Merge pull request #210 from monarch-initiative/issue-209

Refactor VBO definitions #209
monarch-initiative · Dec 11, 2024 · 5a77630 · 5a77630
2 parents 75007a7 + 59f15f1
commit 5a77630
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diff --git a/src/ontology/components/catbreeds.owl b/src/ontology/components/catbreeds.owl
diff --git a/src/ontology/components/catbreeds.tsv b/src/ontology/components/catbreeds.tsv
diff --git a/src/ontology/components/dadisbreedcountry.owl b/src/ontology/components/dadisbreedcountry.owl
diff --git a/src/ontology/components/dadisbreedcountry.tsv b/src/ontology/components/dadisbreedcountry.tsv
diff --git a/src/ontology/components/dadistransbound.tsv b/src/ontology/components/dadistransbound.tsv
@@ -1,5 +1,5 @@
 vbo_id	term_label	to_be_ignored	breed_name_to_be_used_for_label	species_to_be_used_for_label	internal_term_merge_indicator_vboid_into_vboid	internal_date_and_issue_separated_by_pipe_yymmdd_dash_issue	gh_issue_NOT_merge_obsolete	parent_ID	source_for_parents	source_for_parents	parent_ID	source_for_parents	source_for_parents	parent_ID	source_for_parents	source_for_parents	most_common_name	synonym_type_most_common_name	source_for_most_common_name	source_for_most_common_name	synonym_dadis_name_not_used_in_label	source_for_synonym_dadis	source_for_synonym_dadis	synonym_1	source_for_synonym_1	source_for_synonym_1	synonym_2	source_for_synonym_2	source_for_synonym_2	synonym_3	source_for_synonym_3	source_for_synonym_3	synonym_4	source_for_synonym_4	source_for_synonym_4	synonym_5	source_for_synonym_5	source_for_synonym_5	synonym_label_from_merged_term	source_for_merged_term	Breed_code_1	all_source_for_breed_code_1_separated_by_pipe	all_source_for_breed_code_1_separated_by_pipe	Breed_code_2	all_source_for_breed_code_2_separated_by_pipe	all_source_for_breed_code_2_separated_by_pipe	definition 	definition_xref	definition_xref	xref1	source_for_xref1	source_for_xref1	xref2	source_for_xref2	source_for_xref2	omia_xref_internal	recognition_status_1	source_for_recognition_status_1	source_for_recognition_status_1	recognition_status_2	source_for_recognition_status_2	source_for_recognition_status_2	recognition_status_3	source_for_recognition_status_3	source_for_recognition_status_3	source_for_breed	source_for_breed	contributors	contributors	comment	general_comment	comment_from_obsoletion	description_of_origin	source_for_description_of_origin	source_for_description_of_origin	domestication_status	source_for_domestication_status	wikidata_link_for_the_country_exists_in_country_subclass	source_for_country_subclass	source_for_country_subclass	obsoletion_type	obsolete	replacement_term	replacement_label	comment	GH_issue	obsolescence_reason	curator_note	dadis_name	dadis_species_name	dadis_country	dadis_iso3_code	in_subset_transboundary
-ID	LABEL						AT IAO:0000233^^xsd:anyURI SPLIT=|	SC %	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	SC %	>AT oboInOwl:source^^xsd:anyURI	>A oboInOwl:source SPLIT=|	SC %	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasExactSynonym	>AI oboInOwl:hasSynonymType	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasExactSynonym	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasExactSynonym	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasExactSynonym	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasExactSynonym	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasExactSynonym	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasExactSynonym	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasExactSynonym	>A oboInOwl:source SPLIT=|	A http://purl.obolibrary.org/obo/vbo#breed_code	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A http://purl.obolibrary.org/obo/vbo#breed_code	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A IAO:0000115	>AT oboInOwl:hasDbXref^^xsd:anyURI SPLIT=|	>A oboInOwl:hasDbXref SPLIT=|	A oboInOwl:hasDbXref  SPLIT=|	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasDbXref  SPLIT=|	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|		AI http://purl.obolibrary.org/obo/vbo#breed_recognition_status	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	AI http://purl.obolibrary.org/obo/vbo#breed_recognition_status	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	AI http://purl.obolibrary.org/obo/vbo#breed_recognition_status	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	AT dc:source^^xsd:anyURI	A dc:source SPLIT=|	AI dc:contributor SPLIT=|	AI dc:contributor SPLIT=|	A rdfs:comment			A http://purl.obolibrary.org/obo/vbo#origindescription	>AT oboInOwl:source^^xsd:anyURI	>A oboInOwl:source	AI http://purl.obolibrary.org/obo/vbo#hasdomesticationstatus	>AT oboInOwl:source^^xsd:anyURI	SC 'located in' value %	>AT oboInOwl:source^^xsd:anyURI	>A oboInOwl:source	TYPE	AT owl:deprecated^^xsd:boolean	AI IAO:0100001			AT IAO:0000233^^xsd:anyURI	A IAO:0000231						AI oboInOwl:inSubset
