-
Notifications
You must be signed in to change notification settings - Fork 74
/
ChangeLog
1040 lines (890 loc) · 40.1 KB
/
ChangeLog
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
CHANGES
=======
4.2.5
----
* Update biolink-model.yaml for CTKP requirements by @mbrush in https://github.com/biolink/biolink-model/pull/1526
* Remove if absent annotations causing downstream issues in python dataclasses by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1528
* Add disease context qualifier (to the right place this time) by @kevinschaper in https://github.com/biolink/biolink-model/pull/1529
* ready the repo for release by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1530
* Predicate inverses & tests by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1532
* Move disease_context_qualifier up to a higher level mixin by @kevinschaper in https://github.com/biolink/biolink-model/pull/1533
* add subject/object specialization qualifier to help represent extensions in MAXO and GO-CAM by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1534
* Add species context qualifier to macromolecular machine association mixin by @kevinschaper in https://github.com/biolink/biolink-model/pull/1535
**Full Changelog**: https://github.com/biolink/biolink-model/compare/v4.2.4...v4.2.5
4.2.5-rc2
----
* disease_context_qualifier additions [Kevin Schaper]
4.2.5-rc1
-----
* remove if_absent annotations on KL/AT that result in downstream enumeration errors in python dataclasses
representation of the model, see: https://github.com/linkml/linkml/pull/2329 and associated ticket for more details
4.2.4
-----
* regenerating artifacts
* adding disease_context_qualifier
* note: 4.2.3 tag in Biolink is missing key artifacts; this release fixes those issues and updates version info
4.2.2
-----
* Bump requests from 2.31.0 to 2.32.0 by @dependabot in https://github.com/biolink/biolink-model/pull/1508
* fix: flip domain/range for top-level "treats" predicates by @colleenXu in https://github.com/biolink/biolink-model/pull/1512
* Add a description to AgentTypeEnum by @nicholsn in https://github.com/biolink/biolink-model/pull/1510
* Bump urllib3 from 2.1.0 to 2.2.2 by @dependabot in https://github.com/biolink/biolink-model/pull/1513
* Bump certifi from 2023.11.17 to 2024.7.4 by @dependabot in https://github.com/biolink/biolink-model/pull/1518
* Bump zipp from 3.17.0 to 3.19.1 by @dependabot in https://github.com/biolink/biolink-model/pull/1519
* Bump setuptools from 69.0.2 to 70.0.0 by @dependabot in https://github.com/biolink/biolink-model/pull/1520
* restore enumeration to use just for denormalized node properties for … by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1506
* make necessary changes to id_prefixes for chemical entity hierarchy by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1500
* TRAPI multi-CURIE query use cases semantics by @RichardBruskiewich in https://github.com/biolink/biolink-model/pull/150
4.2.1
-----
* administered_to, associated_with moved back to related_to in top level yaml
* make sure treats hierarchy (mixin or not) has its ancestry in "related_to" - Richard B.
* add "url" property to the model to support MolePro, non-curie expandable cross references. - Larry C.
* add two statistical properties p-value and adjusted p-value to association class for use in Monarch KG. - Kevin S.
* bump jinja2 from 3.1.3 to 3.1.4 - dependabot
* bump tqdm from 4.66.1 to 4.66.3 - dependabot
* add RO:0004029 narrow mapping to has_phenotype predicate to support Mondo KG - Kevin S.
4.2.0
-----
* infores catalog has now moved to its own repository.
* onset is reintroduced to ONLY support HP disease-> phenotype annotations, not "treats" associations.
