Merge pull request #191 from monarch-initiative/240729-updates

NTRs and priority issues
monarch-initiative · Jul 30, 2024 · d60e3fd · d60e3fd
2 parents 6e803e0 + 32c6dbb
commit d60e3fd
Show file tree

Hide file tree

Showing 14 changed files with 166 additions and 40 deletions.
diff --git a/src/ontology/components/breedstatus.owl b/src/ontology/components/breedstatus.owl
@@ -58,13 +58,13 @@
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/VBO_0300001">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VBO_0300000"/>
-        <obo:IAO_0000115>Breed status refering to the level of recognition of a group of animal as a breed by an international breed organization.</obo:IAO_0000115>
+        <obo:IAO_0000115>Breed status refering to the level of recognition of a group of animal as a breed by an international breed registration body.</obo:IAO_0000115>
         <rdfs:label>recognition status</rdfs:label>
     </owl:Class>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/VBO_0300001"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
-        <owl:annotatedTarget>Breed status refering to the level of recognition of a group of animal as a breed by an international breed organization.</owl:annotatedTarget>
+        <owl:annotatedTarget>Breed status refering to the level of recognition of a group of animal as a breed by an international 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>
     </owl:Axiom>
@@ -75,13 +75,13 @@
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/VBO_0300002">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VBO_0300001"/>
-        <obo:IAO_0000115>Breed recognition status referring to a breed recognized by an international organization. This status also refers to breeds that are eligible to compete in championship classes. </obo:IAO_0000115>
+        <obo:IAO_0000115>Breed recognition status referring to a breed recognized by an international breed registration body. This status also refers to breeds that are eligible to compete in championship classes. </obo:IAO_0000115>
         <rdfs:label>fully recognized breed</rdfs:label>
     </owl:Class>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/VBO_0300002"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
-        <owl:annotatedTarget>Breed recognition status referring to a breed recognized by an international organization. This status also refers to breeds that are eligible to compete in championship classes. </owl:annotatedTarget>
+        <owl:annotatedTarget>Breed recognition status referring to a breed recognized by an international breed registration body. This status also refers to breeds that are eligible to compete in championship classes. </owl:annotatedTarget>
         <oboInOwl:hasDbXref>https://orcid.org/0000-0002-4142-7153</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>https://orcid.org/0000-0002-5002-8648</oboInOwl:hasDbXref>
     </owl:Axiom>
@@ -92,13 +92,13 @@
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/VBO_0300003">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VBO_0300001"/>
-        <obo:IAO_0000115>Breed recognition status referring to a breed that is in the process of becoming fully recognized by an international organization. This status is given to breeds which are preliminarily or provisionally recognized.</obo:IAO_0000115>
+        <obo:IAO_0000115>Breed recognition status referring to a breed that is in the process of becoming fully recognized by an international breed registration body. This status is given to breeds which are preliminarily or provisionally recognized.</obo:IAO_0000115>
         <rdfs:label>partially recognized breed</rdfs:label>
     </owl:Class>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/VBO_0300003"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
-        <owl:annotatedTarget>Breed recognition status referring to a breed that is in the process of becoming fully recognized by an international organization. This status is given to breeds which are preliminarily or provisionally recognized.</owl:annotatedTarget>
+        <owl:annotatedTarget>Breed recognition status referring to a breed that is in the process of becoming fully recognized by an international breed registration body. This status is given to breeds which are preliminarily or provisionally recognized.</owl:annotatedTarget>
         <oboInOwl:hasDbXref>https://orcid.org/0000-0002-4142-7153</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>https://orcid.org/0000-0002-5002-8648</oboInOwl:hasDbXref>
     </owl:Axiom>
@@ -109,13 +109,13 @@
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/VBO_0300004">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VBO_0300001"/>
-        <obo:IAO_0000115>Breed recognition status referring to a breed that is reported by an international organization but not recognized. </obo:IAO_0000115>
+        <obo:IAO_0000115>Breed recognition status referring to a breed that is reported by an international breed registration body but not recognized. </obo:IAO_0000115>
         <rdfs:label>not recognized breed</rdfs:label>
     </owl:Class>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/VBO_0300004"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
-        <owl:annotatedTarget>Breed recognition status referring to a breed that is reported by an international organization but not recognized. </owl:annotatedTarget>
+        <owl:annotatedTarget>Breed recognition status referring to a breed that is reported by an international breed registration body but not recognized. </owl:annotatedTarget>
         <oboInOwl:hasDbXref>https://orcid.org/0000-0002-4142-7153</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>https://orcid.org/0000-0002-5002-8648</oboInOwl:hasDbXref>
     </owl:Axiom>
@@ -366,5 +366,5 @@
 
