol in PhenX but it is US specific. - + - - + + The transfer of blood components such as erythrocytes, leukocytes, platelets, and plasma from a donor to a recipient or back to the donor. This process differs from the procedures undertaken in plasmapheresis and types of cytapheresis; (plateletpheresis and leukapheresis) where, following the removal of plasma or the specific cell components, the remainder is transfused back to the donor. - http://purl.bioontology.org/ontology/MESH/D016913 - Sufficient - SCDO:0000138 + http://purl.bioontology.org/ontology/MESH/D016913 + Sufficient + SCDO:0000138 MESH:D016913 Blood Component Transfusion - + - - + + Test to determine the presence of blood infection (e.g. sepsis; bacteremia). - - Sufficient - SCDO:0000139 + + Sufficient + SCDO:0000139 MESH:D000071997 BC Culture Blood @@ -23905,185 +23340,185 @@ There is a protocol in PhenX but it is US specific. - + - - - + + + - + - + - + - + - + - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + The introduction of whole blood or blood component directly into the blood stream. (Dorland, 27th ed) + http://purl.bioontology.org/ontology/MESH/D001803 + Sufficient + SCDO:0000147 Radha Raghupathy, Deepa Manwani, and Jane A. Little, “Iron Overload in Sickle Cell Disease,” Advances in Hematology, vol. 2010, Article ID 272940, 9 pages, 2010. doi:10.1155/2010/272940 - http://purl.bioontology.org/ontology/MESH/D001803 - Sufficient - SCDO:0000147 MESH:D001803 Blood Transfusions The major and unavoidable complication of transfusions in sickle cell disease is iron overload. @@ -24094,14 +23529,14 @@ Transfusion is well-defined as prophylaxis (stroke) and as therapy (acute chest - + - + The distance from the sole to the crown of the head with body standing on a flat surface and fully extended. - http://www.ebi.ac.uk/efo/EFO_0004339 - Sufficient - SCDO:0000149 + http://www.ebi.ac.uk/efo/EFO_0004339 + Sufficient + SCDO:0000149 EFO:0004339 Height Height/Length @@ -24111,15 +23546,15 @@ Transfusion is well-defined as prophylaxis (stroke) and as therapy (acute chest - + - + The mass or quantity of heaviness of an individual. It is expressed by units of pounds or kilograms. - Add these terms from PhenX?: -- - Weight Loss/Gain - - Sufficient - SCDO:0000152 + Add these terms from PhenX?: -- - Weight Loss/Gain + + Sufficient + SCDO:0000152 MESH:D001835 Weight Body Weight @@ -24127,16 +23562,16 @@ Transfusion is well-defined as prophylaxis (stroke) and as therapy (acute chest - + - - + + An abnormal hardening or increased density of bone tissue. - + + + Sufficient + SCDO:0000155 Segen's Medical Dictionary. S.v. "bone sclerosis." Retrieved April 30 2019 from https://medical-dictionary.thefreedictionary.com/bone+sclerosis - - Sufficient - SCDO:0000155 MESH:D010026 Bone Scleroses Osteoscleroses @@ -24148,41 +23583,41 @@ Transfusion is well-defined as prophylaxis (stroke) and as therapy (acute chest - + - + - + A noninvasive method to assess the endothelial dysfunction in the brachial artery. - Request inclusion into relevant ontology. - http://en.wikipedia.org/wiki/Endothelial_dysfunction - None + Request inclusion into relevant ontology. + http://en.wikipedia.org/wiki/Endothelial_dysfunction + None BAUI Brachial Artery Ultrasound Imaging - + - - + + - - + + - - + + Voltages between parts of the brain that are detectable with an electroencephalograph. - - Sufficient - SCDO:0000161 + + Sufficient + SCDO:0000161 CRISP:0487-1238 Brain Electrophysiological Activity Brain Oscillography @@ -24192,51 +23627,51 @@ Transfusion is well-defined as prophylaxis (stroke) and as therapy (acute chest - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An episode of severe pain that occurs with rapid onset even when pain-control medication is being used. Breakthrough pain can occur spontaneously or in relation to a specific activity, and can last from a few seconds to a few hours. + + Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 + Few but definitions not specific enough Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 - - Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 - Few but definitions not specific enough NCIT:C9203 There are currently no data that clearly describe or can be used to define breakthrough pain in SCD. Breakthrough Pain @@ -24244,22 +23679,22 @@ Transfusion is well-defined as prophylaxis (stroke) and as therapy (acute chest - + - - + + The Brief IPQ has 9 items, 8 new items from the IPQ plus a causal question. All of the items except the causal question are rated using a 0-to-10-response scale. Five of the items assess Cognitive Illness Representations: Consequences (Item 1), Timeline (Item 2), Personal Control (Item 3), Treatment Control (Item 4), and Identity (Item 5). Two of the items assess Emotional Representations: Concern (Item 6) and Emotions (Item 8). One item assesses Illness Comprehensibility (Item 7). Assessment of the Causal Representation is by an open-ended response item adapted, which asks patients to list the three most important causal factors in their illness (Item 9). Responses to the causal item can be grouped into categories such as stress, lifestyle, hereditary, etc, determined by the particular illness studied, and categorical analysis can then be performed. + Request inclusion into NCIT below "Research or Clinical Assessment Tool". + Broadbent E, Petrie KJ, Main J, Weinman, J. (2006). The brief illness perception questionnaire. Journal of Psychosomatic Research, 60, 631-637. + Multiple countries and cultural groups + Self + Clinic Patients + Many + Good psychometric properties, widely used, has been translated into several languages. + Adults + yes + None Broadbent E, Petrie KJ, Main J, Weinman, J. (2006). The brief illness perception questionnaire. Journal of Psychosomatic Research, 60, 631-637. - Request inclusion into NCIT below "Research or Clinical Assessment Tool". - Broadbent E, Petrie KJ, Main J, Weinman, J. (2006). The brief illness perception questionnaire. Journal of Psychosomatic Research, 60, 631-637. - Multiple countries and cultural groups - Self - Clinic Patients - Many - Good psychometric properties, widely used, has been translated into several languages. - Adults - yes - None B-IPQ Brief Illness Perception Questionnaire Brief Illness Perception Questionnaire (B-IPQ) @@ -24267,44 +23702,44 @@ Transfusion is well-defined as prophylaxis (stroke) and as therapy (acute chest - + - - + + Brief RCOPE is a 14-item instrument that measures religious coping with major life stressors. Responses on the Brief RCOPE indicate the frequency with which participants have used R/S coping behaviors on a Likert scale of 1 (not at all) to 4 (a great deal.) The scale has been used to examine positive and negative religious coping, including in teens with SCD. + Request inclusion into NCIT below "Research or Clinical Assessment Tool". + Pargament K, Koenig H, Perez L. The many methods of religious coping: development and initial validation of the RCOPE. J Clin Psychol. 2000;56:519-543. + Self; Proxy (Parent report) + Children with SCD and their parents. + Demonstrated validity in SCD studies. + Children and adults + None SCDO Pargament K, Koenig H, Perez L. The many methods of religious coping: development and initial validation of the RCOPE. J Clin Psychol. 2000;56:519-543. - Request inclusion into NCIT below "Research or Clinical Assessment Tool". - Pargament K, Koenig H, Perez L. The many methods of religious coping: development and initial validation of the RCOPE. J Clin Psychol. 2000;56:519-543. - Self; Proxy (Parent report) - Children with SCD and their parents. - Demonstrated validity in SCD studies. - Children and adults - None Brief RCOPE - + - + - - + + The improvement of forced expiratory volume in 1 second (FEV1) after inhalation of beta2-agonists and is typically measured as the change in airflow after the administration of short-acting beta2-adrenergic agonists (SABAs). - Suggest that the description be updated in PhenX (https://www.phenxtoolkit.org/protocols/view/90301) - Bauer S, Park HN, Seo HS, et al. Assessment of bronchodilator responsiveness following methacholine-induced bronchoconstriction in children with asthma. Allergy Asthma Immunol Res. 2011;3(4):245-50. - Suggest update to description + Suggest that the description be updated in PhenX (https://www.phenxtoolkit.org/protocols/view/90301) + Bauer S, Park HN, Seo HS, et al. Assessment of bronchodilator responsiveness following methacholine-induced bronchoconstriction in children with asthma. Allergy Asthma Immunol Res. 2011;3(4):245-50. + Suggest update to description BDR Bronchodilator Responsiveness - + BDR @@ -24312,29 +23747,29 @@ Transfusion is well-defined as prophylaxis (stroke) and as therapy (acute chest - + - - + + - + - - + + A test to assess an individual's change in pulmonary function in response to inhaled bronchodilator medications. - Suggest update to label in PhenX (from "Bronchodilator Responsiveness (BDR)") + Suggest update to label in PhenX (from "Bronchodilator Responsiveness (BDR)") -Can also suggest inclusion in MESH below "Respiratory Function Tests" - - PhenX protocol: Bronchodilator Responsiveness (BDR) #90301 - Suggest update to label +Can also suggest inclusion in MESH below "Respiratory Function Tests" + + PhenX protocol: Bronchodilator Responsiveness (BDR) #90301 + Suggest update to label phenX:90301 BDR Test Bronchodilator Responsiveness Testing @@ -24343,14 +23778,14 @@ Can also suggest inclusion in MESH below "Respiratory Function Tests"< - + - - + + A highly-sensitive (in the picomolar range, which is 10,000-fold more sensitive than conventional electrophoresis) and efficient technique that allows separation of proteins; nucleic acids; and carbohydrates. (Segen, Dictionary of Modern Medicine, 1992) - http://purl.bioontology.org/ontology/MESH/D019075 - Sufficient - SCDO:0000182 + http://purl.bioontology.org/ontology/MESH/D019075 + Sufficient + SCDO:0000182 MESH:D019075 Capillary Electrophoreses Capillary Zone Electrophoreses @@ -24360,32 +23795,32 @@ Can also suggest inclusion in MESH below "Respiratory Function Tests"< - + - - + + - - + + An instrument which, by means of a cathode-ray oscillograph, projects an electrocardiographic record on a luminous screen. - Request inclusion into relevant ontology. - http://encyclopedia2.thefreedictionary.com/cardioscope - None + Request inclusion into relevant ontology. + http://encyclopedia2.thefreedictionary.com/cardioscope + None Cardioscope - + - - + + 'Anatomical system that has as its parts the heart and blood vessels. [Curator team: []]' - - http://purl.obolibrary.org/obo/UBERON_0004535 + + http://purl.obolibrary.org/obo/UBERON_0004535 UBERON:0004535 CV system deprecated Cardiovascular System @@ -24394,12 +23829,12 @@ Can also suggest inclusion in MESH below "Respiratory Function Tests"< - + - - + + 'Clinical presentations that may be followed by evaluative studies that eventually lead to a diagnosis. [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D002363 + http://purl.bioontology.org/ontology/MESH/D002363 MESH:D002363 Case Histories Case Studies @@ -24410,14 +23845,14 @@ Can also suggest inclusion in MESH below "Respiratory Function Tests"< - + - - + + Studies which start with the identification of persons with a disease of interest and a control (comparison, referent) group without the disease. The relationship of an attribute to the disease is examined by comparing diseased and non-diseased persons with regard to the frequency or levels of the attribute in each group. - Suggest update to description in MESH - http://purl.bioontology.org/ontology/MESH/D016022 - Suggest update to description + Suggest update to description in MESH + http://purl.bioontology.org/ontology/MESH/D016022 + Suggest update to description MESH:D016022 Case-Referrent Studies Case-Control Studies @@ -24425,22 +23860,22 @@ Can also suggest inclusion in MESH below "Respiratory Function Tests"< - + - - - + + + - + A flexible, tubular device that is used to carry fluids into or from a blood vessel, hollow organ, or body cavity. - Add info (rdfs:comment) about how catheters are used in different therapeutics. -- -- Link relevant Therapeutics term(s) to this term via "has medical device". - http://purl.bioontology.org/ontology/MESH/D057785 - Sufficient - SCDO:0000190 + Add info (rdfs:comment) about how catheters are used in different therapeutics. -- -- Link relevant Therapeutics term(s) to this term via "has medical device". + http://purl.bioontology.org/ontology/MESH/D057785 + Sufficient + SCDO:0000190 MESH:D057785 Cannula Cannulas @@ -24450,90 +23885,90 @@ Can also suggest inclusion in MESH below "Respiratory Function Tests"< - + - - + + A drug adverse event that is caused by a drug administration. Here a causal effect is established between the drug administration and the adverse event. - Suggest definition replaced in OAE. Currenlty it's shown as the definition editor. - http://purl.obolibrary.org/obo/OAE_0000095 - Suggest update to description + Suggest definition replaced in OAE. Currenlty it's shown as the definition editor. + http://purl.obolibrary.org/obo/OAE_0000095 + Suggest update to description OAE:0000095 Causal Adverse Drug Event - + - - + + A causal adverse drug event that is induced by a drug-drug interaction. - http://purl.obolibrary.org/obo/OAE_0000179 - Sufficient - SCDO:0000192 + http://purl.obolibrary.org/obo/OAE_0000179 + Sufficient + SCDO:0000192 OAE:0000179 Causal Adverse Drug Event Due to Drug-Drug Interaction - + - - + + A causal adverse drug event that is induced by a food-drug interaction. - http://purl.obolibrary.org/obo/OAE_0000180 - Sufficient - SCDO:0000193 + http://purl.obolibrary.org/obo/OAE_0000180 + Sufficient + SCDO:0000193 OAE:0000180 Causal Adverse Drug Event Due to Food-Drug Interaction - + - - + + A causal adverse drug event that is induced by genetic predisposition. - Suggest small typo to be fixed in OAE. - http://purl.obolibrary.org/obo/OAE_0000181 - Suggest update to description + Suggest small typo to be fixed in OAE. + http://purl.obolibrary.org/obo/OAE_0000181 + Suggest update to description OAE:0000181 Causal Adverse Drug Event Due to Genetic Predisposition - + - - + + A causal adverse drug event due to genetic predisposition that is specifically induced by SNP. - http://purl.obolibrary.org/obo/OAE_0000182 - Sufficient - SCDO:0000195 + http://purl.obolibrary.org/obo/OAE_0000182 + Sufficient + SCDO:0000195 OAE:0000182 Causal Adverse Drug Event Due to SNP - + - - + + - - + + The determination of the amount of free hemoglobin present in a sample. - Suggest update to label in NCIT (from "Free Hemoglobin Measurement") - - Suggest update to label + Suggest update to label in NCIT (from "Free Hemoglobin Measurement") + + Suggest update to label NCIT:C127617 Cell Free Hemoglobin Assay Cell Free Hemoglobin Blood Assay @@ -24545,22 +23980,22 @@ Can also suggest inclusion in MESH below "Respiratory Function Tests"< - + - + - - + + The level of hemoglobin external to erythrocytes in a biological specimen. - SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology + Request inclusion into relevant ontology -If wanting to include "Plasma Hemoglobin Level" in the future, see CMO:0000588 for a description. synonyms: Plasma Free Hemoglobin (PFHb) Level, Plasma Hemoglobin Level. - None +If wanting to include "Plasma Hemoglobin Level" in the future, see CMO:0000588 for a description. synonyms: Plasma Free Hemoglobin (PFHb) Level, Plasma Hemoglobin Level. + None + SCDO (Jade Hotchkiss) Cell Free Haemoglobin Level Cell Free Hemoglobin Concentration Extracellular Hb Level @@ -24571,148 +24006,148 @@ If wanting to include "Plasma Hemoglobin Level" in the future, see CMO - + - - + + - - + + Cerebral collateral circulation is a subsidiary vascular network which is dynamically recruited after arterial occlusion and may provide residual blood flow to ischemic areas. - The description doesn't actually describe the term. Needs revision. + The description doesn't actually describe the term. Needs revision. Perhaps: Blood flow through cerebral collateral circulation, a subsidiary vascular network which is dynamically recruited after arterial occlusion and which may provide residual blood flow to ischemic areas. -Suggest inclusion into CMO, below "circulation measurement". - Cerebral collateral circulation in experimental ischemic stroke. Elisa Cuccione, Giada Padovano, Alessandro Versace, Carlo Ferrarese, Simone Beretta. Exp Transl Stroke Med. 2016; 8: 2. Published online 2016 Mar 1. doi: 10.1186/s13231-016-0015-0 -PMCID: PMC4772465 - None +Suggest inclusion into CMO, below "circulation measurement". + Cerebral collateral circulation in experimental ischemic stroke. Elisa Cuccione, Giada Padovano, Alessandro Versace, Carlo Ferrarese, Simone Beretta. Exp Transl Stroke Med. 2016; 8: 2. Published online 2016 Mar 1. doi: 10.1186/s13231-016-0015-0 +PMCID: PMC4772465 + None Cerebral Collateral Circulation Cerebral Collateral Flow - + - - + + A test of how well the cerebrum is functioning. + Request inclusion into relevant ontology. + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology. - None Cerebral Function Test Cerebral Function Assay - + - + The movement and the forces involved in the movement of the blood through the blood vessels in the brain. + Request inclusion into relevant ontology. +Perhaps replace with "cerebral blood flow measurement" from the EFO? + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology. -Perhaps replace with "cerebral blood flow measurement" from the EFO? - None Cerebrovascular Hemodynamics - + - - + + The analysis of a sample material, called an analyte, using a set of chemical procedures. - Request inclusion into relevant ontology. - http://www.reference.com/science/chemical-assay-80cfe6f498d34be5 - None + Request inclusion into relevant ontology. + http://www.reference.com/science/chemical-assay-80cfe6f498d34be5 + None Chemical Assay - + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A medical imaging assessment of the chest wall, airways, lungs, pulmonary vessels, heart, mediastinum, and pleura. - - Sufficient - SCDO:0000217 + + Sufficient + SCDO:0000217 phenX:810201 Chest Radiograph Chest X-Ray @@ -24720,23 +24155,23 @@ Perhaps replace with "cerebral blood flow measurement" from the EFO? + - - + + The Child Health Questionnaire (CHQ) is a family of general quality of life surveys that measures 14 unique physical and psychosocial concepts. The parent form is available in 2 lengths - the CHQ-PF50 and the CHQ-PF28. The child self-reported version of the CHQ consists of 87 items (CHQ-CF87). + Multiple countries and cultural groups + Self, Proxy + Healthy Children; Children with Medical Conditions + French, isiXhosa, isiZulu, Portuguese, Punjabi, Sesotho, Temil, Telugu, Gujarati + Demonstrated validity with SCD populations; at least two publications using the measure in SCD. + 5 to 18 years (child report 10 - 18 years; parent report 5 - 18 years) + yes + Few but definitions not specific enough SCDO Landgraf, J. M., Abetz, L., and Ware, J. E. (1996). Child health questionnaire (CHQ): A user's manual (1st Ed.). Boston, M.A.: The Health Institute, New England Medical Center. Panepinto JA, O'Mahar KM, DeBaun MR, Rennie KM, Scott JP. Validity of the child health questionnaire for use in children with sickle cell disease. J Pediatr Hematol Oncol. 2004 Sep;26(9):574-8. Wrotniak BH, Schall JI, Brault ME, Balmer DF, Stallings VA. Health-related quality of life in children with sickle cell disease using the child health questionnaire. J Pediatr Health Care. 2014 Jan-Feb;28(1):14-22. doi: 10.1016/j.pedhc.2012.09.004. Epub 2012 Nov 8. - Multiple countries and cultural groups - Self, Proxy - Healthy Children; Children with Medical Conditions - French, isiXhosa, isiZulu, Portuguese, Punjabi, Sesotho, Temil, Telugu, Gujarati - Demonstrated validity with SCD populations; at least two publications using the measure in SCD. - 5 to 18 years (child report 10 - 18 years; parent report 5 - 18 years) - yes - Few but definitions not specific enough CHQ Child Health Questionnaire Child Health Questionnaire (CHQ) @@ -24744,42 +24179,42 @@ Perhaps replace with "cerebral blood flow measurement" from the EFO? + - - + + - - + + A parent's highest level of education obtained, as reported by the child. - Request inclusion into MESH below "Current Educational Attainment" (also to be suggested), below "Socioeconomic Factors". -Also suggest inclusion in the EFO, below measurement. - - PhenX protocol: Child-Reported Parental Education Attainment #210201 - Negligable + Request inclusion into MESH below "Current Educational Attainment" (also to be suggested), below "Socioeconomic Factors". +Also suggest inclusion in the EFO, below measurement. + + PhenX protocol: Child-Reported Parental Education Attainment #210201 + Negligable phenX:210201 Child-Reported Parental Education Attainment - + - - + + The CDI-2 is a 27-item self-report scale that helps to assess cognitive, affective and behavioral signs of depression in children and adolescents. Each item is scored on a scale from 0 to 2. + Check and show which source was used for the description and whether the description was adapted from the source. + Request inclusion into relevant ontology. Could be as a child of "Symptom Specific Assessment Tool" in the NCIT. + Multiple countries and cultural groups + Self + Clinic Patients + 7 to 17 years + yes + None Kovacs, M. (1985). The Children's Depression, Inventory (CDI). Psychopharmacology Bulletin, 21, 995-998. - Check and show which source was used for the description and whether the description was adapted from the source. - Request inclusion into relevant ontology. Could be as a child of "Symptom Specific Assessment Tool" in the NCIT. - Multiple countries and cultural groups - Self - Clinic Patients - 7 to 17 years - yes - None CDI 2 CDI-2 Children's Depression Inventory 2 @@ -24789,22 +24224,22 @@ Also suggest inclusion in the EFO, below measurement. - + - - + + A measure that seeks to determine the extent to which children and adolescents believe their own health-related behaviors will influence their health. It is a 20 item scale that contains 3 additional practice items and is a yes or no format. It contains 3 factors: belief in internality, belief in powerful others and belief in chance. There is a shorter 9-item version of the scale which is comparable to the full version and adapted for use in Egyptian children. - Abdel Gawwad E, Ahmed MH, Kamal MM. Developing and testing of an Egyptian version of Children's Health Locus of Control scale. J Egypt Public Health Assoc. 1999; 74(1-2):139-73. - Deaux EB. Health Locus of Control in Chukotka children. Alaska Med. 1992 Jul-Sep; 34(3):135-9. - Parcel G.S. and Meyer M.P. (1978) Development of an instrument to measure children's health locus of control. Health Education Monographs, 6, 149-159. - Multiple countries and cultural groups - Self - Healthy Children; Children with Medical Conditions - English, Russian, a 9- item shorter Egyptian version - Has adequate reliability, construct validity and internal consistency. - Children and Adolescents - no - Few but definitions not specific enough + Abdel Gawwad E, Ahmed MH, Kamal MM. Developing and testing of an Egyptian version of Children's Health Locus of Control scale. J Egypt Public Health Assoc. 1999; 74(1-2):139-73. + Deaux EB. Health Locus of Control in Chukotka children. Alaska Med. 1992 Jul-Sep; 34(3):135-9. + Parcel G.S. and Meyer M.P. (1978) Development of an instrument to measure children's health locus of control. Health Education Monographs, 6, 149-159. + Multiple countries and cultural groups + Self + Healthy Children; Children with Medical Conditions + English, Russian, a 9- item shorter Egyptian version + Has adequate reliability, construct validity and internal consistency. + Children and Adolescents + no + Few but definitions not specific enough CHLC Children's Health Locus of Control Scale Children's Health Locus of Control Scale (CHLC) @@ -24812,68 +24247,68 @@ Also suggest inclusion in the EFO, below measurement. - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Surgical removal of the gallbladder. - http://purl.bioontology.org/ontology/MESH/D002763 - Sufficient - SCDO:0000222 + http://purl.bioontology.org/ontology/MESH/D002763 + Sufficient + SCDO:0000222 MESH:D002763 Cholecystectomies Cholecystectomy @@ -24881,141 +24316,141 @@ Also suggest inclusion in the EFO, below measurement. - + - + - + A condition that co-exists or follows from sickle cell disease and that has a slow, creeping onset, slow progress and long continuance of disease manifestations. + Probably too specific to warrant inclusion into anther ontology. + Used info in "Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014" to link to relevant phenotypes. + None SCDO http://purl.bioontology.org/ontology/MESH/Q000150 http://purl.obolibrary.org/obo/HP_0011010 - Probably too specific to warrant inclusion into anther ontology. - Used info in "Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014" to link to relevant phenotypes. - None Chronic Complications of Sickle Cell Disease - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Chronic kidney disease (CKD) is defined as either having a glomerular filtration rate (GFR) of <60 mL/min/1.73 mL for >3 months with or without kidney damage or having evidence of kidney damage for 3 months, with or without decreased GFR. + Suggest update to description in DO (currently no definition). + NHLBI SCD New guidelines 2014. + When assessed by albuminuria, often presents in second decade of life in sickle cell disease and prevalence increases with age. + CKD is classified using a combination of GFR and ACR categories + Sickle cell disease, hypertension, diabetes, polycystic kidney disease, glomerulonephritis, various other causes. + Reduced glomerular filtration, elevated creatinine, anemia, bone disease, uremia. + Few but definitions not specific enough SCDO NHLBI SCD New guidelines 2014. - Suggest update to description in DO (currently no definition). - NHLBI SCD New guidelines 2014. - When assessed by albuminuria, often presents in second decade of life in sickle cell disease and prevalence increases with age. - CKD is classified using a combination of GFR and ACR categories - Sickle cell disease, hypertension, diabetes, polycystic kidney disease, glomerulonephritis, various other causes. - Reduced glomerular filtration, elevated creatinine, anemia, bone disease, uremia. - Few but definitions not specific enough DOID:784 CKD Chronic Kidney Injury @@ -25026,13 +24461,13 @@ Also suggest inclusion in the EFO, below measurement. - + - - + + Is a long-term condition where the kidneys don't work as well as they should. - - There is conflicting positioning of this term in different ontologies. Need an expert to decide descriptions and positioning of this and related terms. + + There is conflicting positioning of this term in different ontologies. Need an expert to decide descriptions and positioning of this and related terms. CKD deprecated-Chronic Kidney Injury true @@ -25040,85 +24475,85 @@ Also suggest inclusion in the EFO, below measurement. - + - - + + - + - + - - + + - - + + - - + + - - + + - - + + Chronic pain caused by damage to nerve fibers. It is usually associated with tissue injury. This pain is usually described as burning, numb, tingling, lancinating, shooting, or paroxysmal in nature and is associated with a sensation of pins and needles. Its severity is also enhanced by exposure to either cold or heat. - Request inclusion into relevant ontology - - Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 - Few but definitions not freely available + Request inclusion into relevant ontology + + Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 + Few but definitions not freely available Chronic Neuropathic Pain - + - - + + This pain occurs in a specific tissue or organ and is usually described as constant and deep, nagging, and achy in nature. - Request inclusion into relevant ontology - Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 - None + Request inclusion into relevant ontology + Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 + None Chronic Pain in a Specific Tissue or Organ - + - - + + The only complaint is the patient's self-report of pain that does not go away. + Request inclusion into relevant ontology + Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 + http://doi.org/10.1182/blood-2012-04-383430 + None Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 - Request inclusion into relevant ontology - Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 - http://doi.org/10.1182/blood-2012-04-383430 - None Intractable Chronic Pain Without Obvious Pathology This type of chronic sickle cell pain may be an extension of recurrent acute painful episodes. Therefore, early and aggressive intervention in treating acute sickle cell @@ -25128,50 +24563,50 @@ pain may reduce the development of chronic pain. - + - + - - + + - - + + - - + + - - + + - - + + - - + + Restrictive lung disease is a category of extrapulmonary, pleural, or parenchymal respiratory diseases that restrict lung expansion, resulting in a decreased lung volume, an increased work of breathing, and inadequate ventilation and/or oxygenation. Pulmonary function test demonstrates a decrease in the forced vital capacity. - The description does not seem complete as it does not address the "chronic" aspect. + The description does not seem complete as it does not address the "chronic" aspect. Request inclusion into relevant ontology -Wikipedia was used as the description source. Perhaps rather use NCIT's "Restrictive Lung Disease", and then use wikipedia as source for additional info. Did not find "Chronic Restrictive Lung Disease" in ontologies, but did find "Chronic Obstructive Lung Disease"...perhaps there was confusion between these terms when giving the name? - - None +Wikipedia was used as the description source. Perhaps rather use NCIT's "Restrictive Lung Disease", and then use wikipedia as source for additional info. Did not find "Chronic Restrictive Lung Disease" in ontologies, but did find "Chronic Obstructive Lung Disease"...perhaps there was confusion between these terms when giving the name? + + None Chronic Restrictive Ventilatory Defect Restrictive Lung Disease Chronic Restrictive Lung Disease @@ -25179,150 +24614,150 @@ Wikipedia was used as the description source. Perhaps rather use NCIT's &qu - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Persistent pain in sickle cell disease. In sickle cell disease, persistent pain (pain that has lasted longer than 3 to 6 months) no longer serves as a warning sign. However, the time distinction is arbitrary and the condition may be difficult to distinguish from frequently recurring acute pain. Chronic pain may occur with objective signs of avascular necrosis, arthropathy, arthritis, leg ulcers or vertebral body collapse, or without objective signs, due to neuroplasticity of the peripheral nervous system. + Request inclusion into relevant ontology + + SCD Management guidelines - Tanzania + None SCDO Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 - Request inclusion into relevant ontology - - SCD Management guidelines - Tanzania - None SCD-Associated Chronic Pain Chronic Sickle Cell Pain - + - - + + - - + + Sickle cell pain management that aims to restore function and improve the quality of life. + Request inclusion into MESH below "Pain Management" / "Sickle Cell Pain Management" (also to be suggested for inclusion) + + None SCDO - Request inclusion into MESH below "Pain Management" / "Sickle Cell Pain Management" (also to be suggested for inclusion) - - None Chronic Sickle Cell Pain Treatment Chronic Sickle Cell Pain Management - + - + - + - - + + - - + + - - + + An indication of a person's current cigarette use as well as some indication of cigarette smoking history. + Request inclusion below "smoking status" in Exposure Ontology + None SCDO (Jade Hotchkiss) - Request inclusion below "smoking status" in Exposure Ontology - None Cigarette Smoking Status Measurement Cigarette Smoking Status - + - - + + Meteorological conditions, including temperature, precipitation, and wind, that characteristically prevail in a particular region; includes regions of the earth having particular meteorological conditions. - http://bioportal.bioontology.org/ontologies/CRISP?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCSP%2F1035-6799 - Sufficient - SCDO:0000236 + http://bioportal.bioontology.org/ontologies/CRISP?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCSP%2F1035-6799 + Sufficient + SCDO:0000236 CRISP:1035-6799 Climate - + - - + + Process of substituting a symbol or code for a term such as a diagnosis or procedure. (from Slee's Health Care Terms, 3d ed.) - Add specific Sickle Cell Disease related codes as instances/individuals below *Clinical Coding*? (see ICD-10 codes here: www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-) - http://purl.bioontology.org/ontology/MESH/D059019 - Sufficient - SCDO:0000245 + Add specific Sickle Cell Disease related codes as instances/individuals below *Clinical Coding*? (see ICD-10 codes here: www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-) + http://purl.bioontology.org/ontology/MESH/D059019 + Sufficient + SCDO:0000245 MESH:D059019 Coding Medical Coding @@ -25331,14 +24766,14 @@ Wikipedia was used as the description source. Perhaps rather use NCIT's &qu - + - - + + The capability to perform acceptably those duties directly related to patient care. - http://purl.bioontology.org/ontology/MESH/D002983 - Sufficient - SCDO:0000246 + http://purl.bioontology.org/ontology/MESH/D002983 + Sufficient + SCDO:0000246 MESH:D002983 Clinical Competencies Clinical Competency @@ -25352,12 +24787,12 @@ Wikipedia was used as the description source. Perhaps rather use NCIT's &qu - + - - + + 'Work that consists of a conference of physicians on their observations of a patient at the bedside, regarding the physical state, laboratory and other diagnostic findings, clinical manifestations, results of current therapy, etc. A clinical conference usually ends with a confirmation or correction of clinical findings by a pathological diagnosis performed by a pathologist. Clinical conference is often referred to as a clinico-pathological conference. [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D016429 + http://purl.bioontology.org/ontology/MESH/D016429 MESH:D016429 Clinico-Pathologic Conference Clinico-Pathological Conference @@ -25367,10 +24802,10 @@ Wikipedia was used as the description source. Perhaps rather use NCIT's &qu - + - - + + 'A quick and accurate way of assessing the patient health states using well defined set of questions and analyzed for an optimal clinical decision for the patient. [Curator team: Gaston K. Mazandu]' obsolete Clinical Diagnostic Questionnaire true @@ -25378,17 +24813,17 @@ Wikipedia was used as the description source. Perhaps rather use NCIT's &qu - + - - + + A physician administered examination to assess peripheral neuropathy. + + PhenX protocol: Neuropathy - Clinical Assessment #130201 + Can be used to assess the severity of symptoms and disability associated with peripheral neuropathy caused by a number of disorders including tumors, infections, autoimmune diseases, and inherited disorders such as Charcot-Marie-Tooth disease. + Sufficient + SCDO:0000250 - - PhenX protocol: Neuropathy - Clinical Assessment #130201 - Can be used to assess the severity of symptoms and disability associated with peripheral neuropathy caused by a number of disorders including tumors, infections, autoimmune diseases, and inherited disorders such as Charcot-Marie-Tooth disease. - Sufficient - SCDO:0000250 phenX:130201 Charcot-Marie-Tooth Neuropathy Score Neuropathy - Clinical Assessment @@ -25397,56 +24832,56 @@ Wikipedia was used as the description source. Perhaps rather use NCIT's &qu - + - - + + - + - - + + - - + + - - + + - - + + Abnormal clinical manifestations of beta thalassemia that are as a result of the underlying genotype. + Could this not rather be "Clinical Subtype of Beta Thalassemia"? See "clinical subtype" in Orphanet. + Request inclusion into relevant ontology + None SCDO (Clair Ingram) - Could this not rather be "Clinical Subtype of Beta Thalassemia"? See "clinical subtype" in Orphanet. - Request inclusion into relevant ontology - None Clinical Phenotype of Beta Thalassemia - + - - + + 'A work that reports on the results of a research study to evaluate interventions or exposures on biomedical or health-related outcomes. The two main types of clinical studies are interventional studies (clinical trials) and observational studies. While most clinical studies concern humans, this publication type may be used for clinical veterinary articles meeting the requisites for humans. [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D000068397 + http://purl.bioontology.org/ontology/MESH/D000068397 MESH:D000068397 obsolete Clinical Study true @@ -25454,27 +24889,27 @@ Wikipedia was used as the description source. Perhaps rather use NCIT's &qu - + - - + + Works about research studies that evaluate interventions or exposures on biomedical or health-related outcomes. The two main types of clinical studies are interventional studies (clinical trials) and observational studies. - Term to be adapted as necessary to match EDDA Study Designs Taxonomy - http://purl.bioontology.org/ontology/MESH/D000068456 - Sufficient - SCDO:0000253 + Term to be adapted as necessary to match EDDA Study Designs Taxonomy + http://purl.bioontology.org/ontology/MESH/D000068456 + Sufficient + SCDO:0000253 MESH:D000068456 Clinical Studies as Topic - + - - + + 'A work that reports on the results of a clinical study in which participants are assigned to receive one or more interventions so that researchers can evaluate the interventions on biomedical or health-related outcomes. The assignments are determined by the study protocol. Participants may receive diagnostic, therapeutic, or other types of interventions. While most clinical trials concern humans, this publication type may be used for clinical veterinary articles meeting the requisites for humans. [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D016430 + http://purl.bioontology.org/ontology/MESH/D016430 MESH:D016430 Intervention Study obsolete Clinical Trial @@ -25483,12 +24918,12 @@ Wikipedia was used as the description source. Perhaps rather use NCIT's &qu - + - - + + 'Work that is the report of a pre-planned, usually controlled, clinical study of the safety and efficacy of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques based on a small number of healthy persons and conducted over the period of about a year in either the United States or a foreign country. [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D017426 + http://purl.bioontology.org/ontology/MESH/D017426 MESH:D017426 Clinical Trial, Phase 1 obsolete Clinical Trial, Phase I @@ -25497,12 +24932,12 @@ Wikipedia was used as the description source. Perhaps rather use NCIT's &qu - + - - + + 'Work that is a report of a pre-planned, usually controlled, clinical study of the safety and efficacy of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques based on several hundred volunteers, including a limited number of patients, and conducted over a period of about two years in either the United States or a foreign country. [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D017427 + http://purl.bioontology.org/ontology/MESH/D017427 MESH:D017427 Clinical Trial, Phase 2 obsolete Clinical Trial, Phase II @@ -25511,12 +24946,12 @@ Wikipedia was used as the description source. Perhaps rather use NCIT's &qu - + - - + + 'Work that is a report of a planned post-marketing study of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques that have been approved for general sale after clinical trials, phases I, II, and III. These studies, conducted in the United States or a foreign country, often garner additional data about the safety and efficacy of a product. [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D017429 + http://purl.bioontology.org/ontology/MESH/D017429 MESH:D017429 Clinical Trial, Phase 4 obsolete Clinical Trial, Phase IV @@ -25525,12 +24960,12 @@ Wikipedia was used as the description source. Perhaps rather use NCIT's &qu - + - - + + 'Work that is a report of a pre-planned, usually controlled, clinical study of the safety and efficacy of diagnostic, therapeutic, or prophylactic drugs, devices, or techniques after phase II trials. A large enough group of patients is studied and closely monitored by physicians for adverse response to long-term exposure, over a period of about three years in either the United States or a foreign country. [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D017428 + http://purl.bioontology.org/ontology/MESH/D017428 MESH:D017428 Clinical Trial, Phase 3 obsolete Clinical Trial, Phase III @@ -25539,58 +24974,58 @@ Wikipedia was used as the description source. Perhaps rather use NCIT's &qu - + - - + + Works about pre-planned studies of the safety, efficacy, or optimum dosage schedule (if appropriate) of one or more diagnostic, therapeutic, or prophylactic drugs, devices, or techniques selected according to predetermined criteria of eligibility and observed for predefined evidence of favorable and unfavorable effects. This concept includes clinical trials conducted both in the U.S. and in other countries. - http://purl.bioontology.org/ontology/MESH/D002986 - Sufficient - SCDO:0000259 + http://purl.bioontology.org/ontology/MESH/D002986 + Sufficient + SCDO:0000259 MESH:D002986 Clinical Trials as Topic - + - - + + - - + + - - + + - - + + - - + + - - + + A direct form of psychotherapy based on the interpretation of situations (cognitive structure of experiences) that determine how an individual feels and behaves. It is based on the premise that cognition, the process of acquiring knowledge and forming beliefs, is a primary determinant of mood and behavior. The therapy uses behavioral and verbal techniques to identify and correct negative thinking that is at the root of the aberrant behavior. - http://purl.bioontology.org/ontology/MESH/D015928 - Sufficient - SCDO:0000262 + http://purl.bioontology.org/ontology/MESH/D015928 + Sufficient + SCDO:0000262 MESH:D015928 CBT Cognition Therapies @@ -25606,14 +25041,14 @@ Wikipedia was used as the description source. Perhaps rather use NCIT's &qu - + - - + + Studies in which subsets of a defined population are identified. These groups may or may not be exposed to factors hypothesized to influence the probability of the occurrence of a particular disease or other outcome. Cohorts are defined populations which, as a whole, are followed in an attempt to determine distinguishing subgroup characteristics. - http://purl.bioontology.org/ontology/MESH/D015331 - Sufficient - SCDO:0000263 + http://purl.bioontology.org/ontology/MESH/D015331 + Sufficient + SCDO:0000263 MESH:D015331 Cohort Analyses Cohort Studies @@ -25621,63 +25056,63 @@ Wikipedia was used as the description source. Perhaps rather use NCIT's &qu - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + A profound state of unconsciousness associated with depressed cerebral activity from which the individual cannot be aroused. Coma generally occurs when there is dysfunction or injury involving both cerebral hemispheres or the brain stem reticular formation. - The specific type of Blood Test (s) used to diagnose a coma should be specified. -- -- Named Individual removed (is diagnosed by): -- As in any neurologic condition, history and examination form the cornerstone of diagnosis when the patient is in a coma; however, history must be obtained from family, friends, or EMS. The Glasgow Coma Scale is a system of examining a comatose patient. It is helpful for evaluating the depth of the coma, tracking the patient's progress, and predicting (somewhat) the ultimate outcome of the coma. The Glasgow Coma Scale assigns a different number of points for exam results in three different categories: opening the eyes, verbal response (using words or voice to respond), and motor response (moving a part of the body). Fifteen is the largest possible number of total points, indicating the highest level of functioning. The highest level of functioning would be demonstrated by an individual who spontaneously opens his/her eyes, gives appropriate answers to questions about his/her situation, and can carry out a command (such as "move your leg" or "nod your head"). Three is the least possible number of total points and would be given to a patient for whom not even a painful stimulus is sufficient to provoke a response. In the middle are those patients who may be able to respond, but who require an intense or painful stimulus, and whose response may demonstrate some degree of brain malfunctioning (such as a person whose only response to pain in a limb is to bend that limb in toward the body). When performed as part of the admission examination, a Glasgow score of three to five points often suggests that the patient has likely suffered fatal brain damage, while eight or more points indicates that the patient's chances for recovery are good. Expansion of the pupils and respiratory pattern are also important. Metabolic causes of coma are diagnosed from blood work and urinalysis to evaluate blood chemistry, drug screen, and blood cell abnormalities that may indicate infection. Anatomic causes of coma are diagnosed from CT (computed tomography) or MRI (magnetic resonance imaging) scans. - http://purl.bioontology.org/ontology/MESH/D003128 - Sufficient - SCDO:0000265 + The specific type of Blood Test (s) used to diagnose a coma should be specified. -- -- Named Individual removed (is diagnosed by): -- As in any neurologic condition, history and examination form the cornerstone of diagnosis when the patient is in a coma; however, history must be obtained from family, friends, or EMS. The Glasgow Coma Scale is a system of examining a comatose patient. It is helpful for evaluating the depth of the coma, tracking the patient's progress, and predicting (somewhat) the ultimate outcome of the coma. The Glasgow Coma Scale assigns a different number of points for exam results in three different categories: opening the eyes, verbal response (using words or voice to respond), and motor response (moving a part of the body). Fifteen is the largest possible number of total points, indicating the highest level of functioning. The highest level of functioning would be demonstrated by an individual who spontaneously opens his/her eyes, gives appropriate answers to questions about his/her situation, and can carry out a command (such as "move your leg" or "nod your head"). Three is the least possible number of total points and would be given to a patient for whom not even a painful stimulus is sufficient to provoke a response. In the middle are those patients who may be able to respond, but who require an intense or painful stimulus, and whose response may demonstrate some degree of brain malfunctioning (such as a person whose only response to pain in a limb is to bend that limb in toward the body). When performed as part of the admission examination, a Glasgow score of three to five points often suggests that the patient has likely suffered fatal brain damage, while eight or more points indicates that the patient's chances for recovery are good. Expansion of the pupils and respiratory pattern are also important. Metabolic causes of coma are diagnosed from blood work and urinalysis to evaluate blood chemistry, drug screen, and blood cell abnormalities that may indicate infection. Anatomic causes of coma are diagnosed from CT (computed tomography) or MRI (magnetic resonance imaging) scans. + http://purl.bioontology.org/ontology/MESH/D003128 + Sufficient + SCDO:0000265 MESH:D003128 Comas Coma @@ -25685,18 +25120,18 @@ Wikipedia was used as the description source. Perhaps rather use NCIT's &qu - + - + A co-existing or additional disease with reference to an initial diagnosis or with reference to the index condition that is the subject of study. + Request inclusion into relevant ontology + +As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Joseph Telfair -- Include here: -- Asthma -- Osteonecrosis of the Femoral Head -- Restrictive Lung Disease (currently Chronic Restrictive Lung Disease in SCDO) -- Retinopathy -- Cardiac Dysfunction -- Renal Dysfunction/Renal Failure -- -- ...and others + Few but definitions not freely available SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - -As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Joseph Telfair -- Include here: -- Asthma -- Osteonecrosis of the Femoral Head -- Restrictive Lung Disease (currently Chronic Restrictive Lung Disease in SCDO) -- Retinopathy -- Cardiac Dysfunction -- Renal Dysfunction/Renal Failure -- -- ...and others - Few but definitions not freely available Additional Disease Co-Existing Disease Co-Morbid Condition @@ -25706,14 +25141,14 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + Comparison of outcomes, results, responses, etc for different techniques, therapeutic approaches or other inputs. - http://purl.bioontology.org/ontology/MESH/D003160 - Sufficient - SCDO:0000268 + http://purl.bioontology.org/ontology/MESH/D003160 + Sufficient + SCDO:0000268 MESH:D003160 Comparative Studies Comparative Study @@ -25721,14 +25156,14 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + Therapeutic practices which are not currently considered an integral part of conventional allopathic medical practice. They may lack biomedical explanations but as they become better researched some (physical therapy modalities; diet; acupuncture) become widely accepted whereas others (humors, radium therapy) quietly fade away, yet are important historical footnotes. Therapies are termed as Complementary when used in addition to conventional treatments and as Alternative when used instead of conventional treatment. Year introduced: 2002(1986). - http://purl.bioontology.org/ontology/MESH/D000529 - Sufficient - SCDO:0000271 + http://purl.bioontology.org/ontology/MESH/D000529 + Sufficient + SCDO:0000271 MESH:D000529 Complementary Medicine Complementary Therapy @@ -25736,10 +25171,10 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + 'Compound heterozygosity in medical genetics is the condition of having two heterogeneous recessive alleles at a particular locus that can cause genetic disease in a heterozygous state. [Curator team: []]' obsolete Compound Heterozygous Hemoglobinopathy true @@ -25747,38 +25182,38 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - + - + - - + + Dark red, comma- or corkscrew-shaped vascular fragment that appears to be isolated from neighboring blood vessels in the conjunctiva. Normally benign, this lesion can serve as the first diagnostic sign of sickle cell retinopathy. The conjunctival comma sign results from transient vaso-occlusive processes in the microvasculature of bulbar conjunctiva. It is not seen in sickle trait, but is common in SCD. - Request inclusion into relevant ontology. - Ballas et al 2010 Am J Hematol - None + Request inclusion into relevant ontology. + Ballas et al 2010 Am J Hematol + None Conjunctival Comma Sign - + - - + + 'A work that consists of summary statements representing the majority and current agreement of physicians, scientists, and other professionals meeting to reach a consensus on a selected subject. [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D016446 + http://purl.bioontology.org/ontology/MESH/D016446 MESH:D016446 obsolete Consensus Development Conference true @@ -25786,12 +25221,12 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + 'Work consisting of summary statements, from a conference sponsored by NIH, representing the majority of current opinion of physicians, scientists, and other professionals on a selected subject. [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D016447 + http://purl.bioontology.org/ontology/MESH/D016447 MESH:D016447 NIH Consensus Development Conference obsolete Consensus Development Conference, NIH @@ -25800,26 +25235,26 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - - + + A tool for collecting standardized information on enrollees' experiences with health plans and their services. + Request inclusion into NCIT below "Research or Clinical Assessment Tool". + + PhenX protocol: Quality of Care - Children #820102 + Proxy (Primary caregiver) + Used to assess the patient-reported health care needs and quality of service from health care providers for individuals with chronic conditions such as sickle cell disease (SCD). + Children and adolescents, ages 17 and younger + yes + None - Request inclusion into NCIT below "Research or Clinical Assessment Tool". - - PhenX protocol: Quality of Care - Children #820102 - Proxy (Primary caregiver) - Used to assess the patient-reported health care needs and quality of service from health care providers for individuals with chronic conditions such as sickle cell disease (SCD). - Children and adolescents, ages 17 and younger - yes - None PhenX:820102 This measure includes general questions about access to care and quality of care and additional questions about the services provided to children with chronic conditions. Items CC1-CC38 of the questionnaire are version 4.0 of the Children with Chronic Conditions Item Set. Consumer Assessment of Healthcare Providers and Systems (CAHPS) Health Plan Survey 4.0 Child Medicaid Questionnaire @@ -25827,14 +25262,14 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + A study in which observations are made before and after an intervention, both in a group that receives the intervention and in a control group that does not. - http://purl.bioontology.org/ontology/MESH/D065187 - Sufficient - SCDO:0000282 + http://purl.bioontology.org/ontology/MESH/D065187 + Sufficient + SCDO:0000282 MESH:D065187 Controlled Before-After Studies Controlled Pre-Post Studies @@ -25842,12 +25277,12 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + 'A work that reports on a clinical trial involving one or more test treatments, at least one control treatment, specified outcome measures for evaluating the studied intervention, and a bias-free method for assigning patients to the test treatment. The treatment may be drugs, devices, or procedures studied for diagnostic, therapeutic, or prophylactic effectiveness. Control measures include placebos, active medicine, no-treatment, dosage forms and regimens, historical comparisons, etc. When randomization using mathematical techniques, such as the use of a random numbers table, is employed to assign patients to test or control treatments, the trial is characterized as a randomized controlled trial. [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D018848 + http://purl.bioontology.org/ontology/MESH/D018848 MESH:D018848 obsolete Controlled Clinical Trial true @@ -25855,28 +25290,28 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + Works about clinical trials involving one or more test treatments, at least one control treatment, specified outcome measures for evaluating the studied intervention, and a bias-free method for assigning patients to the test treatment. The treatment may be drugs, devices, or procedures studied for diagnostic, therapeutic, or prophylactic effectiveness. Control measures include placebos, active medicines, no-treatment, dosage forms and regimens, historical comparisons, etc. When randomization using mathematical techniques, such as the use of a random numbers table, is employed to assign patients to test or control treatments, the trials are characterized as randomized controlled trials as topic. - http://purl.bioontology.org/ontology/MESH/D018849 - Sufficient - SCDO:0000284 + http://purl.bioontology.org/ontology/MESH/D018849 + Sufficient + SCDO:0000284 MESH:D018849 Controlled Clinical Trials as Topic - + - - + + A state of harmony between internal needs and external demands and the processes used in achieving this condition. - http://purl.bioontology.org/ontology/MESH/D000223 - Sufficient - SCDO:0000286 + http://purl.bioontology.org/ontology/MESH/D000223 + Sufficient + SCDO:0000286 MESH:D000223 Adaptive Behavior Adaptive Behaviors @@ -25890,20 +25325,20 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + The CSQ-SCD consists of 78 items, which make up seven scales related to coping with pain in general: Diverting attention, Reinterpreting pain sensations, Calming self-statements, Ignoring pain sensations, Praying and hoping, Catastrophising, and Increasing activity level; together with six scales developed as specifically relevant to sickle cell disease: Fear self-statements, Anger self-statements, Isolation, Taking fluids, Resting, and Heat/cold/massage. Patients rated their use of each response from 0 = never to 6 = always, and scores were averaged to produce a mean for each scale. Two additional aspects were assessed by single items: perceived ability to control pain was rated from 0 = no control to 6 = complete control, and perceived ability to decrease pain was rated from 0 = can't decrease it at all to 6 = can decrease it completely. + Request inclusion into NCIT below "Research or Clinical Assessment Tool". + Abrams M.R., Phillips G. and Keefe F.J. (1989). Sickle cell disease pain: Relation of coping strategies + Multiple countries and cultural groups + Self + Adults with SCD + Demonstrated validity with SCD populations USA and UK; several publications. + Adults + None Gil K.M., Abrams M.R., Phillips G. and Keefe F.J. (1989). Sickle cell disease pain: Relation of coping strategies to adjustment. Journal of Consulting and Clinical Psychology, 57, 725-731. - Request inclusion into NCIT below "Research or Clinical Assessment Tool". - Abrams M.R., Phillips G. and Keefe F.J. (1989). Sickle cell disease pain: Relation of coping strategies - Multiple countries and cultural groups - Self - Adults with SCD - Demonstrated validity with SCD populations USA and UK; several publications. - Adults - None CSQ-SCD Coping Strategies Questionnaire revised for Sickle Cell Disease Coping Strategies Questionnaire revised for Sickle Cell Disease (CSQ-SCD) @@ -25911,77 +25346,77 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + The CSQ-SCD consists of 78 items, which make up seven scales related to coping with pain in general: Diverting attention, Reinterpreting pain sensations, Calming self-statements, Ignoring pain sensations, Praying and hoping, Catastrophising, and Increasing activity level; together with six scales developed as specifically relevant to sickle cell disease: Fear self-statements, Anger self-statements, Isolation, Taking fluids, Resting, and Heat/cold/massage. Patients rated their use of each response from 0 = never to 6 = always, and scores were averaged to produce a mean for each scale. Two additional aspects were assessed by single items: perceived ability to control pain was rated from 0 = no control to 6 = complete control, and perceived ability to decrease pain was rated from 0 = can't decrease it at all to 6 = can decrease it completely. + Request inclusion into NCIT below "Research or Clinical Assessment Tool". + Gil K.M., Williams D.A., Thompson, R.J. and Kinney, T.R. (1991). Sickle cell disease in children and adolescents: The relation of child and parent pain coping strategies to adjustment. Journal of Pediatric Psychology, 16, 643-663. + Multiple countries and cultural groups + Self + Children with SCD + Demonstrated validity with SCD populations USA and UK; several publications. + Children + None Gil K.M., Williams D.A., Thompson, R.J. and Kinney, T.R. (1991). Sickle cell disease in children and adolescents: The relation of child and parent pain coping strategies to adjustment. Journal of Pediatric Psychology, 16, 643-663. - Request inclusion into NCIT below "Research or Clinical Assessment Tool". - Gil K.M., Williams D.A., Thompson, R.J. and Kinney, T.R. (1991). Sickle cell disease in children and adolescents: The relation of child and parent pain coping strategies to adjustment. Journal of Pediatric Psychology, 16, 643-663. - Multiple countries and cultural groups - Self - Children with SCD - Demonstrated validity with SCD populations USA and UK; several publications. - Children - None CSQ-SCD Children Coping Strategies Questionnaire revised for Sickle Cell Disease Children (CSQ-SCD Children) - + - - + + - + A causal adverse drug event that is induced by a corticosteroid. + Request inclusion into OAE below "Causal Adverse Drug Event". + None SCDO (Jade Hotchkiss) - Request inclusion into OAE below "Causal Adverse Drug Event". - None Corticosteroid-Induced Adverse Event - + - - + + - + A corticosteroid-induced adverse event that has the outcome of vaso-occlusion. + Request inclusion into OAE below "Corticosteroid-Induced Adverse Event" (also suggested by us for inclusion). + None SCDO (Jade Hotchkiss) - Request inclusion into OAE below "Corticosteroid-Induced Adverse Event" (also suggested by us for inclusion). - None Corticosteroid-Induced Vaso-Occlusive Adverse Event - + - - - + + + The personal cost of disease which may be economic, social, or psychological. The cost of illness may be reflected in absenteeism, productivity, response to treatment, peace of mind, or quality of life. It differs from health care costs, the societal cost of providing services related to the delivery of health care. - http://purl.bioontology.org/ontology/MESH/D017281 - Sufficient - SCDO:0000294 + http://purl.bioontology.org/ontology/MESH/D017281 + Sufficient + SCDO:0000294 MESH:D017281 Burden of Illness Cost of Disease @@ -25996,14 +25431,14 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + The extent to which a health intervention can be regarded as providing value for money, based on a cost-effectiveness analysis that compares the costs and health effects of the intervention. This informs decision-makers who have to determine where to allocate limited healthcare resources. - Request inclusion into relevant ontology, possibly into MESH, perhaps in an appropriate place below "Quality of Health Care". - http://www.medicine.ox.ac.uk/bandolier/painres/download/whatis/Cost-effect.pdf - Negligable + Request inclusion into relevant ontology, possibly into MESH, perhaps in an appropriate place below "Quality of Health Care". + http://www.medicine.ox.ac.uk/bandolier/painres/download/whatis/Cost-effect.pdf + Negligable Health Care Economics Health Economics Cost-Effectiveness of Healthcare @@ -26011,75 +25446,75 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - - + + + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A bioassay to measure the serum concentration of creatinine, a metabolite of muscle creatine that is filtered out of blood by the kidneys. - - Sufficient - SCDO:0000296 + + Sufficient + SCDO:0000296 phenX:141400 Blood Creatinine Assay Blood Creatinine Test @@ -26090,14 +25525,14 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + Brief therapeutic approach which is ameliorative rather than curative of acute psychiatric emergencies. Used in contexts such as emergency rooms of psychiatric or general hospitals, or in the home or place of crisis occurrence, this treatment approach focuses on interpersonal and intrapsychic factors and environmental modification. (APA Thesaurus of Psychological Index Terms, 7th ed) - http://purl.bioontology.org/ontology/MESH/D003419 - Sufficient - SCDO:0000297 + http://purl.bioontology.org/ontology/MESH/D003419 + Sufficient + SCDO:0000297 MESH:D003419 Crisis Interventions Interventions, Crisis @@ -26106,14 +25541,14 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + Studies in which the presence or absence of disease or other health-related variables are determined in each member of the study population or in a representative sample at one particular time. This contrasts with longitudinal studies which are followed over a period of time. - http://purl.bioontology.org/ontology/MESH/D003430 - Sufficient - SCDO:0000298 + http://purl.bioontology.org/ontology/MESH/D003430 + Sufficient + SCDO:0000298 MESH:D003430 Cross-Sectional Analysis Cross-Sectional Study @@ -26122,14 +25557,14 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - + A collective expression for all behaviour patterns acquired and socially transmitted through symbols. Culture includes customs, traditions, and language. - http://purl.bioontology.org/ontology/MESH/D003469 - Sufficient - SCDO:0000299 + http://purl.bioontology.org/ontology/MESH/D003469 + Sufficient + SCDO:0000299 MESH:D003469 Cultural Beliefs Cultural Values @@ -26138,79 +25573,79 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + Therapeutics relating to or used in the cure of diseases. + Request inclusion into relevant ontology + None SCDO http://www.merriam-webster.com/dictionary/curative - Request inclusion into relevant ontology - None Curative Therapeutics - + - + The length of time that a person has lived since their birth up until the current day. + Few but available definitions not adequate SCDO (Jade Hotchkiss) - Few but available definitions not adequate Current Chronological Age Current Age - + - + - - - + + + - - + + - - + + The respondent's highest level of education at the current time. - Request inclusion into MESH below "Socioeconomic Factors". - - Few but definitions not freely available + Request inclusion into MESH below "Socioeconomic Factors". + + Few but definitions not freely available Educational Attainment Current Educational Attainment - + - + - - + + - - + + The respondent's current employment status. - - PhenX protocol: Current Employment Status #11301 - Sufficient - SCDO:0000306 + + PhenX protocol: Current Employment Status #11301 + Sufficient + SCDO:0000306 phenX:11301 Employment Status Current Employment Status @@ -26218,24 +25653,24 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - + - - + + - - + + The respondent's current marital status. - Can add sub-classes of "Marital Status" from MESH. - - PhenX protocol: Current Marital Status #10902 - Sufficient - SCDO:0000307 + Can add sub-classes of "Marital Status" from MESH. + + PhenX protocol: Current Marital Status #10902 + Sufficient + SCDO:0000307 phenX:10902 Marital Status Marital or Partnership Status @@ -26244,23 +25679,23 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - + - - + + The amount of the protein cystatin C (formerly gamma trace, post-gamma-globulin or neuroendocrine basic polypeptide) found in a specified sample of blood. This extracellular cystatin subtype is abundantly expressed in bodily fluids. + This class is used as a biomarker of kidney function and kidney disease. + + http://purl.bioontology.org/ontology/MESH/D055316 + http://www.ebi.ac.uk/efo/EFO_0004617 + Suggest update to description in CMO - This class is used as a biomarker of kidney function and kidney disease. - - http://purl.bioontology.org/ontology/MESH/D055316 - http://www.ebi.ac.uk/efo/EFO_0004617 - Suggest update to description in CMO CMO:0002777 Blood CC Level Cystatin 3 Level @@ -26275,14 +25710,14 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + A blood disorder characterized by the appearance of sickle-shaped red blood cells and anemia. - http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57- - Sufficient - SCDO:0000311 + http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57- + Sufficient + SCDO:0000311 ICD10CM:D57 D57 D57 Sickle-Cell Disorders @@ -26290,26 +25725,26 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - + - - + + Broad term used to describe several different acute conditions occurring with sickle cell disease, including aplastic crisis, hemolytic crisis, and vasoocclusive crisis. - http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.0 - Sufficient - SCDO:0000312 + http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.0 + Sufficient + SCDO:0000312 ICD10CM:D57.0 D57.0 Hb-SS disease with vasoocclusive pain @@ -26320,31 +25755,31 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - + - + - - + + - + Few but definitions not available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.01 - Few but definitions not available ICD10CM:D57.01 D57.01 Hb-SS disease with acute chest syndrome @@ -26355,25 +25790,25 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - + - - + + - + Few but definitions not available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.02 - Few but definitions not available ICD10CM:D57.02 Acute sickle cell splenic sequestration crisis D57.02 @@ -26384,19 +25819,19 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.1 - Few but definitions not freely available ICD10CM:D57.1 D57.1 Sickle cell anemia without crisis @@ -26406,20 +25841,20 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - - + + One of the sickle cell disorders characterized by the presence of both hemoglobin s and hemoglobin c. It is similar to, but less severe than sickle cell anemia. - http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.2 - Sufficient - SCDO:0000316 + http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.2 + Sufficient + SCDO:0000316 ICD10CM:D57.2 D57.2 D57.2 Sickle-cell/Hb-C disease @@ -26427,25 +25862,25 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - + - - + + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.20 - Few but definitions not freely available ICD10CM:D57.20 D57.20 Sickle Cell Disease-SC without crisis @@ -26455,25 +25890,25 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - - + + - - + + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.21 - Few but definitions not freely available ICD10CM:D57.21 D57.21 Sickle Cell Disease-SC with crisis @@ -26483,31 +25918,31 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - + - - + + - - + + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.211 - Few but definitions not freely available ICD10CM:D57.211 Acute chest syndrome due to sickle cell-hemoglobin c disease crisis Acute chest syndrome sickle cell hb-c crisis @@ -26519,25 +25954,25 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - - + + - - + + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.212 - Few but definitions not freely available ICD10CM:D57.212 D57.212 Sickle Cell Disease-SC with splenic sequestration @@ -26547,25 +25982,25 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - - + + - - + + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.219 - Few but definitions not freely available ICD10CM:D57.219 D57.219 Sickle Cell Disease-SC with crisis NOS @@ -26580,20 +26015,20 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - - + + The condition of being heterozygous for hemoglobin S. - http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.3 - Sufficient - SCDO:0000322 + http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.3 + Sufficient + SCDO:0000322 ICD10CM:D57.3 D57.3 D57.3 Sickle-cell trait @@ -26601,20 +26036,20 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - - + + Hemolytic anemia, in which patients are heterozygous for both the sickle cell gene and a thalassemia gene. - http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.4 - Sufficient - SCDO:0000323 + http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.4 + Sufficient + SCDO:0000323 ICD10CM:D57.4 D57.4 D57.4 Sickle-cell thalassemia @@ -26622,25 +26057,25 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - + - + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.40 - Few but definitions not freely available ICD10CM:D57.40 D57.40 D57.40 Sickle-cell thalassemia without crisis @@ -26648,25 +26083,25 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - + - - + + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.41 - Few but definitions not freely available ICD10CM:D57.41 D57.41 Sickle-cell thalassemia with (painful) crisis @@ -26677,31 +26112,31 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - + - + - - + + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.411 - Few but definitions not freely available ICD10CM:D57.411 D57.411 Sickle-cell thalassemia, unspecified, with acute chest syndrome @@ -26710,25 +26145,25 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - + - - + + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.412 - Few but definitions not freely available ICD10CM:D57.412 D57.412 Sickle cell thalassemia with splenic sequestration @@ -26738,25 +26173,25 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - + - - + + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.419 - Few but definitions not freely available ICD10CM:D57.419 D57.419 Sickle-cell thalassemia with (painful) crisis NOS @@ -26767,13 +26202,13 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.8 - Few but definitions not freely available ICD10CM:D57.8 D57.8 Other sickle-cell disorders @@ -26782,19 +26217,19 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.80 - Few but definitions not freely available ICD10CM:D57.80 D57.80 D57.80 Other sickle-cell disorders without crisis @@ -26802,19 +26237,19 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - - + + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.81 - Few but definitions not freely available ICD10CM:D57.81 D57.81 D57.81 Other sickle-cell disorders with crisis @@ -26822,25 +26257,25 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - + - - + + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.811 - Few but definitions not freely available ICD10CM:D57.811 D57.811 D57.811 Other sickle-cell disorders with acute chest syndrome @@ -26848,19 +26283,19 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - - + + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.812 - Few but definitions not freely available ICD10CM:D57.812 D57.812 D57.812 Other sickle-cell disorders with splenic sequestration @@ -26868,19 +26303,19 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - - + + - + Few but definitions not freely available http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.819 - Few but definitions not freely available ICD10CM:D57.819 D57.819 D57.819 Other sickle-cell disorders with crisis, unspecified @@ -26888,56 +26323,56 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + 'Protein molecule are large, complex molecules that play many critical roles in the body. They do most of the work in cells and are required for the structure, function, and regulation of the body's tissues and organs. [Curator team: []]' - https://ghr.nlm.nih.gov/primer/howgeneswork/protein + https://ghr.nlm.nih.gov/primer/howgeneswork/protein obsolete Protein Molecule true - + - - + + - + - - + + - - + + - - + + - - + + A form of beta-thalassemia characterized by decreased or absent synthesis of the delta- and beta-globin chains with a compensatory increase in expression of fetal gamma-chain synthesis. - - Sufficient - SCDO:0000343 + + Sufficient + SCDO:0000343 ORPHA:231237 Delta Beta Thalassaemia Delta-Beta-Thalassaemia @@ -26948,14 +26383,14 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - + A hereditary disorder characterized by reduced or absent delta-globin thus effecting the level of hemoglobin A2, a minor component of adult hemoglobin monitored in the diagnosis of beta-thalassemia. - http://purl.bioontology.org/ontology/MESH/D055538 - Sufficient - SCDO:0000344 + http://purl.bioontology.org/ontology/MESH/D055538 + Sufficient + SCDO:0000344 MESH:D055538 Delta Thalassaemia Delta Thalassaemias @@ -26968,20 +26403,20 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - + - - + + An acute febrile disease transmitted by the bite of AEDES mosquitoes infected with Dengue Virus. It is self-limiting and characterized by fever, myalgia, headache, and rash. Severe Dengue is a more virulent form of dengue. - http://purl.bioontology.org/ontology/MESH/D003715 - Sufficient - SCDO:0000346 + http://purl.bioontology.org/ontology/MESH/D003715 + Sufficient + SCDO:0000346 MESH:D003715 Break Bone Fever Break-Bone fever @@ -26992,21 +26427,21 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + 'The system pertaining to teeth, oral cavity, and associated structures. [Curator team: []]' - http://medical-dictionary.thefreedictionary.com/dentistry + http://medical-dictionary.thefreedictionary.com/dentistry deprecated Dental System true - + - + Terms that are no longer being used in the ontology. deprecated terms @@ -27014,64 +26449,64 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A common mental disorder, characterized by sadness, hopelessness, loss of interest or pleasure, feelings of guilt or low self-worth, disturbed sleep or appetite, feelings of tiredness, and poor concentration. Depression can be long-lasting or recurrent, substantially impairing an individual's ability to function at work or school or cope with daily life. - http://www.who.int/topics/depression/en/ - Sufficient - SCDO:0000360 + http://www.who.int/topics/depression/en/ + Sufficient + SCDO:0000360 SIO:000824 Depressive Symptoms Low Mood @@ -27080,80 +26515,80 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + Skill in performing tasks, especially with the hands. + Request inclusion into relevant ontology + http://en.oxforddictionaries.com/definition/dexterity + Few but definitions not freely available SCDO - Request inclusion into relevant ontology - http://en.oxforddictionaries.com/definition/dexterity - Few but definitions not freely available Dexterity - + - - + + A medical device used to diagnose medical conditions. - http://purl.obolibrary.org/obo/ERO_0001448 - Sufficient - SCDO:0000376 + http://purl.obolibrary.org/obo/ERO_0001448 + Sufficient + SCDO:0000376 ERO:0001448 Diagnostic Device - + - - + + Diagnostic tools (including the instruments, laboratory assays and methods of patient examination) used for differential diagnosis, the measurements obtained using these tools, and the diagnostic devices used in obtaining the measurements. + Request inclusion into relevant ontology. + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology. - None Diagnostics - + - + - - + + - - + + - - + + - - + + A non-steroidal anti-inflammatory agent (NSAID) with antipyretic and analgesic actions. It is primarily available as the sodium salt. - - Sufficient - SCDO:0000380 + + Sufficient + SCDO:0000380 MESH:D004008 2-((2,6-dichlorophenyl)amino)benzeneacetic acid Diclofenac Acid @@ -27164,105 +26599,105 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - + - + - + - + Concepts involved with nutritional physiology, including categories of substances eaten for sustenance, nutritional phenomena and processes, eating patterns and habits, and measurable nutritional parameters. - Should this term rather be replaced by more specific terms such as Dietary Intake? Or have such terms as sub-classes? - http://purl.bioontology.org/ontology/MESH/D000066888 - Sufficient - SCDO:0000382 + Should this term rather be replaced by more specific terms such as Dietary Intake? Or have such terms as sub-classes? + http://purl.bioontology.org/ontology/MESH/D000066888 + Sufficient + SCDO:0000382 MESH:D000066888 Diet, Food, and Nutrition - + - - + + obsolete Diffusion Capacity by Biochemical Methods true - + - + - + - + - + - - + + - - + + - - + + - - + + The amount of a gas taken up, by the pulmonary capillary blood from the alveolar gas, per minute per unit of average pressure of the gradient of the gas across the blood-air barrier. - http://purl.bioontology.org/ontology/MESH/D011653 - Sufficient - SCDO:0000384 + http://purl.bioontology.org/ontology/MESH/D011653 + Sufficient + SCDO:0000384 MESH:D011653 Alveolar membrane diffusion capacity DL @@ -27274,59 +26709,59 @@ As per: "Transition and Sickle Cell Disease" by Michael R. DeBaun, Jos - + - - + + - + - + - + - - + + - - + + - - + + - - + + Clinical assessment to determine the capacity of an individual's lung to exchange gases (e.g., oxygen and carbon dioxide) across the alveolar-capillary interface. - Suggest update to label in PhenX (from "Lung Function - Diffusion Capacity") + Suggest update to label in PhenX (from "Lung Function - Diffusion Capacity") -Need to add equipment used for this test under "Devices" and link to them below. - - PhenX protocol: Lung Function - Diffusion Capacity #810301 - Suggest update to label +Need to add equipment used for this test under "Devices" and link to them below. + + PhenX protocol: Lung Function - Diffusion Capacity #810301 + Suggest update to label phenX:810301 Pulmonary Diffusing Capacity Test Diffusion Capacity Test @@ -27334,20 +26769,20 @@ Need to add equipment used for this test under "Devices" and link to t - + - - - + + + One DALY can be thought of as one lost year of "healthy" life. The sum of these DALYs across the population, or the burden of disease, can be thought of as a measurement of the gap between current health status and an ideal health situation where the entire population lives to an advanced age, free of disease and disability. - - Multiple countries and cultural groups - Self; Proxy - All - WHO Global Burden of Disease assessment, also used in SCD studies - Children and adults - no - Few but definitions not specific enough + + Multiple countries and cultural groups + Self; Proxy + All + WHO Global Burden of Disease assessment, also used in SCD studies + Children and adults + no + Few but definitions not specific enough DALY Disability-Adjusted Life Year Calculation: DALY = YLL + YLD - The YLL basically correspond to the number of deaths multiplied by the standard life expectancy at the age at which death occurs. The basic formula for YLL (without yet including other social preferences discussed below), is the following for a given cause, age and sex: YLL = N x L where: N = number of deaths L = standard life expectancy at age of death in years. Because YLL measure the incident stream of lost years of life due to deaths, an incidence perspective has also been taken for the calculation of YLD in the original Global Burden of Disease Study for year 1990 and in subsequent WHO updates for years 2000 to 2004. To estimate YLD for a particular cause in a particular time period, the number of incident cases in that period is multiplied by the average duration of the disease and a weight factor that reflects the severity of the disease on a scale from 0 (perfect health) to 1 (dead). The basic formula for YLD is the following (again, without applying social preferences): YLD = I x DW x L where: I = number of incident cases; DW = disability weight; L = average duration of the case until remission or death (years). Prevalence YLD - The recent GBD 2010 study published by IHME in December 2012 used an updated life expectancy standard for the calculation of YLL and based the YLD calculation on prevalence rather than incidence: YLD = P x DW where: P = number of prevalent cases; DW = disability weight. @@ -27356,14 +26791,14 @@ Need to add equipment used for this test under "Devices" and link to t - + - - + + Sudden calamitous events producing great material damage, loss, and distress. They are the result of natural phenomena such as earthquakes, floods, etc. Calamities producing great damage, loss of life, and distress. They include results of natural phenomena and man-made phenomena. Normal conditions of existence are disrupted and the level of impact exceeds the capacity of the hazard-affected community. - http://purl.bioontology.org/ontology/MESH/D004190 - Sufficient - SCDO:0000388 + http://purl.bioontology.org/ontology/MESH/D004190 + Sufficient + SCDO:0000388 MESH:D004190 Disasters Natural Disaster @@ -27373,135 +26808,135 @@ Need to add equipment used for this test under "Devices" and link to t - + - - + + A factor that modifies one or more aspects of a disease, such as sickle cell disease (SCD) (e.g. aspects such as temporal pattern, age of onset and mortality), for specific phenotype(s) of the disease. + Request inclusion into relevant ontology + These article contains a recent description of disease modifiers for SCD: http://www.nejm.org/doi/10.1056/NEJMra1510865 -- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4562292/ -- -- Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/topicpage/sickle-cell-anemia-a-look-at-global-8756219 -- -- Initially, the HP term "Clinical Modifier" (HP:0012823) was used to define this class, but its usage was found to be more "ontology-based" than what the SCDO intended. + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - These article contains a recent description of disease modifiers for SCD: http://www.nejm.org/doi/10.1056/NEJMra1510865 -- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4562292/ -- -- Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/topicpage/sickle-cell-anemia-a-look-at-global-8756219 -- -- Initially, the HP term "Clinical Modifier" (HP:0012823) was used to define this class, but its usage was found to be more "ontology-based" than what the SCDO intended. - None Phenotypic Modifier Disease Modifier - + - + - - + + A diagnostic ultrasound-based imaging technique operating at the frequency range of 2 megahertz. This machine makes use of the doppler effect to measure and visualise blood flow for possible pathology or lesions within blood