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EBISPOT / ols4

Version 4 of the EMBL-EBI Ontology Lookup Service (OLS)
http://www.ebi.ac.uk/ols4/
Apache License 2.0
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hierarchicalChildren present in OLS4 but not in OLS3 #153

Open jamesamcl opened 1 year ago

jamesamcl commented 1 year ago

OLS3 term: https://www.ebi.ac.uk/ols/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000031

OLS3 hierarchicalChildren: https://www.ebi.ac.uk/ols/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000031/hierarchicalChildren

Empty in OLS3. But in OLS4 there are 3 hierarchicalChildren:

{
  "_embedded" : {
    "terms" : [ {
      "iri" : "http://www.ebi.ac.uk/efo/EFO_0005725",
      "lang" : "en",
      "description" : [ "BE(2)-C is a clone of the SK-N-BE(2) neuroblastoma cell line (ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from child with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. The cells grow as clusters of flattened neuroblastic cells with occasional fine cell processes (neurites). Unlike the parent line, they generally do not detach and float." ],
      "synonyms" : [ "BE(2) C", "BE(2)-C cell", "BE(2)_C", "BE2-C", "BE2C", "BE2_C" ],
      "annotation" : {
        "database_cross_reference" : [ "BTO:0000932", "PMID:PMC1531688" ]
      },
      "label" : "BE(2)-C",
      "ontology_name" : "efo",
      "ontology_prefix" : "EFO",
      "ontology_iri" : "http://www.ebi.ac.uk/efo/efo.owl",
      "is_obsolete" : false,
      "term_replaced_by" : null,
      "is_defining_ontology" : true,
      "has_children" : false,
      "is_root" : false,
      "short_form" : "EFO_0005725",
      "obo_id" : "EFO:0005725",
      "in_subset" : null,
      "obo_definition_citation" : null,
      "obo_xref" : [ {
        "database" : "BTO",
        "id" : "0000932",
        "description" : null,
        "url" : "http://purl.obolibrary.org/obo/BTO_0000932"
      }, {
        "database" : "PMID",
        "id" : "PMC1531688",
        "description" : null,
        "url" : "http://www.ncbi.nlm.nih.gov/pubmed/PMC1531688"
      } ],
      "obo_synonym" : null,
      "is_preferred_root" : false,
      "_links" : {
        "self" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005725?lang=en"
        },
        "parents" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005725/parents"
        },
        "ancestors" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005725/ancestors"
        },
        "hierarchicalParents" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005725/hierarchicalParents"
        },
        "hierarchicalAncestors" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005725/hierarchicalAncestors"
        },
        "jstree" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005725/jstree"
        },
        "graph" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005725/graph"
        },
        "bearer_of" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005725/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0000053"
        },
        "has_quality" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005725/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0000086"
        }
      }
    }, {
      "iri" : "http://www.ebi.ac.uk/efo/EFO_0005721",
      "lang" : "en",
      "description" : [ "SK-N-DZ is a neuroblastoma cell line derived in 1978 from a bone marrow metastasis from a child with poorly differentiated embryonal neuroblastoma." ],
      "synonyms" : [ "SK N DZ", "SK-N-DZ cell", "SKNDZ", "SK_N_DZ" ],
      "annotation" : {
        "definition_citation" : [ "http://cancerres.aacrjournals.org/content/47/20/5433.full.pdf" ]
      },
      "label" : "SK-N-DZ",
      "ontology_name" : "efo",
      "ontology_prefix" : "EFO",
      "ontology_iri" : "http://www.ebi.ac.uk/efo/efo.owl",
      "is_obsolete" : false,
      "term_replaced_by" : null,
      "is_defining_ontology" : true,
      "has_children" : false,
      "is_root" : false,
      "short_form" : "EFO_0005721",
      "obo_id" : "EFO:0005721",
      "in_subset" : null,
      "obo_definition_citation" : null,
      "obo_xref" : null,
      "obo_synonym" : null,
      "is_preferred_root" : false,
      "_links" : {
        "self" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005721?lang=en"
        },
        "parents" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005721/parents"
        },
        "ancestors" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005721/ancestors"
        },
        "hierarchicalParents" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005721/hierarchicalParents"
        },
        "hierarchicalAncestors" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005721/hierarchicalAncestors"
        },
        "jstree" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005721/jstree"
        },
        "graph" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005721/graph"
        },
        "part_of" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005721/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FBFO_0000050"
        },
        "bearer_of" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005721/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0000053"
        },
        "has_quality" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005721/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0000086"
        }
      }
    }, {
      "iri" : "http://www.ebi.ac.uk/efo/EFO_0001195",
      "lang" : "en",
      "description" : [ "A cell line derived from vertebrate neuroblastoma." ],
      "synonyms" : [ ],
      "annotation" : {
        "term editor" : [ "James Malone", "Natural Language Generator 8th April 2010" ]
      },
      "label" : "IMR-32",
      "ontology_name" : "efo",
      "ontology_prefix" : "EFO",
      "ontology_iri" : "http://www.ebi.ac.uk/efo/efo.owl",
      "is_obsolete" : false,
      "term_replaced_by" : null,
      "is_defining_ontology" : true,
      "has_children" : false,
      "is_root" : false,
      "short_form" : "EFO_0001195",
      "obo_id" : "EFO:0001195",
      "in_subset" : null,
      "obo_definition_citation" : null,
      "obo_xref" : null,
      "obo_synonym" : null,
      "is_preferred_root" : false,
      "_links" : {
        "self" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0001195?lang=en"
        },
        "parents" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0001195/parents"
        },
        "ancestors" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0001195/ancestors"
        },
        "hierarchicalParents" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0001195/hierarchicalParents"
        },
        "hierarchicalAncestors" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0001195/hierarchicalAncestors"
        },
        "jstree" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0001195/jstree"
        },
        "graph" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0001195/graph"
        },
        "bearer_of" : {
          "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0001195/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FRO_0000053"
        }
      }
    } ]
  },
  "_links" : {
    "self" : {
      "href" : "http://localhost:8080/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000031/hierarchicalChildren?page=0&size=20"
    }
  },
  "page" : {
    "size" : 20,
    "totalElements" : 3,
    "totalPages" : 1,
    "number" : 0
  }
}
jamesamcl commented 1 year ago