* Knowledge level agent type new dir by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1470
* check links in doc by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1465
* Fix category type for pydantic generated models, remove pydantic 1 generation by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1468
* Update links and autogenerated artifacts in README.md by @deepakunni3 in https://github.com/biolink/biolink-model/pull/1476
* fix mislabeled ranges to domain by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1475
* relaxed mappings for a couple of chemicals, made them mappings of Che… by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1474
* remove skos:relatedMatch as an exact mapping to biolink relate… by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1473
* fix order of prefixes for small molecule and chemical entity by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1471
* Adds knowledge_level and agent_type as association slots, makes them required and sets a default value. by @kevinschaper
4.1.6
-----
- remove commas from inverse mixin predicate
- remove rdf:label from in_taxon_ property - Kevin Schaper
https://github.com/biolink/biolink-model/compare/v4.1.5...v4.1.6
4.1.5
-----
- clean up spell config, extend contraindicated to include biological process, add mappings by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1461
https://github.com/biolink/biolink-model/compare/v4.1.4...v4.1.5
4.1.4
-----
- Update README.md by @baig in #1449
- adding inverses for treats hierarchy not currently inversed by @sierra-moxon in #1460
https://github.com/biolink/biolink-model/compare/v4.1.3...v4.1.4
4.1.3
-----
- Remove explicit rdflib dependency by @kevinschaper in #1459
https://github.com/biolink/biolink-model/compare/v4.1.2...v4.1.3
4.1.2
-----
- Bump jinja2 from 3.1.2 to 3.1.3 by @dependabot in #1446
- Add frequency quantifier mixin to disease to phenotypic feature association by @kevinschaper in #1451
- Exploring Agent/Service Provider infores updates Jan2024 by @colleenXu in #1450
https://github.com/biolink/biolink-model/compare/v4.1.1...v4.1.2
4.1.1
-----
- Add RO mapping for gene/condition relations by @cbizon in #1443
- fix whitespace issues by @gprice1129 in #1441
- Adding 'phenotypic feature to disease association' plus related mixins by @RichardBruskiewich in #1444
- Documentation bug fixes and adding more examples and visualizations to help with the treats migration by @sierra-moxon in #1445
https://github.com/biolink/biolink-model/compare/v4.1.0...v4.1.1
4.1.0
-----
Summary: 4.1.0 implements the "treats" refactoring work, making "treats" a mixin. To view the new predicate
hierarchy around this "treats" refactoring, please see https://biolink.github.io/biolink-model/treats_dag.html.
This release also includes a number of bug fixes and documentation updates.
## What's Changed
* ubergraph and sri-reference-kg/monarchinitiative infores updates by @EvanDietzMorris in https://github.com/biolink/biolink-model/pull/1428
* Add infores validation checks to PRs and makefile target by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1434
* add canonical flag to superclass of by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1433
* make subclass of an inverse of superclass of by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1435
* make changes according to https://docs.google.com/spreadsheets/d/12SP… by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1436
* Adds infores:aop-cam (Adverse Outcome Pathways Casual Activity Models) by @gaurav in https://github.com/biolink/biolink-model/pull/1437
* Treats visualization graph including mixins by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1439
* "max predicate approach" for refactoring "treats" by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1328
* Dec 2023 infores updates for Service Provider/BTE by @colleenXu in https://github.com/biolink/biolink-model/pull/1429
* add context at beginning, fix some awkward wording of "using the modeling language documentation" by @nlharris in https://github.com/biolink/biolink-model/pull/1438
**Full Changelog**: https://github.com/biolink/biolink-model/compare/v4.0.0...v4.1.0
4.0.0
-----
Summary: 4.0.0 is a major release that includes many changes to the documentation for Biolink Model as well
as the reorganization of the repository to support the new documentation structure and comply with LinkML best
practices. The model itself has not changed significantly, but the documentation has been updated to reflect
the current state of the model, and includes new visualizations of the model, additional text-based documentation,
and a new gh-pages documentation layout.
3.6.0
-----
## What's Changed
* Removed auto deployment of documentation and artifacts in prep for doc refactor release
* adding aspect qualifier enums by @EvanDietzMorris in https://github.com/biolink/biolink-model/pull/1380
* update name for gtrx infores source to match BTE's name. by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1384
* reorder id_prefixes for small molecule, fixes #1375 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1376
* Update infores_catalog.yaml by @beasleyjonm in https://github.com/biolink/biolink-model/pull/1389
* PFCOR->PFOCR by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1385
* Bump certifi from 2023.5.7 to 2023.7.22 by @dependabot in https://github.com/biolink/biolink-model/pull/1382
* Created new class GeneAffectsChemicalAssociation with qualifiers by @RichardBruskiewich in https://github.com/biolink/biolink-model/pull/1388
* Cx infores edits by @colleenXu in https://github.com/biolink/biolink-model/pull/1391
* Update understanding-the-model.md by @pabloDumas in https://github.com/biolink/biolink-model/pull/1394
* Fix answer appraiser infores by @maximusunc in https://github.com/biolink/biolink-model/pull/1396
* Chemical prefixes - propagate id_prefixes down the chemical entity hierarchy by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1398
* Bump urllib3 from 2.0.2 to 2.0.6 by @dependabot in https://github.com/biolink/biolink-model/pull/1397
* Fix foodb prefixes by @cbizon in https://github.com/biolink/biolink-model/pull/1399
* Update xref URL for infores:arax in infores_catalog.yaml by @saramsey in https://github.com/biolink/biolink-model/pull/1403
* add pydantic-v2 model by @glass-ships in https://github.com/biolink/biolink-model/pull/1404
* Bump urllib3 from 2.0.2 to 2.0.7 by @dependabot in https://github.com/biolink/biolink-model/pull/1400
* add semantic map to STY:T167, fixes #1370 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1406
* Add qualifier to Association by @kevinschaper in https://github.com/biolink/biolink-model/pull/1407
* Bump urllib3 from 2.0.2 to 2.0.7 by @dependabot in https://github.com/biolink/biolink-model/pull/1409
* Adds `deprecated` as a node property slot added to `biolink:Entity` by @kevinschaper in https://github.com/biolink/biolink-model/pull/1421
* Update infores_catalog.yaml by @karafecho in https://github.com/biolink/biolink-model/pull/1422
* Update infores_catalog.yaml by @karafecho in https://github.com/biolink/biolink-model/pull/1423
## New Contributors
* @pabloDumas made their first contribution in https://github.com/biolink/biolink-model/pull/1394
* @maximusunc made their first contribution in https://github.com/biolink/biolink-model/pull/1396
* @saramsey made their first contribution in https://github.com/biolink/biolink-model/pull/1403
* @glass-ships made their first contribution in https://github.com/biolink/biolink-model/pull/1404
**Full Changelog**: https://github.com/biolink/biolink-model/compare/v3.5.4...v3.6.0
3.5.4
-----
Summary: infores catalog URL replacements with TranslatorWiki pages, and a few new infores entries.