+ID	LABEL						AT IAO:0000233^^xsd:anyURI SPLIT=|	SC %	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	SC %	>AT oboInOwl:source^^xsd:anyURI	>A oboInOwl:source SPLIT=|	SC %	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasExactSynonym	>AI oboInOwl:hasSynonymType	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasExactSynonym	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasExactSynonym	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasExactSynonym	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasExactSynonym	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasExactSynonym	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasExactSynonym	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasExactSynonym	>A oboInOwl:source SPLIT=|	A http://purl.obolibrary.org/obo/vbo#breed_code	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A http://purl.obolibrary.org/obo/vbo#breed_code	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A IAO:0000115	>AT oboInOwl:hasDbXref^^xsd:anyURI SPLIT=|	>A oboInOwl:hasDbXref SPLIT=|	A oboInOwl:hasDbXref  SPLIT=|	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	A oboInOwl:hasDbXref  SPLIT=|	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|		AI http://purl.obolibrary.org/obo/vbo#breed_recognition_status	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	AI http://purl.obolibrary.org/obo/vbo#breed_recognition_status	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	AI http://purl.obolibrary.org/obo/vbo#breed_recognition_status	>AT oboInOwl:source^^xsd:anyURI SPLIT=|	>A oboInOwl:source SPLIT=|	AT dc:source^^xsd:anyURI	A dc:source SPLIT=|	AI dc:contributor SPLIT=|	AI dc:contributor SPLIT=|	A rdfs:comment			A http://purl.obolibrary.org/obo/vbo#origindescription	>AT oboInOwl:source^^xsd:anyURI	>A oboInOwl:source	AI http://purl.obolibrary.org/obo/vbo#hasdomesticationstatus	>AT oboInOwl:source^^xsd:anyURI	SC 'breed reported in geographic location' value %	>AT oboInOwl:source^^xsd:anyURI	>A oboInOwl:source	TYPE	AT owl:deprecated^^xsd:boolean	AI IAO:0100001			AT IAO:0000233^^xsd:anyURI	A IAO:0000231						AI oboInOwl:inSubset
 VBO:0000012	Dromedary Bactrian Camel							NCBITaxon:9836		DOI:10.1016/j.jasrep.2021.103038|PMID:31969478|PMID:33409310|PMID:29746547|PMID:26161164|DOI:10.1016/j.jfca.2015.02.006|PMID:25831121|DOI:10.9755/ejfa.v26i4.17271|DOI:10.5252/az2014n2a06								http://purl.obolibrary.org/obo/vbo#most_common_name																																																https://www.fao.org/dad-is		https://orcid.org/0000-0002-4142-7153|https://orcid.org/0000-0002-5520-6597|https://orcid.org/0000-0002-9178-3965																									
 VBO:0000038			Alpaca	Alpaca		231120-126|231212-137	https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126|https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/137	NCBITaxon:30538	https://www.fao.org/dad-is		VBO:0400000		https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153				Alpaca	http://purl.obolibrary.org/obo/vbo#most_common_name	https://www.fao.org/dad-is					Alpaca (Alpaca)		VBO:0000038																																								https://www.fao.org/dad-is		https://orcid.org/0000-0002-4142-7153|https://orcid.org/0000-0002-5520-6597|https://orcid.org/0000-0002-9178-3965																					Alpaca	Alpaca			http://purl.obolibrary.org/obo/vbo#transboundary
 VBO:0000039	Huacaya (Alpaca)		Huacaya	Alpaca		231120-126	https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126	NCBITaxon:30538	https://www.fao.org/dad-is		VBO:0400000		https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153				Huacaya	http://purl.obolibrary.org/obo/vbo#most_common_name	https://www.fao.org/dad-is																																															https://www.fao.org/dad-is		https://orcid.org/0000-0002-4142-7153|https://orcid.org/0000-0002-5520-6597|https://orcid.org/0000-0002-9178-3965																					Huacaya	Alpaca			http://purl.obolibrary.org/obo/vbo#transboundary

