Merge pull request #163 from monarch-initiative/issue-151

Draft foundation stock relation
monarch-initiative · May 1, 2024 · 085dbed · 085dbed
2 parents d9d0e3e + 2c178ff
commit 085dbed
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diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -41,3 +41,4 @@ These are the components in VBO
 | breedstatus.owl | None |
 | highlevelclass.owl | None |
 | lbo.owl | None |
+| relation.owl | None |
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -18,7 +18,7 @@
 # 5. [Run QC](test)
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                d9e82c53b032863094c9b3ad16a3a8c601354db4a25bc9d766a02fe10b199584
+CONFIG_HASH=                2d1bccf970957f84360642eb62b12bfdc9dbed11fb744fafcd2ace889101643b
 
 
 # ----------------------------------------
@@ -61,7 +61,7 @@ OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
 VERSION=                    $(TODAY)
 ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
 ANNOTATE_CONVERT_FILE =     annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@
-OTHER_SRC =                 $(COMPONENTSDIR)/dadistransbound.owl $(COMPONENTSDIR)/dadisbreedcountry.owl $(COMPONENTSDIR)/livestockbreeds.owl $(COMPONENTSDIR)/catbreeds.owl $(COMPONENTSDIR)/dogbreeds.owl $(COMPONENTSDIR)/breedstatus.owl $(COMPONENTSDIR)/highlevelclass.owl $(COMPONENTSDIR)/lbo.owl 
+OTHER_SRC =                 $(COMPONENTSDIR)/dadistransbound.owl $(COMPONENTSDIR)/dadisbreedcountry.owl $(COMPONENTSDIR)/livestockbreeds.owl $(COMPONENTSDIR)/catbreeds.owl $(COMPONENTSDIR)/dogbreeds.owl $(COMPONENTSDIR)/breedstatus.owl $(COMPONENTSDIR)/highlevelclass.owl $(COMPONENTSDIR)/lbo.owl $(COMPONENTSDIR)/relation.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 
@@ -449,6 +449,7 @@ $(COMPONENTSDIR)/%.owl: | $(COMPONENTSDIR)
 
 
 
+
 # ----------------------------------------
 # Mirroring upstream ontologies
 # ----------------------------------------

diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -18,6 +18,7 @@
   <uri name="http://purl.obolibrary.org/obo/vbo/components/dogbreeds.owl" uri="components/dogbreeds.owl"/>
   <uri name="http://purl.obolibrary.org/obo/vbo/components/highlevelclass.owl" uri="components/highlevelclass.owl"/>
   <uri name="http://purl.obolibrary.org/obo/vbo/components/lbo.owl" uri="components/lbo.owl"/>
+  <uri name="http://purl.obolibrary.org/obo/vbo/components/relation.owl" uri="components/relation.owl"/>
 
 
 </group>

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/highlevelclass.owl b/src/ontology/components/highlevelclass.owl
@@ -196,9 +196,9 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/NCBITaxon_9685 -->
+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_9682 -->
 
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_9685"/>
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_9682"/>
 
 
 
@@ -1033,13 +1033,13 @@
         <owl:equivalentClass>
             <owl:Class>
                 <owl:intersectionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_9685"/>
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_9682"/>
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/VBO_0400000"/>
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VBO_0400000"/>
-        <obo:IAO_0000115>Vertebrate breed of the taxon Felis catus. A vertebrate breed is a group of vertebrate animals that share specific characteristics (such as traits, behavior, genetics) that distinguish it from other organisms of the same species, and/or for which cultural or geographical separation has led to the general acceptance of its separate identity. Breeds are formed through genetic isolation and either natural adaptation to the environment or selective breeding, or a combination of the two.</obo:IAO_0000115>
+        <obo:IAO_0000115>Vertebrate breed of the taxon Felis. A vertebrate breed is a group of vertebrate animals that share specific characteristics (such as traits, behavior, genetics) that distinguish it from other organisms of the same species, and/or for which cultural or geographical separation has led to the general acceptance of its separate identity. Breeds are formed through genetic isolation and either natural adaptation to the environment or selective breeding, or a combination of the two.</obo:IAO_0000115>
         <rdfs:comment>Breeds included in VBO have been characterized, defined, and determined by international breed organizations, communities, experts, and/or have been reported in the literature. https://monarch-initiative.github.io/vertebrate-breed-ontology/general/general/</rdfs:comment>
         <rdfs:label>Cat breed</rdfs:label>
     </owl:Class>
@@ -1053,7 +1053,7 @@
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/VBO_0400018"/>
         <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
-        <owl:annotatedTarget>Vertebrate breed of the taxon Felis catus. A vertebrate breed is a group of vertebrate animals that share specific characteristics (such as traits, behavior, genetics) that distinguish it from other organisms of the same species, and/or for which cultural or geographical separation has led to the general acceptance of its separate identity. Breeds are formed through genetic isolation and either natural adaptation to the environment or selective breeding, or a combination of the two.</owl:annotatedTarget>
+        <owl:annotatedTarget>Vertebrate breed of the taxon Felis. A vertebrate breed is a group of vertebrate animals that share specific characteristics (such as traits, behavior, genetics) that distinguish it from other organisms of the same species, and/or for which cultural or geographical separation has led to the general acceptance of its separate identity. Breeds are formed through genetic isolation and either natural adaptation to the environment or selective breeding, or a combination of the two.</owl:annotatedTarget>
         <oboInOwl:source>https://orcid.org/0000-0002-4142-7153</oboInOwl:source>
         <oboInOwl:source>https://orcid.org/0000-0002-5002-8648</oboInOwl:source>
     </owl:Axiom>