vessels. + Request inclusion into relevant ontology + None SCDO (Clair Ingram) - Request inclusion into relevant ontology - None Doppler Ultrasound Machine - 2 Megahertz - + - - + + An adverse event that has an outcome of a decreased amount of the drug excreted by the body. - http://purl.obolibrary.org/obo/OAE_0000887 - Sufficient - SCDO:0000397 + http://purl.obolibrary.org/obo/OAE_0000887 + Sufficient + SCDO:0000397 OAE:0000887 Drug Clearance Decreased AE - + - - + + An adverse drug event that results in the development of a dependence on the drug. - http://purl.obolibrary.org/obo/OAE_0000888 - Sufficient - SCDO:0000398 + http://purl.obolibrary.org/obo/OAE_0000888 + Sufficient + SCDO:0000398 OAE:0000888 Drug Dependence AE - + - - + + The amount of drug substances taken into the body. + This seemed an obvious addition to the modifier class? + None SCDO (Jade Hotchkiss) - This seemed an obvious addition to the modifier class? - None Drug Intake - + - - + + A drug AE that has an outcome of lower threshold to the normal pharmacologic action of a drug. - http://purl.obolibrary.org/obo/OAE_0000891 - Sufficient - SCDO:0000400 + http://purl.obolibrary.org/obo/OAE_0000891 + Sufficient + SCDO:0000400 OAE:0000891 Drug Intolerance AE - + - - + + An adverse event that results in symptoms that occur after the discontinuation of the use of a certain drug. - http://purl.obolibrary.org/obo/OAE_0000893 - Sufficient - SCDO:0000401 + http://purl.obolibrary.org/obo/OAE_0000893 + Sufficient + SCDO:0000401 OAE:0000893 Drug Withdrawal Syndrome AE - + - - + + - + A neuropathy AE that is induced by a drug administration. - http://purl.obolibrary.org/obo/OAE_0000165 - Sufficient - SCDO:0000402 + http://purl.obolibrary.org/obo/OAE_0000165 + Sufficient + SCDO:0000402 OAE:0000165 Drug-Induced Neuropathy AE - + - - + + 'The combined specialties of diseases of the ear, pharynx, and larynx, including the upper respiratory tract and diseases of the head and neck, tracheobronchial tree, and esophagus. [Curator team: []]' - http://medical-dictionary.thefreedictionary.com/ear+nose+and+throat + http://medical-dictionary.thefreedictionary.com/ear+nose+and+throat Otolaryngology deprecated Ear, Nose and Throat true @@ -27509,14 +26944,14 @@ Need to add equipment used for this test under "Devices" and link to t - + - + A small hemorrhagic spot, larger than a petechia, in the skin or mucous membrane forming a nonelevated, rounded or irregular, blue or purplish patch. - Suggest update to description. The term in the HPO was not detailed enough. - - Suggest update to description + Suggest update to description. The term in the HPO was not detailed enough. + + Suggest update to description HP:0031364 Ecchymoses Ecchymosis @@ -27524,44 +26959,44 @@ Need to add equipment used for this test under "Devices" and link to t - + - + - - + + - - + + - - + + - - + + - - + + A physiological assay that uses standard ultrasound techniques to take two-dimensional pictures of the cardiovascular system and can produce accurate assessment of the velocity of blood and cardiac tissue at any arbitrary point using pulsed or continuous wave Doppler ultrasound. - http://purl.obolibrary.org/obo/ERO_0000385 - Sufficient - SCDO:0000409 + http://purl.obolibrary.org/obo/ERO_0000385 + Sufficient + SCDO:0000409 ERO:0000385 Cardiac ECHO Cardiac US Scan @@ -27577,34 +27012,34 @@ Need to add equipment used for this test under "Devices" and link to t - + - - + + - - + + A machine used for ultrasonic recording of the size, motion, and composition of the heart and surrounding tissues. + Request inclusion into relevant ontology. + http://purl.bioontology.org/ontology/MESH/D004452 + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology. - http://purl.bioontology.org/ontology/MESH/D004452 - None Echocardiography Machine - + - + Acquisition of knowledge as a result of instruction in a formal course of study. - http://purl.bioontology.org/ontology/MESH/D004493 - Sufficient - SCDO:0000414 + http://purl.bioontology.org/ontology/MESH/D004493 + Sufficient + SCDO:0000414 MESH:D004493 Schooling Education @@ -27612,14 +27047,14 @@ Need to add equipment used for this test under "Devices" and link to t - + - - + + The visual output that an electrocardiograph produces. - Suggest update to description in ERO? - http://en.wiktionary.org/wiki/electrocardiogram - Suggest update to description + Suggest update to description in ERO? + http://en.wiktionary.org/wiki/electrocardiogram + Suggest update to description ERO:0000383 ECG EKG @@ -27628,20 +27063,20 @@ Need to add equipment used for this test under "Devices" and link to t - + - - + + - + Device which makes prolonged electrocardiographic recordings on a portable tape recorder (Holter-type system) or solid-state device (real-time system), while the patient undergoes normal daily activities; useful in the diagnosis and management of intermittent cardiac arrhythmias and transient myocardial ischemia. - http://bioportal.bioontology.org/ontologies/CRISP/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCSP%2F1393-7164 - Sufficient - SCDO:0000416 + http://bioportal.bioontology.org/ontologies/CRISP/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FCSP%2F1393-7164 + Sufficient + SCDO:0000416 CRISP:1393-7164 Ambulatory Electrocardiographic Monitor Electrocardiocorder @@ -27650,86 +27085,86 @@ Need to add equipment used for this test under "Devices" and link to t - + - - + + - - + + - - + + Recording of the moment-to-moment electromotive forces of the heart as projected onto various sites on the body's surface, delineated as a scalar function of time. The recording is monitored by a tracing on slow moving chart paper or by observing it on a cardioscope, which is a cathode ray tube display. - Request that MESH removes ECG, EKG and Elecrocardiogram as synonyms. - - Sufficient - SCDO:0000417 + Request that MESH removes ECG, EKG and Elecrocardiogram as synonyms. + + Sufficient + SCDO:0000417 MESH:D004562 Electrocardiography - + - - + + A graphic record of the electrical activity of the brain as recorded by an electroencephalograph. - Request inclusion into relevant ontology - http://medical-dictionary.thefreedictionary.com/electroencephalogram - Few but definitions not freely available + Request inclusion into relevant ontology + http://medical-dictionary.thefreedictionary.com/electroencephalogram + Few but definitions not freely available Electroencephalogram - + - - + + - - + + An instrument that measures electrical potentials on the scalp and generates a record of the electrical activity of the brain. - Request inclusion into relevant ontology - http://medical-dictionary.thefreedictionary.com/electroencephalograph - Few but definitions not freely available + Request inclusion into relevant ontology + http://medical-dictionary.thefreedictionary.com/electroencephalograph + Few but definitions not freely available Encephalograph Electroencephalograph - + - - + + - - + + - - + + Recording of electric currents developed in the brain by means of electrodes applied to the scalp, to the surface of the brain, or placed within the substance of the brain. - http://purl.bioontology.org/ontology/MESH/D004569 - Sufficient - SCDO:0000420 + http://purl.bioontology.org/ontology/MESH/D004569 + Sufficient + SCDO:0000420 MESH:D004569 EEG Electroencephalography @@ -27737,14 +27172,14 @@ Need to add equipment used for this test under "Devices" and link to t - + - - + + Media that facilitate transportability of pertinent information concerning patient's illness across varied providers and geographic locations. Some versions include direct linkages to online consumer health information that is relevant to the health conditions and treatments related to a specific patient. - http://purl.bioontology.org/ontology/MESH/D057286 - Sufficient - SCDO:0000423 + http://purl.bioontology.org/ontology/MESH/D057286 + Sufficient + SCDO:0000423 MESH:D057286 Computerized Health Records Computerized Medical Records @@ -27756,30 +27191,30 @@ Need to add equipment used for this test under "Devices" and link to t - + - - + + An electrochemical process in which macromolecules or colloidal particles with a net electric charge migrate in a solution under the influence of an electric current. + Perhaps change label to "Hemoglobin Electrophoresis"? Exactsynonym "Hb ELP". See dc:source provided. + http://purl.bioontology.org/ontology/MESH/D004586 + Sufficient + SCDO:0000424 - Perhaps change label to "Hemoglobin Electrophoresis"? Exactsynonym "Hb ELP". See dc:source provided. - http://purl.bioontology.org/ontology/MESH/D004586 - Sufficient - SCDO:0000424 MESH:D004586 Electrophoresis - + - - + + The system pertaining to the stomach, intestines, and associated organs including liver, gallbladder, and pancreas. - - - http://medical-dictionary.thefreedictionary.com/gastroenterology + + + http://medical-dictionary.thefreedictionary.com/gastroenterology Gastroenterology deprecated Endocrine and Metabolic true @@ -27787,29 +27222,29 @@ Need to add equipment used for this test under "Devices" and link to t - + - - + + An environmental factor that modifies one or more aspects of sickle cell disease (SCD) (such as temporal pattern, age of onset and mortality) for specific phenotype(s) in the Phenotype class. - SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology + Request inclusion into relevant ontology -Perhaps include MESH term "Life Change Events" as a main sub-class, with "Disaster" (under Physical Environment) copied below it? - None +Perhaps include MESH term "Life Change Events" as a main sub-class, with "Disaster" (under Physical Environment) copied below it? + None + SCDO (Jade Hotchkiss) Environmental Disease Modifier - + - - + + A method used to measure the relative activity of a specific enzyme or its concentration in solution. Typically an enzyme substrate is added to a buffer solution containing enzyme and the rate of conversion of substrate to product is measured under controlled conditions. Many classical enzymatic assay methods involve the use of synthetic colorimetric substrates and measuring the reaction rates using a spectrophotometer. - http://purl.bioontology.org/ontology/MESH/D057075 - Sufficient - SCDO:0000436 + http://purl.bioontology.org/ontology/MESH/D057075 + Sufficient + SCDO:0000436 MESH:D057075 Enzyme Assay Enzymatic Assay @@ -27817,15 +27252,15 @@ Perhaps include MESH term "Life Change Events" as a main sub-class, wi - + - - + + Studies designed to examine associations, commonly, hypothesized causal relations. They are usually concerned with identifying or measuring the effects of risk factors or exposures. The common types of analytic study are case-control studies; cohort studies; and cross-sectional studies. - Term to be adapted as necessary to match EDDA Study Designs Taxonomy - http://purl.bioontology.org/ontology/MESH/D016021 - Sufficient - SCDO:0000437 + Term to be adapted as necessary to match EDDA Study Designs Taxonomy + http://purl.bioontology.org/ontology/MESH/D016021 + Sufficient + SCDO:0000437 MESH:D016021 Epidemiological Studies Epidemiologic Studies @@ -27833,13 +27268,13 @@ Perhaps include MESH term "Life Change Events" as a main sub-class, wi - + - - + + Types and formulations of studies used in epidemiological and clinical research. - Term to be adapted as necessary to match EDDA Study Designs Taxonomy - http://purl.bioontology.org/ontology/MESH/D016020 + Term to be adapted as necessary to match EDDA Study Designs Taxonomy + http://purl.bioontology.org/ontology/MESH/D016020 MESH:D016020 Epidemiologic Study Characteristics deprecated Epidemiologic Study Characteristics as Topic @@ -27848,45 +27283,45 @@ Perhaps include MESH term "Life Change Events" as a main sub-class, wi - + - + - + A questionnaire to assess epilepsy, a condition characterized by recurrent seizures and which is a component of over 40 neurological disorders (Aminoff, et al., 2005). - - Sufficient - SCDO:0000440 + + Sufficient + SCDO:0000440 phenX:130401 Epilepsy Screener - + - - + + The GHQ is a screening device for identifying minor psychiatric disorders in the general population and within community or non-psychiatric clinical settings such as primary care or general medical outpatients. Suitable for all ages from adolescent upwards (not children), it assesses the respondent's current state and asks if that differs from his or her usual state. It is therefore sensitive to short-term psychiatric disorders but not to long-standing attributes of the respondent. The self-administered questionnaire focuses on two major areas: inability to carry out normal functions; appearance of new and distressing phenomena. It is available in the following versions: GHQ-60 -- the fully detailed 60-item questionnaire; GHQ-30 -- a short form without items relating to physical illness; GHQ-28 -- a 28 item scaled version -- assesses somatic symptoms, anxiety and insomnia, social dysfunction and severe depression; GHQ-12 -- quick, reliable and sensitive short form, ideal for research studies. + Add the different versions of this questionnaire, as listed in the description here. + Request inclusion into NCIT below "Research or Clinical Assessment Tool". + Goldberg, David; Hillier, Valerie (1979). "A scaled version of the General Health Questionnaire". Psychological Medicine. Cambridge University Press. 9 (01): 139–145. + Few but definitions not freely available SCDO - Add the different versions of this questionnaire, as listed in the description here. - Request inclusion into NCIT below "Research or Clinical Assessment Tool". - Goldberg, David; Hillier, Valerie (1979). "A scaled version of the General Health Questionnaire". Psychological Medicine. Cambridge University Press. 9 (01): 139–145. - Few but definitions not freely available GHQ General Health Questionnaire (GHQ) - + - - - + + + The GAD-7 is a self-administered patient questionnaire used as a screening tool and severity measure for generalised anxiety disorder. The GAD-7 score is calculated by assigning scores of 0, 1, 2, and 3, to the response categories of 'not at all', 'several days', 'more than half the days', and 'nearly every day', respectively, and adding together the scores for the seven questions. Scores of 5, 10, and 15 are taken as the cut-off points for mild, moderate and severe anxiety, respectively. When used as a screening tool, further evaluation is recommended when the score is 10 or greater. - Spitzer RL, Kroenke K, Williams JB, et al; A brief measure for assessing generalized anxiety disorder: the GAD-7. Archives of Internal Medicine. 2006;166(10):1092-7. - Few but definitions not specific enough + Spitzer RL, Kroenke K, Williams JB, et al; A brief measure for assessing generalized anxiety disorder: the GAD-7. Archives of Internal Medicine. 2006;166(10):1092-7. + Few but definitions not specific enough NCIT:C88893 GAD-7 Generalised Anxiety Disorder Questionnaire @@ -27895,20 +27330,20 @@ Perhaps include MESH term "Life Change Events" as a main sub-class, wi - + - - + + - - + + An educational process that provides information and advice to individuals or families about a genetic condition that may affect them. The purpose is to help individuals make informed decisions about marriage, reproduction, and other health management issues based on information about the genetic disease, the available diagnostic tests, and management programs. Psychosocial support is usually offered. - http://purl.bioontology.org/ontology/MESH/D005817 - Sufficient - SCDO:0000443 + http://purl.bioontology.org/ontology/MESH/D005817 + Sufficient + SCDO:0000443 MESH:D005817 Prenatal Genetic Counseling Genetic Counseling @@ -27916,32 +27351,32 @@ Perhaps include MESH term "Life Change Events" as a main sub-class, wi - + - - + + - + A biological disease modifier that is of a genetic nature. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Genetic Disease Modifier - + - - + + Organized services to provide diagnosis, treatment, and prevention of genetic disorders. - http://purl.bioontology.org/ontology/MESH/D033142 - Sufficiient + http://purl.bioontology.org/ontology/MESH/D033142 + Sufficiient MESH:D033142 Genetic Services Genetic Service @@ -27949,15 +27384,15 @@ Perhaps include MESH term "Life Change Events" as a main sub-class, wi - + - - + + Chromosomal, biochemical, intracellular, and other methods used in the study of genetics. - This and its sub-classes need work! - http://purl.bioontology.org/ontology/MESH/D005821 - Sufficient - SCDO:0000448 + This and its sub-classes need work! + http://purl.bioontology.org/ontology/MESH/D005821 + Sufficient + SCDO:0000448 MESH:D005821 Genetic Technic Genetic Technics @@ -27967,105 +27402,105 @@ Perhaps include MESH term "Life Change Events" as a main sub-class, wi - + - + - + - + - - + + - - + + Elevated ocular pressure caused by clogging of the trabecular meshwork and by impaired aqueous humor outflow from blood in the anterior chamber (due to ocular trauma or surgery). - Request inclusion into relevant ontology as more specific type (sub-class) of glaucoma. - Ballas et al 2010 Am J Hematol - None + Request inclusion into relevant ontology as more specific type (sub-class) of glaucoma. + Ballas et al 2010 Am J Hematol + None Glaucomas Glaucoma (Secondary to Presence of Blood in the Anterior Chamber of the Eye) - + - + - + A test to assess the respondent's overall mental capability. - - Sufficient - SCDO:0000455 + + Sufficient + SCDO:0000455 phenX:130700 Global Mental Status Screener - + - - + + A genetic locus responsible for the encoding of globins. + Request inclusion into relevant ontology, perhaps below "Genetic Locus" in MESH. + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology, perhaps below "Genetic Locus" in MESH. - None Globin Locus - + - + - - + + - - + + - - + + - - + + Measurement of the flow rate of filtered fluid through the kidney, calculated either by comparative measurements of substances in the blood and urine, or estimated from a blood test. - http://www.ebi.ac.uk/efo/EFO_0005208 - Sufficient - SCDO:0000457 + http://www.ebi.ac.uk/efo/EFO_0005208 + Sufficient + SCDO:0000457 EFO:0005208 GFR Glomerular Filtration Rate @@ -28073,14 +27508,14 @@ Perhaps include MESH term "Life Change Events" as a main sub-class, wi - + - - + + This gene encodes glucose-6-phosphate dehydrogenase. This protein is a cytosolic enzyme encoded by a housekeeping X-linked gene whose main function is to produce NADPH, a key electron donor in the defense against oxidizing agents and in reductive biosynthetic reactions. G6PD is remarkable for its genetic diversity. Many variants of G6PD, mostly produced from missense mutations, have been described with wide ranging levels of enzyme activity and associated clinical symptoms. G6PD deficiency may cause neonatal jaundice, acute hemolysis, or severe chronic non-spherocytic hemolytic anemia. Two transcript variants encoding different isoforms have been found for this gene. - Exists in other ontologies but we have provided a description more relevant to its relationship with SCD. - http://www.ncbi.nlm.nih.gov/gene/2539 - Not relevant to context of sickle cell + Exists in other ontologies but we have provided a description more relevant to its relationship with SCD. + http://www.ncbi.nlm.nih.gov/gene/2539 + Not relevant to context of sickle cell G-6-PD G6PD1 Glucose-6-Phosphate 1-Dehydrogenase Gene @@ -28090,63 +27525,63 @@ Perhaps include MESH term "Life Change Events" as a main sub-class, wi - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A deficiency or slowing down of growth pre- and postnatally greater than two standard deviations from the age- and sex-related normal. - Suggest update to description in HPO. - http://purl.obolibrary.org/obo/HP_0001510 - Suggest update to description + Suggest update to description in HPO. + http://purl.obolibrary.org/obo/HP_0001510 + Suggest update to description HP:0001510 Delayed Growth Growth Deficiency @@ -28159,32 +27594,32 @@ Perhaps include MESH term "Life Change Events" as a main sub-class, wi - + - - + + - + A bioassay to measure haptoglobin, which is produced by the liver and transports hemoglobin to the liver for recycling. - Suggest update to label in PhenX (from "Haptoglobin Level"). - - Suggest update to label + Suggest update to label in PhenX (from "Haptoglobin Level"). + + Suggest update to label phenX:10801 Haptoglobin Blood Test - + - - + + Individual lifestyle and behavior which may or may not enhance or maintain good health. - Suggest the NCIT updates their description for this term to include negative /risk inreasing behaviour? + Suggest the NCIT updates their description for this term to include negative /risk inreasing behaviour? Include: -- gaining better control of your diabetes @@ -28195,10 +27630,10 @@ Include: -- Include these from MESH: -- Treatment Refusal --- Vaccination Refusal - - Sufficient - SCDO:0000487 +-- Vaccination Refusal + + Sufficient + SCDO:0000487 APAONTO:Health_Behavior Health Behavior Health Behaviour @@ -28206,29 +27641,29 @@ Include: - + - - + + People's beliefs about health problems, perceived benefits of action and barriers to action, and self-efficacy. + + Not relevant to context of sickle cell Health-Belief Model - - Not relevant to context of sickle cell The health belief model suggests that health beliefs explain engagement (or lack of engagement) in health-promoting behaviour. Health Beliefs - + - - + + Health financing is concerned with how financial resources are generated, allocated and used in health systems. Health financing policy focuses on how to move closer to universal coverage with issues related to: (i) how and from where to raise sufficient funds for health; (ii) how to overcome financial barriers that exclude many poor from accessing health services; or (iii) how to provide an equitable and efficient mix of health services. - Request inclusion into relevant ontology - - None + Request inclusion into relevant ontology + + None Health Care Resources Healthcare Resources Health Financing @@ -28236,40 +27671,40 @@ Include: - + - + - + - - + + Whether the respondent is covered by health insurance or some other form of health care coverage at the time of the interview. - Suggest inclusion into MESH. + Suggest inclusion into MESH. The phenX term is actually referring to a protocol for collecting data on Health Insurance Coverage. -The protocol is somewhat U.S. specific. Should probably be modified to be more relevant to the African setting. - - PhenX protocol: Health Insurance Coverage #11502 - Negligable +The protocol is somewhat U.S. specific. Should probably be modified to be more relevant to the African setting. + + PhenX protocol: Health Insurance Coverage #11502 + Negligable Also applicable to a population not just to an individual. Health Insurance Coverage - + - - + + Degree to which individuals have the capacity to obtain, process and understand basic health information and services needed to make appropriate health decisions. - http://purl.bioontology.org/ontology/MESH/D057220 - Sufficient - SCDO:0000491 + http://purl.bioontology.org/ontology/MESH/D057220 + Sufficient + SCDO:0000491 MESH:D057220 Knowledge about Sickle Cell Disease Genetic Counseling @@ -28278,14 +27713,14 @@ The protocol is somewhat U.S. specific. Should probably be modified to be more r - + - - + + Health data accessible to the patient and others. - http://purl.bioontology.org/ontology/MESH/D055991 - Sufficient - SCDO:0000492 + http://purl.bioontology.org/ontology/MESH/D055991 + Sufficient + SCDO:0000492 MESH:D055991 Health Records, Personal Personal Health Information @@ -28298,14 +27733,14 @@ The protocol is somewhat U.S. specific. Should probably be modified to be more r - + - - + + The measure of the population's use of the health care services available to them. This includes the utilization of hospital resources, Personal Care Home (PCH) resources, and physician resources. Health care utilization and health status are used to examine how efficiently a health care system produces health in a population. + + Few but definitions not specific enough - - Few but definitions not specific enough Health Care Service Utilization Health Care Utitlization Healthcare Utitlization @@ -28314,14 +27749,14 @@ The protocol is somewhat U.S. specific. Should probably be modified to be more r - + - - + + A system responsible for delivering services that improve, maintain or restore the health of individuals and their communities. This includes the care provided by hospitals and family doctors, but also less visible tasks such as the prevention and control of communicable disease, health promotion, health workforce planning and improving the social, economic or environmental conditions in which people live. - Suggest update to description in Medline Plus Health Topics - http://www.euro.who.int/en/health-topics/Health-systems/pages/health-systems - Suggest update to description + Suggest update to description in Medline Plus Health Topics + http://www.euro.who.int/en/health-topics/Health-systems/pages/health-systems + Suggest update to description Health Care Delivery Health Care System Health Care Systems @@ -28330,14 +27765,14 @@ The protocol is somewhat U.S. specific. Should probably be modified to be more r - + - - + + Utility measures of health related quality of life are preference values that patients attach to their overall health status. In clinical trials, utility measures summarize both positive and negative effects of an intervention into one value between 0 (equal to death) and 1 (equal to perfect health). These measures allow for comparison of patient outcomes of different diseases, and for comparison between various health care interventions. There are 2 different approaches to utility measurement. - Request inclusion into relevant ontology - http://www.ncbi.nlm.nih.gov/pubmed/7674256 - None + Request inclusion into relevant ontology + http://www.ncbi.nlm.nih.gov/pubmed/7674256 + None Health Utility Index Health Utility Measure Health Utility @@ -28345,18 +27780,18 @@ The protocol is somewhat U.S. specific. Should probably be modified to be more r - + - - + + The ease with which an individual can obtain needed medical services. + Additional WG note: +organization of health system [insurance]; electronic (portable) health records; special issues related to pain and pain medications; levels of care (primary, secondary, tertiary) (Location – [rural/urban; mobile units]; hours; affordability; timeliness). Availability of personnel. Equipment treatments other resources + + Negligable SCDO - Additional WG note: -organization of health system [insurance]; electronic (portable) health records; special issues related to pain and pain medications; levels of care (primary, secondary, tertiary) (Location – [rural/urban; mobile units]; hours; affordability; timeliness). Availability of personnel. Equipment treatments other resources - - Negligable Access to Healthcare Health Care Access The WHO Constitution envisages "...the highest attainable standard of health as a fundamental right of every human being." The right to health includes access to timely, acceptable, and affordable health care of appropriate quality. @@ -28365,63 +27800,63 @@ organization of health system [insurance]; electronic (portable) health records; - + - + - + - + - + - + - + - + - + - + - - + + Dietary patterns which have been found to be important in reducing disease risk. - http://purl.bioontology.org/ontology/MESH/D000072001 - Sufficient - SCDO:0000497 + http://purl.bioontology.org/ontology/MESH/D000072001 + Sufficient + SCDO:0000497 MESH:D000072001 Healthy Eating Healthy Diet @@ -28429,44 +27864,44 @@ organization of health system [insurance]; electronic (portable) health records; - + - - + + - + - + - + - + - - + + A pattern of behavior involving lifestyle choices which ensure optimum health. Examples are eating right; maintaining physical, emotional, and spiritual wellness, and taking preemptive steps against communicable diseases. - http://purl.bioontology.org/ontology/MESH/D000070497 - Sufficient - SCDO:0000498 + http://purl.bioontology.org/ontology/MESH/D000070497 + Sufficient + SCDO:0000498 MESH:D000070497 Healthy Life Style Healthy Lifestyle @@ -28474,14 +27909,14 @@ organization of health system [insurance]; electronic (portable) health records; - + - - + + Examinations used to diagnose and treat heart conditions. - http://purl.bioontology.org/ontology/MESH/D006334 - Sufficient - SCDO:0000500 + http://purl.bioontology.org/ontology/MESH/D006334 + Sufficient + SCDO:0000500 MESH:D006334 Heart Function Tests Pulmonary Function Test @@ -28490,38 +27925,38 @@ organization of health system [insurance]; electronic (portable) health records; - + - - + + - - + + - - + + - - + + - - + + The number of times the heart ventricles contract per unit of time, usually per minute. - http://www.ebi.ac.uk/efo/EFO_0004326 - Sufficient - SCDO:0000501 + http://www.ebi.ac.uk/efo/EFO_0004326 + Sufficient + SCDO:0000501 EFO:0004326 Heart Beat Pulse @@ -28531,73 +27966,73 @@ organization of health system [insurance]; electronic (portable) health records; - + - - + + - + - - + + - - + + - - + + Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart valves. - SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology. Perhaps below "Heart Measurement" in the CMO. + Request inclusion into relevant ontology. Perhaps below "Heart Measurement" in the CMO. Can add sub-classes as per the measurements given in the Diagnostic Criteria below the Protocol section in PhenX for "Heart Valve Function". -Sub-classes that are also morphological measurements can be included below "Body Morphological Measurement" - None +Sub-classes that are also morphological measurements can be included below "Body Morphological Measurement" + None + SCDO (Jade Hotchkiss) Heart Valve Measurement - + - - + + - + - + - + A measurement device used to perform complete blood counts, erythrocyte sedimentation rates (ESRs), or coagulation tests. - http://purl.obolibrary.org/obo/ERO_0000494 - Sufficient - SCDO:0000504 + http://purl.obolibrary.org/obo/ERO_0000494 + Sufficient + SCDO:0000504 ERO:0000494 Haematology Analyser Hematology Analyzer @@ -28605,106 +28040,106 @@ Sub-classes that are also morphological measurements can be included below " - + - - + + A test to detect potential blood disorders or diseases in people who do not have any symptoms of disease. - Request inclusion into relevant ontology. - - Few but definitions not freely available + Request inclusion into relevant ontology. + + Few but definitions not freely available Haematology Screening Test Hematology Screening Test - + - - + + - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Transfer of hematopoietic stem cells from bone marrow or blood between individuals within the same species (transplantation, homologous) or transfer within the same individual (transplantation, autologous). Hematopoietic stem cell transplantation has been used as an alternative to bone marrow transplantation in the treatment of a variety of neoplasms. - http://purl.bioontology.org/ontology/MESH/D018380 - Sufficient - SCDO:0000506 + http://purl.bioontology.org/ontology/MESH/D018380 + Sufficient + SCDO:0000506 MESH:D018380 BMT Bone Marrow Transplant @@ -28714,13 +28149,13 @@ Sub-classes that are also morphological measurements can be included below " - + - - + + The blood-making organs and tissues, principally the bone marrow and lymph nodes. - - http://purl.bioontology.org/ontology/MESH/D006413 + + http://purl.bioontology.org/ontology/MESH/D006413 MESH:D006413 deprecated Hematopoietic System true @@ -28728,74 +28163,74 @@ Sub-classes that are also morphological measurements can be included below " - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Presence of blood in the urine. - http://purl.bioontology.org/ontology/MESH/D006417 - Sufficient - SCDO:0000508 + http://purl.bioontology.org/ontology/MESH/D006417 + Sufficient + SCDO:0000508 MESH:D006417 Blood in Urine Hematurias @@ -28804,15 +28239,15 @@ Sub-classes that are also morphological measurements can be included below " - + - - + + This gene encodes the enzyme, heme oxygenase 1, an essential enzyme in heme catabolism and cellular homeostasis. - Suggest update to description in NCIT (for "HMOX1 Gene") - - http://www.ncbi.nlm.nih.gov/gene/3162 - Suggest update to description + Suggest update to description in NCIT (for "HMOX1 Gene") + + http://www.ncbi.nlm.nih.gov/gene/3162 + Suggest update to description HMOX1 Gene HO-1 HO1 Gene @@ -28826,10 +28261,10 @@ Sub-classes that are also morphological measurements can be included below " - + - - + + Organs involved in the production of BLOOD, including the cellular and the molecular components essential in providing defense against foreign organisms or substances. obsolete Hemic and Immune Systems true @@ -28837,21 +28272,21 @@ Sub-classes that are also morphological measurements can be included below " - + - - - + + + - - + + A commonly occurring abnormal hemoglobin in which lysine replaces a glutamic acid residue at the sixth position of the beta chains. It results in reduced plasticity of erythrocytes. - http://purl.bioontology.org/ontology/MESH/D006444 - Sufficient - SCDO:0000513 + http://purl.bioontology.org/ontology/MESH/D006444 + Sufficient + SCDO:0000513 MESH:D006444 Hb C HbC @@ -28861,21 +28296,21 @@ Sub-classes that are also morphological measurements can be included below " - + - - - + + + - - + + An abnormal hemoglobin resulting from the substitution of valine for glutamic acid at position 6 of the beta chain of the globin moiety. The heterozygous state results in sickle cell trait, the homozygous in sickle cell anemia. - http://purl.bioontology.org/ontology/MESH/D006451 - Sufficient - SCDO:0000514 + http://purl.bioontology.org/ontology/MESH/D006451 + Sufficient + SCDO:0000514 MESH:D006451 Haemoglobin S Hb S @@ -28889,20 +28324,20 @@ Sub-classes that are also morphological measurements can be included below " - + - - + + - - + + An abnormal hemoglobin composed of four beta chains. It is caused by the reduced synthesis of the alpha chain. This abnormality results in alpha-thalassemia. - http://purl.bioontology.org/ontology/MESH/D006447 - Sufficient - SCDO:0000515 + http://purl.bioontology.org/ontology/MESH/D006447 + Sufficient + SCDO:0000515 MESH:D006447 Hb H HbH @@ -28912,33 +28347,33 @@ Sub-classes that are also morphological measurements can be included below " - + - - - - None + + + + None deprecated Hemoglobin A2 Profile true - + - - + + - - + + An abnormal hemoglobin, composed of four gamma globin chains, causing it to have an extremely high affinity for oxygen, resulting in almost no oxygen delivery to the tissues. - Additional info from the definition in HPO: "Hb Barts (Hemoglobin Barts) is a tetramer with four gamma globin chains, and is essentially pathognomonic for one or another form of alpha thalassemia. Hb Barts has an extremely high affinity for oxygen, resulting in almost no oxygen delivery to the tissues." - Suggest update to description in HP as we have done. - http://purl.obolibrary.org/obo/HP_0005507 - Suggest update to description + Additional info from the definition in HPO: "Hb Barts (Hemoglobin Barts) is a tetramer with four gamma globin chains, and is essentially pathognomonic for one or another form of alpha thalassemia. Hb Barts has an extremely high affinity for oxygen, resulting in almost no oxygen delivery to the tissues." + Suggest update to description in HP as we have done. + http://purl.obolibrary.org/obo/HP_0005507 + Suggest update to description HP:0005507 Haemoglobin Bart's Haemoglobin Barts @@ -28950,74 +28385,74 @@ Sub-classes that are also morphological measurements can be included below " - + - - + + - - + + - - + + - - + + - + - - + + - - + + - + - - + + - - + + - - + + The most severe form of alpha-thalassemia and is almost always lethal, and characterized by fetal onset of generalized edema, pleural and pericardial effusions, and severe hypochromic anemia. It is caused by the presence of Hemoglobin Barts, a hemoglobin with four gamma chains, which has an extremely high affinity for oxygen, resulting in almost no oxygen delivery to the tissues - Suggest update to description in ORDO as we have done. - http://www.orpha.net/ORDO/Orphanet_163596 - Suggest update to description + Suggest update to description in ORDO as we have done. + http://www.orpha.net/ORDO/Orphanet_163596 + Suggest update to description Orphanet:163596 Alpha-Thalassemia Hydrops Fetalis Alpha-Thalassemia Major @@ -29032,99 +28467,99 @@ Sub-classes that are also morphological measurements can be included below " - + - - + + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - + + An autosomal recessive disorder resulting from the production of hemoglobin C, secondary to an amino acid substitution of lysine for glutamic acid in the sixth position of the beta chain (E6K), and characterized by mild hemolytic anemia and occasionally jaundice, though most patients are asymptomatic. - Suggest update to description in NCIT - - http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-C - Suggest update to description + Suggest update to description in NCIT + + http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-C + Suggest update to description NCIT:C34675 Haemoglobin C Disease Hb C-Disease @@ -29133,33 +28568,33 @@ Sub-classes that are also morphological measurements can be included below " - + - + - - + + - - + + - + The inheritance of the gene for hemoglobin C from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent. + Request inclusion into NCIT below "Hemoglobin Trait". + http://www.sickle-thal.nwlh.nhs.uk/blood/haemoglobinc.aspx + Few but definitions not freely available - Request inclusion into NCIT below "Hemoglobin Trait". - http://www.sickle-thal.nwlh.nhs.uk/blood/haemoglobinc.aspx - Few but definitions not freely available Haemoglobin C-A Disorder Hb AC Hemoglobin C-A Disorder @@ -29169,13 +28604,13 @@ Sub-classes that are also morphological measurements can be included below " - + - - + + 'A form of beta-thalassemia with a phenotype of mild to moderate hemolytic anemia. Patients are often asymptomatic but if present symptoms include anemia and enlarged spleen.' - The description could be more detailed. - http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=GB&Expert=231242 + The description could be more detailed. + http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=GB&Expert=231242 Hb C-Beta Thalassemia Syndrome Hemoglobin C Beta-Thalassemia deprecated Hemoglobin C-Beta Thalassemia @@ -29184,16 +28619,16 @@ Sub-classes that are also morphological measurements can be included below " - + - - + + A test to measure the presence and amount of a variant of hemoglobin in the blood. - Many terms below "Hemoglobin Variant Test" in SNOMED CT could be added. - Suggest update to label and description in NCIT (from "Hemoglobin Variant Measurement" and "A test to measure the variants of hemoglobin.") -It is not clear whether this term was is in fact a synonym of "Hemoglobin Profile Assay". We assumed it wasn't. If it actually is, we need to address the ambiguity caused. - http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C103845 - Suggest update to label and description + Many terms below "Hemoglobin Variant Test" in SNOMED CT could be added. + Suggest update to label and description in NCIT (from "Hemoglobin Variant Measurement" and "A test to measure the variants of hemoglobin.") +It is not clear whether this term was is in fact a synonym of "Hemoglobin Profile Assay". We assumed it wasn't. If it actually is, we need to address the ambiguity caused. + http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C103845 + Suggest update to label and description NCIT:C103845 Haemoglobin Variant Observation Haemoglobin Variant Test @@ -29206,81 +28641,81 @@ It is not clear whether this term was is in fact a synonym of "Hemoglobin P - + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An autosomal recessive hemoglobinopathy characterized by production of abnormal variant hemoglobin known as hemoglobin D, with no or mild clinical manifestations (splenomegaly, very mild anemia). - Suggest update to description in ORDO - - http://www.doh.wa.gov/Portals/1/Documents/5220/HbDFactSheet.pdf - Suggest update to description + Suggest update to description in ORDO + + http://www.doh.wa.gov/Portals/1/Documents/5220/HbDFactSheet.pdf + Suggest update to description DOID:5378 Hb DD Homozygous Hemoglobin D @@ -29289,81 +28724,81 @@ It is not clear whether this term was is in fact a synonym of "Hemoglobin P - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + The inheritance of the gene for hemoglobin D from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent. + Request inclusion into NCIT below "Hemoglobin Trait". + http://www.doh.wa.gov/Portals/1/Documents/5220/HbDFactSheet.pdf + Few but definitions not freely available SCDO (Jade Hotchkiss) - Request inclusion into NCIT below "Hemoglobin Trait". - http://www.doh.wa.gov/Portals/1/Documents/5220/HbDFactSheet.pdf - Few but definitions not freely available Hb AD Hemoglobin D Trait - + - - + + 'Hemoglobin D/xcexb2xc2xb0 thalassemia is a form of beta-thalassemia which results in a mild to moderate clinical picture. The severity of the condition depends on the degree of thalassemia and how it affects production of Hemoglobin A, however this condition is often considered fairly benign.' - http://www.doh.wa.gov/Portals/1/Documents/5220/HbDFactSheet.pdf + http://www.doh.wa.gov/Portals/1/Documents/5220/HbDFactSheet.pdf HbD - BT Hemoglobin D Beta-Thalassemia deprecated Hemoglobin D-Beta Thalassemia @@ -29372,36 +28807,36 @@ It is not clear whether this term was is in fact a synonym of "Hemoglobin P - + - - + + An unusual hemoglobin that shows all the electrophoretic features of Hb D, but has no inherited disability. This hemoglobin has a beta 87 Thr > Lys mutation. - Request inclusion into NCIT below "Hemoglobin"/"Hemoglobin Variant"/"Unusual Hemoglobin". - - - Few but definitions not freely available + Request inclusion into NCIT below "Hemoglobin"/"Hemoglobin Variant"/"Unusual Hemoglobin". + + + Few but definitions not freely available Hemoglobin D (badan) Hemoglobin D-Ibadan - + - - - + + + - - + + An abnormal hemoglobin (one of the types of hemoglobin D) in which glutamine replaces glutamic acid at codon 121 of beta globin. - Request inclusion in the HPO, below "Abnormal Hemoglobin"/"Hemoglobin D". - http://health.utah.gov/nsp/Disorders/HB/Hb_D_Disease_DD/FactSheet_Provider_HbDD_En.pdf - Few but definitions not freely available + Request inclusion in the HPO, below "Abnormal Hemoglobin"/"Hemoglobin D". + http://health.utah.gov/nsp/Disorders/HB/Hb_D_Disease_DD/FactSheet_Provider_HbDD_En.pdf + Few but definitions not freely available Haemoglobin D-Punjab Hb D-Los Angelese Hb D-Punjab @@ -29416,90 +28851,90 @@ It is not clear whether this term was is in fact a synonym of "Hemoglobin P - + - - + + A disease caused by atypical hemoglobins molecules other than hemoglobin C,D,E, F, H, O-Arab and S. - adapted from description under ID SCDO:0001065 - SCDO:0001065 - http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-and-other-than-A-C-D-E-F-H-O-Arab-S + adapted from description under ID SCDO:0001065 + SCDO:0001065 + http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-and-other-than-A-C-D-E-F-H-O-Arab-S deprecated Hemoglobin Disease Other than C,D,E,F,H,O-Arab,S true - + - - + + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - + - - + + An autosomal recessive haemoglobinopathy characterized by an abnormal form of haemoglobin called haemoglobin E, which disrupts the oxygen-carrying ability of red blood cells. The condition can lead to mild or moderate hemolytic anemia; however, this condition often has no clinical manifestations. with a generally benign, asymptomatic presentation. - - http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-E - Sufficient - SCDO:0000530 + + http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-E + Sufficient + SCDO:0000530 ORPHA:2133 Haemoglobin E Disease Hb E-Disease @@ -29508,28 +28943,28 @@ with a generally benign, asymptomatic presentation. - + - + - - + + - - + + The inheritance of the gene for hemoglobin E from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent. + Request inclusion into NCIT below "Hemoglobin Trait". + http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-A-E + Few but definitions not freely available SCDO - Request inclusion into NCIT below "Hemoglobin Trait". - http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-A-E - Few but definitions not freely available Hb AE Hb E Trait Hb E-carriers generally do not have any signs or symptoms related to abnormal hemoglobin. @@ -29538,12 +28973,12 @@ with a generally benign, asymptomatic presentation. - + - - + + 'Hemoglobin E/xcexb2+ thalassemia is a form of beta-thalassemia that is often, but not always, milder than hemoglobin E/xcexb2xc2xb0 thalassemia. This condition shows a marked clinically diverse picture whereby abnormalities of xcexb2-globin chain synthesis result almost asymptomatic anemia to more severe transfusion-dependant anemia (Vichinsky, 2007).' - http://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN&data_id=19177&Disease_Disease_Search_diseaseGroup=Hemoglobin-D-Beta-Thalassemia&Disease_Disease_Search_diseaseType=Pat&Disease(s)/group%20of%20diseases=Hemoglobin-E-beta-thalassemia-syndrome&title=Hemoglobin-E-beta-thalassemia-syndrome&search=Disease_Search_Simple + http://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN&data_id=19177&Disease_Disease_Search_diseaseGroup=Hemoglobin-D-Beta-Thalassemia&Disease_Disease_Search_diseaseType=Pat&Disease(s)/group%20of%20diseases=Hemoglobin-E-beta-thalassemia-syndrome&title=Hemoglobin-E-beta-thalassemia-syndrome&search=Disease_Search_Simple Haemoglobin E-Beta Thalassemia Hemoglobin E Beta-Thalassemia deprecated Hemoglobin E-Beta Thalassemia @@ -29552,27 +28987,27 @@ with a generally benign, asymptomatic presentation. - + - - + + The score of fetal hemoglobin (Hb F) in the blood of an individual. - + + Description not clear enough. + None SCDO (Gaston K Mazandu) - Description not clear enough. - None deprecated Hemoglobin F Profile true - + - - + + A variant of Hemoglobin Lepore Syndrome. - http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome + http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome Hb Lepore Baltimore obsolete Hemoglobin Lepore Baltimore true @@ -29580,57 +29015,57 @@ with a generally benign, asymptomatic presentation. - + - + - + - + - - + + - + - - + + - - + + - - + + A variant of Hemoglobin Lepore Syndrome. Crossover occurs between glutamine at position 87 of delta chain and histidine at position 116 of beta chain. It is associated with unusual high levels of Hb F. This is the only one of the three variants of described in association with HbS. - Request inclusion into relevant ontology - - http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome - None + Request inclusion into relevant ontology + + http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome + None Hb Lepore Boston Syndrome Hb Lepore Washington Syndrome Hb Lepore Washington-Boston Syndrome @@ -29642,12 +29077,12 @@ with a generally benign, asymptomatic presentation. - + - - + + A variant of Hemoglobin Lepore Syndrome. - http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome + http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome Hb Hollandia obsolete Hemoglobin Lepore Hollandia true @@ -29655,33 +29090,33 @@ with a generally benign, asymptomatic presentation. - + - - + + - + The inheritance of the gene for hemoglobin Lepore from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent. + Request inclusion into relevant ontology + http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome + Few but definitions not freely available SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome - Few but definitions not freely available Heterozygous Hb Lepore Hemoglobin Lepore Trait - + - - + + 'A form of beta-thalassemia in which the patient is compound heterozygous for hemoglobin lepore and beta-thalassemia, which results in beta-thalassemia intermedia to beta-thalassemia major. [Curator team: []]' - Add HBD to Disease Modifiers (below Gene Product)? And link to it. + Add HBD to Disease Modifiers (below Gene Product)? And link to it. Hb Lepore-B-Thalassaemia Hemoglobin Lepore-B-Thalassaemia Hemoglobin Lepore-Beta Thalassaemia Syndrome @@ -29691,48 +29126,48 @@ with a generally benign, asymptomatic presentation. - + - - - + + + - - + + - - + + - + - - + + - - + + A type of dominant hereditary methemoglobinemia resulting from the production of hemoglobin M, which is readily oxidised to yield excess methemoglobin which leads to cyanosis. + Suggest update to description in MESH + + + http://medlineplus.gov/ency/article/000562.htm + Few but definitions not available SCDO (Jade Hotchkiss) - Suggest update to description in MESH - - - http://medlineplus.gov/ency/article/000562.htm - Few but definitions not available Autosomal Dominant Congenital Methemoglobinemia Type II Autosomal Dominant Hereditary Methemoglobinemia Type II Hereditary MetHb Type II @@ -29744,64 +29179,64 @@ with a generally benign, asymptomatic presentation. - + - - - Hemoglobin M Disease is autosomal dominant, thus does not seem to have a "trait" condition. - Requires definition and source. - None + + + Hemoglobin M Disease is autosomal dominant, thus does not seem to have a "trait" condition. + Requires definition and source. + None obsolete - Hemoglobin M Trait true - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A very rare autosomal recessive hemoglobinopathy characterized by an abnormal form of hemoglobin called hemoglobin O-Arab. It is associated with a mild to moderate anemia. - Request inclusion into relevant ontology - - http://onlinelibrary.wiley.com/doi/10.1002/pbc.24414/pdf - None + Request inclusion into relevant ontology + + http://onlinelibrary.wiley.com/doi/10.1002/pbc.24414/pdf + None Hb O-Arab Disease Homozygous Hb O-Arab Homozygous Hemoglobin O-Arab @@ -29810,32 +29245,32 @@ with a generally benign, asymptomatic presentation. - + - + - - + + - - + + - - + + The inheritance of hemoglobin O-Arab from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent. - Request inclusion into NCIT below "Hemoglobin Trait". - http://onlinelibrary.wiley.com/doi/10.1002/pbc.24414/pdf - Few but definitions not freely available + Request inclusion into NCIT below "Hemoglobin Trait". + http://onlinelibrary.wiley.com/doi/10.1002/pbc.24414/pdf + Few but definitions not freely available Hb A/O-Arab Hb AO-Arab Heterozygous Hb O-Arab @@ -29845,65 +29280,65 @@ with a generally benign, asymptomatic presentation. - + - + - - + + The type and relative amounts of various normal and abnormal hemoglobin types. + Request inclusion into relevant ontology. + http://labtestsonline.org/understanding/analytes/sickle/tab/test/ + None SCDO - Request inclusion into relevant ontology. - http://labtestsonline.org/understanding/analytes/sickle/tab/test/ - None Hemoglobin Profile - + - - + + - + - + - - + + - - + + - - + + A bioassay that measures and identifies the different types of hemoglobin in the bloodstream. It can be used to identify and characterize the different variants in structure and synthesis of hemoglobin that cause sickle cell disease. - - PhenX protocol: Hemoglobin Characterization #830301 - Sufficient - SCDO:0000547 + + PhenX protocol: Hemoglobin Characterization #830301 + Sufficient + SCDO:0000547 phenX:830301 Haemoglobin Characterization Haemoglobinopathy Screen @@ -29921,16 +29356,16 @@ with a generally benign, asymptomatic presentation. - + - - + + A test to quantify the presence of hemoglobin S in the blood and therefore determine whether a person has sickle cell trait or sickle cell disease. + In SNOMED CT this term is "Sickle cell identification". +Request inclusion into relevant ontology. + http://www.questdiagnostics.com/testcenter/TestDetail.action?ntc=31852 + Few but definitions not freely available SCDO (Clair Ingram) - In SNOMED CT this term is "Sickle cell identification". -Request inclusion into relevant ontology. - http://www.questdiagnostics.com/testcenter/TestDetail.action?ntc=31852 - Few but definitions not freely available Hemoglobin S Measurement Sickle Cell Identification Hemoglobin S Test @@ -29938,38 +29373,38 @@ Request inclusion into relevant ontology. - + - + The inheritance of one of the faulty genes that causes thalassemia. + Request inclusion into relevant ontology + + Few but definitions not freely available SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - Few but definitions not freely available Thalassemia Trait - + - - + + An inherited disorder of the structure and/or synthesis of hemoglobin, with a variable phenotype expression ranging from benign to severe. - Suggest update to description in NCIT - - Suggest update to description + Suggest update to description in NCIT + + Suggest update to description NCIT:C3092 Hemoglobinopathy - + - - + + Hemoglobinopathy Toms River, is also known as transient neonatal cyanosis and anemia due to toms river hemoglobin. An important gene associated with Hemoglobinopathy Toms River is HBG2 (Hemoglobin Subunit Gamma 2. Anemia due to Toms River Hemoglobin Transient Neonatal Cyanosis @@ -29979,39 +29414,39 @@ Request inclusion into relevant ontology. - + - + - - + + - - + + The distance between the lower border of the liver in the mid-clavicular line, and the upper border of the liver in the mid-clavicular line. - The description needs to be reviewed by an expert. -Request inclusion into Clinical Measurement Ontology, below "liver size measurement". - http://en.wikipedia.org/wiki/Liver_span - None + The description needs to be reviewed by an expert. +Request inclusion into Clinical Measurement Ontology, below "liver size measurement". + http://en.wikipedia.org/wiki/Liver_span + None Liver Span Hepatic Span - + - - + + A test for Hepatitis B Virus. - Which Hepatitis B Test is to be referred to here? (There are various different types below "Immunology Test" in the "Sage Bionetworks Synapse Ontology") + Which Hepatitis B Test is to be referred to here? (There are various different types below "Immunology Test" in the "Sage Bionetworks Synapse Ontology") HBV Test Hepatitis B Virus Test obsolete Hepatitis B Test @@ -30020,26 +29455,26 @@ Request inclusion into Clinical Measurement Ontology, below "liver size mea - + - - + + A test for Hepatitis C Virus. - Is this test for viral load measurement or or antibody measurement? (See terms below "Immunology Test" in the "Sage Bionetworks Synapse Ontology") + Is this test for viral load measurement or or antibody measurement? (See terms below "Immunology Test" in the "Sage Bionetworks Synapse Ontology") obsolete Hepatitis C Test true - + - - + + A rare red cell disorder classified principally into two clinical phenotypes: autosomal recessive congenital (or hereditary) methemoglobinemia types I and II (RCM/RHM type 1; RCM/RHM type 2). - http://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN&data_id=3290&disease=Hereditary-methemoglobinemia&search=Disease_Search_Simple - Sufficient - SCDO:0000559 + http://www.orpha.net/consor/cgi-bin/Disease_Search.php?lng=EN&data_id=3290&disease=Hereditary-methemoglobinemia&search=Disease_Search_Simple + Sufficient + SCDO:0000559 ORPHA:621 Congenital Methemoglobinemia HM @@ -30049,15 +29484,15 @@ Request inclusion into Clinical Measurement Ontology, below "liver size mea - + - - - + + + Replacement of the hip joint. - http://purl.bioontology.org/ontology/MESH/D019644 - Sufficient - SCDO:0000564 + http://purl.bioontology.org/ontology/MESH/D019644 + Sufficient + SCDO:0000564 MESH:D019644 Hip Prosthesis Implantation Hip Replacement Arthroplasty @@ -30069,30 +29504,30 @@ Request inclusion into Clinical Measurement Ontology, below "liver size mea - + - - + + A study that compares a group of participants receiving an intervention with a similar group from the past who did not. - http://purl.bioontology.org/ontology/MESH/D065386 - Sufficient - SCDO:0000565 + http://purl.bioontology.org/ontology/MESH/D065386 + Sufficient + SCDO:0000565 MESH:D065386 Historically Controlled Study - + - + - + A questionnaire to determine whether an individual has had a traumatic brain injury (TBI). - Suggest update to label as we have done. We are using "History of Head Trauma" below Personal Attribute. - - PhenX protocol: History of Head Trauma #130601 - Suggest update to label + Suggest update to label as we have done. We are using "History of Head Trauma" below Personal Attribute. + + PhenX protocol: History of Head Trauma #130601 + Suggest update to label phenX:130600 History of Head Trauma Questionnaire History of Head Trauma Diagnostic Instrument @@ -30100,37 +29535,37 @@ Request inclusion into Clinical Measurement Ontology, below "liver size mea - + - + - + - + - - + + - - + + A questionnaire to determine if the respondent has a history of kidney failure. - Link to? + Link to? -- Kidney Failure --- Personal Attribute---> Personal medical history --> History of Kidney Failure - Suggest update to label as we have done. We are using "History of Kidney Failure" below Personal Attribute. - - PhenX protocol: Personal History of Kidney Failure #140601 - Suggest update to label +-- Personal Attribute---> Personal medical history --> History of Kidney Failure + Suggest update to label as we have done. We are using "History of Kidney Failure" below Personal Attribute. + + PhenX protocol: Personal History of Kidney Failure #140601 + Suggest update to label phenX:140600 History of Kidney Failure Questionnaire History of Kidney Failure Diagnostic Instrument @@ -30138,16 +29573,16 @@ Request inclusion into Clinical Measurement Ontology, below "liver size mea - + - + - + A questionnaire to determine if the respondent has had an ischemic infarction (i.e. stroke) and/or any symptoms related to this event. - Suggest update to label as we have done. We are using "History of Stroke" below Personal Attribute. - - PhenX protocol: History of Stroke - Ischemic Infarction and Hemorrhage #130301 - Suggest update to label + Suggest update to label as we have done. We are using "History of Stroke" below Personal Attribute. + + PhenX protocol: History of Stroke - Ischemic Infarction and Hemorrhage #130301 + Suggest update to label phenX:130300 History of Stroke - Ischemic Infarction and Hemorrhage - Questionnaire History of Stroke - Ischemic Infarction and Hemorrhage - Diagnostic Instrument @@ -30155,68 +29590,68 @@ Request inclusion into Clinical Measurement Ontology, below "liver size mea - + - + - + - + - - + + - - + + A questionnaire to determine a respondent's history of type 1 or type 2 diabetes. - Link to? -- Personal Attribute---> Personal medical history --> History of Type I and Type 2 Diabetes - Suggest update to label as we have done. We are using "History of Type I and Type 2 Diabetes" below Personal Attribute. - - PhenX protocol: Personal History of Type 1 and Type 2 Diabetes #140501 - Suggest update to label + Link to? -- Personal Attribute---> Personal medical history --> History of Type I and Type 2 Diabetes + Suggest update to label as we have done. We are using "History of Type I and Type 2 Diabetes" below Personal Attribute. + + PhenX protocol: Personal History of Type 1 and Type 2 Diabetes #140501 + Suggest update to label phenX:140500 History of Type I and Type 2 Diabetes Diagnostic Instrument - + - - + + - - + + - - + + - - + + A bioassay to measure human immunodeficiency virus (HIV) antibodies and/or HIV antigens in order to determine whether an individual has an HIV infection. - Also below "Immunochemical Assay"? - - - Few but definitions not freely available + Also below "Immunochemical Assay"? + + + Few but definitions not freely available HIV Assay Human Immunodeficiency Virus Assay Human Immunodeficiency Virus Test @@ -30225,20 +29660,20 @@ Request inclusion into Clinical Measurement Ontology, below "liver size mea - + - - - + + + The HADS consists of 2 subscales each with 7 items for measuring anxiety, and 7 items for depression rated from 0 - 3. Anxiety and depression scores are obtained by adding up the ratings of the items on each subscale. A score above 8 in any of the subscales indicates that the patient has experienced clinically significant anxiety or depression over the past week. + Zigmond A.S. and Snaith R.P. (1983). The hospital anxiety and depression scale. Acta Psychiatry Scandinavia, 67, 361-370. Anie, K.A.; Green, J.; Tata, P.; Fotopoulos, C. E.; Oni, L. and Davies, S. C. (2002) Self-help manual-assisted cognitive behavioural therapy for sickle cell disease. Behavioural and Cognitive Psychotherapies, 30, 451-458 + multiple + Patient Reported Outcome + Clinic Patients + Widely used around the world, also used in SCD + Adults (18 to 91 years) + Few but definitions not specific enough - Zigmond A.S. and Snaith R.P. (1983). The hospital anxiety and depression scale. Acta Psychiatry Scandinavia, 67, 361-370. Anie, K.A.; Green, J.; Tata, P.; Fotopoulos, C. E.; Oni, L. and Davies, S. C. (2002) Self-help manual-assisted cognitive behavioural therapy for sickle cell disease. Behavioural and Cognitive Psychotherapies, 30, 451-458 - multiple - Patient Reported Outcome - Clinic Patients - Widely used around the world, also used in SCD - Adults (18 to 91 years) - Few but definitions not specific enough NCIT:C103520 HADS HADS Questionnaire @@ -30251,15 +29686,15 @@ Request inclusion into Clinical Measurement Ontology, below "liver size mea - + - - + + The confinement of a patient in a hospital. - Perhaps "Hospital Utilization" would be better here? - http://purl.bioontology.org/ontology/MESH/D006760 - Sufficient - SCDO:0000573 + Perhaps "Hospital Utilization" would be better here? + http://purl.bioontology.org/ontology/MESH/D006760 + Sufficient + SCDO:0000573 MESH:D006760 Hospital Admission Hospitalisation @@ -30270,282 +29705,282 @@ Request inclusion into Clinical Measurement Ontology, below "liver size mea - + - + - - + + - + - - + + - - + + A record of those living in the respondent's household and about his or her relationship with them. - Request inclusion into MESH below "Social Conditions"? - - PhenX protocol: Household Roster-Relationships #11402 - Negligable + Request inclusion into MESH below "Social Conditions"? + + PhenX protocol: Household Roster-Relationships #11402 + Negligable phenX:11400 Household Roster-Relationships - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A unique treatment that administers electrolyte-packed IV fluids directly into a patient's bloodstream. Depending on the patient's needs, the fluid may be enhanced with additives such as calcium, magnesium sulfate or a Vitamin B complex. It is a far more efficient method of absorption when compared to the traditional method of drinking liquids/electrolytes. + Suggest update to description in NCIT (currently no description) + + Suggest update to description - Suggest update to description in NCIT (currently no description) - - Suggest update to description NCIT:C66896 Hydration Therapy - + - + - + - - + + - - + + - - + + - + - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An antineoplastic agent that inhibits DNA synthesis through the inhibition of ribonucleoside diphosphate reductase. - - Sufficient - SCDO:0000580 + + Sufficient + SCDO:0000580 MESH:D006918 Hydrea Hydroxycarbamide @@ -30555,99 +29990,99 @@ Request inclusion into Clinical Measurement Ontology, below "liver size mea - + - - + + - - + + A causal adverse drug event that is induced by hydroxyurea. + Request inclusion into OAE below "Causal Adverse Drug Event". + None SCDO (Jade Hotchkiss) - Request inclusion into OAE below "Causal Adverse Drug Event". - None Hydroxyurea-Induced Adverse Event - + - - + + - - + + A hydroxyurea-induced adverse event that has an outcome relating to or affecting the skin. - SCDO (Jade Hotchkiss) - Request inclusion into OAE below "Hydroxyurea-Induced Adverse Event" (also suggested by us for inclusion). + Request inclusion into OAE below "Hydroxyurea-Induced Adverse Event" (also suggested by us for inclusion). Or -Obsolete and use an object property (has adverse events) to link Hydroxyea to Cutaneous. - None +Obsolete and use an object property (has adverse events) to link Hydroxyea to Cutaneous. + None + SCDO (Jade Hotchkiss) Hydroxyurea-Induced Cutaneous Adverse Event - + - - + + - - + + A hydroxyurea-induced adverse event that has the outcome of splenomegaly. - SCDO (Jade Hotchkiss) - Request inclusion into OAE below "Hydroxyurea-Induced Adverse Event" (also suggested by us for inclusion). + Request inclusion into OAE below "Hydroxyurea-Induced Adverse Event" (also suggested by us for inclusion). Or -Delete and use an object property (has adverse events) to link Hydroxyea to Splenomegaly. - None +Delete and use an object property (has adverse events) to link Hydroxyea to Splenomegaly. + None + SCDO (Jade Hotchkiss) Hydroxyurea-Induced Splenomegaly Adverse Event - + - - + + - - + + - - + + - - + + - - + + Abnormally high potassium concentration in the blood, most often due to defective renal excretion. It is characterized clinically by electrocardiographic abnormalities (elevated T waves and depressed P waves, and eventually by atrial asystole). In severe cases, weakness and flaccid paralysis may occur. (Dorland, 27th ed). - http://purl.bioontology.org/ontology/MESH/D006947 - Sufficient - SCDO:0000588 + http://purl.bioontology.org/ontology/MESH/D006947 + Sufficient + SCDO:0000588 MESH:D006947 High Blood Potassium Levels Hyperkalemias @@ -30658,14 +30093,14 @@ Delete and use an object property (has adverse events) to link Hydroxyea to Sple - + - + Excessive pigmentation of the skin, usually as a result of increased epidermal or dermal melanin pigmentation, hypermelanosis. Hyperpigmentation can be localized or generalized. The condition may arise from exposure to light, chemicals or other substances, or from a primary metabolic imbalance. - - Sufficient - SCDO:0000593 + + Sufficient + SCDO:0000593 MESH:D017495 Hypermelanoses Hypermelanosis @@ -30676,15 +30111,15 @@ Delete and use an object property (has adverse events) to link Hydroxyea to Sple - + - + - + Drugs used to induce drowsiness or sleep or to reduce psychological excitement or anxiety. - http://purl.bioontology.org/ontology/MESH/D006993 - Sufficient - SCDO:0000598 + http://purl.bioontology.org/ontology/MESH/D006993 + Sufficient + SCDO:0000598 MESH:D006993 Hypnotics Sedatives @@ -30694,35 +30129,35 @@ Delete and use an object property (has adverse events) to link Hydroxyea to Sple - + - - + + The ICD-10-CM diagnosis classification system developed by the Centers for Disease Control and Prevention for use in all U.S. health care treatment settings. Diagnosis coding under this system uses a different number of digits and some other changes, but the format is very much the same as ICD-9-CM. The National Center for Health Statistics (NCHS), the Federal agency responsible for use of the International Statistical Classification of Diseases and Related Health Problems, 10th revision (ICD-10) in the United States, has developed a clinical modification of the classification for morbidity purposes. The ICD-10 is used to code and classify mortality data from death certificates, having replaced ICD-9 for this purpose as of January 1, 1999. ICD-10-CM is the replacement for ICD-9-CM, volumes 1 and 2, effective October 1, 2015. - Request inclusion into relevant ontology, perhaps below "Clinical Coding" in MESH. - https://www.cdc.gov/nchs/icd/icd10cm.htm - https://www.findacode.com/icd-10-cm/icd-10-cm-diagnosis-codes-set.html - None + Request inclusion into relevant ontology, perhaps below "Clinical Coding" in MESH. + https://www.cdc.gov/nchs/icd/icd10cm.htm + https://www.findacode.com/icd-10-cm/icd-10-cm-diagnosis-codes-set.html + None ICD-10-CM Diagnosis Codes - + - - + + The IPQ-R is an 84-item self-completed instrument developed to provide a quantitative measurement of the components of illness representations, as described by Leventhal's Common-Sense Model (CSM) of selfregulation it is divided into 3 sections: identity subscale (14 symptoms), causal subscale (18 causes), and a third section which contains 7 subscales, including consequences, timeline acute/chronic and cyclical, personal and treatment control/cure, illness coherence, and emotional representations. The questionnaire wording can be adapted to the specific illness by replacing the word illness with the name of the condition. For the identity subscale, respondents are asked if they have experienced a number of symptoms since their illness, and if they feel the symptoms are related to their current illness. Response is by circling 'yes' or 'no' to each question. Responses are then summed to give an overall score. For the causal subscale, respondents are asked what they perceive to be the cause of their illness and are asked to respond to each of the listed causes using a 5-point Likert style scale, ranging from strongly disagree to strongly agree. Respondents are also asked to rank the 3 most important factors believed to be the cause of their illness. The third section (7 subscales) is scored by summing responses to each item is on a 5-point Likert style scale, ranging from strongly disagree to strongly agree. All items for each of the subscales are summed to give an overall score. High scores on the identity, consequences, timeline acute/chronic and cyclical subscales represent strongly held beliefs about the number of symptoms attributed, the negative consequences, and the chronicity and cyclical nature of the illness. High scores on the personal and treatment control and coherence subscales represent positive beliefs about controllability and a personal understanding of the illness. + Request inclusion into NCIT below "Research or Clinical Assessment Tool". + Moss-Morris R, Weinman J, Petrie KJ, Horne R, Cameron LD, Buick D (2002). The Revised Illness Perception Questionnaire (IPQ-R). Psychol Health 17:1-16. + multiple + Patient Reported Outcome + Clinic Patients + many + Good psychometric properties, widely used around the world, has been translated into several languages. + Adults + None Moss-Morris R, Weinman J, Petrie KJ, Horne R, Cameron LD, Buick D (2002). The Revised Illness Perception Questionnaire (IPQ-R). Psychol Health 17:1-16. - Request inclusion into NCIT below "Research or Clinical Assessment Tool". - Moss-Morris R, Weinman J, Petrie KJ, Horne R, Cameron LD, Buick D (2002). The Revised Illness Perception Questionnaire (IPQ-R). Psychol Health 17:1-16. - multiple - Patient Reported Outcome - Clinic Patients - many - Good psychometric properties, widely used around the world, has been translated into several languages. - Adults - None IPQ-R Illness Perception Questionnaire Revised Illness Perception Questionnaire Revised (IPQ-R) @@ -30730,13 +30165,13 @@ Delete and use an object property (has adverse events) to link Hydroxyea to Sple - + - - + + The body's defense mechanism against foreign organisms or substances and deviant native cells. It includes the humoral immune response and the cell-mediated response and consists of a complex of interrelated cellular, molecular, and genetic components. - - http://purl.bioontology.org/ontology/MESH/D007107 + + http://purl.bioontology.org/ontology/MESH/D007107 MESH:D007107 deprecated Immune System true @@ -30744,72 +30179,72 @@ Delete and use an object property (has adverse events) to link Hydroxyea to Sple - + - + An assay that identifies a substance (especially a protein) by its action as an antigen. - Request inclusion into relevant ontology - - None + Request inclusion into relevant ontology + + None Immunochemical Assay - + - - + + A drug adverse event that has an outcome of decreased levels of immunosuppressant drugs in the patient's body. - http://purl.obolibrary.org/obo/OAE_0001071 - Sufficient - SCDO:0000618 + http://purl.obolibrary.org/obo/OAE_0001071 + Sufficient + SCDO:0000618 OAE:0001071 Immunosuppressant Drug Level Decreased AE - + - + An assay that employs immunoturbidimetry, a method that measures the absorbance of light from a sample which is used for quantifying an amount of analyte based on the level of turbidity produced by the formation and precipitation of an immune complex containing the analyte. - Request inclusion into relevant ontology. NCIT contains "Immunoturbidimetry", but not "Immunoturbidimetry Assay". Do we rather want to have this term as "Immunoturbidimetry"? - http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C106536 - None + Request inclusion into relevant ontology. NCIT contains "Immunoturbidimetry", but not "Immunoturbidimetry Assay". Do we rather want to have this term as "Immunoturbidimetry"? + http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C106536 + None Immunoturbidimetry Test Immunoturbidimetry Assay - + - - + + Substances causing insects to turn away from them or reject them as food. - http://purl.bioontology.org/ontology/MESH/D007302 - Sufficient - SCDO:0000643 + http://purl.bioontology.org/ontology/MESH/D007302 + Sufficient + SCDO:0000643 MESH:D007302 Insect Repellents - + - + A standardized tool designed to assess a child's development as compared to same-age peers. It has components that involve both direct observation and interaction with a child as well as caregiver questionnaires. It consists of five domains (cognitive, motor, language, social-emotional, and adaptive behavior). - Life stage: Infant, Toddler, Child - Suggest update to description in NCIT (we're not using their description, but their description says "from one to twenty-four months of age") - The Sickle Cell Disease Neurology, Quality of Life, and Health Services Working Group recognizes that there is an age overlap between the Bayley-III and the Wechsler Preschool and Primary Scale of Intelligence-Fourth Edition (WPPSI - IV). The Working Group recommends that providers use their clinical judgment, consider the purpose of testing participants, and refer to the frequently asked questions section of the Pearson website for Bayley-III and the WPPSI-IV for guidance on selecting an age-appropriate test. - http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820504 - PhenX protocol: Intelligence Scale - Birth to 3.5 years #820504 - Suggest update to description + Life stage: Infant, Toddler, Child + Suggest update to description in NCIT (we're not using their description, but their description says "from one to twenty-four months of age") + The Sickle Cell Disease Neurology, Quality of Life, and Health Services Working Group recognizes that there is an age overlap between the Bayley-III and the Wechsler Preschool and Primary Scale of Intelligence-Fourth Edition (WPPSI - IV). The Working Group recommends that providers use their clinical judgment, consider the purpose of testing participants, and refer to the frequently asked questions section of the Pearson website for Bayley-III and the WPPSI-IV for guidance on selecting an age-appropriate test. + http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820504 + PhenX protocol: Intelligence Scale - Birth to 3.5 years #820504 + Suggest update to description NCIT:C99150 Bayley Scale of Infant Development III Bayley Scales of Infant and Toddler Development, Third Edition @@ -30820,28 +30255,28 @@ Delete and use an object property (has adverse events) to link Hydroxyea to Sple - + - - + + An adverse drug event that results in the intentional use of a drug in the wrong way (recreationally etc). - http://purl.obolibrary.org/obo/OAE_0001093 - Sufficient - SCDO:0000650 + http://purl.obolibrary.org/obo/OAE_0001093 + Sufficient + SCDO:0000650 OAE:0001093 Intentional Drug Misuse AE - + - - + + A study that uses observations at multiple time points before and after an intervention (the interruption), in an attempt to detect whether the intervention has had an effect significantly greater than any underlying trend over time. - http://purl.bioontology.org/ontology/MESH/D065186 - Sufficient - SCDO:0000651 + http://purl.bioontology.org/ontology/MESH/D065186 + Sufficient + SCDO:0000651 MESH:D065186 ITS Studies Interrupted Time Series Analysis @@ -30849,13 +30284,13 @@ Delete and use an object property (has adverse events) to link Hydroxyea to Sple - + - - + + Intracerebral hemorrhage (ICH) is when blood suddenly bursts into brain tissue, causing damage to the brain. - - Should this term be merged with "Cerebral Hemorrhage" and "Intracerebral Haemorrhage" made a synonym of "Cerebral Hemorrhage"? -- -- Specify description source and source for additional info. + + Should this term be merged with "Cerebral Hemorrhage" and "Intracerebral Haemorrhage" made a synonym of "Cerebral Hemorrhage"? -- -- Specify description source and source for additional info. Intracerebral Bleeding deprecated-Intracerebral Haemorrhage true @@ -30863,24 +30298,24 @@ Delete and use an object property (has adverse events) to link Hydroxyea to Sple - + - + - - + + CSF pressure less than 6 cm of H2O in patients with clinical presentation compatible with intracranial hypotension, which are postural headache, nausea, vomiting, neck pain, visual and hearing disturbances, and vertigo. It most commonly results from CSF leaks somewhere along the neuraxis. + Suggest update to description in DOID (currently no description) + + Spontaneous intracranial hypotension is typically encountered in middle age (30-50 years of age) and has a predilection for women (F:M 2:1). Of interest, this is a similar demographic to pseudotumour cerebri, which is believed to be an unrecognised predisposing factor. Epidemiology of secondary intracranial hypotension is variable and matches that of the underlying cause. + Intracranial hypotension can broadly be divided into: 1.Primary: usually referred to as spontaneous intracranial hypotension. 2. Secondary: iatrogenic (LP or surgery), over shunting due to diversion devices or traumatic. + Generally, there are no localising symptoms forms directly from the leak, as CSF is absorbed into tissues. The condition often presents as a positional headache which is relieved by a recumbent position, usually within 15-30min. It is confirmed by assessing opening pressure on LP (less than 7 cm CSF). Note that when this is done fluoroscopically, it should be performed in a lateral position to allow for accurate measurement of pressure. Occasionally presentation is more sinister, with even decreased level of consciousness and coma reported. + Suggest update to description - Suggest update to description in DOID (currently no description) - - Spontaneous intracranial hypotension is typically encountered in middle age (30-50 years of age) and has a predilection for women (F:M 2:1). Of interest, this is a similar demographic to pseudotumour cerebri, which is believed to be an unrecognised predisposing factor. Epidemiology of secondary intracranial hypotension is variable and matches that of the underlying cause. - Intracranial hypotension can broadly be divided into: 1.Primary: usually referred to as spontaneous intracranial hypotension. 2. Secondary: iatrogenic (LP or surgery), over shunting due to diversion devices or traumatic. - Generally, there are no localising symptoms forms directly from the leak, as CSF is absorbed into tissues. The condition often presents as a positional headache which is relieved by a recumbent position, usually within 15-30min. It is confirmed by assessing opening pressure on LP (less than 7 cm CSF). Note that when this is done fluoroscopically, it should be performed in a lateral position to allow for accurate measurement of pressure. Occasionally presentation is more sinister, with even decreased level of consciousness and coma reported. - Suggest update to description DOID:4723 Craniospinal Hypotension Decreased Intracranial Pressure @@ -30889,90 +30324,90 @@ Delete and use an object property (has adverse events) to link Hydroxyea to Sple - + - - + + - - + + The hydrostatic pressure of venous blood in the marrow of bones. - Term should be requested for inclusion into the "Ontology of Biological Attributes", perhaps in an appropriate location under "organ system trait". Or perhaps below "bone measurement" or "bone marrow measurement" in the CMO? - http://medical-dictionary.thefreedictionary.com/intraosseous - http://www.ncbi.nlm.nih.gov/pubmed/6456552 - None + Term should be requested for inclusion into the "Ontology of Biological Attributes", perhaps in an appropriate location under "organ system trait". Or perhaps below "bone measurement" or "bone marrow measurement" in the CMO? + http://medical-dictionary.thefreedictionary.com/intraosseous + http://www.ncbi.nlm.nih.gov/pubmed/6456552 + None IOP Intraosseous Pressure - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A hypoperfusion of the blood through an organ or tissue caused by a pathologic constriction or obstruction of its blood vessels, or an absence of blood circulation. - Should this be under "Abnormal Cardiovascular System Morphology" or ""Abnormal Cardiovascular System Physiology"? - http://purl.bioontology.org/ontology/MESH/D007511 - Sufficient - SCDO:0000665 + Should this be under "Abnormal Cardiovascular System Morphology" or ""Abnormal Cardiovascular System Physiology"? + http://purl.bioontology.org/ontology/MESH/D007511 + Sufficient + SCDO:0000665 MESH:D007511 Ischemias Ischemia @@ -30980,17 +30415,17 @@ Delete and use an object property (has adverse events) to link Hydroxyea to Sple - + - - - + + + Electrophoresis in which a pH gradient is established in a gel medium and proteins migrate until they reach the site (or focus) at which the pH is equal to their isoelectric point. + Perhaps change label to "Hemoglobin Isoeletcric Focusing"? Exactsynonym "Hb IEF". See dc:source provided. + http://purl.bioontology.org/ontology/MESH/D007525 + Sufficient + SCDO:0000666 - Perhaps change label to "Hemoglobin Isoeletcric Focusing"? Exactsynonym "Hb IEF". See dc:source provided. - http://purl.bioontology.org/ontology/MESH/D007525 - Sufficient - SCDO:0000666 MESH:D007525 Electrofocusing IEF @@ -30999,14 +30434,14 @@ Delete and use an object property (has adverse events) to link Hydroxyea to Sple - + - - + + Laboratory tests used to evaluate how well the kidneys are working through examination of blood and urine. - http://purl.bioontology.org/ontology/MESH/D007677 - Sufficient - SCDO:0000676 + http://purl.bioontology.org/ontology/MESH/D007677 + Sufficient + SCDO:0000676 MESH:D007677 Kidney Function Tests Renal Function Test @@ -31016,92 +30451,92 @@ Delete and use an object property (has adverse events) to link Hydroxyea to Sple - + - - + + A specialized area of medicine in which exercise and movement are used as the primary form of rehabilitation. + Request inclusion into relevant ontology + http://medical-dictionary.thefreedictionary.com/kinesiotherapy + Few but definitions not freely available SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - http://medical-dictionary.thefreedictionary.com/kinesiotherapy - Few but definitions not freely available Kinesiotherapy - + - - + + Collections of facts, assumptions, beliefs and practices that health professionals hold about the aetiology, pathophysiology, quality management of SCD and related social support systems based on global standards. + Probably too specific to SCD to be included in other ontologies. + https://www.ncbi.nlm.nih.gov/mesh/?term=base%2C+knowledge; + https://www.ncbi.nlm.nih.gov/pubmed/20353928 + None SCDO - Probably too specific to SCD to be included in other ontologies. - https://www.ncbi.nlm.nih.gov/mesh/?term=base%2C+knowledge; - https://www.ncbi.nlm.nih.gov/pubmed/20353928 - None Knowledge about Sickle Cell Disease - + - + - + - + - - + + - - + + - - + + - + - - + + - - + + The level of lactate dehydrogenase, an enzyme released during tissue damage and injury, found in a specified biological specimen. + Request inclusion into relevant ontology +Should this term's name be changed to "L-Lactate Dehydrogenase Level"? + Few but definitions not freely available SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology -Should this term's name be changed to "L-Lactate Dehydrogenase Level"? - Few but definitions not freely available LD Level LDH Level Lactate Dehydrogenase Levels @@ -31112,38 +30547,38 @@ Should this term's name be changed to "L-Lactate Dehydrogenase Level&q - + - - + + - + - + - - + + - - + + A bioassay to measure levels of lactate dehydrogenase, an enzyme released during tissue damage and injury. - Suggest update to label in PhenX (from "Lactate Dehydrogenase Level"). - - Suggest update to label + Suggest update to label in PhenX (from "Lactate Dehydrogenase Level"). + + Suggest update to label phenX:811001 LDH Test Lactate Dehydrogenase Level Test @@ -31153,74 +30588,74 @@ Should this term's name be changed to "L-Lactate Dehydrogenase Level&q - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Ulceration of the skin and underlying structures of the lower extremity. About 90% of the cases are due to venous insufficiency (varicose ulcer), 5% to arterial disease, and the remaining 5% to other causes. - http://purl.bioontology.org/ontology/MESH/D007871 - Sufficient - SCDO:0000685 + http://purl.bioontology.org/ontology/MESH/D007871 + Sufficient + SCDO:0000685 MESH:D007871 Leg Ulcers Leg Ulcer @@ -31228,14 +30663,14 @@ Should this term's name be changed to "L-Lactate Dehydrogenase Level&q - + - - + + Typical way of life or manner of living characteristic of an individual or group. (From APA, Thesaurus of Psychological Index Terms, 8th ed). - http://purl.bioontology.org/ontology/MESH/D008019 - Sufficient - SCDO:0000689 + http://purl.bioontology.org/ontology/MESH/D008019 + Sufficient + SCDO:0000689 MESH:D008019 Life Style Lifestyle @@ -31243,14 +30678,14 @@ Should this term's name be changed to "L-Lactate Dehydrogenase Level&q - + - - + + The coagulation of tissue by an intense beam of light, including laser (laser coagulation). In the eye it is used in the treatment of retinal detachments, retinal holes, aneurysms, hemorrhages, and malignant and benign neoplasms. (Dictionary of Visual Science, 3d ed) - http://purl.bioontology.org/ontology/MESH/D008028 - Sufficient - SCDO:0000691 + http://purl.bioontology.org/ontology/MESH/D008028 + Sufficient + SCDO:0000691 MESH:D008028 Light Coagulations Photocoagulation @@ -31260,46 +30695,46 @@ Should this term's name be changed to "L-Lactate Dehydrogenase Level&q - + - - + + - - + + - - + + - - + + Any process carried out to determine the condition of a patient's liver. - http://bioportal.bioontology.org/ontologies/IDODEN?