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Variant Interpretation using Biomedical literature Evidence
GNU Lesser General Public License v3.0
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Automatically include alternative HPO id's #25

Open svandenhoek opened 4 years ago

svandenhoek commented 4 years ago

Currently the application simply uses the given HPO term(s), and if used, terms related to these according to the ontology. However, if the user doesn't also add alternative HPO id's (for example when an HPO id gets deprecated and not including the new HPO id as well), the results of these alternative HPO id's will not be included.

Including the HPO terms from hp.owl as defined in the oboInOwl:hasAlternativeId field could result in a better user-experience.

Example of information stored in the hp.owl file:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/HP_0006121">
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/HP_0007460"/>
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/HP_0031917"/>
        <obo:IAO_0000115>A type of digital ulcer that manifests as an open sore on the surface of the skin at the tip of a finger or toe.</obo:IAO_0000115>
        <oboInOwl:hasAlternativeId>HP:0001226</oboInOwl:hasAlternativeId>
        <oboInOwl:hasAlternativeId>HP:0001862</oboInOwl:hasAlternativeId>
        <oboInOwl:hasAlternativeId>HP:0005040</oboInOwl:hasAlternativeId>
        <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UMLS:C1860099</oboInOwl:hasDbXref>
        <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">human_phenotype</oboInOwl:hasOBONamespace>
        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HP:0006121</oboInOwl:id>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Acral ulceration</rdfs:label>
    </owl:Class>

<owl:Class rdf:about="http://purl.obolibrary.org/obo/HP_0001226">
        <obo:IAO_0100001>HP:0006121</obo:IAO_0100001>
        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HP:0001226</oboInOwl:id>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete Acral ulceration and osteomyelitis leading to autoamputation of digits</rdfs:label>
        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
    </owl:Class>

<owl:Class rdf:about="http://purl.obolibrary.org/obo/HP_0001862">
        <obo:IAO_0100001>HP:0006121</obo:IAO_0100001>
        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HP:0001862</oboInOwl:id>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete Acral ulceration and osteomyelitis leading to autoamputation of the digits (feet)</rdfs:label>
        <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
    </owl:Class>
svandenhoek commented 4 years ago

Not processing alternative HPO IDs might also lead to missing results when using the -n argument to retrieve child/related HPO terms.