* adding infores for MolePro new data source. by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1377
* many URL updates to the infores catalog to conform with Translator Wiki requirements.
**Full Changelog**: https://github.com/biolink/biolink-model/compare/v3.5.3...v3.5.4
3.5.3
-----
* fix: chemical-affects-gene-association aspect qualifier range by @colleenXu in https://github.com/biolink/biolink-model/pull/1362
* add association slot annotation to support graphs slot, add 'semmed agreement count' as an association slot by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1364
* Adds synonym to named thing, removes it from gene by @kevinschaper in https://github.com/biolink/biolink-model/pull/1369
* Update domain and range of gene condition association by @nicholsn in https://github.com/biolink/biolink-model/pull/1367
* Bump certifi from 2023.5.7 to 2023.7.22 by @dependabot in https://github.com/biolink/biolink-model/pull/1365
**Full Changelog**: https://github.com/biolink/biolink-model/compare/v3.5.2...v3.5.3
3.5.1
----
Summary: added more xrefs for infores catalog and added a semmeddb exclude list
* a few new entries for the infores catalog by @EvanDietzMorris in https://github.com/biolink/biolink-model/pull/1350
* fix duplicated 'deprecated' syntax by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1349
* Semmed exclusion yaml by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1356
* Information resource updates - per TAQA curation by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1357
**Full Changelog**: https://github.com/biolink/biolink-model/compare/v3.5.0...v3.5.1
3.5.0
----
Summary: introduced many changes to infores_catalog.yaml to capture more information about each resource.
From GitHub automated Changelog:
* Adding xref for Text Mining KP by @edgargaticaCU in https://github.com/biolink/biolink-model/pull/1332
* Update MolePro xref in infores catalog by @vdancik in https://github.com/biolink/biolink-model/pull/1334
* Fix broken link in guidelines/README.md by @Daniel-Mietchen in https://github.com/biolink/biolink-model/pull/1336
* update BTE link in infores catalog by @andrewsu in https://github.com/biolink/biolink-model/pull/1337
* Add "full name" slot to the "named thing" slot list by @kevinschaper in https://github.com/biolink/biolink-model/pull/1335
* log odds ratio 95 ci by @CaseyTa in https://github.com/biolink/biolink-model/pull/1340
* Update dataset iri mappings by @nicholsn in https://github.com/biolink/biolink-model/pull/1338
* Stop gap changes to infores_catalog.yaml including knowledge_level and agent_type fields by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1331
* Update BTE link to point to Translator wiki page by @andrewsu in https://github.com/biolink/biolink-model/pull/1342
* add simple script to extract infores resources without URLs or with g… by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1343
* Updated infores catalog according to spreadsheet curation by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1345
* fix : in url by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1346
## New Contributors
* @Daniel-Mietchen made their first contribution in https://github.com/biolink/biolink-model/pull/1336
* @nicholsn made their first contribution in https://github.com/biolink/biolink-model/pull/1338
**Full Changelog**: https://github.com/biolink/biolink-model/compare/v3.4.3...v3.5.0
3.4.3
----
in_taxon_label addition
3.4.2
----
move GeneToPhenotypeAssociation to GeneToPhenotypicFeatureAssociation
3.4.1
-----
recreate wheel with pydantic included
3.4.0
-----
remove support for dynamic enumerations in anatomical context qualifier
reinstate gene to disease and gene to phenotype associations as subclasses of
gene to disease or phenotypic feature association.
more infores URL updates
3.3.4
-----
infores updates and format change
infores TSV IS NOW DEPRECATED in favor of the infores-catalog.yaml file. please make changes here going forward.
bug fixes for documentation.