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FIDODEN_0003652 - Sufficient - SCDO:0000694 + http://bioportal.bioontology.org/ontologies/IDODEN?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FIDODEN_0003652 + Sufficient + SCDO:0000694 IDODEN:0003652 Liver Examination - + - - + + Personality construct referring to an individual's perception of the locus of events as determined internally by his or her own behaviour versus fate, luck, or external forces. - http://purl.bioontology.org/ontology/MESH/D007389 - Sufficient - SCDO:0000698 + http://purl.bioontology.org/ontology/MESH/D007389 + Sufficient + SCDO:0000698 MESH:D007389 Control Locus External-Internal Control @@ -31311,14 +30746,14 @@ Should this term's name be changed to "L-Lactate Dehydrogenase Level&q - + - - + + Studies in which variables relating to an individual or group of individuals are assessed over a period of time. - http://purl.bioontology.org/ontology/MESH/D008137 - Sufficient - SCDO:0000699 + http://purl.bioontology.org/ontology/MESH/D008137 + Sufficient + SCDO:0000699 MESH:D008137 Heart Study, Jackson Longitudinal Studies @@ -31326,14 +30761,14 @@ Should this term's name be changed to "L-Lactate Dehydrogenase Level&q - + - - + + A sampling methodology using small sample sizes when conducting surveys in small geographical or population-based areas or lots. - http://purl.bioontology.org/ontology/MESH/D055810 - Sufficient - SCDO:0000702 + http://purl.bioontology.org/ontology/MESH/D055810 + Sufficient + SCDO:0000702 MESH:D055810 LQAS Lot Quality Assurance Sampling @@ -31341,75 +30776,75 @@ Should this term's name be changed to "L-Lactate Dehydrogenase Level&q - + - + - + - + - + - - + + - - + + - - + + - + - - + + - - + + - - + + Measurement of the amount of air that the lungs may contain at various points in the respiratory cycle. - Perhaps use the "DEFINITIONS AND SUBDIVISIONS OF LUNG VOLUME" section in the "Lung Function - Lung Volume #810401" protocol source in PhenX to include types of lung volume as subclasses. Can also use subclasses of Experimental Factor Ontology -- (EFO) term "pulmonary function measurement or sub-classes of "Lung Volume Measurements" in MESH. - http://purl.bioontology.org/ontology/MESH/D008176 - Sufficient - SCDO:0000704 + Perhaps use the "DEFINITIONS AND SUBDIVISIONS OF LUNG VOLUME" section in the "Lung Function - Lung Volume #810401" protocol source in PhenX to include types of lung volume as subclasses. Can also use subclasses of Experimental Factor Ontology -- (EFO) term "pulmonary function measurement or sub-classes of "Lung Volume Measurements" in MESH. + http://purl.bioontology.org/ontology/MESH/D008176 + Sufficient + SCDO:0000704 MESH:D008176 Lung Capacities Lung Capacity @@ -31420,69 +30855,69 @@ Should this term's name be changed to "L-Lactate Dehydrogenase Level&q - + - - + + - + - + - + - - + + - - + + - - + + - - + + - - + + Clinical assessment to determine the volume of gas within an individual's lung. - Suggest update to label in PhenX (from "Lung Function - Lung Volume") + Suggest update to label in PhenX (from "Lung Function - Lung Volume") Perhaps use the protocol source in PhenX to include different ways of measuring FRC (functional residual capacity) as subclasses (e.g. Measurement of FRC using body plethysmography, Measurement of FRC using nitrogen washout, Measurement of FRC using helium dilution, Measurement of lung volume using imaging techniques). SNOMED has more terms below "Lung Volume Test" -Link to necessary medical device. - - PhenX protocol: Protocol - Lung Function - Lung Volume #810401 - Suggest update to label +Link to necessary medical device. + + PhenX protocol: Protocol - Lung Function - Lung Volume #810401 + Suggest update to label phenX:810401 Lung Function - Lung Volume Lung Volume Assay @@ -31493,12 +30928,12 @@ Link to necessary medical device. - + - - + + 'The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system. [Curator team: []]' - http://purl.obolibrary.org/obo/UBERON_0002465 + http://purl.obolibrary.org/obo/UBERON_0002465 UBERON:0002465 obsolete Lymphoid System true @@ -31506,131 +30941,131 @@ Link to necessary medical device. - + - - + + - + - - + + - - + + - - + + - - + + The use of drugs or other agents to prevent malarial infection. Examples: Proguanil, mefloquine, artesunate, insect repellant, insecticide-treated-bednet. - Request inclusion into relevant ontology - http://www.cdc.gov/malaria/travelers/drugs.html - Few but definitions not freely available + Request inclusion into relevant ontology + http://www.cdc.gov/malaria/travelers/drugs.html + Few but definitions not freely available Malaria Prevention Malaria Prophylaxis - + - - + + - - + + An instrument that is used for measuring the pressure of liquids and gases. - Request inclusion into "Eagle-I Research Resource Ontology", below the "instrument" term. + Request inclusion into "Eagle-I Research Resource Ontology", below the "instrument" term. -Perhaps the specific manometer used for measuring "Intraosseous Pressure" should be added as a sub-class and linked to directly. - The American Heritage Science Dictionary. Retrieved October 20, 2016 from Dictionary.com website - http://www.dictionary.com/browse/manometer - Negligable +Perhaps the specific manometer used for measuring "Intraosseous Pressure" should be added as a sub-class and linked to directly. + The American Heritage Science Dictionary. Retrieved October 20, 2016 from Dictionary.com website + http://www.dictionary.com/browse/manometer + Negligable Manometer - + - + - - + + - - + + The current marital status of the respondent's caregiver (i.e. family member or another individual who takes primary responsibility for the respondent). - Request inclusion into MESH below "Family Characteristics". - - PhenX protocol: Marital Status of Primary Caregiver #840101 - Negligable + Request inclusion into MESH below "Family Characteristics". + + PhenX protocol: Marital Status of Primary Caregiver #840101 + Negligable phenX:840101 Marital Status of Primary Caregiver - + - + - - + + - - + + A questionnaire to capture the frequency of acute pain episodes within a defined time frame due to sickle cell disease (SCD). It includes three self-administered questions from the Cooperative Study of Sickle Cell Disease (CSSCD) that capture number of painful episodes that required visits to the emergency room or hospital or interfered with daily activities. - Suggest update to label in PhenX as we have done here because we have used "Frequency of Sickle Cell Pain Episodes Per Year" for the Diagnostic Instrument Measurement. - - PhenX protocol: Frequency of Sickle Cell Pain Episodes Per Year #830101 - Suggest update to label + Suggest update to label in PhenX as we have done here because we have used "Frequency of Sickle Cell Pain Episodes Per Year" for the Diagnostic Instrument Measurement. + + PhenX protocol: Frequency of Sickle Cell Pain Episodes Per Year #830101 + Suggest update to label phenX:830100 Measure of Frequency of Sickle Cell Pain Episodes - + - - + + Measure of disease specific stigma based on patient reported outcome measurements that assesses 4 MoSCS factors: Social exclusion, Internalized Stigma, Expected Discrimination and Disclosure concerns. Measure includes stigma scores; perceived disease severity, acute care service utilization, hospital admission levels. N=262. + Request inclusion into NCIT below "Research or Clinical Assessment Tool". + J Health Psychol. 2016 May; 21(5): 808–820. + African-Americans + Patient Reported Outcome + Adults with Sickle Cell Disease + Adults 18 years and older + None Bediako, Shawn M et al. “The Measure of Sickle Cell Stigma: Initial Findings from the Improving Patient Outcomes through Respect and Trust Study.” Journal of health psychology (2014): 1359105314539530. PMC. Web. 13 Mar. 2016. PMCID: PMC4627860 - Request inclusion into NCIT below "Research or Clinical Assessment Tool". - J Health Psychol. 2016 May; 21(5): 808–820. - African-Americans - Patient Reported Outcome - Adults with Sickle Cell Disease - Adults 18 years and older - None Measure of Sickle Cell Stigma MoSCS Measure of Sickle Cell Stigma (MoSCS) @@ -31638,50 +31073,50 @@ Perhaps the specific manometer used for measuring "Intraosseous Pressure&qu - + - - + + The weight of the participant in kilograms. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Measured Weight - + - - + + An information entity used in the diagnosis of medical conditions. It could be the recording of the output of a diagnostic device or the outcome of a diagnostic tool. + Request inclusion into relevant ontology. + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology. - None Diagnostic Quantitative Measurement Diagnostic Measurement - + - - + + The MOS Social Support Survey is a self-administered questionnaire that includes 19 items across four functional support subscales: emotional/informational support (8 items), tangible/instrumental support (4 items), affectionate support (3 items), and positive social interaction (3 items). Each item is scored on a 5-point Likert style scale (1 = None of the Time; 5 = All of the Time) to indicate how often that type of support is available to them. A score for each social support subscale can be computed by averaging across the individual items or by adding scores individual items together. Higher scores indicate more support. + Check and show which source was used for the description and whether the description was adapted from the source. + Suggest update to description in NCIT for "Medical Outcomes Study Social Support Survey". + Sherbourne CD, Stewart A. The MOS Social Support Survey. Social Science and Medicine, v. 32, 1991, pp. 705-714. + Sherbourne, Cathy D. and Anita Stewart. The MOS Social Support Survey. Santa Monica, CA: RAND Corporation, 1993. + Multiple countries and cultural groups + Self + Clinic patients + Adults 18 years and older + no + Suggest update to description - Check and show which source was used for the description and whether the description was adapted from the source. - Suggest update to description in NCIT for "Medical Outcomes Study Social Support Survey". - Sherbourne CD, Stewart A. The MOS Social Support Survey. Social Science and Medicine, v. 32, 1991, pp. 705-714. - Sherbourne, Cathy D. and Anita Stewart. The MOS Social Support Survey. Santa Monica, CA: RAND Corporation, 1993. - Multiple countries and cultural groups - Self - Clinic patients - Adults 18 years and older - no - Suggest update to description NCIT:C110969 MOS Social Support Survey Medical Outcomes Study Social Support Survey @@ -31690,72 +31125,72 @@ Perhaps the specific manometer used for measuring "Intraosseous Pressure&qu - + - - + + Recording of pertinent information concerning patient's illness or illnesses. - http://purl.bioontology.org/ontology/MESH/D008499 - Sufficient - SCDO:0000738 + http://purl.bioontology.org/ontology/MESH/D008499 + Sufficient + SCDO:0000738 MESH:D008499 Medical Records - + - - + + Voluntary cooperation of the patient in taking drugs or medicine as prescribed. This includes timing, dosage, and frequency. - http://purl.bioontology.org/ontology/MESH/D055118 - Sufficient - SCDO:0000739 + http://purl.bioontology.org/ontology/MESH/D055118 + Sufficient + SCDO:0000739 MESH:D055118 Medication Adherence - + - + - + - + - - + + A record of the type and dosage of all prescription and over-the-counter medications as well as dietary supplements currently being taken by the individual. + Request inclusion into relevant ontology + +Would it also be appropriate to add this to "Diagnostic Instrument" below "Diagnostics"? + PhenX protocol: Medication Inventory #140301 + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - -Would it also be appropriate to add this to "Diagnostic Instrument" below "Diagnostics"? - PhenX protocol: Medication Inventory #140301 - Negligable Medication Inventory - + - - + + A state of consciousness in which the individual eliminates environmental stimuli from awareness so that the mind can focus on a single thing, producing a state of relaxation and relief from stress. A wide variety of techniques are used to clear the mind of stressful outside interferences. It includes meditation therapy. (Mosby's Medical, Nursing, and Allied Health Dictionary, 4th ed) - http://purl.bioontology.org/ontology/MESH/D019122 - Sufficient - SCDO:0000741 + http://purl.bioontology.org/ontology/MESH/D019122 + Sufficient + SCDO:0000741 MESH:D019122 Transcendental Meditation Meditation @@ -31763,20 +31198,20 @@ Would it also be appropriate to add this to "Diagnostic Instrument" be - + - + - - + + A phospholipid-interacting antimalarial drug (antimalarials). It is very effective against plasmodium falciparum with very few side effects. - - Sufficient - SCDO:0000742 + + Sufficient + SCDO:0000742 MESH:D015767 Lariam Mephloquine @@ -31786,24 +31221,24 @@ Would it also be appropriate to add this to "Diagnostic Instrument" be - + - + - - + + A type of glomerulonephropathy characterized by histology with thickening of the basement membrane and deposition of immune complexes in the subepithelial space. - Suggest update to description in HPO - - Typically seen in adult population; rare in children. - Idiopathic - may be related to M-type phosplipase A2 receptor antibodies; secondary forms may be related to autoimmune disease, underlying maligancies, drugs or infections. Has been reported in patients with sickle cell disease. - Nephrotic syndrome with histologic features specific to membranous nephropathy. - Suggest update to description + Suggest update to description in HPO + + Typically seen in adult population; rare in children. + Idiopathic - may be related to M-type phosplipase A2 receptor antibodies; secondary forms may be related to autoimmune disease, underlying maligancies, drugs or infections. Has been reported in patients with sickle cell disease. + Nephrotic syndrome with histologic features specific to membranous nephropathy. + Suggest update to description HP:0012578 MN Membranous Glomerulopathy @@ -31812,20 +31247,20 @@ Would it also be appropriate to add this to "Diagnostic Instrument" be - + - + - + Emotional, psychological, and social well-being of an individual or group. - - Sufficient - SCDO:0000746 + + Sufficient + SCDO:0000746 MESH:D008603 Emotional Health Mental Hygiene @@ -31834,30 +31269,30 @@ Would it also be appropriate to add this to "Diagnostic Instrument" be - + - - + + Works consisting of studies using a quantitative method of combining the results of independent studies (usually drawn from the published literature) and synthesizing summaries and conclusions which may be used to evaluate therapeutic effectiveness, plan new studies, etc. It is often an overview of clinical trials. It is usually called a meta-analysis by the author or sponsoring body and should be differentiated from reviews of literature. - http://purl.bioontology.org/ontology/MESH/D017418 - Sufficient - SCDO:0000747 + http://purl.bioontology.org/ontology/MESH/D017418 + Sufficient + SCDO:0000747 MESH:D017418 Meta-Analysis - + - - + + The state of the chemical reactions that occur within the cells, tissues, or an organism. These processes include both the biosynthesis (anabolism) and the breakdown (catabolism) of organic materials utilized by the living organism. - Request inclusion into relevant ontology. + Request inclusion into relevant ontology. -Add as sub-classes: Metabolic Function Normal and Metabolic Function Abnormal? (from SNOMED CT) - http://purl.bioontology.org/ontology/MESH/D008660 - None +Add as sub-classes: Metabolic Function Normal and Metabolic Function Abnormal? (from SNOMED CT) + http://purl.bioontology.org/ontology/MESH/D008660 + None MESH:D008660 Metabolic Function Metabolic State @@ -31865,14 +31300,14 @@ Add as sub-classes: Metabolic Function Normal and Metabolic Function Abnormal? ( - + - + The presence of methemoglobin in the blood, resulting in cyanosis. A small amount of methemoglobin is present in the blood normally, but injury or toxic agents convert a larger proportion of hemoglobin into methemoglobin, which does not function reversibly as an oxygen carrier. Methemoglobinemia may be due to a defect in the enzyme NADH methemoglobin reductase (an autosomal recessive trait) or to an abnormality in hemoglobin M (an autosomal dominant trait). (Dorland, 27th ed) - http://purl.bioontology.org/ontology/MESH/D008708 - Sufficient - SCDO:0000753 + http://purl.bioontology.org/ontology/MESH/D008708 + Sufficient + SCDO:0000753 MESH:D008708 MetHb Methemoglobinemia @@ -31880,14 +31315,14 @@ Add as sub-classes: Metabolic Function Normal and Metabolic Function Abnormal? ( - + - - + + 'Any procedure or test to diagnose a disease or disorder. [Curator team: []]' - - Perhaps move other sibling classes below this class? (Imaging Test/Diagnostic Imaging, -- -- Include sub-class "Biopsy" and include specific types below that? - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C18020 + + Perhaps move other sibling classes below this class? (Imaging Test/Diagnostic Imaging, -- -- Include sub-class "Biopsy" and include specific types below that? + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C18020 NCIT:C18020 Diagnostic Procedure deprecated Diagnostic Method @@ -31896,15 +31331,15 @@ Add as sub-classes: Metabolic Function Normal and Metabolic Function Abnormal? ( - + - + - + A questionnaire to assess migraines and headaches. - Suggest update to label in PhenX (from "Migraine") as we have done. - - Suggest update to label + Suggest update to label in PhenX (from "Migraine") as we have done. + + Suggest update to label phenX:130500 Headache Disability Questionnaire Migraine Questionnaire @@ -31912,29 +31347,29 @@ Add as sub-classes: Metabolic Function Normal and Metabolic Function Abnormal? ( - + - + Transportable radiographic equipment allowing imaging services to be brought to the patient. + Request inclusion into relevant ontology + http://www.who.int/medical_devices/innovation/hospt_equip_26.pdf + https://radiologykey.com/mobile-radiography/ + None SCDO - Request inclusion into relevant ontology - http://www.who.int/medical_devices/innovation/hospt_equip_26.pdf - https://radiologykey.com/mobile-radiography/ - None Mobile Radiographic Unit - + - - + + Difficulty moving from place to place or from one position to another without assistance. - Suggest update to description in MESH. - http://purl.bioontology.org/ontology/MESH/D051346 - Suggest update to description + Suggest update to description in MESH. + http://purl.bioontology.org/ontology/MESH/D051346 + Suggest update to description MESH:D051346 Ambulation Difficulty Ambulatory Difficulty @@ -31946,14 +31381,14 @@ Add as sub-classes: Metabolic Function Normal and Metabolic Function Abnormal? ( - + - - + + The biological processes, properties, and objects that are involved in maintaining, expressing, and transmitting from one organism to another, genetically encoded traits. - - Sufficient - SCDO:0000765 + + Sufficient + SCDO:0000765 MESH:D055614 Concepts, Genetic Genetic Phenomena @@ -31961,97 +31396,97 @@ Add as sub-classes: Metabolic Function Normal and Metabolic Function Abnormal? ( - + - - - http://bioportal.bioontology.org/ontologies/ADO/?p=classes&conceptid=http%3A%2F%2Fscai.fraunhofer.de%2FAlzheimerOntology%23Modifying_the_home_enviornment_and_make_it_safer_for_the_patient + + + http://bioportal.bioontology.org/ontologies/ADO/?p=classes&conceptid=http%3A%2F%2Fscai.fraunhofer.de%2FAlzheimerOntology%23Modifying_the_home_enviornment_and_make_it_safer_for_the_patient obsolete Modifying the Home Environment and Making it Safer For the Patient true - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + The principal alkaloid in opium and the prototype opiate analgesic and narcotic. Morphine has widespread effects in the central nervous system and on smooth muscle. - - Sufficient - SCDO:0000771 + + Sufficient + SCDO:0000771 MESH:D009020 17-methyl-7,8-didehydro-4,5alpha-epoxymorphinan-17-ium-3,6alpha-diol Morphia @@ -32061,12 +31496,12 @@ Add as sub-classes: Metabolic Function Normal and Metabolic Function Abnormal? ( - + - - + + 'A work that reports on a study executed by several cooperating institutions. [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D016448 + http://purl.bioontology.org/ontology/MESH/D016448 MESH:D016448 obsolete Multicenter Study true @@ -32074,14 +31509,14 @@ Add as sub-classes: Metabolic Function Normal and Metabolic Function Abnormal? ( - + - - + + Works about controlled studies which are planned and carried out by several cooperating institutions to assess certain variables and outcomes in specific patient populations, for example, a multicenter study of congenital anomalies in children. - - Sufficient - SCDO:0000775 + + Sufficient + SCDO:0000775 MESH:D015337 Multicenter Trial Multicenter Trials @@ -32093,22 +31528,22 @@ Add as sub-classes: Metabolic Function Normal and Metabolic Function Abnormal? ( - + - - + + The multidimensional health locus of control (MHLC) scale is a widely used measure of the factors that people believe exert some measures of control over their health. The MHLC originally developed by Wallston and colleagues contained 3 subscales describing various types of control-related cognitions an individual may have about the current state of his or her health. These were: Internal Health Locus of Control (IHLC), Powerful Others Health Locus of Control (PHLC) and Chance Health Locus of Control (CHLC). Subsequently, a fourth subscale, the God Locus of Health Control (G LHC) scale was developed to assess the extent of an individual's belief that God controls his or her health status was added to the measure. Thus, the expanded MHLC Consists of 4 sub-scales: one Internal and 3 external subscales namely, powerful others, chance and God. Each of the 4 sub-scales has 6 items making a total of 24 items. The two original versions of the MHLC (forms A & B) deal with the general health status whereas the third version (Form C) assesses control-related cognitions about a specific disease state. + Request inclusion into NCIT below "Research or Clinical Assessment Tool". + Multiple countries and cultural groups + Self + Healthy population and patients with specific medical conditions + Spanish; Chinese; Persian + Has adequate construct validity and acceptable metric properties + 15 years and above + no + Few but definitions not freely available Wallston K., Wallston B. and De Vellis R. (1978). Development of the multidimensional health locus of control (MHLC) scales. Health Education Monographs, 6, 160-169. Wallston KA, Malcarne VL, Flores L, Hansdottir I, Smith CA, Stein MJ, Weisman MH, Clements PJ. Does God Determine Your Health? The God Locus of Health Control Scale. Cognitive Therapy and Research . April 1999, Volume 23 (2):131-142. - Request inclusion into NCIT below "Research or Clinical Assessment Tool". - Multiple countries and cultural groups - Self - Healthy population and patients with specific medical conditions - Spanish; Chinese; Persian - Has adequate construct validity and acceptable metric properties - 15 years and above - no - Few but definitions not freely available MHLC MHLC Scales Multidimensional Health Locus of Control Scales @@ -32117,16 +31552,16 @@ Add as sub-classes: Metabolic Function Normal and Metabolic Function Abnormal? ( - + - - + + The presence of skeletal muscular atrophy, reduction in the muscle bulk. - Suggest update to description in HPO. + Suggest update to description in HPO. -Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0003202 - Suggest update to description +Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0003202 + Suggest update to description HP:0003202 Amyotrophy Muscle Wasting @@ -32138,14 +31573,14 @@ Provide source for additional info. - + - - + + Anatomical system that consists of the muscular and skeletal systems. - - - http://purl.obolibrary.org/obo/UBERON_0002204 + + + http://purl.obolibrary.org/obo/UBERON_0002204 UBERON:0002204 Musculo-Skeletal System deprecated Musculoskeletal System @@ -32154,15 +31589,15 @@ Provide source for additional info. - + - + The process of identifying carriers/heterozygotes of a genetic mutation that can result in a severe recessive condition. Carrier screening is done using various laboratory techniques. + Request inclusion into relevant ontology (MESH) or suggest inclusion of description in NCIT. + Alswaidi, F.M. and O'brien, S.J., 2009. Premarital screening programmes for haemoglobinopathies, HIV and hepatitis viruses: review and factors affecting their success. Journal of medical screening, 16(1), pp.22-28. + Few but definitions not freely available SCDO (Clair Ingram) - Request inclusion into relevant ontology (MESH) or suggest inclusion of description in NCIT. - Alswaidi, F.M. and O'brien, S.J., 2009. Premarital screening programmes for haemoglobinopathies, HIV and hepatitis viruses: review and factors affecting their success. Journal of medical screening, 16(1), pp.22-28. - Few but definitions not freely available MESH:D006580 Mutation Carrier Detection This term is very similar to but different (more specific) from the term "Genetic Carrier Screening" in MESH. @@ -32171,15 +31606,15 @@ Provide source for additional info. - + - - + + This gene encodes a protein with three HTH DNA-binding domains that functions as a transcription regulator. This protein plays an essential role in the regulation of hematopoiesis. This gene may be aberrently expressed or rearranged or undergo translocation in leukemias and lymphomas, and is considered to be an oncogene. Alternative splicing results in multiple transcript variants. - Exists in other ontologies but we have provided a description more relevant to its relationship with SCD. - Link to "Hereditary Persistence of fetal hemoglobin". - http://www.ncbi.nlm.nih.gov/gene/4602 - Not relevant to context of sickle cell + Exists in other ontologies but we have provided a description more relevant to its relationship with SCD. + Link to "Hereditary Persistence of fetal hemoglobin". + http://www.ncbi.nlm.nih.gov/gene/4602 + Not relevant to context of sickle cell MYB Gene MYB Proto-Oncogene, Transcription Factor MYB-HSP1 @@ -32188,44 +31623,44 @@ Provide source for additional info. - + - - + + - + - + - + - - + + - + A bioassay to determine an individual's level of N-terminal pro-brain natriuretic peptide (NT-proBNP). - Label different from source's "N-terminal Pro-brain Natriuretic Peptide (NT-proBNP)" - - Suggest update to label + Label different from source's "N-terminal Pro-brain Natriuretic Peptide (NT-proBNP)" + + Suggest update to label phenX:810501 NT-proBNP Test Equipment needed: Phlebotomy supplies, centrifuge for serum separation, and freezer for sample storage is required. @@ -32234,39 +31669,39 @@ Provide source for additional info. - + - + - - + + - - + + - - + + - - + + A specific opiate antagonist that has no agonist activity. It is a competitive antagonist at mu, delta, and kappa opioid receptors. - Are the synonyms included relevant to SCD? Should other synonyms from the description source be included? - - Sufficient - SCDO:0000789 + Are the synonyms included relevant to SCD? Should other synonyms from the description source be included? + + Sufficient + SCDO:0000789 MESH:D009270 1-N-Allyl-14-hydroxynordihydromorphinone 17-allyl-3,14-dihydroxy-4,5α-epoxymorphinan-6-one @@ -32276,15 +31711,15 @@ Provide source for additional info. - + - + - + Drugs designed to treat inflammation of the nasal passages, generally the result of an infection (more often than not the common cold) or an allergy related condition, e.g., hay fever. The inflammation involves swelling of the mucous membrane that lines the nasal passages and results in inordinate mucus production. The primary class of nasal decongestants are vasoconstrictor agents. (From PharmAssist, The Family Guide to Health and Medicine, 1993) - - Sufficient - SCDO:0000791 + + Sufficient + SCDO:0000791 MESH:D014663 Nasal Vasoconstrictor Agents Nasal Vasoconstrictors @@ -32293,12 +31728,12 @@ Provide source for additional info. - + - - + + 'A subspecialty of internal medicine concerned with the anatomy, physiology, and pathology of the kidney. [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D009398 + http://purl.bioontology.org/ontology/MESH/D009398 MESH:D009398 obsolete Nephrology true @@ -32306,77 +31741,77 @@ Provide source for additional info. - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Nephrotic syndrome is a collection of findings resulting from glomerular dysfunction with an increase in glomerular capillary wall permeability associated with pronounced proteinuria >3.5 g per 24 hours (in children, >40 mg/m2/hr or PCR >2000 mg/g [>200 mg/mmol] or >300 mg/dl or 3+ on urine dipstick) plus hypoalbuminemia (<3gm/dl) and edema. - Suggest update to description in the HPO - - Nephrotic syndrome related to sickle cell disease typically occurs in adulthood and preceded by lesser degree of proteinuria, other forms may occur at any age with different histologic lesions occurring at different ages. - Variety of causes - in sickle cell disease, most common lesion is focal segmental glomerulosclerosis (FSGS). Other causes may be other forms of primary glomerular disease including membranous nephropathy, minimmal change disease, membranoproliferative glomerulonephritis. Secondary forms may result from diabetes, amyloidosis. - Heavy proteinuria, edema, hyperlipidemia. May also be associated with hypertension and increased risk of venous thrombosis. - Suggest update to description + Suggest update to description in the HPO + + Nephrotic syndrome related to sickle cell disease typically occurs in adulthood and preceded by lesser degree of proteinuria, other forms may occur at any age with different histologic lesions occurring at different ages. + Variety of causes - in sickle cell disease, most common lesion is focal segmental glomerulosclerosis (FSGS). Other causes may be other forms of primary glomerular disease including membranous nephropathy, minimmal change disease, membranoproliferative glomerulonephritis. Secondary forms may result from diabetes, amyloidosis. + Heavy proteinuria, edema, hyperlipidemia. May also be associated with hypertension and increased risk of venous thrombosis. + Suggest update to description HP:0000100 Nephrosis Nephrotic Syndrome @@ -32384,62 +31819,62 @@ Provide source for additional info. - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Severely increased amount of excretion of protein in the urine, defined as 3.5 grams per day or more in adults and 40 mg per meter-squared body surface area per hour in children, or urine protein to creatinine ratio >2000 mg/g [>200 mg/mmol] in children. + Suggest update to description in HPO. + + + In sickle cell disease, seen primarily in adult population but may develop in childhood if secondary cause occurs. + Glomerular diseases that lead to protein loss in the urine (See Nephrotic Syndrome). + Severely increased amount of excretion of protein in the urine, defined as 3.5 grams per day or more in adults and 40 mg per meter-squared body surface area per hour in children, or urine protein to creatinine ratio >2000 mg/g [>200 mg/mmol] in children. + Suggest update to description - Suggest update to description in HPO. - - - In sickle cell disease, seen primarily in adult population but may develop in childhood if secondary cause occurs. - Glomerular diseases that lead to protein loss in the urine (See Nephrotic Syndrome). - Severely increased amount of excretion of protein in the urine, defined as 3.5 grams per day or more in adults and 40 mg per meter-squared body surface area per hour in children, or urine protein to creatinine ratio >2000 mg/g [>200 mg/mmol] in children. - Suggest update to description HP:0012593 Nephrotic-Range Proteinuria Is diagnosed by assessment of proteinuria (see Proteinuria) by 24hr urine collection or by urine protein-creatinine ratio on spot urine sample [KDIGO 2012]. @@ -32448,13 +31883,13 @@ Provide source for additional info. - + - - + + The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior. - - http://purl.obolibrary.org/obo/UBERON_0001016 + + http://purl.obolibrary.org/obo/UBERON_0001016 UBERON:0001016 Neurological System deprecated Nervous System @@ -32463,29 +31898,29 @@ Provide source for additional info. - + - + - + An invisible complication of sickle cell anemia (SSA) that defies detection by imaging and other routine diagnostic methods. Impaired neurocognitive function in seemingly neurologically intact patients is not related to vasoocclusion or hemolysis. It is detected by neuropsychiatric and neurobehavioral testing and is associated with anemia and age. + Request inclusion into relevant ontology + http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415156/ + None SCDO - Request inclusion into relevant ontology - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415156/ - None Neurocognitive Impairment - + - - + + Physician-supervised programs designed to rehabilitate people with diseases, trauma, or disorders of the nervous system. - http://purl.bioontology.org/ontology/MESH/D000066530 - Sufficient - SCDO:0000801 + http://purl.bioontology.org/ontology/MESH/D000066530 + Sufficient + SCDO:0000801 MESH:D000066530 Neurologic Rehabilitation Neurorehabilitation @@ -32496,38 +31931,38 @@ Provide source for additional info. - + - - + + Testing of neonates to identify those with major sickling diseases. - Link to "Hb isoelectric focusing" and "HPLC fractionation" ? + Link to "Hb isoelectric focusing" and "HPLC fractionation" ? -Request inclusion into relevant ontology. Perhaps in SNOMED CT below "Screening for sickle cell disease"? - Newborn Screening for Sickle Cell Disease and Other Hemoglobinopathies. JAMA. 1987;258(9):1205–1209. doi:10.1001/jama.1987.03400090089040 - None +Request inclusion into relevant ontology. Perhaps in SNOMED CT below "Screening for sickle cell disease"? + Newborn Screening for Sickle Cell Disease and Other Hemoglobinopathies. JAMA. 1987;258(9):1205–1209. doi:10.1001/jama.1987.03400090089040 + None Newborn Infant Screening for Sickle Cell Neonatal Screening for Sickle Cell - + - - + + - - + + A physical assessment of the various symptoms associated with a stroke, consisting of 11 categories. For each category, the test administrator asks the respondent to perform an activity or respond to stimuli. Respondents receive a score for each category based upon their ability to complete the activity or respond to the action. Each score typically ranges from 0 to 3. Each category of the NIHSS is designed to determine the respondent's level of consciousness (LOC), visual, motor, or language ability. - http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820801 - PhenX protocol: NIH Stroke Scale (NIHSS) #820801 - 18 years and older - Examiners must be trained to administer, score, and interpret the NIH Stroke Scale (NIHSS). The National Institute of Neurological Disorders and Stroke (NINDS) provides a comprehensive interactive training DVD for the NIHSS. Information and purchasing details for this training are available on the NINDS website. - Few but definitions not freely available + http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820801 + PhenX protocol: NIH Stroke Scale (NIHSS) #820801 + 18 years and older + Examiners must be trained to administer, score, and interpret the NIH Stroke Scale (NIHSS). The National Institute of Neurological Disorders and Stroke (NINDS) provides a comprehensive interactive training DVD for the NIHSS. Information and purchasing details for this training are available on the NINDS website. + Few but definitions not freely available phenX:820801 NIH Stroke Scale NIHSS @@ -32536,14 +31971,14 @@ Request inclusion into relevant ontology. Perhaps in SNOMED CT below "Scree - + - - + + Patients who do not turn up for scheduled healthcare appointments. - http://purl.bioontology.org/ontology/MESH/D000067455 - Sufficient - SCDO:0000807 + http://purl.bioontology.org/ontology/MESH/D000067455 + Sufficient + SCDO:0000807 MESH:D000067455 No Show Patient Patient No Show @@ -32553,38 +31988,38 @@ Request inclusion into relevant ontology. Perhaps in SNOMED CT below "Scree - + - + - - + + - - + + - - + + - - + + Frequent urination at night that interrupts sleep. It is often associated with outflow obstruction, diabetes mellitus, or bladder inflammation (cystitis). - http://purl.bioontology.org/ontology/MESH/D053158 - Sufficient - SCDO:0000808 + http://purl.bioontology.org/ontology/MESH/D053158 + Sufficient + SCDO:0000808 MESH:D053158 Nycturia Often occuring as a result of heart insufficiency. @@ -32593,50 +32028,50 @@ Request inclusion into relevant ontology. Perhaps in SNOMED CT below "Scree - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A subclass of analgesic agents that typically do not bind to opioid receptors and are not addictive. Many non-narcotic analgesics are offered as nonprescription drugs. - http://purl.bioontology.org/ontology/MESH/D018712 - Sufficient - SCDO:0000809 + http://purl.bioontology.org/ontology/MESH/D018712 + Sufficient + SCDO:0000809 MESH:D018712 Non-Narcotic Nonnarcotic @@ -32648,117 +32083,117 @@ Request inclusion into relevant ontology. Perhaps in SNOMED CT below "Scree - + - + A gene that does not encode a globin family protein. + Perhaps too specific to the SCDO to be included in other ontologies? + None SCDO (Jade Hotchkiss) - Perhaps too specific to the SCDO to be included in other ontologies? - None Non-Globin Gene - + - - + + - - + + - - + + - - + + - - + + Sickle retinopathy caused by direct damage or remodeling of the small blood vessels supplying the retina secondary to vaso-occlusion and local ischemia. + Request inclusion into HPO below "Retinopathy/Sickle Retinopathy". + http://en.wikipedia.org/wiki/Retinopathy + http://eyewiki.aao.org/Sickle_Cell_Retinopathy + None SCDO (Jade Hotchkiss) - Request inclusion into HPO below "Retinopathy/Sickle Retinopathy". - http://en.wikipedia.org/wiki/Retinopathy - http://eyewiki.aao.org/Sickle_Cell_Retinopathy - None Non-Proliferative Sickle Retinopathy - + - + - + - - + + - + - - + + - - + + - - + + Includes acute respiratory episodes with lower respiratory tract signs that do not meet the criteria for other diagnoses. May include episodes which would have been diagnosed as ACS were radiographic facilities available. - SCDO - Request inclusion into relevant ontology + Request inclusion into relevant ontology -Provide source for additional info. - Several possible etiologies including infections by various classes of microorganisms, pulmonary fat emobolism, infarction and pulmonary embolism. - Acute onset of respiratory symptoms and signs including cough, coryza +/- fever. - None +Provide source for additional info. + Several possible etiologies including infections by various classes of microorganisms, pulmonary fat emobolism, infarction and pulmonary embolism. + Acute onset of respiratory symptoms and signs including cough, coryza +/- fever. + None + SCDO Non-specific Acute Lower Respiratory Tract Episode - + - - + + 'A work that reports on the results of a clinical study in which participants may receive diagnostic, therapeutic, or other types of interventions, but the investigator does not assign participants to specific interventions (as in an interventional study). [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D064888 + http://purl.bioontology.org/ontology/MESH/D064888 MESH:D064888 obsolete Observational Study true @@ -32766,88 +32201,88 @@ Provide source for additional info. - + - - + + Works about clinical studies in which participants may receive diagnostic, therapeutic, or other types of interventions, but the investigator does not assign participants to specific interventions (as in an interventional study). - http://purl.bioontology.org/ontology/MESH/D064887 - Sufficient - SCDO:0000819 + http://purl.bioontology.org/ontology/MESH/D064887 + Sufficient + SCDO:0000819 MESH:D064887 Observational Studies as Topic - + - - + + - + - + - + - + - + - + - - + + - - + + - - + + - - + + Skilled treatment that helps individuals achieve independence in all facets of their lives. It assists in the development of skills needed for independent living. - http://purl.bioontology.org/ontology/MESH/D009788 - Sufficient - SCDO:0000822 + http://purl.bioontology.org/ontology/MESH/D009788 + Sufficient + SCDO:0000822 MESH:D009788 Occupational Therapies Therapies, Occupational @@ -32857,32 +32292,32 @@ Provide source for additional info. - + - + - - + + - + - - + + Low output of urine, defined as an output below 5mL/kg/hr over 6 hours. - Suggest update to description in HPO - - Suggest update to description + Suggest update to description in HPO + + Suggest update to description HP:0100520 Reduced Urine Output Oliguria @@ -32890,14 +32325,14 @@ Provide source for additional info. - + - - + + Surgery performed on the eye or any of its parts. - http://purl.bioontology.org/ontology/MESH/D013508 - Sufficient - SCDO:0000833 + http://purl.bioontology.org/ontology/MESH/D013508 + Sufficient + SCDO:0000833 MESH:D013508 Ophthalmologic Surgical Procedures Ophthalmological Surgical Procedure @@ -32906,26 +32341,26 @@ Provide source for additional info. - + - - + + - + - - + + Device for examining the interior of the eye, permitting the clear visualization of the structures of the eye at any depth. - http://purl.bioontology.org/ontology/MESH/D019721 - Sufficient - SCDO:0000834 + http://purl.bioontology.org/ontology/MESH/D019721 + Sufficient + SCDO:0000834 MESH:D019721 Funduscope Ophthalmoscopes @@ -32934,51 +32369,51 @@ Provide source for additional info. - + - + - - + + Examination of the interior of the eye with an ophthalmoscope. - Include "Direct Ophthalmoscopy" and "Indirect Ophthalmoscopy" from NCIT as sub-classes? (Direct could be used to diagnose "Conjunctival Comma Sign") - http://purl.bioontology.org/ontology/MESH/D009887 - Sufficient - SCDO:0000835 + Include "Direct Ophthalmoscopy" and "Indirect Ophthalmoscopy" from NCIT as sub-classes? (Direct could be used to diagnose "Conjunctival Comma Sign") + http://purl.bioontology.org/ontology/MESH/D009887 + Sufficient + SCDO:0000835 MESH:D009887 Ophthalmoscopy - + - + - - + + - - + + A general term for bone weakness owing to a defect in mineralization of the protein framework known as osteoid. This defective mineralization is mainly caused by lack in vitamin D. Osteomalacia in children is known as rickets. - Suggest update to description in HPO. (remove "Osteomalacia" from start of definitiion) + Suggest update to description in HPO. (remove "Osteomalacia" from start of definitiion) -Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0002749 - Abnormal vitamin D metabolism: 1) Deficient intake or absorption;2) Defective 25-hydroxylation due to biliary cirrhosis- alcoholic cirrhosis- anticonvulsants; 3) Loss of vitamin D binding protein- nephrotic syndrome; 4) Defective 1-alpha 25-hydroxylation: Hypoparathyroidism, Renal failure, Vitamin D-dependent rickets type 1; 5) Defective target organ response to calcitriol: Vitamin D-dependent rickets, type II (Hereditary vitamin D resistant rickets, HVDRR). Mineralization defects: 1) Abnormal matrix: Chronic renal failure, Osteogenesis imperfecta, Fibrogenesis imperfecta, Axial osteomalacia; 2) Enzyme deficiency: Hypophosphatasia; 3) Mineralization inhibitors: bisphosphonates, Aluminum, fluoride. Phosphate deficiency: 1) Decreased intake ( antiacids); 2) Impaired renal reabsorption, that can be Primary defects = X-linked hypophosphatemic rickets (vitamin D resistant rickets, VDRR), Hereditary hypophosphatemic rickets with hypercalciuria, Sporadic acquired hypophosphatemic rickets, Fanconi syndrome, Wilson disease, cystinosis, multiple myeloma; or can be Secondary defects = 2) Secondary hyperparathyroidism (renal tubular acidosis, type 1 and disorders of vitamin D metabolism), 2) Oncogenic osteomalacia. - May be asymptomatic and present radiologically as osteopenia. Or it may present as diffuse bone and joint pain, muscle weakness, and difficulty walking, Fractures, Muscle spasms, cramps. - Suggest update to description +Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0002749 + Abnormal vitamin D metabolism: 1) Deficient intake or absorption;2) Defective 25-hydroxylation due to biliary cirrhosis- alcoholic cirrhosis- anticonvulsants; 3) Loss of vitamin D binding protein- nephrotic syndrome; 4) Defective 1-alpha 25-hydroxylation: Hypoparathyroidism, Renal failure, Vitamin D-dependent rickets type 1; 5) Defective target organ response to calcitriol: Vitamin D-dependent rickets, type II (Hereditary vitamin D resistant rickets, HVDRR). Mineralization defects: 1) Abnormal matrix: Chronic renal failure, Osteogenesis imperfecta, Fibrogenesis imperfecta, Axial osteomalacia; 2) Enzyme deficiency: Hypophosphatasia; 3) Mineralization inhibitors: bisphosphonates, Aluminum, fluoride. Phosphate deficiency: 1) Decreased intake ( antiacids); 2) Impaired renal reabsorption, that can be Primary defects = X-linked hypophosphatemic rickets (vitamin D resistant rickets, VDRR), Hereditary hypophosphatemic rickets with hypercalciuria, Sporadic acquired hypophosphatemic rickets, Fanconi syndrome, Wilson disease, cystinosis, multiple myeloma; or can be Secondary defects = 2) Secondary hyperparathyroidism (renal tubular acidosis, type 1 and disorders of vitamin D metabolism), 2) Oncogenic osteomalacia. + May be asymptomatic and present radiologically as osteopenia. Or it may present as diffuse bone and joint pain, muscle weakness, and difficulty walking, Fractures, Muscle spasms, cramps. + Suggest update to description HP:0002749 Adult Rickets Osteomalacia @@ -32986,85 +32421,85 @@ Provide source for additional info. - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An inflammatory process accompanied by bone destruction and caused by an infecting microorganism. - Suggest update to description in HPO (remove "Osteomyelitis is" from the start of the definition. + Suggest update to description in HPO (remove "Osteomyelitis is" from the start of the definition. -Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0002754 - Bacteria, blunt trauma, fracture, bone surgery. - Tenderness, redness, and warmth in the area of infection, fever, fatigue, bone pain, swelling around the affected bone, lost range of motion. - Suggest update to description +Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0002754 + Bacteria, blunt trauma, fracture, bone surgery. + Tenderness, redness, and warmth in the area of infection, fever, fatigue, bone pain, swelling around the affected bone, lost range of motion. + Suggest update to description HP:0002754 Bone Infection Osteomyelitis can be acute or chronic and can be caused by a variety of microbial agents. @@ -33073,33 +32508,33 @@ Provide source for additional info. - + - + - - + + - - + + - - + + The amount of oxygen bound to hemoglobin in arterial blood expressed as a percentage of the maximal binding capacity, as determined by an arterial blood gas test. - Request inclusion into CMO below "Oxygen Saturation" - - Few but definitions not freely available + Request inclusion into CMO below "Oxygen Saturation" + + Few but definitions not freely available Arterial HbO2 Arterial Oxyhemoglobin Saturation Arterial SaO2 @@ -33113,110 +32548,110 @@ Provide source for additional info. - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An unpleasant sensory and emotional experience triggered in the nervous system, associated with actual or potential tissue damage, or described in terms of such damage. - Suggest update to description in HPO. + Suggest update to description in HPO. -Provide source for additional info. - http://purl.obolibrary.org/obo/HP_0012531 - Somatic pain is caused by injury to skin, muscles, bone, joint, and connective tissues. Deep somatic pain is usually described as dull or aching, and localized in one area. Visceral pain refers to pain that originates from ongoing injury to the internal organs or the tissues that support them. Somatic pain from injury to the skin or the tissues just below it often is sharper and may have a burning or pricking quality. - Nociceptive pain is believed to be caused by the ongoing activation of pain receptors in either the surface or deep tissues of the body. There are two types: "somatic" pain and "visceral" pain. Neuropathic pain is believed to be caused by changes in the nervous system that sustain pain even after an injury heals. "Psychogenic" pain is a simple label for all kinds of pain that can be best explained by psychological problems. - Suggest update to description +Provide source for additional info. + http://purl.obolibrary.org/obo/HP_0012531 + Somatic pain is caused by injury to skin, muscles, bone, joint, and connective tissues. Deep somatic pain is usually described as dull or aching, and localized in one area. Visceral pain refers to pain that originates from ongoing injury to the internal organs or the tissues that support them. Somatic pain from injury to the skin or the tissues just below it often is sharper and may have a burning or pricking quality. + Nociceptive pain is believed to be caused by the ongoing activation of pain receptors in either the surface or deep tissues of the body. There are two types: "somatic" pain and "visceral" pain. Neuropathic pain is believed to be caused by changes in the nervous system that sustain pain even after an injury heals. "Psychogenic" pain is a simple label for all kinds of pain that can be best explained by psychological problems. + Suggest update to description HP:0012531 Pain - + - - + + The impact of sickle cell pain on the daily activities of patients. The degree to which pain interferes with their quality of life. This pain is related to the unique features of Sickle Cell Disease. + Request inclusion into relevant ontology + None SCDO - Request inclusion into relevant ontology - None Pain Burden Pain Disability Pain Impact @@ -33226,28 +32661,28 @@ Provide source for additional info. - + - - + + A method of determining the shape and consistency of the liver by feeling with the fingers or hands. + Request inclusion into relevant ontology + Few but definitions not freely available SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - Few but definitions not freely available Liver Palpation Palpation of Liver - + - + Invertebrate organisms that live on or in another organism (the host), and benefit at the expense of the other. Traditionally excluded from definition of parasites are pathogenic bacteria; fungi; viruses; and plants; though they may live parasitically. - http://purl.bioontology.org/ontology/MESH/D010271 - Sufficient - SCDO:0000866 + http://purl.bioontology.org/ontology/MESH/D010271 + Sufficient + SCDO:0000866 MESH:D010271 Parasites Parasite @@ -33255,21 +32690,21 @@ Provide source for additional info. - + - - - + + + - + Voluntary cooperation of the patient in following a prescribed regimen. - http://purl.bioontology.org/ontology/MESH/D010349 - Sufficient - SCDO:0000869 + http://purl.bioontology.org/ontology/MESH/D010349 + Sufficient + SCDO:0000869 MESH:D010349 Adherence Patient Adherence @@ -33279,15 +32714,15 @@ Provide source for additional info. - + - - + + A headache disability questionnaire which is completed by the patient and his/her parent and is reviewed with the clinician or study staff. It captures the impact of headaches on school performance (three questions), activities at home (one question on homework or chores), and social and/or sports functions (two questions). It is scored by summing the answers across the six questions. If a range is provided as an answer, either use the high end of the range or prompt for a single answer. The frequency and severity are not scored but can be used for clinical reference. - Suggest update to label in PhenX (from "Migraine - Children") as we have done. - - PhenX protocol: Migraine - Children #130502 - Suggest update to label + Suggest update to label in PhenX (from "Migraine - Children") as we have done. + + PhenX protocol: Migraine - Children #130502 + Suggest update to label phenX:130502 PedMIDAS Pediatric Migraine Questionnaire @@ -33296,22 +32731,22 @@ Provide source for additional info. - + - - + + - - + + A physical assessment of the various symptoms associated with a stroke, consisting of eleven categories. The PedNIHSS was developed by a panel of pediatric and adult stroke experts and is a modification of the adult NIH stroke scale (NIHSS). Modifications were made to allow individuals age 18 or younger to be assessed and are identified in the PedNIHSS by bold italic text. - http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820802 - PhenX protocol: Pediatric NIH Stroke Scale (PedNIHSS) #820802 - 2-18 years old - Examiners must be trained to administer, score, and interpret the NIHSS. The National Institute of Neurological Disorders and Stroke (NINDS) provides a comprehensive interactive training DVD for the National Institutes of Health Stroke Scale (NIHSS). Information and purchasing details for this training is available on the NINDS website. - None + http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820802 + PhenX protocol: Pediatric NIH Stroke Scale (PedNIHSS) #820802 + 2-18 years old + Examiners must be trained to administer, score, and interpret the NIHSS. The National Institute of Neurological Disorders and Stroke (NINDS) provides a comprehensive interactive training DVD for the National Institutes of Health Stroke Scale (NIHSS). Information and purchasing details for this training is available on the NINDS website. + None phenX:820802 PedNIHSS Pediatric NIH Stroke Scale @@ -33321,191 +32756,191 @@ Provide source for additional info. - + - - - + + + - - + + A questionnaire to assess educational performance and learning accommodations. + Suggest update to label in PhenX as we have done. + + PhenX protocol: Pediatric School Performance #840201 + Many rare genetic conditions (e.g., sickle cell disease) and other diseases are associated with developmental delays, damage to the central nervous system, and frequent absences from school due to illness, all of which can impact school performance. + Suggest update to label - Suggest update to label in PhenX as we have done. - - PhenX protocol: Pediatric School Performance #840201 - Many rare genetic conditions (e.g., sickle cell disease) and other diseases are associated with developmental delays, damage to the central nervous system, and frequent absences from school due to illness, all of which can impact school performance. - Suggest update to label phenX:840200 Pediatric School Performance Measure - + - + A generic symptom-specific instrument to measure fatigue across pediatric populations. - Request inclusion into NCIT below "Pediatric Quality of Life Inventory". - Panepinto JA, Torres S, Bendo CB, McCavit TL, Dinu B, Sherman-Bien S, Bemrich-Stolz C, Varni JW (2014). PedsQL Multidimensional Fatigue Scale in sickle cell disease: feasibility, reliability, and validity. Pediatric Blood & Cancer, 61,171-177 - Self; Proxy (Parent report) - Clinic patients - Validation study in SCD - Children 2 - 18 (child report ages 5 - 18 years; parent proxy report of children ages 2 - 18 years) - None + Request inclusion into NCIT below "Pediatric Quality of Life Inventory". + Panepinto JA, Torres S, Bendo CB, McCavit TL, Dinu B, Sherman-Bien S, Bemrich-Stolz C, Varni JW (2014). PedsQL Multidimensional Fatigue Scale in sickle cell disease: feasibility, reliability, and validity. Pediatric Blood & Cancer, 61,171-177 + Self; Proxy (Parent report) + Clinic patients + Validation study in SCD + Children 2 - 18 (child report ages 5 - 18 years; parent proxy report of children ages 2 - 18 years) + None The 18-item PedsQL Multidimensional Fatigue Scale encompasses three domains: 1) General Fatigue, 2) Sleep/Rest Fatigue and 3) Cognitive Fatigue. The format, instructions, Likert response scale, and scoring method are identical to the PedsQL 4.0 Generic Core Scales [16], with higher scores indicating better HRQOL (lower fatigue symptoms). The instructions ask how much of a problem each item has been during the past one month. PedsQL Multidimensional Fatigue Scale - + - + - + - - + + The PedsQL Sickle Cell Disease Module includes 43 items from 9 subscales: Pain and Hurt (9 items); Pain Impact (10 items); Pain Management and Control (2 items); Worry (5 items); Worry II (2 items); Emotions (2 items); Treatment (7 items); Communication I (3 items); and Communication II (3 items). For all ages, each item asks how much of a problem there has been in the past month. There are self- or parent-reported forms for ages 8 to 18, and responses are scored on a 5-point Likert-style scale (0 = never a problem; 1 = almost never a problem; 2 = sometimes a problem; 3 = often a problem; 4 = almost always a problem). Forms for children ages 5 to 7 are interviewer-administered, and responses include a 3-point Likert-style scale (0 = not at all a problem; 2 = sometimes a problem; 4 = a lot of a problem). Items are reversed-scored and converted to a 100-point scale (0 = 100, 1 = 75, 2 = 50, 3 = 25, 4 = 0) with higher scores indicating better quality of life. Scores for individual subscales are the sum of items divided by the total number or items answered. The total score for the PedsQL Sickle Cell Disease Module is the sum of the items divided by the number of items answered. + Request inclusion into NCIT below "Pediatric Quality of Life Inventory". + + PhenX protocol: PedsQL Sickle Cell Disease Module #820202 + Self; Proxy (Parent report) + Clinic Patients (Children with SCD) + Ages 2 to 18 + No. The PedsQ Sickle Cell Disease Module is a proprietary instrument and administration requires permission and a license from the MAPI Research Trust. + None Panepinto JA, Torres S, Bendo CB, McCavit TL, Dinu B, Sherman-Bien S, Bemrich-Stolz C, Varni JW (2013).PedsQL sickle cell disease module: feasibility, reliability, and validity.Pediatric Blood & Cancer, 60,1338-1344. - Request inclusion into NCIT below "Pediatric Quality of Life Inventory". - - PhenX protocol: PedsQL Sickle Cell Disease Module #820202 - Self; Proxy (Parent report) - Clinic Patients (Children with SCD) - Ages 2 to 18 - No. The PedsQ Sickle Cell Disease Module is a proprietary instrument and administration requires permission and a license from the MAPI Research Trust. - None PedsQL Sickle Cell Disease Module - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Use of penicillin for the prevention of infections with penicillin-susceptible organisms, e.g. Streptococcus pneumoniae. + Request inclusion into relevant ontology + Few but definitions not freely available SCDO - Request inclusion into relevant ontology - Few but definitions not freely available Penicillin Prophylaxis - + - - + + A method of determining the size of the liver by tapping on the surface of the abdomen. + To be requested for inclusion into SNOMED CT, below "Diagnostic procedure on liver". + None SCDO (Jade Hotchkiss) - To be requested for inclusion into SNOMED CT, below "Diagnostic procedure on liver". - None Percussion of Liver - + - + - - + + - - + + An estimation of the oxygen saturation level usually measured with a pulse oximeter device. - Request inclusion into CMO below "Oxygen Saturation" - http://en.wikipedia.org/wiki/Oxygen_saturation_(medicine) - Few but definitions not freely available + Request inclusion into CMO below "Oxygen Saturation" + http://en.wikipedia.org/wiki/Oxygen_saturation_(medicine) + Few but definitions not freely available SNOMEDCT:431314004 Oxygen Saturation of Peripheral Blood Peripheral SaO2 @@ -33518,119 +32953,119 @@ Provide source for additional info. - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A (combination of) quality(ies) of some or all sickle cell disease individuals, determined by the interaction of the genetic make-up of these individuals (with regard to sickle cell disease) and their environment. - SCDO - Probably too specific to warrant inclusion into anther ontology. + Probably too specific to warrant inclusion into anther ontology. -Make sure complications as described in "Definitions of the Phenotypic Manifestations of Sickle Cell Disease" (Ballas, 2010) are included in Phenotype. - http://bioportal.bioontology.org/ontologies/OGMS?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000023 - None +Make sure complications as described in "Definitions of the Phenotypic Manifestations of Sickle Cell Disease" (Ballas, 2010) are included in Phenotype. + http://bioportal.bioontology.org/ontologies/OGMS?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000023 + None + SCDO OGMS:0000023 Phenotype of Sickle Cell Disease - + - - + + The physical method (technology) used to measure / readout the effect caused by a perturbagen in the assay environment. - - Sufficient - SCDO:0000896 + + Sufficient + SCDO:0000896 BAO:0000035 Physical Detection Method - + - - + + The part of the human environment that consists of purely physical factors, including the natural environment (such as soil, climate, water supply) and the built environment. - Request inclusion into relevant ontology - Physical Environment. Merriam-Webster.com. Merriam-Webster, n.d. Web. 9 Nov. 2016. - Few but definitions not freely available + Request inclusion into relevant ontology + Physical Environment. Merriam-Webster.com. Merriam-Webster, n.d. Web. 9 Nov. 2016. + Few but definitions not freely available Physical Environment - + - - + + Systematic and thorough inspection of the patient for physical signs of disease or abnormality. - http://purl.bioontology.org/ontology/MESH/D010808 - Sufficient - SCDO:0000898 + http://purl.bioontology.org/ontology/MESH/D010808 + Sufficient + SCDO:0000898 MESH:D010808 Physical Assessment Physical Examination @@ -33638,21 +33073,21 @@ Make sure complications as described in "Definitions of the Phenotypic Mani - + - + - + One's ability to carry out activities that require physical actions, ranging from self-care (activities of daily living) to more complex activities that require a combination of skills, often within a social context. Physical function is inclusive of the term disability and includes the full spectrum of physical functioning from severe impairment to exceptional physical abilities. + Determine and specify the description source. -- -- Include a term to do with level of independence? + + Few but definitions not specific enough SCDO - Determine and specify the description source. -- -- Include a term to do with level of independence? - - Few but definitions not specific enough Mobility Motor Function Physical Function @@ -33662,148 +33097,148 @@ Make sure complications as described in "Definitions of the Phenotypic Mani - + - - + + An organismal assay designed to capture information pertaining to the organic processes and phenomena of an organism or any of its parts or of a particular bodily process. - http://purl.obolibrary.org/obo/ERO_0001292 - Sufficient - SCDO:0000902 + http://purl.obolibrary.org/obo/ERO_0001292 + Sufficient + SCDO:0000902 ERO:0001292 Physiological Assay - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A therapeutic intervention that remediates impairments and promotes mobility, function, and quality of life through examination, diagnosis, and physical intervention. - http://purl.obolibrary.org/obo/OAE_0002476 - Sufficient - SCDO:0000903 + http://purl.obolibrary.org/obo/OAE_0002476 + Sufficient + SCDO:0000903 OAE:0002476 Physical Therapy Physiotherapy @@ -33811,14 +33246,14 @@ Make sure complications as described in "Definitions of the Phenotypic Mani - + - - + + Small-scale tests of methods and procedures to be used on a larger scale if the pilot study demonstrates that these methods and procedures can work. - http://purl.bioontology.org/ontology/MESH/D010865 - Sufficient - SCDO:0000905 + http://purl.bioontology.org/ontology/MESH/D010865 + Sufficient + SCDO:0000905 MESH:D010865 Pilot Study Pilot Projects @@ -33826,27 +33261,27 @@ Make sure complications as described in "Definitions of the Phenotypic Mani - + - - + + A nonincisional procedure that has become a well-accepted alternative to scleral buckling and vitrectomy for the repair of selected cases of rhegmatogenous retinal detachment. - Request inclusion into relevant ontology - http://emedicine.medscape.com/article/1844217-overview - Few but definitions not freely available + Request inclusion into relevant ontology + http://emedicine.medscape.com/article/1844217-overview + Few but definitions not freely available Pneumatic Retinopexy - + - - + + The process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As the process progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified. - Suggest update to description in OBI - http://purl.obolibrary.org/obo/OBI_0000415 - Suggest update to description + Suggest update to description in OBI + http://purl.obolibrary.org/obo/OBI_0000415 + Suggest update to description OBI:0000415 PCR Polymerase Chain Reaction @@ -33854,12 +33289,12 @@ Make sure complications as described in "Definitions of the Phenotypic Mani - + - - + + 'Works about randomized clinical trials that compare interventions in clinical settings and which look at a range of effectiveness outcomes and impacts. [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D065007 + http://purl.bioontology.org/ontology/MESH/D065007 MESH:D065007 Pragmatic Clinical Trial true @@ -33867,29 +33302,29 @@ Make sure complications as described in "Definitions of the Phenotypic Mani - + - - + + Prenatal detection of a fetus affected with Sickle Cell Disease using appropriate laboratory techniques. Detection of affected fetuses allows couples to make informed decisions regarding the pregnancy. + Request inclusion into relevant ontology. Perhaps in SNOMED CT below "Screening for sickle cell disease". + None SCDO (Clair Ingram) - Request inclusion into relevant ontology. Perhaps in SNOMED CT below "Screening for sickle cell disease". - None Prenatal Screening for Sickle Cell - + - - + + Activities to prevent Sickle Cell Disease or its complications. - SCDO - Probably too specific to SCD to be included in other ontologies. + Probably too specific to SCD to be included in other ontologies. -Consider making the description more generic (e.g. "Activities to prevent a disease or its complications.") - None +Consider making the description more generic (e.g. "Activities to prevent a disease or its complications.") + None + SCDO Preventive Therapeutics Prophylactic Therapeutics Preventative Therapeutics @@ -33897,97 +33332,97 @@ Consider making the description more generic (e.g. "Activities to prevent a - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A prolonged painful erection that may last hours and is not associated with sexual activity. It is seen in patients with sickle cell anemia, advanced malignancy, spinal trauma, and certain drug treatments. - http://purl.bioontology.org/ontology/MESH/D011317 - Sufficient - SCDO:0000923 + http://purl.bioontology.org/ontology/MESH/D011317 + Sufficient + SCDO:0000923 MESH:D011317 Priapism - + - - + + Care which provides integrated, accessible health care services by clinicians who are accountable for addressing a large majority of personal health care needs, developing a sustained partnership with patients, and practicing in the context of family and community. - This term is not below Quality of Health Care in MESH, but below "Health Services Administration" ---> "Patient Care Management" ---> "Comprehensive Health Care - http://purl.bioontology.org/ontology/MESH/D011320 - Sufficient - SCDO:0000924 + This term is not below Quality of Health Care in MESH, but below "Health Services Administration" ---> "Patient Care Management" ---> "Comprehensive Health Care + http://purl.bioontology.org/ontology/MESH/D011320 + Sufficient + SCDO:0000924 MESH:D011320 Primary Care Primary Health Care @@ -33996,27 +33431,27 @@ Consider making the description more generic (e.g. "Activities to prevent a - + - + - - + + - - + + A biguanide compound which metabolizes in the body to form cycloguanil, an anti-malaria agent. Cycloguanil stops the malaria parasite, Plasmodium falciparum and Plasmodium vivax, from reproducing once it is in the red blood cells. It does this by inhibiting the enzyme, dihydrofolate reductase, which is involved in the reproduction of the parasite. - Suggest update to description in MESH - - - Suggest update to description + Suggest update to description in MESH + + + Suggest update to description MESH:D002727 1-(P-Chlorophenyl)-5-isopropylbiguanide Chlorguanid @@ -34028,75 +33463,75 @@ Consider making the description more generic (e.g. "Activities to prevent a - + - - + + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Sickle retinopathy that involves the upregulation of vascular growth factors due to chronic changes of local hypoxia and ischemia. + Request inclusion into HPO below "Retinopathy/Sickle Retinopathy". + http://eyewiki.aao.org/Sickle_Cell_Retinopathy + None SCDO (Jade Hotchkiss) - Request inclusion into HPO below "Retinopathy/Sickle Retinopathy". - http://eyewiki.aao.org/Sickle_Cell_Retinopathy - None Retinopathy due to SCD Characterized by Neovascularization Sickle Cell Proliferative Retinopathy Proliferative Sickle Retinopathy @@ -34104,54 +33539,54 @@ Consider making the description more generic (e.g. "Activities to prevent a - + - + - + - - + + This protocol includes 29 self-administered quality of life-type questions from the PROMIS Profile 29 for adults. The quality of life questions include physical function, anxiety, depression, fatigue, sleep disturbance, ability to participate in social roles and activities, and pain intensity over the past 7 days. Each question, except for the pain intensity question, is measured on a 5-point scale. - Suggest update to label in PhenX as we have done. - http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=221302 - PhenX protocol: Quality of Life - Adult #221302 - Suggest update to label + Suggest update to label in PhenX as we have done. + http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=221302 + PhenX protocol: Quality of Life - Adult #221302 + Suggest update to label PROMIS 25 Profie v2.0 PROMIS Adult Profile 29 - + - + - + - - + + This protocol includes 25 quality of life-type questions relating to physical function mobility, anxiety, depressive symptoms, fatigue, peer relationships, pain interference, and pain intensity over the past 7 days. - Suggest update to label in PhenX as we have done. - http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=221301 - PhenX protocol: Quality of Life - Pediatric #221301 - Suggest update to label + Suggest update to label in PhenX as we have done. + http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=221301 + PhenX protocol: Quality of Life - Pediatric #221301 + Suggest update to label PROMIS 25 PROMIS 25 Profie PROMIS Pediatric Profile 25 @@ -34159,88 +33594,88 @@ Consider making the description more generic (e.g. "Activities to prevent a - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A planned process that has the objective to reduce the risk of acquiring one or more infections. + Few but definitions not freely available http://purl.obolibrary.org/obo/OGMS_0000103 - Few but definitions not freely available Disease Prevention Infection Prophylaxis - + - - + + Observation of a population for a sufficient number of persons over a sufficient number of years to generate incidence or mortality rates subsequent to the selection of the study group. - http://purl.bioontology.org/ontology/MESH/D011446 - Sufficient - SCDO:0000931 + http://purl.bioontology.org/ontology/MESH/D011446 + Sufficient + SCDO:0000931 MESH:D011446 Prospective Study Prospective Studies @@ -34248,109 +33683,109 @@ Consider making the description more generic (e.g. "Activities to prevent a - + - + - - + + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Increased amounts of any protein (including albumin) in the urine - typically more than 300mg in a 24hr period. + Suggest update to description in HPO. + http://purl.obolibrary.org/obo/HP_0000093 + In sickle cell disease, overt proteinuria (distinguised from albuminuria) may be noted in childhood although less common (4.5% in ages 2-21 [Wigfall 2000] v. 26% in adults [Guasch 2006]). + At most severe form - lead to nephrotic syndrome. + Caused by a variety of kidney diseases, including sickle cell disease, diabetes, glomerular disease, arteriosclerosis. + Elevated amounts of protein in the urine - typically greater than 300mg in 24 hrs. + Suggest update to description - Suggest update to description in HPO. - http://purl.obolibrary.org/obo/HP_0000093 - In sickle cell disease, overt proteinuria (distinguised from albuminuria) may be noted in childhood although less common (4.5% in ages 2-21 [Wigfall 2000] v. 26% in adults [Guasch 2006]). - At most severe form - lead to nephrotic syndrome. - Caused by a variety of kidney diseases, including sickle cell disease, diabetes, glomerular disease, arteriosclerosis. - Elevated amounts of protein in the urine - typically greater than 300mg in 24 hrs. - Suggest update to description HP:0000093 High Urine Protein Levels Screening Recommendations: Screen all individuals with SCD, beginning by age 10, for proteinuria. If the result is negative, repeat screening annually. If the result is positive, perform a first morning void urine albumin-creatinine ratio and if abnormal, consult with or refer to a renal specialist. @@ -34359,57 +33794,57 @@ Consider making the description more generic (e.g. "Activities to prevent a - + - - + + This is a 17-item scale, separated into 4 subscales with good psychometric properties. Negative Attitudes Scale comprises six items grouped together (Mean=36.5, SD=21.9, Potential range = 0 to 100). Higher scores on this scale indicate an endorsement of more negative views about SCD patients. Positive Attitudes Scale comprises four items grouped together (Mean=45.7, SD=24.3, Potential range = 0 to 100). Higher scores indicate an endorsement of more positive views about SCD patients. Concern Raising Behaviors Scale comprises four items grouped together (Mean = 53.7, SD = 22.0, Potential range = 0 to 100). Higher scores indicate greater endorsement of the belief that certain SCD patient behaviors raise clinician concern that the patient is inappropriately drug-seeking. Red-Flag Behaviors Scale comprises three items grouped together (Mean = 58.7, SD = 22.7, Potential range = 0 to 100). Higher scores on this scale indicate greater endorsement of the belief that certain SCD patient behaviors raise clinician concern about patient drug-seeking. + Request inclusion into NCIT below "Research or Clinical Assessment Tool". + Haywood, Jr., C., Lanzkron, S., Hughes, MD3, Brown, R., Massa, M., Ratanawongsa, N., and Beach, MC. (2010). A Video-Intervention to Improve Clinician Attitudes Toward Patients with Sickle Cell Disease: The Results of a Randomized Experiment. J Gen Intern Med 26(5):518–23. + African Americans + Self + Heath care providers + Demonstrated validity with SCD populations in the US + Adults + None Haywood, Jr., C., Lanzkron, S., Hughes, MD3, Brown, R., Massa, M., Ratanawongsa, N., and Beach, MC. (2010). A Video-Intervention to Improve Clinician Attitudes Toward Patients with Sickle Cell Disease: The Results of a Randomized Experiment. J Gen Intern Med 26(5):518–23. - Request inclusion into NCIT below "Research or Clinical Assessment Tool". - Haywood, Jr., C., Lanzkron, S., Hughes, MD3, Brown, R., Massa, M., Ratanawongsa, N., and Beach, MC. (2010). A Video-Intervention to Improve Clinician Attitudes Toward Patients with Sickle Cell Disease: The Results of a Randomized Experiment. J Gen Intern Med 26(5):518–23. - African Americans - Self - Heath care providers - Demonstrated validity with SCD populations in the US - Adults - None Provider Attitudes Toward Patients with Sickle Cell Disease - + - + - - + + - - + + - - + + - - + + Pruritus, or itch, is defined as an unpleasant sensation that provokes the desire to scratch. - Suggest update to description. The current description seems to be describing two different things in the same description. - - Suggest update to description + Suggest update to description. The current description seems to be describing two different things in the same description. + + Suggest update to description HP:0000989 Itchy Skin Skin Itching @@ -34418,32 +33853,32 @@ Consider making the description more generic (e.g. "Activities to prevent a - + - - + + - - + + - - + + - - + + Stress wherein emotional factors predominate. - - Sufficient - SCDO:0000937 + + Sufficient + SCDO:0000937 MESH:D013315 Emotional Stress Life Stress @@ -34453,16 +33888,16 @@ Consider making the description more generic (e.g. "Activities to prevent a - + - - - + + + The absence of appropriate stimuli in the physical or social environment which are necessary for the emotional, social, and intellectual development of the individual. - This term is placed below "Culture" in MESH. - http://purl.bioontology.org/ontology/MESH/D011610 - Sufficient - SCDO:0000938 + This term is placed below "Culture" in MESH. + http://purl.bioontology.org/ontology/MESH/D011610 + Sufficient + SCDO:0000938 MESH:D011610 Psychosocial Deprivations Psychosocial Deprivation @@ -34470,26 +33905,26 @@ Consider making the description more generic (e.g. "Activities to prevent a - + - - + + - - + + - - + + A generic term for the treatment of mental illness or emotional disturbances primarily by verbal or nonverbal communication. - http://purl.bioontology.org/ontology/MESH/D011613 - Sufficient - SCDO:0000940 + http://purl.bioontology.org/ontology/MESH/D011613 + Sufficient + SCDO:0000940 MESH:D011613 Logotherapy Psycho-Therapy @@ -34498,26 +33933,26 @@ Consider making the description more generic (e.g. "Activities to prevent a - + - - + + 'Describes the type of material the article represents (e.g., Review, Clinical Trial, Retracted Publication, Letter); see the PubMed Publication Types, e.g., review[pt]. Publication Types are arranged hierarchically with more specific terms arranged beneath broader terms. [Curator team: []]' - http://bioportal.bioontology.org/ontologies/EDDA_PT?p=classes&conceptid=http%3A%2F%2Fontologies.dbmi.pitt.edu%2Fedda%2FPublicationType.owl%23publication_type + http://bioportal.bioontology.org/ontologies/EDDA_PT?p=classes&conceptid=http%3A%2F%2Fontologies.dbmi.pitt.edu%2Fedda%2FPublicationType.owl%23publication_type obsolete Publication Type true - + - - + + Measurement of the various processes involved in the act of respiration: inspiration, expiration, oxygen and carbon dioxide exchange, lung volume and compliance, etc. - - Sufficient - SCDO:0000942 + + Sufficient + SCDO:0000942 MESH:D012129 Lung Function Test PFT @@ -34527,94 +33962,94 @@ Consider making the description more generic (e.g. "Activities to prevent a - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An elevation of mean pulmonary arterial systolic pressure (mPASP) (>20 mmHg at rest or >30 mmHg with exercise). The 6th World Symposium on PH reduced it from >25mmHg to >20mmHg for at rest, but did not adjust the definition for PH with exercise. + Br J Haematol. 2006 Jul;134(1):109-15. + Simonneau et al 2013 J Am Coll Cardiol; Ataga et al. + Multifactorial, including chronic thromboembolism, splenectomy, high cardiac output, left-heart disease, and hyperviscosity; the role of an inactivation of nitric oxide by free plasma hemoglobin due to chronic hemolysis is controversial. + Few but definitions not specific enough - Br J Haematol. 2006 Jul;134(1):109-15. - Simonneau et al 2013 J Am Coll Cardiol; Ataga et al. - Multifactorial, including chronic thromboembolism, splenectomy, high cardiac output, left-heart disease, and hyperviscosity; the role of an inactivation of nitric oxide by free plasma hemoglobin due to chronic hemolysis is controversial. - Few but definitions not specific enough Increased Blood Pressure in Blood Vessels of Lungs Pulmonary Arterial Hypertension Pulmonary hypertension can be secondary to known cardiac, pulmonary, or hepatic disease. If no cause is identifiable, the term primary pulmonary hypertension is used. @@ -34623,27 +34058,27 @@ Consider making the description more generic (e.g. "Activities to prevent a - + - - + + - - + + - - + + A measurement device, usually attached to the earlobe or fingertip, that measures the oxygen saturation of arterial blood. - This consists of 2 parts, the "pulse oximeter monitor" and the "pulse oximeter probe". Perhaps can be included as sub-classes or siblings? See "Pulse Oximetry (Rest)" in PhenX. - http://purl.obolibrary.org/obo/ERO_0000876 - Sufficient - SCDO:0000944 + This consists of 2 parts, the "pulse oximeter monitor" and the "pulse oximeter probe". Perhaps can be included as sub-classes or siblings? See "Pulse Oximetry (Rest)" in PhenX. + http://purl.obolibrary.org/obo/ERO_0000876 + Sufficient + SCDO:0000944 ERO:0000876 Blood Oxygen Monitor Oxygen Monitor @@ -34652,43 +34087,43 @@ Consider making the description more generic (e.g. "Activities to prevent a - + - + - - + + - - + + The application of pulse oximetry to measure a patient's saturation of oxyhemoglobin when the patient is at rest. - Suggest update to description in PhenX + Suggest update to description in PhenX -Suggest inclusion of term below "Pulse Oximetry" in the CMO. - - PhenX protocol: Pulse Oximetry (Rest) #91102 - Suggest update to description +Suggest inclusion of term below "Pulse Oximetry" in the CMO. + + PhenX protocol: Pulse Oximetry (Rest) #91102 + Suggest update to description phenX:91102 Pulse Oximetry (Rest) - + - - + + The systemic measurement of the quality of health care that includes a broad set of perfomance measures such as the quality of services and the outcomes analysis for particular diseases and conditions, mortality and morbidity, patient safety, data on maternal and child health, as well as evaluation of quality of diagnosis, care accessibility, implementation of proven evidence-based practices, quality of reporting systems for errors and adverse events, reliability and accessibility of health and health care-related information, and health care organizations infrastructure. - Suggest update to description in EDDA (replace "excessability" with "accessibility". - - Suggest update to description + Suggest update to description in EDDA (replace "excessability" with "accessibility". + + Suggest update to description EDDA:health_care_quality_assessment Health Care Quality Assessment Quality of Health Care Assessment @@ -34697,20 +34132,20 @@ Suggest inclusion of term below "Pulse Oximetry" in the CMO. + - - + + - + The levels of excellence which characterize the health service or health care provided based on accepted standards of quality. - http://purl.bioontology.org/ontology/MESH/D011787 - Sufficient - SCDO:0000948 + http://purl.bioontology.org/ontology/MESH/D011787 + Sufficient + SCDO:0000948 MESH:D011787 Health Care Quality Healthcare Quality @@ -34720,81 +34155,81 @@ Suggest inclusion of term below "Pulse Oximetry" in the CMO. + - - + + The subjective measurement of an individual's sense of well-being and ability to enjoy life, and the levels of excellence which characterize the health service or health care provided to individuals based on accepted standards of quality. + Request inclusion into relevant ontology. + +Include the term "Transition from pediatric care" somewhere...see the source provided here. + None SCDO - Request inclusion into relevant ontology. - -Include the term "Transition from pediatric care" somewhere...see the source provided here. - None Quality of Life and Care - + - - + + A measurement tool that is useful in aiding routine clinical practice with regard to quality of life and/or quality of care. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Quality of Life and Care Measurement Scales Quality of Life and Care Measure - + - - - + + + - + - - + + - - + + - - + + - - + + - - + + A questionnaire to assess the physical, emotional, and social impact of chronic conditions, such as sickle cell disease (SCD). - Suggest update to label in PhenX. - - Suggest update to label + Suggest update to label in PhenX. + + Suggest update to label phenX:820200 Quality of Life in SCD Quality of Life in Sickle Cell Disease Measure @@ -34802,58 +34237,58 @@ Include the term "Transition from pediatric care" somewhere...see the - + - - + + - + - - + + A measurement tool with eight potential uses in aiding routine clinical practice. It can be used to prioritise problems, facilitate communication, screen for potential problems, identify preferences, monitor changes or response to treatment, and train new staff. It can also be used in clinical audit and in clinical governance. The first five of these can be used in the clinical encounter, while the last three contribute to training, reviewing care, and improving care in the future. + Request inclusion into relevant ontology + + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - None Quality of Life Measure - + - + Sickle cell symptoms where there is evidence of some relation with quality of life. + Probably too specific to be included in other ontologies. + None SCDO - Probably too specific to be included in other ontologies. - None Quality of Life Related SCD Symptoms and Complications - + - - - + + + QALYs are used primarily to correct a person's life expectancy based on the levels of health-related quality of life they are predicted to experience throughout the course of their life, or part of it. - Multiple countries and cultural groups - Self; Proxy - All - Standard global assessment of health interventions, also used in SCD studies - Children and adults - no - Few but definitions not specific enough + Multiple countries and cultural groups + Self; Proxy + All + Standard global assessment of health interventions, also used in SCD studies + Children and adults + no + Few but definitions not specific enough QALY Quality-Adjusted Life Year The number of QALYs lived by an individual in one year is simply: QALYs lived in one year = 1 * Q with Q <= 1; where Q is the health-related quality of life weight attached to the relevant year of life. I.e. QALY assumes a utility value (quality of life) of 1 = perfect health and a utility value of 0 = dead: Years of Life x Utility Value = Number of QALYs. E.g. If a person lives in perfect health for one year, that person will have 1 QALY (1 Year of Life x 1 Utility Value = 1 QALY), If a person lives in perfect health but only for half a year, that person will have 0.5 QALYs (0.5 Years of Life x 1 Utility Value = 0.5 QALYs) OR if a person lives for 1 year in a situation with 0.5 utility (half of perfect health), that person will also have 0.5 QALYs (1 Year of Life x 0.5 Utility Value = 0.5 QALYs). In cost-effectiveness evaluations the QALY is used to quantify the effectiveness of, for instance, a new medication versus the current one. In other words, the current standard of care is taken as the baseline, and the QALYs gained from the new (improved) intervention are counted in addition. @@ -34862,12 +34297,12 @@ Include the term "Transition from pediatric care" somewhere...see the - + - - + + 'Collection of data obtained from voluntary subjects. The information usually takes the form of answers to questions, or suggestions. Predetermined sets of questions used to collect data - clinical data, social status, occupational group, etc. [Curator team: []]' - http://bioportal.bioontology.org/ontologies/MESH?p=classes&conceptid=D011795 + http://bioportal.bioontology.org/ontologies/MESH?p=classes&conceptid=D011795 MESH:D011795 obsolete Questionnaire true @@ -34875,32 +34310,32 @@ Include the term "Transition from pediatric care" somewhere...see the - + - + - + - - + + - - + + Examination of any part of the body for diagnostic purposes by means of x-rays or gamma rays, recording the image on a sensitized surface (such as photographic film). - http://purl.bioontology.org/ontology/MESH/D011859 - Sufficient - SCDO:0000963 + http://purl.bioontology.org/ontology/MESH/D011859 + Sufficient + SCDO:0000963 MESH:D011859 Imaging by X-Ray X-Ray @@ -34909,14 +34344,14 @@ Include the term "Transition from pediatric care" somewhere...see the - + - + The production of an image obtained by cameras that detect the radioactive emissions of an injected radionuclide as it has distributed differentially throughout tissues in the body. The image obtained from a moving detector is called a scan, while the image obtained from a stationary camera device is called a scintiphotograph. - http://purl.bioontology.org/ontology/MESH/D011877 - Sufficient - SCDO:0000964 + http://purl.bioontology.org/ontology/MESH/D011877 + Sufficient + SCDO:0000964 MESH:D011877 Imaging by Radionuclide Scintigraphy @@ -34925,12 +34360,12 @@ Include the term "Transition from pediatric care" somewhere...see the - + - - + + 'A work that reports on a clinical trial that involves at least one test treatment and one control treatment, concurrent enrollment and follow-up of the test- and control-treated groups, and in which the treatments to be administered are selected by a random process, such as the use of a random-numbers table. [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D016449 + http://purl.bioontology.org/ontology/MESH/D016449 MESH:D016449 obsolete Randomized Controlled Trial true @@ -34938,21 +34373,21 @@ Include the term "Transition from pediatric care" somewhere...see the - + - - + + The Rapid Estimate of Adolescent Literacy or REALM-Teen is a valid, reliable, easy-to-administer tool that will allow health professionals to screen youth in grades 6-12 for below-grade reading. The REALM-Teen is a reading recognition instrument, modeled after the Rapid Estimate of Adult Literacy in Medicine (REALM), the most commonly used tool to screen adults for low literacy in health care settings. The REALM-Teen is a reading recognition instrument which measures an individual's ability to pronounce words in ascending order of difficulty. All test words are commonly used adolescent health terms. + Request inclusion into NCIT below "Research or Clinical Assessment Tool". + +Add these annotation properties: -- has cross-cultural adaptation -- freely available -- has translations + Davis TC, Wolf MS, Arnold CL, Byrd RS, Long SW, Springer T, Kennen E, Bocchini JA. (2006). Development and validation of the Rapid Estimate of Adolescent Literacy in Medicine (REALM-Teen): a tool to screen adolescents for below-grade reading in health care settings. Pediatrics 118(6):e1707-14. + Self + Adolescents with SCD + Used in SCD studies + Adolescents + None Davis TC, Wolf MS, Arnold CL, Byrd RS, Long SW, Springer T, Kennen E, Bocchini JA. (2006). Development and validation of the Rapid Estimate of Adolescent Literacy in Medicine (REALM-Teen): a tool to screen adolescents for below-grade reading in health care settings. Pediatrics 118(6):e1707-14. - Request inclusion into NCIT below "Research or Clinical Assessment Tool". - -Add these annotation properties: -- has cross-cultural adaptation -- freely available -- has translations - Davis TC, Wolf MS, Arnold CL, Byrd RS, Long SW, Springer T, Kennen E, Bocchini JA. (2006). Development and validation of the Rapid Estimate of Adolescent Literacy in Medicine (REALM-Teen): a tool to screen adolescents for below-grade reading in health care settings. Pediatrics 118(6):e1707-14. - Self - Adolescents with SCD - Used in SCD studies - Adolescents - None REALM-Teen Rapid Estimate of Adolescent Literacy in Medicine Rapid Estimate of Adolescent Literacy in Medicine (REALM-Teen) @@ -34960,27 +34395,27 @@ Add these annotation properties: -- has cross-cultural adaptation -- freely avai - + - - + + - + - - + + A questionnaire that assesses recovery and recurrence of stroke in children. It is completed by a parent about their child. - Suggest update to description in PhenX. - http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820702 - PhenX protocol: Recovery and Recurrence Questionnaire (RRQ) - Pediatrics #820702 - Suggest update to description + Suggest update to description in PhenX. + http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820702 + PhenX protocol: Recovery and Recurrence Questionnaire (RRQ) - Pediatrics #820702 + Suggest update to description phenX:820702 RRQ Recovery and Recurrence Questionnaire (RRQ) - Pediatrics @@ -34989,60 +34424,60 @@ Add these annotation properties: -- has cross-cultural adaptation -- freely avai - + - - + + - - + + - - + + Recurrent episodes of wheezing in persons with SCD who have no co-morbid asthma. - Probably too specific to warrant inclusion into anther ontology. - Glassberg et al 2014 Curr Opin Pediatr. - Knight-Madden et al 2014 Ped Resp Rev - Likely related to inflammation of SCD. - Other markers of severity of SCD- eg complications of SCD, high LDH. - None + Probably too specific to warrant inclusion into anther ontology. + Glassberg et al 2014 Curr Opin Pediatr. + Knight-Madden et al 2014 Ped Resp Rev + Likely related to inflammation of SCD. + Other markers of severity of SCD- eg complications of SCD, high LDH. + None RWIS Recurrent Wheeze in Sickle Cell Disease - + - + - - + + - - + + The amount of red blood cell derived microparticles in a specific volume of blood. - SCDO (Jade Hotchkiss) - - Request inclusion into relevant ontology + Request inclusion into relevant ontology More info can be taken from the dc:source provided. -Perhaps add MeSH term "Cell-Derived Microparticles" as a superclass of this term? - None +Perhaps add MeSH term "Cell-Derived Microparticles" as a superclass of this term? + None + SCDO (Jade Hotchkiss) + Cell-Derived Microparticles EMP Level Erythrocyte-Derived Microparticles Level @@ -35054,47 +34489,47 @@ Perhaps add MeSH term "Cell-Derived Microparticles" as a superclass of - + - + - + - - + + - - + + - - + + Hemoglobin A (HbA) contains two alpha-globin chains and two beta-globin chains. HbA is normally the main adult hemoglobin, representing about 96-98 percent of all hemoglobin. This term represents a decrease in the proportion of HbA below this limit, and can be seen in various forms of thalassemia. - Suggest update to description in HPO. - http://purl.obolibrary.org/obo/HP_0011905 - Suggest update to description + Suggest update to description in HPO. + http://purl.obolibrary.org/obo/HP_0011905 + Suggest update to description HP:0011905 Reduced Hemoglobin A - + - - + + Restoration of human functions to the maximum degree possible in a person or persons suffering from disease or injury. - http://purl.bioontology.org/ontology/MESH/D012046 - Sufficient - SCDO:0000978 + http://purl.bioontology.org/ontology/MESH/D012046 + Sufficient + SCDO:0000978 MESH:D012046 Habilitation Rehabilitation @@ -35102,15 +34537,15 @@ Perhaps add MeSH term "Cell-Derived Microparticles" as a superclass of - + - - + + Reincarnation is the philosophical or religious concept that an aspect of a living being starts a new life in a different physical body or form after each biological death. + Request inclusion into relevant ontology + http://en.wikipedia.org/wiki/Reincarnation + None SCDO - Request inclusion into relevant ontology - http://en.wikipedia.org/wiki/Reincarnation - None Rebirth Transmigration Reincarnation @@ -35118,15 +34553,15 @@ Perhaps add MeSH term "Cell-Derived Microparticles" as a superclass of - + - + - + A set of beliefs concerning the nature, cause, and purpose of the universe, especially when considered as the creation of a superhuman agency. It usually involves devotional and ritual observances and often a moral code for the conduct of human affairs. - http://purl.bioontology.org/ontology/MESH/D012067 - Sufficient - SCDO:0000981 + http://purl.bioontology.org/ontology/MESH/D012067 + Sufficient + SCDO:0000981 MESH:D012067 Religious Beliefs Religious Ethics @@ -35135,87 +34570,87 @@ Perhaps add MeSH term "Cell-Derived Microparticles" as a superclass of - + - - + + - + - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + Therapy for the insufficient cleansing of the BLOOD by the kidneys based on dialysis and including hemodialysis, peritoneal dialysis, and hemodiafiltration. - Include types of renal dialysis as sub-classes: -- Peritoneal dialysis -- Hemodialysis -- Pediatric dialysis? -- Hemofiltration -- Hemodiafiltration - http://purl.bioontology.org/ontology/MESH/D006435 - Sufficient - SCDO:0000983 + Include types of renal dialysis as sub-classes: -- Peritoneal dialysis -- Hemodialysis -- Pediatric dialysis? -- Hemofiltration -- Hemodiafiltration + http://purl.bioontology.org/ontology/MESH/D006435 + Sufficient + SCDO:0000983 MESH:D006435 Dialyses, Renal Extracorporeal Dialyses @@ -35228,44 +34663,44 @@ Perhaps add MeSH term "Cell-Derived Microparticles" as a superclass of - + - + - - + + - + - - + + - - + + - - + + Inadequate blood flow to one or both kidneys, or nephrons, usually due to functional constriction or actual obstruction of blood vessels. - Suggest update to description in Mammalian Phenotype ontology. + Suggest update to description in Mammalian Phenotype ontology. -Provide source for additional info. - - Loss of adequate blood flow may be due to obstruction of blood vessels - large or small or due to low flow states such as prolonged hypotension. - Usually associated with kidney injury as noted by decrease in urine output and/or elevation in serum creatinine. - Suggest update to description +Provide source for additional info. + + Loss of adequate blood flow may be due to obstruction of blood vessels - large or small or due to low flow states such as prolonged hypotension. + Usually associated with kidney injury as noted by decrease in urine output and/or elevation in serum creatinine. + Suggest update to description MP:0011758 Kidney Ischaemia Kidney Ischemia @@ -35277,26 +34712,26 @@ Provide source for additional info. - + - - + + - + - - + + The transference of a kidney from one human or animal to another. - http://purl.bioontology.org/ontology/MESH/D016030 - Sufficient - SCDO:0000985 + http://purl.bioontology.org/ontology/MESH/D016030 + Sufficient + SCDO:0000985 MESH:D016030 Kidney Grafting Kidney Transplant @@ -35309,37 +34744,37 @@ Provide source for additional info. - + - + - - + + - - + + - - + + Acidosis owing to malfunction of the kidney tubules with accumulation of metabolic acids and hyperchloremia. - Suggest update to description in HPO. - -Provide source for additional info. - - Has multiple types - Type 1 (Distal RTA), Type 2 (Proximal RTA), Type 4 (Hyperkalemic RTA). Sickle cell disease may demonstrate a voltage dependent Type 1 RTA. - Defects in the kidneys in reabsorption of bicarbonate (HCO3), the excretion of hydrogen ions (H+), or both. - A relatively normal GFR and a metabolic acidosis accompanied by hyperchloremia and a normal plasma anion gap. - Suggest update to description + Suggest update to description in HPO. + +Provide source for additional info. + + Has multiple types - Type 1 (Distal RTA), Type 2 (Proximal RTA), Type 4 (Hyperkalemic RTA). Sickle cell disease may demonstrate a voltage dependent Type 1 RTA. + Defects in the kidneys in reabsorption of bicarbonate (HCO3), the excretion of hydrogen ions (H+), or both. + A relatively normal GFR and a metabolic acidosis accompanied by hyperchloremia and a normal plasma anion gap. + Suggest update to description HP:0001947 Accumulation of Acid in Body Due to Kidney Problem RTA @@ -35348,35 +34783,35 @@ Provide source for additional info. - + - + - + - + A questionnaire to assess either male or females' pregnancy history. Females are asked about the number of pregnancies, description of pregnancies and smoking during pregnancy. Males are asked whether they have ever fathered a pregnancy and, if so, the description of the pregnancy. - Suggest update to labels of as we have done. We are using "Reproductive History" below Personal Attribute. -Also suggest update to description as we have done. - - Suggest update to label and description + Suggest update to labels of as we have done. We are using "Reproductive History" below Personal Attribute. +Also suggest update to description as we have done. + + Suggest update to label and description phenX:101300 Reproductive History Diagnostic Instrument - + - - + + 'Anatomical system that has as its parts the organs concerned with reproduction. [Curator team: []]' - - http://purl.obolibrary.org/obo/UBERON_0000990 + + http://purl.obolibrary.org/obo/UBERON_0000990 UBERON:0000990 deprecated Reproductive System true @@ -35384,13 +34819,13 @@ Also suggest update to description as we have done. - + - - + + 'Systematic investigation into a subject in order to discover facts, establish or revise a theory, or develop a plan of action based on the facts discovered. [Curator team: []]' - Consider other sub-classes of this in NCIT. - http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C15429 + Consider other sub-classes of this in NCIT. + http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C15429 NCIT:C15429 obsolete Research Activity true @@ -35398,26 +34833,26 @@ Also suggest update to description as we have done. - + - + - + - + The number of times an organism breathes with the lungs (respiration) per unit time, usually per minute. - - Sufficient - SCDO:0000993 + + Sufficient + SCDO:0000993 MESH:D056152 Breathing Frequency Pulmonary Ventilation Rate @@ -35427,12 +34862,12 @@ Also suggest update to description as we have done. - + - - + + Lungs and respiratory system of the body. - + Pulmonary System deprecated Respiratory System true @@ -35440,27 +34875,27 @@ Also suggest update to description as we have done. - + - + Root of all terms in the Sickle Cell Disease Ontology, an effort of unambiguously describing all concepts and unifying up-to-date knowledge in sickle cell disease. + None SCDO (Gaston K. Mazandu) - None Sickle Cell Disease Ontology SCDO - + - - + + PCR-restriction fragment length polymorphism (RFLP)-based analysis, also known as cleaved amplified polymorphic sequence (CAPS), is a popular technique for genetic analysis. It has been applied for the detection of intraspecies as well as interspecies variation. There exist several techniques that are related with PCR-RFLP and also involve gel electrophoresis including techniques for DNA fingerprinting and expression profiling. - Request inclusion into relevant ontology. - Henrik Berg Rasmussen (April 4th 2012). Restriction Fragment Length Polymorphism Analysis of PCR-Amplified Fragments (PCR-RFLP) and Gel Electrophoresis - Valuable Tool for Genotyping and Genetic Fingerprinting, Gel Electrophoresis Sameh Magdeldin, IntechOpen, DOI: 10.5772/37724. Available from: https://www.intechopen.com/books/gel-electrophoresis-principles-and-basics/restriction-fragment-length-polymorphism-analysis-of-pcr-amplified-fragments-pcr-rflp-and-related-te - Few but definitions not freely available + Request inclusion into relevant ontology. + Henrik Berg Rasmussen (April 4th 2012). Restriction Fragment Length Polymorphism Analysis of PCR-Amplified Fragments (PCR-RFLP) and Gel Electrophoresis - Valuable Tool for Genotyping and Genetic Fingerprinting, Gel Electrophoresis Sameh Magdeldin, IntechOpen, DOI: 10.5772/37724. Available from: https://www.intechopen.com/books/gel-electrophoresis-principles-and-basics/restriction-fragment-length-polymorphism-analysis-of-pcr-amplified-fragments-pcr-rflp-and-related-te + Few but definitions not freely available PCR-RFLP Restriction Fragment Length Polymorphism - Polymerase Chain Reaction Restriction Fragment Length Polymorphism PCR @@ -35468,111 +34903,111 @@ Also suggest update to description as we have done. - + - + - + - + - - + + - - + + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + The number of reticulocytes per unit volume of blood. The values are expressed as a percentage of the erythrocyte count or in the form of an index ("corrected reticulocyte index"), which attempts to account for the number of circulating erythrocytes. - - PhenX protocol: Reticulocyte Count #810601 - Sufficient - SCDO:0001004 + + PhenX protocol: Reticulocyte Count #810601 + Sufficient + SCDO:0001004 MESH:D017701 Reticulocyte Number Reticulocyte Count @@ -35580,128 +35015,128 @@ Also suggest update to description as we have done. - + - - + + A reticulocyte count that was performed with an electronic haematology analyzer. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Reticulocyte Count by Hematology Analyzer - + - - + + A reticulocyte count that was performed with microscopy. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Reticulocyte Count by Microsocopy - + - - + + A procedure that uses intense cold to induce a chorioretinal scar and to destroy retinal or choroidal tissue. - Request inclusion into relevant ontology - http://www.surgeryencyclopedia.com/Pa-St/Retinal-Cryopexy.html - None + Request inclusion into relevant ontology + http://www.surgeryencyclopedia.com/Pa-St/Retinal-Cryopexy.html + None Retinal Cryotherapy Retinal Cryopexy - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Separation of the retina from the choroid and eye wall due to holes in the retina and traction on the retina by vitreous bands and condensed preretinal membranes (usually as sequelae of proliferative sickle retinopathy). Retinal detachment is the most severe complication (Stage V) of proliferative sickle retinopathy. - We provided a more SCD specific description than the generic descriptions provided in existing ontologies. - Ballas et al 2010 Am J Hematol - Not relevant to context of sickle cell + We provided a more SCD specific description than the generic descriptions provided in existing ontologies. + Ballas et al 2010 Am J Hematol + Not relevant to context of sickle cell Retinal Detachment - + - - + + Studies used to test etiologic hypotheses in which inferences about an exposure to putative causal factors are derived from data relating to characteristics of persons under study or to events or experiences in their past. The essential feature is that some of the persons under study have the disease or outcome of interest and their characteristics are compared with those of unaffected persons. - http://purl.bioontology.org/ontology/MESH/D012189 - Sufficient - SCDO:0001010 + http://purl.bioontology.org/ontology/MESH/D012189 + Sufficient + SCDO:0001010 MESH:D012189 Retrospective Study Retrospective Studies @@ -35709,15 +35144,15 @@ Also suggest update to description as we have done. - + - + - + An open swath of land that has few homes or other buildings, and not very many people. - Request inclusion into relevant ontology - - None + Request inclusion into relevant ontology + + None Rural Rural Area Rural Setting @@ -35726,53 +35161,53 @@ Also suggest update to description as we have done. - + - + - + - - + + - - + + - - + + Round or oval-shaped intraretinal accumulation of erythrocytes that may be up to 2 mm in diameter. This small intraretinal hematoma is initially red and becomes salmon colored with time. - Request inclusion into relevant ontology. - Ballas et al 2010 Am J Hematol - None + Request inclusion into relevant ontology. + Ballas et al 2010 Am J Hematol + None Salmon Patch Hemorrhages Salmon Patch Hemorrhage - + - - + + Studies in which a number of subjects are selected from all subjects in a defined population. Conclusions based on sample results may be attributed only to the population sampled. - http://purl.bioontology.org/ontology/MESH/D012494 - Sufficient - SCDO:0001020 + http://purl.bioontology.org/ontology/MESH/D012494 + Sufficient + SCDO:0001020 MESH:D012494 Probability Sample Probability Samples @@ -35782,29 +35217,29 @@ Also suggest update to description as we have done. - + - - - - + + + + - - + + - - + + Pain resulting from the presence of Sickle Cell Disease (SCD). Such pain can be acute, chronic or a mixture of the two. + Request inclusion into relevant ontology + None SCDO Okpala I., Tawil A. Management of pain in sickle-cell disease. Journal of the Royal Society of Medicine. 2002;95(9):456-458. doi: 10.1258/jrsm.95.9.456 - Request inclusion into relevant ontology - None SCD Pain SCD-Related Pain SCD Related Pain @@ -35812,14 +35247,14 @@ Also suggest update to description as we have done. - + - - + + An operation for retinal detachment which reduces the size of the globe by indenting the sclera so that it approximates the retina. - http://purl.bioontology.org/ontology/MESH/D012591 - Sufficient - SCDO:0001025 + http://purl.bioontology.org/ontology/MESH/D012591 + Sufficient + SCDO:0001025 MESH:D012591 Scleral Buckle Surgery Scleral Bucklings @@ -35828,14 +35263,14 @@ Also suggest update to description as we have done. - + - - + + Specialized healthcare delivered as a follow-up or referral from a primary care provider. - http://purl.bioontology.org/ontology/MESH/D063127 - Sufficient - SCDO:0001027 + http://purl.bioontology.org/ontology/MESH/D063127 + Sufficient + SCDO:0001027 MESH:D063127 Secondary Care Secondary Health Care @@ -35844,28 +35279,28 @@ Also suggest update to description as we have done. - + - - + + Usual level of physical activity that is less than 30 minutes of moderate-intensity activity on most days of the week. - http://purl.bioontology.org/ontology/MESH/D057185 - Sufficient - SCDO:0001029 + http://purl.bioontology.org/ontology/MESH/D057185 + Sufficient + SCDO:0001029 MESH:D057185 Sedentary Lifestyle - + - - + + Caring for self when ill or positive actions and adopting behaviors to prevent illness. - http://purl.bioontology.org/ontology/MESH/D012648 - Sufficient - SCDO:0001034 + http://purl.bioontology.org/ontology/MESH/D012648 + Sufficient + SCDO:0001034 MESH:D012648 Self Management Self-Care @@ -35875,14 +35310,14 @@ Also suggest update to description as we have done. - + - - + + Cognitive mechanism based on expectations or beliefs about one's ability to perform actions necessary to produce a given effect. - - Sufficient - SCDO:0001035 + + Sufficient + SCDO:0001035 MESH:D020377 Self-Concept Self Efficacy @@ -35890,27 +35325,27 @@ Also suggest update to description as we have done. - + - - + + The weight in kilograms or pounds as reported by the participant. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Self-Reported Weight - + - - + + Epidemiologic studies based on the detection through serological testing of characteristic change in the serum level of specific antibodies. Latent subclinical infections and carrier states can thus be detected in addition to clinically overt cases. - http://purl.bioontology.org/ontology/MESH/D016036 - Sufficient - SCDO:0001041 + http://purl.bioontology.org/ontology/MESH/D016036 + Sufficient + SCDO:0001041 MESH:D016036 Seroprevalences Seroepidemiologic Studies @@ -35918,21 +35353,21 @@ Also suggest update to description as we have done. - + - + - - + + The amount of the HDL cholesterol, the small lipoprotein:cholesterol complex that transports cholesterol out of the arteries and to the liver for reprocessing or excretion, in a specified volume of serum. + Request inclusion into relevant ontology + + Few but definitions not freely available SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - Few but definitions not freely available Blood HDL Cholesterol Amount Blood High Density Lipoprotein Cholesterol Amount Circulating HDL Cholesterol Amount @@ -35944,36 +35379,36 @@ Also suggest update to description as we have done. - + - - + + A 36-item instrument for measuring health status and outcomes via patient self-report. It is designed for use in surveys of general and specific populations, health policy evaluations, and clinical practice and research. The SF-36v2 measures the following eight health concepts, which are relevant across age, disease, and treatment groups: physical functioning, role limitations due to physical health problems, bodily pain, general health, vitality (energy/fatigue), social functioning, role limitations due to emotional problems, and mental health (psychological distress and psychological well-being). Both standard (4-week) and acute (1-week) recall versions are available. The survey's standardized scoring system yields a profile of eight health scores and two summary measures (physical and mental health) and a self-evaluated change in health status. - Add these annotation properties: -- has cross-cultural adaptation -- freely available -- has translations - Suggest update to label in PhenX (from "Physical, Social, and Mental Health Functioning (SF-36V2)") - - PhenX protocol: #191201 - Self - Healthy people; Clinic patients - Demonstrated validity with SCD populations; multiple publications using the measure in SCD; very widely used with healthy populations and those with chronic conditions - Adults 18 years and older - Suggest update to label + Add these annotation properties: -- has cross-cultural adaptation -- freely available -- has translations + Suggest update to label in PhenX (from "Physical, Social, and Mental Health Functioning (SF-36V2)") + + PhenX protocol: #191201 + Self + Healthy people; Clinic patients + Demonstrated validity with SCD populations; multiple publications using the measure in SCD; very widely used with healthy populations and those with chronic conditions + Adults 18 years and older + Suggest update to label SF-36v2 Health Survey - + - - + + A measure of stigma among adults living with Sickle Cell disease. Focus on; depressive symptoms, pain, assertive communication, satisfaction with pain management experience, and health-related stigma. - Jenerette C, Brewer CA, Crandell J, Ataga KI. Preliminary validity and reliability of the Sickle Cell Disease Health-Related Stigma Scale.Issues Ment Health Nurs.2012 Jun;33(6):363-9. - Request inclusion into NCIT below "Research or Clinical Assessment Tool". + Request inclusion into NCIT below "Research or Clinical Assessment Tool". -Add these annotation properties: -- has respondents -- has target population -- selection criteria met -- validated for age ranges -- has cross-cultural adaptation -- freely available -- has translations - Jenerette C, Brewer CA, Crandell J, Ataga KI. Preliminary validity and reliability of the Sickle Cell Disease Health-Related Stigma Scale.Issues Ment Health Nurs.2012 Jun;33(6):363-9. - None +Add these annotation properties: -- has respondents -- has target population -- selection criteria met -- validated for age ranges -- has cross-cultural adaptation -- freely available -- has translations + Jenerette C, Brewer CA, Crandell J, Ataga KI. Preliminary validity and reliability of the Sickle Cell Disease Health-Related Stigma Scale.Issues Ment Health Nurs.2012 Jun;33(6):363-9. + None + Jenerette C, Brewer CA, Crandell J, Ataga KI. Preliminary validity and reliability of the Sickle Cell Disease Health-Related Stigma Scale.Issues Ment Health Nurs.2012 Jun;33(6):363-9. SCD-HRSS Sickle Cell Disease Health-Related Stigma Scale Sickle Cell Disease Health-Related Stigma Scale (SCD-HRSS) @@ -35981,95 +35416,95 @@ Add these annotation properties: -- has respondents -- has target population -- - + - - + + The SCPBI-Y is a brief clinical interview designed to assess pain burden for children and adolescents with SCD. - Request inclusion into NCIT below "Research or Clinical Assessment Tool". + Request inclusion into NCIT below "Research or Clinical Assessment Tool". -Add these annotation properties: -- has respondents -- has target population -- selection criteria met -- validated for age ranges -- has cross-cultural adaptation -- freely available -- has translations - Zempsky WT, O'Hara EA, Santanelli JP, Palermo TM, New T, Smith-Whitley K, Casella JF. Validation of the sickle cell disease pain burden interview-youth. J Pain. 2013 Sep;14(9):975-82. - None +Add these annotation properties: -- has respondents -- has target population -- selection criteria met -- validated for age ranges -- has cross-cultural adaptation -- freely available -- has translations + Zempsky WT, O'Hara EA, Santanelli JP, Palermo TM, New T, Smith-Whitley K, Casella JF. Validation of the sickle cell disease pain burden interview-youth. J Pain. 2013 Sep;14(9):975-82. + None SCPBI-Y Sickle Cell Disease Pain Burden Interview - Youth - + - - + + Sickle cell tests are used to help diagnose sickle cell anemia (also called sickle cell disease) and to identify those who may have sickle cell trait. Sickle cell anemia is an inherited disorder that leads to the production of an abnormal hemoglobin called hemoglobin S (Hb S or Hgb S). Sickle cell tests determine the presence and relative amount of hemoglobin S in a blood sample. - Request inclusion into relevant ontology - https://labtestsonline.org/tests/sickle-cell-tests - Few but definitions not freely available + Request inclusion into relevant ontology + https://labtestsonline.org/tests/sickle-cell-tests + Few but definitions not freely available Screening for Sickle Cell Disease Sickle Cell Disease Screening Test - + - - - + + + - + - - + + A nine-item self-administered questionnaire that measures disease-specific perceptions of the ability to manage day-to-day issues resulting from sickle cell disease (SCD). Items are scores according to a five-point scale ranging from 1 - Not sure at all to 5 - Very sure. Responses from individual items are summed to give an overall score with higher scores indicating greater self-efficacy. + Suggest update to label in PhenX as we have done. + + PhenX protocol: Self-efficacy in Sickle Cell Disease #820401 + Self + Clinic Patients (Adults with SCD) + Self-efficacy, or one’s perceptions that they can exercise control over their behaviors and environment, may play an important role in determining the ability to adjust to chronic conditions such as sickle cell disease (SCD). + 18 and older + Suggest update to label - Suggest update to label in PhenX as we have done. - - PhenX protocol: Self-efficacy in Sickle Cell Disease #820401 - Self - Clinic Patients (Adults with SCD) - Self-efficacy, or one’s perceptions that they can exercise control over their behaviors and environment, may play an important role in determining the ability to adjust to chronic conditions such as sickle cell disease (SCD). - 18 and older - Suggest update to label Scale of Self-efficacy in Sickle Cell Disease Sickle Cell Disease Self-Efficacy Scale - + - - + + - + - + - - + + A variant form of sickle cell disease that results from inheriting the sickle mutation in combination with another beta-globin gene mutation. These hemoglobinopathies may have different clinical severity compared to the homozygous form of sickle cell disease (HbSS). - Request inclusion into relevant ontology - http://www.uptodate.com/contents/overview-of-variant-sickle-cell-syndromes - None + Request inclusion into relevant ontology + http://www.uptodate.com/contents/overview-of-variant-sickle-cell-syndromes + None SCD Variant Sickle Cell Disease Variant Variant Sickle Cell Syndromes @@ -36078,37 +35513,37 @@ Add these annotation properties: -- has respondents -- has target population -- - + - - + + - - + + A form of therapy that employs a coordinated and interdisciplinary approach for easing the suffering and improving the quality of life of those experiencing sickle cell related pain. + Request inclusion into MESH below "Pain Management". + http://purl.bioontology.org/ontology/MESH/D059408 + None SCDO - Request inclusion into MESH below "Pain Management". - http://purl.bioontology.org/ontology/MESH/D059408 - None Sickle Cell Pain Managements Sickle Cell Pain Management - + - - + + Pain lasting at least two hours that requires an unscheduled emergency room visit or hospitalization or that disrupts daily activities. + Could be categorised as a phenotype "Finding". + Request inclusion into relevant ontology + None SCDO http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=830101 - Could be categorised as a phenotype "Finding". - Request inclusion into relevant ontology - None Pain Episode Painful Crisis Painful Event @@ -36119,88 +35554,88 @@ Add these annotation properties: -- has respondents -- has target population -- - + - + A cancer that is almost exclusively associated with sickle cell trait and/or sickle cell disease. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Sickle Cell Associated Cancer Sickle Cell Related Cancer - + - + - - + + - - + + - - + + - + - + - - + + - - + + - - + + - - + + - - + + The condition of being heterozygous for hemoglobin S. - http://purl.bioontology.org/ontology/MESH/D012805 - Sufficient - SCDO:0001055 + http://purl.bioontology.org/ontology/MESH/D012805 + Sufficient + SCDO:0001055 MESH:D012805 AS Genotype Haemoglobin Genotype AS @@ -36210,176 +35645,176 @@ Add these annotation properties: -- has respondents -- has target population -- - + - + - + - + - - + + - + - - + + - - + + - - + + - - + + - - + + - + - + - - + + - - + + - - + + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A mild form of sickle cell thalassemia characterized by the presence of hemoglobin S and a reduced amount of hemoglobin A in the red blood cells. It is characterized by the presence of small red blood cells and mild anemia. - Suggest update to label in NCIT from "Sickle Beta Plus Thalassemia" to "Sickle Beta Minus Thalassemia" - http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C98837 - Suggest update to label + Suggest update to label in NCIT from "Sickle Beta Plus Thalassemia" to "Sickle Beta Minus Thalassemia" + http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C98837 + Suggest update to label NCIT:C98837 S beta-minus Sickle B- Thalassemia @@ -36392,141 +35827,141 @@ Add these annotation properties: -- has respondents -- has target population -- - + - - - + + + - - + + - + - + - - + + - - + + - - + + - - + + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + One of the sickle cell disorders characterized by the presence of both hemoglobin S and hemoglobin C. It is similar to, but less severe than sickle cell anemia. - http://purl.bioontology.org/ontology/MESH/D006450 - Sufficient - SCDO:0001059 + http://purl.bioontology.org/ontology/MESH/D006450 + Sufficient + SCDO:0001059 MESH:D006450 Hb SC-disease Hemoglobin S / Hemoglobin C Disease @@ -36542,69 +35977,69 @@ Add these annotation properties: -- has respondents -- has target population -- - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A rare compound heterozygous hemoglobinopathy characterised by the presence of two beta globin gene variants: that of hemoglobin S (beta-6(GAG-->GTG)) and that of hemoglobin D-Punjab (beta-121(GAA-->CAA)). + Request inclusion into relevant ontology. Perhaps as sub-class of "Sickle Cell-Hemoglobin D Disease" in the NCIT. + Rahimah Ahmad*, Syahira Lazira Omar*, Siti Hida H M Arif*, Faidatul Syazlin A Hamid*, Nur Aisyah Aziz*, Nik Hafidzah N Mustapha**, Zubaidah Zakaria*Haemoglobin Sickle D Punjab: - A Case Report. Med J Malaysia. 2014. Vol 69 No 1. + Few but definitions not freely available - Request inclusion into relevant ontology. Perhaps as sub-class of "Sickle Cell-Hemoglobin D Disease" in the NCIT. - Rahimah Ahmad*, Syahira Lazira Omar*, Siti Hida H M Arif*, Faidatul Syazlin A Hamid*, Nur Aisyah Aziz*, Nik Hafidzah N Mustapha**, Zubaidah Zakaria*Haemoglobin Sickle D Punjab: - A Case Report. Med J Malaysia. 2014. Vol 69 No 1. - Few but definitions not freely available Haemoglobin S/D-Punjab Hemoglobin S/D-Punjab Sickle Cell-Haemoglobin D-Punjab @@ -36614,129 +36049,129 @@ Add these annotation properties: -- has respondents -- has target population -- - + - - - + + + - + - - + + - - + + - - + + - - + + - - + + - + - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A variant of sickle cell disease due to heterozygosity for hemoglobin S and hemoglobin E mutations, which can cause mild hemolytic anemia. - Suggest update to description of "Sickle Cell-Hemoglobin D Disease" in the NCIT. - http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-S-E - Few but definitions not specific enough + Suggest update to description of "Sickle Cell-Hemoglobin D Disease" in the NCIT. + http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-S-E + Few but definitions not specific enough Hb SE-Disease Hemoglobin SE Disease Hemoglobin SE-Disease @@ -36748,70 +36183,70 @@ Add these annotation properties: -- has respondents -- has target population -- - + - + - + - - + + - - + + - - + + - - + + - - + + - + - - + + - - + + Sickle cell-Hb Lepore Boston syndrome is a type of sickle cell disease that differs from homozygous sickle cell disease where both parents carry sickle hemoglobin. In this variant one parent has the sickle cell hemoglobin the second parent has Hb Lepore Boston, the only one of the three Hb Lepore variants described in association with HbS. + Request inclusion into relevant ontology + + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - None SCD-S/Lepore Boston Sickle Cell Disease-S/Lepore Sickle Cell-Hb Lepore Boston Syndrome @@ -36822,82 +36257,82 @@ Add these annotation properties: -- has respondents -- has target population -- - + - - - + + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - - + + - - + + One of the sickle cell disorders characterized by the presence of both hemoglobin S and hemoglobin O-Arab. It can cause anemia, repeated infections, and periodic episodes of pain and organ damage. + Request inclusion into relevant ontology + http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-S-O-Arab + Few but definitions not freely available - Request inclusion into relevant ontology - http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-S-O-Arab - Few but definitions not freely available Hb F,S,O-Arab Hb S O-Arab disease Hb S,O-Arab @@ -36910,12 +36345,12 @@ Add these annotation properties: -- has respondents -- has target population -- - + - - + + 'A variant of sickle cell disease in which individuals have atypical hemoglobin molecules called hemoglobin S together with another form of abnormal hemoglobin, other than hemoglobin C,D,E and O-Arab. [Curator team: []]' - http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-S-and-other-than-A-C-D-E-O-Arab + http://newbornscreeningcodes.nlm.nih.gov/nb/sc/condition/Hb-F-S-and-other-than-A-C-D-E-O-Arab Hb S Other than A,C,D,E,O-Arab obsolete Sickle Cell-Hemoglobin Other than A,C,D,E,O-Arab true @@ -36923,77 +36358,77 @@ Add these annotation properties: -- has respondents -- has target population -- - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Retinal changes of sickle cell disease that can be either proliferative or non-proliferative. In both cases, the changes are caused by erythrostasis secondary to sickling. - Request inclusion into HPO below "Retinopathy". + Request inclusion into HPO below "Retinopathy". -Use the scielo source to add info on diagnosis and treatment. - Bonanomi et al 2013 Arq Bras Oftalmol - Few but definitions not freely available +Use the scielo source to add info on diagnosis and treatment. + Bonanomi et al 2013 Arq Bras Oftalmol + Few but definitions not freely available Retinopathy due to SCD Sickle Cell Retinopathy Sickle Retinopathy @@ -37001,34 +36436,34 @@ Use the scielo source to add info on diagnosis and treatment. + - - - + + + A qualitative screening test for sickling haemoglobins, especially HbS. In the SCT, sodium metabisulfite or sodium dithionate is used to desolubilise haemoglobin S to the crystallised deoxygenated form, which causes the abnormal RBCs to sickle, as detected by light microscopy. - In SNOMED CT this term seems to be both "Sickle cell identification, slide method" and "Sickling Test". Request they merge these terms? - Segen's Medical Dictionary. © 2012 Farlex, Inc. - Few but definitions not freely available. + In SNOMED CT this term seems to be both "Sickle cell identification, slide method" and "Sickling Test". Request they merge these terms? + Segen's Medical Dictionary. © 2012 Farlex, Inc. + Few but definitions not freely available. Sickle Cell Identification, Slide Method Sickling Test - + - - + + A generic measure used to evaluate the impact of SCD on both physical and emotional functioning of an affected person. SIP is designed to measure perceived health status and to be used as an outcome measure for evaluation, program planning, and policy formation related to health care. It is designed in such a way as to reflect sensitivity to changes and/or differences in health status and to be applicable across a broad range of types and severities of the SCD illness, as well as different demographic and cultural groups. + Too specific to SCD to be included in other ontologies. + +These annotation properties still required: -- has respondents -- has target population -- selection criteria met -- validated for age ranges -- has cross-cultural adaptation -- freely available -- has translations + http://link.springer.com/referenceworkentry/10.1007%2F978-0-387-79948-3_1833 + http://qol.thoracic.org/sections/instruments/pt/pages/sick.html + Few but definitions not specific enough SCDO Bergner M., Bobbitt R.A., Carter W.B. and Gilson B.S. (1981). The Sickness Impact Profile: development and final revision of a health status measure. Medical Care 19,787-805. - Too specific to SCD to be included in other ontologies. - -These annotation properties still required: -- has respondents -- has target population -- selection criteria met -- validated for age ranges -- has cross-cultural adaptation -- freely available -- has translations - http://link.springer.com/referenceworkentry/10.1007%2F978-0-387-79948-3_1833 - http://qol.thoracic.org/sections/instruments/pt/pages/sick.html - Few but definitions not specific enough SIP Sickness Impact Profile Sickness Impact Profile (SIP) @@ -37036,13 +36471,13 @@ These annotation properties still required: -- has respondents -- has target pop - + - - + + 'The bodily system consisting of the skin and its associated structures, such as the hair, nails, sweat glands, and sebaceous glands. [Curator team: []]' - - integumentary system. (n.d.) The American Heritage Medical Dictionary. (2007). Retrieved December 14 2016 + + integumentary system. (n.d.) The American Heritage Medical Dictionary. (2007). Retrieved December 14 2016 Dermatologic System Integumentary System deprecated Skin @@ -37051,50 +36486,50 @@ These annotation properties still required: -- has respondents -- has target pop - + - + - + - - + + - - + + - - + + - - + + - - + + An abnormal change in skin color, appearance, or texture. - Suggest update to description in HPO. - - Suggest update to description + Suggest update to description in HPO. + + Suggest update to description HP:0000988 Exanthem Skin Rash @@ -37102,43 +36537,43 @@ These annotation properties still required: -- has respondents -- has target pop - + - + - - + + - - + + - - + + - - + + - - + + An intrinsic sleep disorder characterized by breathing abnormalities. - http://purl.obolibrary.org/obo/NBO_0000494 - Suffcient + http://purl.obolibrary.org/obo/NBO_0000494 + Suffcient NBO:0000494 SBD Sleep Breathing Disorder @@ -37146,15 +36581,15 @@ These annotation properties still required: -- has respondents -- has target pop - + - - + + An interviewer-administered questionnaire which captures routine sleep schedule, sleep deprivation, morningness-eveningness, insomnia, narcolepsy, cataplexy and associated distress. - Suggest update to label in PhenX (from "Suggest update to label") as we have done. - - PhenX protocol: Sleep Disorders Screener #121001 - Suggest update to label + Suggest update to label in PhenX (from "Suggest update to label") as we have done. + + PhenX protocol: Sleep Disorders Screener #121001 + Suggest update to label phenX:121001 National Institute of Mental Health (NIMH) Sleep Patterns and Problems Instrument Sleep Disorders Screener - Adult @@ -37162,48 +36597,48 @@ These annotation properties still required: -- has respondents -- has target pop - + - - + + - + A microscope with a light source that can be projected into a linear beam. It allows cross-sectional viewing of the aqueous humor; conjuncteiva; cornea; eyelids; iris; and lens of the eye. - http://purl.bioontology.org/ontology/MESH/D066167 - Sufficient - SCDO:0001077 + http://purl.bioontology.org/ontology/MESH/D066167 + Sufficient + SCDO:0001077 MESH:D066167 Slit Lamp - + - - + + Inhaling and exhaling the smoke of burning tobacco (Cigar, Cigarette, Hookah, Pipe, Smoking, Waterpipe). - http://purl.bioontology.org/ontology/MESH/D012907 - Sufficient - SCDO:0001079 + http://purl.bioontology.org/ontology/MESH/D012907 + Sufficient + SCDO:0001079 MESH:D012907 Smoking - + - - + + Discontinuing the habit of smoking. - http://purl.bioontology.org/ontology/MESH/D016540 - Sufficient - SCDO:0001080 + http://purl.bioontology.org/ontology/MESH/D016540 + Sufficient + SCDO:0001080 MESH:D016540 Quit Smoking Smoking Cessation @@ -37211,14 +36646,14 @@ These annotation properties still required: -- has respondents -- has target pop - + - - + + The aggregate of social and cultural institutions, forms, patterns, and processes that influence the life of an individual or community. - http://purl.bioontology.org/ontology/MESH/D012931 - Sufficient - SCDO:0001082 + http://purl.bioontology.org/ontology/MESH/D012931 + Sufficient + SCDO:0001082 MESH:D012931 Social Ecology Social Environment @@ -37226,30 +36661,30 @@ These annotation properties still required: -- has respondents -- has target pop - + - + Social functioning defines an individual's interactions with their environment and the ability to fulfill their role within such environments as work, social activities, and relationships with partners and family. - PROMIS Domain Frameworks/Definitions nih.promis.org - Request inclusion into relevant ontology + Request inclusion into relevant ontology -Include terms for social relationships; social activities? - Compr Psychiatry. 2000 Jan-Feb;41(1):63-9. Assessment of social functioning in depression. - Few but definitions not freely available +Include terms for social relationships; social activities? + Compr Psychiatry. 2000 Jan-Feb;41(1):63-9. Assessment of social functioning in depression. + Few but definitions not freely available + PROMIS Domain Frameworks/Definitions nih.promis.org Social Functioning - + - - + + The separation of individuals or groups resulting in the lack of or minimizing of social contact and/or communication. This separation may be accomplished by physical separation, by social barriers and by psychological mechanisms. In the latter, there may be interaction but no real communication. - http://purl.bioontology.org/ontology/MESH/D012934 - Sufficient - SCDO:0001084 + http://purl.bioontology.org/ontology/MESH/D012934 + Sufficient + SCDO:0001084 MESH:D012934 Social Isolations Social Isolation @@ -37257,14 +36692,14 @@ Include terms for social relationships; social activities? + - - + + A role that is ascribed to individuals in a community. - http://semanticscience.org/resource/SIO_000676 - Sufficient - SCDO:0001085 + http://semanticscience.org/resource/SIO_000676 + Sufficient + SCDO:0001085 SIO:000676 Social Function Social Role @@ -37272,27 +36707,27 @@ Include terms for social relationships; social activities? + - - + + An extent/ degree to which an individual fulfills the expectations of his/her social role. + Request inclusion into relevant ontology + None SCDO - Request inclusion into relevant ontology - None Social Role Fulfillment - + - - + + The personal set of abilities required to successfully interact and communicate with others, both verbally and non-verbally through gestures, body language and personal appearance. - http://purl.bioontology.org/ontology/MESH/D066107 - Sufficient - SCDO:0001087 + http://purl.bioontology.org/ontology/MESH/D066107 + Sufficient + SCDO:0001087 MESH:D066107 Interpersonal Skill Social Ability @@ -37303,14 +36738,14 @@ Include terms for social relationships; social activities? + - - + + Support systems that provide assistance and encouragement to individuals with physical or emotional disabilities in order that they may better cope. Informal social support is usually provided by friends, relatives, or peers, while formal assistance is provided by churches, groups, etc. - http://purl.bioontology.org/ontology/MESH/D012944 - Sufficient - SCDO:0001088 + http://purl.bioontology.org/ontology/MESH/D012944 + Sufficient + SCDO:0001088 MESH:D012944 Psychosocial Support System Social Network @@ -37319,14 +36754,14 @@ Include terms for social relationships; social activities? + - - + + Abstract standards or empirical variables in social life which are believed to be important and/or desirable. - http://purl.bioontology.org/ontology/MESH/D012945 - Sufficient - SCDO:0001089 + http://purl.bioontology.org/ontology/MESH/D012945 + Sufficient + SCDO:0001089 MESH:D012945 Value Orientation Value Orientations @@ -37335,74 +36770,74 @@ Include terms for social relationships; social activities? + - - + + Social and economic factors that characterize the individual or group within the social structure. - Maybe include some sub-classes of this term in MESH? There would be overlap with terms in QOL, so would need to work around that. - http://purl.bioontology.org/ontology/MESH/D012959 - Sufficient - SCDO:0001090 + Maybe include some sub-classes of this term in MESH? There would be overlap with terms in QOL, so would need to work around that. + http://purl.bioontology.org/ontology/MESH/D012959 + Sufficient + SCDO:0001090 MESH:D012959 Socioeconomic Factors - + - - + + The combination of one's social class and income level. Includes socioeconomic differences between individuals or groups. - http://bioportal.bioontology.org/ontologies/APAONTO/?p=classes&conceptid=http%3A%2F%2Fontology.apa.org%2Fapaonto%2FtermsonlyOUT%2520%285%29.owl%23Socioeconomic_Status - Sufficient - SCDO:0001091 + http://bioportal.bioontology.org/ontologies/APAONTO/?p=classes&conceptid=http%3A%2F%2Fontology.apa.org%2Fapaonto%2FtermsonlyOUT%2520%285%29.owl%23Socioeconomic_Status + Sufficient + SCDO:0001091 APAONTO:Socioeconomic_Status Socioeconomic Status - + - - - + + + A basic first line test that looks for the presence of abnormal Hemoglobin S in a blood sample. Sodium metabisulfite is added to the blood sample which causes Hb S polymerisation and sickling of red blood cells if Hb S is present. A positive result means that a person has either Sickle Cell Disease or Sickle Cell Trait. Confirmatory tests are needed to distinguish which form of SCD the patient has. - SCDO (Clair Ingram) - In SNOMED CT this term is "Hemoglobin S Solubility Test" + In SNOMED CT this term is "Hemoglobin S Solubility Test" -Commonly used tests include hemoglobin electrophoresis, isoelectric focusing (IEF), high performance liquid chromatography (HPLC), and DNA analysis. - Few but definitions not freely available. +Commonly used tests include hemoglobin electrophoresis, isoelectric focusing (IEF), high performance liquid chromatography (HPLC), and DNA analysis. + Few but definitions not freely available. + SCDO (Clair Ingram) Hemoglobin S Solubility Test Solubility Test - + - - + + Instruments for measuring arterial blood pressure consisting of an inflatable cuff, inflating bulb, and a gauge showing the blood pressure. - http://purl.bioontology.org/ontology/MESH/D019722 - Sufficient - SCDO:0001097 + http://purl.bioontology.org/ontology/MESH/D019722 + Sufficient + SCDO:0001097 MESH:D019722 Sphygmomanometer - + - - + + Sensitivity or attachment to religious values, or to things of the spirit as opposed to material or worldly interests. - http://purl.bioontology.org/ontology/MESH/D029181 - Sufficient - SCDO:0001098 + http://purl.bioontology.org/ontology/MESH/D029181 + Sufficient + SCDO:0001098 MESH:D029181 Spiritual Beliefs Spiritualities @@ -37411,76 +36846,76 @@ Commonly used tests include hemoglobin electrophoresis, isoelectric focusing (IE - + - - + + - - + + - + - - + + A spirometer is an apparatus for measuring the volume of air inspired and expired by the lungs. It is a precision differential pressure transducer for the measurements of respiration flow rates. The spirometer records the amount of air and the rate of air that is breathed in and out over a specified period of time. - http://purl.obolibrary.org/obo/ERO_0000452 - Sufficient - SCDO:0001099 + http://purl.obolibrary.org/obo/ERO_0000452 + Sufficient + SCDO:0001099 ERO:0000452 Spirometer - + - - + + - - + + - - + + A form of nephrotic syndrome that does not respond to treatment with steroid medication after 8 weeks, specifically in children. - Suggest update to description in HPO + Suggest update to description in HPO -Provide source for additional info. - - May represent underlying focal segmental glomerulosclerosis, minimal change disease, or other underlying cause. Can be subseqeunt to known mutations. - Persistence of nephrotic syndrome despite appropriate treatment with corticosteroids. - Suggest update to description +Provide source for additional info. + + May represent underlying focal segmental glomerulosclerosis, minimal change disease, or other underlying cause. Can be subseqeunt to known mutations. + Persistence of nephrotic syndrome despite appropriate treatment with corticosteroids. + Suggest update to description HP:0012588 Steroid-Resistant Nephrotic Syndrome - + - + A perceived attribute that is deeply discrediting and is considered to be a violation of social norms. - http://purl.bioontology.org/ontology/MESH/D057545 - Sufficient - SCDO:0001107 + http://purl.bioontology.org/ontology/MESH/D057545 + Sufficient + SCDO:0001107 MESH:D057545 Social Stigma Social Stigmas @@ -37490,14 +36925,14 @@ Provide source for additional info. - + - + An oversimplified perception or conception, especially or persons, social groups, etc. - http://purl.bioontology.org/ontology/MESH/D013240 - Sufficient - SCDO:0001108 + http://purl.bioontology.org/ontology/MESH/D013240 + Sufficient + SCDO:0001108 MESH:D013240 Stereotyping Stigmatization @@ -37505,88 +36940,88 @@ Provide source for additional info. - + - - - + + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A group of pathological conditions characterized by sudden loss of neurological function due to brain ischemia or intracranial hemorrhages. Stroke is classified by the type of tissue necrosis, such as the anatomic location, vasculature involved, etiology, age of the affected individual, and hemorrhagic vs. non-hemorrhagic nature. - Types of stroke relevant to SCD to be added as children of this class. - http://purl.bioontology.org/ontology/MESH/D020521 - Sufficient - SCDO:0001111 + Types of stroke relevant to SCD to be added as children of this class. + http://purl.bioontology.org/ontology/MESH/D020521 + Sufficient + SCDO:0001111 MESH:D020521 Brain Vascular Accident CVA @@ -37599,22 +37034,22 @@ Provide source for additional info. - + - - - + + + - - + + This measure is a physical assessment to determine neurological deficits due to a stroke. - Suggest update to label in PhenX - - This measure is used to describe the consequences of a stroke and to monitor the effects of treatment and recovery. - Suggest update to label + Suggest update to label in PhenX + + This measure is used to describe the consequences of a stroke and to monitor the effects of treatment and recovery. + Suggest update to label phenX:820800 Stroke Impact/Outcome Measure Stroke Outcome Measure @@ -37623,27 +37058,27 @@ Provide source for additional info. - + - - + + - + - - + + This questionnaire includes 59 proxy- or self-report items in 8 domains that assess multidimensional stroke outcomes in adults. - Suggest update to description in PhenX. - http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820701 - PhenX protocol: Stroke Impact Scale (SIS) - Adults #820701 - Suggest update to description + Suggest update to description in PhenX. + http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820701 + PhenX protocol: Stroke Impact Scale (SIS) - Adults #820701 + Suggest update to description phenX:820701 Stroke Impact Scale (SIS) - Adults Stroke Impact Scale (SIS) @@ -37651,149 +37086,149 @@ Provide source for additional info. - + - + - - + + - - + + - + A clinical test to measure the blood flow velocities in intracranial arteries. Elevated intracranial arterial blood flow rates are indicative of expanding vessel lesions and a subsequent increased risk of stroke. - Include below "Cerebral Flow Test"? -- Include below "Vascular Endothelial Function Test"? - - Sufficient - SCDO:0001114 + Include below "Cerebral Flow Test"? -- Include below "Vascular Endothelial Function Test"? + + Sufficient + SCDO:0001114 phenX:821001 Stroke Risk Test in Children with Sickle Cell Disease - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + The occurrence of multiple self-limited episodes of unwanted, often painful erections lasting <4 hours. + Request inclusion into relevant ontology, perhaps below "Priapism" in MESH. + Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014 + Few but definitions not freely available SCDO - Request inclusion into relevant ontology, perhaps below "Priapism" in MESH. - Evidence-Based Management of Sickle Cell Disease, Expert Panel Report, 2014 - Few but definitions not freely available Recurrent Priapism Stuttering Priapism - + - + Assessment with the goal to obtain a relevant drug and alcohol history and perform a physical examination in order to establish whether there is a diagnosis of a substance use disorder. + Few but definitions not specific enough SCDO - Few but definitions not specific enough If substance use disorder diagnosed, the patient’s readiness to change should be categorized and information from the assessment should be used to formulate a management plan based on the individual’s needs. Substance Use History - + - - - + + + - - + + An indication of whether the respondent has ever used a drug during his or her entire life. + Request inclusion into relevant ontology + Not relevant to context of sickle cell SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - Not relevant to context of sickle cell Substances - Lifetime Use - + - - + + - - + + Frequent thinking about or preoccupation with killing oneself. - Suggest update to description in HPO (correct typo in "oneself") - - Suggest update to description + Suggest update to description in HPO (correct typo in "oneself") + + Suggest update to description HP:0031589 Suicidal Ideation Suicidal Thoughts @@ -37801,14 +37236,14 @@ Provide source for additional info. - + - - + + Organizations which provide an environment encouraging social interactions through group activities or individual relationships especially for the purpose of rehabilitating or supporting patients, individuals with common health problems, or the elderly. They include therapeutic social clubs. - http://purl.bioontology.org/ontology/MESH/D012657 - Sufficient - SCDO:0001123 + http://purl.bioontology.org/ontology/MESH/D012657 + Sufficient + SCDO:0001123 MESH:D012657 Self Help Group Self-Help Group @@ -37819,68 +37254,68 @@ Provide source for additional info. - + - - + + - + - + - + - + - + - + - + - - + + - - + + Measures aimed at providing appropriate supportive and rehabilitative services to minimize morbidity and maximize quality of life after a long-term disease or injury is present. - http://purl.bioontology.org/ontology/MESH/D055512 - Sufficient - SCDO:0001129 + http://purl.bioontology.org/ontology/MESH/D055512 + Sufficient + SCDO:0001129 MESH:D055512 Supportive Therapy Tertiary Prevention @@ -37889,22 +37324,22 @@ Provide source for additional info. - + - + - + - - + + A computerized test for the assessment of visual attention problems in individuals ages 8 years old and older. - Suggest update to label in PhenX as we have done. - http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=821201 - PhenX protocol: Sustained and Selective Attention #821201 - Suggest update to label + Suggest update to label in PhenX as we have done. + http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=821201 + PhenX protocol: Sustained and Selective Attention #821201 + Suggest update to label phenX:821201 Conners CPT 3 Conners Continuous Performance Test 3rd Edition @@ -37914,96 +37349,96 @@ Provide source for additional info. - + - - + + - - + + - - + + Therapeutics that ease the symptoms without addressing the basic cause of the disease. + Request inclusion into relevant ontology + http://www.medicinenet.com/script/main/art.asp?articlekey=10701 + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - http://www.medicinenet.com/script/main/art.asp?articlekey=10701 - None Symptomatic Treatment Symptomatic Therapeutics - + - - - + + + - - + + - - + + - - + + - - + + Refers to a worsening, over a short period of time, of the symptoms and signs of SCD; usually associated with pain and/or shortage of blood (anaemia). Can be suspected in a person with sickle cell disease who presents with a sudden onset of pain, infection, anemia or other symptoms such as stroke or priapism. Acute pain frequently occurs spontaneously, but may be precipitated by infections, skin cooling, dehydration or stress. + Request inclusion into relevant ontology + This is a difficult one to describe, as I think it can also be referred to as an 'acute painful crisis' (this is not clear from the literature). Have tried to merge descriptions from different sources - please review. + + Rees, D. C., Olujohungbe, A. D., Parker, N. E., Stephens, A. D., Telfer, P. and Wright, J. (2003), Guidelines for the management of the acute painful crisis in sickle cell disease. British Journal of Haematology, 120: 744-752. doi:10.1046/j.1365-2141.2003.04193.x + SCD Management guidelines - Nigeria + None SCDO - Request inclusion into relevant ontology - This is a difficult one to describe, as I think it can also be referred to as an 'acute painful crisis' (this is not clear from the literature). Have tried to merge descriptions from different sources - please review. - - Rees, D. C., Olujohungbe, A. D., Parker, N. E., Stephens, A. D., Telfer, P. and Wright, J. (2003), Guidelines for the management of the acute painful crisis in sickle cell disease. British Journal of Haematology, 120: 744-752. doi:10.1046/j.1365-2141.2003.04193.x - SCD Management guidelines - Nigeria - None Acute Sickle Cell Crisis - + - - + + 'Affecting a number of tissues relating to the entire organism as distinguished from and of its individual parts. [Curator team: []]' - - http://medical-dictionary.thefreedictionary.com/systemic + + http://medical-dictionary.thefreedictionary.com/systemic deprecated Systemic true - + - - + + Care of a highly technical and specialized nature, provided in a medical center, usually one affiliated with a university, for patients with unusually severe, complex, or uncommon health problems. - http://purl.bioontology.org/ontology/MESH/D063128 - Sufficient - SCDO:0001140 + http://purl.bioontology.org/ontology/MESH/D063128 + Sufficient + SCDO:0001140 MESH:D063128 Tertiary Care Tertiary Health Care @@ -38012,18 +37447,18 @@ Provide source for additional info. - + - - + + The Test of Functional Health Literacy Assessment (TOFHLA) assesses a patient's level of comprehension of health-related material. It is available in a full-format (a 22-minute test, with 50 reading comprehension items in three passages and 17 numeracy items), an abbreviated format (a 12-minute test, with 36 reading comprehension items in two passages and four numeracy items) and a shortened version (the S-TOFHLA, a 7-minute test, with 36 reading comprehension items in 2 passages.). The passages on the S-TOFHLA use a modified Cloze procedure where every fifth to seventh word is omitted and subjects select the correct word from among a set of four options. The passages contain information about an upper gastrointestinal tract x-ray procedure, and the "Rights and Responsibilities" section from a Medicaid application, and have Gunning-Fox readability indices of fourth and tenth grade, respectively. In early developmental studies, the reading comprehension passages in the S-TOFHLA had a reliability coefficient (Cronbach's alpha) of 0.97 and correlation with the Rapid Estimate of Adult Literacy in Medicine (REALM) of 0.81. Each selection is scored a "1" for correct or a "0" for incorrect and scores are summed over items to create a total score. The 36-point scale of the S-TOFHLA is divided into three categories of functional literacy: inadequate (0-16), adequate (17-22) and functional (23-36). - Parker RM, Baker DW, Williams MV, Nurss JR. The test of functional health literacy in adults: a new instrument for measuring patients' literacy skills. Journal of General Internal Medicine. 1995;10(10):537-41. - Request inclusion into NCIT below "Research or Clinical Assessment Tool". + Request inclusion into NCIT below "Research or Clinical Assessment Tool". -Still must add these annotation properties: -- has respondents -- has target population -- selection criteria met -- validated for age ranges -- has cross-cultural adaptation -- freely available - Parker RM, Baker DW, Williams MV, Nurss JR. The test of functional health literacy in adults: a new instrument for measuring patients' literacy skills. Journal of General Internal Medicine. 1995;10(10):537-41. - Spanish - None +Still must add these annotation properties: -- has respondents -- has target population -- selection criteria met -- validated for age ranges -- has cross-cultural adaptation -- freely available + Parker RM, Baker DW, Williams MV, Nurss JR. The test of functional health literacy in adults: a new instrument for measuring patients' literacy skills. Journal of General Internal Medicine. 1995;10(10):537-41. + Spanish + None + Parker RM, Baker DW, Williams MV, Nurss JR. The test of functional health literacy in adults: a new instrument for measuring patients' literacy skills. Journal of General Internal Medicine. 1995;10(10):537-41. TOFHLA Test of Functional Health Literacy in Adults Test of Functional Health Literacy in Adults (TOFHLA) @@ -38031,22 +37466,22 @@ Still must add these annotation properties: -- has respondents -- has target pop - + - - + + The Duke Religion Index (DUREL) is a five item scale which measures religiosity in three areas: organizational religiosity (OR), non-organizational religiosity (NOR), and intrinsic religiosity. Two of the questions were derived from large epidemiologic studies and have been shown to have a strong predictive value for many health outcomes. OR has been related to less depression, more social support, better physical health, lower resource utilization, and lower mortality. NOR has been shown to be related to poorer physical health, and greater social support. The other three items were taken from the Hoge 10- item religiosity scale (Hodge et al 1972). The DUREL has high test-retest reliability (intra-class correlation = 0.91), high internal consistency (Cronbach's alpha's = 0.78--0.91). + Request inclusion into NCIT below "Research or Clinical Assessment Tool". + +Also requires these properties: -- has cross-cultural adaptation -- has translations + Koenig, HG and Büssing A. (2010). The Duke University Religion Index (DUREL): A Five-Item Measure for Use in Epidemological Studies. Religions, 1, 78-85. + Self + Adults with SCD + Used in at least one SCD study + Adults + no + None Koenig, HG and Büssing A. (2010). The Duke University Religion Index (DUREL): A Five-Item Measure for Use in Epidemological Studies. Religions, 1, 78-85. - Request inclusion into NCIT below "Research or Clinical Assessment Tool". - -Also requires these properties: -- has cross-cultural adaptation -- has translations - Koenig, HG and Büssing A. (2010). The Duke University Religion Index (DUREL): A Five-Item Measure for Use in Epidemological Studies. Religions, 1, 78-85. - Self - Adults with SCD - Used in at least one SCD study - Adults - no - None DUREL The Duke Religion Index The Duke Religion Index (DUREL) @@ -38054,27 +37489,27 @@ Also requires these properties: -- has cross-cultural adaptation -- has translat - + - - + + A medical device used to prevent and treat medical conditions, or to alleviate pain or injury. + Request inclusion into relevant ontology + Negligable SCDO - Request inclusion into relevant ontology - Negligable Therapeutic Device - + - - + + The washing of a body cavity or surface by flowing water or solution for therapy or diagnosis. - http://purl.bioontology.org/ontology/MESH/D007507 - Sufficient - SCDO:0001151 + http://purl.bioontology.org/ontology/MESH/D007507 + Sufficient + SCDO:0001151 MESH:D007507 Lavage Lavages @@ -38084,16 +37519,16 @@ Also requires these properties: -- has cross-cultural adaptation -- has translat - + - - + + Procedures, agents or devices concerned with the remedial treatment or prevention of diseases. - Chemotherapy to be added in this class? If so, would have to be specific types of chemotherapy relevant to the type of therapeutics class. - Include as subclasses: -- Prosthesis -- Phototherapy (therapy for Jaundice) -- Risk Reduction? Copy relevant disease modifiers below this. - Suggest update to description in MESH - - Suggest update to description + Chemotherapy to be added in this class? If so, would have to be specific types of chemotherapy relevant to the type of therapeutics class. + Include as subclasses: -- Prosthesis -- Phototherapy (therapy for Jaundice) -- Risk Reduction? Copy relevant disease modifiers below this. + Suggest update to description in MESH + + Suggest update to description MESH:D013812 Therapy Treatment @@ -38102,14 +37537,14 @@ Also requires these properties: -- has cross-cultural adaptation -- has translat - + - + A mutation named with the blend of insertion and deletion. It refers to a length difference between two alleles where it is unknowable if the difference was originally caused by a sequence insertion or by a sequence deletion. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a frameshift mutation. - http://purl.bioontology.org/ontology/MESH/D054643 - Sufficient - SCDO:0001158 + http://purl.bioontology.org/ontology/MESH/D054643 + Sufficient + SCDO:0001158 MESH:D054643 Insertion-Deletion Mutation Indel Mutation @@ -38117,20 +37552,20 @@ Also requires these properties: -- has cross-cultural adaptation -- has translat - + - - + + - + Ending the tobacco habits of smoking, chewing, or snuff use. - http://purl.bioontology.org/ontology/MESH/D020340 - Sufficient - SCDO:0001159 + http://purl.bioontology.org/ontology/MESH/D020340 + Sufficient + SCDO:0001159 MESH:D020340 Tobacco Cessation Tobacco Use Cessation @@ -38138,15 +37573,15 @@ Also requires these properties: -- has cross-cultural adaptation -- has translat - + - - + + A person who practices the art of healing using traditional medicine, a system of medicine based on cultural beliefs and practices handed down from generation to generation. The concept includes mystical and magical rituals (spiritual therapies); phytotherapy (plant therapy) and other treatments which may not be explained by modern medicine. + Request inclusion into relevant ontology, perhaps MESH. + Few but definitions not specific enough SCDO - Request inclusion into relevant ontology, perhaps MESH. - Few but definitions not specific enough Faith Healer Folk Healer Healer @@ -38157,15 +37592,15 @@ Also requires these properties: -- has cross-cultural adaptation -- has translat - + - - + + An interviewer-administered, two-part test that requires the respondent to organize numerical and alphabetical sequences that are randomly distributed on a piece of paper. The protocol includes instructions for correcting mistakes and instructions for scoring based on speed and accuracy. - Suggest update to label in PhenX. - - PhenX protocol: #131101 - Suggest update to label + Suggest update to label in PhenX. + + PhenX protocol: #131101 + Suggest update to label phenX:131101 Executive Function - Adult Trail Making Test @@ -38173,58 +37608,58 @@ Also requires these properties: -- has cross-cultural adaptation -- has translat - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A non-invasive technique using ultrasound for the measurement of cerebrovascular hemodynamics, particularly cerebral blood flow velocity and cerebral collateral flow. With a high-intensity, low-frequency pulse probe, the intracranial arteries may be studied transtemporally, transorbitally, or from below the foramen magnum. - http://purl.bioontology.org/ontology/MESH/D017585 - Sufficient - SCDO:0001166 + http://purl.bioontology.org/ontology/MESH/D017585 + Sufficient + SCDO:0001166 MESH:D017585 TCD Transcranial Doppler @@ -38234,20 +37669,20 @@ Also requires these properties: -- has cross-cultural adaptation -- has translat - + - - + + - - + + The use of specifically placed small electrodes to deliver electrical impulses across the skin to relieve pain. It is used less frequently to produce anesthesia. - http://purl.bioontology.org/ontology/MESH/D004561 - Sufficient - SCDO:0001167 + http://purl.bioontology.org/ontology/MESH/D004561 + Sufficient + SCDO:0001167 MESH:D004561 Analgesic Cutaneous Electrostimulation Electroanalgesia @@ -38266,64 +37701,64 @@ Also requires these properties: -- has cross-cultural adaptation -- has translat - + - + - + - - + + - - + + - + - - + + - - + + - - + + - - + + Temporary loss of vision in one eye due to a lack of blood flow to the retina. + Request inclusion into HP below "Blindness". + + None SCDO - Request inclusion into HP below "Blindness". - - None Amaurosis Fugax TMB Temporary Blindness @@ -38332,12 +37767,12 @@ Also requires these properties: -- has cross-cultural adaptation -- has translat - + - - + + 'Work consisting of reporting using a method of detecting genetic causes in human traits and genetic factors in behavior using sets of twins. [Curator team: []]' - http://purl.bioontology.org/ontology/MESH/D018486 + http://purl.bioontology.org/ontology/MESH/D018486 MESH:D018486 obsolete Twin Study true @@ -38345,28 +37780,28 @@ Also requires these properties: -- has cross-cultural adaptation -- has translat - + - - + + Works about methods of detecting genetic etiology in human traits. The basic premise of twin studies is that monozygotic twins carry identical genes, while zygotic twins are genetically no more similar than two siblings born after separate pregnancies. (Last, J.M., A Dictionary of Epidemiology, 2d ed) - http://purl.bioontology.org/ontology/MESH/D018433 - Sufficient - SCDO:0001198 + http://purl.bioontology.org/ontology/MESH/D018433 + Sufficient + SCDO:0001198 MESH:D018433 Twin Studies as Topic - + - - + + This gene encodes a UDP-glucuronosyltransferase, an enzyme of the glucuronidation pathway that transforms small lipophilic molecules, such as steroids, bilirubin, hormones, and drugs, into water-soluble, excretable metabolites. This gene is part of a complex locus that encodes several UDP-glucuronosyltransferases. The preferred substrate of this enzyme is bilirubin, although it also has moderate activity with simple phenols, flavones, and C18 steroids. Mutations in this gene result in Crigler-Najjar syndromes types I and II and in Gilbert syndrome. - Request inclusion into relevant ontology - - Few but definitions not freely available + Request inclusion into relevant ontology + + Few but definitions not freely available GNT1 UDP Glucuronosyltransferase Family 1 Member A1 UGT1 @@ -38376,15 +37811,15 @@ Also requires these properties: -- has cross-cultural adaptation -- has translat - + - + - + The region surrounding a city. Most inhabitants of urban areas have nonagricultural jobs. Urban areas are very developed, meaning there is a density of human structures such as houses, commercial buildings, roads, bridges, and railways. - Request inclusion into relevant ontology - - None + Request inclusion into relevant ontology + + None Urban Urban Area Urban Environment @@ -38394,66 +37829,66 @@ Also requires these properties: -- has cross-cultural adaptation -- has translat - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + A bioassay to measure urine concentration of albumin, which is produced by the liver and is the most abundant protein in the blood. + Label different from source's "Urinary Microalbumin - Assay" + + + PhenX protocol: Urinary Microalbumin Assay #141501 + Suggest update to label - Label different from source's "Urinary Microalbumin - Assay" - - - PhenX protocol: Urinary Microalbumin Assay #141501 - Suggest update to label In the protocol provided, albumin concentration is measured according to a fluorescent immunoassay (FIA). The protocol also lists reference ranges for healthy adults. The criteria for clinically significant proteinuria have been changed from an albumin-creatinine ratio (ACR) of 30 mg/mmol or more to 3 mg/mmol or more. This is because there is evidence that the risk of adverse outcomes is a continuum and starts at an ACR well below 30 mg/mmol. @@ -38466,47 +37901,47 @@ Because albuminuria may be affected by non-pathological factors (exercise, menst - + - + - + - + - - + + - - + + - - + + - - + + A bioassay to measure urine concentration of creatinine, a muscle metabolite that is filtered out of blood by the kidneys. - - - PhenX protocol: Urinary Creatinine - Assay #141601 - Sufficient - SCDO:0001206 + + + PhenX protocol: Urinary Creatinine - Assay #141601 + Sufficient + SCDO:0001206 phenX:141601 Urinary Creatinine Assay Urine Creatinine Analysis @@ -38515,39 +37950,39 @@ Because albuminuria may be affected by non-pathological factors (exercise, menst - + - + - - + + - - + + Any measurement of protein present in urine. - Suggest update to description in CMO. - - Suggest update to description (currently no description provided). + Suggest update to description in CMO. + + Suggest update to description (currently no description provided). CMO:0000770 Urinary Protein Measurement - + - - + + The organs and passageways concerned with the production and excretion of urine, including the kidneys, ureters, urinary bladder, and urethra. - - http://purl.obolibrary.org/obo/BTO_0003092 + + http://purl.obolibrary.org/obo/BTO_0003092 BTO:0003092 deprecated Urinary System true @@ -38555,81 +37990,81 @@ Because albuminuria may be affected by non-pathological factors (exercise, menst - + - - + + - + - + - - + + - - + + - - + + - - + + - + - - + + - - + + - - + + - - + + The amount of albumin in a specified volume of urine. + Suggest that the CMO removes the second part of the definition and puts as comment, as we have done. Also suggest the change to this second part. + + Suggest update to description - Suggest that the CMO removes the second part of the definition and puts as comment, as we have done. Also suggest the change to this second part. - - Suggest update to description CMO:0000130 Urinary Albumin Concentration Urinary Albumin Level @@ -38641,14 +38076,14 @@ Because albuminuria may be affected by non-pathological factors (exercise, menst - + - - + + The amount of albumin excreted into the urine within a specified period of time. - Suggest that the CMO removes the second part of the definition and puts as comment, as we have done. Also suggest the change to this second part. - http://purl.obolibrary.org/obo/CMO_0000757 - Suggest update to description + Suggest that the CMO removes the second part of the definition and puts as comment, as we have done. Also suggest the change to this second part. + http://purl.obolibrary.org/obo/CMO_0000757 + Suggest update to description CMO:0000757 Urinary Albumin Excretion Rate If the level of albumin in the urine is above normal but not high enough to be detectable with routine protein testing it is referred to as low level albuminuria (the old term is microalbuminuria). @@ -38657,14 +38092,14 @@ Because albuminuria may be affected by non-pathological factors (exercise, menst - + - - + + A comparison of urine microalbumin, that is, a level of albumin in the urine which is above normal but not detectable with routine protein testing, to the amount of creatinine in a specified volume of urine. Often expressed as albumin concentration divided by creatinine concentration times 1000 mg per gram. - Suggest update to description as we have done. - http://purl.obolibrary.org/obo/CMO_0000384 - Suggest update to description + Suggest update to description as we have done. + http://purl.obolibrary.org/obo/CMO_0000384 + Suggest update to description CMO:0000384 ACR ALBCREAT @@ -38681,51 +38116,51 @@ Because albuminuria may be affected by non-pathological factors (exercise, menst - + - + - + - - + + - - + + - + - + - - + + The concentration of creatinine in a urine specimen. + Request inclusion below "urine creatinine measurement" in the CMO. + None SCDO (Jade Hotchkiss) - Request inclusion below "urine creatinine measurement" in the CMO. - None Urinary Creatinine Concentration Urine Creatinine Amount Urine Creatinine Concentration Measurement Datum @@ -38735,14 +38170,14 @@ Because albuminuria may be affected by non-pathological factors (exercise, menst - + - - + + A method in which sulfosalicylic acid (that is, the SSA reagent) is added to a small and equal volume of clear urine. The acidification causes precipitation of protein in the sample (seen as increasing turbidity), which can be subjectively quantitated visually or more precisely quantitated using photometry. - http://purl.obolibrary.org/obo/MMO_0000504 - Sufficient - SCDO:0001215 + http://purl.obolibrary.org/obo/MMO_0000504 + Sufficient + SCDO:0001215 MMO:0000504 SSA Protein Precipitation Test Urine SSA Turbidimetry @@ -38753,12 +38188,12 @@ Because albuminuria may be affected by non-pathological factors (exercise, menst - + - - + + The medical specialty concerned with the study, diagnosis, and treatment of diseases of the genitourinary tract. - http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17243 + http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17243 NCIT:C17243 obsolete Urology true @@ -38766,28 +38201,28 @@ Because albuminuria may be affected by non-pathological factors (exercise, menst - + - - + + Works consisting of research using processes by which the reliability and relevance of a procedure for a specific purpose are established. - http://purl.bioontology.org/ontology/MESH/D023361 - Sufficient - SCDO:0001223 + http://purl.bioontology.org/ontology/MESH/D023361 + Sufficient + SCDO:0001223 MESH:D023361 Validation Studies - + - - + + Smoking vapors produced from electronic nicotene delivery systems. - http://purl.bioontology.org/ontology/MESH/D000072137 - Sufficient - SCDO:0001224 + http://purl.bioontology.org/ontology/MESH/D000072137 + Sufficient + SCDO:0001224 MESH:D000072137 Electronic Cigarrete Use Vaping @@ -38795,14 +38230,14 @@ Because albuminuria may be affected by non-pathological factors (exercise, menst - + - - + + A measure of vascular endothelial cell response to stimulation, for example, by vasoactive substances released by or those that interact with the vascular endothelium. - Request inclusion into relevant ontology - http://circ.ahajournals.org/content/108/17/2054 - None + Request inclusion into relevant ontology + http://circ.ahajournals.org/content/108/17/2054 + None Assessment of Endothelial Cell Function Endothelium Dysfunction Test Vascular Endothelial Function Test @@ -38811,75 +38246,75 @@ Because albuminuria may be affected by non-pathological factors (exercise, menst - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Pain resulting from tissue ischemia as a result of blockage of blood vessels, occurring in a variety of vascular beds, but most commonly in the bone or bone marrow and requiring analgesic medication. + Request inclusion into relevant ontology + Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 + Few but definitions not specific enough SCDO - Request inclusion into relevant ontology - Evidence-Based Management of Sickle Cell Disease: Expert Panel Report (EPR), 2014 - Few but definitions not specific enough Acute Pain Crisis Sickle Crisis VOC @@ -38890,45 +38325,45 @@ Because albuminuria may be affected by non-pathological factors (exercise, menst - + - - + + Extraction of blood from a vein using a needle. In human, the basilic, cephalic and median cubital veins are most commonly used as well as the femoral vein. - http://purl.obolibrary.org/obo/MMO_0000090 - Sufficient - SCDO:0001230 + http://purl.obolibrary.org/obo/MMO_0000090 + Sufficient + SCDO:0001230 MMO:0000090 Venipuncture - + - - - + + + - + - - + + A parent or caregiver questionnaire administered as part of a structured interview that measures day-to-day performance on communication, daily living, socialization, and motor skills. Standard scores can be derived for communication, daily living, socialization, and motor skills subtests or combined to create an Adaptive Behavior Composite (ABC). - Suggest update to label in PhenX as we have done. - http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820601 - PhenX protocol: Adaptive Behavior/Adaptive Function #820601 - Proxy - This measure can be used to identify individuals with developmental disabilities or delays, perform diagnostic evaluations, monitor progress, and develop programs. - All ages from birth through age 90 - Suggest update to label + Suggest update to label in PhenX as we have done. + http://www.phenxtoolkit.org/index.php?pageLink=browse.protocoldetails&id=820601 + PhenX protocol: Adaptive Behavior/Adaptive Function #820601 + Proxy + This measure can be used to identify individuals with developmental disabilities or delays, perform diagnostic evaluations, monitor progress, and develop programs. + All ages from birth through age 90 + Suggest update to label phenX:820601 VABS Vineland Adaptive Behavior Scales @@ -38938,17 +38373,17 @@ Because albuminuria may be affected by non-pathological factors (exercise, menst - + - + Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells. - Add sub-classes: + Add sub-classes: Hepatitis C Virus (term in NCIT) -Hepatitis B Virus (term not found in other ontologies) - http://purl.bioontology.org/ontology/MESH/D014780 - Sufficient - SCDO:0001234 +Hepatitis B Virus (term not found in other ontologies) + http://purl.bioontology.org/ontology/MESH/D014780 + Sufficient + SCDO:0001234 MESH:D014780 Viruses Virus @@ -38956,20 +38391,20 @@ Hepatitis B Virus (term not found in other ontologies) - + - - + + - + Removal of the whole or part of the vitreous body in treating endophthalmitis, diabetic retinopathy, retinal detachment, intraocular foreign bodies, and some types of glaucoma. - http://purl.bioontology.org/ontology/MESH/D014821 - Sufficient - SCDO:0001237 + http://purl.bioontology.org/ontology/MESH/D014821 + Sufficient + SCDO:0001237 MESH:D014821 Vitrectomies Vitrectomy @@ -38977,15 +38412,15 @@ Hepatitis B Virus (term not found in other ontologies) - + - - + + Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes. - Can this term also be below "Immunological Assay"? - - Sufficient - SCDO:0001240 + Can this term also be below "Immunological Assay"? + + Sufficient + SCDO:0001240 MESH:D015153 Western Immunoblot Western Blot @@ -38993,57 +38428,57 @@ Hepatitis B Virus (term not found in other ontologies) - + - - + + - + - - + + - - + + - - + + An acute onset of wheezing in a person with SCD and co-morbid asthma. + Glassberg, Jeffrey A., Robert Strunk, and Michael R. DeBaun. “Wheezing in Children with Sickle Cell Disease.” Current opinion in pediatrics 26.1 (2014): 9–18. PMC. Web. 2 Aug. 2017. + Paediatr Respir Rev. 2014 Mar;15(1):13-6. doi: 10.1016/j.prrv.2013.10.005. Epub 2013 Oct 31. + Synergistic inflammatory response due to both SCD and asthma. + Increased severity of episodes. + None SCDO Glassberg, Jeffrey A., Robert Strunk, and Michael R. DeBaun. “Wheezing in Children with Sickle Cell Disease.” Current opinion in pediatrics 26.1 (2014): 9–18. PMC. Web. 2 Aug. 2017. Paediatr Respir Rev. 2014 Mar;15(1):13-6. doi: 10.1016/j.prrv.2013.10.005. Epub 2013 Oct 31. - Glassberg, Jeffrey A., Robert Strunk, and Michael R. DeBaun. “Wheezing in Children with Sickle Cell Disease.” Current opinion in pediatrics 26.1 (2014): 9–18. PMC. Web. 2 Aug. 2017. - Paediatr Respir Rev. 2014 Mar;15(1):13-6. doi: 10.1016/j.prrv.2013.10.005. Epub 2013 Oct 31. - Synergistic inflammatory response due to both SCD and asthma. - Increased severity of episodes. - None Asthma Attack Wheezing Episode with Co-Morbid Asthma - + - - + + An act of employing sorcery (the use of power gained from the assistance or control of spirits), especially with malevolent intent, and the exercise of supernatural powers and alleged intercourse with the devil or a familiar. (From Webster, 3rd Ed). - http://purl.bioontology.org/ontology/MESH/D018599 - Sufficient - SCDO:0001246 + http://purl.bioontology.org/ontology/MESH/D018599 + Sufficient + SCDO:0001246 MESH:D018599 Sorceries Sorcery @@ -39052,19 +38487,19 @@ Hepatitis B Virus (term not found in other ontologies) - + - - + + The WHOQOL is a quality of life assessment developed by the WHOQOL Group with fifteen international field centres, simultaneously, in an attempt to develop a quality of life assessment that would be applicable cross-culturally. - WHOQOL Group (1993). Measuring quality of life: The development of the World Health Organisation quality of life instrument (WHOQOL). Geneva: WHO. - Request inclusion into NCIT below "Research or Clinical Assessment Tool". + Request inclusion into NCIT below "Research or Clinical Assessment Tool". -Still must add these annotation properties: -- validated for age ranges -- has cross-cultural adaptation -- freely available -- has translations - Self - Healthy people; Clinic patients - Demonstrated validity with SCD populations; at least two publications using the measure - None +Still must add these annotation properties: -- validated for age ranges -- has cross-cultural adaptation -- freely available -- has translations + Self + Healthy people; Clinic patients + Demonstrated validity with SCD populations; at least two publications using the measure + None + WHOQOL Group (1993). Measuring quality of life: The development of the World Health Organisation quality of life instrument (WHOQOL). Geneva: WHO. WHOQOL World Health Organisation Quality of Life Instrument World Health Organisation Quality of Life Instrument (WHOQOL) @@ -39072,192 +38507,192 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + The visual output that an X-ray machine produces. + Request inclusion into relevant ontology. + Not relevant to context of sickle cell SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology. - Not relevant to context of sickle cell X-Ray Image - + - - + + - - + + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + The visual output that an X-ray machine produces when imaging the chest. + Request inclusion into relevant ontology. + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology. - Negligable Chest X-Ray Image X-Ray Image of Chest - + - - + + - + Medical treatment involving the use of controlled amounts of X-Rays. + http://purl.bioontology.org/ontology/MESH/D014964 + Sufficient + SCDO:0001252 - http://purl.bioontology.org/ontology/MESH/D014964 - Sufficient - SCDO:0001252 MESH:D014964 Roentgenotherapy X Ray Therapy @@ -39268,69 +38703,69 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Penetrating, high-energy electromagnetic radiation emitted when the inner orbital electrons of an atom are excited and release radiant energy. X-ray wavelengths range from 1 pm to 10 nm. Hard X-rays are the higher energy, shorter wavelength X-rays. Soft x-rays or Grenz rays are less energetic and longer in wavelength. The short wavelength end of the X-ray spectrum overlaps the gamma rays wavelength range. The distinction between gamma rays and X-rays is based on their radiation source. - This should probably be removed. - http://purl.bioontology.org/ontology/MESH/D014965 - Sufficient - SCDO:0001253 + This should probably be removed. + http://purl.bioontology.org/ontology/MESH/D014965 + Sufficient + SCDO:0001253 MESH:D014965 X-Radiation X-Ray Electromagnetic Radiation @@ -39339,21 +38774,21 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + The EQ-5D is a widely-used generic instrument for describing health-related quality of life states in five dimensions scored from 1 to 3 or 1 to 5, and a visual analogue scale to record self-rated health state from 0 to100. These provide a simple descriptive profile and a single index value for health status. The EQ-5D can also be used to calculate health utilities and determine the quality-adjusted life years associated with a health state. There is also a youth version (EQ-5D-Y). + The EuroQol Group. EuroQol-a new facility for the measurement of health-related quality of life. Health Policy. 1990; 16(3):199-208. + Multiple countries and cultural groups + Self + Healthy People; Clinic Patients + Widely used around the world, also used in SCD + Adults and Youth (8 to 18 years) + Few but definitions not specific enough Anie KA, Grocott H, White L, Dzingina M, Rogers G, Cho G (2012). Patient self-assessment of hospital pain, mood and health-related quality of life in adults with sickle cell disease. BMJ Open, 2, e001274. doi:10.1136/bmjopen-2012-001274. Howard, J, Malfroy, M, Llewelyn, C et al. The Transfusion Alternatives Preoperatively in Sickle Cell Disease (TAPS) study: a randomised, controlled, multicentre clinical trial. Lancet. 2013; 381(9870):930–938. The EuroQol Group. EuroQol-a new facility for the measurement of health-related quality of life. Health Policy. 1990; 16(3):199-208. - The EuroQol Group. EuroQol-a new facility for the measurement of health-related quality of life. Health Policy. 1990; 16(3):199-208. - Multiple countries and cultural groups - Self - Healthy People; Clinic Patients - Widely used around the world, also used in SCD - Adults and Youth (8 to 18 years) - Few but definitions not specific enough EQ-5D EuroQol Five Dimension Self-Report Questionnaire EuroQol Five Dimensions Questionnaire @@ -39364,19 +38799,19 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + The FACIT-Sp is a 12-item measure that asks participants to indicate how true various statements are about them on a Likert scale of 0 ("not at all") to 4 ("very much"). Responses on the FACIT-Sp are summed to create a total score, ranging from 0 to 48, with higher scores representing higher levels of spirituality. + Request inclusion into NCIT below "Research or Clinical Assessment Tool". + Peterman AH, Fitchett G, Brady MJ, et al. Measuring spiritual well-being in people with cancer: the functional assessment of chronic illness therapy—Spiritual Well-being Scale (FACIT- Sp). Ann Behav Med. 2002;24:49–58. + Self; Proxy (Parent report) + Children with SCD and their parents + Demonstrated validity in SCD studies. + Children and adults + None Peterman AH, Fitchett G, Brady MJ, et al. Measuring spiritual well-being in people with cancer: the functional assessment of chronic illness therapy—Spiritual Well-being Scale (FACIT- Sp). Ann Behav Med. 2002;24:49–58. - Request inclusion into NCIT below "Research or Clinical Assessment Tool". - Peterman AH, Fitchett G, Brady MJ, et al. Measuring spiritual well-being in people with cancer: the functional assessment of chronic illness therapy—Spiritual Well-being Scale (FACIT- Sp). Ann Behav Med. 2002;24:49–58. - Self; Proxy (Parent report) - Children with SCD and their parents - Demonstrated validity in SCD studies. - Children and adults - None FACIT-Sp Scale Functional Assessment of Chronic Illness Therapy-Spirituality Scale Functional Assessment of Chronic Illness Therapy-Spirituality (FACIT-Sp) Scale @@ -39384,26 +38819,26 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + - - + + - + The application of modern theories of learning and conditioning in the treatment of behavior disorders. - http://purl.bioontology.org/ontology/MESH/D001521 - Sufficient - SCDO:0001284 + http://purl.bioontology.org/ontology/MESH/D001521 + Sufficient + SCDO:0001284 MESH:D001521 Behavior Modification Behavior Modifications @@ -39416,52 +38851,52 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - + - - + + - + - - + + - - + + - - + + - - + + - - + + A primary headache disorder that is characterized by severe, strictly unilateral pain which is orbital, supraorbital, temporal or in any combination of these sites, lasting 15-180 min. occurring 1 to 8 times a day. The attacks are associated with one or more of the following, all of which are ipsilateral: conjunctival injection, lacrimation, nasal congestion, rhinorrhea, facial sweating, eyelid edema, and miosis. - http://purl.bioontology.org/ontology/MESH/D003027 - Sufficient - SCDO:0001288 + http://purl.bioontology.org/ontology/MESH/D003027 + Sufficient + SCDO:0001288 MESH:D003027 Acute Severe Headache Cluster Headaches @@ -39471,26 +38906,26 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + - + - - + + Broad term used to describe several different acute conditions occurring with sickle cell disease, including aplastic crisis, hemolytic crisis, and vasoocclusive crisis. + Sufficient + SCDO:0001292 http://www.icd10data.com/ICD10CM/Codes/D50-D89/D55-D59/D57-/D57.00 - Sufficient - SCDO:0001292 ICD10CM:D57.00 D57.00 Hb-SS disease with (painful) crisis NOS @@ -39503,20 +38938,20 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + - - + + An instrument used in the detection and diagnosis of heart abnormalities that measures electrical potentials on the body surface and generates a record of the electrical currents associated with heart muscle activity. - Request inclusion into relevant ontology - http://en.wiktionary.org/wiki/electrocardiograph - Few but definitions not freely available + Request inclusion into relevant ontology + http://en.wiktionary.org/wiki/electrocardiograph + Few but definitions not freely available Cardiograph Electrocardiographic Instrument Electrocardiograph @@ -39524,20 +38959,20 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + - - + + The transfer of erythrocytes from a donor to a recipient or reinfusion to the donor. - http://purl.bioontology.org/ontology/MESH/D017707 - Sufficient - SCDO:0001296 + http://purl.bioontology.org/ontology/MESH/D017707 + Sufficient + SCDO:0001296 MESH:D017707 Erythrocyte Transfusions Red Blood Cell Transfusion @@ -39549,34 +38984,34 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + Works consisting of studies determining the effectiveness or utility of processes, personnel, and equipment. - http://purl.bioontology.org/ontology/MESH/D023362 - Sufficient - SCDO:0001299 + http://purl.bioontology.org/ontology/MESH/D023362 + Sufficient + SCDO:0001299 MESH:D023362 Evaluation Studies - + - - + + - + Repetitive withdrawal of small amounts of blood and replacement with donor blood until a large proportion of the blood volume has been exchanged. Used in treatment of fetal erythroblastosis, hepatic coma, sickle cell anemia, disseminated intravascular coagulation, septicemia, burns, thrombotic thrombopenic purpura, and fulminant malaria. - - Sufficient - SCDO:0001303 + + Sufficient + SCDO:0001303 MESH:D005078 Exchange Blood Transfusion Exchange Transfusion, Whole Blood @@ -39584,28 +39019,28 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - + - + An interviewer-administered test to measure a respondent's system of high-level cognitive functions such as abstract thinking, rule acquisition, cognitive flexibility, and goal-oriented behavior. - - Sufficient - SCDO:0001304 + + Sufficient + SCDO:0001304 phenX:131100 Executive Function Measure - + - - + + The organ of vision that consists of the eyeball and the optic nerve. - - http://medical-dictionary.thefreedictionary.com/eye + + http://medical-dictionary.thefreedictionary.com/eye Oculus deprecated Eye true @@ -39613,13 +39048,13 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + Facial paralysis is loss of facial movement because of nerve damage. - - Is this not the same thing as "Facial Nerve Palsy"? + + Is this not the same thing as "Facial Nerve Palsy"? DOID:13934 obsolete Facial Paralysis true @@ -39627,50 +39062,50 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + Inability to function due to tiredness related to sickle cell disease. - Use the literature cited here to link to other phenotypes. - Not relevant to context of sickle cell + Use the literature cited here to link to other phenotypes. + Not relevant to context of sickle cell Fatigability Fatigable Lassitude @@ -39681,47 +39116,47 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + Studies to determine the advantages or disadvantages, practicability, or capability of accomplishing a projected plan, study, or project. - http://purl.bioontology.org/ontology/MESH/D005240 - Sufficient - SCDO:0001320 + http://purl.bioontology.org/ontology/MESH/D005240 + Sufficient + SCDO:0001320 MESH:D005240 Feasibility Studies - + - + - - + + - - + + - - + + A potent narcotic analgesic, abuse of which leads to habituation or addiction. It is primarily a mu-opioid agonist. Fentanyl is also used as an adjunct to general anesthetics, and as an anesthetic for induction and maintenance. - Were these specific synonyms selected form the long list in the description source because of specific relevance to SCD? - - Sufficient - SCDO:0001321 + Were these specific synonyms selected form the long list in the description source because of specific relevance to SCD? + + Sufficient + SCDO:0001321 MESH:D005283 Duragesic Durogesic @@ -39732,50 +39167,50 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + - + - + - + - - + + - - + + - - + + A bioassay to measure the serum concentration of ferritin (i.e., iron). - Suggest update to label in PhenX (from "Serum or Plasma Ferritin") - - Suggest update to label + Suggest update to label in PhenX (from "Serum or Plasma Ferritin") + + Suggest update to label phenX:811301 Ferritin Blood Test Ferritin Measurement @@ -39787,80 +39222,80 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + The amount of ferritin found in a specified volume of serum. + Suggest update to description and label of "ferritin measurement" in the EFO. + Suggest update to description SCDO (Jade Hotchkiss) - Suggest update to description and label of "ferritin measurement" in the EFO. - Suggest update to description Blood Serum Ferritin Concentration Blood Serum Ferritin Concentration Measurement Datum Serum Ferritin Level @@ -39868,73 +39303,73 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + - - + + An instrument which is used to count and sort microscopic particles suspended in a buffer. This instrument consists of a flow cell, at least one lamp or laser, a variable number of emission detectors or photomultipliers, a system that converts analog signals to digital, and a computer to run the system and collect and analyze the data output. - Not sure whether this can be classified as a "Medical Device". - http://purl.bioontology.org/ontology/npo#NPO_1769 - Sufficient - SCDO:0001325 + Not sure whether this can be classified as a "Medical Device". + http://purl.bioontology.org/ontology/npo#NPO_1769 + Sufficient + SCDO:0001325 NPO:1769 Flow Cytometer - + - - + + - - + + - - + + Flow cytometry uses the principles of light scattering and fluorescence from fluorochrome molecules to generate specific multi-parameter data from particles and cells in the size range of 0.5um to 40um diameter. - - Sufficient - SCDO:0001326 + + Sufficient + SCDO:0001326 BAO:0000005 Flow Cytometry - + - + - - + + - - + + Visualization of a vascular system after intravenous injection of a fluorescein solution. The images may be photographed or televised. It is used especially in studying the retinal and uveal vasculature. - http://purl.bioontology.org/ontology/MESH/D005451 - Sufficient - SCDO:0001327 + http://purl.bioontology.org/ontology/MESH/D005451 + Sufficient + SCDO:0001327 MESH:D005451 Fluorescence Angiography Fluorescein Angiography @@ -39942,114 +39377,114 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - + A rare neurologic movement disorder characterized by sustained muscle contractions of a single body region, usually producing twisting and repetitive movements or abnormal postures or positions. - - Sufficient - SCDO:0001328 + + Sufficient + SCDO:0001328 ORPHA:1866 Focal Dystonia - + - + - - + + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A member of the vitamin B family that stimulates the hematopoietic system. It is present in the liver and kidney and is found in mushrooms, spinach, yeast, green leaves, and grasses (poaceae). Folic acid is used in the treatment and prevention of folate deficiencies and megaloblastic anemia. - - Sufficient - SCDO:0001329 + + Sufficient + SCDO:0001329 MESH:D005492 Folacin Folate @@ -40063,14 +39498,14 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + Studies in which individuals or populations are followed to assess the outcome of exposures, procedures, or effects of a characteristic, e.g., occurrence of disease. - http://purl.bioontology.org/ontology/MESH/D005500 - Sufficient - SCDO:0001330 + http://purl.bioontology.org/ontology/MESH/D005500 + Sufficient + SCDO:0001330 MESH:D005500 Follow Up Studies Follow-Up Study @@ -40080,16 +39515,16 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - + An observable characteristic of disease that is persistent and long standing. + Request inclusion into relevant ontology + http://purl.obolibrary.org/obo/NCIT_C14141 + http://semanticscience.org/resource/SIO_010056 + None SCDO (Clair Ingram) - Request inclusion into relevant ontology - http://purl.obolibrary.org/obo/NCIT_C14141 - http://semanticscience.org/resource/SIO_010056 - None NCIT:C14141 SIO:010056 Chronic Phenotype @@ -40097,37 +39532,37 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + Terms deprecated in the "Phenotype" class. from phenotype - + - - - + + + - + - - + + A questionnaire to measure the health status of individuals who had a stroke. - - Sufficient - SCDO:0001339 + + Sufficient + SCDO:0001339 phenX:820700 Functionality After Stroke Diagnostic Instrument Functionality After Stroke Measure @@ -40135,13 +39570,13 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + 'The system concerned with the function and disorders of the gastrointestinal tract, including stomach, intestines, and associated organs including liver, pancreas and gall bladder. [Curator team: []]' - - http://medical-dictionary.thefreedictionary.com/gastroenterology + + http://medical-dictionary.thefreedictionary.com/gastroenterology gastrointestinal tract deprecated Gastrointestinal System true @@ -40149,108 +39584,108 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + Combined effects of genotypes and environmental factors together to affect phenotypic characteristics. - http://purl.bioontology.org/ontology/MESH/D059647 - Sufficient - SCDO:0001342 + http://purl.bioontology.org/ontology/MESH/D059647 + Sufficient + SCDO:0001342 MESH:D059647 Gene-Environment Interaction - + - - + + - + Deviation(s) in the nucleotide sequence of the genetic material of an individual from that typical of the group to which the individual belongs, or deviation(s) in the nucleotide sequence of the genetic material of offspring from that of its parents. - Suggest update to description in NCIT - http://purl.obolibrary.org/obo/NCIT_C17248 - Suggest update to description + Suggest update to description in NCIT + http://purl.obolibrary.org/obo/NCIT_C17248 + Suggest update to description NCIT:C17248 Genetic Variation - + - - + + 'To be defined by an expert [Curator team: []]' - - made a synonym of HBB, GLU6LYS + + made a synonym of HBB, GLU6LYS deprecated beta C mutation true - + - - + + obsolete heterozygous beta c mutation true - + - - + + obsolete homozygous beta c mutation true - + - - + + 'To be defined by an expert [Curator team: []]' - - Made a synonym of "HBB, GLU26LYS" + + Made a synonym of "HBB, GLU26LYS" deprecated beta E mutation true - + - - + + 'To be defined by an expert [Curator team: []]' - - Made a synonym of HBB, GLU6VAL + + Made a synonym of HBB, GLU6VAL deprecated beta S mutation true - + - - + + This gene provides instructions for making a protein called alpha-globin, which is involved in oxygen transport. This protein is also produced from a nearly identical gene called HBA2. - Suggest update to description in NCIT. - - http://www.ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C75429 - Suggest update to description + Suggest update to description in NCIT. + + http://www.ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C75429 + Suggest update to description NCIT:C75429 HBA1 Gene Hemoglobin Subunit Alpha 1 Gene @@ -40260,15 +39695,15 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + This gene provides instructions for making a protein called alpha-globin, which is involved in oxygen transport. This protein is also produced from a nearly identical gene called HBA1. - Suggest update to description in NCIT. - - http://purl.obolibrary.org/obo/NCIT_C75432 - Suggest update to description + Suggest update to description in NCIT. + + http://purl.obolibrary.org/obo/NCIT_C75432 + Suggest update to description HBA2 Gene Hemoglobin Subunit Alpha 2 Gene Hemoglobin, Alpha 2 Gene @@ -40277,15 +39712,15 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - - + + Gamma Globin is a type of polypeptide chain that when in combination with alpha globin chains forms fetal hemoglobin. Beta-Hemoglobin subunits gamma-1 (147 aa, ~16 kDa) and gamma-2 (147 aa, ~16 kDa) are encoded by the human HBG1 and HBG2 gene respectively, in the beta-globin gene cluster. These proteins play a role in the transport of oxygen to tissues of the fetal body. + Request inclusion into relevant ontology. + https://www.genecards.org/cgi-bin/carddisp.pl?gene=HBG1 + None - Request inclusion into relevant ontology. - https://www.genecards.org/cgi-bin/carddisp.pl?gene=HBG1 - None Gamma-Globin Haemoglobin Gamma Chain Haemoglobin Subunit Gamma @@ -40295,68 +39730,68 @@ Still must add these annotation properties: -- validated for age ranges -- has c - + - + - - + + A reduction in the ratio of production of alpha globin to that of gamma globin. + Request inclusion into the HPO below "Imbalanced Hemoglobin Synthesis". + None SCDO (Nicole Vasilevsky) - Request inclusion into the HPO below "Imbalanced Hemoglobin Synthesis". - None Increased Gamma/Alpha Synthesis Ratio Reduced Alpha/Gamma Synthesis Ratio - + - - + + - - + + The state, in utero or shortly after birth, in which all four alpha globin genes are deleted or inactivated resulting in absent alpha globin synthesis. If gamma globin synthesis persists, then the resulting phenotype is hemoglobin Barts (four gamma chains) and hemoglobin Bart hydrops fetalis. + Request inclusion into HPO below "Reduced Alpha/Gamma Synthesis Ratio" (also requested for inclusion). + Marengo-Rowe, A.J., 2007, January. The thalassemias and related disorders. In Baylor university medical center proceedings (Vol. 20, No. 1, pp. 27-31). Taylor & Francis. + None SCDO (Clair Ingram) - Request inclusion into HPO below "Reduced Alpha/Gamma Synthesis Ratio" (also requested for inclusion). - Marengo-Rowe, A.J., 2007, January. The thalassemias and related disorders. In Baylor university medical center proceedings (Vol. 20, No. 1, pp. 27-31). Taylor & Francis. - None Absence of Alpha Globin Synthesis with Gamma Globin Synthesis - + - + - - + + - - + + A deletion in or of the HBA1 or HBA2 gene that can result in some form of alpha thalassemia. + Request inclusion into relevant ontology + Still need to add one sub-class: +the complete deletion of the HBA1 and HBA2 genes on one chromosome 16, combined with a defect (deletional or nondeletional) in either the HBA1 or HBA2 gene on the other chromosome 16, leaving one functioning gene present (https://www.snpedia.com/index.php/Alpha_Thalassemia) + None SCDO (Clair Ingram) - Request inclusion into relevant ontology - Still need to add one sub-class: -the complete deletion of the HBA1 and HBA2 genes on one chromosome 16, combined with a defect (deletional or nondeletional) in either the HBA1 or HBA2 gene on the other chromosome 16, leaving one functioning gene present (https://www.snpedia.com/index.php/Alpha_Thalassemia) - None Alpha-Globin Cluster Deletion Alpha-Globin Gene Cluster Deletion HBA Locus Deletion @@ -40365,33 +39800,33 @@ the complete deletion of the HBA1 and HBA2 genes on one chromosome 16, combined - + - - + + - + Deletion of all four alpha-globin genes resulting in the most severe form of alpha thalassemia, Hemoglobin Barts Hydrops Fetalis. + Request inclusion into relevant ontology + None SCDO (Clair Ingram) - Request inclusion into relevant ontology - None Homozygous Deletion of HBA1 and HBA2 - + - + Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt genetic translation of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation. - http://purl.bioontology.org/ontology/MESH/D016254 - Sufficient - SCDO:0001388 + http://purl.bioontology.org/ontology/MESH/D016254 + Sufficient + SCDO:0001388 MESH:D016254 Gene Insertion Insertion Mutation @@ -40400,78 +39835,78 @@ the complete deletion of the HBA1 and HBA2 genes on one chromosome 16, combined - + - - + + - - + + - - + + - - + + The administration of oxygen to an individual. It is of paramount importance in the peri-operative care of SCD patients as hypoxaemia predisposes to sickling. - - - Few but definitions not specific enough + + + Few but definitions not specific enough Supplemental Oxygen Therapy Oxygen Therapy - + - + - + - - + + - - + + - - + + - - + + - - + + Renal medullary carcinoma is a rare, aggressive subtype of renal cell carcinoma characterized by a large, white or tan, firm, infiltrative tumor with microabscess-like foci centered in the renal medulla, typically presenting with hematuria, abdominal/flank pain, weight loss and fever. It is associated with sickle cell trait and disease and metastasis to the bones and lungs is common at time of diagnosis. + http://www.orpha.net/ORDO/Orphanet_319319 + Sufficient + SCDO:0001511 Shetty A, Matrana MR. Renal medullary carcinoma: a case report and brief review of the literature. Ochsner J. 2014;14(2):270-5. - http://www.orpha.net/ORDO/Orphanet_319319 - Sufficient - SCDO:0001511 ORPHA:319319 Kidney Medullary Carcinoma RMC @@ -40481,197 +39916,197 @@ the complete deletion of the HBA1 and HBA2 genes on one chromosome 16, combined - + - + A part of anthropological linguistics concerned with the interrelation between a language and the cultural behavior of those who speak it. + + Sufficient + SCDO:0001551 - - Sufficient - SCDO:0001551 APAONTO:Ethnolinguistics Ethnolinguistics - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + That period when the patient with sickle cell anaemia is free of infection, pain, or other disease processes. - Request inclusion into relevant ontology. - Juwah, A. I., Nlemadim, E. U., & Kaine, W. (2004). Types of anaemic crises in paediatric patients with sickle cell anaemia seen in Enugu, Nigeria. Archives of disease in childhood, 89(6), 572-576. - Not relevant to context of sickle cell + Request inclusion into relevant ontology. + Juwah, A. I., Nlemadim, E. U., & Kaine, W. (2004). Types of anaemic crises in paediatric patients with sickle cell anaemia seen in Enugu, Nigeria. Archives of disease in childhood, 89(6), 572-576. + Not relevant to context of sickle cell SCD Steady State Steady State - + - - + + A reduction in the level of performance of the kidneys in areas of function comprising the concentration of urine, removal of wastes, the maintenance of electrolyte balance, homeostasis of blood pressure, and calcium metabolism. - + deprecated-Renal Insufficiency true - + - + Not anemic, i.e. no reduction in erythrocytes volume and/or hemoglobin concentration. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Nonanemic Non-Anemic - + - - + + An amino acid-specifying codon that has been converted to a stop codon by mutation. Its occurance is abnormal causing premature termination of protein translation and results in production of truncated and non-functional proteins. A nonsense mutation is one that converts an amino acid-specific codon to a stop codon. - http://purl.bioontology.org/ontology/MESH/D018389 - Sufficient - SCDO:0001626 + http://purl.bioontology.org/ontology/MESH/D018389 + Sufficient + SCDO:0001626 MESH:D018389 Nonsense Codon - + - - + + Chronic pain caused by damage to nerve fibers. It is usually associated with tissue injury. This pain is usually described as burning, numb, tingling, lancinating, shooting, or paroxysmal in nature and is associated with a sensation of pins and needles. Its severity is also enhanced by exposure to either cold or heat. - - This term already exists in the ontology as 'Chronic Neuropathic Pain' (SCDO:0000228), however when searching other ontologies, the term 'chronic' is included in the definition. I have therefore edited the definition to include the term 'chronic'. Please review as to whether we need to change the label that currently exists in SCDO. Is treated with: amitriptyline, duloxetine, gabapentin, or pregabalin. + + This term already exists in the ontology as 'Chronic Neuropathic Pain' (SCDO:0000228), however when searching other ontologies, the term 'chronic' is included in the definition. I have therefore edited the definition to include the term 'chronic'. Please review as to whether we need to change the label that currently exists in SCDO. Is treated with: amitriptyline, duloxetine, gabapentin, or pregabalin. deprecated-Neuropathic Pain true - + - - + + Deletion of both HBA2 genes, which results in an alpha-thal-2 (alpha-/alpha-) form of alpha thalassemia trait. With this deletion there is nearly normal production of red blood cells, but there may be a mild anemia. + Request inclusion into relevant ontology + + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - None Trans Deletion of HBA2 Homozygous Deletion of HBA2 - + - - + + - + - - + + A mutation in the beta-globin gene, HBB, that results in reduced beta globin synthesis. + Request inclusion into relevant ontology + None SCDO - Request inclusion into relevant ontology - None Beta-Minus Thalassemia Mutation - + - + - - + + - - + + - - + + A rapid heartrate that exceeds the range of the normal resting heartrate for age, gender or patient population. - Suggest update to description in HPO. -The original description stated 'A rapid heartrate that exceeds the range of the normal resting heartrate for age', however I think it should be recommended that gender and patient population be included. - http://purl.obolibrary.org/obo/HP_0001649 - Suggest update to description + Suggest update to description in HPO. +The original description stated 'A rapid heartrate that exceeds the range of the normal resting heartrate for age', however I think it should be recommended that gender and patient population be included. + http://purl.obolibrary.org/obo/HP_0001649 + Suggest update to description HP:0001649 Fast Heart Rate Heart Racing @@ -40681,20 +40116,20 @@ The original description stated 'A rapid heartrate that exceeds the range o - + - - + + - - + + The process whereby a mutation in a hemoglobin molecule causes conformational changes in the hemoglobin molecule, which cause increased hydrophobicity of the molecule, which result in the formation of crystals consisting of the mutated hemoglobin molecules. This type of crystallisation is observed in hemoglobins with the HbC mutation. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Crystallisation of Haemoglobin Crystallization of Haemoglobin Crystallization of Hemoglobin @@ -40707,62 +40142,62 @@ The original description stated 'A rapid heartrate that exceeds the range o - + - - + + A deficiency of the essential metal Zinc; an essential cofactor for many enzymes. Zinc deficiency is caused by a lack of zinc in the diet, loss of zinc after absorption, for example through loss through burns, inability to absorb Zinc, or increased loss through exercise. - - Sufficient - SCDO:0002039 + + Sufficient + SCDO:0002039 EFO:1000003 Zinc Deficiency - + - + - - + + - - + + - - + + - - + + Insufficiency of arterial or venous blood supply to the spleen due to emboli, thrombi, vascular torsion, or pressure that produces a macroscopic area of necrosis. - http://www.ebi.ac.uk/efo/EFO_1001190 - Sufficient - SCDO:0002106 + http://www.ebi.ac.uk/efo/EFO_1001190 + Sufficient + SCDO:0002106 EFO:1001190 Splenic Infarction - + - - + + This represents the phenotypic feature of mutational effects on a given property of an organism biological system [Gaston K. Mazandu, []]. deprecated-Nature of Mutations true @@ -40770,14 +40205,14 @@ The original description stated 'A rapid heartrate that exceeds the range o - + - - + + The privacy of information and its protection against unauthorized disclosure. - http://purl.bioontology.org/ontology/MESH/D003219 - Sufficient - SCDO:0002125 + http://purl.bioontology.org/ontology/MESH/D003219 + Sufficient + SCDO:0002125 MESH:D003219 Privileged Communications Confidentiality @@ -40785,14 +40220,14 @@ The original description stated 'A rapid heartrate that exceeds the range o - + - - + + The pattern of gene expression at the level of genetic transcription in a specific organism or under specific circumstances in specific cells. - http://purl.bioontology.org/ontology/MESH/D059467 - Sufficient - SCDO:0002130 + http://purl.bioontology.org/ontology/MESH/D059467 + Sufficient + SCDO:0002130 MESH:D059467 Gene Expression Levels Gene Expression Profile @@ -40802,32 +40237,32 @@ The original description stated 'A rapid heartrate that exceeds the range o - + - + The presence and extensiveness of a disease in the body. It is objectively evaluated through diagnostic testing and physiological examination of the impaired biological organs or tissues, in cases in which disease severity can be distinguished from other realms of health, as in heart disease. - Request inclusion into relevant ontology. -This exists in the Influenza Ontology, but their definition is not ideal. - - Negligable + Request inclusion into relevant ontology. +This exists in the Influenza Ontology, but their definition is not ideal. + + Negligable Severity Disease Severity - + - + Reimbursement of research participants for costs directly incurred during the research, such as travel costs and reasonable compensation for their inconvenience and time spent. Compensation can be monetary or non-monetary. - SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology + Request inclusion into relevant ontology -The label for this term has been changed to be more specific than the original "Compensation". - International Ethical Guidelines for Health-related Research Involving Humans, Fourth Edition. Geneva, Council for International Organizations of Medical Sciences (CIOMS); 2016. - Few but definitions not freely available +The label for this term has been changed to be more specific than the original "Compensation". + International Ethical Guidelines for Health-related Research Involving Humans, Fourth Edition. Geneva, Council for International Organizations of Medical Sciences (CIOMS); 2016. + Few but definitions not freely available + SCDO (Jade Hotchkiss) Study Participant Compensation Research participants should be reasonably reimbursed for costs directly incurred during the research, such as travel costs, and compensated reasonably for their inconvenience and time spent. Compensation can be monetary or non-monetary. Compensation must not be so large as to induce potential participants to consent to participate in the research against their better judgment ("undue inducement"). A local research ethics committee must approve reimbursement and compensation for research participants. Research Participant Compensation @@ -40835,69 +40270,69 @@ The label for this term has been changed to be more specific than the original & - + - + A mutation wholly or partly responsible for causing Hemoglobin D Disease. + None SCDO (Jade Hotchkiss) - None Hemoglobin D Disease Causal Mutation - + - - + + The abiding by applicable principles such as 1. compliance by research institutions; 2. obtaining and documenting informed consent; 3. Research Ethics Committee membership function, operations, review of research, and record keeping; 4. additional protection for certain vulnerable research subjects - pregnant women, prisoners, and children + Request inclusion into relevant ontology + National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research. The Belmont Report: Ethical Principles and Guidelines for the Protection of Human Subjects of Research. [Bethesda, Md.] + Research ethics committees: Basic concepts for capacity building. International Ethical Guidelines for Health-related Research Involving Humans, Fourth Edition. Geneva. Council for International Organizations of Medical Sciences (CIOMS); 2016. + The Commission, 1978. World Health Organization. Geneva: WHO Document Production Services; 2009. + None SCDO - Request inclusion into relevant ontology - National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research. The Belmont Report: Ethical Principles and Guidelines for the Protection of Human Subjects of Research. [Bethesda, Md.] - Research ethics committees: Basic concepts for capacity building. International Ethical Guidelines for Health-related Research Involving Humans, Fourth Edition. Geneva. Council for International Organizations of Medical Sciences (CIOMS); 2016. - The Commission, 1978. World Health Organization. Geneva: WHO Document Production Services; 2009. - None Ethical Conduct - + - - + + - + - - + + A mutation in the beta-globin gene, HBB, that results in absent beta globin synthesis. + Request inclusion into relevant ontology + None SCDO - Request inclusion into relevant ontology - None Beta Null Mutation Beta-Zero Thalassemia Mutation - + - + An abnormality of the body's metabolism or homeostasis. - Suggest update to description in HPO. Currenlty the HPO does not have a description. - - Suggest update to description + Suggest update to description in HPO. Currenlty the HPO does not have a description. + + Suggest update to description HP:0001939 Homeostasis Abnormality Metabolism Abnormality @@ -40906,63 +40341,63 @@ The label for this term has been changed to be more specific than the original & - + - + Naturally occurring genetic variations associated with drug response. While these variants are not markers for genetic predisposition to disease, they influence pharmacokinetics and pharmacodynamics and often occur on genes encoding drug metabolism enzymes and transporters (e.g., angiotensin converting enzyme; cytochrome P-450 CYP2D6). - - Sufficient - SCDO:0002798 + + Sufficient + SCDO:0002798 MESH:D000071184 Pharmacogenomic Variants - + - - + + 'The hemoglobin molecule that transports oxygen in the blood is made up of a number of components. Human hemoglobin is a tetramer: in adults it is made up of two alpha globins and two beta globins; in the fetus, of two alpha and two g globins; and in the embryo, two e and two z globins. The sequences of these five globin types are similar and the genes that code for them occur in clusters on the chromosomes. In humans, there are two main clusters of globin genes: the alpha globin cluster on chromosome 16 and the beta globin cluster on chromosome 11. [Curator team: []]' - - http://www2.nau.edu/~bio372-c/class/evolution/glbgnclst.htm + + http://www2.nau.edu/~bio372-c/class/evolution/glbgnclst.htm deprecated Globin Gene true - + - + A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a material) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. - - Sufficient - SCDO:0002829 + + Sufficient + SCDO:0002829 SIO:001050 Sample - + - - + + - - + + Deoxygenated malfunctioning or mutated hemoglobins which clump together and form a long polymer in a process called polymerisation. - SCDO (Khuthala Mnika) - Request inclusion in the HPO, below "Abnormal Hemoglobin". + Request inclusion in the HPO, below "Abnormal Hemoglobin". -Description still needs work. - None +Description still needs work. + None + SCDO (Khuthala Mnika) Hemoglobin Polymer Polymerised Haemoglobin Polymerized Hemoglobin @@ -40973,40 +40408,40 @@ Description still needs work. - + - - + + A person's ethnic status, whether conserved or mixed ethnicity. + Request inclusion into relevant ontology + None SCDO (curators) - Request inclusion into relevant ontology - None Tribe Ethnic Status - + - - + + Genetic variation in the structure leading to the abnomality of protein structure in non-sickle cell disease hemoglobin. - Curation completed by the SCDO curator team: Clair. + Curation completed by the SCDO curator team: Clair. obsolete Non-SCD Structural Variants true - + - - + + Documents describing a medical treatment or research project, including proposed procedures, risks, and alternatives, that are to be signed by an individual, or the individual's proxy, to indicate his/her understanding of the document and a willingness to undergo the treatment or to participate in the research. - http://purl.bioontology.org/ontology/MESH/D032962 - Sufficient - SCDO:0003572 + http://purl.bioontology.org/ontology/MESH/D032962 + Sufficient + SCDO:0003572 MESH:D032962 Consent Forms Consent Form @@ -41014,28 +40449,28 @@ Description still needs work. - + - + A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population. - - Sufficient - SCDO:0003675 + + Sufficient + SCDO:0003675 MESH:D020641 Single Nucleotide Polymorphism - + - + A procedure in which a sample of peripheral blood is viewed under a microscope to count different circulating blood cells (red blood cells, white blood cells, platelets, etc.) and see whether the cells look normal. - Request inclusion into relevant ontology - - None + Request inclusion into relevant ontology + + None Peripheral Blood Film Examination Peripheral Blood Smear Peripheral Blood Film @@ -41043,43 +40478,43 @@ Description still needs work. - + - + A legal representation or family member of the participant gives consent on behalf of the patient. + Request inclusion into the Informed Consent Ontology. +MESH has the term Third-party consent, but the description's not suitable. + None SCDO (Victoria Nembaware) - Request inclusion into the Informed Consent Ontology. -MESH has the term Third-party consent, but the description's not suitable. - None Third-Party Consent Proxy Consent - + - - + + Dynamic consent is a personalised, communication interface to enable greater participant engagement in clinical and research activities.The interface facilitates two-way communication to stimulate a more engaged, informed and scientifically literate participant population where individuals can tailor and manage their own consent preferences. It has the potential to be applied more broadly to situations where there are multiple and varied uses of data requiring different kinds of consent over a period of time. + Request inclusion into ICO below "Informed Consent". + https://www.nature.com/articles/ejhg201471 + None SCDO - Request inclusion into ICO below "Informed Consent". - https://www.nature.com/articles/ejhg201471 - None Dynamic Consent - + - - + + Surgical procedure involving either partial or entire removal of the spleen. - - Sufficient - SCDO:0003742 + + Sufficient + SCDO:0003742 MESH:D013156 Splenectomies Splenectomy @@ -41087,18 +40522,18 @@ MESH has the term Third-party consent, but the description's not suitable.< - + - + - + Hemoglobin characterized by structural alterations within the molecule that confer an inherited health condition phenotype. The alteration can be either absence, addition or substitution of one or more amino acids in the globin part of the molecule at selected positions in the polypeptide chains. - - Suggest HPO to update their term description and to move terms related to hemoglobin concentration below "Abnormal Hemoglobin Concentration". + Suggest HPO to update their term description and to move terms related to hemoglobin concentration below "Abnormal Hemoglobin Concentration". -Include as a sub-class "Hemoglobin S-Providence"? - - Suggest update to description +Include as a sub-class "Hemoglobin S-Providence"? + + Suggest update to description + Abnormal Hemoglobin Variant Abnormal Hemoglobins Abnormal Variant of Hemoglobin @@ -41107,72 +40542,72 @@ Include as a sub-class "Hemoglobin S-Providence"? + - - + + The polymerase chain reaction (PCR) is the most common method to detect the deletional thalassaemias. Gap-PCR amplifies the deleted DNA sequence using the primers flanking the deleted region 10. Three primers are designed for each deletion to amplify the normal (undeleted) and deleted gene sequences. - Request inclusion into relevant ontology. - Kho SL, Chua KH, George E, Tan JA. A novel gap-PCR with high resolution melting analysis for the detection of α-thalassaemia Southeast Asian and Filipino β°-thalassaemia deletion. Sci Rep. 2015;5:13937. Published 2015 Sep 14. doi:10.1038/srep13937 - None + Request inclusion into relevant ontology. + Kho SL, Chua KH, George E, Tan JA. A novel gap-PCR with high resolution melting analysis for the detection of α-thalassaemia Southeast Asian and Filipino β°-thalassaemia deletion. Sci Rep. 2015;5:13937. Published 2015 Sep 14. doi:10.1038/srep13937 + None Gap PCR - + - - + + The genetic constitution of the individual, comprising the alleles present at each genetic locus. - - Sufficient - SCDO:0004061 + + Sufficient + SCDO:0004061 MESH:D005838 Genotype - + - + - - + + - - + + Characterized by an established ileus, with vomiting, a silent distended abdomen and distended bowel loops and fluid levels on abdominal x-ray. Some hepatic enlargement is common, and it is often associated with bilateral basal lung consolidation (chest syndrome). - SCDO - Request inclusion into relevant ontology + Request inclusion into relevant ontology -Can be treated with analgesia, IV fluids, and antibiotics if patient is febrile. - - SCD Management guidelines - Tanzania - None +Can be treated with analgesia, IV fluids, and antibiotics if patient is febrile. + + SCD Management guidelines - Tanzania + None + SCDO Mesenteric Syndrome Girdle Syndrome - + - - + + The most common and normal adult human hemoglobin tetramer, comprising over 97% of the total red blood cell hemoglobin and consisting of two alpha chains and two beta chains. - Request inclusion into NCIT below "Hemoglobin"/"Normal Hemoglobin". -Suggest update to description in MESH. - - Few but definitions not specific enough + Request inclusion into NCIT below "Hemoglobin"/"Normal Hemoglobin". +Suggest update to description in MESH. + + Few but definitions not specific enough MESH:D006441 Adult Haemoglobin Haemoglobin A @@ -41187,54 +40622,54 @@ Suggest update to description in MESH. - + - + - - + + - - + + May be caused by an acute VOC, malarial infection or oxidant drug exposure in individuals with concomitant glucose-6-phosphate dehydrogenase (G6PD) deficiency. Haemolytic crisis may be distinguished from aplastic crisis by the finding of a reticulocytosis as opposed to a reticulocytopenia. + Request inclusion into relevant ontology + SCD Management guidelines - South Africa + Few but definitions not freely available SCDO - Request inclusion into relevant ontology - SCD Management guidelines - South Africa - Few but definitions not freely available Hemolytic Crisis - + - - + + A term used to express willingness to participate in research by persons who are by definition too young to give informed consent but who are old enough to understand the proposed research in general, its expected risks and possible benefits, and the activities expected of them as subjects. - The source term seems to be deprecated in the ICO. - - Suggest update to description + The source term seems to be deprecated in the ICO. + + Suggest update to description ICO:0000143 Assent - + - - + + The protein product of the fusion of the gene products of the HBD and HBB genes that causes the mutation which causes the Hemoglobin Lepore Trait. - Request inclusion into relevant ontology - - None + Request inclusion into relevant ontology + + None Crossover between delta and beta globin gene loci Delta Beta Globin Chain Fusion Product Delta Beta Globin Fusion Chain @@ -41242,70 +40677,70 @@ Suggest update to description in MESH. - + - - - + + + - - + + - - + + Chronic splenic sequestration associated with enlarged spleen and cytopaenia with anaemia and reduction in white blood cells and platelets. The anaemia is usually chronic in nature and patients rarely present with signs of heart failure. + Request inclusion into the HPO below "Hypersplenism". + Management of Sickle Cell Disease - The United Republic of Tanzania (By Ministry of Health) + None SCDO - Request inclusion into the HPO below "Hypersplenism". - Management of Sickle Cell Disease - The United Republic of Tanzania (By Ministry of Health) - None Chronic Hypersplenism - + - - + + The sequential set of three nucleotides in transfer RNA that interacts with its complement in messenger RNA, the Codon, during translation in the ribosome. - http://purl.bioontology.org/ontology/MESH/D000926 - Sufficient - SCDO:0004598 + http://purl.bioontology.org/ontology/MESH/D000926 + Sufficient + SCDO:0004598 MESH:D000926 Anticodon - + - - + + Also known as sense codon, a set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (terminator codon). Most codons are universal, but some organisms do not produce the transfer RNAs complementary to all codons. These codons are referred to as unassigned codons (nonsense codons). - Add "Terminator Codon" as a parent of "Nonsense Codon" as in MESH? - http://purl.bioontology.org/ontology/MESH/D003062 - Sufficient - SCDO:0004623 + Add "Terminator Codon" as a parent of "Nonsense Codon" as in MESH? + http://purl.bioontology.org/ontology/MESH/D003062 + Sufficient + SCDO:0004623 MESH:D003062 Codon - + - - + + A codon that directs initiation of protein translation (Translation, Genetic) by stimulating the binding of initiator tRNA (RNA, TRANSFER, MET). In prokaryotes, the codons AUG or GUG can act as initiators while in eukaryotes, AUG is the only initiator codon. - http://purl.bioontology.org/ontology/MESH/D018387 - Sufficient - SCDO:0004716 + http://purl.bioontology.org/ontology/MESH/D018387 + Sufficient + SCDO:0004716 MESH:D018387 Codon, Initiation Codon, Initiator @@ -41319,50 +40754,50 @@ Suggest update to description in MESH. - + - + - - + + - - + + - - + + - - + + - - + + - - + + Brief reversible episodes of focal, nonconvulsive ischemic dysfunction of the brain having a duration of less than 24 hours, and usually less than one hour, caused by transient thrombotic or embolic blood vessel occlusion or stenosis. Events may be classified by arterial distribution, temporal pattern, or etiology (e.g., embolic vs. thrombotic). - http://www.ebi.ac.uk/efo/EFO_0003764 - Sufficient - SCDO:0004829 + http://www.ebi.ac.uk/efo/EFO_0003764 + Sufficient + SCDO:0004829 EFO:0003764 Mini Stroke TIA @@ -41372,66 +40807,66 @@ Suggest update to description in MESH. - + - + A chest pain that is caused when your heart muscle doesn't get enough oxygen-rich blood. - - Sufficient - SCDO:0004836 + + Sufficient + SCDO:0004836 OAE:0002122 Angina - + - + - - + + - - + + - - + + - - + + A rarely recognized complication of vaso-occlusive crisis. It is characterized by a presentation of right upper quadrant pain in the liver. A smooth, tender, enlarged liver is noted on physical exam. The lab values show a decrease in the hemoglobin/hematocrit. An increase in reticulocyte count is also seen. + Request inclusion into relevant ontology + Norris, W. E. (2004). Acute hepatic sequestration in sickle cell disease. Journal of the National Medical Association, 96(9), 1235-1239. The Management of Sickle Cell Disease. 1984. (Revised June 2002). NIH publication 02-2117. Available at http:/www.nhlbi.nih.gov/health/prof/blood/sickle/sc. + None SCDO - Request inclusion into relevant ontology - Norris, W. E. (2004). Acute hepatic sequestration in sickle cell disease. Journal of the National Medical Association, 96(9), 1235-1239. The Management of Sickle Cell Disease. 1984. (Revised June 2002). NIH publication 02-2117. Available at http:/www.nhlbi.nih.gov/health/prof/blood/sickle/sc. - None Acute Hepatic Sequestration - + - - + + 'A penicillin in which the substituent at position 6 of the penam ring is a 2-amino-2-(4-hydroxyphenyl)acetamido group. [Curator team: []]' - - http://purl.obolibrary.org/obo/CHEBI_2676 + + http://purl.obolibrary.org/obo/CHEBI_2676 CHEBI:2676 deprecated-Amoxicillin true @@ -41439,56 +40874,56 @@ Suggest update to description in MESH. - + - + - - + + - - + + - - + + - - + + An acquired disorder caused by several hematological and immunological diseases and characterized by impairment of splenic function. + Request inclusion into relevant ontology, perhaps below "Abnormality of the Spleen" in the HPO. + Few but definitions not freely available SCDO Kirkineska L, Perifanis V, Vasiliadis T. Functional hyposplenism. Hippokratia. 2014;18(1):7–11. Vijay, V., Cavenagh, J.D. and Yate, P., 1998. The anaesthetist's role in acute sickle cell crisis. British journal of anaesthesia, 80(6), pp.820-828. - Request inclusion into relevant ontology, perhaps below "Abnormality of the Spleen" in the HPO. - Few but definitions not freely available FH Functional Hyposplenism - + - + Deletion of a part of the beta-globin locus. + Request inclusion into relevant ontology + + None SCDO - Request inclusion into relevant ontology - - None Beta-Globin Cluster Deletion Beta-Globin Gene Cluster Deletion Hemaglobin Beta Gene Deletion @@ -41497,110 +40932,110 @@ Suggest update to description in MESH. - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Long lasting form of anemia. - SCDO - Request inclusion into relevant ontology + Request inclusion into relevant ontology -No online description for this term exists, would it be sufficient to say 'Long lasting form of anemia'? or is there a better definition specific for sickle cell anemia? - Few but definitions not freely available +No online description for this term exists, would it be sufficient to say 'Long lasting form of anemia'? or is there a better definition specific for sickle cell anemia? + Few but definitions not freely available + SCDO Chronic Anemia - + - + - + An increase in the rate of hemolysis, in conjunction with specific clinical complications of sickle cell disease. - SCDO - Request inclusion into Mammalian Phenotype ontology below "Hemolysis". + Request inclusion into Mammalian Phenotype ontology below "Hemolysis". -Info also provided by the definition source: 'Hyperhemolysis should be typified by an acute reduction in hemoglobin level associated with higher than usual reticulocyte counts and perhaps an unaccountable and sudden increase in LDH.' - Request inclusion into relevant ontology - Disorders of Hemoglobin: Genetics, Pathophysiology, and Clinical Management. Martin H. Steinberg, Bernard G. Forget, Douglas R. Higgs, David J. Weatherall. Cambridge University Press, 17 Aug 2009 - None +Info also provided by the definition source: 'Hyperhemolysis should be typified by an acute reduction in hemoglobin level associated with higher than usual reticulocyte counts and perhaps an unaccountable and sudden increase in LDH.' + Request inclusion into relevant ontology + Disorders of Hemoglobin: Genetics, Pathophysiology, and Clinical Management. Martin H. Steinberg, Bernard G. Forget, Douglas R. Higgs, David J. Weatherall. Cambridge University Press, 17 Aug 2009 + None + SCDO Hyperhemolysis - + - - + + A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations. - - Sufficient - SCDO:0005243 + + Sufficient + SCDO:0005243 MESH:D055028 CGH Comparative Genome Hybridization @@ -41611,18 +41046,18 @@ Info also provided by the definition source: 'Hyperhemolysis should be typi - + - - + + An abnormally high number of reticulocytes per unit volume of blood. The normal fraction of reticulocytes in the blood depends on the clinical situation but is usually 0.5% to 2.5% in adults and 2% to 6% in infants. - - SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology + + Request inclusion into relevant ontology -Symptom of splenic sequestration, or increased haemolysis. - - Negligable +Symptom of splenic sequestration, or increased haemolysis. + + Negligable + SCDO (Jade Hotchkiss) Reticulocyte Count High deprecated High Reticulocyte Count true @@ -41630,28 +41065,28 @@ Symptom of splenic sequestration, or increased haemolysis. + - - + + The physical characteristics of the globin polypeptides that form hemoglobins. - Request inclusion into relevant ontology. - https://www.ncbi.nlm.nih.gov/pubmed/20339107 - None + Request inclusion into relevant ontology. + https://www.ncbi.nlm.nih.gov/pubmed/20339107 + None Globin Chain Phenotype Globin Phenotype - + - - + + Work consisting of a structured file of information or a set of logically related data stored and retrieved using computer-based means. - http://purl.bioontology.org/ontology/MESH/D019991 - Sufficient - SCDO:0005379 + http://purl.bioontology.org/ontology/MESH/D019991 + Sufficient + SCDO:0005379 MESH:D019991 Data Base Database @@ -41659,15 +41094,15 @@ Symptom of splenic sequestration, or increased haemolysis. + - - + + The major component of hemoglobin in the fetus. This hemoglobin has two alpha and two gamma polypeptide subunits in comparison to normal adult hemoglobin, which has two alpha and two beta polypeptide subunits. Fetal hemoglobin concentrations can be elevated (usually above 0.5%) in children and adults affected by leukemia and several types of anemia. - Request inclusion into NCIT below "Hemoglobin"/"Normal Hemoglobin", for completion sake. - - Sufficient - SCDO:0005446 + Request inclusion into NCIT below "Hemoglobin"/"Normal Hemoglobin", for completion sake. + + Sufficient + SCDO:0005446 MESH:D005319 Fetal Haemoglobin Foetal Haemoglobin @@ -41680,39 +41115,39 @@ Symptom of splenic sequestration, or increased haemolysis. + - - + + - - + + - - + + A disorder of cardiac function caused by insufficient blood flow to the muscle tissue of the heart. The decreased blood flow may be due to narrowing of the coronary arteries (coronary artery disease), to obstruction by a thrombus (coronary thrombosis), or less commonly, to diffuse narrowing of arterioles and other small vessels within the heart. Severe interruption of the blood supply to the myocardial tissue may result in necrosis of cardiac muscle (myocardial infarction). - http://www.ebi.ac.uk/efo/EFO_1001375 - Sufficient - SCDO:0005464 + http://www.ebi.ac.uk/efo/EFO_1001375 + Sufficient + SCDO:0005464 EFO:1001375 Myocardial Ischemia - + - + Avascular necrosis of femoral head (ANFH) is a severely disabling disease characterised by progressive groin pain, a limping gait, leg length discrepancy, collapse of the subchondral bone, limitation of hip function and eventual degeneration of the hip joint requiring total hip arthroplasty. - - http://www.orpha.net/ORDO/Orphanet_86820 + + http://www.orpha.net/ORDO/Orphanet_86820 Orphanet:86820 ANFH deprecated-Avascular Necrosis of the Femoral Head @@ -41721,48 +41156,48 @@ Symptom of splenic sequestration, or increased haemolysis. + - - + + The meaning ascribed to the base sequence with respect to how it is translated into amino acid sequence. The start, stop, and order of amino acids of a protein is specified by consecutive triplets of nucleotides called codons. - http://purl.bioontology.org/ontology/MESH/D005815 - Sufficient - SCDO:0005593 + http://purl.bioontology.org/ontology/MESH/D005815 + Sufficient + SCDO:0005593 MESH:D005815 Genetic Code - + - - - + + + - + Deletion of the HBB and HBD genes that results in delta-beta thalassemia. + Request inclusion into relevant ontology + None SCDO - Request inclusion into relevant ontology - None HBB and HBD Deletion - + - - + + A biological object that contains genetic information and that is involved in transmitting genetically encoded traits from one organism to another. - - Sufficient - SCDO:0005722 + + Sufficient + SCDO:0005722 MESH:D040342 Genetic Structures Genetic Structure @@ -41770,97 +41205,97 @@ Symptom of splenic sequestration, or increased haemolysis. + - + An ethical principle that obligates one to treat people fairly. Distributive justice refers to allocating benefits and harms fairly; procedural justice refers to using fair processes to make decisions that affect people; formal justice refers to treating similar cases in the same way. In human subjects research, the principle of justice implies that subjects should be selected equitably. + Request inclusion into relevant ontology + https://www.niehs.nih.gov/research/resources/bioethics/glossary/index.cfm#human-subjects-research + Few but definitions not specific enough SCDO - Request inclusion into relevant ontology - https://www.niehs.nih.gov/research/resources/bioethics/glossary/index.cfm#human-subjects-research - Few but definitions not specific enough Justice - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Elevated body temperature due to failed thermoregulation, or inflammation or immune responses. - Merged the two descriptions from NCIT and HP + Merged the two descriptions from NCIT and HP -Suggest update to description in NCIT and HP. - - - Suggest update to description +Suggest update to description in NCIT and HP. + + + Suggest update to description HP:0001945 NCIT:C3038 Pyrexia @@ -41870,107 +41305,107 @@ Suggest update to description in NCIT and HP. - + - - + + A person who has not attained the age at which full civil rights are accorded. - http://purl.bioontology.org/ontology/MESH/D033242 - Sufficient - SCDO:0006036 + http://purl.bioontology.org/ontology/MESH/D033242 + Sufficient + SCDO:0006036 MESH:D033242 Minor - + - - + + An ethnic group that includes persons with significant ethnic contributions from more than one group. - http://purl.obolibrary.org/obo/ERO_0002032 - Sufficient - SCDO:0006070 + http://purl.obolibrary.org/obo/ERO_0002032 + Sufficient + SCDO:0006070 ERO:0002032 Mixed Ethnicity - + - - + + Critical and exhaustive investigation or experimentation, having for its aim the discovery of new facts and their correct interpretation, the revision of accepted conclusions, theories, or laws in the light of newly discovered facts, or the practical application of such new or revised conclusions, theories, or laws. - http://purl.bioontology.org/ontology/MESH/D012106 - Sufficient - SCDO:0006339 + http://purl.bioontology.org/ontology/MESH/D012106 + Sufficient + SCDO:0006339 MESH:D012106 Research - + - + An uncommon complication of cholecystitis and refers to a situation where the gallbladder lumen is filled and distended by purulent material (pus). + Request inclusion into relevant ontology + https://radiopaedia.org/articles/gallbladder-empyema + Few but definitions not freely available SCDO - Request inclusion into relevant ontology - https://radiopaedia.org/articles/gallbladder-empyema - Few but definitions not freely available Gallbladder Empyema - + - + - + - - + + Aplasia or hemolysis may be precipitated by another illness/infection in sickle cell disease patients. Acutely severe anemia is defined as Hb < 5g/dl or a recent acute drop in HB > 2g/dl below the individual's steady state value. If no steady state value is available, it can be detected by the presence of acutely symptomatic anemia (i.e. tachycardia, cardiac failure, shock). - SCDO - Request inclusion into relevant ontology. + Request inclusion into relevant ontology. -Please check with the working group as to how they feel about the label for this term. - SCD Management guidelines - Tanzania - None +Please check with the working group as to how they feel about the label for this term. + SCD Management guidelines - Tanzania + None + SCDO Acutely Severe Anemia - + - - + + Research involving the collection, storage, or use of private data or biological samples from living individuals by means of interactions, interventions, surveys, or other research methods or procedures. - https://www.niehs.nih.gov/research/resources/bioethics/glossary/index.cfm#human-subjects-research - Not relevant to context of sickle cell + https://www.niehs.nih.gov/research/resources/bioethics/glossary/index.cfm#human-subjects-research + Not relevant to context of sickle cell Human Subject Research - + - - - + + + The collecting of fetal blood samples typically via endoscopic ultrasound guided fine needle aspiration from the umbilical vein, followed by examination of the blood to detect fetal abnormalities. - Suggest update to description in MESH. - - - Suggest update to description + Suggest update to description in MESH. + + + Suggest update to description MESH:D017218 Fetal Blood Sampling PUBS @@ -41981,28 +41416,28 @@ Please check with the working group as to how they feel about the label for this - + - - + + A material transfer agreement (MTA) is a type of legally enforceable contract employed by research institutions and companies to set the terms under which their materials and associated data may be obtained and used by others. - Request inclusion into relevant ontology - Henderson J (2007) Counterpoint: MTAs are a practical necessity. Nat Biotechnol 25: 722–724. - None + Request inclusion into relevant ontology + Henderson J (2007) Counterpoint: MTAs are a practical necessity. Nat Biotechnol 25: 722–724. + None MTA Material Transfer Agreement - + - + A branch of applied ethics that studies the value implications of practices and developments in life sciences, medicine, and health care. - http://purl.bioontology.org/ontology/MESH/D001675 - Sufficient - SCDO:0006706 + http://purl.bioontology.org/ontology/MESH/D001675 + Sufficient + SCDO:0006706 MESH:D001675 Biomedical Ethics Health Care Ethics @@ -42011,14 +41446,14 @@ Please check with the working group as to how they feel about the label for this - + - - + + A condition due to a dietary deficiency of ascorbic acid (vitamin C), characterized by malaise, lethargy, and weakness. As the disease progresses, joints, muscles, and subcutaneous tissues may become the sites of hemorrhage. Ascorbic acid deficiency frequently develops into SCURVY in young children fed unsupplemented cow's milk exclusively during their first year. It develops also commonly in chronic alcoholism. (Cecil Textbook of Medicine, 19th ed, p1177) - - Sufficient - SCDO:0006832 + + Sufficient + SCDO:0006832 MESH:D001206 Ascorbic Acid Deficiencies Vitamin C Deficiencies @@ -42028,38 +41463,38 @@ Please check with the working group as to how they feel about the label for this - + - - + + - - + + - - + + - - + + - - + + A rare intracranial arteriopathy involving progressive stenosis of the cerebral vasculature located at the base of the brain causing transient ischemic attacks or strokes. - http://www.orpha.net/ORDO/Orphanet_2573 - Sufficient - SCDO:0006833 + http://www.orpha.net/ORDO/Orphanet_2573 + Sufficient + SCDO:0006833 ORPHA:2573 MMD Moyamoya Disease @@ -42067,15 +41502,15 @@ Please check with the working group as to how they feel about the label for this - + - + - + Hemoglobin that presents no inherited health condition phenotype. + Request inclusion into NCIT below "Hemoglobin". + Few but definitions not freely available SCDO (Jade Hotchkiss) - Request inclusion into NCIT below "Hemoglobin". - Few but definitions not freely available Hemoglobin Normal Hemoglobin Normal Variant Normal Hemoglobin @@ -42083,133 +41518,133 @@ Please check with the working group as to how they feel about the label for this - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An acute form of acquired red cell aplasia. A significant change in blood picture is observed, characterised by a precipitous fall in the haemoglobin level (>20 g/l beyond steady state level) and reduced (<1%) or absent reticulocytes in the peripheral blood. The total white blood cell or platelet counts may or may not be affected. In addition, there is no significant increase in the unconjugated fraction of serum bilirubin.The most common cause is infection by parvovirus B19, a DNA virus that replicates inside immature red blood cells in the bone marrow, resulting in severe anaemia (hemoglobin levels well below steady state) and low reticulocyte count. It is rarely recurrent. + Request inclusion into relevant ontology + Juwah, A. I., Nlemadim, E. U., & Kaine, W. (2004). Types of anaemic crises in paediatric patients with sickle cell anaemia seen in Enugu, Nigeria. Archives of disease in childhood, 89(6), 572-576. + SCD Management guidelines - Jamaica + SCD Management guidelines - Nigeria + SCD Management guidelines - South Africa + Few but definitions not freely available SCDO - Request inclusion into relevant ontology - Juwah, A. I., Nlemadim, E. U., & Kaine, W. (2004). Types of anaemic crises in paediatric patients with sickle cell anaemia seen in Enugu, Nigeria. Archives of disease in childhood, 89(6), 572-576. - SCD Management guidelines - Jamaica - SCD Management guidelines - Nigeria - SCD Management guidelines - South Africa - Few but definitions not freely available Aplastic Crises Aplastic Crisis - + - + - - + + Mutations in the HBG1 and/or HBG2 genes. Such mutations can lead to variably increased levels of fetal hemoglobin (Hb) (Hb F, alpha2gamma2) in the syndrome of hereditary persistence of fetal Hb (HPFH). + Request inclusion into relevant ontology. + +Perhaps add sub-classes of specific mutations as in the dc:source. + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology. - -Perhaps add sub-classes of specific mutations as in the dc:source. - None HBG1 and/or HBG2 Mutations - + - + - - + + - - + + - - + + - - + + Condition characterized by splenomegaly, some reduction in the number of circulating blood cells in the presence of a normal or hyperactive bone marrow, and the potential for reversal by splenectomy. + http://www.ebi.ac.uk/efo/EFO_1000975 + Sufficient + SCDO:0006905 Al-Salem, A. H. (2011). Splenic Complications of Sickle Cell Anemia and the Role of Splenectomy. ISRN Hematology, 2011, 864257. http://doi.org/10.5402/2011/864257 - http://www.ebi.ac.uk/efo/EFO_1000975 - Sufficient - SCDO:0006905 EFO:1000975 Hypersplenia Hypersplenism @@ -42217,140 +41652,140 @@ Perhaps add sub-classes of specific mutations as in the dc:source. + - - + + - - + + Significant change in blood picture characterised by a precipitous fall in the haemoglobin level associated with jaundice, marked reticulocytosis, and polychromasia on the blood smear, increased unconju- gated hyperbilirubinaemia, and increased urobilinogen content in urine above the steady state level for each individual patient. + Request inclusion into relevant ontology + Juwah, A. I., Nlemadim, E. U., & Kaine, W. (2004). Types of anaemic crises in paediatric patients with sickle cell anaemia seen in Enugu, Nigeria. Archives of disease in childhood, 89(6), 572-576. + None SCDO - Request inclusion into relevant ontology - Juwah, A. I., Nlemadim, E. U., & Kaine, W. (2004). Types of anaemic crises in paediatric patients with sickle cell anaemia seen in Enugu, Nigeria. Archives of disease in childhood, 89(6), 572-576. - None Hyper-Hemolytic Crisis - + - - + + An ethnic group that includes persons with ethnic contributions from only one ethnic group. + Request inclusion into relevant ontology + None SCDO (curators) - Request inclusion into relevant ontology - None Conserved Ethnicity - + - + - + Hemoglobin with altered structural and biochemical properties. + Request inclusion into NCIT below "Hemoglobin". + https://www.ncbi.nlm.nih.gov/pubmed/23388674 + None SCDO (Clair Ingram) - Request inclusion into NCIT below "Hemoglobin". - https://www.ncbi.nlm.nih.gov/pubmed/23388674 - None Hemoglobin Variant - + - + Voluntary authorization, by a patient or research subject, with full comprehension of the risks involved, for diagnostic or investigative procedures, and for medical and surgical treatment. - - Sufficient - SCDO:0007087 + + Sufficient + SCDO:0007087 MESH:D007258 Informed Consent - + - - - + + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Significant change in blood picture characterised by a precipitous fall in the haemoglobin level of at least 20 g/l and accompanied by a rapidly enlarging spleen or liver (greater than 2 cm from the steady state level) and reticulocytosis above the steady state level for each individual patient. Signs of acute circulatory insufficiency such tachypnoea, tachycardia, and hypotension may or may not be present. It is the earliest life-threatening complication seen in patients with SCD besides pneumococcal infections. + Request inclusion into relevant ontology + Vijay, V., Cavenagh, J.D. and Yate, P., 1998. The anaesthetist's role in acute sickle cell crisis. British journal of anaesthesia, 80(6), pp.820-828. + Few but definitions not freely available SCDO - Request inclusion into relevant ontology - Vijay, V., Cavenagh, J.D. and Yate, P., 1998. The anaesthetist's role in acute sickle cell crisis. British journal of anaesthesia, 80(6), pp.820-828. - Few but definitions not freely available Acute Crisis Splenic Sequestration Acute Splenic Sequestration Crisis - + - - + + A hemoglobinopathy caused by a reduced or imbalanced synthesis of a normal globin chain or by a defect in the switch between synthesis of different types of normal hemoglobin. + None SCDO (Jade Hotchkiss) - None Abnormal Hemoglobin Synthesis Abnormal Synthesis Hemoglobinopathy Synthesis Hemoglobinopathy @@ -42359,10 +41794,10 @@ Perhaps add sub-classes of specific mutations as in the dc:source. + - - + + 'Other molecules are complexes which do not contain protein or RNA, including lipids, carbohydrates, etc.' obsolete Other Molecules true @@ -42370,14 +41805,14 @@ Perhaps add sub-classes of specific mutations as in the dc:source. + - + Insufficient production of steroid hormones (primarily cortisol) by the adrenal glands as a result of a primary defect in the glands themselves. - Suggest update to description. Not sure if they changed their description or if we adapted it. - - Suggest update to description + Suggest update to description. Not sure if they changed their description or if we adapted it. + + Suggest update to description HP:0000846 Hypoadrenalism Adrenal Insufficiency @@ -42385,213 +41820,213 @@ Perhaps add sub-classes of specific mutations as in the dc:source. + - - + + The probability that an event will occur. It encompasses a variety of measures of the probability of a generally unfavorable outcome. - http://purl.bioontology.org/ontology/MESH/D012306 - Sufficient - SCDO:0007495 + http://purl.bioontology.org/ontology/MESH/D012306 + Sufficient + SCDO:0007495 MESH:D012306 Risk - + - - + + A process of inclusive participation that supports mutual respect of values, strategies, and actions for authentic partnership of people affiliated by geographic location, shared interest, or similar circumstances to address issues affecting community wellbeing. - Request inclusion into relevant ontology - Holzer et al 2014 Doi:10.1097/JIM.0000000000000097 - Few but definitions not available + Request inclusion into relevant ontology + Holzer et al 2014 Doi:10.1097/JIM.0000000000000097 + Few but definitions not available Community Engagement - + - - + + Distinct geographical area. - - This term was too general. Was replaced by "Geographic Area". + + This term was too general. Was replaced by "Geographic Area". deprecated Major Area true - + - - + + Information or a description of consent (hypothetical or obtained) or any aspect involved in or captured in the consent process. + Request inclusion into relevant ontology, perhaps the ICO. + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology, perhaps the ICO. - None Descriptor of Consent - + - + In situ death of bone within the humeral head due to disruption of blood supply. - - Has synonym: Osteonecrosis of the humeral head - http://www.wheelessonline.com/ortho/Humeral_Head_Osteonecrosis + + Has synonym: Osteonecrosis of the humeral head + http://www.wheelessonline.com/ortho/Humeral_Head_Osteonecrosis deprecated-Avascular necrosis of the humeral head true - + - + The molecular characteristics of a cell of tissue including expressed coding and non-coding RNAs, proteins and their post-translational modifications, lipids, carbohydrates and small molecules that characterize the state in a cell or tissue and that result from the interaction of its genotype and the environment. - - http://www.bioassayontology.org/bao#BAO_0170001 - Sufficient - SCDO:0007623 + + http://www.bioassayontology.org/bao#BAO_0170001 + Sufficient + SCDO:0007623 BAO:0170001 Molecular Phenotype - + - - + + - + - - + + - - + + HBB genetic variants that result in reduced or absent hemoglobin subunit beta production. + Request inclusion into relevant ontology + PMID: 20301599 + None SCDO - Request inclusion into relevant ontology - PMID: 20301599 - None Beta Thalassemia Genotype - + - - - + + + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Hemolytic anemia, in which patients are compound or double heterozygous for both the sickle cell gene and a thalassemia gene. - Suggest update to description in NCIT - - Suggest update to description + Suggest update to description in NCIT + + Suggest update to description NCIT:C61237 Sickle Cell-Thalassemia Sickle Cell Thalassemia @@ -42599,57 +42034,57 @@ Perhaps add sub-classes of specific mutations as in the dc:source. + - - - + + + A document containing the determination of the Research Ethics Committee (REC) that the clinical study with human subject participation has been reviewed and may be conducted at a particular study site within the constraints set forth by the REC and other institutional and federal requirements. The regulations require that an REC conduct continuing review of research at intervals appropriate to the degree of risk, but not less than once a year. + Request inclusion into relevant ontology + None SCDO - Request inclusion into relevant ontology - None Ethics Approval - + - - + + Hemoglobin produced in the blood islands in the embryonic yolk sac during the mesoblastic stage of gestation. There are four different embryonic hemoglobins, Hemoglobin Gower 1, Hemoglobin Gower 2, Hemoglobin Portland 1 and Hemoglobin Portland 2. - Request inclusion into NCIT below "Hemoglobin"/"Normal Hemoglobin". + Request inclusion into NCIT below "Hemoglobin"/"Normal Hemoglobin". Add sub-classes: Hemoglobin Gower 1 Hemoglobin Gower 2 Hemoglobin Portland 1 -Hemoglobin Portland 2 - - R Al-Mufti, H Hambley, F Farzaneh, KH Nicolaides -Haematologica Jan 2000, 85 (7) 690-693; - None +Hemoglobin Portland 2 + + R Al-Mufti, H Hambley, F Farzaneh, KH Nicolaides +Haematologica Jan 2000, 85 (7) 690-693; + None Hemoglobin Epsilon Embryonic Hemoglobin - + - - + + - - + + A seizure that occurs in the context of a brain insult (systemic, toxic, or metabolic) and may not recur when the underlying cause has been removed or the acute phase has elapsed. It is often associated with infections, infarctions, and severe metabolic or sickle cell complications. - Suggest update to description in HPO. - - SCD Management guidelines - Jamaica - Suggest update to description + Suggest update to description in HPO. + + SCD Management guidelines - Jamaica + Suggest update to description HP:0011145 Provoked Seizures Situation-Related Seizures @@ -42658,82 +42093,82 @@ Haematologica Jan 2000, 85 (7) 690-693; - + - - + + Deletion of both HBA1 genes, which results in an alpha-thal-2 (alpha-/alpha-) form of alpha thalassemia trait. With this deletion there is nearly normal production of red blood cells, but there may be a mild anemia. + Request inclusion into relevant ontology + + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - None Trans Deletion of HBA1 Homozygous Deletion of HBA1 - + - - + + A hemoglobinopathy caused by the presence of structurally abnormal hemoglobins. