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DiseaseOntology / HumanDiseaseOntology

Repository for the Human Disease Ontology.
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parsing doid.owl with rdf2x tool encountering error #781

Closed zengxianhua closed 4 years ago

zengxianhua commented 4 years ago

when dealing with HumanDiseaseOntology rdf representation file(url:https://github.com/DiseaseOntology/HumanDiseaseOntology/blob/master/src/ontology/doid.owl) using rdf2x tool(https://github.com/Merck/rdf2x), occurs parsing errors such as InstanceAggregator:194 - Error parsing quad [urn:x-arq:DefaultGraphNode -3be79fdb:16f03ccdbaf:-5dd9 http://www.w3.org/1999/02/22-rdf-syntax-ns#first http://purl.obolibrary.org/obo/DOID_0111104]: Subject has to be a URI, encountered: -3be79fdb:16f03ccdbaf:-5dd9

can anybody give any advices?

beckyjackson commented 4 years ago

What are you trying to accomplish with the rdf2x package?

The error that you're showing looks like a blank node, potentially coming from here (starting on line 298037 in doid.owl):

<rdf:Description>
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AllDisjointClasses"/>
    <owl:members rdf:parseType="Collection">
        <rdf:Description rdf:about="http://purl.obolibrary.org/obo/DOID_0111099"/>
        <rdf:Description rdf:about="http://purl.obolibrary.org/obo/DOID_0111100"/>
        <rdf:Description rdf:about="http://purl.obolibrary.org/obo/DOID_0111101"/>
        <rdf:Description rdf:about="http://purl.obolibrary.org/obo/DOID_0111102"/>
        <rdf:Description rdf:about="http://purl.obolibrary.org/obo/DOID_0111103"/>
        <rdf:Description rdf:about="http://purl.obolibrary.org/obo/DOID_0111104"/>
        <rdf:Description rdf:about="http://purl.obolibrary.org/obo/DOID_0111105"/>
        <rdf:Description rdf:about="http://purl.obolibrary.org/obo/DOID_0111106"/>
        <rdf:Description rdf:about="http://purl.obolibrary.org/obo/DOID_0111107"/>
        <rdf:Description rdf:about="http://purl.obolibrary.org/obo/DOID_0111108"/>
        <rdf:Description rdf:about="http://purl.obolibrary.org/obo/DOID_0111109"/>
        <rdf:Description rdf:about="http://purl.obolibrary.org/obo/DOID_0111110"/>
        <rdf:Description rdf:about="http://purl.obolibrary.org/obo/DOID_0111111"/>
    </owl:members>
</rdf:Description>

-3be79fdb:16f03ccdbaf:-5dd9 is a reference to the blank node, which has no URI, so perhaps this package does not support anonymous subjects.

zengxianhua commented 4 years ago

Appreicate for your response.I want to dump the ontologies and the relations between ontologies into relation database such as mysql.The rdf2x tool can solve it, however it encouts some errors which result in exporting out data failure.Do you know any tools to dump the doid rdf/owl format data into relation database?

beckyjackson commented 4 years ago

I'm not aware of any tools specifically for that purpose, but I do a lot of work between MySQL databases and ontologies. I've had to write my own scripts in the past for this purpose. I use the following tools:

You could potentially write SPARQL queries to generate a CSV file with ROBOT and then load it into your database.

Alternatively, you could write a python script using rdflib to parse the data and PyMySQL to add it to your database.

zengxianhua commented 4 years ago

Thanks a lot.I will try it.