3.3.3
-----
Infores formatting fixes and validation script updates.
3.3.2
-----
added mappings identified from semmeddb domain/range analysis
3.3.1
----
changes to support fixing documentation links and accessing biolink-model.yaml for use as an import.
3.3.0
-----
* codespell: configuration, github action + typos fixed by @yarikoptic in https://github.com/biolink/biolink-model/pull/1285
* Update codespell to ignore regenerated files by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1286
* Poetry for artifacts by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1287
* Add infores by @gloriachin in https://github.com/biolink/biolink-model/pull/1288
* Improved CAM-KP infores entries by @gaurav in https://github.com/biolink/biolink-model/pull/1293
* Update COHD URLs to Translator Wiki landing pages in Infores Catalog by @CaseyTa in https://github.com/biolink/biolink-model/pull/1290
* fix prefix for biolink by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1297
* Semmeddb mappings per analysis in #1292, fixes #1295 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1294
* fixes #1279 fixes #1216 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1296
## New Contributors
* @yarikoptic made their first contribution in https://github.com/biolink/biolink-model/pull/1285
* @gloriachin made their first contribution in https://github.com/biolink/biolink-model/pull/1288
* @gaurav made their first contribution in https://github.com/biolink/biolink-model/pull/1293
**Full Changelog**: https://github.com/biolink/biolink-model/compare/v3.2.8...v3.3.0
3.2.8
-----
infores catalog URL updates
some changes to mappings for deprecated predicates
update xref definition to be more explicit
3.2.7
-----
minor fixes to infores URL properties
remove singular_name from attributes
3.2.6
-----
some minor fixes to infores URL properties
add denormalized edge properties to association class to support KGX sqlite sink
3.2.5
-----
add supporting_graphs property
3.2.4
-----
add slot usage required instead of broad slot required by @sierra-moxon in #1252
3.2.3
-----
deprecate a few infores entries for automat KGs no longer in use.
3.2.2
----
several new infores parameters added
replaced smart-api URLs in the infores registry with github projects where possible
added support for reasoner-validator to validate retrieval source object
3.2.1
----
add domain to biolink:type to help KGX recognize it as a node property. by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1221
3.2.0
-----
add entity as a domain of name by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1208
fix the regex pattern used to check for the biolink:category CURIE by @vemonet in https://github.com/biolink/biolink-model/pull/1213
add SHACL gen to the `Makefile` by @vemonet in https://github.com/biolink/biolink-model/pull/1214
update doc to use curie form of predicates by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1209
make type slot multivalued by @vincentvialard in https://github.com/biolink/biolink-model/pull/1212
remove cycle in permissible values, fixes #1215, remove degradation from abundance hierarchy in permissible values, fixes #1206 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1217
create `publication type` slot to fix SHACL validation and avoid confusion by @vemonet in https://github.com/biolink/biolink-model/pull/1218
add grouping class for qualifiers, add subset translator, fix range o… by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1219
3.1.2
-----
documentation consistency updates and minor bug fixes
update dependencies
3.1.1
-----
adding more predicate mappings, refactored location and naming conventions here to remove "deprecated"
some opposite/inverse refactoring
loosened the domain of ameliorates predicate to include ClinicalEntities
added several slots to a variety of association classes
refactored build so that pydantic classes are generated and pypi release is automatic
3.1.0
-----
remove deprecated classes, slots
add deprecated predicate mappings to predicate_mappings.yaml
refine documentation with regard to associations, add several chemical->gene examples
general cleanup and maintenance
3.0.3
-----
add missing inverses or missing symmetric properties
add explicit mappings for phenotype and anatomical ontologies
add UMLS as an id prefix for requested class
3.0.2
-----
add side effect predicate
add 'abundance or activity' enum value
deprecate 'original knowledge source', add documentation to the description and examples
3.0.1
-----
minor syntax changes/typo fixes
adding requested attributes for COHD supporting data properties
3.0.0
-----
deprecated/refactored predicate hierarchy to move semantics from predicates into qualifiers (edge properties)
