From c736ca59ce28005495a928e01cac58b3fbe2f920 Mon Sep 17 00:00:00 2001 From: helenamachado Date: Thu, 14 Sep 2023 16:14:28 -0700 Subject: [PATCH] adding facial skeleton terms issue #151 adding: lacrimal bone length nasal bone length to nasomaxillary suture facial skeleton lateral length to infra-orbital foramen of maxilla facial skeleton lateral length to frontolacrimal suture --- src/ontology/fovt-edit.owl | 55 ++++++++++++++++++++ src/ontology/imports/bco_import.owl | 4 +- src/ontology/imports/bfo_import.owl | 4 +- src/ontology/imports/bspo_import.owl | 4 +- src/ontology/imports/iao_import.owl | 4 +- src/ontology/imports/ncbitaxon_import.owl | 8 +-- src/ontology/imports/oba_import.owl | 41 ++++++++++++++- src/ontology/imports/oba_terms.txt | 3 +- src/ontology/imports/pato_import.owl | 4 +- src/ontology/imports/ro_import.owl | 4 +- src/ontology/imports/uberon_import.owl | 62 ++++++++++++++++++++++- src/ontology/imports/uberon_terms.txt | 3 +- 12 files changed, 176 insertions(+), 20 deletions(-) diff --git a/src/ontology/fovt-edit.owl b/src/ontology/fovt-edit.owl index 7ec06e3..1a5ddc0 100644 --- a/src/ontology/fovt-edit.owl +++ b/src/ontology/fovt-edit.owl @@ -1153,6 +1153,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -13472,6 +13476,57 @@ AnnotationAssertion(Annotation( "facial skeleton breadth at nasal bone"@en) SubClassOf( ) +# Class: (lacrimal bone length) + +AnnotationAssertion( ) +AnnotationAssertion(Annotation( "ISBN: 9780873659505") "The length of a lacrimal bone along the anterior-posterior axis."@en) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(dcterms:contributor "https://orcid.org/0000-0001-8415-4848") +AnnotationAssertion(Annotation( "ISBN: 9780873659505") "greatest length of lacrimal"@en) +AnnotationAssertion(Annotation( "ISBN: 9780873659505") rdfs:comment "The following is the measurement number and genus for this trait in von den Driesch (1979): 14 Ovis and Capra"@en) +AnnotationAssertion(Annotation( "ISBN: 9780873659505") rdfs:comment "This measurement is taken from the most lateral point of the lacrimal bone to the most oral point of the lacrimomaxillary suture."@en) +AnnotationAssertion(rdfs:label "lacrimal bone length"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) + +# Class: (nasal bone length to nasomaxillary suture) + +AnnotationAssertion( ) +AnnotationAssertion(Annotation( "ISBN: 9780873659505") "The length of a nasal bone from a nasion to a midsagittal point of anteriormost points of nasomaxillary suture."@en) +AnnotationAssertion( ) +AnnotationAssertion(dcterms:contributor "https://orcid.org/0000-0001-8415-4848") +AnnotationAssertion(Annotation( "ISBN: 9780873659505") "short nasal length"@en) +AnnotationAssertion(Annotation( "ISBN:9780873659505"^^xsd:decimal) rdfs:comment "The following is the measurement number and genus for this trait in von den Driesch (1979): 15a Sus"@en) +AnnotationAssertion(rdfs:label "nasal bone length to nasomaxillary suture"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (facial skeleton lateral length to infra-orbital foramen of maxilla) + +AnnotationAssertion( ) +AnnotationAssertion(Annotation( "ISBN: 9780873659505") "The length of a facial skeleton from a entorbitale to an infra-orbital foramen of maxilla."@en) +AnnotationAssertion( ) +AnnotationAssertion(dcterms:contributor "https://orcid.org/0000-0001-8415-4848") +AnnotationAssertion(Annotation( "ISBN: 9780873659505") "entorbitale to infraorbitale"@en) +AnnotationAssertion(Annotation( "ISBN: 9780873659505") rdfs:comment "The following is the measurement number and genus for this trait in von den Driesch (1979): 19 Sus."@en) +AnnotationAssertion(rdfs:label "facial skeleton lateral length to infra-orbital foramen of maxilla"@en) +SubClassOf( ) +SubClassOf( ) + +# Class: (facial skeleton lateral length to frontolacrimal suture) + +AnnotationAssertion( ) +AnnotationAssertion(Annotation( "ISBN: 9780873659505") "The lenght of a facial skeleton from a posteriormost point of a lacrimal bone at the margin of orbit of skull to a posteriormost point of a frontolacrimal suture."