 
 
-<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->
 
diff --git a/src/ontology/components/breedstatus.tsv b/src/ontology/components/breedstatus.tsv
@@ -1,10 +1,10 @@
 VBO id	Breed name	Parent ID NCBITaxon:	Definition 	Definition Xref	Comment
 ID	LABEL	SC %	A IAO:0000115	>A oboInOwl:hasDbXref SPLIT=| 	A rdfs:comment
 VBO:0300000	breed status				
-VBO:0300001	recognition status	VBO:0300000	Breed status refering to the level of recognition of a group of animal as a breed by an international breed organization.	https://orcid.org/0000-0002-4142-7153|https://orcid.org/0000-0002-5002-8648	
-VBO:0300002	fully recognized breed	VBO:0300001	Breed recognition status referring to a breed recognized by an international organization. This status also refers to breeds that are eligible to compete in championship classes. 	https://orcid.org/0000-0002-4142-7153|https://orcid.org/0000-0002-5002-8648	
-VBO:0300003	partially recognized breed	VBO:0300001	Breed recognition status referring to a breed that is in the process of becoming fully recognized by an international organization. This status is given to breeds which are preliminarily or provisionally recognized.	https://orcid.org/0000-0002-4142-7153|https://orcid.org/0000-0002-5002-8648	
-VBO:0300004	not recognized breed	VBO:0300001	Breed recognition status referring to a breed that is reported by an international organization but not recognized. 	https://orcid.org/0000-0002-4142-7153|https://orcid.org/0000-0002-5002-8648	
+VBO:0300001	recognition status	VBO:0300000	Breed status refering to the level of recognition of a group of animal as a breed by an international breed registration body.	https://orcid.org/0000-0002-4142-7153|https://orcid.org/0000-0002-5002-8648	
+VBO:0300002	fully recognized breed	VBO:0300001	Breed recognition status referring to a breed recognized by an international breed registration body. This status also refers to breeds that are eligible to compete in championship classes. 	https://orcid.org/0000-0002-4142-7153|https://orcid.org/0000-0002-5002-8648	
+VBO:0300003	partially recognized breed	VBO:0300001	Breed recognition status referring to a breed that is in the process of becoming fully recognized by an international breed registration body. This status is given to breeds which are preliminarily or provisionally recognized.	https://orcid.org/0000-0002-4142-7153|https://orcid.org/0000-0002-5002-8648	
+VBO:0300004	not recognized breed	VBO:0300001	Breed recognition status referring to a breed that is reported by an international breed registration body but not recognized. 	https://orcid.org/0000-0002-4142-7153|https://orcid.org/0000-0002-5002-8648	
 VBO:0300005	domestication status	VBO:0300000	Breed status refering to the level of domestication of a group of animals.	https://orcid.org/0000-0002-4142-7153	
 VBO:0300006	feral breed	VBO:0300005	Domestication status given to a group of animals that has been domesticated and has adapted to existence in the wild state but remains distinct from other wild individuals of the same species.	https://orcid.org/0000-0002-4142-7153|https://orcid.org/0000-0002-5002-8648|https://www.fao.org/dad-is	
 VBO:0300007	domestic breed	VBO:0300005	Domestication status given to a group of animals that has been domesticated, that is have been selectively bred and genetically adapted over generations to live alongside humans.	https://orcid.org/0000-0002-4142-7153|https://orcid.org/0000-0002-5002-8648|https://www.fao.org/dad-is	

diff --git a/src/ontology/components/catbreeds.owl b/src/ontology/components/catbreeds.owl
@@ -15810,5 +15810,5 @@
 