added several enumerations for qualifiers, depending on their usage in associations
added gene->chemical associations with restrictions on subject/predicate/object values (as defined in enumerations)
restructured annotations syntax to comply with LinkML including a change to canonical predicate and opposite syntax
2.4.7
-----
* add pydantic class to the wheel
* update LinkML dependency
2.4.5
-----
* add BioPlanet and Inxight prefixes
* rename pydantic class to model.py
2.4.4
-----
* updated documentation to reference the Biolink Model publication
* added molecular activity to pathway association
* added gene to pathway association
2.4.3
-----
* DRY refactoring of the biolink:ThingWithTaxon mixin by @RichardBruskiewich in https://github.com/biolink/biolink-model/pull/1033
* Adding a biolink:GeneToPathwayAssociation by @RichardBruskiewich in https://github.com/biolink/biolink-model/pull/1031
**Full Changelog**: https://github.com/biolink/biolink-model/compare/v2.4.2...v2.4.3
2.4.2
-----
* fix exposure classes
* more documentation
2.4.1
-----
* bug fixes
2.4.0
-----
* make attribute a child of named thing
* add id to ontology class
2.3.1
-----
* reinstantiate food class with correct prefixes
* add pydantic gen to artifacts
2.3.0
----
* Define subject and/or object on several associations by @kevinschaper in https://github.com/biolink/biolink-model/pull/997
* Replace recursive category range on NamedThing with regex by @kevinschaper in https://github.com/biolink/biolink-model/pull/998
* fixes #1002 - remove underscores from some model components by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1004
* fixes #937 - deprecate approved_to_treat in favor of worldwide FDA status slot. by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1005
* add xref to named thing, fixes #934 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1006
* move around SEMMED mappings according to 936, fixes #936 fixes #935 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1007
* remove relation from association fixes #922 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1009
* add remaining inverses fixes #831 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1010
* Fix prefix mismatches by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1011
**Full Changelog**: https://github.com/biolink/biolink-model/compare/v2.2.16...v2.3.0
2.2.16
------
small maintenance fixes, new prefixes, roles for chemical entities
2.2.15
------
update doc regeneration to use DocGenerator as a first pass.
fix annotations syntax.
2.2.14
------
small maintenance fixes, pin LinkML for testing purposes.
2.2.13
------
small refactors to better use description field consistently.
2.2.12
------
fix dependebot security announcement
remove subclass of from slot_usage
add canonical inverse for increased/decreased activity of pairs
and mondo disease susceptibility term to narrow mappings of disease
update license to apache 2.0
2.2.11
------
Update actions to use github user
2.2.10
------
mapping fixes - remove obsolete mappings, swap text based mappings with ids where applicable
add associated with predicate along with associated with sensitivity to predicates.
2.2.9
-----
many fixes to mappings
2.2.8
-----
add a prefix mapping file artifact generated with LinkML upgrade.
2.2.7
-----
get pypi releases working via github actions
2.2.6
-----
small new additions: several new prefixes, UMLS for chemical entity hierarchy, reactions and pathway additions.
remove drugbank, drugcentral from some members of the chemical hierarchy
added drug regulatory status world wide
added two new predicates under related to, related to at concept level, related to at instance level to
add ways of excluding concept level triples from instance level ones.
fixed chemical entity domain/range constraints after second round of chemical hierarchy refactor
added two new associations that help relate wellness gut/blood microbiome sampling to blood analytes
added literature co-occurence
added has_evidence to association object
fix KGX warnings
fix doc links
added pypi github action
2.2.5
-----
bug fixes: add FYPO prefix, add toxicant, add canonical tag to genetically_interacts_with
setup.py to include name variable in order to enable dependents graph
add README info including link to presention on biolink.
2.2.4
-----
bug fixes: various ID expansion cleanups, remove redundancy in ID prefixes (ie: DBSNP)
upgrade to linkml-1.0.5 to address some issues with the context.jsonld file
2.2.3
-----
bug fixes: inverse predicate is_a hierarchy for 'affects' vs. 'affected by'
2.2.2
-----
UMLS->STY prefix management
adding back in missing mixins for increases/decreases amount activity of.