diff --git a/src/ontology/components/highlevelclass.tsv b/src/ontology/components/highlevelclass.tsv
@@ -23,7 +23,7 @@ VBO:0400037	Pheasant breed	VBO:0400006	https://orcid.org/0000-0002-5002-8648|htt
 VBO:0400038	Partridge breed	VBO:0400006	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153	https://www.fao.org/dad-is		Vertebrate breed of the taxon Perdicinae. A vertebrate breed is a group of vertebrate animals that share specific characteristics (such as traits, behavior, genetics) that distinguish it from other organisms of the same species, and/or for which cultural or geographical separation has led to the general acceptance of its separate identity. Breeds are formed through genetic isolation and either natural adaptation to the environment or selective breeding, or a combination of the two.	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153		NCBITaxon:466544		Breeds included in VBO have been characterized, defined, and determined by international breed organizations, communities, experts, and/or have been reported in the literature. https://monarch-initiative.github.io/vertebrate-breed-ontology/general/general/		
 VBO:0001223	Quail breed	VBO:0400006	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153	https://www.fao.org/dad-is		Vertebrate breed of the taxon Coturnix. A vertebrate breed is a group of vertebrate animals that share specific characteristics (such as traits, behavior, genetics) that distinguish it from other organisms of the same species, and/or for which cultural or geographical separation has led to the general acceptance of its separate identity. Breeds are formed through genetic isolation and either natural adaptation to the environment or selective breeding, or a combination of the two.	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153		NCBITaxon:9090		Breeds included in VBO have been characterized, defined, and determined by international breed organizations, communities, experts, and/or have been reported in the literature. https://monarch-initiative.github.io/vertebrate-breed-ontology/general/general/		
 VBO:0400017	Turkey breed	VBO:0400006	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153	https://www.fao.org/dad-is		Vertebrate breed of the taxon Meleagris gallopavo. A vertebrate breed is a group of vertebrate animals that share specific characteristics (such as traits, behavior, genetics) that distinguish it from other organisms of the same species, and/or for which cultural or geographical separation has led to the general acceptance of its separate identity. Breeds are formed through genetic isolation and either natural adaptation to the environment or selective breeding, or a combination of the two.	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153		NCBITaxon:9103		Breeds included in VBO have been characterized, defined, and determined by international breed organizations, communities, experts, and/or have been reported in the literature. https://monarch-initiative.github.io/vertebrate-breed-ontology/general/general/		
-VBO:0400018	Cat breed	VBO:0400000	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153			Vertebrate breed of the taxon Felis catus. A vertebrate breed is a group of vertebrate animals that share specific characteristics (such as traits, behavior, genetics) that distinguish it from other organisms of the same species, and/or for which cultural or geographical separation has led to the general acceptance of its separate identity. Breeds are formed through genetic isolation and either natural adaptation to the environment or selective breeding, or a combination of the two.	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153		NCBITaxon:9685		Breeds included in VBO have been characterized, defined, and determined by international breed organizations, communities, experts, and/or have been reported in the literature. https://monarch-initiative.github.io/vertebrate-breed-ontology/general/general/		
+VBO:0400018	Cat breed	VBO:0400000	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153			Vertebrate breed of the taxon Felis. A vertebrate breed is a group of vertebrate animals that share specific characteristics (such as traits, behavior, genetics) that distinguish it from other organisms of the same species, and/or for which cultural or geographical separation has led to the general acceptance of its separate identity. Breeds are formed through genetic isolation and either natural adaptation to the environment or selective breeding, or a combination of the two.	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153		NCBITaxon:9682		Breeds included in VBO have been characterized, defined, and determined by international breed organizations, communities, experts, and/or have been reported in the literature. https://monarch-initiative.github.io/vertebrate-breed-ontology/general/general/		
 VBO:0400019	Bovine breed	VBO:0400000	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153			Vertebrate breed of the taxon Bovinae. A vertebrate breed is a group of vertebrate animals that share specific characteristics (such as traits, behavior, genetics) that distinguish it from other organisms of the same species, and/or for which cultural or geographical separation has led to the general acceptance of its separate identity. Breeds are formed through genetic isolation and either natural adaptation to the environment or selective breeding, or a combination of the two.	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153		NCBITaxon:27592		Breeds included in VBO have been characterized, defined, and determined by international breed organizations, communities, experts, and/or have been reported in the literature. https://monarch-initiative.github.io/vertebrate-breed-ontology/general/general/		
 VBO:0400020	Cattle breed	VBO:0400019	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153	LBO:0000001	Vertebrate breed of the taxon Bos. A vertebrate breed is a group of vertebrate animals that share specific characteristics (such as traits, behavior, genetics) that distinguish it from other organisms of the same species, and/or for which cultural or geographical separation has led to the general acceptance of its separate identity. Breeds are formed through genetic isolation and either natural adaptation to the environment or selective breeding, or a combination of the two.	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153		NCBITaxon:9903		Breeds included in VBO have been characterized, defined, and determined by international breed organizations, communities, experts, and/or have been reported in the literature. https://monarch-initiative.github.io/vertebrate-breed-ontology/general/general/		
 VBO:0000041	American bison breed	VBO:0400019	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153	https://www.fao.org/dad-is		Vertebrate breed of the taxon Bison bison. A vertebrate breed is a group of vertebrate animals that share specific characteristics (such as traits, behavior, genetics) that distinguish it from other organisms of the same species, and/or for which cultural or geographical separation has led to the general acceptance of its separate identity. Breeds are formed through genetic isolation and either natural adaptation to the environment or selective breeding, or a combination of the two.	https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153		NCBITaxon:9901		Breeds included in VBO have been characterized, defined, and determined by international breed organizations, communities, experts, and/or have been reported in the literature. https://monarch-initiative.github.io/vertebrate-breed-ontology/general/general/