Here is one of the supposed OLS4 hierarchical children in EFO

    <!-- http://www.ebi.ac.uk/efo/EFO_0005725 -->

    <owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0005725">
        <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0002888"/>
        <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0005214"/>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
                <owl:someValuesFrom rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000621"/>
            </owl:Restriction>
        </rdfs:subClassOf>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000086"/>
                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PATO_0000384"/>
            </owl:Restriction>
        </rdfs:subClassOf>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0001000"/>
                <owl:someValuesFrom>
                    <owl:Class>
                        <owl:intersectionOf rdf:parseType="Collection">
                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/CL_0000031"/>
                            <owl:Restriction>
                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
                                <owl:someValuesFrom>
                                    <owl:Class>
                                        <owl:intersectionOf rdf:parseType="Collection">
                                            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/UBERON_0000955"/>
                                            <owl:Restriction>
                                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
                                            </owl:Restriction>
                                        </owl:intersectionOf>
                                    </owl:Class>
                                </owl:someValuesFrom>
                            </owl:Restriction>
                        </owl:intersectionOf>
                    </owl:Class>
                </owl:someValuesFrom>
            </owl:Restriction>
        </rdfs:subClassOf>
        <obo1:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BE(2)-C is a clone of the SK-N-BE(2) neuroblastoma cell line (ATCC CRL-2271) that was established in November of 1972 from a bone marrow biopsy taken from child with disseminated neuroblastoma after repeated courses of chemotherapy and radiotherapy. The cells grow as clusters of flattened neuroblastic cells with occasional fine cell processes (neurites). Unlike the parent line, they generally do not detach and float.</obo1:IAO_0000115>
        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BTO:0000932</oboInOwl:hasDbXref>
        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PMID:PMC1531688</oboInOwl:hasDbXref>
        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BE(2) C</oboInOwl:hasExactSynonym>
        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BE(2)-C cell</oboInOwl:hasExactSynonym>
        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BE(2)_C</oboInOwl:hasExactSynonym>
        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BE2-C</oboInOwl:hasExactSynonym>
        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BE2C</oboInOwl:hasExactSynonym>
        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BE2_C</oboInOwl:hasExactSynonym>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BE(2)-C</rdfs:label>
    </owl:Class>