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Qualitative Hemoglobinopathy Structural Hemoglobinopathy - + - + - + - - + + Persistence of an inflammatory event in the articulation overtime. + Request inclusion into relevant ontology + None SCDO - Request inclusion into relevant ontology - None Chronic Arthritis - + - + The obstruction of blood vessels by altered erythrocytes that can result in pain, anemia and tissue ischemia. + Request inclusion into relevant ontology + None SCDO - Request inclusion into relevant ontology - None Vaso-Occlusion - + - - + + - - + + Characterized by pain and discomfort in the right upper quadrant (RUQ) of the abdomen caused by a number of possible aetiologies in sickle cell disease. Causes of RUQ pain may be divided into pain originating from the liver or gall bladder versus other origins of abdominal pain in that region. - Request inclusion into relevant ontology - SCD Management guidelines - Jamaica - Few but definitions not freely available + Request inclusion into relevant ontology + SCD Management guidelines - Jamaica + Few but definitions not freely available RUQ Pain Right Upper Quadrant Pain Right Upper Quadrant Syndrome @@ -42741,42 +42176,42 @@ Haematologica Jan 2000, 85 (7) 690-693; - + - - + + A biobank is a collections of samples of biological substances (e.g. tissue, blood, DNA) which are linked to data about the samples and their donors. They have a dual nature as collections of samples and data and usually require investigators or institutions to agree to certain conditions as a condition for sharing samples or data with them. - Suggest update to description in OMIABIS - - - Suggest update to description + Suggest update to description in OMIABIS + + + Suggest update to description OMIABIS:0000000 Biobank - + - - + + - - + + - - + + The concurrence of sickle cell anemia and alpha-thalassemia. This condition is thought to result in less severe hemolytic anemia due to reduced concentration of hemoglobin S and its polymerization within red blood cells. + Request inclusion into relevant ontology + Few but definitions not freely available SCDO (Clair Ingram) - Request inclusion into relevant ontology - Few but definitions not freely available Co-Inheritance of Alpha-Thalassemia and Sickle Cell Anemia Co-Inheritance of Sickle Cell Anemia and Alpha-Thalassemia Sickle Cell Anemia Associated with Coexistent Alpha Thalassemia @@ -42785,144 +42220,144 @@ Haematologica Jan 2000, 85 (7) 690-693; - + - - + + A radiograph of dental structures made on x-ray film or stored as a digital image. The radiographs may be extraoral or intraoral. Three common types of intraoral dental images are periapical, interproximal, and occlusal radiographs. - Request inclusion into relevant ontology - "dental radiograph." Mosby's Medical Dictionary, 8th edition. 2009. Elsevier 7 Nov. 2018 https://medical-dictionary.thefreedictionary.com/dental+radiograph - None + Request inclusion into relevant ontology + "dental radiograph." Mosby's Medical Dictionary, 8th edition. 2009. Elsevier 7 Nov. 2018 https://medical-dictionary.thefreedictionary.com/dental+radiograph + None Radiologic Examination, Teeth Dental Radiograph - + - - + + - + - + - + - - + + - - + + The removal of excess iron from the body with special drugs. - Request inclusion into MESH below "Chelation Therapy" - - None + Request inclusion into MESH below "Chelation Therapy" + + None Iron Chelation Therapy - + - + The capacity for self-governance, i.e. the ability to make reasonable decisions. + Request inclusion into relevant ontology + + Few but definitions not freely available SCDO https://www.hhs.gov/ohrp/sites/default/files/the-belmont-report-508c_FINAL.pdf - Request inclusion into relevant ontology - - Few but definitions not freely available Autonomy - + - + - - + + - - + + - - + + - - + + Blockage of blood flow in the central retinal artery. Results in sudden painless loss of vision and occurs in children and young adults. Thrombus formation in the retinal artery occurs spontaneously or in association with hyphema, Moyamoya and acute chest sydrome. There is no associated pain and it may be unilateral or bilateral. - Suggest update to description in HPO - - SCD Management guidelines - Jamaica - Suggest update to description + Suggest update to description in HPO + + SCD Management guidelines - Jamaica + Suggest update to description HP:0025342 Central Retinal Artery Occlusion - + - + - - + + - - + + - - + + Occurs where there is infarction of vertebral bone marrow, leading to collapse of the vertebrae with a typical 'fish mouth' appearance. It is often asymptomatic, but may cause acute and/or long term pain requiring analgesia and mechanical support such as a brace. Can be an acute or chronic bone problem in SCD. + Suggest update to description in HPO (currently no description). + + Few but definitions not freely available SCDO - Suggest update to description in HPO (currently no description). - - Few but definitions not freely available HP:0002953 Compression Fracture Fractures of Vertebral Bodies @@ -42935,30 +42370,30 @@ Haematologica Jan 2000, 85 (7) 690-693; - + - + Principle dictating that harm should not come to individuals as a result of their participation in a research project. - Request inclusion into relevant ontology - Shamoo AE and Resnik DB, Responsible Conduct of Research, 3rd ed. (New York: Oxford University Press, 2015). - None + Request inclusion into relevant ontology + Shamoo AE and Resnik DB, Responsible Conduct of Research, 3rd ed. (New York: Oxford University Press, 2015). + None Non-Maleficience - + - - + + A nutritional condition produced by a deficiency of folic acid in the diet. + + Alcohol interferes with its intermediate metabolism and absorption. Folic acid deficiency may develop in long-term anticonvulsant therapy or with use of oral contraceptives. + This deficiency causes anemia, macrocytic anemia, and megaloblastic anemia. It is indistinguishable from vitamin B 12 deficiency in peripheral blood and bone marrow findings, but the neurologic lesions seen in B 12 deficiency do not occur. (Merck Manual, 16th ed) + Sufficient + SCDO:0009117 - - Alcohol interferes with its intermediate metabolism and absorption. Folic acid deficiency may develop in long-term anticonvulsant therapy or with use of oral contraceptives. - This deficiency causes anemia, macrocytic anemia, and megaloblastic anemia. It is indistinguishable from vitamin B 12 deficiency in peripheral blood and bone marrow findings, but the neurologic lesions seen in B 12 deficiency do not occur. (Merck Manual, 16th ed) - Sufficient - SCDO:0009117 EFO:0001070 Deficiency of Folic Acid Deficiency of Folic Acid (Disorder) @@ -42969,107 +42404,107 @@ Haematologica Jan 2000, 85 (7) 690-693; - + - - + + A hemoglobinopathy caused by compound heterozygous inheritance of one hemoglobin S allele and one hemoglobin allele that produces structurally abnormal hemoglobin. - + obsolete Sickle Plus Structural Variant true - + - - + + Hemoglobin with decreased solubility in the red cell due to substitutions in the primary sequence of globin which alters the tertiary or quaternary structure of the molecule and results in a globin polypeptide/hemoglobin tetramer that is unstable and precipitates intracellularly, reducing the red blood cell lifespan. + Request inclusion in the HPO, below "Abnormal Hemoglobin". + + Few but definitions not freely available SCDO (Jade Hotchkiss) - Request inclusion in the HPO, below "Abnormal Hemoglobin". - - Few but definitions not freely available Unstable Hemoglobin - + - + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An acute condition of intrasplenic pooling of large amounts of blood. + Suggest update to description in the Radiology Lexicon, or use their description "Splenic sequestration occurs in sickle cell disease when sickled red blood cells become trapped in the spleen, causing it to enlarge." + + Suggest update to description SCDO - Suggest update to description in the Radiology Lexicon, or use their description "Splenic sequestration occurs in sickle cell disease when sickled red blood cells become trapped in the spleen, causing it to enlarge." - - Suggest update to description Blood Trapped in the Spleen Can cause severely acute anemia. Splenic Sequestration @@ -43077,56 +42512,56 @@ Haematologica Jan 2000, 85 (7) 690-693; - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A complication of kidney diseases characterized by cell death involving kidney papilla in the kidney medulla. Damages to this area may hinder the kidney to concentrate urine resulting in polyuria. Sloughed off necrotic tissue may block kidney pelvis or ureter. Necrosis of multiple renal papillae can lead to kidney failure. - http://www.ebi.ac.uk/efo/EFO_1001004 - Sufficient - SCDO:0009445 + http://www.ebi.ac.uk/efo/EFO_1001004 + Sufficient + SCDO:0009445 EFO:1001004 Kidney Papillary Necrosis Necrotising Renal Papillitis @@ -43139,12 +42574,12 @@ Haematologica Jan 2000, 85 (7) 690-693; - + - - + + 'Any single chemical entity that is an electrically neutral entity consisting of more than one atom. Each atom carries a certain number of electrons that orbit around the nucleus.[Curator team: []]' - http://purl.obolibrary.org/obo/CHEBI_25367 + http://purl.obolibrary.org/obo/CHEBI_25367 CHEBI:25367 obsolete Molecule true @@ -43152,151 +42587,151 @@ Haematologica Jan 2000, 85 (7) 690-693; - + - + Effort made to secure the well-being of persons, maximizing possible benefits and minimizing possible harms. + https://www.hhs.gov/ohrp/sites/default/files/the-belmont-report-508c_FINAL.pdf + Few but definitions not specific enough SCDO - https://www.hhs.gov/ohrp/sites/default/files/the-belmont-report-508c_FINAL.pdf - Few but definitions not specific enough MESH:D026686 Beneficence - + - - + + The physical characteristics and levels of proteins that characterize the state in a cell or tissue and that result from the interaction of its genotype and the environment. - SCDO (Jade Hotchkiss) - Request inclusion into BioAssay Ontology below "biochemical phenotype". + Request inclusion into BioAssay Ontology below "biochemical phenotype". Can all sub-classes of the "Gene Product" class not be included here? -Can this class not be removed but its sub-classes kept? - None +Can this class not be removed but its sub-classes kept? + None + SCDO (Jade Hotchkiss) Protein Phenotype - + - - + + An abnormally low number of reticulocytes per unit volume of blood. - + + Request inclusion into relevant ontology + +Symptom of aplastic crisis, possibly due to parvovirus B19 infection. Is there a certain value below which is considered a low reticulocyte count? + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - -Symptom of aplastic crisis, possibly due to parvovirus B19 infection. Is there a certain value below which is considered a low reticulocyte count? - Negligable deprecated Low Reticulocyte Count true - + - - + + 'The aplastic crisis is temporary cessation of red cell production. This usually affect sickle cell patients, because of the markedly shortened red cell survival time in patients with sickle cell disease, a precipitous drop in hemoglobin occurs in the absence of adequate reticulocytosis. [Curator team: []]' - - http://www.ihtc.org/medical-professionals/blood-disorders/sickle-cell-disease/aplastic-crisis-intervention/ + + http://www.ihtc.org/medical-professionals/blood-disorders/sickle-cell-disease/aplastic-crisis-intervention/ deprecated Aplastic Crises true - + - - + + - - + + - - + + - - + + Pain resulting from tissue ischemia as a result of blockage of mesenteric blood vessels. - Request inclusion into relevant ontology - Akingbola TS, Kolude B, Aneni EC, et al. ABDOMINAL PAIN IN ADULT SICKLE CELL DISEASE PATIENTS: A NIGERIAN EXPERIENCE. Annals of Ibadan Postgraduate Medicine. 2011;9(2):100-104. - SCD Management guidelines - Tanzania - Abdominal distension with generalised abdominal tenderness (no rebound tenderness) and reduced bowel sounds. Abdomen moves with respiration. Vomiting/diarrhoea are not common. - None + Request inclusion into relevant ontology + Akingbola TS, Kolude B, Aneni EC, et al. ABDOMINAL PAIN IN ADULT SICKLE CELL DISEASE PATIENTS: A NIGERIAN EXPERIENCE. Annals of Ibadan Postgraduate Medicine. 2011;9(2):100-104. + SCD Management guidelines - Tanzania + Abdominal distension with generalised abdominal tenderness (no rebound tenderness) and reduced bowel sounds. Abdomen moves with respiration. Vomiting/diarrhoea are not common. + None Abdominal Vaso-Occlusive Crisis - + - + - + A mutation in the beta-globin gene, HBB, that causes decreased or absent beta-globin synthesis. + Request inclusion into relevant ontology + None SCDO - Request inclusion into relevant ontology - None Beta Thalassemia Mutation - + - - + + A genetic mutation in the HBB gene that results in absent or decreased hemoglobin subunit beta or an abnormal hemoglobin other than Hb S. + Too specific to SCD to be included in other ontologies. + None SCDO - Too specific to SCD to be included in other ontologies. - None Other HBB Variants - + - - + + The proteins and their post-translational modifications, lipids, carbohydrates and small molecules that characterize the state in a cell or tissue and that result from the interaction of its genotype and the environment. - - Sufficient - SCDO:0009884 + + Sufficient + SCDO:0009884 BAO:0170003 Biochemical Phenotype - + - - + + 'Genotypes which are not specific to sickle cell trait.' obsolete Other Genotypes true @@ -43304,112 +42739,112 @@ Symptom of aplastic crisis, possibly due to parvovirus B19 infection. Is there a - + - + - + The moral obligations governing the conduct of research. Used for discussions of research ethics as a general topic. - http://purl.bioontology.org/ontology/MESH/D032984 - Sufficient - SCDO:0300002 + http://purl.bioontology.org/ontology/MESH/D032984 + Sufficient + SCDO:0300002 MESH:D032984 Research Ethics - + - - + + Specific genre of publication. - http://purl.bioontology.org/ontology/MESH/D052180 - Sufficient - SCDO:0300003 + http://purl.bioontology.org/ontology/MESH/D052180 + Sufficient + SCDO:0300003 MESH:D052180 Publication Formats - + - - + + Types and formulations of studies used in epidemiological and clinical research. - Suggest update to description in MESH - http://purl.bioontology.org/ontology/MESH/D016020 - Suggest update to description + Suggest update to description in MESH + http://purl.bioontology.org/ontology/MESH/D016020 + Suggest update to description MESH:D016020 Epidemiologic Study Characteristics - + - - + + Elements, types, descriptions and formulations of a research study. + Request inclusion into relevant ontology + None SCDO (Gaston K. Mazandu) - Request inclusion into relevant ontology - None Research Characteristics - + - - + + Revealing of information, by oral or written communication. - http://purl.bioontology.org/ontology/MESH/D030881 - Sufficient - SCDO:0300006 + http://purl.bioontology.org/ontology/MESH/D030881 + Sufficient + SCDO:0300006 MESH:D030881 Information Disclosure - + - - + + Reporting to parents or guardians about care to be provided to a minor (minors). - http://purl.bioontology.org/ontology/MESH/D035622 - Sufficient - SCDO:0300007 + http://purl.bioontology.org/ontology/MESH/D035622 + Sufficient + SCDO:0300007 MESH:D035622 Parental Notification - + - - + + A legal requirement that designated types of information acquired by professionals or institutions in the course of their work be reported to appropriate authorities. - http://purl.bioontology.org/ontology/MESH/D019221 - Sufficient - SCDO:0300008 + http://purl.bioontology.org/ontology/MESH/D019221 + Sufficient + SCDO:0300008 MESH:D019221 Mandatory Reporting - + - - + + Making information permanently non-identifiable that is associated with the identity of specific entities via encryption or other methods. - Suggest update to description in MESH - http://purl.bioontology.org/ontology/MESH/D000068240 - Suggest update to description + Suggest update to description in MESH + http://purl.bioontology.org/ontology/MESH/D000068240 + Suggest update to description MESH:D000068240 Data De-Identification Data Masking @@ -43419,117 +42854,117 @@ Symptom of aplastic crisis, possibly due to parvovirus B19 infection. Is there a - + - + An observable characteristic of disease that has a severe and rapid onset of symptoms with short duration. + Request inclusion into relevant ontology + http://purl.obolibrary.org/obo/NCIT_C14140 + http://semanticscience.org/resource/SIO_010056 + None SCDO (Clair Ingram) - Request inclusion into relevant ontology - http://purl.obolibrary.org/obo/NCIT_C14140 - http://semanticscience.org/resource/SIO_010056 - None Acute Phenotype - + - - + + A unique identifier generated either manually or electronically when adding a subject to a study. - + deprecated Research Subject ID true - + - - + + - + - + Procedures which temporarily or permanently remedy insufficient cleansing of body fluids by the kidneys. - Could this and it's sub-classes not fall below any of the other main Therapeutics classes? Symptomatic? - http://purl.bioontology.org/ontology/MESH/D017582 - Sufficient - SCDO:1000004 + Could this and it's sub-classes not fall below any of the other main Therapeutics classes? Symptomatic? + http://purl.bioontology.org/ontology/MESH/D017582 + Sufficient + SCDO:1000004 MESH:D017582 Renal Replacement Therapy - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + An abnormal hemoglobin caused by various point mutations within the HBB gene. This form of hemoglobin prevents red blood cells from carrying oxygen effectively. There are at least 8 different types of hemoglobin D. - Request inclusion in the HPO, below "Abnormal Hemoglobin". - - - Few but definitions not freely available + Request inclusion in the HPO, below "Abnormal Hemoglobin". + + + Few but definitions not freely available Haemoglobin D Hb D HbD @@ -43538,15 +42973,15 @@ Symptom of aplastic crisis, possibly due to parvovirus B19 infection. Is there a - + - - + + A group of abnormal hemoglobins in which amino acid substitutions take place in either the alpha, beta or gamma chains but near the heme iron. This results in facilitated oxidation of the hemoglobin to yield excess methemoglobin which leads to cyanosis. - Suggest update to description in MESH (to include "gamma chains") -Suggest this term replaces "Methemoglobinemia" below "Abnormal Hemoglobin" in the HPO. - http://purl.bioontology.org/ontology/MESH/D006449 - Suggest update to description + Suggest update to description in MESH (to include "gamma chains") +Suggest this term replaces "Methemoglobinemia" below "Abnormal Hemoglobin" in the HPO. + http://purl.bioontology.org/ontology/MESH/D006449 + Suggest update to description MESH:D006449 Hb M HbM Hemoglobin @@ -43555,22 +42990,22 @@ Suggest this term replaces "Methemoglobinemia" below "Abnormal He - + - - - + + + - - + + An abnormal hemoglobin that results from the substitution of lysine for glutamic acid at position 26 of the beta chain. It is most frequently observed in southeast Asian populations. - Request inclusion in the HPO, below "Abnormal Hemoglobin", for the sake of completion. - http://purl.bioontology.org/ontology/MESH/D006446 - Sufficient - SCDO:1000009 + Request inclusion in the HPO, below "Abnormal Hemoglobin", for the sake of completion. + http://purl.bioontology.org/ontology/MESH/D006446 + Sufficient + SCDO:1000009 MESH:D006446 Hb E Hemoglobin E @@ -43578,75 +43013,75 @@ Suggest this term replaces "Methemoglobinemia" below "Abnormal He - + - - - + + + - + - - + + - - + + - - + + - - + + - - + + - + - + - + - - + + A group of disorders caused by large deletions of the beta-globin gene complex; typically 30% fetal haemoglobin. - Request inclusion into relevant ontology - http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf?_tid=691c25c0-5826-11e7-b704-00000aacb35e&acdnat=1498230953_4d1264c47385275daf8fc2a1e1de62e3 - None + Request inclusion into relevant ontology + http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf?_tid=691c25c0-5826-11e7-b704-00000aacb35e&acdnat=1498230953_4d1264c47385275daf8fc2a1e1de62e3 + None HPFH-Sickle Cell Disease Syndrome Hereditary Persistence of Fetal Hemoglobin-Sickle Cell Disease Syndrome Sickle Cell Disease Syndrome-Hereditary Persistence of Fetal Hemoglobin @@ -43657,15 +43092,15 @@ Suggest this term replaces "Methemoglobinemia" below "Abnormal He - + - - - + + + Members of the beta-globin family. In humans, they are encoded in a gene cluster on chromosome 11. They include hemoglobin subunit epsilon, hemoglobin subunit gamma, hemoglobin subunit delta and hemoglobin subunit beta. There is also a pseudogene of beta (theta-beta) in the gene cluster. Adult hemoglobin is comprised of two alpha globin chains and two beta-globin chains. - - Sufficient - SCDO:1000012 + + Sufficient + SCDO:1000012 MESH:D055544 Beta-Globins Beta-Globin Family Members @@ -43673,14 +43108,14 @@ Suggest this term replaces "Methemoglobinemia" below "Abnormal He - + - - + + This gene encodes the hemoglobin subunit beta and is located on chromosome 11 mapped at 11p15.5. - Request inclusion into relevant ontology - - Negligable + Request inclusion into relevant ontology + + Negligable NCBIGene:3043 Beta-Globin Gene HBB Gene @@ -43693,15 +43128,15 @@ Suggest this term replaces "Methemoglobinemia" below "Abnormal He - + - - + + This gene encodes the hemoglobin subunit delta, which is a component of hemoglobin A2, which plays a role in the transport of oxygen to tissues of the adult body, but exists only in small amounts in all adult humans (1.5-3.1% of all hemoglobin molecules). - Suggest update to description in NCIT - - http://purl.obolibrary.org/obo/NCIT_C84961 - Suggest update to description + Suggest update to description in NCIT + + http://purl.obolibrary.org/obo/NCIT_C84961 + Suggest update to description NCIT:C84961 HBD Gene Hemoglobin Delta Gene @@ -43711,21 +43146,21 @@ Suggest this term replaces "Methemoglobinemia" below "Abnormal He - + - - - + + + - - + + An abnormal hemoglobin that results from the substitution of glutamic acid with lysine at position 121 of the beta chain. - Request inclusion in the HPO, below "Abnormal Hemoglobin". - MESH and Zimmerman SA. Am J Hematol. 1999 Apr; 60(4) 279-84 - Few but definitions not freely available + Request inclusion in the HPO, below "Abnormal Hemoglobin". + MESH and Zimmerman SA. Am J Hematol. 1999 Apr; 60(4) 279-84 + Few but definitions not freely available Hb O-Arab Hb-Arab Hemoglobin-Arab @@ -43734,503 +43169,503 @@ Suggest this term replaces "Methemoglobinemia" below "Abnormal He - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - + + - - + + - - + + - - + + A material processing technique that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury or to help improve bodily function or appearance. - http://purl.obolibrary.org/obo/ERO_0000378 - Sufficient - SCDO:1000017 + http://purl.obolibrary.org/obo/ERO_0000378 + Sufficient + SCDO:1000017 ERO:0000378 Surgery - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Treatment of factors associated with the definitive onset of a disease, illness, accident, behavioral response, or course of action. Usually one factor is more important or more obviously recognizable than others, if several are involved, and one may often be regarded as necessary. Examples include exposure to specific disease; amount or level of an infectious organism, drug, or noxious agent, etc. + Request inclusion into relevant ontology + http://purl.bioontology.org/ontology/MESH/D015985 + None SCDO - Request inclusion into relevant ontology - http://purl.bioontology.org/ontology/MESH/D015985 - None Management of Precipitating Factors Management of Underlying Cause Treatment of Underlying Cause @@ -44239,35 +43674,35 @@ Suggest this term replaces "Methemoglobinemia" below "Abnormal He - + - - + + 'Every annotation must be attributed to a source, which may be a literature reference, another database or a computational analysis. The annotation must indicate what kind of evidence is found in the cited source to support the association between the gene product and the GO term. A simple controlled vocabulary is used to record evidence; and the evidence codes are simply the three-letter codes used to signify the type of evidence cited. [Curator team: Exact []]' - The information in this class and its sub-classes will be migrated to evidence code properties. - http://www.geneontology.org/faq/what-evidence-code + The information in this class and its sub-classes will be migrated to evidence code properties. + http://www.geneontology.org/faq/what-evidence-code obsolete Evidence Code true - + - - + + 'Used for annotations that depend directly on computation or automated transfer of annotations from a database, particularly when the analysis is performed internally and not published. A key feature that distinguishes this evidence code from others is that it is not made by a curator; use IEA when no curator has checked the specific annotation to verify its accuracy. [Curator team: Exact []]' - http://geneontology.org/page/automatically-assigned-evidence-codes + http://geneontology.org/page/automatically-assigned-evidence-codes obsolete IEA (inferred from electronic annotation) true - + - - + + 'This should be used for information extracted from articles in the medical literature. [Curator team: []]' obsolete PCS (published clinical study) true @@ -44275,10 +43710,10 @@ Suggest this term replaces "Methemoglobinemia" below "Abnormal He - + - - + + 'Can be used for annotations based on individual clinical experience. [Curator team: []]' obsolete ICE (individual clinical experience) true @@ -44286,10 +43721,10 @@ Suggest this term replaces "Methemoglobinemia" below "Abnormal He - + - - + + 'Not described [Curator team: []]' obsolete ITM (inferred by text-mining) true @@ -44297,10 +43732,10 @@ Suggest this term replaces "Methemoglobinemia" below "Abnormal He - + - - + + 'Usually reviews or disease entries (e.g. OMIM) that only refers to the original publication. [Curator team: []]' obsolete TAS (traceable author statement) true @@ -44308,94 +43743,94 @@ Suggest this term replaces "Methemoglobinemia" below "Abnormal He - + - - + + 'used in all cases where the author makes a statement that a curator wants to capture but for which there are neither results presented nor a specific reference cited in the source used to make the annotation. [Curator team: []]' - http://www.geneontology.org/page/nas-non-traceable-author-statement + http://www.geneontology.org/page/nas-non-traceable-author-statement obsolete NAS (non-traceable author statement) true - + - - + + 'Used for those cases where an annotation is not supported by any direct evidence, but can be reasonably inferred by a curator from other annotations, for which evidence is available. [Curator team: []]' - http://www.geneontology.org/page/ic-inferred-curator + http://www.geneontology.org/page/ic-inferred-curator obsolete IC (inferred by curator) true - + - - + + Terms deprecated in the "Personal Attribute" class. from personal attribute - + - - + + A diagnostic instrument, technique, laboratory assay or test, or method of patient examination used for differential diagnosis. + Request inclusion into relevant ontology. + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology. - None Diagnostic Tool - + - - + + A research instrument consisting of a series of questions and other prompts for the purpose of gathering information from respondents to assist with differential diagnosis. - Request inclusion into relevant ontology - http://en.wikipedia.org/wiki/Questionnaire - Few but definitions not freely available + Request inclusion into relevant ontology + http://en.wikipedia.org/wiki/Questionnaire + Few but definitions not freely available Diagnostic Questionnaire Diagnostic Instrument - + - - + + Terms deprecated in the "Diagnostics" class. from diagnostics - + - - + + Terms deprecated in the "Therapeutics" class. from therapeutics - + - + When the abnormal hemoglobin, hemoglobin C (HbC), has been detected in a blood sample. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Haemoglobin C Present Haemoglobin C in Blood HbC Present @@ -44406,13 +43841,13 @@ Suggest this term replaces "Methemoglobinemia" below "Abnormal He - + - + An abnormality of the cerebral vasculature. - - Few but definitions not available + + Few but definitions not available HP:0100659 Abnormality of the Cerebral Blood Vessels Cerebrovascular Disorder @@ -44421,25 +43856,25 @@ Suggest this term replaces "Methemoglobinemia" below "Abnormal He - + - + A mutation wholly or partly responsible for causing a sickle cell disease. - SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology + Request inclusion into relevant ontology -B-Thal mutations: -- http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.2004.tb00278.x/pdf -- https://www.ncbi.nlm.nih.gov/pubmed/15153712 - None +B-Thal mutations: -- http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.2004.tb00278.x/pdf -- https://www.ncbi.nlm.nih.gov/pubmed/15153712 + None + SCDO (Jade Hotchkiss) SCD Causal Mutation - + - - + + @@ -44449,235 +43884,235 @@ B-Thal mutations: -- http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.200 - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + The glutamic acid in position 6 in the primary sequence of a beta-chain produced by the HBB gene is replaced by valine. - Request inclusion into relevant ontology - http://www.bloodjournal.org/content/bloodjournal/46/3/363.full.pdf?sso-checked=true - Negligable + Request inclusion into relevant ontology + http://www.bloodjournal.org/content/bloodjournal/46/3/363.full.pdf?sso-checked=true + Negligable Beta S Mutation E6V Glu6Val @@ -44687,76 +44122,76 @@ B-Thal mutations: -- http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.200 - + - - + + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + A mutation where the glutamic acid in position 121 in the primary sequence of a beta-chain produced by the HBB gene is replaced by lysine. This mutation is found as a single alteration in Hemoglobin O-Arab and is one of the two contributing mutations to the production of Hemoglobin S-Oman. + Request inclusion into relevant ontology + + + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - - Negligable Beta O-Arab Mutation Contributing Beta S-Oman Mutation Glu121Lys @@ -44765,69 +44200,69 @@ B-Thal mutations: -- http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.200 - + - - + + - + - + - + - + - - + + - - + + - - + + - - + + - - + + A mutation where the glutamic acid in position 6 in the primary sequence of a beta-chain produced by the HBB gene is replaced by lysine. This mutation results in the production of Hemoglobin C and confers resistance to malaria. + Request inclusion into relevant ontology + + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - Negligable Beta C mutation HbC Mutation HBB, GLU6LYS @@ -44835,53 +44270,53 @@ B-Thal mutations: -- http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.200 - + - - - + + + - + - + - - + + - - + + - - + + - - + + A mutation in the HBB gene causing substitution of glutamic acid for lysine at the 26th position of the beta-globin chain. + Request inclusion into relevant ontology + + + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - - Negligable Beta E Mutation HbE Mutation HBB, GLU26LYS @@ -44889,53 +44324,53 @@ B-Thal mutations: -- http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.200 - + - + A person's concept of self as being male and masculine or female and feminine, or ambivalent, based in part on physical characteristics, parental responses, and psychological and social pressures. It is the internal experience of gender role. - - Sufficient - SCDO:1000043 + + Sufficient + SCDO:1000043 MESH:D005783 Gender Identity - + - - + + - + - + - - + + - - + + A mutation where the aspartic acid in position 73 in the primary sequence of a beta-chain produced by the HBB gene is replaced by asparagine. This mutation is found as a single alteration in Hemoglobin Korle Bu and is one of the two contributing mutations to the production of Hemoglobin C-Harlem. + Request inclusion into relevant ontology + http://www.bloodjournal.org/content/bloodjournal/46/3/363.full.pdf?sso-checked=true + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - http://www.bloodjournal.org/content/bloodjournal/46/3/363.full.pdf?sso-checked=true - Negligable Asp73Asn D73N HBB, ASP73ASN @@ -44943,33 +44378,33 @@ B-Thal mutations: -- http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.200 - + - - + + - + - - + + - - + + A mutation where the valine in position 23 in the primary sequence of a beta-chain produced by the HBB gene is replaced by isoleucine. When compounded with the HbS mutation in the same gene, the sickling Hemoglobin S-Antilles is produced. + Request inclusion into relevant ontology + + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - Negligable Contributing Beta S-Antilles Mutation Contributing Hb S-Antilles Mutation HBB, VAL23ILE @@ -44977,92 +44412,92 @@ B-Thal mutations: -- http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.200 - + - - + + - + - - + + - - + + A mutation where the threonine in position 87 in the primary sequence of a beta-chain produced by the HBB gene is replaced by isoleucine. This mutation is found as a single alteration in Hemoglobin Quebec-Chori. Compound heterozygosity for Hb Quebec-chori and Hb S results in sickle cell disease. + Request inclusion into relevant ontology + + Witkowska, H. E., Lubin, B. H., Beuzard, Y., Baruchel, S., Esseltine, D. W., Vichinsky, E. P., Kleman, K. M., Bardakdjian-Michau, J., Pinkoski, L., Cahn, S., Roitman, E., Green, B. N., Falick, A. M., Shackleton, C. H. L. Sickle cell disease in a patient with sickle cell trait and compound heterozygosity for hemoglobin S and hemoglobin Quebec-Chori. New Eng. J. Med. 325: 1150-1154, 1991. + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - Witkowska, H. E., Lubin, B. H., Beuzard, Y., Baruchel, S., Esseltine, D. W., Vichinsky, E. P., Kleman, K. M., Bardakdjian-Michau, J., Pinkoski, L., Cahn, S., Roitman, E., Green, B. N., Falick, A. M., Shackleton, C. H. L. Sickle cell disease in a patient with sickle cell trait and compound heterozygosity for hemoglobin S and hemoglobin Quebec-Chori. New Eng. J. Med. 325: 1150-1154, 1991. - Negligable Hb Quebec-Chori Mutation HBB, THR87ILE - + - - + + - + - - + + - - + + A mutation where the leusine residue in position 6 in the primary sequence of a beta-chain produced by the HBB gene is replaced by phenylalanine. This mutation on its own produces a stable hemoglobin that does not result in hemolysis (Hb Rockford), but when in combination with the Hb S mutation (HBB, GLU6VAL), the symptomatic Hb Jamaica Plain is produced. + Request inclusion into relevant ontology + + Perrault, J., Fairbanks, V. F., McCormick, D. J., Kubik, K., Madden, B. J., Holmes, M. W., Hoyer, J. D. Hemoglobin Rockford, beta68(E12)leu-to-phe: a new HB variant associated with mild anemia. (Abstract) Blood 90 (Suppl. 1): 30b, 1997. + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - Perrault, J., Fairbanks, V. F., McCormick, D. J., Kubik, K., Madden, B. J., Holmes, M. W., Hoyer, J. D. Hemoglobin Rockford, beta68(E12)leu-to-phe: a new HB variant associated with mild anemia. (Abstract) Blood 90 (Suppl. 1): 30b, 1997. - Negligable Contributing Hb Jamaica Plain Mutation HBB, LEU68PHE - + - - + + - - + + The alleles, or variant forms of the HBB gene, that are carried by an SCD sufferer. + Probably too specific to be included in other ontologies. + +Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/topicpage/sickle-cell-anemia-a-look-at-global-8756219 -- -- Table of SCD Genotypes: -- http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.2004.tb00278.x/pdf -- -- HBB allelic variants: -- https://www.omim.org/entry/141900#0243 -- -- Perhaps have parent class Hemoglobinopathy Genotype, with Hemoglobinopathy Trait below that? + http://www.nature.com/scitable/definition/genotype-234 + None SCDO (Jade Hotchkiss) - Probably too specific to be included in other ontologies. - -Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/topicpage/sickle-cell-anemia-a-look-at-global-8756219 -- -- Table of SCD Genotypes: -- http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.2004.tb00278.x/pdf -- -- HBB allelic variants: -- https://www.omim.org/entry/141900#0243 -- -- Perhaps have parent class Hemoglobinopathy Genotype, with Hemoglobinopathy Trait below that? - http://www.nature.com/scitable/definition/genotype-234 - None Sickle Cell Disease Genotype Sickle Genotype SCD Genotype @@ -45070,45 +44505,45 @@ Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/top - + - - + + - + - - + + - - + + - - + + - - + + The genotype when an individual has the Hb C gene from one parent and the Hb S gene from the other. Individuals with Hb SC have similar symptoms to individuals with Hb SS, however, the anemia is less severe. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Haemoglobin Genotype SC SC Genotype beta6Glu>Val/beta6Glu>Lys @@ -45117,44 +44552,44 @@ Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/top - + - - + + - + - - + + - - + + - - + + - - + + Compound heterozygosity for the hemoglobin S (HBB Glu6Val) and hemoglobin D-Punjab (HBB Glu121Gln) variants. - Hemoglobin Genotype S/D-Punjab - Torres LS, Okumura JV, Silva DG, Bonini-Domingos CR. Hemoglobin D-Punjab: origin, distribution and laboratory diagnosis. Rev Bras Hematol Hemoter. 2015;37(2): 120–126. pmid:25818823 - None + Hemoglobin Genotype S/D-Punjab + Torres LS, Okumura JV, Silva DG, Bonini-Domingos CR. Hemoglobin D-Punjab: origin, distribution and laboratory diagnosis. Rev Bras Hematol Hemoter. 2015;37(2): 120–126. pmid:25818823 + None Haemoglobin Genotype S/D-Punjab S/D-Punjab Genotype beta6Glu>Val/beta121Glu>Gln @@ -45163,44 +44598,44 @@ Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/top - + - - + + - + - - + + - - + + - - + + - - + + Compound heterozygosity for the hemoglobin S (HBB Glu6Val) and hemoglobin O-Arab (HBB GluU121Lys) variants. - Request inclusion into relevant ontology - Lancet. 2010 Dec 11;376(9757):2018-31. doi: 10.1016/S0140-6736(10)61029-X. Epub 2010 Dec 3. - None + Request inclusion into relevant ontology + Lancet. 2010 Dec 11;376(9757):2018-31. doi: 10.1016/S0140-6736(10)61029-X. Epub 2010 Dec 3. + None Haemoglobin Genotype S/OArab S/O-Arab Genotype beta6Glu>Val/beta121Glu>Lys @@ -45209,44 +44644,44 @@ Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/top - + - - + + - + - - + + - - + + - - + + - - + + Compound heterozygosity for the hemoglobin S (HBB Glu6Val) and hemoglobin E (HBB Glu26Lys) variants. - Request inclusion into relevant ontology - Lancet. 2010 Dec 11;376(9757):2018-31. doi: 10.1016/S0140-6736(10)61029-X. Epub 2010 Dec 3. - None + Request inclusion into relevant ontology + Lancet. 2010 Dec 11;376(9757):2018-31. doi: 10.1016/S0140-6736(10)61029-X. Epub 2010 Dec 3. + None Haemoglobin Genotype SE SE Genotype SE Hemoglobin Genotype @@ -45256,10 +44691,10 @@ Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/top - + - - + + @@ -45268,20 +44703,20 @@ Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/top - - + + - - + + The homozygous genotype that involves a substitution of glutamic acid for a valine at position 6 of beta-globin chains produced by both beta-globin gene (HBB) alleles. + Request inclusion into relevant ontology + Few but definitions not specific enough SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - Few but definitions not specific enough Haemoglobin Genotype SS Hemoglobin S Genotype SS Genotype @@ -45291,10 +44726,10 @@ Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/top - + - - + + @@ -45303,75 +44738,75 @@ Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/top - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Compound heterozygous inheritance of Hb S and Hb D mutations. Hb S occurs from substitution of valine for glutamic acid in the beta-6 position (beta6Glu>Val). Hb D generally results from substitution of glutamic acid for glutamine at beta-121 (beta121Glu>Gln); such as the Hb D-Punjab/Hb D-Los Angeles variants. There are several other Hb D variants, including Hb D-Iband where threonine is substituted by lysine at beta-87 (beta87Thr>Lys) and Hb D-Iran where glutamic acid is substituted by glutamine at beta-22 (beta22Glu>Gln). + Request inclusion into relevant ontology + + None SCDO - Request inclusion into relevant ontology - - None Haemoglobin Genotype SD SD Genotype Hemoglobin Genotype SD @@ -45379,45 +44814,45 @@ Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/top - + - - + + - + - - + + - - + + - - + + - - + + Compound heterozygous inheritance of Hb S and Hb C-Harlem mutations. Hb S occurs from substitution of valine for glutamic acid in the beta-6 position (beta6Glu>Val). Hb C-Harlem involves two substitutions in each beta-chain: the first being identical to that found in Hb S, and the second being a substitution of aspartic acid at position 73 by asparagine (beta73Asp>Asn). + Request inclusion into relevant ontology + PMID: 1148394 + None SCDO - Request inclusion into relevant ontology - PMID: 1148394 - None Haemoglobin Genotype S/C-Harlem S/C-Harlem Genotype beta6Glu>Val/beta6Glu>Val, beta73Asp>Asn @@ -45426,27 +44861,27 @@ Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/top - + - - + + - - + + - - + + An abnormal hemoglobin in which two mutations occur in its beta-chains results in the sickling of red blood cells containing this hemoglobin. The sickling is the result of the mutation in which glutamic acid in position 6 is replaced by valine, which is not counteracted by the second mutation, in which the aspartic acid in position 73 is replaced by asparagine. + Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions". + https://www.omim.org/entry/141900#0243 + Few but definitions not freely available SCDO (Jade Hotchkiss) - Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions". - https://www.omim.org/entry/141900#0243 - Few but definitions not freely available HbS-HBC-Harlem Hemoglobin C-Georgetown Hemoglobin S-Hemoglobin C-Harlem @@ -45455,22 +44890,22 @@ Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/top - + - - + + - - + + The inheritance of the gene for hemoglobin D-Punjab from one parent and a gene for normal adult hemoglobin (hemoglobin A) from the other parent. + Request inclusion into NCIT below "Hemoglobin Trait". + + None SCDO (Jade Hotchkiss) - Request inclusion into NCIT below "Hemoglobin Trait". - - None Hb AD-Punjab Hemoglobin D-Punjab Trait causes no clinical or hematological alterations Hemoglobin D-Punjab Trait @@ -45478,98 +44913,98 @@ Paper mentioning haplotypes and severity: -- https://www.nature.com/scitable/top - + - - + + - - + + The underlying molecular makeup resulting in sickle cell disease. - SCDO (Clair Ingram) - Probably too specific to warrant inclusion into anther ontology. + Probably too specific to warrant inclusion into anther ontology. -Consider inclusion of other sub-classes of this term in the Human Phenotype Ontology. -- - Elevated hemoglobin A1c -- - Imbalanced Hemoglobin Synthesis (and the 2 terms below this) -- Methemoglobina -- Others from MESH?: -- J, M, Methemoglobin? - None +Consider inclusion of other sub-classes of this term in the Human Phenotype Ontology. -- - Elevated hemoglobin A1c -- - Imbalanced Hemoglobin Synthesis (and the 2 terms below this) -- Methemoglobina -- Others from MESH?: -- J, M, Methemoglobin? + None + SCDO (Clair Ingram) SCD Molecular Phenotype - + - - + + - - + + An altered level of normal hemoglobin (Hemoglobin A (Hb A), Hemoglobin A2 (Hb A2) or Hemoglobin F (Hb F, fetal hemoglobin) in the blood, which may be seen in those suffering with Sickle Cell Disease (SCD). + Probably too specific to SCD be included in other ontologies. + None SCDO (Jade Hotchkiss) - Probably too specific to SCD be included in other ontologies. - None Altered Level of Normal Hemoglobin in SCD - + - - - + + + - + - + - - + + - - + + - - + + - - + + - - + + A rare type of sickle cell disease with the compound heterozygous genotype involving the mutations for Hemoglobin S and Hemoglobin C-Harlem. This condition is described to have a clinical course similar to sickle cell anemia. + Request inclusion into relevant ontology + Moo-Penn, W., Bechtel, K., Jue, D., Chan, M.S., Hopkins, G., Schneider, N.J., Wright, J. and Schmidt, R.M., 1975. The presence of hemoglobin S and C Harlem in an individual in the United States. Blood, 46(3), pp.363-367. + None SCDO (Clair Ingram) - Request inclusion into relevant ontology - Moo-Penn, W., Bechtel, K., Jue, D., Chan, M.S., Hopkins, G., Schneider, N.J., Wright, J. and Schmidt, R.M., 1975. The presence of hemoglobin S and C Harlem in an individual in the United States. Blood, 46(3), pp.363-367. - None SC(Harlem) Disease Sickle Cell-Hemoglobin C-Harlem Disease Sickle Cell Disease-S/C-Harlem @@ -45577,11 +45012,11 @@ Consider inclusion of other sub-classes of this term in the Human Phenotype Onto - + - - - + + + @@ -45591,81 +45026,81 @@ Consider inclusion of other sub-classes of this term in the Human Phenotype Onto - + - - + + - - + + - - + + - + A 106-kb deletion of the beta globin gene cluster. + Request inclusion into relevant ontology + + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - Negligable HPFH1 HBB, 106-KB DEL - + - + A consent model in which participants are given a set of options allowing them to select how they want to participate in the research. - Request inclusion into the Informed Consent Ontology. - https://www.genome.gov/27559022/informed-consent-glossary/ - None + Request inclusion into the Informed Consent Ontology. + https://www.genome.gov/27559022/informed-consent-glossary/ + None Tiered Consent - + - - + + Requires that consent to the use of human samples be specific to the 'purpose' for which the sample is to be used and that where previously collected samples are to be used for a different 'research purpose' further consent should generally be obtained. + Request inclusion into the ICO below "Informed Consent". + https://www.alrc.gov.au/publications/15-human-genetic-research-and-consent/specific-consent + None SCDO - Request inclusion into the ICO below "Informed Consent". - https://www.alrc.gov.au/publications/15-human-genetic-research-and-consent/specific-consent - None Specific Consent - + - - + + The determination of the amount of hemoglobin F present in a sample. - Suggest update to label in NCIT (from "Hemoglobin F Measurement") + Suggest update to label in NCIT (from "Hemoglobin F Measurement") -Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? - - Suggest update to label +Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + + Suggest update to label NCIT:C92262 Fetal Hemoglobin Test HGBF Test @@ -45674,10 +45109,10 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + - - + + @@ -45686,32 +45121,32 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? - - + + - - + + - - + + - - + + When one beta-globin gene carries the hemoglobin S mutation (beta6Glu>Val) whereas the other carries a null mutation, called beta-zero, because of the resulting inability to synthesize any beta-globin chain. - Request inclusion into relevant ontology - - None + Request inclusion into relevant ontology + + None S/Beta-Zero-Thal Genotype S/Beta-Zero-Thalassaemia Genotype S/Beta-Zero-Thalassemia @@ -45720,13 +45155,13 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + - - + + 'Genotype where a person is a compound heterozygote for the hemoglobin S mutation and a severe beta plus thalassemia mutation. Source: CLAIR [Curator team: []]' - - Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031. + + Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031. Severe S/Beta-Plus-Thal Severe S/Beta-Plus-Thal Genotype Severe S/Beta-Plus-Thalassaemia Genotype @@ -45736,51 +45171,51 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + - - + + - + - - + + - - + + - - + + - + - - + + Genotype whereby a person is heterozygous for a hemoglobin S mutation and heterozygous for a mutation that causes persistant fetal hemoglobin production into adulthood. HPFH causative mutations are largely due to deletions in the beta-globin locus, but also by point mutations in the gamma-globin gene promoters. + Request inclusion into relevant ontology + Stamatoyannopoulos, G. (2005). Control of globin gene expression during development and erythroid differentiation. Experimental Hematology, 33(3), 259. http://doi.org/10.1016/j.exphem.2004.11.007 + None SCDO (Clair Ingram) - Request inclusion into relevant ontology - Stamatoyannopoulos, G. (2005). Control of globin gene expression during development and erythroid differentiation. Experimental Hematology, 33(3), 259. http://doi.org/10.1016/j.exphem.2004.11.007 - None Haemoglobin Genotype S/HPFH S/HPFH Genotype Hemoglobin Genotype S/HPFH @@ -45788,45 +45223,45 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + - - + + - + - - + + - - + + - - + + - - + + A compound heterozygous genotype, involving the mutations for Hemoglobin S (beta6Glu>Val) and Hemoglobin Lepore Boston. - Request inclusion into relevant ontology - PMID: 7055103 - Stevens MC, Lehmann H, Mason KP, Serjeant BE, Serjeant GR. 1982. Sickle cell Hb Lepore Boston syndrome. Uncommon differential diagnosis to homozygous sickle cell disease. Am J Dis Child. 136(1):19-22. - None + Request inclusion into relevant ontology + PMID: 7055103 + Stevens MC, Lehmann H, Mason KP, Serjeant BE, Serjeant GR. 1982. Sickle cell Hb Lepore Boston syndrome. Uncommon differential diagnosis to homozygous sickle cell disease. Am J Dis Child. 136(1):19-22. + None Haemoglobin Genotype S/Lepore S/Lepore S/Lepore Boston Genotype @@ -45836,38 +45271,38 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + - - + + - + - - + + - - + + - - + + A genotype that involves a double mutation in one beta-globin gene that results in hemoglobin with low oxygen affinity, which results in the polymerisation of the hemoglobin variant (hemoglobin Jamaica Plain) and thus sickling of erythorcytes. - Request inclusion into relevant ontology - http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf?_tid=691c25c0-5826-11e7-b704-00000aacb35e&acdnat=1498230953_4d1264c47385275daf8fc2a1e1de62e3 - None + Request inclusion into relevant ontology + http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf?_tid=691c25c0-5826-11e7-b704-00000aacb35e&acdnat=1498230953_4d1264c47385275daf8fc2a1e1de62e3 + None A/Jamaica Plain Genotype A/Jamaica Plain Haemoglobin Genotype A/Jamaica Plain Hemoglobin Genotype @@ -45877,27 +45312,27 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + - - + + - - + + - - + + A sickling hemoglobin with reduced oxygen affinity that causes severe hemolytic anemia and sickling of erythrocytes. + Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions". + http://www.nejm.org/doi/full/10.1056/NEJMoa040771#t=article + None SCDO (Jade Hotchkiss) - Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions". - http://www.nejm.org/doi/full/10.1056/NEJMoa040771#t=article - None Hb JP Hb Jamaica Plain Hemoglobin JP @@ -45906,54 +45341,54 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + - - + + - - + + - - + + A form of hemoglobin caused by two mutations in its beta-chains, the classic beta S mutation (beta 6 Glu>Val) and beta 23 Val>Ile. Hemoglobin S-Antilles has the same electrophoretic mobility as Hemoglobin S but a distinct isoelectric focus and produces sickling in the carriers of the Hb A/S Antilles trait. + Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions". + + Few but definitions not freely available SCDO (Jade Hotchkiss) - Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions". - - Few but definitions not freely available Hemoglobin S-Antilles - + - - + + - - + + - - + + A form of hemoglobin caused by two mutations in a beta-globin chain, the classic beta S mutation (beta6 Glu> Val) and a beta121 Glu > Lys mutation identical to that of Hb-O Arab. The hemoglobin variant has reduced solubility and there is an apparent increase in red cell sickling tendency. It is reported to cause a rare dominant form of sickle cell disease, Sickle Cell Disease A/S-Oman. + Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions". + + Nagel, R.L., Daar, S., Romero, J.R., Suzuka, S.M., Gravell, D., Bouhassira, E., Schwartz, R.S., Fabry, M.E. and Krishnamoorthy, R., 1998. HbS-Oman heterozygote: a new dominant sickle syndrome. Blood, 92(11), pp.4375-4382. + Negligable SCDO (Jade Hotchkiss) - Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions". - - Nagel, R.L., Daar, S., Romero, J.R., Suzuka, S.M., Gravell, D., Bouhassira, E., Schwartz, R.S., Fabry, M.E. and Krishnamoorthy, R., 1998. HbS-Oman heterozygote: a new dominant sickle syndrome. Blood, 92(11), pp.4375-4382. - Negligable Hb S-Oman Hemoglobin S (Oman) Hemoglobin S-Oman @@ -45961,39 +45396,39 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + - - + + - + - - + + - - + + - - + + Dominant heterozygosity for the double HBB Glu6Val and Glu121Lys mutation. - Request inclusion into relevant ontology - - PMID: 9834244 - None + Request inclusion into relevant ontology + + PMID: 9834244 + None A/S-Oman Genotype A/S-Oman Haemoglobin Genotype A/S-Oman Hemoglobin Genotype @@ -46003,28 +45438,28 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + - - + + - - + + - - + + A form of sickle cell thalassemia, with a mild clinical phenotype, characterized by the presence of hemoglobin S and a small amount of hemoglobin A in the red blood cells. + Request inclusion into relevant ontology + + Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031. + None SCDO (Clair Ingram) - Request inclusion into relevant ontology - - Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031. - None Mild Sickle Cell Disease-S Beta Minus Thalassaemia Mild Sickle Cell-Beta Minus Thalassaemia Mild Sickle Cell-Beta Minus Thalassemia @@ -46033,40 +45468,40 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + - - + + - - + + - - + + - - + + - - + + A form of sickle cell thalassemia, with a moderate clinical phenotype, characterized by the presence of hemoglobin S and a small amount of hemoglobin A in the red blood cells. + Request inclusion into relevant ontology + + Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031. + None SCDO (Clair Ingram) - Request inclusion into relevant ontology - - Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031. - None Moderate Sickle Cell Disease-S Beta Minus Thalassaemia Moderate Sickle Cell-Beta Minus Thalassaemia Moderate Sickle Cell-Beta Minus Thalassemia @@ -46075,40 +45510,40 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + - - + + - - + + - - + + - - + + - - + + A form of sickle cell thalassemia, with a severe clinical phenotype, characterized by the presence of hemoglobin S and a small amount of hemoglobin A in the red blood cells. + Request inclusion into relevant ontology + + Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031. + None SCDO (Clair Ingram) - Request inclusion into relevant ontology - - Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031. - None Severe Sickle Cell Disease-S Beta Minus Thalassaemia Severe Sickle Cell-Beta Minus Thalassaemia Severe Sickle Cell-Beta Minus Thalassemia @@ -46117,13 +45552,13 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + - - + + 'Genotype where a person is a compound heterozygote for the hemoglobin S mutation and a moderate beta plus thalassemia mutation. Source: CLAIR [Curator team: []]' - - Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031. + + Rees, D.C., Williams, T.N. and Gladwin, M.T., 2010. Sickle-cell disease. The Lancet, 376(9757), pp.2018-2031. Moderate S/Beta-Plus-Thalassaemia deprecated Moderate S/Beta-Plus-Thal true @@ -46131,12 +45566,12 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + - - + + 'Not described [Curator team: []]' - + Mild S/Beta-Plus-Thalassaemia deprecated Mild S/Beta-Plus-Thal true @@ -46144,51 +45579,51 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + - - + + - + - - + + - - + + - - + + - - + + - - + + Compound heterozygosity for the hemoglobin C (HBB Glu6Lys) mutation and the double HBB Glu6Val, Val23Ile mutation of hemoglobin S-Antilles. - Request inclusion into relevant ontology - DOI: 10.1016/S0140-6736(10)61029-X - PMID: 21131035 - None + Request inclusion into relevant ontology + DOI: 10.1016/S0140-6736(10)61029-X + PMID: 21131035 + None C/S Antilles Genotype C/S Antilles Haemoglobin Genotype C/S Antilles Hemoglobin Genotype @@ -46199,88 +45634,88 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + - - - + + + A hemoglobin that sickles due to the presence of two beta-globin gene mutations within the same HBB gene. + Request inclusion into the HPO, below "Abnormal Hemoglobin". + None - Request inclusion into the HPO, below "Abnormal Hemoglobin". - None Doubly Substituted Sickling Hemoglobin Sickling Hemoglobin with Two Beta-Globin Gene Substitutions - + - - + + - - + + - - + + An abnormal hemoglobin in which two mutations occurring in its beta-chains results in the sickling of red blood cells containing this hemoglobin. The sickling is the result of the mutation in which glutamic acid in position 6 is replaced by valine, which is not counteracted by the second mutation, in which the lysine in position 132 is replaced by asparagine. + Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions". + Luo, H.Y., Adewoye, A.H., Eung, S.H., Skelton, T.P., Quillen, K., McMahon, L., Steinberg, M.H. and Chui, D.H., 2004. A novel sickle hemoglobin: Hemoglobin S-South End. Journal of pediatric hematology/oncology, 26(11), pp.773-776. + Negligable SCDO (Jade Hotchkiss) - Request inclusion into the HPO, below "Abnormal Hemoglobin"/"Sickling Hemoglobin with Two Beta-Globin Gene Substitutions". - Luo, H.Y., Adewoye, A.H., Eung, S.H., Skelton, T.P., Quillen, K., McMahon, L., Steinberg, M.H. and Chui, D.H., 2004. A novel sickle hemoglobin: Hemoglobin S-South End. Journal of pediatric hematology/oncology, 26(11), pp.773-776. - Negligable Hemoglobin S-South End - + - - + + - + - - + + - - + + - - + + - - + + A compound heterozygous genotype, involving the mutations for Hemoglobin S and Hemoglobin Quebec Chori, which shows an electrophoretic pattern similar to that of the Hb A/S Genotype, but shows sickling. + Request inclusion into relevant ontology + Pediatr Blood Cancer. 2007 Aug;49(2):207-10. + None SCDO - Request inclusion into relevant ontology - Pediatr Blood Cancer. 2007 Aug;49(2):207-10. - None Haemoglobin Genotype S/Quebec-Chori S/Quebec-Chori Genotype beta6Glu>Val/beta87Thr>Ile @@ -46289,25 +45724,25 @@ Add sub-classes of "Fetal hemoglobin determination" in SNOMED CT? + - - - + + + - - + + An abnormal hemoglobin in which a threonine is replaced by an isoleucine residue at the eighty-seventh position of beta chains. It migrates like HbA but promotes sickling. + Suggest update to description in MESH (the term in MESH doesn't currently have a description). +Also request inclusion in the HPO, below "Abnormal Hemoglobin", for the sake of completion. + + Witkowska, H.E., Lubin, B.H., Beuzard, Y., Baruchel, S., Esseltine, D.W., Vichinsky, E.P. et al. Sickle cell disease in a patient with sickle cell trait and compound heterozygosity for hemoglobin S and hemoglobin Quebec-Chori. N Engl J Med. 1991; 325: 1150–1154 + Suggest update to description http://ac.els-cdn.com/S014067361061029X/1-s2.0-S014067361061029X-main.pdf?_tid=691c25c0-5826-11e7-b704-00000aacb35e&acdnat=1498230953_4d1264c47385275daf8fc2a1e1de62e3 - Suggest update to description in MESH (the term in MESH doesn't currently have a description). -Also request inclusion in the HPO, below "Abnormal Hemoglobin", for the sake of completion. - - Witkowska, H.E., Lubin, B.H., Beuzard, Y., Baruchel, S., Esseltine, D.W., Vichinsky, E.P. et al. Sickle cell disease in a patient with sickle cell trait and compound heterozygosity for hemoglobin S and hemoglobin Quebec-Chori. N Engl J Med. 1991; 325: 1150–1154 - Suggest update to description MESH:C070823 Hb Quebec-Chori Hemoglobin Quebec Chori @@ -46315,96 +45750,96 @@ Also request inclusion in the HPO, below "Abnormal Hemoglobin", for th - + - - + + - + - + - - + + - - + + - - + + - - + + - - + + - - + + A severe compound heterozygous sickling disorder characterized by the presence of both hemoglobin S and hemoglobin Quebec Chori. + Request inclusion into relevant ontology + + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - None Sickle Cell-Hemoglobin Quebec Chori Disease Sickle Cell Disease-S/Quebec Chori - + - - + + - + - - + + - - + + A mutation where the lysine residue in position 132 in the primary sequence of a beta-chain produced by the HBB gene is replaced by asparagine. This mutation on its own produces Hb Yamagata which has reduced oxygen affinity, but no distinctive clinical abnormalities. However, when present in the same gene as the Hb S mutation (HBB, GLU6VAL), the sickling HbS-South End is produced. + Request inclusion into relevant ontology + + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - Negligable Contributing Beta S-South End Mutation Contributing Hb S-South End Mutation Hb Yamagata Mutation @@ -46414,44 +45849,44 @@ Also request inclusion in the HPO, below "Abnormal Hemoglobin", for th - + - - + + - + - - + + - - + + - - + + - - + + A compound heterozygous genotype, involving the mutations for hemoglobin S and hemoglobin S-South End. - Request inclusion into relevant ontology - - None + Request inclusion into relevant ontology + + None Haemoglobin Genotype S/S-South End S/S-South End Genotype beta Glu6Val, GAG>GTG/beta Glu6Val, GAG>GTG; beta Lys132Asn, AAA>AAC @@ -46461,22 +45896,22 @@ Also request inclusion in the HPO, below "Abnormal Hemoglobin", for th - + - - - + + + The most common Hemoglobin Lepore type and the only type of the three known variants described in association with HbS. This abnormal hemoglobin consists of two normal alpha globin chains (HBA) and two deltabeta globin fusion chains which occur due to a crossover between the delta (HBD) and beta globin (HBB) gene loci during meiosis. - Suggest inclusion in the HPO, below "Abnormal Hemoglobin". + Suggest inclusion in the HPO, below "Abnormal Hemoglobin". Hb Lepore is produced at a reduced rate and this is why the disease is related to the Β-thalassemic syndromes. Quantity in heterozygotes 7-13%; found in combination with Hb S, Hb C, beta+-thal, and in the homozygous state. -The most common Hb Lepore type; found mainly in Italian families; it has also been observed in families from Rumania, Yugoslavia, Turkey, Cyprus, Jamaica, Cuba, Greece, England, Australia, Mexico, etc - http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome#Homozygous_Hb_Lepore - http://globin.cse.psu.edu/html/huisman/variants/hybrid/Lepore-Boston-Washington.html - Few but definitions not freely available +The most common Hb Lepore type; found mainly in Italian families; it has also been observed in families from Rumania, Yugoslavia, Turkey, Cyprus, Jamaica, Cuba, Greece, England, Australia, Mexico, etc + http://en.wikipedia.org/wiki/Hemoglobin_Lepore_syndrome#Homozygous_Hb_Lepore + http://globin.cse.psu.edu/html/huisman/variants/hybrid/Lepore-Boston-Washington.html + Few but definitions not freely available Hb Lepore Boston-Washington Hb Lepore-B-W Hb Lepore-Boston-Washington @@ -46489,96 +45924,96 @@ The most common Hb Lepore type; found mainly in Italian families; it has also be - + - - - + + + - + - - + + - - + + - - + + - - + + - - + + - + - - + + - - + + A rare, reported severe, type of sickle cell disease with the compound heterozygous genotype involving the mutations for Hemoglobin S and Hemoglobin S-South End. + Request inclusion into relevant ontology + Luo, H.Y., Adewoye, A.H., Eung, S.H., Skelton, T.P., Quillen, K., McMahon, L., Steinberg, M.H. and Chui, D.H., 2004. A novel sickle hemoglobin: Hemoglobin S-South End. Journal of pediatric hematology/oncology, 26(11), pp.773-776. + None SCDO (Clair Ingram) - Request inclusion into relevant ontology - Luo, H.Y., Adewoye, A.H., Eung, S.H., Skelton, T.P., Quillen, K., McMahon, L., Steinberg, M.H. and Chui, D.H., 2004. A novel sickle hemoglobin: Hemoglobin S-South End. Journal of pediatric hematology/oncology, 26(11), pp.773-776. - None Sickle Cell-Hemoglobin S-South End Disease Sickle Cell Disease-S/S-South End - + - - + + 'Sb+ thalassemia is an inherited condition. Hemoglobin S comes from one parent and Beta plus thalassemia comes from the other parent. Instead of appearing round (like donuts), red blood cells are somewhat small, pale and misshapen. [Curator team: []]' - + deprecated Sickle beta plus thalassemia true - + - - + + A primary headache disorder that is characterized by severe, strictly unilateral PAIN which is orbital, supraorbital, temporal or in any combination of these sites, lasting 15-180 min. occurring 1 to 8 times a day. The attacks are associated with one or more of the following, all of which are ipsilateral: conjunctival injection, lacrimation, nasal congestion, rhinorrhea, facial SWEATING, eyelid EDEMA, and miosis. - - Ask a clinician if this is different to a cluster headache? - https://meshb.nlm.nih.gov/record/ui?ui=D003027 + + Ask a clinician if this is different to a cluster headache? + https://meshb.nlm.nih.gov/record/ui?ui=D003027 MESH:D003027 deprecated-Acute Severe Headache true @@ -46586,14 +46021,14 @@ The most common Hb Lepore type; found mainly in Italian families; it has also be - + - - + + A medically undesirable event occurring in a research subject, such as an abnormal sign, symptom, worsening of a disease, injury, etc. A serious adverse event (SAE) results in death, hospitalization (or increased hospital stay), persistent disability, birth defect, or any other outcome that seriously jeopardizes the subject's health. - - Sufficient - SCDO:1000093 + + Sufficient + SCDO:1000093 OAE:0000001 Adverse Reaction Adverse Event (AE) @@ -46601,28 +46036,28 @@ The most common Hb Lepore type; found mainly in Italian families; it has also be - + - - + + A desirable research outcome or state of affairs, such as medical treatment, clinically useful information, or self-esteem. In the oversight of human subjects research, money is usually not treated as a benefit. + Request inclusion into relevant ontology + Shamoo AE and Resnik DB, Responsible Conduct of Research, 3rd ed. (New York: Oxford University Press, 2015). + None SCDO - Request inclusion into relevant ontology - Shamoo AE and Resnik DB, Responsible Conduct of Research, 3rd ed. (New York: Oxford University Press, 2015). - None Research Benefit - + - - - + + + A situation in which an individual or their close associates might benefit personally from official or professional actions. It includes a conflict between a person's private interests and official responsibilities in a position of trust.The concept refers both to actual conflict of interest and the appearance or perception of conflict. - http://purl.bioontology.org/ontology/MESH/D016265 - Few but definitions not specific enough + http://purl.bioontology.org/ontology/MESH/D016265 + Few but definitions not specific enough MESH:D016265 Interest Conflict Conflict of Interest @@ -46630,42 +46065,42 @@ The most common Hb Lepore type; found mainly in Italian families; it has also be - + - - + + An homo sapiens that bears an experimental subject role which is realized through his/her participation in a scientific technique as the subject of interest (ie as the subject about which data is generated in an assay or study, or the entity that is transformed or modified in a material processing technique). - - Sufficient - SCDO:1000097 + + Sufficient + SCDO:1000097 ERO:0001964 Human Subject - + - - + + A paper or electronic questionnaire specifically used in research by the sponsor of the research to collect data from each research participant. All data on each participant in the study are held and/or documented in the CRF, including adverse events. + Request inclusion into relevant ontology, perhaps as parent of "electronic case report form" in the Ontology for Biomedical Investigations (OBI) + Debbie Kennedy, CRF Designer, Canary Publications, ISBN 0-9531174-7-2 + None SCDO - Request inclusion into relevant ontology, perhaps as parent of "electronic case report form" in the Ontology for Biomedical Investigations (OBI) - Debbie Kennedy, CRF Designer, Canary Publications, ISBN 0-9531174-7-2 - None Case Report Form (CRF) - + - - + + Genes with alleles that affect the phenotype associated with a nonallelic gene. - - Sufficient - SCDO:1000099 + + Sufficient + SCDO:1000099 MESH:D060045 Gene, Modifier Modifier Gene @@ -46673,26 +46108,26 @@ The most common Hb Lepore type; found mainly in Italian families; it has also be - + - - + + The type of ICD-10-CM code, in terms of a code's usability for reimbursement purposes. + None SCDO (Jade Hotchkiss) - None ICD-10-CM Code Type - + - - + + A specific region that is mapped within a genome. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or hereditary disease. - - Sufficient - SCDO:1000103 + + Sufficient + SCDO:1000103 MESH:D056426 Genetic Loci Loci, Genetic @@ -46702,29 +46137,29 @@ The most common Hb Lepore type; found mainly in Italian families; it has also be - + - + The protein subunits that comprise multimeric hemoglobins. - - Sufficient - SCDO:1000104 + + Sufficient + SCDO:1000104 MESH:D055554 Hemoglobin Subunits - + - - - + + + Members of the alpha-globin family. In humans, they are encoded in a gene cluster on chromosome 16. They include hemoglobin subunit zeta and hemoglobin subunit alpha. There are also pseudogenes of zeta (theta-zeta) and alpha (theta-alpha) in the cluster. Adult hemoglobin is comprised of 2 alpha-globin chains and 2 beta-globin chains. - - Sufficient - SCDO:1000105 + + Sufficient + SCDO:1000105 MESH:D055542 Alpha-Globins Alpha-Globin Family Members @@ -46732,40 +46167,40 @@ The most common Hb Lepore type; found mainly in Italian families; it has also be - + - - + + - - + + - - + + - - + + Sickle cell disease (SCD) is a pleiotropic inherited disorder of the blood, characterised by the appearance of sickle-shaped red blood cells and anemia. It results from homozygosity for the sickle beta-globin gene mutation at position 6 (glu > val), or compound heterozygosity for the sickle gene and either another mutation for a different hemoglobin variant or one of numerous beta-thalassemia mutations. - - Suggest update to description in NCIT. + Suggest update to description in NCIT. Sickle cell diseases include inheritance of the gene for sickle hemoglobin from one parent and one of the following: A gene for sickle hemoglobin from the other parent (Hb SS), A gene for another abnormal hemoglobin from the other parent (Hb SC, HbSD Punjab, HbSO Arab, HbS Leopore, or Hb SE), -A gene that limits hemoglobin production from the other parent (sickle beta +/0 thalassemia). In S beta (+) thalassemia there is some production of beta globin, and in S beta (0) thalassemia there is no production of beta globin. - - - Few but definitions not specific enough +A gene that limits hemoglobin production from the other parent (sickle beta +/0 thalassemia). In S beta (+) thalassemia there is some production of beta globin, and in S beta (0) thalassemia there is no production of beta globin. + + + Few but definitions not specific enough + Banana Cell Disease Drepanocytosis SCD @@ -46778,10 +46213,10 @@ A gene that limits hemoglobin production from the other parent (sickle beta +/0 - + - - + + @@ -46790,32 +46225,32 @@ A gene that limits hemoglobin production from the other parent (sickle beta +/0 - - + + - - + + - - + + - - + + The combination of the hemoglobin S mutation (beta6Glu>Val) and a beta-thalassemia mutation. - Request inclusion into relevant ontology - - None + Request inclusion into relevant ontology + + None Hemoglobin Genotype S/Beta Thalassaemia S/Beta -Thal Genotype S/Beta -Thalassaemia Genotype @@ -46824,98 +46259,98 @@ A gene that limits hemoglobin production from the other parent (sickle beta +/0 - + - - + + - - + + - - + + - - + + - - + + A mutation where the serine in position 9 in the primary sequence of a beta-chain produced by the HBB gene is replaced by tyrosine. This mutation is one of 2 amino acid substitutions in the same beta chain that produces the asymptomatic Hemoglobin D-Agri, the other mutation being HBB, GLU121GLN, which on its own produces Hemoglobin D-Punjab. + Request inclusion into relevant ontology + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - Negligable Beta D-Agri Mutation HBB, SER9TYR - + - - - + + + - + - + - - + + - - + + - - + + - - + + - - + + A mutation where the glutamic acid in position 121 in the primary sequence of a beta-chain produced by the HBB gene is replaced by glutamine. + Request inclusion into relevant ontology + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - Negligable Beta 121Glu>Gln Beta D-Punjab Mutation Derived from a point mutation in the beta-globin gene (HBB: c.364G>C; rs33946267). @@ -46924,387 +46359,387 @@ A gene that limits hemoglobin production from the other parent (sickle beta +/0 - + - - + + - - + + - - + + - - + + - - + + A mutation where the glycine in position 16 in the primary sequence of a beta-chain produced by the HBB gene is replaced by arginine. + Request inclusion into relevant ontology + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - Negligable Beta D-Bushman Mutation HBB, GLY16ARG - + - - + + - - + + - - + + - - + + - - + + A mutation where the asparargine acid in position 19 in the primary sequence of a beta-chain produced by the HBB gene is replaced by lysine. + Request inclusion into relevant ontology + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - Negligable Beta D-Ouled Rabah Mutation HBB, ASN19LYS - + - - + + - - + + - - + + - - + + - - + + A mutation where the glutamic acid in position 22 in the primary sequence of a beta-chain produced by the HBB gene is replaced by glutamine. + Request inclusion into relevant ontology + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - Negligable Beta D-Iran Mutation HBB, GLU22GLN - + - - + + - - + + - - + + - - + + - - + + A mutation where the glutamic acid in position 22 in the primary sequence of a beta-chain produced by the HBB gene is replaced by valine. + Request inclusion into relevant ontology + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - Negligable Beta D-Granada Mutation HBB, GLU22VAL - + - - + + - - + + - - + + - - + + - - + + A mutation where the threonine in position 87 in the primary sequence of a beta-chain produced by the HBB gene is replaced by lysine. + Request inclusion into relevant ontology + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - Negligable Beta D-Ibadan Mutation HBB, THR87LYS - + - - + + - - + + - - + + - - + + - - + + A mutation where the glutamic acid in position 121 in the primary sequence of a beta-chain produced by the HBB gene is replaced by alanine. + Request inclusion into relevant ontology + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - Negligable Beta D-Neath Mutation HBB, GLU121ALA - + - + The Adja ethnic group are mostly farmers and live in the southern part of Benin Republic. They make up 15% of the general country population. This group of people migrated into Benin between the 12th and 13th centuries from River Mono. The primary language is Aja-Gbe with a majority of the people being trilingual. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + Negigable Demographic and Health Surveys Program (2011-2012) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - Negigable Adja Ethnic Group Adja - + - + Bariba is the ethnic group dominating the northern side of Benin, who constitute 9% of the population. They are the first inhabitants of Benin and are concentrated in the capital city, Nikki. One of their leading practices is horse riding, which is a practice that has been enjoyed from generation to generation. With agriculture being their dominant occupation, Bariba people have a diverse range of produce such as corn, rice and palm oil. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + Negligable Demographic and Health Surveys Program (2011-2012) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - Negligable Bariba Ethnic Group Bariba - + - + - Negligable + Negligable Dendi Ethnic Group Dendi - + - + The largest ethnic group in Benin is Fon/Dahomey which constitutes 39% of the total population. Established in 1600 by the Fon, a group that came about through the intermarriage between the Adja and local Gedevi. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + None Demographic and Health Surveys Program (2011-2012) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - None Fon Ethnic Group Fon - + - + - None + None Yoa Ethnic Group Yoa - + - + - None + None Betamaribe Ethnic Group Betamaribe - + - + The Embu are a Bantu-speaking people who are closely related to the Gikuyu of Ndia and Gicugu to the west, the Mbeere and the Kamba to the southeast, and the Chuka and the Meru to the north in Kenya. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + Negligable Demographic and Health Surveys Program (2015) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - Negligable Embu Ethnic Group Embu - + - + The Kalenjin ethnic group are one of the five largest ethnic groups in Kenya. They are a Nilotic ethnic group and they are mainly farmers. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + None Demographic and Health Surveys Program (2015) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - None Kalenjin Ethnic Group Kalenjin - + - + The Kamba ethnic group, also known as Akamba is one of the five largest ethnic groups in Kenya. They are Bantu-speaking people and primarily agriculturists. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + None Demographic and Health Surveys Program (2015) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - None Kamba Ethnic Group Kamba - + - + The Kikuyu are the largest single ethnic tribe in Kenya, making up 22% of the country's population. It is believed that the Kikuyu people migrated from Lake Chad to East Africa in 1000 AD, settling in the fertile central highlands of Kenya and engaging in farming. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + Few but definitions not freely available Demographic and Health Surveys Program (2015) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - Few but definitions not freely available Kikuyu Ethnic Group Kikuyu - + - + The Kisii tribe (also known as the Gusii tribe) is a Bantu ethnic group who occupy the Kisii highlands in Nyanza, Western Kenya. The Kisiis constitute the sixth largest ethnic group, comprising about seven percent of the national population. Kisii, which is their ethnic language, is also traditionally known as Ekegusii. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + Few but definitions not specific enough Demographic and Health Surveys Program (2015) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - Few but definitions not specific enough Gusii Kisii Ethnic Group Kisii @@ -47312,101 +46747,101 @@ A gene that limits hemoglobin production from the other parent (sickle beta +/0 - + - + The Luhya ethnic group, also known as the Abaluhya, Baluhya, or Abaluyia, is a Bantu tribe living in Kenya's agriculturally fertile western region. They are the second largest tribe in Kenya and neighbors to some of the Nilotic tribes, including the Luo, Kalenjin, Maasai and Teso (Iteso). + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + None Demographic and Health Surveys Program (2015) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - None Luhya Ethnic Group Luhya - + - + Luo, also called Joluo or Kavirondo constitute the fourth largest ethnic group in Kenya. The Luo speak a Nilotic language of the Nilo-Saharan language family. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + Few but definitions not freely available Demographic and Health Surveys Program (2015) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - Few but definitions not freely available Luo Ethnic Group Luo - + - + A smaller ethnic group, accounting for only about 0.7 percent of Kenya's population, with a similar number living in Tanzania. Maasais speak Maa, a Nilotic ethnic language from their origin in the Nile region of North Africa. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + None Demographic and Health Surveys Program (2015) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - None Maasai Ethnic Group Maasai - + - + - None + None Peulh Ethnic Group Peulh - + - + Yoruba is an ethnic group coming from Nigeria and well settled along the eastern boundary of Benin. They are more than 18% of the population. The majority of the Yoruba people in Benin are descendants of the Ife tribe, and the Yoruba people are predominantly of the Muslim religion. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + Few but definitions not specific enough Demographic and Health Surveys Program (2011-2012) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - Few but definitions not specific enough Yoruba Ethnic Group Yoruba - + - + The Meru tribe or Merus is a Bantu ethnic group. They reside on Mount Kenya's agriculturally rich northeastern slopes, in Kenya's Eastern Province. The name Meru refers to both the people and the location. Merus are primarily agrarian, raising a few domestic animals. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + Not relevant to context of sickle cell Demographic and Health Surveys Program (2015) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - Not relevant to context of sickle cell Meru Ethnic Group Meru - + - + The Mijikenda tribe is a Kenyan coastal Bantu tribe that consists of nine closely related sub-tribes. "Mijikenda" literally means nine homes or nine homesteads (in Swahili), referring to the common ancestry of the Mijikenda people. The nine Mijikenda sub-tribes are believed to be nine different homes of the same tribe. Each sub-tribe speaks its own dialect of the Mijikenda language. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + Negligable Demographic and Health Surveys Program (2015) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - Negligable Mijikenda Mijikenda Ethnic Group Mijikenda/Swahili @@ -47414,32 +46849,32 @@ A gene that limits hemoglobin production from the other parent (sickle beta +/0 - + - + A Cushitic speaking people comprising a small minority of Kenya's population. The Somali tend large herds of cattle, goats, sheep, and camels in the dry, arid lands of Northern Kenya. They are politically well organized and are united by both family allegiances and political treaties. The Somali also produce exquisitely carved headrests and woven artifacts. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + Few but definitions not freely available Demographic and Health Surveys Program (2015) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - Few but definitions not freely available Somali Ethnic Group Somali - + - + The Taita people are a Bantu tribe living in the Taita Hills on Kenya's southwest, near the Tanzania border and surrounding plains. Taita tribe actually consists of three separate but closely-related tribes: Wadawida (or Taita), Wasaghala (Sagalla) and Wataveta (Taveta). - Demographic Health and Surveys Program (2015) - Perhaps change label to "Taveta"? + Perhaps change label to "Taveta"? Include the Wadawida (or Taita), Wasaghala (Sagalla) and Wataveta (Taveta) as sub-classes? -Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - Negligable +Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + Negligable + Demographic Health and Surveys Program (2015) Taita/Taveta Ethnic Group Taveta Ethnic Group Taita/Taveta @@ -47447,89 +46882,89 @@ Request inclusion into relevant ontology, possibly below "Ethnic Group" - + - + The Borana are a branch of the populous Oromo people found in southern Ethiopia and northern Kenya. