Add UBERON bridge between species-specific and taxon-neutral ontology terms

[brianraymor]

General Design

See #data-discovery for report.

obs (Cell Metadata)

tissue_ontology_term_id

No schema change is required.

organism_tissue_ontology_term_id

If there is a species-specific ontology for tissue type, then a term from that ontology must be annotated by the curator in organism_tissue_ontology_term_id. Otherwise, the value must be "na".

Editorial Notes

Explore the possibility of adding a --map-species option to cellxgene-schema CLI to annotate the UBERON term based on the mapping referenced in the UBERON bridge.

Is there a case where there is a species-specific ontology but not a bridge to UBERON?

SSSOM

Simple Standard for Sharing Ontological Mappings (SSSOM)

Also noting the possibility of Switching mappings from cross-reference annotations to SSSOM

current_release :

Note that the bridge files, used to merge Uberon/CL with
the taxon-specific ontologies, are treated as intermediate products and
are not available as release artifacts. Consequently, they must be
obtained directly from the GitHub
repository.
The mappings from which the bridges are derived are available as a
SSSOM file.

UBERON bridges

Available bridges to UBERON

Species	UBERON bridge
Danio rerio (zebrafish)	uberon-bridge-to-zfa.owl
Drosophila melanogaster (fruit fly)	uberon-bridge-to-fbbt.owl
Xenopus laevis (African clawed frog)	uberon-bridge-to-xao.owl
Xenopus tropicalis (tropical clawed frog)	uberon-bridge-to-xao.owl

Sample in bridge.owl

    <!-- http://purl.obolibrary.org/obo/ZFA_0000047 -->

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/ZFA_0000047">
        <owl:equivalentClass>
            <owl:Class>
                <owl:intersectionOf rdf:parseType="Collection">
                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0000004"/>
                    <owl:Restriction>
                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_7954"/>
                    </owl:Restriction>
                </owl:intersectionOf>
            </owl:Class>
        </owl:equivalentClass>
        <obo:IAO_0000589>nose (zebrafish)</obo:IAO_0000589>
    </owl:Class>

Sample in uberon.owl

    <!-- http://purl.obolibrary.org/obo/UBERON_0000004 -->

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000004">
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000475"/>
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0002268"/>
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0004121"/>
        <rdfs:subClassOf rdf:nodeID="genid67361"/>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002160"/>
                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_7742"/>
            </owl:Restriction>
        </rdfs:subClassOf>
        <rdfs:subClassOf rdf:nodeID="genid67364"/>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002216"/>
                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0007608"/>
            </owl:Restriction>
        </rdfs:subClassOf>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002433"/>
                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001004"/>
            </owl:Restriction>
        </rdfs:subClassOf>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002433"/>
                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001456"/>
            </owl:Restriction>
        </rdfs:subClassOf>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002551"/>
                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0006813"/>
            </owl:Restriction>
        </rdfs:subClassOf>
        <obo:IAO_0000115>The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity.</obo:IAO_0000115>
        <obo:UBPROP_0000001>Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047].</obo:UBPROP_0000001>
        <obo:UBPROP_0000001>a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose].</obo:UBPROP_0000001>
        <obo:UBPROP_0000001>the organ that is specialized for smell and is part of the respiratory system</obo:UBPROP_0000001>
        <obo:UBPROP_0000008>the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359]</obo:UBPROP_0000008>
        <oboInOwl:hasDbXref>BTO:0000840</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>CALOHA:TS-2037</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>EHDAA2:0001274</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>EHDAA:1502</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>EMAPA:16542</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>EV:0100037</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>EV:0100370</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>FMA:46472</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>GAID:77</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>MA:0000281</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>MAT:0000139</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>MESH:D009666</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>MIAA:0000139</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>NCIT:C12756</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>SCTID:181195007</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>TAO:0000047</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>UMLS:C0028429</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>Wikipedia:Nose</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>ZFA:0000047</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref>galen:Nose</oboInOwl:hasDbXref>
        <oboInOwl:hasExactSynonym>nasal sac</oboInOwl:hasExactSynonym>
        <oboInOwl:hasExactSynonym>nose</oboInOwl:hasExactSynonym>
        <oboInOwl:hasExactSynonym>peripheral olfactory organ</oboInOwl:hasExactSynonym>
        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
        <oboInOwl:hasRelatedSynonym>nasus</oboInOwl:hasRelatedSynonym>
        <oboInOwl:hasRelatedSynonym>olfactory apparatus</oboInOwl:hasRelatedSynonym>
        <oboInOwl:hasRelatedSynonym>proboscis</oboInOwl:hasRelatedSynonym>
        <oboInOwl:id>UBERON:0000004</oboInOwl:id>
        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#efo_slim"/>
        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#major_organ"/>
        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#pheno_slim"/>
        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#uberon_slim"/>
        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#vertebrate_core"/>
        <rdfs:label>nose</rdfs:label>
        <foaf:depiction rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg</foaf:depiction>
    </owl:Class>
    <owl:Restriction rdf:nodeID="genid67361">
        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001456"/>
    </owl:Restriction>
    <owl:Restriction rdf:nodeID="genid67364">
        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002202"/>
        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0003050"/>
    </owl:Restriction>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000004"/>
        <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
        <owl:annotatedTarget rdf:nodeID="genid67361"/>
        <oboInOwl:source>FMA</oboInOwl:source>
        <oboInOwl:source>ZFA-def</oboInOwl:source>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000004"/>
        <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
        <owl:annotatedTarget rdf:nodeID="genid67364"/>
        <oboInOwl:source>ZFA</oboInOwl:source>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000004"/>
        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
        <owl:annotatedTarget>The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity.</owl:annotatedTarget>
        <oboInOwl:hasDbXref>UBERON:cjm</oboInOwl:hasDbXref>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000004"/>
        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/UBPROP_0000001"/>
        <owl:annotatedTarget>Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047].</owl:annotatedTarget>
        <oboInOwl:source>ZFA:0000047</oboInOwl:source>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000004"/>
        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/UBPROP_0000001"/>
        <owl:annotatedTarget>a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose].</owl:annotatedTarget>
        <oboInOwl:source>Wikipedia:Nose</oboInOwl:source>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000004"/>
        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/UBPROP_0000001"/>
        <owl:annotatedTarget>the organ that is specialized for smell and is part of the respiratory system</owl:annotatedTarget>
        <oboInOwl:source>MP:0002233</oboInOwl:source>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000004"/>
        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
        <owl:annotatedTarget>UMLS:C0028429</owl:annotatedTarget>
        <oboInOwl:source>ncithesaurus:Nose</oboInOwl:source>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000004"/>
        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
        <owl:annotatedTarget>nasal sac</owl:annotatedTarget>
        <oboInOwl:hasDbXref>ZFA:0000047</oboInOwl:hasDbXref>
        <oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/uberon/core#SENSU"/>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000004"/>
        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
        <owl:annotatedTarget>nose</owl:annotatedTarget>
        <oboInOwl:hasDbXref>MA:0000281</oboInOwl:hasDbXref>
        <oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/uberon/core#HUMAN_PREFERRED"/>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000004"/>
        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
        <owl:annotatedTarget>peripheral olfactory organ</owl:annotatedTarget>
        <oboInOwl:hasDbXref>ZFA:0000047</oboInOwl:hasDbXref>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000004"/>
        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
        <owl:annotatedTarget>nasus</owl:annotatedTarget>
        <oboInOwl:hasDbXref>Wikipedia:Nose</oboInOwl:hasDbXref>
        <oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/OMO_0003011"/>
    </owl:Axiom>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000004"/>
        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
        <owl:annotatedTarget>olfactory apparatus</owl:annotatedTarget>
        <oboInOwl:hasDbXref>UBERON:cjm</oboInOwl:hasDbXref>
    </owl:Axiom>