 
 
-<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi -->
 
diff --git a/src/ontology/components/dadisbreedcountry.owl b/src/ontology/components/dadisbreedcountry.owl
@@ -223104,7 +223104,7 @@
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VBO_0400000"/>
         <rdfs:subClassOf rdf:nodeID="genid25022"/>
         <vbo:hasdomesticationstatus rdf:resource="http://purl.obolibrary.org/obo/VBO_0300007"/>
-        <vbo:origindescription>Natibe breed of the Bos indicus specie. There is no written record on the origin of the Khailla cattle. It is believed that these cattle (Doteli Gai) came from Doti and Dadeldhura districts.</vbo:origindescription>
+        <vbo:origindescription>Native breed of the Bos indicus species. There is no written record on the origin of the Khailla cattle. It is believed that these cattle (Doteli Gai) came from Doti and Dadeldhura districts.</vbo:origindescription>
         <terms:contributor rdf:resource="https://orcid.org/0000-0002-4142-7153"/>
         <terms:contributor rdf:resource="https://orcid.org/0000-0002-5520-6597"/>
         <terms:contributor rdf:resource="https://orcid.org/0000-0002-9178-3965"/>
@@ -223144,7 +223144,7 @@
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/VBO_0005152"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/vbo#origindescription"/>
-        <owl:annotatedTarget>Natibe breed of the Bos indicus specie. There is no written record on the origin of the Khailla cattle. It is believed that these cattle (Doteli Gai) came from Doti and Dadeldhura districts.</owl:annotatedTarget>
+        <owl:annotatedTarget>Native breed of the Bos indicus species. There is no written record on the origin of the Khailla cattle. It is believed that these cattle (Doteli Gai) came from Doti and Dadeldhura districts.</owl:annotatedTarget>
         <oboInOwl:source rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://www.fao.org/dad-is</oboInOwl:source>
     </owl:Axiom>
     <owl:Axiom>

