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Merge pull request #194 from monarch-initiative/240806-updates
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Add new breed classifications and breeds for Cellosaurus request
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sabrinatoro authored Aug 9, 2024
2 parents c91d7de + 680ea22 commit c9830ec
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Showing 24 changed files with 33,839 additions and 30,437 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/qc.yml
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Expand Up @@ -19,7 +19,7 @@ jobs:
ontology_qc:
# The type of runner that the job will run on
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.5
container: obolibrary/odkfull:v1.5.1

# Steps represent a sequence of tasks that will be executed as part of the job
steps:
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1 change: 1 addition & 0 deletions docs/odk-workflows/RepositoryFileStructure.md
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Expand Up @@ -42,3 +42,4 @@ These are the components in VBO
| highlevelclass.owl | None |
| lbo.owl | None |
| relation.owl | None |
| otherbreeds.owl | None |
9 changes: 5 additions & 4 deletions src/ontology/Makefile
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@@ -1,7 +1,7 @@
# ----------------------------------------
# Makefile for vbo
# Generated using ontology-development-kit
# ODK Version: v1.5
# ODK Version: v1.5.1
# ----------------------------------------
# IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use vbo.Makefile instead

Expand All @@ -18,7 +18,7 @@
# 5. [Run QC](test)

# Fingerprint of the configuration file when this Makefile was last generated
CONFIG_HASH= 2d1bccf970957f84360642eb62b12bfdc9dbed11fb744fafcd2ace889101643b
CONFIG_HASH= f908deda2051faa7b93669cd38b2393ec8e6f9b7b25761ef1ecb817e463e8b7a


# ----------------------------------------
Expand Down Expand Up @@ -54,14 +54,14 @@ REPORT_PROFILE_OPTS =
OBO_FORMAT_OPTIONS =
SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by
SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms
ODK_VERSION_MAKEFILE = v1.5
ODK_VERSION_MAKEFILE = v1.5.1

TODAY ?= $(shell date +%Y-%m-%d)
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 $(COMPONENTSDIR)/relation.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 $(COMPONENTSDIR)/otherbreeds.owl
ONTOLOGYTERMS = $(TMPDIR)/ontologyterms.txt
EDIT_PREPROCESSED = $(TMPDIR)/$(ONT)-preprocess.owl

Expand Down Expand Up @@ -450,6 +450,7 @@ $(COMPONENTSDIR)/%.owl: | $(COMPONENTSDIR)




# ----------------------------------------
# Mirroring upstream ontologies
# ----------------------------------------
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1 change: 1 addition & 0 deletions src/ontology/catalog-v001.xml
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Expand Up @@ -19,6 +19,7 @@
<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"/>
<uri name="http://purl.obolibrary.org/obo/vbo/components/otherbreeds.owl" uri="components/otherbreeds.owl"/>


</group>
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60,865 changes: 30,478 additions & 30,387 deletions src/ontology/components/dadisbreedcountry.owl

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18 changes: 9 additions & 9 deletions src/ontology/components/dadisbreedcountry.tsv