2.2.1
-----
bug fixes: handling one-off prefix requests
added epistemic qualifier enumeration
2.2.0
-----
add original_subject and original_object edge properties
refactor id prefixes in chemical hierarchy
remove spurious mapping
2.1.0
-----
remove gene and polypeptide (and children) from chemical entity is_a hierarchy
add chemical entity and gene or gene product mixin
add chemical entity and polypeptide and protein mixin
add fda approval status enumeration and definitions
remove is_a parents from exposure classes
add prefixes back to protein
2.0.2
-----
First pass at property chain specification
2.0.0 bug fixes and documentation updates
Upgrade to linkml-1.0.0
2.0.1
-----
Add NCBIGene prefix (with correct capitalization) to accommodate jsonld context requirements
2.0.0
-----
Refactor of the 'Molecular Entity' and 'Chemical Substance' classes and hierarchy
New 'Information Resource' class and EPC slots
New 'reactions' associations and slots
Added inverses for the majority of biolink predicates
1.8.2
-----
Added documentation and examples for mixins
Added id_prefixes to gene, protein
Added id_prefixes to gross anatomical structure
1.8.1
-----
Fixed typo in 'treatement' -> 'treatment'
Removed UniProtKB from Gene class ID prefix list
Changed contact email from Deepak->Sierra
1.8.0
-----
BiolinkML->LinkML name change support
1.7.0
-----
Updated identifiers to canonical forms
Added predicates for increase/decrease expression predicates, opposite of predicate, generalized
domain for treats and transcription/translation predicates
Domain/range changes for 'interacts with' predicate
Add owlstart enumerations for logical interpretations
Fixed part of the documentation bug for 'types' (linkml changes in progress), added environmental context
as another doc fix
Bump urllib to 1.26.3
Added last broad mappings from wikidata to the model
1.6.1
-----
Corrected NCBIGene prefix (from NCBIGENE)
Reverted ontology taxon parent to named thing
1.6.0
-----
Corrected the exact mappings for CTD positive and negative correlation predicates
Refined the modeling of ontology class as a mixin
Removed slot_uri for 'subclass of' predicate
Moved CTD:therapeutic from 'exacerbates' to 'ameliorates'
Fixed range for category slot in the 'association' class
Cleaned up prefixes for INO and HANCESTRO
Removed commas in class and predicate names
1.5.0
-----
Fixed mapping for CTD
Added catalyst qualifier slot
Updated guidelines with examples
Extended the model to represent spatiotemporal exposures, outcomes, and cohorts
Added 'pathological process' class
Predicates that are symmetric are defined explicitly
Added a new 'activity' class
Fixed mixin hierarchy of transcript and RNA products
Extended the model to represent entities from MODs
Reorganized the chemical substance hierarchy
Added a class to represent siRNA
Improved the organization of 'pathological process'
Added more prefixes for various classes
Changed category slot required for 'named thing' and optional for 'association'
1.4.0
-----
Added an enhanced Publication model
Replaced biolink-model.owl with biolink-model.owl.ttl
Differentiated mappings for classes into related, broad, narrow, close, and exact mappings
Differentiated mappings for slots into related, broad, narrow, close, and exact mappings
Fixed typos in class and slot definitions
Fixed inconsistent domain and range constraints
Added classes to represent food
Fixed parent for relation enables
Deprecate edge_label in favor of predicate
Added missing prefixes
Added guidelines to the documentation
Tidied the representation and use of mixins
Differentiated the mixin hierarchy from the class hierarchy
Rearranged properties like id, name, type, description to a generic grouping entity class
1.3.9
-----
Added genomic entities and common properties for these entities
Added mappings to GPI 2.0 specification
Fixed prefixes for mappings in the model
Fixed definition of interacts_with relation to be symmetric
Added missing predicates referenced in associations
Added entities and properties for representing sequence locations
Added mappings from Monarch Initiative
Added an inverse property of subclass_of
Fixed description for edge_label and relation slots
Added more mappings for different entities and relations
Added chi_squared_statistic and p_value association slots
Expanded the scope of correlated_with relation
Added clarification to RDF mappings
Fixed provided_by property to be multivalued
Added enables relation
1.3.0
-----
* association_id property should be an association property
* Added or updated id_prefixes for many types
* add caused by property as inverse of causes
* Chemical structure --> chemical substance
* adding has-output
* OBAN to all upper case. Fix Issue #271
* Adding RHEA to prefixes that can be used for reactions, #269
* First pass at chem2chem associations and hyperedges to catalysts,
* fixes #269
* adding node properties for exposure events
* added new associations for exposures
* identifier type changed to anyURI and linked to metamodel ElementIdentifier
* iri type changed to support both URI or Curie
* changed subclass of to reference an iri instead of a defined ontology class, and made it multivalued
* association_id now defaults to bnode so it doesn't have to be supplied
* range of association slot is named thing (meaning that it has to be typed in the model)
* systematic synonym changed to multivalued
* changed subject and object of association to named thing instead of just a iri
* changed relation type to uriorcurie vs. straight uri
* moved association_id in the association class so the creation order is subject, relation, object instead of association_id, subject, relation, object
1.2.5
-----
* fixed ID type
* adding support for samples and generic attributes
* tiny typo
* Change type off association\_id from identifier type (URI or CURIE) to nodeidentifier (URI, CURIE or BNODE)
* Newest biolinkml output + changes from dataset push
* TBD: tag looks like an JSON object tag - quote it!
