From 5331655917a6e0f5fdbd7b564ad28efd83d0ee05 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Thu, 12 Sep 2024 16:09:23 +0100 Subject: [PATCH 1/3] Fix incompatibility with ZFA's "head". In ZFA, the "head" (ZFA:0001114) corresponds to what Uberon calls the "craniocervical region" (UBERON:0007811), comprising the head proper and the neck. So we remap ZFA:0001114 to UBERON:0007811, rather than UBERON:0000033). Also, the axiom stating that 'pharyngeal arch' (UBERON:0002539) is part of the 'embryonic head' (UBERON:0008816) is bogus, as some pharyngeal arches are located in the neck rather than the head. So we create a new term 'embryonic craniocervical region' to be the embryonic counterpart of 'craniocervical region' (as 'embryonic head' is the embryonic counterpart of 'head'), and rewrite the aforementioned axiom to state that 'pharyngeal arch' is part of the 'embryonic craniocervical region'. Combined together, these two changes fix about 80 unsatisfiable classes in the merge product of Uberon and ZFA. closes #379 --- src/ontology/uberon-edit.obo | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index a28d01127..5b7335d49 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -1137,7 +1137,6 @@ xref: VHOG:0001644 xref: WBbt:0005739 xref: Wikipedia:Head xref: XAO:0003024 -xref: ZFA:0001114 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: has_skeleton UBERON:0003129 {gci_relation="part_of", gci_filler="NCBITaxon:7776"} ! skull relationship: in_taxon NCBITaxon:33213 ! Bilateria @@ -53567,7 +53566,7 @@ relationship: developmentally_induced_by UBERON:0007690 {source="PMID:16313389"} relationship: has_developmental_contribution_from UBERON:0002342 {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neural crest relationship: in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata relationship: part_of UBERON:0008814 ! pharyngeal arch system -relationship: part_of UBERON:0008816 {source="PMID:16313389"} ! embryonic head +relationship: part_of UBERON:8450003 {source="PMID:16313389"} ! embryonic craniocervical region property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png" xsd:anyURI property_value: external_definition "One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010359", ontology="AAO", source="NLM:branchial+arch"} property_value: homology_notes "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000155", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} @@ -123558,6 +123557,7 @@ xref: NCIT:C12418 xref: SCTID:361355005 xref: UMLS:C0460004 {source="ncithesaurus:Head_and_Neck"} xref: WikipediaCategory:Head_and_neck +xref: ZFA:0001114 is_a: UBERON:0000475 {source="MA"} ! organism subdivision relationship: has_part UBERON:0000033 ! head relationship: has_part UBERON:0000974 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! neck @@ -223135,6 +223135,15 @@ intersection_of: capable_of GO:0046903 ! secretion created_by: http://orcid.org/0000-0002-6095-8718 creation_date: 2022-05-25T18:21:29Z +[Term] +id: UBERON:8450003 +name: embryonic craniocervical region +def: "A craniocervical region that is part of an embryo." [] +intersection_of: UBERON:0007811 ! craniocervical region +intersection_of: part_of UBERON:0000922 ! embryo +relationship: dc-contributor https://orcid.org/0000-0002-6095-8718 ! Damien Goutte-Gattat +property_value: dcterms-date "2024-09-12T14:40:00Z" xsd:dateTime + [Term] id: UBERON:8470000 name: placental blood From 1d7f882d9612474c7a855c78d5fd124dcefe41ed Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Thu, 12 Sep 2024 16:26:30 +0100 Subject: [PATCH 2/3] Add xref for definition of 'embryonic craniocervical region'. Not really useful for a definition that is merely the English translation of the logical definition, but it keeps the CI checks happy. --- src/ontology/uberon-edit.obo | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 5b7335d49..ef3d0b91c 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -223138,7 +223138,7 @@ creation_date: 2022-05-25T18:21:29Z [Term] id: UBERON:8450003 name: embryonic craniocervical region -def: "A craniocervical region that is part of an embryo." [] +def: "A craniocervical region that is part of an embryo." [https://orcid.org/0000-0002-6095-8718] intersection_of: UBERON:0007811 ! craniocervical region intersection_of: part_of UBERON:0000922 ! embryo relationship: dc-contributor https://orcid.org/0000-0002-6095-8718 ! Damien Goutte-Gattat From 95cc4af6e5b5f4c98c7f01e119d99afd8fd57490 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Thu, 24 Oct 2024 17:08:20 +0100 Subject: [PATCH 3/3] Add GCI for 'part of some embryonic craniocervical region'. Add the following GCI axiom ('part of' some embryo) and ('part of' some 'craniocervical region') SubClassOf: 'part of' some 'embryonic craniocervical region' --- src/ontology/components/disjoint_union_over.owl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/ontology/components/disjoint_union_over.owl b/src/ontology/components/disjoint_union_over.owl index d53841bb5..96268fea5 100644 --- a/src/ontology/components/disjoint_union_over.owl +++ b/src/ontology/components/disjoint_union_over.owl @@ -16,6 +16,7 @@ EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) EquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) +SubClassOf(ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))