diff --git a/src/ontology/components/dadisbreedcountry.tsv b/src/ontology/components/dadisbreedcountry.tsv
@@ -3431,7 +3431,7 @@ VBO:0005148	Telemarkfe, Norway (Cattle)		Telemarkfe, Norway	Cattle				NCBITaxon:
 VBO:0005149	Vestlandsk fjordfe, Norway (Cattle)		Vestlandsk fjordfe, Norway	Cattle				NCBITaxon:9913	https://www.fao.org/dad-is		VBO:0400000		https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153	VBO:0017011		https://orcid.org/0000-0002-9178-3965	Vestlandsk fjordfe	http://purl.obolibrary.org/obo/vbo#most_common_name	https://www.fao.org/dad-is					Western Fjord Cattle	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					Developed in the western fjord areas of Norway, based on local animals, during the last period of the nineteenth century.	https://www.fao.org/dad-is		VBO:0300007	https://www.fao.org/dad-is	wikidata:Q20	wikidata:Q20	https://www.fao.org/dad-is										Vestlandsk fjordfe	Norway	Cattle	NOR
 VBO:0005150	Vestlandsk raudkolle, Norway (Cattle)		Vestlandsk raudkolle, Norway	Cattle				NCBITaxon:9913	https://www.fao.org/dad-is		VBO:0400000		https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153	VBO:0017012		https://orcid.org/0000-0002-9178-3965	Vestlandsk raudkolle	http://purl.obolibrary.org/obo/vbo#most_common_name	https://www.fao.org/dad-is					Western Red Polled Cattle	https://www.fao.org/dad-is		sør- og vestlandsfe	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					Developed in the western part of Norway during the 1880`s and -90`s.	https://www.fao.org/dad-is		VBO:0300007	https://www.fao.org/dad-is	wikidata:Q20	wikidata:Q20	https://www.fao.org/dad-is										Vestlandsk raudkolle	Norway	Cattle	NOR
 VBO:0005151	Achhami, Nepal (Cattle)		Achhami, Nepal	Cattle				NCBITaxon:9913	https://www.fao.org/dad-is		VBO:0400000		https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153				Achhami	http://purl.obolibrary.org/obo/vbo#most_common_name	https://www.fao.org/dad-is					Acchami	https://www.fao.org/dad-is		Naumuthe Gai	https://www.fao.org/dad-is		Sano gai	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					This is a indigenous breed of Nepal.	https://www.fao.org/dad-is		VBO:0300007	https://www.fao.org/dad-is	wikidata:Q837	wikidata:Q837	https://www.fao.org/dad-is										Achhami	Nepal	Cattle	NPL
-VBO:0005152	Khaila, Nepal (Cattle)		Khaila, Nepal	Cattle				NCBITaxon:9913	https://www.fao.org/dad-is		VBO:0400000		https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153				Khaila	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					Natibe breed of the Bos indicus specie. There is no written record on the origin of the Khailla cattle. It is believed that these cattle (Doteli Gai) came from Doti and Dadeldhura districts.	https://www.fao.org/dad-is		VBO:0300007	https://www.fao.org/dad-is	wikidata:Q837	wikidata:Q837	https://www.fao.org/dad-is										Khaila	Nepal	Cattle	NPL
+VBO:0005152	Khaila, Nepal (Cattle)		Khaila, Nepal	Cattle				NCBITaxon:9913	https://www.fao.org/dad-is		VBO:0400000		https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153				Khaila	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					Native breed of the Bos indicus species. There is no written record on the origin of the Khailla cattle. It is believed that these cattle (Doteli Gai) came from Doti and Dadeldhura districts.	https://www.fao.org/dad-is		VBO:0300007	https://www.fao.org/dad-is	wikidata:Q837	wikidata:Q837	https://www.fao.org/dad-is										Khaila	Nepal	Cattle	NPL
 VBO:0005153	Morang, Nepal (Cattle)		Morang, Nepal	Cattle				NCBITaxon:9913	https://www.fao.org/dad-is		VBO:0400000		https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153				Morang	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					hill type, similar to Purnea	https://www.fao.org/dad-is		VBO:0300007	https://www.fao.org/dad-is	wikidata:Q837	wikidata:Q837	https://www.fao.org/dad-is										Morang	Nepal	Cattle	NPL
 VBO:0005154	Pahadi, Nepal (Cattle)		Pahadi, Nepal	Cattle				NCBITaxon:9913	https://www.fao.org/dad-is		VBO:0400000		https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153				Pahadi	http://purl.obolibrary.org/obo/vbo#most_common_name	https://www.fao.org/dad-is					Nepalese Hill	https://www.fao.org/dad-is		Nepali Hill Zebu	https://www.fao.org/dad-is		Pahari	https://www.fao.org/dad-is		Pahari Guie	https://www.fao.org/dad-is		Pahari Sandhe	https://www.fao.org/dad-is		Black Hill Zebu	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					Native breed of the Bos indicus species.	https://www.fao.org/dad-is		VBO:0300007	https://www.fao.org/dad-is	wikidata:Q837	wikidata:Q837	https://www.fao.org/dad-is										Pahadi	Nepal	Cattle	NPL
 VBO:0005155	Terai, Nepal (Cattle)		Terai, Nepal	Cattle				NCBITaxon:9913	https://www.fao.org/dad-is		VBO:0400000		https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153				Terai	http://purl.obolibrary.org/obo/vbo#most_common_name	https://www.fao.org/dad-is					Tarai	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					Native cattle breed of the Bos indicus specie with Hariana influence.	https://www.fao.org/dad-is		VBO:0300007	https://www.fao.org/dad-is	wikidata:Q837	wikidata:Q837	https://www.fao.org/dad-is										Terai	Nepal	Cattle	NPL