* first passing test
* Make run against new model
* Adjustments to type system and association
* Fix merge issue on contextn
* Add native URIs and shexJ format
* Add context that uses metamodel uris instead of slot\_uri and class\_uri
* Add context that uses metamodel uris instead of slot\_uri and class\_uri
* Fix JSON object/array parsing conflict
* SIO:010004 duplication resolved
* Needed double quotes around string..
1.2.1
-----
* Bump version to 1.2.1
* Fix typo
* Add ChangeLog
* Switched to png for UML images
1.2.0
-----
* Update .gitignore
* Update setup.cfg
* Revert "Update setup.py"
* Use the official uniprot PURLs for uniprot entries
* Update setup.py
* Update remaining artifacts
* Update Makefile and tests
* Rename biolinkmodel folder to biolink
* Switch to newer biolinkml
* Fix issue #227
* Point travis at tests (vs. test)
* Fix issue #225
* Backing up to Travis 3.6
* updating index docs
* Update UML diagrams
* Change travis build to 3.7
* Build from new makefile
* Update biolink-model.yaml
* Update biolink-model.yaml
* Fixes #212
* Undoing committed change, intended to open pull request
* Fixes #212
* Update tests for Semantic Net updates
* Commit cosmetic changes so we can merge the latest Semantic Net elements
* Added UMLS Semantic Types and Codes to the Biolink YAML model (#209)
* Update all content for model changes
* Update documentation (#194)
* remove useless evidence instance and use evidence type for has evidence to fix https://github.com/biolink/biolink-model/issues/153 (#195)
* Add description for population (#196)
* Update biolink-model.yaml (#203)
* Add Gitter badge
* Fixed null pointer exception
* Regen tests (#192)
* model refactoring (#187)
* Add Python 3.7 badge to README
* Fix issue #188. Use non-aliased slot names in RDF (#190)
* Update tests, requirements and version
* chembl id prefixes (#180)
* Adding PMID as id prefix for publications (#181)
* Resolve merge conflicts
* Detect ALL unused prefixes (#183)
* Partial fix for issue #175 - missing prefix fix
* Partial fix for issue #175 - missing prefix fix
* Changed ANCESTRO to HANCESTRO
* Update tests to reflect changes
* Fixing type in RO mapping of the 'prevents' slot
* Changed graphviz output to .gv and .svg. Fixes issue #176 (#177)
* extend mappings with new slots (#173)
* Change base URI to http://w3id.org/biolink/vocab
* Detect ALL unused prefixes
* merge
* Update secondary files Also removed a few more false change positives
* Test and build of patch change
* Remove GMODChado mapping
* Make category an IRI type
* Fix issue #163. Also added pipenv files and fixed make file bug
* Checkpoint
* Added comparefiles tool and added to makefile
* Sort markdown index files
* Sort markdown output
* Sample test code for RDF files
* Update tests to reflect ancestors fix
* Fixed scope error
* Correct error in shex compact grammar generation
* Update to fix a bug in the shexc generator
* Updates ShEx testing and generation
* Fixed issue in ShEx generation
* Fix for issue #138. Also updated version number
* Remove a debug statement
* Make test file case sensitive
* Fix issue #131 by changing the name of the test script and adding a pattern to the Makefile
* Add COLUMNS to travis build
* Fixes issue #133 and does complete build
* Updated tests to reflect issue 120 fix
* Fix for issue #119. Also includes a complete make
* Fix for issue #119. Also includes a complete make
* Fixed issue #120
* Updated version for ShExJSG
* Update requirements to match setup
* Update biolink-model.yaml
* Update images
* Build fix
* Resync build
* adding 48 new predicates to support CTD data
* Start of documentation for using the schema loader
* fixed erroneous BFO:0000066 mappings
* Fix for issue #106 - regenerate all documents
* Completely merge biolink-model.yaml
* Set the test refresh\_files variable to false
* Completed the biolink-model.yaml merge and regenerated the ouutput
* Conflict resolution
* Order related differences?