@en) +AnnotationAssertion( ) +AnnotationAssertion(dcterms:contributor "https://orcid.org/0000-0001-8415-4848") +AnnotationAssertion(Annotation( "ISBN: 9780873659505") "upper length of the lacrimal"@en) +AnnotationAssertion(Annotation( "ISBN: 9780873659505") rdfs:comment "The following is the measurement number and genus for this trait in von den Driesch (1979): 21 Sus"@en) +AnnotationAssertion(rdfs:label "facial skeleton lateral length to frontolacrimal suture"@en) +SubClassOf( ) +SubClassOf( ) + # Class: (pelvic girdle bone/zone size) SubClassOf( ) diff --git a/src/ontology/imports/bco_import.owl b/src/ontology/imports/bco_import.owl index 64b5c1d..4d0469b 100644 --- a/src/ontology/imports/bco_import.owl +++ b/src/ontology/imports/bco_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2023-09-13"^^xsd:string) +Annotation(owl:versionInfo "2023-09-14"^^xsd:string) Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl index 89c8af1..ad04295 100644 --- a/src/ontology/imports/bfo_import.owl +++ b/src/ontology/imports/bfo_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2023-09-13"^^xsd:string) +Annotation(owl:versionInfo "2023-09-14"^^xsd:string) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) diff --git a/src/ontology/imports/bspo_import.owl b/src/ontology/imports/bspo_import.owl index 6653c76..7d5eb8b 100644 --- a/src/ontology/imports/bspo_import.owl +++ b/src/ontology/imports/bspo_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2023-09-13"^^xsd:string) +Annotation(owl:versionInfo "2023-09-14"^^xsd:string) Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl index 47cabde..db27d86 100644 --- a/src/ontology/imports/iao_import.owl +++ b/src/ontology/imports/iao_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2023-09-13"^^xsd:string) +Annotation(owl:versionInfo "2023-09-14"^^xsd:string) Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/ncbitaxon_import.owl b/src/ontology/imports/ncbitaxon_import.owl index 6ec776d..a658a59 100644 --- a/src/ontology/imports/ncbitaxon_import.owl +++ b/src/ontology/imports/ncbitaxon_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2023-09-13"^^xsd:string) + +Annotation( ) +Annotation(owl:versionInfo "2023-09-14") Declaration(Class()) Declaration(Class()) @@ -148,6 +148,8 @@ AnnotationAssertion(rdfs:label (root) AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "PMID:30365038") +AnnotationAssertion( "PMID:32761142") AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( ) "all") AnnotationAssertion( "NCBITaxon:1") diff --git a/src/ontology/imports/oba_import.owl b/src/ontology/imports/oba_import.owl index 1e10db1..b895518 100644 --- a/src/ontology/imports/oba_import.owl +++ b/src/ontology/imports/oba_import.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -9938,6 +9938,39 @@ + + + + + + + + + + + + + + + The morphology of a lacrimal bone. + morphology of lacrimal bone + lacrimal bone morphology trait + + + + + The morphology of a lacrimal bone. + obo:oba/patterns/entity_attribute_part_of + + + + + morphology of lacrimal bone + obo:oba/patterns/entity_attribute_part_of + + + + @@ -11630,6 +11663,12 @@ + + + + + + diff --git a/src/ontology/imports/oba_terms.txt b/src/ontology/imports/oba_terms.txt index d9f5132..366e82b 100644 --- a/src/ontology/imports/oba_terms.txt +++ b/src/ontology/imports/oba_terms.txt @@ -105,4 +105,5 @@ OBA:VT0003047 #thoracic vertebra morphology trait OBA:0004048 #lumbar vertebra length OBA:0002828 #lumbar vertebra 5 size OBA:0002399 #nasal bone length -OBA:0003446 #premaxilla length \ No newline at end of file +OBA:0003446 #premaxilla length +OBA:VT0005271 #lacrimal bone morphology trait \ No newline at end of file diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index ec4c717..9561745 100644 --- a/src/ontology/imports/pato_import.owl +++ b/src/ontology/imports/pato_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2023-09-13"^^xsd:string) +Annotation(owl:versionInfo "2023-09-14"^^xsd:string) Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 6bd59d2..47a7fdf 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2023-09-13"^^xsd:string) +Annotation(owl:versionInfo "2023-09-14"^^xsd:string) Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/uberon_import.owl b/src/ontology/imports/uberon_import.owl index 25c66f4..1c954be 100644 --- a/src/ontology/imports/uberon_import.owl +++ b/src/ontology/imports/uberon_import.owl @@ -7,7 +7,7 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) Annotation( ) Annotation( ) @@ -68,7 +68,7 @@ Annotation( "https://docs.google.com/doc Annotation( "https://docs.google.com/document/d/1cPWBqrl_Qy7XHEWFqtR_PgQX61yRkgGuLaiDpnEXxkE/edit"^^xsd:anyURI) Annotation( "https://docs.google.com/document/d/1r9kNPpFYGdu0SpJDLyFAVQczBlG0wAZCBMd18gG3Ot8/edit#"^^xsd:anyURI) Annotation( "https://docs.google.com/spreadsheet/ccc?key=0Aj8NJdyb-leqdDM0R3hTVTRHRExDVjRCSkZEbDc5N1E#gid=0"^^xsd:anyURI) -Annotation(owl:versionInfo "2023-09-13"^^xsd:string) +Annotation(owl:versionInfo "2023-09-14"^^xsd:string) Declaration(Class()) Declaration(Class()) @@ -6368,6 +6368,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9614,6 +9615,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -115699,6 +115701,48 @@ SubClassOf( ObjectSomeValuesFrom( SubClassOf(Annotation( "definitional") ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (lacrimal bone) + +AnnotationAssertion(Annotation( "ISBN:0-683-40008-8") Annotation( "MP:0005271") "The irregularly thin plate that forms part of the medial wall of the orbit behind the frontal process of the maxilla.") +AnnotationAssertion(Annotation( "Wikipedia") ) +AnnotationAssertion( ) +AnnotationAssertion(Annotation( "2012-09-17") Annotation( "VHOG:0001149") Annotation( "VHOG") Annotation( "ISBN:978-3899370805 Arratia G, Schultze HP, Wilson MVH, Mesozoic Fishes 4 - Homology and Phylogeny (2008) p.23-48") Annotation( "http://bgee.unil.ch/") "The infraorbital bone 1 of actinopterygians is homologous with the lacrimal bone (...).