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Update OBO test file to new obo syntax
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matentzn committed May 9, 2024
1 parent 8abb40d commit 944eb34
Showing 1 changed file with 8 additions and 6 deletions.
14 changes: 8 additions & 6 deletions docs/examples/example.obo
Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
format-version: 1.2
idspace: foaf http://xmlns.com/foaf/0.1/
idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl#
remark: Comment from annotations.ttl file.
ontology: https://github.com/ontodev/robot/examples/edit.owl
owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(Class(<http://purl.obolibrary.org/obo/UBERON_0001062>))\n############################\n# Classes\n############################\n\n# Class: <http://purl.obolibrary.org/obo/UBERON_0001062> (<http://purl.obolibrary.org/obo/UBERON_0001062>)\n\nSubClassOf(<http://purl.obolibrary.org/obo/UBERON_0001062> owl:Thing)\n\n\n)
Expand Down Expand Up @@ -377,8 +379,8 @@ xref: XAO:0000165
is_a: UBERON:0001851 ! cortex
intersection_of: UBERON:0001851 ! cortex
intersection_of: part_of UBERON:0002369 ! adrenal gland
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/thumb/5/5c/Gray1185.png/200px-Gray1185.png
property_value: foaf:depicted_by http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png
property_value: foaf:depicted_by http://upload.wikimedia.org/wikipedia/commons/thumb/5/5c/Gray1185.png/200px-Gray1185.png
property_value: homology_notes "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001481", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9"}
property_value: taxon_notes "Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO" xsd:string

Expand Down Expand Up @@ -469,7 +471,7 @@ is_a: UBERON:0002530 ! gland
intersection_of: UBERON:0002530 ! gland
intersection_of: part_of UBERON:0000949 ! endocrine system
relationship: part_of UBERON:0000949 ! endocrine system
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png
property_value: foaf:depicted_by http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png

[Term]
id: UBERON:0002369
Expand Down Expand Up @@ -514,9 +516,9 @@ xref: XAO:0000164
is_a: UBERON:0006858 ! adrenal/interrenal gland
relationship: part_of UBERON:0000916 ! abdomen
relationship: part_of UBERON:0000949 ! endocrine system
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/9d/Illu_endocrine_system_New.png
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/thumb/c/c6/Illu_endocrine_system.jpg/200px-Illu_endocrine_system.jpg
property_value: external_definition "Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010551", ontology="AAO", source="AAO:BJB"}
property_value: foaf:depicted_by http://upload.wikimedia.org/wikipedia/commons/9/9d/Illu_endocrine_system_New.png
property_value: foaf:depicted_by http://upload.wikimedia.org/wikipedia/commons/thumb/c/c6/Illu_endocrine_system.jpg/200px-Illu_endocrine_system.jpg
property_value: function_notes "suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n." xsd:string
property_value: homology_notes "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001141", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9"}
property_value: taxon_notes "The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole" xsd:string
Expand Down Expand Up @@ -572,7 +574,7 @@ xref: OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA
xref: UMLS:C1285092 {source="ncithesaurus:Gland"}
xref: WikipediaCategory:Glands
is_a: UBERON:0000062 ! organ
property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png
property_value: foaf:depicted_by http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png
property_value: has_relational_adjective "glandular" xsd:string

[Term]
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