* Integrated last change to biolink-model.yaml on biolink repository
* Remove contrib PNG's and use direct reference
* docs
* Everything is more or less solid
* Everything is more or less solid
* Get the right context for the metamodel
* Added a RDF directory to the make file
* Checkpoint. Metamodel seems completely sound in JSON/RDF and the like
* RDF generating from JSON-LD
* Updated the python to type the slots
* First cut at ShEx generator
* Theoretically complete except for ShEx
* Undoing earlier name fix -- need another approach
* Fix for issue #14
* Undo fix for issue #12
* Fix for issue #12
* Fix for issue #12
* Fix for issue #11
* Fix for issue #10
* Update test and make output to reflect changes in json schema generator
* Fixed a typo in Generator.visit\_all\_\_class slots
* Fixes issue #9
* Test files updated to reflect biolink-model.yaml refactoring for issue #8
* Misc test files that were missed in previous submissions
* Temporary fix for issue #8 -- added expected failure decorators
* Fix for issue #7
* Fixes for issue #5
* Fixes for issue #4
* Additional changes for yuml determinacy problem
* Fixed non-determinacy issue in emission order
* Cleaned up contextgen comments and clicktestcase editing of it
* Fix issue #6
* Part of issue 2 fix
* Removed Generator.root\_closure, as it was only called from here
* Fix Issue #3 - extra asterisk
* Fix Issue #5
* Fix Issue #2
* Added link to the metamodel markdown documentation
* Approaching beta version of markdown and yuml diagrams
* Switch to inline UML
* Update to YUML and markdown generators
* OWl Generation is close to working
* Set theme jekyll-theme-dinky
* Updated the docs
* Passes 3.6 and 3.7 tox tests
* Removed bin directory and added scripts to setup.py
* Checkpoint -- all generators running
* Checkpoint -- YUML generator approaching complete
* Checkpoint -- Generating everything through markdown
* Checkpoint -- generating complete python for metamodel and biolink
* Checkpoint -- metamodel is (almost) self generating
* Proposed dataclasses representation of metamodel
* test for shex etc
1.1.1
-----
* added generated docs for new elements
* Additional association paths
* Added zenodo badge, see #87
* added predisposes and has input slots
* added missing generated docs
* evidence
* Additional mappings
* semweb prefixes
* Ensure all prefixes added
* regen
* add 'in taxon' slot to translator\_minimal subset
* imports
* trim leading 'is' from several predicate names
* changing in\_subset values to lists
* regen
* Fixes #77
* Added example property for chemical entity, fixes #64
* pop2pop
* Update biolink-model.yaml
* regen docs
* fix syntax errs
* stub code for generating nested objects in contextld
* Fixed invalid YAML file
* update treats condition->treats
* fix typos, minor updates to deescriptions
* Added in\_subset and inverse annotations to TKG min predicates, and WD and SemMedDB mappings
* added in\_subset and inverse slot definitions
* renamed 4 predicates, deprecated two predicates, added numerous new predicates
* re-prioritized
* re-prioritized
* Added chembl, fixes #65
* added links to context file, see #65
* missing docs
* Using reactome for now, but see https://github.com/monarch-initiative/dipper/issues/582
* include all prefixes
* JSON-LD context generation
* link to kgx
1.1.0
-----
* docs
* regen
* fix typo
* updated docs
* Added grouping for BP+MF, fixes #59
* Update biolink-model.yaml
* add SEMMEDDB:PRECEDES mapping
* neo4j-names
* proposed for #49
* tr
* Added UMLS Semantic Group LIVB as a mapping
* category
* expanding UML
* new classes
* restored
* regen
* variant to pop frequencies
* add missing
* Use correct UPHENO Phenotype IRI
* upgraded marshmallow
* fixed typo
* Added metabolite, fixes #35
* Fix upheno mapping, fixes #41
* Update biolink-model.yaml
* Update biolink-model.yaml
* Update biolink-model.yaml
* nu
* yUML
* variants
* protobuf
* regen
* regen
* regen
* regulates
* local-names
* Adding predicates
* NT: haplotype
* sequence variant changes, from #21
* Update biolink-model.yaml
* Issue #26
* regenerated
* regenerated
* regen
* ontol
* regen
* ontology iri
* license
* license
* license
* adding license
1.0.0
-----
* regenerated derived artefacts
* fixing typo
* removing occupation, was added for #7
* First pass at modeling isoforms in schema, see also discussion at https://github.com/The-Sequence-Ontology/MSO/issues/1
* improved metamodel def
* reorganized README
* regen
* Fix list typo
* add\_wikidata\_class\_mappings
* sio mappings
* Added mappings from @micheldumontier in https://github.com/NCATS-Tangerine/translator-knowledge-beacon/pull/45
* pheno qualifiers
* Added mappings to the small number of Wikidata concept types
* Gitignore local Eclipse IDE configuration
* first pass at ShEx, #12
* csvs
* moved docs from top level
* csv export
* regen
* regen
* docs
* moved
* moved
* remove stale
* split some out into contrib
* additional mappings