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12 changes: 12 additions & 0 deletions src/ontology/components/dadistransbound.owl
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Expand Up @@ -17331,10 +17331,12 @@
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9031"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VBO_0400000"/>
<obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126</obo:IAO_0000233>
<obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/181</obo:IAO_0000233>
<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"/>
<terms:source rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://www.fao.org/dad-is</terms:source>
<oboInOwl:hasExactSynonym>Arbor Acres</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>Commercial strain- broiler- Arbor Acres AA broiler breeders</oboInOwl:hasExactSynonym>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/vbo#transboundary"/>
<rdfs:label>Commercial strain- broiler- Arbor Acres AA broiler breeders (Chicken)</rdfs:label>
Expand All @@ -17352,6 +17354,13 @@
<oboInOwl:source>https://orcid.org/0000-0002-4142-7153</oboInOwl:source>
<oboInOwl:source>https://orcid.org/0000-0002-5002-8648</oboInOwl:source>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/VBO_0000472"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
<owl:annotatedTarget>Arbor Acres</owl:annotatedTarget>
<oboInOwl:source>https://orcid.org/0000-0002-5002-8648</oboInOwl:source>
<oboInOwl:source>https://orcid.org/0000-0003-2826-6444</oboInOwl:source>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/VBO_0000472"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
Expand Down Expand Up @@ -46723,9 +46732,12 @@
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9986"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/VBO_0400000"/>
<obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126</obo:IAO_0000233>
<obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/181</obo:IAO_0000233>
<terms:contributor rdf:resource="https://orcid.org/0000-0002-4142-7153"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0002-5002-8648"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0002-5520-6597"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0002-9178-3965"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0003-2826-6444"/>
<terms:source rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://www.fao.org/dad-is</terms:source>
<oboInOwl:hasExactSynonym>Fauve de Borgogne</oboInOwl:hasExactSynonym>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/vbo#transboundary"/>
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4 changes: 2 additions & 2 deletions src/ontology/components/dadistransbound.tsv
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Expand Up @@ -429,7 +429,7 @@ VBO:0000468 Chantecler (Chicken) Chantecler Chicken 231120-126 https://github.
VBO:0000469 Cochin (Chicken) Cochin Chicken 231120-126 https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126 NCBITaxon:9031 https://www.fao.org/dad-is VBO:0400000 https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153 Cochin 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 Cochin Chicken http://purl.obolibrary.org/obo/vbo#transboundary
VBO:0000470 Cochin Bantam (Chicken) Cochin Bantam Chicken 231120-126 https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126 NCBITaxon:9031 https://www.fao.org/dad-is VBO:0400000 https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153 Cochin Bantam 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 Cochin Bantam Chicken http://purl.obolibrary.org/obo/vbo#transboundary
VBO:0000471 Columbian Rock (Chicken) Columbian Rock Chicken 231120-126 https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126 NCBITaxon:9031 https://www.fao.org/dad-is VBO:0400000 https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153 Columbian Rock http://purl.obolibrary.org/obo/vbo#most_common_name https://www.fao.org/dad-is Columbian Rock https://omia.org OMIA:507 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 Columbian Rock Chicken http://purl.obolibrary.org/obo/vbo#transboundary
VBO:0000472 Commercial strain- broiler- Arbor Acres AA broiler breeders (Chicken) Commercial strain- broiler- Arbor Acres AA broiler breeders Chicken 231120-126 https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126 NCBITaxon:9031 https://www.fao.org/dad-is VBO:0400000 https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153 Commercial strain- broiler- Arbor Acres AA broiler breeders 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 Commercial strain- broiler- Arbor Acres AA broiler breeders Chicken http://purl.obolibrary.org/obo/vbo#transboundary
VBO:0000472 Commercial strain- broiler- Arbor Acres AA broiler breeders (Chicken) Commercial strain- broiler- Arbor Acres AA broiler breeders Chicken 231120-126|240807-181 https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126|https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/181 NCBITaxon:9031 https://www.fao.org/dad-is VBO:0400000 https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153 Commercial strain- broiler- Arbor Acres AA broiler breeders http://purl.obolibrary.org/obo/vbo#most_common_name https://www.fao.org/dad-is Arbor Acres https://orcid.org/0000-0003-2826-6444|https://orcid.org/0000-0002-5002-8648 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 Commercial strain- broiler- Arbor Acres AA broiler breeders Chicken http://purl.obolibrary.org/obo/vbo#transboundary