[well established][VHOG]") +AnnotationAssertion( "In early lobe-finned fishes and ancestral tetrapods, the lacrimal bone is a relatively large and robust bone, running from the orbit to the nostrils. It forms part of the side of the face, between the nasal bones and the maxilla. In primitive forms, it is often accompanied by a much smaller septomaxilla bone, lying immediately behind the nasal opening, but this is lost in most modern species. The lacrimal bone is often smaller in living vertebrates, and is no longer always directly associated with the nasal opening, although it retains its connection with the orbit. The bone is entirely absent in living amphibians, as well as some reptilian species[ISBN 0-03-910284-X]") +AnnotationAssertion( "lacrimal") +AnnotationAssertion( "FMA:52741") +AnnotationAssertion( "MA:0001486") +AnnotationAssertion( "NCIT:C32906") +AnnotationAssertion( "SCTID:272675007") +AnnotationAssertion(Annotation( "ncithesaurus:Lacrimal_Bone") "UMLS:C0222733") +AnnotationAssertion( "VHOG:0001149") +AnnotationAssertion( "Wikipedia:Lacrimal_bone") +AnnotationAssertion( "lachrymal bone") +AnnotationAssertion( "lacrymal bone") +AnnotationAssertion( "uberon") +AnnotationAssertion(Annotation( "VHOG:0001149") Annotation( "ZFA:0000223") Annotation( ) "infraorbital 1") +AnnotationAssertion(Annotation( "VHOG:0001149") "lachrymal bone - infraorbital 1") +AnnotationAssertion(Annotation( "VHOG:0001149") "lacrimal - infraorbital 1") +AnnotationAssertion(Annotation( "VHOG:0001149") "lacrymal bone - infraorbital 1") +AnnotationAssertion(Annotation( "Wikipedia:Lacrimal_bone") Annotation( ) "os lacrimale") +AnnotationAssertion( "UBERON:0001680") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "lacrimal bone") +AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray164.png"^^xsd:anyURI) +SubClassOf( ) +SubClassOf(Annotation( "FMA") ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf(Annotation( "orbital series") Annotation( "ISBN:0073040584") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "FMA-abduced-lr") ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "ZFA-modified") ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (nasal bone) AnnotationAssertion(Annotation( "Wikipedia:Nasal_bone") Annotation( "ZFIN:curator") Annotation( "https://github.com/obophenotype/uberon/issues/265") "One of two small oblong bones, varying in size and form in different individuals; they are placed side by side at the middle and upper part of the face, and form, by their junction, 'the bridge' of the nose[WP]. Paired dermal bones, likened to a bone tube, positioned lateral to the supraethmoid. Nasal bones are transversed by the anterior most part of the supraorbital canals and bear one neuromast foramen in zebrafish[ZFA].") @@ -181855,6 +181899,20 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (lacrimomaxillary suture) + +AnnotationAssertion(Annotation( "http://medical-dictionary.thefreedictionary.com/lacrimomaxillary+suture") "A suture between the lacrimal bone and the maxilla.") +AnnotationAssertion( "FMA:52961") +AnnotationAssertion(Annotation( "FMA:52961") "lacrimomaxillary suture of skull") +AnnotationAssertion(Annotation( "FMA:TA") Annotation( ) "sutura lacrimomaxillaris") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0035883") +AnnotationAssertion(rdfs:label "lacrimomaxillary suture") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (maxillary-premaxillary suture) AnnotationAssertion(Annotation( "MGI:csmith") Annotation( "PMID:21538817") Annotation( "https://github.com/obophenotype/mammalian-phenotype-ontology/issues/2139") "A suture between the maxilla and premaxilla.") diff --git a/src/ontology/imports/uberon_terms.txt b/src/ontology/imports/uberon_terms.txt index 4f7c413..02a1d31 100644 --- a/src/ontology/imports/uberon_terms.txt +++ b/src/ontology/imports/uberon_terms.txt @@ -319,4 +319,5 @@ UBERON:0004616 #mammalian cervical vertebra 7 UBERON:0008462 #postzygapophysis of cervical vertebra UBERON:0008459 #prezygapophysis of cervical vertebra UBERON:0018143 #transverse process of cervical vertebra -UBERON:7500103 #preorbital fossa \ No newline at end of file +UBERON:7500103 #preorbital fossa +UBERON:0001680 #lacrimal bone \ No newline at end of file