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + Negligable Demographic and Health Surveys Program (2015) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - Negligable Borana Ethnic Group Borana - + - + It is the second largest sub-tribe of the Luhya ethnic group in Kenya. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + None Demographic and Health Surveys Program (2015) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - None Maragoli Ethnic Group Maragoli - + - + The Pokot are a Kalenjin-speaking people whose language incorporates words from the neighboring Karamojong and Turkana. The Pokot live in an ecologically complex region that extends from the plains of eastern Uganda across the highlands of northwestern Kenya to the plains of Lake Baringo. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + None Demographic Health and Surveys Program (2015) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - None Pokot Ethnic Group Pokot - + - + The Turkana tribe is a nomadic pastoralist people that inhabit the Turkana district in Kenya's Rift Valley Province. Turkana tribe is part of the Nilotic tribes and constitutes the second largest pastoralist community in Kenya after the Maasais. They speak the Turkana language, which is Nilotic and similar to the Maasai language. + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + None Demographic and Health Surveys Program (2015) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - None Turkana Ethnic Group Turkana - + - + Bassa is a Niger-Congo Kru language. Historians have traced the Bassa's origins back to Egypt nearly six thousand years ago. Due to their migration from Egypt to other parts of Africa, the Bassa in Liberia share a similar history with Bassa groups in other parts of the continent such as Nigeria (Bassa Nge), The Democratic Republic of the Congo (Bassaa la Mpasu), Togo (Basa'r), Senegal (Bassa-Ri), and Cameroon (Basaa Mpoo). + Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? + + Negligable Demographic and Health Surveys Program (2013) - Request inclusion into relevant ontology, possibly below "Ethnic Group" in NCIT? - - Negligable Bassa Ethnic Group Bassa - + - - + + Spectrophotometry involves the use of a spectrophotometer to measure the amount of light that a sample absorbs. The instrument operates by passing a beam of light through a sample and measuring the intensity of light reaching a detector. - - Sufficient - SCDO:1000142 + + Sufficient + SCDO:1000142 BAO:0000049 Spectrophotometry Method Spectrophotometry @@ -47537,15 +46972,15 @@ Request inclusion into relevant ontology, possibly below "Ethnic Group" - + - - + + A recommendation on the appropriate treatment and care of people with a specific disease or condition, based on the best available evidence, designed to help healthcare professionals in their work. + + Sufficient + SCDO:1000143 SCDO (Jade Hotchkiss) - - Sufficient - SCDO:1000143 FaBiO:d4e2515 Clinical Guideline Disease Management Guideline @@ -47553,170 +46988,170 @@ Request inclusion into relevant ontology, possibly below "Ethnic Group" - + - - + + Management protocols for the purposes of consistency and standardisation, which could also facilitate sharing of resources between centers for maximal utility. These recommendations have been developed for the South African setting, and it is intended to update them regularly to meet new demands and challenges. - Probably not necessary to include in other ontologies. - N A Alli, M Patel, H D Alli, et al. Recommendations for the management of sickle cell disease in South Africa. SAMJ. 2014, Vol. 104, No. 11. - None + Probably not necessary to include in other ontologies. + N A Alli, M Patel, H D Alli, et al. Recommendations for the management of sickle cell disease in South Africa. SAMJ. 2014, Vol. 104, No. 11. + None South African Management Guidelines Recommendations for the Management of Sickle Cell Disease in South Africa - + - - + + Guidelines for the management of specific clinical problems and protocols for various therapeutic procedures for patients with sickle cell disease and thalassaemia; to facilitate uniformity and standardization of care across different disciplines. - Probably not necessary to include in other ontologies. - National guideline for the control and management of sickle cell disease. 2014. - None + Probably not necessary to include in other ontologies. + National guideline for the control and management of sickle cell disease. 2014. + None A Nigerian document. National Guideline for the Control and Management of Sickle Cell Disease - + - - + + Guidelines for health care professionals for management of sickle cell disease in patients in the Tanzanian context. + Probably not necessary to include in other ontologies. + Management of Sickle Cell Disease - The United Republic of Tanzania + None SCDO (Jade Hotchkiss) - Probably not necessary to include in other ontologies. - Management of Sickle Cell Disease - The United Republic of Tanzania - None Tanzania Management Guidelines Management of Sickle Cell Disease - The United Republic of Tanzania - + - - + + A booklet with information and standard guidelines to help parents learn about sickle cell disease and how to take care of their children with sickle cell disease. - Probably not necessary to include in other ontologies. - A parent's guide to managing sickle cell disease. Brent Sickle Cell and Thalassaemia Centre. 3rd Edition 2012. - None + Probably not necessary to include in other ontologies. + A parent's guide to managing sickle cell disease. Brent Sickle Cell and Thalassaemia Centre. 3rd Edition 2012. + None A UK document.(for parents) A Parental Guide to Managing Sickle Cell Disease - + - - + + A document that includes standards and guidelines for clinical care and recommendations for how care for adults with sickle cell disease should be delivered. - Probably not necessary to include in other ontologies. - Standards for Clinical Care of Adults with Sickle Cell Disease in the UK, 2nd Edition. 2018, Sickle Cell Society. - None + Probably not necessary to include in other ontologies. + Standards for Clinical Care of Adults with Sickle Cell Disease in the UK, 2nd Edition. 2018, Sickle Cell Society. + None A UK document (for adults with SCD) Standards for Clinical Care of Adults with Sickle Cell Disease in the UK - + - - + + The second edition of the Clinical Care Guidelines of the Sickle Cell Unit, containing revised and expanded guidelines for the management of sickle cell disease. It outlines a standard of care that is informed by best practice, taking into account resource limitations locally and regionally. It also contains patient information leaflets. + Probably not necessary to include in other ontologies. + Sickle Cell Disease: The Clinical Care Guidelines of the Sickle Cell Unit, 2015 + None SCDO (Jade Hotchkiss) - Probably not necessary to include in other ontologies. - Sickle Cell Disease: The Clinical Care Guidelines of the Sickle Cell Unit, 2015 - None Jamaican Management Guidelines Sickle Cell Disease: The Clinical Care Guidelines of the Sickle Cell Unit - + - - + + Standard of care guidelines that promote excellence in sickle cell care, and that lead to improved patient experiences around care and treatment. - Probably not necessary to include in other ontologies. - Segbefia C, Pendergrast J, Amid A, et al. 2015. Consensus Statement on the Care of Patients with Sickle Cell Disease in Canada. The Canadian Haemoglobinopathy Association. - None + Probably not necessary to include in other ontologies. + Segbefia C, Pendergrast J, Amid A, et al. 2015. Consensus Statement on the Care of Patients with Sickle Cell Disease in Canada. The Canadian Haemoglobinopathy Association. + None A Canadian document. Consensus Statement on the Care of Patients with Sickle Cell Disease in Canada - + - - + + A document that include standards and guidelines for clinical care and recommendations for how care for children with sickle cell disease should be delivered. - Probably not necessary to include in other ontologies. - Sickle cell disease in children, standards and guidelines for clinic care. 2nd edition. October 2010 - None + Probably not necessary to include in other ontologies. + Sickle cell disease in children, standards and guidelines for clinic care. 2nd edition. October 2010 + None A UK document (for children with SCD) Sickle Cell Disease in Children, Standards and Guidelines for Clinic Care - + - - + + Guidelines providing the best science-based recommendations to guide practice decisions for primary care providers and other clinicians, nurses, and staff who provide emergency or continuity care to individuals with sickle cell disease (SCD). They assist health care professionals in the management of common issues, including routine health maintenance, the recognition and treatment of common acute and chronic complications and comorbidities of SCD, as well as the indications for and monitoring of hydroxyurea and blood transfusion therapy. The guidelines address the care of infants, children, adolescents, and adults with SCD, with the goal of facilitating high-quality and appropriate care for all individuals with this disease. - Probably not necessary to include in other ontologies. - Evidence-Based Management of Sickle Cell Disease: Expert Panel Report, 2014 - None + Probably not necessary to include in other ontologies. + Evidence-Based Management of Sickle Cell Disease: Expert Panel Report, 2014 + None USA Management Guidelines Children Evidence-Based Management of Sickle Cell Disease - + - - + + A review of service delivery across Europe to children with sickle cell disease (SCD), reporting on the available minimum standards of care and future perspectives. + Probably not necessary to include in other ontologies. + None Colombatti R and Sainati L. Management of children with sickle cell disease in Europe: current situation and future perspectives. EMJ Hematol. 2016;4[1]:129-135. - Probably not necessary to include in other ontologies. - None European document (Colombatti) Management of Children with Sickle Cell Disease in Europe: Current Situation and Future Perspectives - + - - + + A document that describes various ways in which sickle cell disease can be managed and its complications can be prevented in children. + Probably not necessary to include in other ontologies. + None Am J Hematol. 2011 Jan;86(1):72-5. doi: 10.1002/ajh.21865. - Probably not necessary to include in other ontologies. - None European document for children with SCD (Montalambert) ENERCA Clinical Recommendations for Disease Management and Prevention of Complications of Sickle Cell Disease in Children - + - - + + Research conducted on members of families, examining the affects of genetics, the environment, or twin offspring. - - Sufficient - SCDO:1000155 + + Sufficient + SCDO:1000155 EDDA:familial_study Familial Studies Familial Study @@ -47727,27 +47162,27 @@ Request inclusion into relevant ontology, possibly below "Ethnic Group" - + - + The distinguishing qualities or prominent aspects of an individual person that have some relation with quality of life. + Probably too specific to SCDO to be included in other ontologies? + None SCDO (Jade Hotchkiss) - Probably too specific to SCDO to be included in other ontologies? - None Quality of Life Related Personal Attribute - + - - + + Hemoglobin that has undergone conformational changes resulting in increased hydrophobicity that results in the formation of solid crystals consisting of hemoglobin particles. + Request inclusion into the HPO, below "Abnormal Hemoglobin". + None SCDO (Jade Hotchkiss) - Request inclusion into the HPO, below "Abnormal Hemoglobin". - None Crystallised Haemoglobin Crystallized Haemoglobin Crystallized Hemoglobin @@ -47758,90 +47193,90 @@ Request inclusion into relevant ontology, possibly below "Ethnic Group" - + - - + + - + - - + + - - + + - - + + - - + + When one beta-globin gene carries the hemoglobin S mutation (beta6Glu>Val) whereas the other carries a mutation that reduces the amount of beta-globin chain synthesised. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Hemoglobin Genotype S/Beta Minus Thalassaemia - + - - + + Work consisting of a set of statements, directions, or principles presenting current or future rules or policy. Guidelines may be developed by government agencies at any level, institutions, organizations such as professional societies or governing boards, or by the convening of expert panels. The text may be cursive or in outline form, but it is generally a comprehensive guide to problems and approaches in any discipline or activity. This concept relates to the general conduct and administration of health care activities rather than to specific decisions for a particular clinical condition. - Do we rather want to use the more specific MESH term "Practice Guideline"? - - Sufficient - SCDO:1000160 + Do we rather want to use the more specific MESH term "Practice Guideline"? + + Sufficient + SCDO:1000160 MESH:D016431 Guideline - + - - + + - + - - + + - - + + A genotype whereby one HBB allele produces hemoglobin beta chains for normal adult hemoglobin and the other produces the abnormal hemoglobin beta chains of hemoglobin S. Individuals with this genotype are known to be carriers of the sickle cell trait. + Request inclusion into relevant ontology + None SCDO - Request inclusion into relevant ontology - None Haemoglobin Genotype AS Sickle Cell Trait Genotype Hemoglobin Genotype AS @@ -47849,14 +47284,14 @@ Request inclusion into relevant ontology, possibly below "Ethnic Group" - + - - + + The condition in which an individual with sickle cell trait shows symptoms of sickle cell disease such as anemia or acute chest syndrome. - + + - Clinical Sickle Cell Disease in the Heterozygous State Dominant Sickle Cell Disease Often these individuals have co-inherited another hemoglobin mutation that decreases hemoglobin solubility (eg, HbS-Antilles; Hb-Quebec-Chori; HbS-Oman; Hb Jamaica Plain). @@ -47868,253 +47303,253 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - + + A hemoglobinopathy in which the sickle mutation (HBB, Glu6Val) is inherited in combination with another beta-globin gene mutation, other thanHBB, Glu6Val. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Compound Heterozygous Sickling Disorder Compound Heterozygous Sickle Cell Disease - + - - - + + + - + - - + + - - + + - - + + - + - + - - + + Sickle cell disease caused by two mutations in the same beta globin allele, specifically the sickle cell mutation beta6 Glu > Val and a second beta68 Leu > Phe mutation.The other beta globin allele produces normal beta globin chains. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Sickle Cell Disease A/Jamaica Plain - + - - - + + + - + - - + + - - + + - - + + - - + + Sickle cell disease caused by two mutations in the same beta globin allele, specifically the sickle cell mutation (beta6 Glu > Val) and the hemoglobin O-Arab mutation (beta121 Glu > Lys). The other beta globin allele produces normal beta globin chains. + Request inclusion into relevant ontology + + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - None Sickle Cell Disease A/S-Oman - + - - - + + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Sickle cell disease caused by two mutations in the same beta globin allele, specifically the sickle cell mutation beta6 Glu > Val and a second beta 23 Val>Ile mutation. The other beta globin allele produces normal beta globin chains. + Request inclusion into relevant ontology + + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - None Sickle Cell Disease C/S Antilles - + - - + + A directive information entity that specifies how to establish a diagnosis based on clinical findings. - - Sufficient - SCDO:1000170 + + Sufficient + SCDO:1000170 AERO:0000001 Diagnosis Guideline - + - - + + An ICD-10-CM code that can be used to indicate a diagnosis for reimbursement purposes as there are no codes with a greater level of specificity under each code. + None SCDO (Jade Hotchkiss) - None Specific ICD-10-CM Code Billable ICD-10-CM Code - + - - + + An ICD-10-CM diagnosis code that is not billable as there are more specific codes below it that contain a greater level of detail. + None SCDO (Jade Hotchkiss) - None Non-specific ICD-10-CM Code Non-Billable ICD-10-CM Code - + - - + + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:N48.32 N48.32 Priapism due to disease classified elsewhere @@ -48123,26 +47558,26 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - + + A data element in the SickleInAfrica Extended Demographics data capture instrument. + None SCDO (Jade Hotchkiss) - None SickleInAfrica Extended Demographics DE SickleInAfrica Extended Demographics Data Element - + - - + + A lack of production of hemoglobin E. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Absent Haemoglobin E Haemoglobin E Absent Hemoglobin E Absent @@ -48153,13 +47588,13 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - + When the abnormal hemoglobin, hemoglobin E (HbE), has been detected in a blood sample. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Haemoglobin E Present Haemoglobin E in Blood HbE Present @@ -48170,13 +47605,13 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - + + When the level of hemoglobin A2 detected in a sample of blood falls in the normal range for HbA2. + None SCDO (Jade Hotchkiss) - None Normal Haemoglobin A2 Level Normal HbA2 Level Normal Hemoglobin A2 Concentration @@ -48185,15 +47620,15 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - + + A test to detect both HIV antibodies and HIV antigens (a part of the virus) in blood. + Request inclusion into relevant ontology. + + None SCDO (Khuthala Mnika) - Request inclusion into relevant ontology. - - None Antibody/Antigen Tests It can take 2 to 6 weeks for a person’s body to make enough antigens and antibodies for a combination test to detect HIV infection. HIV Combination Test @@ -48201,22 +47636,22 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - + + A test to detect HIV in a person's blood. + Request inclusion into relevant ontology. The more specific term "HIV-1 nucleic acid testing" is found in the OBI. + + None SCDO (Khuthala Mnika) - Request inclusion into relevant ontology. The more specific term "HIV-1 nucleic acid testing" is found in the OBI. - - None NAT NATS can detect HIV infection about 7 to 28 days after a person has been infected with HIV. NATs are very expensive and not routinely used for HIV screening unless the person had a high-risk exposure or a possible exposure with early symptoms of HIV infection. HIV Nucleic Acid Test - + NAT @@ -48224,14 +47659,14 @@ NATs are very expensive and not routinely used for HIV screening unless the pers - + - - + + An abnormal albumin excretion rate of more than 300 mg/g urine creatinine. - Request inclusion into relevant ontology - - Few but definitions not freely available + Request inclusion into relevant ontology + + Few but definitions not freely available Macro-albuminuria Macroalbuminuria High Level Albuminuria @@ -48239,52 +47674,52 @@ NATs are very expensive and not routinely used for HIV screening unless the pers - + - - + + - + - - + + - - + + - - + + A clinically severe form of sickle cell disease resulting when a person is homozygous for Hemoglobin C-Harlem. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Hemoglobin C-Harlem Disease - + - - + + Production of new arrangements of DNA by various mechanisms such as assortment and segregation, crossing over; gene conversion; genetic transformation; genetic conjugation; genetic transduction; or mixed infection of viruses. - - Sufficient - SCDO:1000206 + + Sufficient + SCDO:1000206 MESH:D011995 Recombination Recombination, Genetic @@ -48293,14 +47728,14 @@ NATs are very expensive and not routinely used for HIV screening unless the pers - + - - + + An exchange of DNA between matching or similar sequences. - - Sufficient - SCDO:1000207 + + Sufficient + SCDO:1000207 MESH:D059765 Homologous Recombinations Homologous Recombination @@ -48308,15 +47743,15 @@ NATs are very expensive and not routinely used for HIV screening unless the pers - + - - + + The reciprocal exchange of segments at corresponding positions along pairs of homologous chromosomes by symmetrical breakage and crosswise rejoining forming cross-over sites (Holliday junctions) that are resolved during chromosome segregation. Crossing-over typically occurs during meiosis but it may also occur in the absence of meiosis, for example, with bacterial chromosomes, organelle chromosomes, or somatic cell nuclear chromosomes. - link this term to - - Sufficient - SCDO:1000208 + link this term to + + Sufficient + SCDO:1000208 MESH:D003434 Crossing Over, Genetic Genetic Crossing Over @@ -48324,26 +47759,26 @@ NATs are very expensive and not routinely used for HIV screening unless the pers - + - - + + - + - + - + @@ -48354,43 +47789,43 @@ NATs are very expensive and not routinely used for HIV screening unless the pers - - + + - - + + - - + + The homologous recombination event that occurs during meiosis and results in the delta beta globin fusion chains that replace hemoglobin subunit beta chains in the abnormal hemoglobin, Hemoglobin Lepore. + Request inclusion into relevant ontology + + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - None Crossover between delta (HBD) and beta globin (HBB) gene loci - + - + - + Clinical sickle cell disease in the heterozygous state due to an additional mutation on the same allele as the beta S mutation. + Hemoglobin Jamaica Plain is an example of an abnormal hemoglobin structure caused by a double mutation in 1 Hb allele. + + None SCDO (Jade Hotchkiss) - Hemoglobin Jamaica Plain is an example of an abnormal hemoglobin structure caused by a double mutation in 1 Hb allele. - - None Dominant Sickle Cell Syndrome Dominant Sickle Syndrome Often these individuals have co-inherited another hemoglobin mutation that decreases hemoglobin solubility (eg, HbS-Antilles; Hb-Quebec-Chori; HbS-Oman; Hb Jamaica Plain). @@ -48401,22 +47836,22 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - - + + + deprecated Disease Caused by A/Jamaica Plain Genotype true - + - - - + + + deprecated Disease Caused by A/S-Oman Genotype true @@ -48424,33 +47859,33 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - - + + + deprecated Disease Caused by C/S Antilles Genotype true - + - - + + A hemoglobinopathy involving the presence of structurally abnormal hemoglobins and defects in the quantity of hemoglobins synthesised. + Probably too specific to the SCDO to be included in other ontologies. + None SCDO (Jade Hotchkiss) - Probably too specific to the SCDO to be included in other ontologies. - None Structural and Quantitative Hemoglobinopathy - + - + @@ -48460,42 +47895,42 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - - + + - + A genotype whereby one of the four alpha-globin genes is faulty, either as a result of a single nucleotide variant (SNP) or of a deletion. + Request inclusion into relevant ontology + + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - None -/alpha alpha/alpha Alpha Thalassemia Silent Genotype - + - + - - + + Increased susceptibility to bruising. + Suggest update to label of HPO's "Bruising Susceptibility". +"Bruising Susceptibility" and "Easy Bruisability" are not actually the same thing. + Suggest update to label SCDO (Jade Hotchkiss) - Suggest update to label of HPO's "Bruising Susceptibility". -"Bruising Susceptibility" and "Easy Bruisability" are not actually the same thing. - Suggest update to label Bruisability, Bruising susceptibility, Easy bruising Bruise Easily Bruising Susceptibility @@ -48505,31 +47940,31 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - + + - + - - + + - - + + A genotype whereby one HBB allele produces hemoglobin beta chains for normal adult hemoglobin and the other produces the abnormal hemoglobin beta chains for hemoglobin C. Individuals with this genotype are known to be carriers of the hemoglobin C trait. + None SCDO (Clair Ingram) - None AC Genotype AC Hemoglobin Genotype Haemoglobin Genotype AC @@ -48540,73 +47975,73 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + A genotype whereby one HBB allele produces hemoglobin beta chains for normal adult hemoglobin and the other produces the abnormal hemoglobin beta chains for hemoglobin D. Individuals with this genotype are known to be carriers of the hemoglobin D trait. + None SCDO (Clair Ingram) - None AD Genotype AD Hemoglobin Genotype Haemoglobin Genotype AD @@ -48616,32 +48051,32 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - + + - + - - + + - - + + A genotype whereby one HBB allele produces hemoglobin beta chains for normal adult hemoglobin and the other produces the abnormal hemoglobin beta chains for hemoglobin E. Individuals with this genotype are known to be carriers of the hemoglobin E trait. + Request inclusion into relevant ontology + None SCDO (Clair Ingram) - Request inclusion into relevant ontology - None AE Genotype AE Hemoglobin Genotype Haemoglobin Genotype AE @@ -48652,32 +48087,32 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - + + - + - - + + - - + + A genotype whereby one HBB allele produces hemoglobin beta chains for normal adult hemoglobin and the other produces the abnormal hemoglobin beta chains for hemoglobin O-Arab. Individuals with this genotype are known to be carriers of the hemoglobin O-Arab trait. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None AO-Arab Genotype AO-Arab Hemoglobin Genotype Haemoglobin Genotype AO-Arab @@ -48687,32 +48122,32 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - + + - + - - + + - - + + The homozygous genotype that involves a substitution of glutamic acid for a lysine at position 26 of beta-globin chains (hemoglobin E mutation) produced by both beta-globin gene (HBB) alleles. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None EE Genotype EE Hemoglobin Genotype Haemoglobin Genotype EE @@ -48723,74 +48158,74 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - + + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + The homozygous genotype that involves a hemoglobin D mutation in both beta-globin gene (HBB) alleles. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None DD Genotype DD Hemoglobin Genotype Haemoglobin Genotype DD @@ -48800,32 +48235,32 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - + + - + - - + + - - + + The homozygous genotype that involves a substitution of glutamic acid for a lysine at position 121 of beta-globin chains (hemoglobin O-Arab mutation) produced by both beta-globin gene (HBB) alleles. + Probably not necessary to include in other ontologies. + None SCDO (Jade Hotchkiss) - Probably not necessary to include in other ontologies. - None Haemoglobin Genotype O-Arab O-Arab Genotype O-Arab Hemoglobin Genotype @@ -48835,32 +48270,32 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - + + - + - - + + - - + + The homozygous genotype that involves a substitution of glutamic acid for a lysine at position 6 of beta-globin chains (hemoglobin C mutation) produced by both beta-globin gene (HBB) alleles. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None CC Genotype CC Hemoglobin Genotype Haemoglobin Genotype CC @@ -48871,28 +48306,28 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - + + - + - - + + The presence of an amino acid substitution in either an alpha-, beta-, or gamma-globin chain such that its proximity to the heme iron in the hemoglobin molecule results in facilitated oxidation of the hemoglobin to yield excess methemoglobin. This can occur in either one or both alleles of the effected gene. + Request inclusion into relevant ontology + + + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - - None Haemoglobin Genotype M Hemoglobin M Genotype Hemoglobin Genotype M @@ -48900,21 +48335,21 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - - Hemoglobin M Disease is autosomal dominant, thus does not seem to have a "trait" condition. + + + Hemoglobin M Disease is autosomal dominant, thus does not seem to have a "trait" condition. obsolete - Hemoglobin M trait Genotype true - + - - + + @@ -48923,67 +48358,67 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - - + + - - + + - + Either homozygosity or heterozygosity for the HPFH1 mutation, a 106-KB deletion in the beta globin gene cluster. + Request inclusion into relevant ontology + + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - None Hereditary Persistence of Fetal Hemoglobin Genotype - + - - + + - + - - + + The homozygous genotype for Hemoglobin Lepore Boston that involves a crossover between both sets of delta (HBD) and beta globin (HBB) gene loci during meiosis. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Hemoglobin Lepore Boston Genotype - + - + The inheritance of one normal HBB gene along with an abnormal HBB gene that contains two amino acid substitutions, namely Glu6Val (HbS) and Asp73Asn. + Request inclusion into NCIT below "Hemoglobin Trait". + + None SCDO (Jade Hotchkiss) - Request inclusion into NCIT below "Hemoglobin Trait". - - None Hb CH-Trait Erythrocytes from persons with Hb CH trait show some sickling in hypertonic saline without deoxygenation; this finding and the renal functional abnormalities are similar to those seen in persons with sickle cell trait and suggest that the renal concentrating defects in the two disorders have similar pathogeneses. Hemoglobin C-Harlem Trait @@ -48991,19 +48426,19 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - + - - + + A mutation in the NADH-Cytochrome b5 Reductase 3 gene, CYB5R3, that contributes to the presence of methemoglobinemia (type I or II). - Request inclusion into relevant ontology - None + Request inclusion into relevant ontology + None DIA 1 Mutation Diaphorase Mutation Methemoglobinemia Mutation @@ -49013,108 +48448,108 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - + + - - + + Deletion of one alpha-globin gene, either an HBA1 or HBA2 gene, which results in Alpha Thalassemia Silent (the person with the mutation is a silent carrier). + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Heterozygous Deletion of HBA1 or HBA2 - + - - + + Either a decrease in the proportion of hemoglobin A to below 96-98% of all hemoglobin, or a complete lack of hemoglobin A production. + Probably too specific to be added to existing ontologies? + None SCDO (Jade Hotchkiss) - Probably too specific to be added to existing ontologies? - None Reduced or Absent Hemoglobin A - + - + - + A lack of production of normal adult hemoglobin. + Request inclusion into HPO below "Abnormal Hemoglobin Concentration". + Negligable SCDO (Jade Hotchkiss) - Request inclusion into HPO below "Abnormal Hemoglobin Concentration". - Negligable Hemoglobin A Absent Absent Hemoglobin A - + - + A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in individuals that are homozygotes (having two copies of the same mutant allele). + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Autosomal Homozygous Recessive Inheritance Autosomal Recessive Homozygous - + - + A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in individuals that are compound heterozygotes (whereby each copy of a gene has a distinct mutant allele). + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Autosomal Recessive Compound Heterozygous Inheritance Autosomal Recessive Compound Heterozygous - + - - + + A sickle cell disease phenotype in which an individual heterozygous for hemoglobin S also has a severe pyruvate kinase deficiency, which lowers the hemoglobin oxygen affinity, resulting in hemoglobin S polymerization and sickling. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Sickle Cell Trait with a Severe Pyruvate Kinase Deficiency - + - + - + A powder form of the optically active form of glutamine having L-configuration; to be administered orally. + Suggest update to description in the Drug Ontology (DRON) for "Glutamine Oral Powder" (currently no description provided). + + + Few but definitions not freely available SCDO (Jade Hotchkiss) - Suggest update to description in the Drug Ontology (DRON) for "Glutamine Oral Powder" (currently no description provided). - - - Few but definitions not freely available Glutamine Oral Powder Glutamine Oral Powder Product Glutamine Powder @@ -49126,14 +48561,14 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - - + + A phenotype in which a specific molecular function is abnormal. - - Sufficient - SCDO:1000250 + + Sufficient + SCDO:1000250 FYPO:0000707 deprecated Abnormal Molecular Function true @@ -49141,21 +48576,21 @@ Other rare causes of symptomatic sickle cell trait include: mosaicism for cells - + - + An increase in red blood cell sensitivity to change in osmotic pressure. More specifically, the degree or proportion of hemolysis that occurs when a sample of red blood cells are subjected to osmotic stress by being placed in a hypotonic solution. - SCDO (Jade Hotchkiss) - What is normal osmotic fragility? Perhaps this can be included in the description. + What is normal osmotic fragility? Perhaps this can be included in the description. Suggest update to description in the HPO. Currently no description given. -Include "Osmotic Fragility Test" in an appropriate location below "Diagnostics Tools" and link to this term. - - - - Suggest update to description. +Include "Osmotic Fragility Test" in an appropriate location below "Diagnostics Tools" and link to this term. + + + + Suggest update to description. + SCDO (Jade Hotchkiss) HP:0005502 Increased Erythrocyte Osmotic Fragility Increased Red Cell Fragility @@ -49164,149 +48599,149 @@ Include "Osmotic Fragility Test" in an appropriate location below &quo - + - + - - Is this not the same as "Increased Red Cell Osmotic Fragility"? See dc:source provided. + Is this not the same as "Increased Red Cell Osmotic Fragility"? See dc:source provided. What is normal osmotic resistance? Perhaps this can be included in the description. Suggest update to description in the HPO. Currently no description given. -Include "Osmotic Fragility Test" in an appropriate location below "Diagnostics Tools" and link to this term. - - Few but definitions not freely available +Include "Osmotic Fragility Test" in an appropriate location below "Diagnostics Tools" and link to this term. + + Few but definitions not freely available + HP:0005546 Increased Red Cell Osmotic Resistance - + - + A situation in which a specific biological process within an organism is abnormal. - Include here "Intrahepatic Sinusoidal -Sickling"? See paper "Liver involvement in sickle cell disease" by Emel GÜRKAN et al. - - Sufficient - SCDO:1000253 + Include here "Intrahepatic Sinusoidal +Sickling"? See paper "Liver involvement in sickle cell disease" by Emel GÜRKAN et al. + + Sufficient + SCDO:1000253 FYPO:0005447 Abnormal Biological Process - + - - + + When deoxygenated, malfunctioning or mutated hemoglobins clump together and form a long polymer. + + None SCDO (Jade Hotchkiss) - - None Hemoglobin Polymerisation Polymerisation of Hemoglobin - + - - + + Guidelines that examine current available evidence on indications for transfusion in sickle cell disease. - Probably not necessary to include in other ontologies. - Br J Haematol. 2017 Jan;176(2):192-209. doi: 10.1111/bjh.14383. Epub 2016 Nov 18. - None + Probably not necessary to include in other ontologies. + Br J Haematol. 2017 Jan;176(2):192-209. doi: 10.1111/bjh.14383. Epub 2016 Nov 18. + None Guidelines on Red Cell Transfusion in Sickle Cell Disease - Part II: Indications for Transfusion - + - - + + This guideline addresses the management of an acute painful sickle cell episode in patients presenting to hospital until discharge. This includes the use of pharmacological and non-pharmacological interventions, identifying the signs and symptoms of acute complications, skills and settings for managing an acute painful episode, and the information and support needs of patients. + Probably not necessary to include in other ontologies. + + None SCDO - Probably not necessary to include in other ontologies. - - None Sickle Cell Acute Painful Episode - Management of an Acute Painful Sickle Cell Episode in Hospital - + - - + + A factsheet that shares steps to improve care in emergency departments (ED) of hospitals and clinics for people with sickle cell disease (SCD). It was created to help improve healthcare in the ED for patients with SCD. - Probably not necessary to include in other ontologies. - - None + Probably not necessary to include in other ontologies. + + None Three Tips About Sickle Cell Disease Every Emergency Provider Needs to Know - + - - + + A comprehensive guideline to aid physicians and other health care professionals in the management of patients with acute and chronic pain associated with sickle cell disease (SCD). The guideline covers the following information: an overview of the disease, the types and characteristics of pain associated with the disease, recommendations for pain assessment, methods for treatment of pain and a discussion of pain in the various developmental stages. It also includes discussions of pain assessment instruments. + Probably not necessary to include in other ontologies. + Am Fam Physician. 2000 Mar 1;61(5):1544-1550. + None SCDO - Probably not necessary to include in other ontologies. - Am Fam Physician. 2000 Mar 1;61(5):1544-1550. - None Practice Guidelines: Management of Pain in Sickle Cell Disease - + - - + + A hemoglobin that shows characteristics of an abnormal hemoglobin, but its inheritance does not accompany any disability. + Request inclusion into NCIT below "Hemoglobin"/"Hemoglobin Variant". + + None SCDO (Jade Hotchkiss) - Request inclusion into NCIT below "Hemoglobin"/"Hemoglobin Variant". - - None Unusual Hemoglobin Variant Unusual Hemoglobin - + - + Any feeling of illness or physical or mental change that results from strenuous exercise. + Suggest update to description in OMIM (currently no description provided). + Few but definitions not freely available - Suggest update to description in OMIM (currently no description provided). - Few but definitions not freely available OMIM:MTHU024836 Symptom Induced by Strenuous Exercise - + - + A condition due to a deficiency of one or more essential vitamins. (Dorland, 27th ed) - - Sufficient - SCDO:1000261 + + Sufficient + SCDO:1000261 MESH:D001361 Vitamin Deficiencies Vitamin Deficiency @@ -49315,40 +48750,40 @@ Sickling"? See paper "Liver involvement in sickle cell disease" b - + - + Abnormality originating in one or more muscles of the set of muscles in the body. - - Suggest update to description + + Suggest update to description HP:0003011 Abnormality of the Musculature - + - - + + An abnormal level of hemoglobin that occurs in one or more forms of Sickle Cell Disease (SCD). + Probably too specific to SCD be included in other ontologies. + None SCDO (Jade Hotchkiss) - Probably too specific to SCD be included in other ontologies. - None Abnormal Hemoglobin Level in SCD - + - - + + Hemochromatosis that results from repeated blood transfusions. + Request inclusion into relevant ontology + None SCDO - Request inclusion into relevant ontology - None Transfusion Haemochromatosis Transfusion-Induced Iron Overload Transfusion Hemochromatosis @@ -49356,26 +48791,26 @@ Sickling"? See paper "Liver involvement in sickle cell disease" b - + - + An acquired metabolic disorder characterized by iron accumulation in the tissues. + Suggest inclusion into existing ontology. + Few but definitions not freely available SCDO (Jade Hotchkiss) - Suggest inclusion into existing ontology. - Few but definitions not freely available Secondary Hemochromatosis - + - + When the abnormal hemoglobin, hemoglobin D-Punjab (Hb D-Punjab), has been detected in a blood sample. + None SCDO (Jade Hotchkiss) - None Haemoglobin D-Punjab Present Haemoglobin D-Punjab in Blood Hb D-Punjab Present @@ -49386,13 +48821,13 @@ Sickling"? See paper "Liver involvement in sickle cell disease" b - + - + When the abnormal hemoglobin, hemoglobin G-Philadelphia (Hb G-Philadelphia), has been detected in a blood sample. + None SCDO (Jade Hotchkiss) - None Haemoglobin G-Philadelphia Present Haemoglobin G-Philadelphia in Blood Hb G-Philadelphia Present @@ -49403,13 +48838,13 @@ Sickling"? See paper "Liver involvement in sickle cell disease" b - + - + When the abnormal hemoglobin, hemoglobin O-Arab (Hb O-Arab), has been detected in a blood sample. + None SCDO (Jade Hotchkiss) - None Haemoglobin O-Arab Present Haemoglobin O-Arab in Blood Hb O-Arab Present @@ -49420,13 +48855,13 @@ Sickling"? See paper "Liver involvement in sickle cell disease" b - + - - + + When the level of hemoglobin F detected in a sample of blood falls in the normal range for HbF. + None SCDO (Jade Hotchkiss) - None Normal Haemoglobin F Level Normal HbF Level Normal Hemoglobin F Concentration @@ -49435,29 +48870,29 @@ Sickling"? See paper "Liver involvement in sickle cell disease" b - + - - + + The score obtained from a quality of life-related diagnostic instrument. + Request inclusion into relevant ontology + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - Negligable Quality of Life Score Quality of Life Assessment Score - + - - + + The score obtained from the Adult Sickle Cell Quality-of-Life Measurement Information System (ASCQ-Me) diagnostic instrument. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None ASCQ-Me - Quality of Life in SCD Score Sickle Cell Disease Adult Quality of Life Questionnaire Assessment Score ASCQ-Me Score @@ -49465,28 +48900,28 @@ Sickling"? See paper "Liver involvement in sickle cell disease" b - + - - + + A diagnostic instrument that involves an assessment of quality of life- and/or quality of care-related elements. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Quality of Life and Care Diagnostic Instrument - + - - + + A deteremination of the presence of hepatitis B virus surface antigen. + Suggest update to label in NCIT (from "Hepatitis B Virus Surface Antigen Measurement") + + Suggest update to label - Suggest update to label in NCIT (from "Hepatitis B Virus Surface Antigen Measurement") - - Suggest update to label NCIT:C64850 HBSAG Test HBsAg Test @@ -49500,14 +48935,14 @@ A positive HBsAg test result means that you are infected and can spread the hepa - + - - + + The determination of the surface antibody reaction of a sample to the Hepatitis B virus. - Suggest update to label in NCIT (from "Hepatitis B Surface Antibody Measurement") - - Suggest update to label + Suggest update to label in NCIT (from "Hepatitis B Surface Antibody Measurement") + + Suggest update to label NCIT:C74711 HBSAB Test HBsAb Test @@ -49519,15 +48954,15 @@ A positive HBsAg test result means that you are infected and can spread the hepa - + - - + + The determination of the amount of Hepatitis B virus core antibody present in a sample. + Suggest update to label in nCIT (from "Hepatitis B Virus Core Antibody Measurement") + + Suggest update to label - Suggest update to label in nCIT (from "Hepatitis B Virus Core Antibody Measurement") - - Suggest update to label NCIT:C96660 Anti-HBc Test HBCAB Test @@ -49543,15 +48978,15 @@ A positive anti-HBc (or HBcAb) test result requires talking to your health care - + - - + + A set of three blood tests (Hepatitis B Core Antibody Test, Hepatitis B Surface Antibody Test, and Hepatitis B Virus Surface Antigen Test) needed to fully understand whether a person is infected with Hepatitis B or not. + Request inclusion into relevant ontology + + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - - None Hepatitis B Panel Hepatitis B Panel of Blood Tests Hepatitis B Blood Panel @@ -49559,14 +48994,14 @@ A positive anti-HBc (or HBcAb) test result requires talking to your health care - + - - + + The determination of the amount of hepatitis B virus antibody present in a sample. - Suggest update to label in NCIT (from "Hepatitis B Virus Antibody Measurement") - - Suggest update to label + Suggest update to label in NCIT (from "Hepatitis B Virus Antibody Measurement") + + Suggest update to label NCIT:C125944 HBAB Test Hepatitis B Antibody Test @@ -49575,14 +49010,14 @@ A positive anti-HBc (or HBcAb) test result requires talking to your health care - + - - + + The determination of the amount of hepatitis B virus core IgG antibody in a biological specimen. - Suggest update to label in NCIT (from "Hepatitis B Virus Core IgG Antibody Measurement") - - Suggest update to label + Suggest update to label in NCIT (from "Hepatitis B Virus Core IgG Antibody Measurement") + + Suggest update to label NCIT:C119280 HBCIGGAB Test Hepatitis B Virus Core IgG Antibody Test @@ -49591,14 +49026,14 @@ A positive anti-HBc (or HBcAb) test result requires talking to your health care - + - - + + The determination of the amount of Hepatitis B virus core IgM antibody present in a sample. - Suggest update to label in NCIT (from "Hepatitis B Virus Core IgM Antibody Measurement") - - Suggest update to label + Suggest update to label in NCIT (from "Hepatitis B Virus Core IgM Antibody Measurement") + + Suggest update to label NCIT:C96661 HBCIGMAB Test Hepatitis B Virus Core IgM Antibody Test @@ -49607,30 +49042,30 @@ A positive anti-HBc (or HBcAb) test result requires talking to your health care - + - + Exercise testing for evaluation of hypoxemia and/or desaturation that occurs on exertion. - Suggest inclusion of term below "Pulse Oximetry" in the CMO. - - PhenX protocol: Pulse Oximetry (Exercise) #91001 - Sufficient - SCDO:1000305 + Suggest inclusion of term below "Pulse Oximetry" in the CMO. + + PhenX protocol: Pulse Oximetry (Exercise) #91001 + Sufficient + SCDO:1000305 phenX:91001 Pulse Oximetry (Exercise) - + - - + + The determination of the amount of hepatitis C virus antigen present in a sample. - Suggest update to label in NCIT (from "Hepatitis C Virus Antigen Measurement" - - Suggest update to label + Suggest update to label in NCIT (from "Hepatitis C Virus Antigen Measurement" + + Suggest update to label NCIT:C116196 HCAG Test Hepatitis C Virus Antigen Measurement @@ -49639,14 +49074,14 @@ A positive anti-HBc (or HBcAb) test result requires talking to your health care - + - - + + A determination of the presence of the hepatitis C virus antibody in a biological specimen. - Suggest update to label and description in NCIT (from "Hepatitis C Antibody Measurement") - - Suggest update to label and description + Suggest update to label and description in NCIT (from "Hepatitis C Antibody Measurement") + + Suggest update to label and description NCIT:C92535 HCAB Test Hepatitis C Antibody Measurement @@ -49656,14 +49091,14 @@ A positive anti-HBc (or HBcAb) test result requires talking to your health care - + - - + + The determination of the amount of hepatitis C virus core antigen in a biological sample. - Suggest update to label in NCIT (from "Hepatitis C Virus Core Antigen Measurement") - - Suggest update to label + Suggest update to label in NCIT (from "Hepatitis C Virus Core Antigen Measurement") + + Suggest update to label NCIT:C135424 HCCAG Test HCV Core Antigen Measurement @@ -49675,14 +49110,14 @@ A positive anti-HBc (or HBcAb) test result requires talking to your health care - + - - + + The determination of the surface antibody reaction of a sample to the Hepatitis C virus. - Suggest update to label in NCIT (from "Hepatitis C Surface Antibody Measurement") - - Suggest update to label + Suggest update to label in NCIT (from "Hepatitis C Surface Antibody Measurement") + + Suggest update to label NCIT:C74712 Hepatitis C Surface Antibody Measurement Hepatitis C Surface Antibody Test @@ -49690,21 +49125,21 @@ A positive anti-HBc (or HBcAb) test result requires talking to your health care - + - - - + + + - - + + The determination of the amount of cystatin C present in a sample. - Suggest update to label in NCIT (from "Cystatin C Measurement") - - Suggest update to label + Suggest update to label in NCIT (from "Cystatin C Measurement") + + Suggest update to label NCIT:C92290 CYSTATC Blood Test Cystatin C Blood Test @@ -49712,53 +49147,53 @@ A positive anti-HBc (or HBcAb) test result requires talking to your health care - + - - + + The visual output that a specific diagnostic device produces. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Visual Output of a Diagnostic Device Diagnostic Device Visual Output - + - - + + - - + + A bioassay to measure levels of red blood cell microparticles. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Red Blood Cell Microparticles Assay - + - - + + - - + + A quantitative measurement of the amount of HDL cholesterol present in a sample of serum. - Suggest update to label in NCIT (from "Serum HDL Cholesterol Measurement") - - Suggest update to label + Suggest update to label in NCIT (from "Serum HDL Cholesterol Measurement") + + Suggest update to label NCIT:C61041 Serum HDL Cholesterol Measurement Serum HDL Cholesterol Test @@ -49766,230 +49201,230 @@ A positive anti-HBc (or HBcAb) test result requires talking to your health care - + - - + + A technique used to measure velocity and amount of blood flow and circulation in the living system. + None SCDO (Jade Hotchkiss) - None Blood Flow Test - + - + Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart. - Suggest this description for this term in the CMO (it was recently described separately from another similar term" but's it's definition has not yet been ascribed). - - Suggest update to description + Suggest this description for this term in the CMO (it was recently described separately from another similar term" but's it's definition has not yet been ascribed). + + Suggest update to description CMO:0000670 Heart Measurement - + - - + + An information entity, used in the diagnosis of medical conditions, that is a recording of the output of a diagnostic instrument. - SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology + Request inclusion into relevant ontology Add terms/Variables obtained from: -History of Head Trauma Diagnostic Instrument - None +History of Head Trauma Diagnostic Instrument + None + SCDO (Jade Hotchkiss) Diagnostic Instrument Outcome Diagnostic Instrument Measurement - + - - + + Questions asking the respondent about smoking status in his or her entire life. - Request inclusion into relevant ontology - - None + Request inclusion into relevant ontology + + None Cigarette Smoking Status Diagnostic Instrument - + - - + + - - + + Questions asking an adult respondent about smoking status in his or her entire life. + Request inclusion into relevant ontology + PhenX protocol: Cigarette Smoking Status - Adult #30604 + None SCDO (Jade hotchkiss) - Request inclusion into relevant ontology - PhenX protocol: Cigarette Smoking Status - Adult #30604 - None Cigarette Smoking Status Diagnostic Instrument - Adult - + - - + + - - + + Questions asking an adolescentt respondent about smoking status in his or her entire life. + Request inclusion into relevant ontology + PhenX protocol: Cigarette Smoking Status - Adolescent #30603 + None SCDO (Jade hotchkiss) - Request inclusion into relevant ontology - PhenX protocol: Cigarette Smoking Status - Adolescent #30603 - None Cigarette Smoking Status Diagnostic Instrument - Adolescent - + - - + + A person who has never smoked a cigarette, not even one or two puffs. + Other ontologies define this as "A person who was not smoking at the time of the interview and has smoked less than 100 cigarettes in their life." + Not relevant to context of sickle cell SCDO (Jade Hotchkiss) - Other ontologies define this as "A person who was not smoking at the time of the interview and has smoked less than 100 cigarettes in their life." - Not relevant to context of sickle cell Never Smoker - + - - + + A person who was smoking on a daily basis at the time of the interview. + Other ontologies define this as "Indicates a person who has smoked at least 100 cigarettes in his or her lifetime and who currently smokes every day." + Not relevant to context of sickle cell SCDO (Jade Hotchkiss) - Other ontologies define this as "Indicates a person who has smoked at least 100 cigarettes in his or her lifetime and who currently smokes every day." - Not relevant to context of sickle cell Current Every-Day Smoker - + - - + + A person who had smoked a cigarette in the past, and was smoking on some days, but not daily, at the time of the interview. + Other ontologies define this as "Indicates a person who has smoked at least 100 cigarettes in his or her lifetime, who smokes now, but does not smoke every day." + Not relevant to context of sickle cell SCDO (Jade Hotchkiss) - Other ontologies define this as "Indicates a person who has smoked at least 100 cigarettes in his or her lifetime, who smokes now, but does not smoke every day." - Not relevant to context of sickle cell Current Some-Day Smoker - + - - + + A person who was not smoking at the time of the interview but has smoked a cigarette in the past, even if just one or two puffs + Other ontologies define this as "A person who was not smoking at the time of the interview but has smoked at least 100 cigarettes in their life." + Not relevant to context of sickle cell SCDO (Jade Hotchkiss) - Other ontologies define this as "A person who was not smoking at the time of the interview but has smoked at least 100 cigarettes in their life." - Not relevant to context of sickle cell Former Smoker - + - - + + A person who has smoked a cigarette in the past, even if just one or two puffs, but was unable to or refused to answer when asked when the last time was that they smoked a cigarette, even one or two puffs. + None SCDO (Jade Hotchkiss) - None Ever-Smoker - + - - + + A person who had smoked in the past 30 days at the time of the interview, but who had not smoked every day of the past 30 days. + None SCDO (Jade Hotchkiss) - None Past 30-Day Smoker - + - - + + A person who had smoked every day of the past 30 days at the time of the interview. + None SCDO (Jade Hotchkiss) - None Past 30-Day Every-Day Smoker - + - - + + - - + + Question asking the respondent if s/he has ever consumed any alcoholic beverage during his or her entire life. - Suggest update to label in PhenX - - PhenX protocol: #30101 - Suggest update to label + Suggest update to label in PhenX + + PhenX protocol: #30101 + Suggest update to label phenX:030100 Alcohol - Lifetime Use Diagnostic Instrument - + - - + + A nine-item, interviewer-administered questionnaire to screen for the presence of epilepsy in adults. + Request inclusion into "PhenX Phenotypic Terms". +This is in the PhenX toolkit but not in the ontology in BioPortal. It should probably be included there. + + None SCDO (Jade Hotchkiss) - Request inclusion into "PhenX Phenotypic Terms". -This is in the PhenX toolkit but not in the ontology in BioPortal. It should probably be included there. - - None phenX:130401 Epilepsy Screener for Adults Epilepsy Screener - Adult @@ -49997,16 +49432,16 @@ This is in the PhenX toolkit but not in the ontology in BioPortal. It should pro - + - - + + A nine-item, interviewer-administered questionnaire to screen for the presence of epilepsy in family members, including children and those who are deceased. + Request inclusion into "PhenX Phenotypic Terms". +This is in the PhenX toolkit but not in the ontology in BioPortal. It should probably be included there. + + None SCDO (Jade Hotchkiss) - Request inclusion into "PhenX Phenotypic Terms". -This is in the PhenX toolkit but not in the ontology in BioPortal. It should probably be included there. - - None phenX:130402 Family History of Epilepsy Screening Interview Ottman Brief Epilepsy Screener - Proxy-reported Version @@ -50015,20 +49450,20 @@ This is in the PhenX toolkit but not in the ontology in BioPortal. It should pro - + - + - - + + A disruption to the efficacy of the executive functions, which is a group of cognitive processes that regulate, control, and manage other cognitive processes. - Request inclusion into relevant ontology. Perhaps below "Behavioral Abnormality" in the HPO. - - Few but definitions not freely available + Request inclusion into relevant ontology. Perhaps below "Behavioral Abnormality" in the HPO. + + Few but definitions not freely available Defects in Executive Function Executive Function Deficit Executive Dysfunction @@ -50036,81 +49471,81 @@ This is in the PhenX toolkit but not in the ontology in BioPortal. It should pro - + - - + + A series of 21 age-specific questionnaires and scoring sheets designed to screen a child's skills in five developmental areas: fine motor, gross motor, problem solving, communication, and personal-social. A child's scores for each area are compared to cut-off scores to determine a need for monitoring or further assessment. - Request inclusion into relevant ontology. Maybe below "Clinical or Research Assessment Questionnaire" in the NCIT. - - Global Mental Status Screener - Child #130702 - Few but definitions not freely available + Request inclusion into relevant ontology. Maybe below "Clinical or Research Assessment Questionnaire" in the NCIT. + + Global Mental Status Screener - Child #130702 + Few but definitions not freely available The Ages & Stages Questionnaires, Third Edition (ASQ-3) Global Mental Status Screener - Child - + - - + + - - + + The frequency of acute pain episodes due to sickle cell disease (SCD). - Request inclusion into relevant ontology + Request inclusion into relevant ontology Add as sub-classes: (from protocol questions) - a term for the number of times an emergency room was visited because of a sickle cell painful event in the last 6 months -- a term for the number of times the person was admitted to a hospital because of a sickle cell painful event in the last 12 months - Not relevant to context of sickle cell. This term in PhenX currently refers to a diagnostic instrument. +- a term for the number of times the person was admitted to a hospital because of a sickle cell painful event in the last 12 months + Not relevant to context of sickle cell. This term in PhenX currently refers to a diagnostic instrument. Frequency of Sickle Cell Pain Episodes - + - + - + - - + + - - + + Questions from the National Epidemiologic Survey on Alcohol and Related Conditions-III (NESARC-III) related to their lifetime use of illicit and prescribed substances. - Suggest update to label in PhenX - - PhenX protocol: Substances - Lifetime Use #31102 - Suggest update to label + Suggest update to label in PhenX + + PhenX protocol: Substances - Lifetime Use #31102 + Suggest update to label Substances - Lifetime Use Diagnostic Instrument - + - - + + A 26-item, self-administered scale completed by the parent that assesses the child's sleep behaviors in the past 6 months. The scale includes six subscales: disorders of initiating and maintaining sleep (items 1, 2, 3, 4, 5, 10, 11); sleep breathing disorders (items 13, 14, 15); disorders of arousal (items 17, 20, 21); sleep-wake transition disorders (items 6, 7, 8, 12, 18, 19); disorders of excessive somnolence (items 22, 23, 24, 25, 26); and sleep hyperhidrosis (score of the items 9, 16). Each item is rated on a 5-point, Likert-type scale (1 = Never; 5 = Always [daily]). Scores from individual items of each subscale are added together to give a subscale score, with higher scores indicating greater symptoms. Scores from the individual subscales can be added together to give a total score. + Request inclusion into relevant ontology. +Separate adult vs children instruments not shown in "PhenX Phenotypic Terms". + + PhenX protocol: Sleep Disorders Screener - Children #121002 + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology. -Separate adult vs children instruments not shown in "PhenX Phenotypic Terms". - - PhenX protocol: Sleep Disorders Screener - Children #121002 - None phenX:121002 Sleep Disturbances Scale for Children Sleep Disorders Screener - Children @@ -50118,196 +49553,196 @@ Separate adult vs children instruments not shown in "PhenX Phenotypic Terms - + - + A record of an individual's background in regard to head trauma. - SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology. Perhaps as a sub-class of "History of Trauma" in "The Stroke Ontology"? + Request inclusion into relevant ontology. Perhaps as a sub-class of "History of Trauma" in "The Stroke Ontology"? -PhenX uses this as their label for a questionnaire, but we're going to suggest they change that. Otherwise, don't see it in other ontologies. - Not relevant to context of sickle cell +PhenX uses this as their label for a questionnaire, but we're going to suggest they change that. Otherwise, don't see it in other ontologies. + Not relevant to context of sickle cell + SCDO (Jade Hotchkiss) History of Head Trauma - + - + A record of an individual's history of stroke(s) and associated symptoms such as slurred speech, double vision, loss of vision, and paralysis. + Request inclusion into NCIT below "Personal Medical History". Note: Is present in The Stroke Ontology. + Few but definitions not freely available SCDO (Jade Hotchkiss) - Request inclusion into NCIT below "Personal Medical History". Note: Is present in The Stroke Ontology. - Few but definitions not freely available History of Stroke - + - + A record of an individual's history of kidney failure. - SCDO (Jade Hotchkiss) - Request inclusion into NCIT as a sub-class of "Personal Medical History". + Request inclusion into NCIT as a sub-class of "Personal Medical History". -PhenX uses this as their label for a questionnaire, but we're going to suggest they change that. Otherwise, don't see it in other ontologies. - Not relevant to context of sickle cell +PhenX uses this as their label for a questionnaire, but we're going to suggest they change that. Otherwise, don't see it in other ontologies. + Not relevant to context of sickle cell + SCDO (Jade Hotchkiss) History of Kidney Failure - + - + - + - + - - + + A questionnaire to assess history of transfusion. - Suggest update to label as we have done. We are using "History of Transfusion" below Personal Attribute. - - PhenX protocol: History of Transfusion #830201 - Suggest update to label + Suggest update to label as we have done. We are using "History of Transfusion" below Personal Attribute. + + PhenX protocol: History of Transfusion #830201 + Suggest update to label phenX:830200 History of Transfusion Diagnostic Instrument - + - + A record of an individual's history of type 1 and type 2 diabetes. - SCDO (Jade Hotchkiss) - Request inclusion into NCIT as a sub-class of "Personal Medical History". + Request inclusion into NCIT as a sub-class of "Personal Medical History". -PhenX uses this as their label for a questionnaire, but we're going to suggest they change that. Otherwise, don't see it in other ontologies. - Not relevant to context of sickle cell +PhenX uses this as their label for a questionnaire, but we're going to suggest they change that. Otherwise, don't see it in other ontologies. + Not relevant to context of sickle cell + SCDO (Jade Hotchkiss) History of Type 1 and Type 2 Diabetes - + - - + + A questionnaire to assess males' pregnancy history. + Suggest update to label and description in PhenX as we have done. We are using "Reproductive History" below Personal Attribute. + PhenX protocol: Reproductive History - Male #101302 + Suggest update to label and description. SCDO (Jade Hotchkiss) - Suggest update to label and description in PhenX as we have done. We are using "Reproductive History" below Personal Attribute. - PhenX protocol: Reproductive History - Male #101302 - Suggest update to label and description. Reproductive History Diagnostic Instrument - Male - + - - + + A questionnaire to assess females' pregnancy history. + Suggest update to label and description in PhenX as we have done. We are using "Reproductive History" below Personal Attribute. + PhenX protocol: Reproductive History - Female #101301 + Suggest update to label and description. SCDO (Jade Hotchkiss) - Suggest update to label and description in PhenX as we have done. We are using "Reproductive History" below Personal Attribute. - PhenX protocol: Reproductive History - Female #101301 - Suggest update to label and description. Reproductive History Diagnostic Instrument - Female - + - + - + A questionnaire to assess sleep disorders, a broad group of disorders that can be caused by endogenous disturbances in the sleep-wake or timing cycles (American Psychiatric Association, 2000). - - Sufficient - SCDO:1000348 + + Sufficient + SCDO:1000348 phenX:121000 Sleep Disorders Screener - + - - + + - - + + A test to assess the structure and function of the heart valves. - Suggest update to label in PhenX (from "Heart Valve Function") - - PhenX protocol: Heart Valve Function #40501 - Suggest update to label + Suggest update to label in PhenX (from "Heart Valve Function") + + PhenX protocol: Heart Valve Function #40501 + Suggest update to label phenX:40501 Heart Valve Function Test - + - + Measurement of the breathing capacity of an adult's lung by means of a spirometer. + Suggest update to description in PhenX (currently the same for both adult and child protocols) + PhenX protocol: Spirometry - Adult #91601 + Suggest update to description SCDO (Jade Hotchkiss) - Suggest update to description in PhenX (currently the same for both adult and child protocols) - PhenX protocol: Spirometry - Adult #91601 - Suggest update to description Spirometry - Adult - + - + Measurement of the breathing capacity of a child's lung by means of a spirometer. + Suggest update to description in PhenX (currently the same for both adult and child protocols) + PhenX protocol: Spirometry - Child #91602 + Suggest update to description SCDO (Jade Hotchkiss) - Suggest update to description in PhenX (currently the same for both adult and child protocols) - PhenX protocol: Spirometry - Child #91602 - Suggest update to description Spirometry - Child - + - - + + Pattern of behavior which predisposes certain individuals to increased risk for contracting disease or sustaining personal injury. These behaviors may cluster into a risky lifestyle. - - Sufficient - SCDO:1000354 + + Sufficient + SCDO:1000354 MESH:D000073599 Health Risk Behaviors Risky Health Behavior @@ -50317,57 +49752,57 @@ PhenX uses this as their label for a questionnaire, but we're going to sugg - + - + Physical surroundings or conditions of a hospital or other health facility and influence of these factors on patients and staff. - - Sufficient - SCDO:1000355 + + Sufficient + SCDO:1000355 MESH:D006272 Health Facility Environment - + - - + + Height above sea level or above the earth's surface. - - Sufficient - SCDO:1000356 + + Sufficient + SCDO:1000356 CSP:1035-6505 Altitude - + - - + + A measure of educational progress reported using a questionnaire based approach, often used as a proxy for cognitive performance as the two are correlated. - - PhenX protocol: Current Educational Attainment #11001 - Sufficient - SCDO:1000357 + + PhenX protocol: Current Educational Attainment #11001 + Sufficient + SCDO:1000357 EFO:0004784 Self Reported Educational Attainment - + - + A gene that encodes one of the globin family proteins, which are globular heme-containing proteins and include androglobin, cryoglobin, hemoglobin subunits, myoglobin and neuroglobin. - Suggest update to description in NCIT. - - Suggest update to description + Suggest update to description in NCIT. + + Suggest update to description NCIT:C142196 Globin Gene Family Globin Genes @@ -50376,49 +49811,49 @@ PhenX uses this as their label for a questionnaire, but we're going to sugg - + - - + + A gene that provides instructions for making a protein called alpha-globin. + Request inclusion into relevant ontology + Negligable SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - Negligable Alpha-Globin Gene - + - - + + A gene located in the beta-globin locus (or gene cluster) on chromosome 11. - SCDO (Jade Hotchkiss) - Include sub-classes?: + Include sub-classes?: HBE1 (encodes hemoglobin subunit epsilon) HBG1 HBG2 HBM HBQ1 -HBZ - Should this perhaps rather be something like "Beta-Globin Locus Gene"? To prevent confusion with the HBB Gene. +HBZ + Should this perhaps rather be something like "Beta-Globin Locus Gene"? To prevent confusion with the HBB Gene. -Request inclusion into relevant ontology. - Negligable +Request inclusion into relevant ontology. + Negligable + SCDO (Jade Hotchkiss) Beta-Globin Gene - + - - + + A member of the alpha-globin family. In humans, it is encoded in the alpha-globin gene cluster or locus, located on chromosome 16. Two hemoglobin subunit zeta chains combine with two hemoglobin subunit epsilon chains to form the embryonic Hemoglobin Gower 1. - - Sufficient - SCDO:1000363 + + Sufficient + SCDO:1000363 MESH:D055543 HBAZ Haemoglobin Subunit Zeta @@ -50431,15 +49866,15 @@ Request inclusion into relevant ontology. - + - - + + An adult hemoglobin component normally present in hemolysates from human erythrocytes in concentrations of about 3%. The hemoglobin is composed of two alpha chains and two delta chains. The percentage of HbA2 varies in some hematologic disorders, but is about double in beta-thalassemia. - Request inclusion into NCIT below "Hemoglobin"/"Normal Hemoglobin". - - Sufficient - SCDO:1000364 + Request inclusion into NCIT below "Hemoglobin"/"Normal Hemoglobin". + + Sufficient + SCDO:1000364 MESH:D006443 A2, Hemoglobin HbA2 @@ -50450,29 +49885,29 @@ Request inclusion into relevant ontology. - + - - + + A mutation that contributes to decreased or absent synthesis of the delta- and beta-globin chains with a compensatory increase in expression of fetal gamma-chain synthesis. + Request inclusion into relevant ontology + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology - None Delta Beta Thalassaemia Mutation Delta Beta Thalassemia Mutation - + - + A health abnormality in a woman during pregnancy. + Suggest update to description in HP. Currently no description. + + Suggest update to description SCDO (Jade Hotchkiss) - Suggest update to description in HP. Currently no description. - - Suggest update to description HP:0002686 Maternal Health Problem Prenatal Maternal Abnormality @@ -50480,33 +49915,33 @@ Request inclusion into relevant ontology. - + - + - - + + - - + + - - + + In situ death of bone within the humeral head due to disruption of blood supply. + Request inclusion into NCIT as sub-class of "Avascular Necrosis of Humerus". + + None SCDO (Jade Hotchkiss) - Request inclusion into NCIT as sub-class of "Avascular Necrosis of Humerus". - - None Aseptic Necrosis of the Humeral Head Avascular Necrosis of the Humeral Head Osteonecrosis of the Humeral Head @@ -50514,14 +49949,14 @@ Request inclusion into relevant ontology. - + - - + + Health care services that are respectful of and responsive to the health beliefs, practices and cultural and linguistic needs of diverse patients. The provider and the patient each bring their individual learned patterns of language and culture to the health care experience which must be transcended to achieve equal access and quality health care. - - Sufficient - SCDO:1000379 + + Sufficient + SCDO:1000379 MESH:D065246 Care, Culturally Congruent Culturally Congruent Care @@ -50530,27 +49965,27 @@ Request inclusion into relevant ontology. - + - + Any kidney disorder occurring as a consequence of injury to the kidney. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Kidney Complication Renal Complication - + - + Promoter-specific RNA polymerase II transcription factor that binds to the GC box, one of the upstream promoter elements, in mammalian cells. The binding of Sp1 is necessary for the initiation of transcription in the promoters of a variety of cellular and viral GENES. - - Sufficient - SCDO:1000392 + + Sufficient + SCDO:1000392 MESH:D016329 Transcription Factor, Sp1 Sp1 Transcription Factor @@ -50558,135 +49993,135 @@ Request inclusion into relevant ontology. - + - - + + A gene component is a component of a gene. - - Sufficient - SCDO:1000394 + + Sufficient + SCDO:1000394 SIO:010444 Gene Component - + - - + + A gene regulatory component is a gene component that exerts a regulatory function. - - Sufficient - SCDO:1000395 + + Sufficient + SCDO:1000395 SIO:010085 Gene Regulatory Component - + - - + + A gene enhancer is a short region of DNA that can be bound with proteins to enhance transcription levels of genes in a gene cluster. - - Sufficient - SCDO:1000396 + + Sufficient + SCDO:1000396 SIO:010086 Gene Enhancer - + - - + + A gene promoter is a region of DNA that initiates transcription of a particular gene. - - Sufficient - SCDO:1000397 + + Sufficient + SCDO:1000397 SIO:010446 Gene Promoter - + - - + + + None - None Erythroid Specific Enhancer of Bcl11A BCL11A Erythroid Enhancer - + - - + + A characteristic that further describes the nature of data. + None SCDO (Jade Hotchkiss) - None Data Descriptor - + - - + + The predominant publication type for articles and other items indexed for NLM databases. - - Sufficient - SCDO:1000402 + + Sufficient + SCDO:1000402 MESH:D016428 Journal Article - + - - + + A characteristic or directive that further describes the nature of data sharing. + None SCDO (Jade Hotchkiss) - None Data Sharing Descriptor - + - - + + Requirements indicate additional conditions set for use of data. - Suggest update to description in DUO - - Suggest update to description + Suggest update to description in DUO + + Suggest update to description DUO:0000017 Data Use Requirements - + - - - + + + The standard method of providing feedback to study participants regarding their information (data, biological samples, genetic material) that has been shared. + None SCDO (Jade Hotchkiss) - None Policy for Feedback to Participant Policy for Returning Results Policy for Returning Results to Participant @@ -50695,103 +50130,103 @@ Request inclusion into relevant ontology. - + - - + + An element or information entity that is required to be provided in consent forms. + None SCDO (Jade Hotchkiss) - None Basic Element of a Consent Form - + - - - + + + The policy regarding participants' right to withdraw their participation in a study. + None SCDO (Jade Hotchkiss) - None Participant Withdrawal Policy - + - - + + A course or principle of action adopted or proposed by a study. + None SCDO (Jade Hotchkiss) - None Study Policy - + - - + + A statement of what the key investigational purpose of the study is. + None SCDO (Jade Hotchkiss) - None Study Focus Statement - + - - + + A statement about how the researcher is obligated by law to report if the participant is found to have a communicable disease. + None SCDO (Jade Hotchkiss) - None Communicable Disease - Report by Law Statement - + - - + + The principles of professional conduct concerning the rights and duties of the physician, relations with patients and fellow practitioners, as well as actions of the physician in patient care and interpersonal relations with patient families. - - Sufficient - SCDO:1000429 + + Sufficient + SCDO:1000429 MESH:D004992 Medical Ethics - + - - + + Concepts related to ethics, excluding types of ethics. + None SCDO (Jade Hotchkiss) - None Ethics Related Concept - + - + A protein expressed in enterocytes of the small intestine and released into the systemic circulation when there is intestinal damage. This protein plays a role in binding to saturated long-chain fatty acids with a high affinity and to unsaturated long-chain fatty acids with less affinity. + Suggest update to description in NCIT + + + Few but definitions not specific enough - Suggest update to description in NCIT - - - Few but definitions not specific enough NCIT:C29616 FABPI Fatty Acid-Binding Protein, Intestinal @@ -50803,15 +50238,15 @@ Request inclusion into relevant ontology. - + - + The level of intestinal fatty-acid binding protein in the systemic circulation (serum). + Used to provide the evidence for intestinal injury due to VOC affecting the splanchnic vasculature. + None SCDO (Jade Hotchkiss) - Used to provide the evidence for intestinal injury due to VOC affecting the splanchnic vasculature. - None Serum Intestinal Fatty-Acid Binding Protein Level Measured in ng/ml Serum iFABP Level @@ -50819,30 +50254,30 @@ Request inclusion into relevant ontology. - + - + Damage inflicted on the intestine. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Intestinal Damage Intestinal Injury - + - + Adverse functional, metabolic, or structural changes in ischemic tissues resulting from the restoration of blood flow to the tissue (reperfusion), including swelling; hemorrhage; necrosis; and damage from free radicals. The most common instance is myocardial reperfusion injury. + + Sufficient + SCDO:1000436 - - Sufficient - SCDO:1000436 EFO:0002687 Hypoxia-Reoxygenation Injury Hypoxia/Reperfusion Injury @@ -50855,27 +50290,27 @@ Request inclusion into relevant ontology. - + - + An increased circulating blood concentration of the intestinal fatty-acid binding protein. + None SCDO (Jade Hotchkiss) - None Significantly high serum iFABP levels is evidence of intestinal injury. Elevated Serum iFABP Level - + - + The level of L-selectin in the systemic circulation (serum). + None SCDO (Jade Hotchkiss) - None Serum CD62L Level Soluble CD62L Serum L-Selectin Level @@ -50883,54 +50318,54 @@ Request inclusion into relevant ontology. - + - + The number of aged neutrophils in a specified volume of blood, usually 1 cubic millimeter. + None SCDO (Jade Hotchkiss) - None Activated Neutrophil Count Aged Neutrophil Count - + - - + + A medication that is typically used for indications other than pain control but provides control of pain in some painful diseases. + None - None Adjuvant Analgesic Agent Adjunct Analgesic Agent - + - - + + An infusion of ketamine at a low dose (up to 5 µg/kg/min). + None - None Low-dose ketamine infusion may be considered as an adjunct analgesic agent in patients with vaso-occlusive episodes who report continued severe pain despite high-dose opioid therapy, particularly those experiencing opioid-induced adverse effects. Low-Dose Ketamine Infusion - + - - + + Pain that may be caused by or related to cellular, tissue, and systemic changes that occur during neoplasm growth, tissue invasion, and metastasis. - - Sufficient - SCDO:1000452 + + Sufficient + SCDO:1000452 MESH:D000072716 Cancer-Related Pain Pains, Neoplasm-Related @@ -50939,958 +50374,958 @@ Request inclusion into relevant ontology. - + - - + + The current age of a patient, calculated using the current date and the patient's date of birth and provided in years. + None SCDO (Jade Hotchkiss) - None Calculated Current Age in Years Calculated Current Age (Years) - + - + A type of consent that includes an aspect of timing (i.e. an indication of when consent was acquired). + Request inclusion into ICO below "Informed Consent". + None SCDO (Jade Hotchkiss) - Request inclusion into ICO below "Informed Consent". - None Temporal Consent Concept - + - - + + Consent given prior to enrollment. + Request inclusion into the Informed Consent Ontology. + None SCDO (Jade Hotchkiss) - Request inclusion into the Informed Consent Ontology. - None Prospective Consent - + - - + + Consent that is taken later after enrollment into study especially in emergency situations. + Request inclusion into the Informed Consent Ontology. + None SCDO (Victoria Nembaware) - Request inclusion into the Informed Consent Ontology. - None Deferred Consent - + - - - + + + Informed consent given prior to enrollment. + Request inclusion into ICO below "Informed Consent". + None SCDO (Victoria Nembaware) - Request inclusion into ICO below "Informed Consent". - None Prospective Informed Consent - + - + Consent obtained at a population level through public/community engagement where individual consenting is not feasible. This is normally done for low risk studies and/or in case of emergencies. + Request inclusion into the Informed Consent Ontology. + None SCDO (Victoria Nembaware) - Request inclusion into the Informed Consent Ontology. - None Waived Consent - + - - + + A decision made by a research ethics committee. + Request inclusion into the Informed Consent Ontology. + None SCDO (Jade Hotchkiss) - Request inclusion into the Informed Consent Ontology. - None Research Ethics Committee Decision - + - - + + When a research ethics committee approves a study's application for approval of their proposed research. + Request inclusion into the Informed Consent Ontology. + None SCDO (Jade Hotchkiss) - Request inclusion into the Informed Consent Ontology. - None Approval of Ethics - + - - + + When a research ethics committee declines a study's application for approval of their proposed research. + Request inclusion into the Informed Consent Ontology. + None SCDO (Jade Hotchkiss) - Request inclusion into the Informed Consent Ontology. - None Disapproval of Ethics - + - - + + A method in which a patient or their legal representative provides consent. + Request inclusion into the Informed Consent Ontology. + None SCDO (Jade Hotchkiss) - Request inclusion into the Informed Consent Ontology. - None Mode of Providing Consent - + - - + + When the participant or a legal representative or family member provides consent by filling out and/or signing a written form. + Request inclusion into the Informed Consent Ontology. + None SCDO (Jade Hotchkiss) - Request inclusion into the Informed Consent Ontology. - None Written Consent - + - - + + When the participant communicates consent orally rather than by filling out and signing a written form. Normally a witness is present when verbal consent is given. + Request inclusion into the Informed Consent Ontology. + None SCDO - Request inclusion into the Informed Consent Ontology. - None Verbal Consent - + - + A unique identifier assigned to a study participant's data when it is registered in the SickleInAfrica data registry. + None SCDO (Jade Hotchkiss) - None SickleInAfrica Participant Number - + - - + + The name of the country where the sample or data was collected. - - Few but definitions not specific enough + + Few but definitions not specific enough FLU:0000831 Country of Data Collection - + - - + + The rules by which data are described and recorded. + + Not relevant to context of sickle cell SCDO (Jade Hotchkiss) - - Not relevant to context of sickle cell Data Standards - + - - + + A data element used to capture or facilitate the capture of data in a clinical or research assessment. + None SCDO (Jade Hotchkiss) - None Clinical or Research Assessment Data Element - + - - + + A type of question pertaining to a clinical or research assessment data element. + None SCDO (Jade Hotchkiss) - None Clinical or Research Assessment Question Type - + - - + + deprecated Field Type true - + - - + + deprecated Calculation Field Type true - + - - + + deprecated Checkbox Field Type true - + - - + + deprecated Descriptive Field Type true - + - - + + deprecated Dropdown Field Type true - + - - + + deprecated Dropdown Multiple Choice Field Type true - + - - + + deprecated Dropdown Single Choice Field Type true - + - - + + deprecated File Upload Field Type true - + - - + + deprecated Radio Field Type true - + - - + + deprecated Text Box Field Type true - + - - + + deprecated Notes Box Field Type true - + - - + + deprecated Slider - Visual Analog Scale true - + - - + + The situation, with regard to obtaining consent from a respondent, at a particular stage during a process. + None SCDO (Jade Hotchkiss) - None Consent Status - + - - + + A question that provides the respondent with specific answer options to choose from. + None SCDO (Jade Hotchkiss) - None Close-Ended Question - + - - + + A question that allows the respondent to give their own answer instead of selecting an answer from answer options. + None SCDO (Jade Hotchkiss) - None Open-Ended Question - + - - + + A close-ended question that provides two possible answers. + + None SCDO (Jade Hotchkiss) - - None Dichotomous Question - + - - + + A close-ended question that provides multiple answers for respondents to select from and allows for the selection of multiple options. + None SCDO (Jade Hotchkiss) - None Multiple Choice Multiple Selection Question - + - - + + A close-ended question that provides multiple answers for respondents to select from but allows for the selection of only one option. + None SCDO (Jade Hotchkiss) - None Multiple Choice Single Selection Question - + - - + + A dichotomous question that has answer options "true" and "false". + None SCDO (Jade Hotchkiss) - None True-False Question - + - - + + A dichotomous question that has answer options "yes" and "no". + None SCDO (Jade Hotchkiss) - None Yes-No Question - + - - + + A open ended question that restricts the nature of the text answer that can be provided by the respondent. + None SCDO (Jade Hotchkiss) - None Open-Ended Question - Restricted - + - - + + A open ended question that allows the respondent to respond in free text, without any restrictions on the nature of the text answer provided. + None SCDO (Jade Hotchkiss) - None Open-Ended Question - Free Text - + - - + + A data element in a SickleInAfrica data capture instrument. + None SCDO (Jade Hotchkiss) - None SickleInAfrica DE SickleInAfrica Data Element - + - - + + A data element in the SickleInAfrica core data capture instrument. + None SCDO (Jade Hotchkiss) - None SickleInAfrica Core DE SickleInAfrica Core Data Element - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the concentration of albumin in the respondent's urine. - Urinary albumin concentration - urinary_microalbumin_conc - Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise) - µg/mL; PX141501 - 3 - Number - text + Urinary albumin concentration + urinary_microalbumin_conc + Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise) + µg/mL; PX141501 + 3 + Number + text SickleInAfrica CDE - Urinary Albumin Concentration Question - + - - + + - - + + - + - + - + - + - - + + The Sickle in Africa core data element that records whether the respondent has consented as necessary. - 1, Yes + 1, Yes 2, No -7, Refused --9, Don't Know - Has the patient consented? - consent_obtained - Consent - 1 - radio +-9, Don't Know + Has the patient consented? + consent_obtained + Consent + 1 + radio SickleInAfrica CDE - Informed Consent Obtained Question - + - - + + An indication of whether informed consent was obtained from the respondent and/or their proxy. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Informed Consent Obtained - + - - + + Voluntary authorization given by a respondent and/or their proxy to be enrolled into a study as a research subject. + Request inclusion into relevant ontology, perhaps the ICO. + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology, perhaps the ICO. - None Study Enrollment Consent - + - - + + Voluntary authorization given by a study respondent and/or their proxy to have their specimen(s) stored. + Request inclusion into relevant ontology, perhaps the ICO. + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology, perhaps the ICO. - None Specimen Storage Consent - + - - + + Voluntary authorization given by a study paticipant to have their genetic material stored. + Request inclusion into relevant ontology, perhaps the ICO. + None SCDO (Jade Hotchkiss) - Request inclusion into relevant ontology, perhaps the ICO. - None Genetic Material Storage Consent - + - - + + - - + + - + - - + + - - + + - - + + - - + + - + 0 - + 4 The Sickle in Africa core data element that records the type(s) of informed consent obtained from the participant. - 1, Study Enrollment Consent + 1, Study Enrollment Consent 2, Specimen Storage Consent 3, Genetic Material Storage Consent -4, Broad Consent - Type(s) of informed consent obtained - consent_type - Consent - 2 - checkbox +4, Broad Consent + Type(s) of informed consent obtained + consent_type + Consent + 2 + checkbox SickleInAfrica CDE - Type of Informed Consent Obtained Question - + - - + + An indication of the type of informed consent that was obtained from the respondent and/or their proxies. + None SCDO (Jade Hotchkiss) - None Type of Informed Consent Obtained - + - - - + + + Time-related information that can be observed and is related to consent. + None SCDO (Jade Hotchkiss) - None Temporal Observable of Consent - + - - + + The current age of a patient, calculated using the current date and the patient's date of birth. + None SCDO (Jade Hotchkiss) - None Calculated Current Age - + - - + + - - + + - + The Sickle in Africa core data element that records the date on which the respondent signed the consent form for the relevant study. - Date subject signed consent (dd/mm/yyyy) - consent_date - Consent - 3 - date_dmy - text + Date subject signed consent (dd/mm/yyyy) + consent_date + Consent + 3 + date_dmy + text SickleInAfrica CDE - Date of Signing Consent Question - + - - + + - - + + - - + + The Sickle in Africa core data element that records the name of the person who managed the process of consenting the respondent. - Consented by: - consented_by - Consent - 4 - text + Consented by: + consented_by + Consent + 4 + text SickleInAfrica CDE - Consented By Question - + - - + + An indication of whether the respondent has had a blood transfusion since their last hospital visit. This is any transfusion before enrolment if it is the patient's first hospital visit. + None SCDO (Jade Hotchkiss) - None Blood Transfusion Since Last Visit - + - - + + An indication of whether the consent form used for obtaining informed consent from the respondent has been uploaded to the relevant electronic system. + None SCDO (Jade Hotchkiss) - None Consent Form Uploaded - + - - + + The name of the person who conducted consenting of the respondent. + None SCDO (Jade Hotchkiss) - None Consented By - + - - + + Time-related information that can be observed. + Few but definitions not freely available SCDO (Jade Hotchkiss) - Few but definitions not freely available Temporal Observable - + - - - + + + Time-related information that can be observed and is related to a diagnosis. + None SCDO (Jade Hotchkiss) - None Diagnosis Temporal Observable - + - - + + - - + + - + The Sickle in Africa core data element that records the visit date, in the format dd/mm/yyyy. - Visit date (dd/mm/yyyy) - date_today - Demographics - 1 - date_dmy - text + Visit date (dd/mm/yyyy) + date_today + Demographics + 1 + date_dmy + text SickleInAfrica CDE - Visit Date Question - + - - + + - - + + - - + + The Sickle in Africa core data element that records the site-specific unique identifier that was assigned to the study participant by the data collectors at the data collection site. - Site participant number - participant_number - Demographics - Site-specific ID eg. GH20181234 for Ghana, NG20184321 for Nigeria or TZ20180001 for Tanzania - 3 - text + Site participant number + participant_number + Demographics + Site-specific ID eg. GH20181234 for Ghana, NG20184321 for Nigeria or TZ20180001 for Tanzania + 3 + text SickleInAfrica CDE - Site Participant Number Question - + - - + + - - + + - + The Sickle in Africa core data element that records the respondent's date of birth in the format dd/mm/yyyy. - Date of birth (dd/mm/yyyy) - date_of_birth - Demographics - 9 - date_dmy - text + Date of birth (dd/mm/yyyy) + date_of_birth + Demographics + 9 + date_dmy + text SickleInAfrica CDE - Date of Birth Question - + - - + + The current age of a patient, calculated using the current date and the patient's date of birth and provided in months. + None SCDO (Jade Hotchkiss) - None Calculated Current Age in Months Calculated Current Age (Months) - + - - + + The length of time that a person has lived since their birth up until the current day, as reported in years by the respondent. + None SCDO (Jade Hotchkiss) - None Self-Reported Age in Years Self-Reported Current Age in Years Self-Reported Current Age (Years) @@ -51898,386 +51333,386 @@ Request inclusion into relevant ontology. - + - - + + - - + + - - + + The Sickle in Africa core data element that records the respondent's age, as reported by the respondent in years. - Self-reported age (in years) - age_on_day_of_visit - Demographics - Age on day of visit - 11 - Number - 0 - 125 - RH - text + Self-reported age (in years) + age_on_day_of_visit + Demographics + Age on day of visit + 11 + Number + 0 + 125 + RH + text SickleInAfrica CDE - Self-Reported Age Question - + - - + + - - + + - + - + - + - + - + - - + + The Sickle in Africa core data element that records the respondent's current marital status. - 1, Married + 1, Married 2, Widowed 3, Divorced 4, Separated -5, Never been married/Annulled - Current marital status - marital_status - Demographics - 15 - radio +5, Never been married/Annulled + Current marital status + marital_status + Demographics + 15 + radio SickleInAfrica CDE - Current Marital Status Question - + - - + + - - + + - - + + The Sickle in Africa core data element that records the date on which the respondent last received a blood transfusion. + Date of blood transfusion + transfusion_date + Management Details + 8 + date_dmy + [blood_transfusion] = "Yes" + text SCDO (Jade Hotchkiss) - Date of blood transfusion - transfusion_date - Management Details - 8 - date_dmy - [blood_transfusion] = "Yes" - text SickleInAfrica CDE - Date of Transfusion Question - + - - + + - - + + - - + + The Sickle in Africa core data element that records the type of SCD test that was used to diagnose the respondent, in the case where the type of test was not listed as an answer option in a previous data element. - If other test, please specify: - other_test - SCD Diagnosis Details - 6 - [type_of_test] = '6' - text + If other test, please specify: + other_test + SCD Diagnosis Details + 6 + [type_of_test] = '6' + text SickleInAfrica CDE - SCD Other Test Question - + - - + + - - + + - + - + - + - + - + The Sickle in Africa core data element that records the respondent's sex. - 1, Male + 1, Male 2, Female 3, Intersex --7, Refused - Respondent's sex - respondent_sex - Demographics - 14 - radio +-7, Refused + Respondent's sex + respondent_sex + Demographics + 14 + radio SickleInAfrica CDE - Sex Question - + - - + + - - + + - + - + - - + + The Sickle in Africa core data element that records whether the respondent knows the date of their SCD diagnosis. - 1, Yes -0, No - Is date of SCD diagnosis known? - diagnosis_date_known - SCD Diagnosis Details - 1 - yesno + 1, Yes +0, No + Is date of SCD diagnosis known? + diagnosis_date_known + SCD Diagnosis Details + 1 + yesno SickleInAfrica CDE - Date of Diagnosis Known Question - + - - + + Information or a description that further describes a diagnosis. + None SCDO (Jade Hotchkiss) - None Diagnosis Descriptor - + - - + + An indication of whether the date of the respondent's diagnosis of a disease is known by the respondent or the respondent's guardian. + None SCDO (Jade Hotchkiss) - None Date of Diagnosis Known - + - - + + An indication of whether the date of the respondent's SCD diagnosis is known by the respondent or the respondent's guardian. + None SCDO (Jade Hotchkiss) - None Date of SCD Diagnosis Known - + - - + + - - + + - - + + The Sickle in Africa core data element that records the respondent's date of diagnosis in the format dd/mm/yyyy. - Date of SCD diagnosis (dd/mm/yyyy) - exact_diagnosis_date - SCD Diagnosis Details - 2 - date_dmy - [diagnosis_date_known] = '1' - text + Date of SCD diagnosis (dd/mm/yyyy) + exact_diagnosis_date + SCD Diagnosis Details + 2 + date_dmy + [diagnosis_date_known] = '1' + text SickleInAfrica CDE - Date of Diagnosis Question - + - + The date on which a diagnosis of sickle cell disease was made. + None SCDO (Jade Hotchkiss) - None Date of SCD Diagnosis - + - - - + + + The date on which a patient received a blood transfusion. + None SCDO (Jade Hotchkiss) - None Date of Blood Transfusion - + - + The year in which a sickle cell disease diagnosis was made. + None SCDO (Jade Hotchkiss) - None Year of SCD Diagnosis - + - - + + The month when a diagnosis was assigned to an individual's condition. + None SCDO (Jade Hotchkiss) - None Month of Diagnosis - + - - + + The month when a sickle cell disease diagnosis was made. + None SCDO (Jade Hotchkiss) - None Month of SCD Diagnosis - + - - + + The Sickle in Africa core data element that records the month of the year in which the respondent was diagnosed with SCD. - -9, Don't know + -9, Don't know 1, 1 2, 2 3, 3 @@ -52289,332 +51724,332 @@ Request inclusion into relevant ontology. 9, 9 10, 10 11, 11 -12, 12 - Month of SCD diagnosis - month_of_diagnosis - SCD Diagnosis Details - 4 - [diagnosis_date_known] = '0' - dropdown +12, 12 + Month of SCD diagnosis + month_of_diagnosis + SCD Diagnosis Details + 4 + [diagnosis_date_known] = '0' + dropdown SickleInAfrica CDE - Month of Diagnosis Question - + - + A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms. - - Sufficient - SCDO:1000572 + + Sufficient + SCDO:1000572 SIO:001331 Diagnosis - + - - + + - - + + - + - + - + - - + + - - + + - - + + The Sickle in Africa core data element that records the respondent's SCD test result. - 1, SS + 1, SS 2, SBThal 3, SC 4, AS -5, Other - SCD test result - scd_test_result - SCD Diagnosis Details - SS = Sickle Cell Disease-SS | SBThal = Sickle Beta Thalassemia | SC = Sickle Cell Disease-SC | AS = Sickle Cell Trait - 3 - RH - dropdown +5, Other + SCD test result + scd_test_result + SCD Diagnosis Details + SS = Sickle Cell Disease-SS | SBThal = Sickle Beta Thalassemia | SC = Sickle Cell Disease-SC | AS = Sickle Cell Trait + 3 + RH + dropdown SickleInAfrica CDE - SCD Test Result Question - + - + - + The result of a medical investigation to identify the type of sickle cell disease that a person has. + None SCDO (Jade Hotchkiss) - None SCD Test Result - + - - + + - - + + - + - + - - + + - - + + - - + + - - + + - - + + - - + + The Sickle in Africa core data element that records the type of SCD test that was used to diagnose the respondent. - 1, HPLC + 1, HPLC 2, HBE 3, IEF 4, Basique 5, Acide 6, Sickle SCAN rapid test -7, Other - Type of test? - type_of_test - SCD Diagnosis Details - HPLC = High-Performance Liquid Chromatography| HBE = Hemoglobin Electrophoresis | IEF = Isoelectric Focusing| Basique = Basique SCD Test | Acide = Acide SCD Test - 5 - dropdown +7, Other + Type of test? + type_of_test + SCD Diagnosis Details + HPLC = High-Performance Liquid Chromatography| HBE = Hemoglobin Electrophoresis | IEF = Isoelectric Focusing| Basique = Basique SCD Test | Acide = Acide SCD Test + 5 + dropdown SickleInAfrica CDE - Type of SCD Test Question - + - - + + A piece of information that further describes a diagnostic measurement. + None SCDO (Jade Hotchkiss) - None Diagnostic Measurement Descriptor - + - - + + The type of test that was used to obtain a sickle cell disease diagnosis. + None SCDO (Jade Hotchkiss) - None Type of SCD Test - + - - + + - - + + - - + + The Sickle in Africa core data element that records the respondent's SCD test result, in the case where the specific result was not listed as an answer option in a previous data element. - If other SCD test result, please specify: - other_scd_test_result - SCD Diagnosis Details - 4 - text + If other SCD test result, please specify: + other_scd_test_result + SCD Diagnosis Details + 4 + text SickleInAfrica CDE - SCD Test Other Result Question - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + The Sickle in Africa core data element that records the respondent's ABO Blood Group. - SCDO (Jade Hotchkiss) - 1, A+ + 1, A+ 2, A- 3, B+ 4, B- 5, O+ 6, O- 7, AB+ -8, AB- - ABO blood group - abo_blood_group - SCD Diagnosis Details - 7 - dropdown +8, AB- + ABO blood group + abo_blood_group + SCD Diagnosis Details + 7 + dropdown + SCDO (Jade Hotchkiss) SickleInAfrica CDE - Blood Group Question - + - - - - + + + + A blood test that uses the principles of gel electrophoresis to separate out the various types of hemoglobin in order to determine the level of different types of hemoglobin in the blood. + Placed as sub-class here according to position in the "Read Codes, Clinical Terms Version 3 (CTV3)" Ontology + Few but definitions not available - Placed as sub-class here according to position in the "Read Codes, Clinical Terms Version 3 (CTV3)" Ontology - Few but definitions not available Electrophoresis - hemoglobin HBE Haemoglobin Electrophoresis @@ -52629,13 +52064,13 @@ Request inclusion into relevant ontology. - + - + A blood type containing type A red blood cell surface markers, with the presence of a protein called rhesus (Rh) factor. + Few but definitions not available SCDO (Kambe Banda) - Few but definitions not available A+ Blood group A Rh(D) positive Type A blood, Rh positive @@ -52644,13 +52079,13 @@ Request inclusion into relevant ontology. - + - + A blood type containing type A red blood cell surface markers, with the absence of a protein called rhesus (Rh) factor. SCDO (Kambe Banda) - Few but definitions not available + Few but definitions not available A- Blood group A Rh(D) negative Type A blood, Rh negative @@ -52659,13 +52094,13 @@ Request inclusion into relevant ontology. - + - + A blood type containing type B red blood cell surface markers, with the presence of a protein called rhesus (Rh) factor. + Few but definitions not available SCDO (Kambe Banda) - Few but definitions not available B+ Blood group B Rh(D) positive Type B blood, Rh positive @@ -52674,13 +52109,13 @@ Request inclusion into relevant ontology. - + - + A blood type containing type B red blood cell surface markers, with the absence of a protein called rhesus (Rh) factor. + Few but definitions not available SCDO (Kambe Banda) - Few but definitions not available B- Blood group B Rh(D) negative Type B blood, Rh negative @@ -52689,13 +52124,13 @@ Request inclusion into relevant ontology. - + - + A blood type containing no surface markers on red blood cells, with the presence of a protein called rhesus (Rh) factor. + Few but definitions not available SCDO (Kambe Banda) - Few but definitions not available Blood group O Rh(D) positive O+ Type O blood, Rh positive @@ -52704,13 +52139,13 @@ Request inclusion into relevant ontology. - + - + A blood type containing no surface markers on red blood cells, with the absence of a protein called rhesus (Rh) factor. + Few but definitions not available SCDO (Kambe Banda) - Few but definitions not available Blood group O Rh(D) negative O- Type O blood, Rh negative @@ -52719,13 +52154,13 @@ Request inclusion into relevant ontology. - + - + A blood type containing both type A and B red blood cell surface markers, with the presence of a protein called rhesus (Rh) factor. + Few but definitions not available SCDO (Kambe Banda) - Few but definitions not available AB+ Blood group AB Rh(D) positive Type AB blood, Rh positive @@ -52734,13 +52169,13 @@ Request inclusion into relevant ontology. - + - + A blood type containing both type A and B red blood cell surface markers, with the absence of a protein called rhesus (Rh) factor + Few but definitions not available SCDO (Kambe Banda) - Few but definitions not available AB- Blood group AB Rh(D) negative Type AB blood, Rh negative @@ -52749,710 +52184,710 @@ Request inclusion into relevant ontology. - + - + - + Information about how a patient's SCD is being managed. + None SCDO (Jade Hotchkiss) - None SCD Management Details - + - - + + - - + + - + - + - - + + The Sickle in Africa core data element that records the respondent's hydroxyurea use status (i.e. an indication of whether the respondent is using hydroxyurea). - 1, Yes -0, No - Using hydroxyurea - using_hydroxyurea - Management Details - 1 - RH - yesno + 1, Yes +0, No + Using hydroxyurea + using_hydroxyurea + Management Details + 1 + RH + yesno SickleInAfrica CDE - Hydroxyurea Use Question - + - - - + + + An indication of whether the respondent is using hydroxyurea. + None SCDO (Jade Hotchkiss) - None Hydroxyurea Use Status - + - - + + - - + + - - + + The Sickle in Africa core data element that records the date on which the respondent started hydroxyurea therapy, in the format dd/mm/yyyy. - Date of initiation of hydroxyurea therapy (dd/mm/yyyy) - date_of_initiation_of_hydr - Management Details - 2 - date_dmy - text + Date of initiation of hydroxyurea therapy (dd/mm/yyyy) + date_of_initiation_of_hydr + Management Details + 2 + date_dmy + text SickleInAfrica CDE - Hydroxyurea Initiation Date Question - + - - + + The date on which hydroxyurea therapy was initiated. + None SCDO (Jade Hotchkiss) - None Date of Hydroxyurea Therapy Initiation - + - - + + - - + + - + - + - + - - + + The Sickle in Africa core data element that records whether the respondent is using penicillin V as a prophylaxis against bacterial infections. - 1, Yes + 1, Yes 2, No --6, NA - Using penicillin V (prophylaxis) - penicillin_v_prophylaxis - Management Details - 3 - RH - radio +-6, NA + Using penicillin V (prophylaxis) + penicillin_v_prophylaxis + Management Details + 3 + RH + radio SickleInAfrica CDE - Penicillin V Use Question - + - - - + + + An indication of whether the respondent is using penicillin V prophylaxis. + None SCDO (Jade Hotchkiss) - None Penicillin V Prophylaxis Use Status - + - - + + - - + + - + - + - - + + The Sickle in Africa core data element that records the respondent's folic acid use status (i.e. an indication of whether the respondent is using folic acid). - 1, Yes -0, No - Using folic acid - folic_acid - Management Details - 5 - RH - yesno + 1, Yes +0, No + Using folic acid + folic_acid + Management Details + 5 + RH + yesno SickleInAfrica CDE - Folic Acid Use Question - + - - - + + + An indication of whether the respondent is using folic acid. + None SCDO (Jade Hotchkiss) - None Folic Acid Use Status - + - - - + + + An indication of whether the respondent is using malaria prophylaxis. + None SCDO (Jade Hotchkiss) - None Malaria Prophylaxis Status - + - - + + - - + + - + - + - + - - + + The Sickle in Africa core data element that records whether the respondent is using malaria chemoprophylaxis (drugs that prevent malaria). - 1, Yes + 1, Yes 2, No --6, NA - Using malaria chemoprophylaxis - antimalaria_prophylaxis - Management Details - 4 - radio +-6, NA + Using malaria chemoprophylaxis + antimalaria_prophylaxis + Management Details + 4 + radio SickleInAfrica CDE - Malaria Prophylaxis Question - + - - + + - - + + - + - + - - + + The Sickle in Africa core data element that records whether the respondent's pneumococcal vaccination is up to date. - 1, Yes -0, No - Pneumococcal vaccination up to date - pneumococcal_vacc_uptodate - Management Details - 6 - RH - yesno + 1, Yes +0, No + Pneumococcal vaccination up to date + pneumococcal_vacc_uptodate + Management Details + 6 + RH + yesno SickleInAfrica CDE - Pneumococcal Vaccination Question - + - - + + An indication of whether the respondent is up to date with their pneumococcal vaccinations. + None SCDO (Jade Hotchkiss) - None Pneumococcal Vaccination Status - + - - + + The person who recorded the information about how a patient's condition is being managed. + None SCDO (Jade Hotchkiss) - None Management Details Added By - + - - + + - + Any assay which measures the amount, level or concentration of urea in whole blood. - - Sufficient - SCDO:1000605 + + Sufficient + SCDO:1000605 MMO:0000272 Blood Urea Analysis - + - - - + + + The date on which the respondent's management details were added/recorded. + None SCDO (Jade Hotchkiss) - None Management Details Add Date - + - - + + - - + + - + - + The Sickle in Africa core data element that collects the red blood cell count in the respondent's blood, as measured by a complete blood count. - Red blood cell count (RBC) - cbc_redbloodcount - Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) - million cells/µL - 1 - text + Red blood cell count (RBC) + cbc_redbloodcount + Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) + million cells/µL + 1 + text SickleInAfrica CDE - Red Blood Cell Count Question - + - - + + - - + + - + - + The Sickle in Africa core data element that collects the white blood cell count in the respondent's blood, as measured by a complete blood count. - White blood cell count (WBC) - cbc_whitebloodcount - Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) - 1000 cells/µL - 2 - text + White blood cell count (WBC) + cbc_whitebloodcount + Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) + 1000 cells/µL + 2 + text SickleInAfrica CDE - White Blood Cell Count Question - + - + Any structural abnormality of leukocytes (nucleated cells of the myeloid or lymphoid lineages, found in blood or other tissue). - Suggest the HPO update their definition. Theirs currently is "An abnormality of leukocytes." - - Suggest update to description + Suggest the HPO update their definition. Theirs currently is "An abnormality of leukocytes." + + Suggest update to description HP:0001881 Abnormal Leukocyte Morphology - + - - + + - - + + - + - + The Sickle in Africa core data element that collects the platelet count in the respondent's blood, as measured by a complete blood count. - Platelet count - cbc_platelet_count - Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) - 1000 cells/µL - 3 - text + Platelet count + cbc_platelet_count + Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) + 1000 cells/µL + 3 + text SickleInAfrica CDE - Platelet Count Question - + - - + + - - + + - + - + The Sickle in Africa core data element that collects the concentration of hemoglobin in the respondent's blood, as measured by a complete blood count. - Hemoglobin - cbc_hemoglobin - Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) - g/dL - 4 - text + Hemoglobin + cbc_hemoglobin + Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) + g/dL + 4 + text SickleInAfrica CDE - Hemoglobin - CBC Question - + - - + + - - + + - + - + The Sickle in Africa core data element that collects the respondent's mean cell volume (MCV), as measured by a complete blood count. - Mean cell volume (MCV) - cbc_mean_cell_volume - Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) - fL - 5 - text + Mean cell volume (MCV) + cbc_mean_cell_volume + Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) + fL + 5 + text SickleInAfrica CDE - Mean Cell Volume Question - + - - + + - - + + - + - + The Sickle in Africa core data element that collects the respondent's mean cell hemoglobin (MCH), as measured by a complete blood count. - Mean cell hemoglobin (MCH) - cbc_mean_cell_hemoglobin - Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) - pg - 6 - text + Mean cell hemoglobin (MCH) + cbc_mean_cell_hemoglobin + Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) + pg + 6 + text SickleInAfrica CDE - Mean Cell Hemoglobin Question - + - - + + - - + + - + - + The Sickle in Africa core data element that collects the respondent's mean cell hemoglobin concentration (MCHC), as measured by a complete blood count. - Mean cell hemoglobin concentration (MCHC) - cbc_mchc - Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) - g/dL - 7 - text + Mean cell hemoglobin concentration (MCHC) + cbc_mchc + Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) + g/dL + 7 + text SickleInAfrica CDE - Mean Cell Hemoglobin Concentration Question - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the respondent's red cell distribution width, as measured by a complete blood count. - Red cell distribution width (RDW) - cbc_redcelldistributionwidth - Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) - % - 8 - text + Red cell distribution width (RDW) + cbc_redcelldistributionwidth + Laboratory Results: Complete Blood Count (PhenX protocol PX220501 unless stated otherwise) + % + 8 + text SickleInAfrica CDE - Red Cell Distribution Width Question - + - + - + - + - + - - + + Red blood cell distribution width (RDW or RDW-CV or RCDW and RDW-SD) is a measure of the range of variation of red blood cell (RBC) volume that is reported as part of a standard complete blood count. Usually red blood cells are a standard size of about 6-8 μm in diameter. Certain disorders, however, cause a significant variation in cell size. Higher RDW values indicate greater variation in size. Normal reference range of RDW-CV in human red blood cells is 11.5-14.5%.[1] If anemia is observed, RDW test results are often used together with mean corpuscular volume (MCV) results to determine the possible causes of the anemia. It is mainly used to differentiate an anemia of mixed causes from an anemia of a single cause. - - Sufficient - SCDO:1000638 + + Sufficient + SCDO:1000638 EFO:0009188 RCDW RDW @@ -53462,50 +52897,50 @@ Request inclusion into relevant ontology. - + - - + + - - + + - + - + The Sickle in Africa core data element that collects the level of serum creatinine in the respondent's blood. - Serum creatinine concentration - serum_creatinine_conc - Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise) - mg/dL; PX141401 - 1 - Number - text + Serum creatinine concentration + serum_creatinine_conc + Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise) + mg/dL; PX141401 + 1 + Number + text SickleInAfrica CDE - Serum Creatinine Concentration Question - + - + An abnormally increased amount of creatinine in the blood. - Suggest update to description in HPO (include the word "abnormally") - - Suggest update to description + Suggest update to description in HPO (include the word "abnormally") + + Suggest update to description HP:0003259 Elevated Creatinine High Blood Creatinine Level @@ -53516,279 +52951,279 @@ Request inclusion into relevant ontology. - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the concentration of creatinine in the respondent's urine. - Urinary creatinine concentration - urinary_creatinine_conc - Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise) - mg/dL; PX141601 - 4 - Number - text + Urinary creatinine concentration + urinary_creatinine_conc + Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise) + mg/dL; PX141601 + 4 + Number + text SickleInAfrica CDE - Urinary Creatinine Concentration Question - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the level of alanine aminotransferase in the respondent's blood. + Alanine aminotransferase level + results_of_alanine_at_assay + Liver Function Assay (PhenX protocol PX190801 unless stated otherwise) + IU/L + 1 + Number + text SCDO (Jade Hotchkiss) - Alanine aminotransferase level - results_of_alanine_at_assay - Liver Function Assay (PhenX protocol PX190801 unless stated otherwise) - IU/L - 1 - Number - text SickleInAfrica CDE - Alanine Aminotransferase Level Question - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the level of aspartate aminotransferase in the respondent's blood. + Aspartate aminotransferase level + results_of_aspartate_at_assay + Liver Function Assay (PhenX protocol PX190801 unless stated otherwise) + IU/L + 2 + Number + text SCDO (Jade Hotchkiss) - Aspartate aminotransferase level - results_of_aspartate_at_assay - Liver Function Assay (PhenX protocol PX190801 unless stated otherwise) - IU/L - 2 - Number - text SickleInAfrica CDE - Aspartate Aminotransferase Level Question - + - - + + - - + + - + - + The Sickle in Africa core data element that collects the level of alkaline phosphatase in the respondent's blood. + Alkaline phosphatase level + results_of_alkaline_phosphatase_assay + Liver Function Assay (PhenX protocol PX190801 unless stated otherwise) + IU/L + 3 + Number + text SCDO (Jade Hotchkiss) - Alkaline phosphatase level - results_of_alkaline_phosphatase_assay - Liver Function Assay (PhenX protocol PX190801 unless stated otherwise) - IU/L - 3 - Number - text SickleInAfrica CDE - Alkaline Phosphatase Level Question - + - + - + A quantitative measurement of alkaline phosphatase present in a blood sample. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Alkaline Phosphatase Test Alkaline Phosphatase Blood Test - + - - - + + + A multiplexed qualitative point-of-care immunoassay used for the rapid diagnosis of sickle cell disorders. The test is made up of three indicators which detect the presence of hemoglobins A, S, and C, allowing the user to rapidly distinguish between normal, carrier, and sickle cell samples. + None SCDO (Jade Hotchkiss) - None Sickle SCAN Rapid Test - + - + An indication of a person's current status in terms of living with a person as though married (in a romantic relationship and living together but not married). + None SCDO (Jade Hotchkiss) - None Current Partner Status - + - + An indication of whether a person has previously lived with someone as though married (in a romantic relationship and lived together but were not married). + None SCDO (Jade Hotchkiss) - None Past Partner Status - + - - + + - - + + - + - + The Sickle in Africa core data element that collects the level of billirubin in the respondent's blood. - Total billirubin concentration - billirubin_total_billirubin_conc - Laboratory Results: Bilirubin Level (PhenX protocol PX0810901 unless stated otherwise) - mg/dL - 1 - Number - text + Total billirubin concentration + billirubin_total_billirubin_conc + Laboratory Results: Bilirubin Level (PhenX protocol PX0810901 unless stated otherwise) + mg/dL + 1 + Number + text SickleInAfrica CDE - Total Bilirubin Concentration Question - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the level of lactate dehydrogenase in the respondent's blood. - Lactate dehydrogenase level - lactate_dehydrogenase_conc - Laboratory Results: Lactate Dehydrogenase Level (PhenX protocol PX0811001 unless stated otherwise) - IU/L - 1 - Number - text + Lactate dehydrogenase level + lactate_dehydrogenase_conc + Laboratory Results: Lactate Dehydrogenase Level (PhenX protocol PX0811001 unless stated otherwise) + IU/L + 1 + Number + text SickleInAfrica CDE - Lactate Dehydrogenase Level Question - + - + A decreased or reduced level of the enzyme lactate dehydrogenase in serum. - The current label in HPO is "Reduced lactate dehydrogenase B level". Seems the "B" in the label and the comment that refers to the B subunit should be removed. - - Suggest update to label + The current label in HPO is "Reduced lactate dehydrogenase B level". Seems the "B" in the label and the comment that refers to the B subunit should be removed. + + Suggest update to label HP:0045041 Decreased Lactate Dehydrogenase Level Reduced Lactate Dehydrogenase Level @@ -53796,49 +53231,49 @@ Request inclusion into relevant ontology. - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the reticulocyte count in the respondent's blood, as measured by a complete blood count. - Number of reticulocytes - reticulocyte_amount - Laboratory Results: Reticulocyte Count (PhenX protocol PX0810601 unless stated otherwise) - 1000 cells/µL - 1 - Number - text + Number of reticulocytes + reticulocyte_amount + Laboratory Results: Reticulocyte Count (PhenX protocol PX0810601 unless stated otherwise) + 1000 cells/µL + 1 + Number + text SickleInAfrica CDE - Reticulocyte Count Question - + - - + + A test used to measure the reticulocyte count (number of reticulocytes in a given volume of blood). + + Few but definitions not available SCDO (Jade Hotchkiss) - - Few but definitions not available Retic Count Reticulocyte Count Test Reticulocyte Count Assay @@ -53846,78 +53281,78 @@ Request inclusion into relevant ontology. - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + The Sickle in Africa core data element that records the hemoglobins for which assay results were recorded. - 1, Hb A + 1, Hb A 2, Hb F 3, Hb S 4, Hb C @@ -53925,39 +53360,39 @@ Request inclusion into relevant ontology. 6, Hb A2 7, Hb D-Punjab 8, Hb G-Philadelphia -9, Hb O-Arab - For which hemoglobins were assay results recorded? - scd_hemoglobin_assay_results - Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) - Select all relevant options - 1 - LH - checkbox +9, Hb O-Arab + For which hemoglobins were assay results recorded? + scd_hemoglobin_assay_results + Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) + Select all relevant options + 1 + LH + checkbox SickleInAfrica CDE - Hb Assay Results Recorded Question - + - - + + The hemoglobins for which assay results were recorded. + None SCDO (Jade Hotchkiss) - None Hemoglobin Assay Results Recorded - + - - + + Hemoglobin G Philadelphia (HbG Phil) is a structural variant of the hemoglobin molecule that involves the alpha chain rather than the beta chain. It has a frequency of about 1 in 5,000 African Americans, but has been reported in other ethnic groups in the Mediterranean region as well, HbG Phil itself has no clinical consequences. The only finding of clinical interest is the mild microcytosis. While this molecule has no clinical consequences, the presence helps to distinguish HbG from HbD that shares its electrophoretic migration on HPLC and gel electrophoresis and which does have consequences when it occurs with sickle trait. - - Sufficient - SCDO:1000689 + + Sufficient + SCDO:1000689 LNC:LP16433-2 Hb G-Phil Hb G-Philadelphia @@ -53968,854 +53403,854 @@ Request inclusion into relevant ontology. - + - - + + - - + + - - + + - - + + The amount of hemoglobin A present in a specified volume of blood. + Negligible SCDO (Jade Hotchkiss) - Negligible Haemoglobin A Level Hemoglobin A Level - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin A. - Record the levels of Hb A if measured. - hba2 - Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) - % - 2 - Number - [scd_hemoglobin_assay_results(1)] = '1' - text + Record the levels of Hb A if measured. + hba2 + Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) + % + 2 + Number + [scd_hemoglobin_assay_results(1)] = '1' + text SickleInAfrica CDE - Hemoglobin A Level Question - + - - + + - - + + - - + + - - + + The amount of hemoglobin S present in a specified volume of blood. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Haemoglobin S Level Hemoglobin S Level - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin S. - Record the levels of Hb S if measured. - hbs - Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) - % - 4 - Number - [scd_hemoglobin_assay_results(3)] = '1' - text + Record the levels of Hb S if measured. + hbs + Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) + % + 4 + Number + [scd_hemoglobin_assay_results(3)] = '1' + text SickleInAfrica CDE - Hemoglobin S Level Question - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin C. - Record the levels of Hb C if measured. - hbc - Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) - % - 5 - Number - [scd_hemoglobin_assay_results(4)] = '1' - text + Record the levels of Hb C if measured. + hbc + Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) + % + 5 + Number + [scd_hemoglobin_assay_results(4)] = '1' + text SickleInAfrica CDE - Hemoglobin C Level Question - + - - + + - - + + - - + + - - + + The amount of hemoglobin C present in a specified volume of blood. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Haemoglobin C Level Hemoglobin C Level - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin E. - Record the levels of Hb E if measured. - hbe - Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) - % - 6 - Number - [scd_hemoglobin_assay_results(5)] = '1' - text + Record the levels of Hb E if measured. + hbe + Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) + % + 6 + Number + [scd_hemoglobin_assay_results(5)] = '1' + text SickleInAfrica CDE - Hemoglobin E Level Question - + - - + + - - + + - - + + - - + + The amount of hemoglobin E present in a specified volume of blood. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Haemoglobin E Level Hemoglobin E Level - + - - + + - - + + - + - - + + The amount of hemoglobin A2 present in a specified volume of blood. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Haemoglobin A2 Level Hemoglobin A2 Level - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin A2. - Record the levels of Hb A2 if measured. - hb_a2 - Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) - % - 7 - Number - [scd_hemoglobin_assay_results(6)] = '1' - text + Record the levels of Hb A2 if measured. + hb_a2 + Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) + % + 7 + Number + [scd_hemoglobin_assay_results(6)] = '1' + text SickleInAfrica CDE - Hemoglobin A2 Level Question - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin D-Punjab. - Record the levels of Hb D-Punjab if measured. - hb_dpunjab - Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) - % - 8 - Number - [scd_hemoglobin_assay_results(7)] = '1' - text + Record the levels of Hb D-Punjab if measured. + hb_dpunjab + Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) + % + 8 + Number + [scd_hemoglobin_assay_results(7)] = '1' + text SickleInAfrica CDE - Hemoglobin D-Punjab Level Question - + - - + + - - + + - - + + - - + + The amount of hemoglobin D-Punjab present in a specified volume of blood. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Haemoglobin D-Punjab Level Hemoglobin D-Punjab Level - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin G-Philadelphia. - Record the levels of Hb G-Philadelphia if measured. - hb_gphilidelphia - Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) - % - 9 - Number - [scd_hemoglobin_assay_results(8)] = '1' - text + Record the levels of Hb G-Philadelphia if measured. + hb_gphilidelphia + Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) + % + 9 + Number + [scd_hemoglobin_assay_results(8)] = '1' + text SickleInAfrica CDE - Hemoglobin G-Philadelphia Level Question - + - - + + - - + + - - + + - - + + The amount of hemoglobin G-Philadelphia present in a specified volume of blood. + None SCDO (Jade Hotchkiss) - None Haemoglobin G-Philadelphia Level Hemoglobin G-Philadelphia Level - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin O-Arab. - Record the levels of Hb O-Arab if measured. - hb_o_arab - Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) - % - 10 - Number - [scd_hemoglobin_assay_results(9)] = '1' - text + Record the levels of Hb O-Arab if measured. + hb_o_arab + Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) + % + 10 + Number + [scd_hemoglobin_assay_results(9)] = '1' + text SickleInAfrica CDE - Hemoglobin O-Arab Level Question - + - - + + - - + + - - + + - - + + The amount of hemoglobin O-Arab present in a specified volume of blood. + None SCDO (Jade Hotchkiss) - None Haemoglobin O-Arab Level Hemoglobin O-Arab Level - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the proportion of the respondent's hemoglobin that consists of hemoglobin F. - Record the levels of Hb F if measured. - hbf_percent - Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) - % - 3 - Number - [scd_hemoglobin_assay_results(2)] = '1' - text + Record the levels of Hb F if measured. + hbf_percent + Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) + % + 3 + Number + [scd_hemoglobin_assay_results(2)] = '1' + text SickleInAfrica CDE - Hemoglobin F Level Question - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - - + + - - + + - + - - + + The amount of hemoglobin F present in a specified volume of blood. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Haemoglobin F Level Hemoglobin F Level - + - + The sex of the respondent's spouse, as provided by the respondent. + None SCDO (Jade Hotchkiss) - None Sex of Spouse - + - + The sex of the respondent's partner (where the partner is not a spouse), as provided by the respondent. + None SCDO (Jade Hotchkiss) - None Sex of Partner - + - - + + - - + + - + - + The Sickle in Africa core data element that collects the respondent's body temperature. + Patient's body temperature + body_temperature + Vital Signs + degrees Celsius + 1 + Number + 13 + 46 + text SCDO (Jade Hotchkiss) - Patient's body temperature - body_temperature - Vital Signs - degrees Celsius - 1 - Number - 13 - 46 - text SickleInAfrica CDE - Body Temperature Question - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the respondent's respiratory rate. - Patient's respiratory rate - respiratory_rate - Vital Signs - breaths per minute - 3 - Number - text + Patient's respiratory rate + respiratory_rate + Vital Signs + breaths per minute + 3 + Number + text SickleInAfrica CDE - Respiratory Rate Question - + - - + + - - + + - + - + The Sickle in Africa core data element that collects the respondent's partial pressure of carbon dioxide in their arterial blood, as measured by an arterial blood gas test. - Partial pressure of carbon dioxide (PaCO2) - partial_pressure_co2 - Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) - mmHg - 1 - Number - text + Partial pressure of carbon dioxide (PaCO2) + partial_pressure_co2 + Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + mmHg + 1 + Number + text SickleInAfrica CDE - Partial Pressure CO2 Question - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the respondent's partial pressure of oxygen their arterial blood, as measured by an arterial blood gas test. - Partial pressure of oxygen (PaO2) - partial_pressure_of_oxygen - Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) - mmHg - 2 - Number - text + Partial pressure of oxygen (PaO2) + partial_pressure_of_oxygen + Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + mmHg + 2 + Number + text SickleInAfrica CDE - Partial Pressure O2 Question - + - + - - + + - - + + - - + + The pressure exerted by oxygen dissolved in the blood, indicating how well oxygen is able to move from the airspace of the lungs into the blood. - Few but available definitions not adequate + Few but available definitions not adequate CMO:0000381 Oxygen Tension PaO2 @@ -54828,137 +54263,137 @@ Request inclusion into relevant ontology. - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the respondent's arterial oxygen saturation (oxyhemoglobin saturation), as measured by an arterial blood gas test. - Oxyhemoglobin saturation (HbO2) - oxyhemoglobin_saturation - Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) - % - 3 - Number - text + Oxyhemoglobin saturation (HbO2) + oxyhemoglobin_saturation + Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + % + 3 + Number + text SickleInAfrica CDE - Oxyhemoglobin Saturation Question - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the respondent's carboxyhemoglobin to total hemoglobin ratio, as measured by an arterial blood gas test. + Carboxyhemoglobin (COHb) + carboxyhemoglobin + Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + % + 4 + Number + text SCDO (Jade Hotchkiss) - Carboxyhemoglobin (COHb) - carboxyhemoglobin - Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) - % - 4 - Number - text SickleInAfrica CDE - Carboxyhemoglobin Question - + - - + + - - + + - - + + - + The Sickle in Africa core data element that collects the respondent's methemoglobin to total hemoglobin ratio, as measured by an arterial blood gas test. - Methemoglobin (MetHb) - methemoglobin - Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) - % - 5 - Number - text + Methemoglobin (MetHb) + methemoglobin + Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + % + 5 + Number + text SickleInAfrica CDE - Methemoglobin Question - + - + - - + + - - + + - - + + The ratio of methemoglobin compared to total hemoglobin present in a sample. The measurement may be expressed as a ratio or percentage. - - Used term from existing ontology but will suggest they update their label and description to ours. + + Used term from existing ontology but will suggest they update their label and description to ours. EFO:0009226 HGBMHGB MetHb Saturation @@ -54970,31 +54405,31 @@ Request inclusion into relevant ontology. - + - + - - + + - - + + - - + + The ratio of carboxyhemoglobin compared to total hemoglobin present in a sample. The measurement may be expressed as a ratio or percentage. - - Used term from existing ontology but will suggest they update their label and description to ours. + + Used term from existing ontology but will suggest they update their label and description to ours. EFO:0009203 COHb Saturation Carboxyhemoglobin Saturation @@ -55004,13 +54439,13 @@ Request inclusion into relevant ontology. - + - + An elevated concentration in the blood of methemoglobin, which is the ferric (Fe(3+)) form of hemoglobin. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Methemoglobin Increased Raised Methemoglobin Injury or toxic agents can convert a larger proportion of hemoglobin to methemoglobin, which does not function reversibly as an oxygen carrier and thus less oxygen is made available to the tissues. @@ -55019,82 +54454,81 @@ Request inclusion into relevant ontology. - + - + A site-specific unique identifier assigned to a study participant by the data collectors at the data collection site. + None SCDO (Jade Hotchkiss) - None Site Participant Number - + - + A unique identifier provided on SCD passports. + None SCDO (Jade Hotchkiss) - None SCD Passport Number - + - - + + - - + + The Sickle in Africa core data element that records the unique identifier that was assigned to the study participant's data when it was registered in the SickleInAfrica data registry. - SickleInAfrica Participant Number - record_id - text + SickleInAfrica Participant Number + record_id + text SickleInAfrica CDE - SickleInAfrica Participant Number - + - - + + - - + + The Sickle in Africa core data element that calculates the respondent's age in months, using the visit date and birth date collected by other core data elements. + Calculated age (in months) + calc_age_on_day_of_visit + Demographics + datediff([date_today],[date_of_birth], "M","dmy") + Age on day of visit + 10 + RH + calc SCDO (Jade Hotchkiss) - Calculated age (in months) - calc_age_on_day_of_visit - Demographics - datediff([date_today],[date_of_birth], "M","dmy") - Age on day of visit - 10 - RH - calc SickleInAfrica CDE - Age In Months Calculation - + - + A data capture instrument designed and applied by the Sickle In Africa Consortium. - SCDO (Jade Hotchkiss) - None - Consent + None + Consent Demographics SCD Diagnosis Details Management Details @@ -55105,84 +54539,85 @@ Laboratory Results: Bilirubin Level (PhenX protocol PX0810901 unless stated othe Laboratory Results: Lactate Dehydrogenase Level (PhenX protocol PX0811001 unless stated otherwise) Laboratory Results: Reticulocyte Count (PhenX protocol PX0810601 unless stated otherwise) Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) -Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) +Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + SCDO (Jade Hotchkiss) SickleInAfrica Core Data Element Instrument - + - - + + - - + + - + - + The Sickle in Africa core data element that collects the total concentration of hemoglobin in the respondent's blood. - Total hemoglobin (Hbtotal) - total_hemoglobin - Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) - g/dL - 11 - Number - text + Total hemoglobin (Hbtotal) + total_hemoglobin + Laboratory Results: Hemoglobin Characterisation (PhenX protocol PX0830301 unless stated otherwise) + g/dL + 11 + Number + text SickleInAfrica CDE - Total Hemoglobin Question - + - + An assay to determine the body temperature of an evaluant using an oral thermometer. + + PhenX protocol: Body Temperature - Oral Thermometers #810102 + None SCDO (Jade Hotchkiss) - - PhenX protocol: Body Temperature - Oral Thermometers #810102 - None Oral Temperature Taking Body Temperature - Oral Measurement Assay - + - + An assay to determine the body temperature of an evaluant using a tympanic (i.e. ear) thermometer. + PhenX protocol: Body Temperature - Tympanic Thermometers #810101 + None SCDO (Jade Hotchkiss) - PhenX protocol: Body Temperature - Tympanic Thermometers #810101 - None Tympanic Temperature Taking Body Temperature - Tympanic Measurement Assay - + - + The temperature of the oral cavity. - - Sufficient - SCDO:1000755 + + Sufficient + SCDO:1000755 VSO:0000025 Oral Body Temperature Oral Temperature @@ -55190,14 +54625,14 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - + The temperature of the external acoustic tube. - - Sufficient - SCDO:1000756 + + Sufficient + SCDO:1000756 VSO:0000045 Tympanic (ear) Temperature Tympanic Body Temperature @@ -55206,14 +54641,14 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - + The temperature of the lumen of the rectum. - - Sufficient - SCDO:1000757 + + Sufficient + SCDO:1000757 VSO:0000033 Rectal Body Temperature Rectal Temperature @@ -55221,14 +54656,14 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - + The temperature of the axillary fossa. - - Sufficient - SCDO:1000758 + + Sufficient + SCDO:1000758 VSO:0000003 Armpit Temperature Axillary (armpit) Temperature @@ -55237,139 +54672,139 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - - + + - - + + - - + + - - + + - - + + - - + + The Sickle in Africa core data element that records the type of body temperature that was taken for the respondent. - 1, Oral Temperature + 1, Oral Temperature 2, Tympanic (ear) Temperature 3, Axillary (armpit) Temperature -4, Rectal Temperature - Type of body temperature taken - type_of_temp - Vital Signs - 2 - dropdown +4, Rectal Temperature + Type of body temperature taken + type_of_temp + Vital Signs + 2 + dropdown SickleInAfrica CDE - Type of Temperature Question - + - - + + Type of Body Temperature - + - + An answer to a question where the answer is a year between 1900 and the current year, selected from a provided list of years. + None SCDO (Jade Hotchkiss) - None Year 1900 - Current - + - + An answer to a question where the answer is a month between 1 - 12, selected form a list of months. + None SCDO (Jade Hotchkiss) - None Month 1 - 12 - + - - - Waiting for description for this. + + + Waiting for description for this. Acide - + - - + + Waiting for description for this. Basique - + - - + + - + - - + + - - + + - + Few but definitions not available - Few but definitions not available ICD10CM:D57.03 D57.03 Hb-SS disease with cerebral vascular involvement @@ -55379,26 +54814,26 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - + - - + + - + yes + Few but definitions not available - yes - Few but definitions not available ICD10CM:D57.09 D57.09 Hb-SS disease with crisis with other specified complication @@ -55408,26 +54843,26 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - - + + + When there is no deviation from the normal concentration of hemoglobin in the blood. + None SCDO (Jade Hotchkiss) - None Normal Hemoglobin Concentration - + - - + + A lack of production of hemoglobin S. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available MEDDRA:10055604 Absent Haemoglobin S Haemoglobin S Absent @@ -55439,31 +54874,31 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - - + + - - + + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.213 D57.213 Sickle Cell Disease-SC with cerebral vascular involvement @@ -55473,25 +54908,25 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - - + + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.218 D57.218 Sickle Cell Disease-SC with crisis with other specified complication @@ -55501,31 +54936,31 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - + - - + + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.413 D57.413 D57.413 Sickle-cell thalassemia, unspecified, with cerebral vascular involvement @@ -55533,25 +54968,25 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.418 D57.418 Sickle-cell thalassemia, unspecified, with crisis with other specified complication @@ -55560,25 +54995,25 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - + - + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.42 D57.42 Sickle-cell thalassemia beta zero without crisis @@ -55587,25 +55022,25 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.43 D57.43 Sickle-cell thalassemia beta zero with crisis @@ -55614,31 +55049,31 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - + - + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.431 D57.431 Sickle-cell thalassemia beta zero with acute chest syndrome @@ -55647,25 +55082,25 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.432 D57.432 Sickle-cell thalassemia beta zero with splenic sequestration @@ -55674,31 +55109,31 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - + - - + + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.433 D57.433 Sickle-cell thalassemia beta zero with cerebral vascular involvement @@ -55707,25 +55142,25 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.438 D57.438 Sickle-cell thalassemia beta zero with crisis with other specified complication @@ -55734,25 +55169,25 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.439 D57.439 Sickle-cell thalassemia beta zero with crisis, unspecified @@ -55761,25 +55196,25 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.44 D57.44 Sickle-cell thalassemia beta minus without crisis @@ -55789,25 +55224,25 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - - + + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.45 D57.45 Sickle-cell thalassemia beta minus with crisis @@ -55817,31 +55252,31 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - + - - + + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.451 D57.451 Sickle-cell thalassemia beta minus with acute chest syndrome @@ -55851,25 +55286,25 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - - + + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.452 D57.452 Sickle-cell thalassemia beta minus with splenic sequestration @@ -55879,31 +55314,31 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - - + + - - + + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.453 D57.453 Sickle-cell thalassemia beta minus with cerebral vascular involvement @@ -55913,25 +55348,25 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - - + + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.458 D57.458 Sickle-cell thalassemia beta minus with crisis with other specified complication @@ -55941,25 +55376,25 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - - + + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.459 D57.459 Sickle-cell thalassemia beta minus with crisis, unspecified @@ -55969,19 +55404,19 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.818 D57.818 D57.818 Other sickle-cell disorders with crisis with other specified complication @@ -55989,25 +55424,25 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - - + + - - + + - + Few but definitions not freely available - Few but definitions not freely available ICD10CM:D57.813 D57.813 D57.813 Other sickle-cell disorders with cerebral vascular involvement @@ -56015,13 +55450,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + A lack of production of hemoglobin C. + None SCDO (Jade Hotchkiss) - None Absent Haemoglobin C Haemoglobin C Absent Hemoglobin C Absent @@ -56032,13 +55467,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - + An elevated concentration in the blood of carboxyhemoglobin, which is the form of hemoglobin where the heme group has formed a stable complex with carbon monoxide (CO). + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Carboxyhemoglobin Increased Raised Carboxyhemoglobin Increased Carboxyhemoglobin @@ -56046,13 +55481,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - + An abnormal reduction in the amount of oxygen bound to hemoglobin in arterial blood expressed as a percentage of the maximal binding capacity. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Arterial Oxygen Saturation Decreased Decreased Arterial HbO2 Decreased Arterial Oxyhemoglobin Saturation @@ -56066,38 +55501,38 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - + A phenotype of the body's metabolism or homeostasis that is not clinically abnormal. + None SCDO (Jade Hotchkiss) - None Normal Metabolism/Homeostasis Phenotype - + - - + + When the degree to which oxygen is bound to hemoglobin in arterial blood is in the normal range. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Normal Arterial Blood Oxygen Saturation Normal Arterial Oxygen Saturation - + - - + + When the level of carboxyhemoglobin detected in a sample of blood falls in the normal range for carboxyhemoglobin. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Carboxyhemoglobin Normal Normal Carboxyhemoglobin Concentration Normal Carboxyhemoglobin Level @@ -56105,13 +55540,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + When the level of methemoglobin detected in a sample of blood falls in the normal range for methemoglobin. + None SCDO (Jade Hotchkiss) - None MetHb Normal Normal MetHb Level Normal Methemoglobin Concentration @@ -56120,13 +55555,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + A lack of production of hemoglobin D-Punjab. + None SCDO (Jade Hotchkiss) - None Absent Haemoglobin D-Punjab Haemoglobin D-Punjab Absent Hemoglobin D-Punjab Absent @@ -56137,13 +55572,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + A lack of production of hemoglobin G-Philadelphia. + None SCDO (Jade Hotchkiss) - None Absent Haemoglobin G-Philadelphia Haemoglobin G-Philadelphia Absent Hemoglobin G-Philadelphia Absent @@ -56154,13 +55589,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + A lack of production of hemoglobin O-Arab. + None SCDO (Jade Hotchkiss) - None Absent Haemoglobin O-Arab Haemoglobin O-Arab Absent Hemoglobin O-Arab Absent @@ -56171,13 +55606,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - + An abnormal reduction in the pressure exerted by oxygen dissolved in the blood. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Arterial Oxygen Partial Pressure Decreased Decreased Oxygen Tension Decreased PO2 @@ -56189,13 +55624,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - + The observable morphological and physiological characteristics of the human blood cells or the organs associated with the development and formation of blood cells that are manifested through development and lifespan. + Few but definitions not specific enough - Few but definitions not specific enough Haematopoietic System Phenotype Haemopoietic System Phenotype Hemopoietic System Phenotype @@ -56204,25 +55639,25 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + A phenotype of the body's hematopoietic system that is not clinically abnormal. + None SCDO (Jade Hotchkiss) - None Normal Hematopoietic System Phenotype - + - - + + When the number of red blood cells in a specified volume of blood falls in the normal range. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Normal RBC Count RBC Count Normal Red Blood Cell Count Normal @@ -56231,13 +55666,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + When the number of white blood cells in a specified volume of blood falls in the normal range. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Normal WBC Count WBC Count Normal White Blood Cell Count Normal @@ -56246,26 +55681,26 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + When the number of platelets in a specified volume of blood falls in the normal range. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Platelet Count Normal Normal Platelet Count - + - - + + When the average volume or size of a single red blood cell falls in the normal range. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available MCV Normal Mean Cell Volume Normal Mean Corpuscular Volume Normal @@ -56276,13 +55711,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + When the average amount of hemoglobin per red blood cell (calculated by dividing the total mass of hemoglobin by the number of red blood cells in a volume of blood) falls in the normal range. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available MCH Normal Mean Cell Hemoglobin Normal Mean Corpuscular Hemoglobin Level Normal @@ -56296,13 +55731,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + When the amount of hemoglobin in a given volume of packed red blood cells falls in the normal range. + None SCDO (Jade Hotchkiss) - None MCHC Normal Mean Corpuscular Hemoglobin Concentration Normal Normal MCHC @@ -56312,13 +55747,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + When the range of variation of red blood cell (RBC) volume falls in the normal range. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Normal RBC Distribution Width Normal RCDW RBC Distribution Width Normal @@ -56329,13 +55764,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + When the level of serum creatinine is in the normal range. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Normal Serum Creatinine Level Serum Creatinine Level Normal Serum Creatinine Normal @@ -56344,13 +55779,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + When the level of serum alanine aminotransferase is in the normal range. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available ALT Level Normal ALT Normal Normal ALT @@ -56365,13 +55800,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + When the level of serum aspartate aminotransferase is in the normal range. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available AST Level Normal AST Normal Normal AST @@ -56386,13 +55821,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + When the level of serum alkaline aminotransferase is in the normal range. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available AP Level Normal AP Normal Alkaline Phosphatase Level Normal @@ -56406,13 +55841,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + When the level of the enzyme lactate dehydrogenase in the serum is in the normal range. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available LD Level Normal LD Normal LDH Level Normal @@ -56428,26 +55863,26 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + When the number of reticulocytes in a specified volume of blood falls in the normal range. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Reticulocyte Count Normal Normal Reticulocyte Count - + - - + + When the total bilirubin level in the serum is in the normal range. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Serum Bilirubin Total Normal Total Serum Bilirubin Level Normal Total Serum Bilirubin Normal @@ -56456,13 +55891,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + When the concentration of urinary albumin falls in the normal range. + None SCDO (Jade Hotchkiss) - None Normal Urinary Albumin Concentration Urinary Albumin Concentration Normal Urine Albumin Concentration Normal @@ -56471,13 +55906,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + When the concentration of urine creatinine falls in the normal range. + Few but definitions not available SCDO (Jade Hotchkiss) - Few but definitions not available Creatinine Urine Normal Normal Urinary Creatinine Normal Urinary Creatinine Level @@ -56489,13 +55924,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + When the pressure exerted by oxygen dissolved in the blood falls in the normal range. + None SCDO (Jade Hotchkiss) - None Normal Oxygen Tension Normal PO2 Normal PaO2 @@ -56509,13 +55944,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + When the pressure exerted by carbon dioxide dissolved in the blood falls in the normal range. + None SCDO (Jade Hotchkiss) - None Normal Carbon Dioxide Tension Normal PaCO2 Normal Partial Pressure of Blood Carbon Dioxide @@ -56527,13 +55962,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - + An abnormal reduction in the pressure exerted by carbon dioxide dissolved in the blood. + None SCDO (Jade Hotchkiss) - None Decreased PCO2 Decreased PaCO2 Decreased Partial Pressure of Blood Carbon Dioxide @@ -56545,13 +55980,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - + An abnormal increase in the pressure exerted by carbon dioxide dissolved in the blood. + None SCDO (Jade Hotchkiss) - None Elevated Partial Pressure of Carbon Dioxide Increased PCO2 Increased PaCO2 @@ -56565,14 +56000,14 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - + Clinical manifestation consisting of a deficiency of carbon dioxide in arterial blood. - - Sufficient - SCDO:1000842 + + Sufficient + SCDO:1000842 MESH:D016857 Hypocarbia Hypocapnia @@ -56580,14 +56015,14 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - + A clinical manifestation of abnormal increase in the amount of carbon dioxide in arterial blood. - - Sufficient - SCDO:1000843 + + Sufficient + SCDO:1000843 MESH:D006935 Hypercarbia Hypercapnia @@ -56595,13 +56030,13 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - + When the abnormal hemoglobin, hemoglobin S (HbS), has been detected in a blood sample. + None SCDO (Jade Hotchkiss) - None Haemoglobin S Present Haemoglobin S in Blood HbS Present @@ -56612,95 +56047,95 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - - + + - + - - + + - - + + - - + + - + The Sickle in Africa core data element that records the type of visit undertaken by a patient. - 1, Routine + 1, Routine 2, Acute 3, Review -4, First visit - Type of visit - visit_type - Demographics - 2 - dropdown +4, First visit + Type of visit + visit_type + Demographics + 2 + dropdown SickleInAfrica CDE - Type of Visit Question - + - + A clinical visit occuring because of an acute (severe with sudden onset) health condition. + Few but definitions not specific enough SCDO (Jade Hotchkiss) - Few but definitions not specific enough Acute Clinical Visit - + - - + + - - + + - + The Sickle in Africa core data element that records the patient's medical record number. - Medical record number (MRN) - medical_record_number - Demographics - 4 - text + Medical record number (MRN) + medical_record_number + Demographics + 4 + text MRN Medical record number SickleInAfrica CDE - Medical Record Number Question @@ -56708,107 +56143,107 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - - + + - - + + - - + + The Sickle in Africa core data element that records the name of the hospital that a patient visited. - Hospital name - hospital_name - Demographics - 5 - text + Hospital name + hospital_name + Demographics + 5 + text SickleInAfrica CDE - Hospital Name Question - + - + The name of the hospital visited by a patient. + None SCDO (Jade Hotchkiss) - None Hospital Name - + - - + + - - + + - - + + The Sickle in Africa core data element that records a respondent's first name. - First name - first_name - Demographics - 6 - text + First name + first_name + Demographics + 6 + text SickleInAfrica CDE - First Name Question - + - - + + - - + + - - + + The Sickle in Africa core data element that records a respondent's middle name. - Middle name - middle_name - Demographics - 7 - text + Middle name + middle_name + Demographics + 7 + text SickleInAfrica CDE - Middle Name Question - + - + A first name is a name that denotes a specific individual between members of a group of individuals, whose members usually share the same surname. - - Sufficient - SCDO:1000858 + + Sufficient + SCDO:1000858 sio:FirstName Forename Given Name @@ -56817,906 +56252,1470 @@ Arterial blood gas - ABG (PhenX protocol PX090201 unless stated otherwise) + - + A middle name is a name assigned to an individual that is not the first or last name. - - Sufficient - SCDO:1000860 + + Sufficient + SCDO:1000860 sio:MiddleName Middle Name - + - + A last name (surname) is a name added to a given name and is part of a personal name and is often the family name. - - Sufficient - SCDO:1000861 + + Sufficient + SCDO:1000861 sio:LastName Last Name - + - - + + - - + + - - + + The Sickle in Africa core data element that records a respondent's last name. - Last name - last_name - Demographics - 8 - text + Last name + last_name + Demographics + 8 + text SickleInAfrica CDE - Last Name Question - + - - + + - - + + - - + + - + The Sickle in Africa core data element that records a respondent's height. - Height/Length - height_length - Demographics - cm - 12 - Number - text + Height/Length + height_length + Demographics + cm + 12 + Number + text SickleInAfrica CDE - Height Question - + - - + + - - + + - - + + - + The Sickle in Africa core data element that records a respondent's measured weight. - Weight - weight - Demographics - kg - 13 - Number - text + Weight + weight + Demographics + kg + 13 + Number + text SickleInAfrica CDE - Weight Question - + - - + + - - + + - + The Sickle in Africa core data element that records the ethnic group to which a respondent belongs. - Ethnic Group - tribe - Demographics - 16 - text + Ethnic Group + tribe + Demographics + 16 + text SickleInAfrica CDE - Ethnic Group Question - + - - + + - - + + - - + + The Sickle in Africa core data element that records the religion of a respondent. - Religion - religion - Demographics - 17 - text + Religion + religion + Demographics + 17 + text SickleInAfrica CDE - Religion Question - + - - + + - - + + - + The Sickle in Africa core data element that records the region in which the respondent lives. - Region - region - Demographics - 18 - text + Region + region + Demographics + 18 + text SickleInAfrica CDE - Region Question - + - + A street name is the token given to identify a particular street. - - Sufficient - SCDO:1000871 + + Sufficient + SCDO:1000871 SIO:000766 Street Name - + - - + + - - + + - - + + The Sickle in Africa core data element that records the name of the street in which the respondent lives. - Street - street - Demographics - 19 - text + Street + street + Demographics + 19 + text SickleInAfrica CDE - Street Question - + - - + + - - + + - - + + The Sickle in Africa core data element that records the landmark that is nearest to where the participant lives. - Nearest landmark - nearest_landmark - Demographics - 20 - text + Nearest landmark + nearest_landmark + Demographics + 20 + text SickleInAfrica CDE - Nearest Landmark Question - + - + A recognizable natural or artificial geographic feature, used for navigation (often visible from long distances), that is nearest to where the participant lives. + None SCDO (Jade Hotchkiss) - None Nearest Geographical Landmark - + - + The name of a respondent's next of kin. + None SCDO (Jade Hotchkiss) - None Next of Kin Name - + - - + + - - + + - - + + The Sickle in Africa core data element that records the participant's primary telephone number. - Telephone 1 - telephone_1 - Demographics - 21 - text + Telephone 1 + telephone_1 + Demographics + 21 + text SickleInAfrica CDE - Telephone 1 Question - + - - + + - - + + - - + + The Sickle in Africa core data element that records the participant's secondary telephone number. - Telephone 2 - telephone_2 - Demographics - 22 - text + Telephone 2 + telephone_2 + Demographics + 22 + text SickleInAfrica CDE - Telephone 2 Question - + - - + + - - + + - - + + The Sickle in Africa core data element that records the name of the participant's next of kin. - Next of kin name - next_of_kin_name - Demographics - 23 - text + Next of kin name + next_of_kin_name + Demographics + 23 + text SickleInAfrica CDE - Next of Kin Name Question - + - - + + - - + + - - + + The Sickle in Africa core data element that records the telephone number of the participant's next of kin. - Next of kin telephone number - next_of_kin_telephone_numb - Demographics - 24 - text + Next of kin telephone number + next_of_kin_telephone_numb + Demographics + 24 + text SickleInAfrica CDE - Next of Kin Number Question - + - - + + - - + + - - + + The Sickle in Africa core data element that records the participant's next of kin's relationship to the participant. - Relationship to participant - next_of_kin_relationship - Demographics - 25 - text + Relationship to participant + next_of_kin_relationship + Demographics + 25 + text SickleInAfrica CDE - Relationship to Participant Question - + - + A respondent's primary telephone number. + None SCDO (Jade Hotchkiss) - None Telephone Number 1 - + - + A respondent's secondary telephone number. + None SCDO (Jade Hotchkiss) - None Telephone Number 2 - + - + The telephone number of a respondent's next of kin. + None SCDO (Jade Hotchkiss) - None Next of Kin Telephone Number - + - + The relationship that the participant's next of kin has with the participant. + None SCDO (Jade Hotchkiss) - None Next of Kin Relationship to Patient Next of Kin Relationship to Participant - + - - + + - - + + - + - + - - + + The Sickle in Africa core data element that records whether the participant was given a blood transfusion. + 1, Yes +0, No + Blood transfusion + blood_transfusion + Management Details + 7 + yesno SCDO (Jade Hotchkiss) - 1, Yes -0, No - Blood transfusion - blood_transfusion - Management Details - 7 - yesno SickleInAfrica CDE - Blood Transfusion Question - + - - + + - - + + - - + + The Sickle in Africa core data element that records the number of units of blood that a participant was given during a blood transfusion. - Units transfused - units_transfused - Management Details - 9 - Number - [blood_transfusion] = "Yes" - text + Units transfused + units_transfused + Management Details + 9 + Number + [blood_transfusion] = "Yes" + text SickleInAfrica CDE - Units Transfused Question - + - - + + The number of units of blood that a patient received during a blood transfusion. + None SCDO (Jade Hotchkiss) - None Number of Units Transfused - + - - + + - - + + - + - + - + The Sickle in Africa core data element that records whether a participant has difficulty in breathing. - 1, Yes -0, No - Difficulty in breathing - difficulty_in_breathing - Vital Signs - 4 - yesno + 1, Yes +0, No + Difficulty in breathing + difficulty_in_breathing + Vital Signs + 4 + yesno SickleInAfrica CDE - Difficulty in Breathing Question - + - - + + - - + + - + - + The Sickle in Africa core data element that records a participant's systolic blood pressure. - Systolic blood pressure - systolic_blood_press - Vital Signs - mmHg - 5 - text + Systolic blood pressure + systolic_blood_press + Vital Signs + mmHg + 5 + text SickleInAfrica CDE - Systolic Blood Pressure Question - + - - + + - - + + - + - + The Sickle in Africa core data element that records a participant's diastolic blood pressure. - Diastolic blood pressure - diastol_blood_press - Vital Signs - mmHg - 6 - text + Diastolic blood pressure + diastol_blood_press + Vital Signs + mmHg + 6 + text SickleInAfrica CDE - Diastolic Blood Pressure Question - + - - + + - - + + - + - + - - + + The Sickle in Africa core data element that records whether a participant has priapism. - 1, Yes -0, No - Priapism - priapism - Vital Signs - 7 - yesno + 1, Yes +0, No + Priapism + priapism + Vital Signs + 7 + yesno SickleInAfrica CDE - Priapism Question - + - - + + - - + + - + - + - + The Sickle in Africa core data element that records whether a participant has chest pain. + 1, Yes +0, No + Chest Pain + chest_pain + Vital Signs + 8 + yesno SCDO (Jade Hotchkiss) - 1, Yes -0, No - Chest Pain - chest_pain - Vital Signs - 8 - yesno SickleInAfrica CDE - Chest Pain Question - + - - + + - - + + - + - + - + The Sickle in Africa core data element that records whether a participant has anaemia. + 1, Yes +0, No + Anaemia + anaemia + Vital Signs + 9 + yesno SCDO (Jade Hotchkiss) - 1, Yes -0, No - Anaemia - anaemia - Vital Signs - 9 - yesno SickleInAfrica CDE - Anaemia Question - + - - + + - - + + - + - + - + The Sickle in Africa core data element that records whether a participant has jaundice. - 1, Yes -0, No - Jaundice - jaundice - Vital Signs - 10 - yesno + 1, Yes +0, No + Jaundice + jaundice + Vital Signs + 10 + yesno SickleInAfrica CDE - Jaundice Question - + - - + + - - + + - + - + The Sickle in Africa core data element that collects the concentration of urea in the respondent's blood. - Urea - urea - Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise) - mmol/L - 2 - Number - text + Urea + urea + Kidney Function Assay (Phenx protocols PX141401, PX141501 and PX141601 unless stated otherwise) + mmol/L + 2 + Number + text SickleInAfrica CDE - Urea Question - + - + A clinical visit that is the patient's first clinical visit. + None SCDO (Jade Hotchkiss) - None First Visit - + - + A clinical visit that is a follow-up for a previous visit. + Not relevant to context of sickle cell SCDO (Jade Hotchkiss) - Not relevant to context of sickle cell Review Visit Follow-Up Visit + + + + + Genome wide association study is a kind of study whose objective is to detect association between genetic markers (SNP or otherwise) accross the genome and a trait which may be a disease or another phenotype (e.g. trait of agronomic relevance in animal or plant studies). Genome wide association study compare the allele frequencies in 2 populations, one free of the trait used as control, the other one showing the trait use as 'case'. GWAS studies implement case-control design. + http://purl.obolibrary.org/obo/STATO_0000091 + Sufficient + SCDO:0000450 + STATO:0000091 + GWAS + Genome Wide Association Study + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A neurological and physiological symptom characterized by a painful or apprehensive uneasiness of mind usually over an impending or anticipated ill. + http://purl.obolibrary.org/obo/SYMP_0000412 + Sufficient + SCDO:0000068 + http://www.apa.org/topics/anxiety/ + SYMP:0000412 + Anxiety Symptoms + Panic + Worry + Physical symptoms include increased blood pressure (rapid heartbeat), trembling or dizziness. + Anxiety + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Muscle pain is a pain characterized by pain in one or more muscles. + Provide source for additional info + http://purl.obolibrary.org/obo/SYMP_0019161 + Over-stretching of one muscle or a group of muscles, trauma, infections ( influenza, Lyme, Ebola, Dengue fever, Chicungunya fever, Babesiosis, Malaria, Toxoplasmosis, Hemorrhage fever, polio, Rocky Mountain spotted fever, Trichinosis), vaccines, muscle hematoma, autoimmune disorders ( lupus, polymyalgia, polymyositis, nutricional deficiencies, chronic fatigue syndrome, acute rejection after heart transplant surgery, rhabdomyolysis, severe potassium deficiency, fibromialgia, muscle abscess , reaction to drugs ( statins, fibrates, ACE inhibitors, cocaine), repetitive strain injury,withdrawal syndrome of certain drugs ( corticosteroids, opioids, barbiturates, benzodiazepines, caffeine, alcohol). + Pain of a muscle or a group of muscles. + Sufficient + SCDO:0000779 + SYMP:0019161 + Myalgia + Muscle Pain + + + + + + + + + A standardized quantity of a physical quality. + + Sufficient + SCDO:1000478 + UO:0000000 + Unit + Unit of Measure + Units + Unit of Measurement + + + + + + + + + A unit which is a standard measure of the distance between two points. + + Sufficient + SCDO:1000864 + UO:0000001 + Length Unit + + + + + + + + + A unit which is a standard measure of the amount of matter/energy of a physical object. + + Sufficient + SCDO:1000628 + UO:0000002 + Mass Unit + + + + + + + + + A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. + + Sufficient + SCDO:1000712 + UO:0000005 + Temperature Unit + + + + + + + + + A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. + + Sufficient + SCDO:1000867 + UO:0000009 + Kilogram + + + + + + + + + A length unit which is equal to one hundredth of a meter or 10^[-2] m. + + Sufficient + SCDO:1000865 + UO:0000015 + Centimeter + + + + + + + + + A mass unit which is equal to 10^[-12] g. + + Sufficient + SCDO:1000629 + UO:0000025 + picogram + pg + + + + + + + + + A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. + + Sufficient + SCDO:1000491 + UO:0000051 + Concentration Unit + + + + + + + + + A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. + + Sufficient + SCDO:1000622 + UO:0000095 + Volume Unit + + + + + + + + + A volume unit which is equal to 10^[-15] L. + + Sufficient + SCDO:1000623 + UO:0000104 + cubic micrometre + femtoliter + femtolitre + μm^3 + fL + + + + + + + + + A unit which is a standard measure of the force applied to a given area. + + Sufficient + SCDO:1000720 + UO:0000109 + Pressure Unit + + + + + + + + + A concentration unit which is a standard measure of the mass of a substance in a given volume (density). + + Sufficient + SCDO:1000506 + UO:0000180 + Unit of Density + Definition from BioAssay Ontology + Mass Per Unit Volume + + + + + + + + + A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. + + Sufficient + SCDO:1000642 + UO:0000186 + Dimensionless Unit + + + + + + + + + A dimensionless ratio unit which denotes numbers as fractions of 100. + + Sufficient + SCDO:1000644 + UO:0000187 + % + Percent + + + + + + + + + A dimensionless unit which denotes an amount or magnitude of one quantity relative to another. + + Sufficient + SCDO:1000643 + UO:0000190 + Ratio + + + + + + + + + A concentration unit which denotes the average cell number in a given volume. + + Sufficient + SCDO:1000503 + UO:0000200 + Cell Concentration Unit + + + + + + + + + A unit of pressure equal to the amount of fluid pressure one millimeter deep in mercury at zero degrees centigrade on Earth. + + Sufficient + SCDO:1000721 + UO:0000272 + millimetres of mercury + mmHg + + + + + + + + + A unit which represents a standard measurement occurrence of a process per unit time. + + Sufficient + SCDO:1000715 + UO:0000280 + Rate Unit + + + + + + + + + A unit of cell concentration which is equal to one cell in a volume of 1 microliter. + + Sufficient + SCDO:1000507 + UO:0000316 + cells per microliter + cells/µL + cells per microliter + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine. + http://purl.obolibrary.org/obo/VO_0000001 + Sufficient + SCDO:0001221 + VO:0000001 + Vaccine + + + + + + + + + + + + + + + A viral vaccine that protects against infection with influenza virus. + http://purl.obolibrary.org/obo/VO_0000642 + Sufficient + SCDO:0000642 + VO:0000642 + Influenza Virus Vaccine + + + + + + + + + + + + + + + + + + + + + + + + + + + A Streptococcal vaccine that is used against S. pneumoniae infection, which causes pneumococcal diseases. + http://purl.obolibrary.org/obo/VO_0000675 + Sufficient + SCDO:0001109 + VO:0000675 + Pneumococcal Vaccine + Streptococcus Pneumoniae Vaccine + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The amount of alkaline phosphatase present in a specified volume of blood. + The proportion, quantity, or volume in whole blood, serum, or plasma of this enzyme, which hydrolyzes orthophosphoric monoesters. + + Sufficient + SCDO:1000499 + VT:0000202 + AP Level + Blood Alkaline Phosphatase Amount + Circulating ALP Level + Circulating Alkaline Phosphatase Level + Alkaline Phosphatase Level + + + +