diff --git a/src/ontology/components/dogbreeds.owl b/src/ontology/components/dogbreeds.owl
@@ -56585,7 +56585,7 @@
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/VBO_0200902">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9615"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VBO_0400000"/>
-        <obo:IAO_0000115>A group of dogs derived from more than one breed of the same species. A breed is defined as a group of animals that share specific characteristics that distinguish it from other organisms of the same species, and/or which cultural or geographical separation has led to the general acceptance of its separate identity.</obo:IAO_0000115>
+        <obo:IAO_0000115>A dog breed that has not been given a recognition status by an official breed registration body.</obo:IAO_0000115>
         <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/111</obo:IAO_0000233>
         <terms:contributor rdf:resource="https://orcid.org/0000-0001-7688-1770"/>
         <terms:contributor rdf:resource="https://orcid.org/0000-0002-4142-7153"/>
@@ -56596,6 +56596,7 @@
         <oboInOwl:hasExactSynonym>Mixed Breed</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Mongrel</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym>Mongrel (Dog)</oboInOwl:hasExactSynonym>
+        <rdfs:comment>A mixed breed dog may or may not have known ancestry, may or may not be intentionally bred, and may through time develop into a purebred if the breed is given a recognition status by an official breed registration body.</rdfs:comment>
         <rdfs:label>Mixed Breed (Dog)</rdfs:label>
     </owl:Class>
     <owl:Axiom>
@@ -56608,10 +56609,12 @@
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/VBO_0200902"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
-        <owl:annotatedTarget>A group of dogs derived from more than one breed of the same species. A breed is defined as a group of animals that share specific characteristics that distinguish it from other organisms of the same species, and/or which cultural or geographical separation has led to the general acceptance of its separate identity.</owl:annotatedTarget>
+        <owl:annotatedTarget>A dog breed that has not been given a recognition status by an official breed registration body.</owl:annotatedTarget>
         <oboInOwl:hasDbXref>https://orcid.org/0000-0002-4142-7153</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>https://orcid.org/0000-0002-5002-8648</oboInOwl:hasDbXref>
-        <oboInOwl:hasDbXref>https://venomcoding.org/venom-codes/</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref>https://orcid.org/0000-0002-7356-1779</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://en.wikipedia.org/wiki/Mongrel</oboInOwl:hasDbXref>
+        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://venomcoding.org/venom-codes/</oboInOwl:hasDbXref>
     </owl:Axiom>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/VBO_0200902"/>
@@ -57956,8 +57959,8 @@
         <terms:contributor rdf:resource="https://orcid.org/0000-0002-5520-6597"/>
         <terms:contributor rdf:resource="https://orcid.org/0000-0002-9178-3965"/>
         <terms:source rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://omia.org</terms:source>
-        <oboInOwl:hasExactSynonym>Navasota (mixed breed)</oboInOwl:hasExactSynonym>
-        <rdfs:label>Navasota (mixed breed) (Dog)</rdfs:label>
+        <oboInOwl:hasExactSynonym>Navasota Mixed Breed</oboInOwl:hasExactSynonym>
+        <rdfs:label>Navasota Mixed Breed (Dog)</rdfs:label>
     </owl:Class>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/VBO_0200929"/>
@@ -57969,7 +57972,7 @@
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/VBO_0200929"/>
         <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
-        <owl:annotatedTarget>Navasota (mixed breed)</owl:annotatedTarget>
+        <owl:annotatedTarget>Navasota Mixed Breed</owl:annotatedTarget>
         <oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/vbo#most_common_name"/>
         <oboInOwl:source rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://omia.org</oboInOwl:source>
     </owl:Axiom>