Sample in uberon.json

      "id" : "http://purl.obolibrary.org/obo/UBERON_0000004",
      "lbl" : "nose",
      "type" : "CLASS",
      "meta" : {
        "definition" : {
          "val" : "The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity.",
          "xrefs" : [ "UBERON:cjm" ]
        },
        "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ],
        "synonyms" : [ {
          "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU",
          "pred" : "hasExactSynonym",
          "val" : "nasal sac",
          "xrefs" : [ "ZFA:0000047" ]
        }, {
          "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#HUMAN_PREFERRED",
          "pred" : "hasExactSynonym",
          "val" : "nose",
          "xrefs" : [ "MA:0000281" ]
        }, {
          "pred" : "hasExactSynonym",
          "val" : "peripheral olfactory organ",
          "xrefs" : [ "ZFA:0000047" ]
        }, {
          "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011",
          "pred" : "hasRelatedSynonym",
          "val" : "nasus",
          "xrefs" : [ "Wikipedia:Nose" ]
        }, {
          "pred" : "hasRelatedSynonym",
          "val" : "olfactory apparatus",
          "xrefs" : [ "UBERON:cjm" ]
        }, {
          "pred" : "hasRelatedSynonym",
          "val" : "proboscis"
        } ],
        "xrefs" : [ {
          "val" : "BTO:0000840"
        }, {
          "val" : "CALOHA:TS-2037"
        }, {
          "val" : "EHDAA2:0001274"
        }, {
          "val" : "EHDAA:1502"
        }, {
          "val" : "EMAPA:16542"
        }, {
          "val" : "EV:0100037"
        }, {
          "val" : "EV:0100370"
        }, {
          "val" : "FMA:46472"
        }, {
          "val" : "GAID:77"
        }, {
          "val" : "MA:0000281"
        }, {
          "val" : "MAT:0000139"
        }, {
          "val" : "MESH:D009666"
        }, {
          "val" : "MIAA:0000139"
        }, {
          "val" : "NCIT:C12756"
        }, {
          "val" : "SCTID:181195007"
        }, {
          "val" : "TAO:0000047"
        }, {
          "val" : "UMLS:C0028429"
        }, {
          "val" : "Wikipedia:Nose"
        }, {
          "val" : "ZFA:0000047"
        }, {
          "val" : "galen:Nose"
        } ],
        "basicPropertyValues" : [ {
          "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001",
          "val" : "Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]."
        }, {
          "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001",
          "val" : "a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose]."
        }, {
          "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001",
          "val" : "the organ that is specialized for smell and is part of the respiratory system"
        }, {
          "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008",
          "val" : "the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359]"
        }, {
          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
          "val" : "uberon"
        }, {
          "pred" : "http://xmlns.com/foaf/0.1/depiction",
          "val" : "http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg"
        } ]
      }
    },