VBO:0000473 Commercial strain- broiler- Avian (Chicken) Commercial strain- broiler- Avian Chicken 231120-126 https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126 NCBITaxon:9031 https://www.fao.org/dad-is VBO:0400000 https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153 Commercial strain- broiler- Avian 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 Commercial strain- broiler- Avian Chicken http://purl.obolibrary.org/obo/vbo#transboundary
VBO:0000474 Commercial strain- broiler- Euribrid Hybro (Chicken) Commercial strain- broiler- Euribrid Hybro Chicken 231120-126 https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126 NCBITaxon:9031 https://www.fao.org/dad-is VBO:0400000 https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153 Commercial strain- broiler- Euribrid Hybro 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 Commercial strain- broiler- Euribrid Hybro Chicken http://purl.obolibrary.org/obo/vbo#transboundary
VBO:0000475 Commercial strain- broiler- Euribrid Hybro N (Chicken) Commercial strain- broiler- Euribrid Hybro N Chicken 231120-126 https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126 NCBITaxon:9031 https://www.fao.org/dad-is VBO:0400000 https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153 Commercial strain- broiler- Euribrid Hybro N 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 Commercial strain- broiler- Euribrid Hybro N Chicken http://purl.obolibrary.org/obo/vbo#transboundary
Expand Down Expand Up @@ -1194,7 +1194,7 @@ VBO:0001244 Deilenaar (Rabbit) Deilenaar Rabbit 231120-126 https://github.com/
VBO:0001245 Dutch (Rabbit) Dutch Rabbit 231120-126 https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126 NCBITaxon:9986 https://www.fao.org/dad-is VBO:0400000 https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153 Dutch 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 Dutch Rabbit http://purl.obolibrary.org/obo/vbo#transboundary
VBO:0001246 English Spot (Rabbit) English Spot Rabbit 231120-126 https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126 NCBITaxon:9986 https://www.fao.org/dad-is VBO:0400000 https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153 English Spot 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 English Spot Rabbit http://purl.obolibrary.org/obo/vbo#transboundary
VBO:0001247 English Wether (Rabbit) English Wether Rabbit 231120-126 https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126 NCBITaxon:9986 https://www.fao.org/dad-is VBO:0400000 https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153 English Wether 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 English Wether Rabbit http://purl.obolibrary.org/obo/vbo#transboundary
VBO:0001248 Fauve de Borgogne (Rabbit) Fauve de Borgogne Rabbit 231120-126 https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126 NCBITaxon:9986 https://www.fao.org/dad-is VBO:0400000 https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153 Fauve de Borgogne 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 Fauve de Borgogne Rabbit http://purl.obolibrary.org/obo/vbo#transboundary
VBO:0001248 Fauve de Borgogne (Rabbit) Fauve de Borgogne Rabbit 231120-126|240807-181 https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126|https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/181 NCBITaxon:9986 https://www.fao.org/dad-is VBO:0400000 https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153 Fauve de Borgogne 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|https://orcid.org/0000-0003-2826-6444|https://orcid.org/0000-0002-5002-8648 Fauve de Borgogne Rabbit http://purl.obolibrary.org/obo/vbo#transboundary
VBO:0001249 Flemish Giant (Rabbit) Flemish Giant Rabbit 231120-126 https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126 NCBITaxon:9986 https://www.fao.org/dad-is VBO:0400000 https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153 Flemish Giant http://purl.obolibrary.org/obo/vbo#most_common_name https://www.fao.org/dad-is Flemish Giant https://omia.org OMIA:455 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 Flemish Giant Rabbit http://purl.obolibrary.org/obo/vbo#transboundary
VBO:0001250 Fox (Rabbit) Fox Rabbit 231120-126 https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126 NCBITaxon:9986 https://www.fao.org/dad-is VBO:0400000 https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153 Fox 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 Fox Rabbit http://purl.obolibrary.org/obo/vbo#transboundary
VBO:0001251 French Lop (Rabbit) French Lop Rabbit 231120-126 https://github.com/monarch-initiative/vertebrate-breed-ontology/issues/126 NCBITaxon:9986 https://www.fao.org/dad-is VBO:0400000 https://orcid.org/0000-0002-5002-8648|https://orcid.org/0000-0002-4142-7153 French Lop 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 French Lop Rabbit http://purl.obolibrary.org/obo/vbo#transboundary
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