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dbmi-pitt / DIKB-Micropublication

Micropublication and Open Data Annotation for drug-drug interaction evidence synthesis
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problems with rdf:subClassOf mp:Data/mp:Method #43

Closed jodischneider closed 8 years ago

jodischneider commented 8 years ago

I'd expect Data and Method to be disjoint. So I'd expect e.g. #EV_CT_PK_Phenotype_Data and #EV_CT_PK_Phenotype_Method here, rather than:

<owl:Class rdf:about="http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/DIKB_evidence_ontology_v1.3.owl#EV_CT_PK_Phenotype">
    <rdfs:subClassOf rdf:resource="&mp;Data"/>
    <rdfs:subClassOf rdf:resource="&mp;Method"/>
</owl:Class>

Similarly this looks wrong:

<!-- http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/DIKB_evidence_ontology_v1.3.owl#EV_CT_Pharmacokinetic -->

<owl:Class rdf:about="http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/DIKB_evidence_ontology_v1.3.owl#EV_CT_Pharmacokinetic">
    <rdfs:subClassOf rdf:resource="&mp;Data"/>
    <rdfs:subClassOf rdf:resource="&mp;Method"/>
</owl:Class>

<!-- http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/DIKB_evidence_ontology_v1.3.owl#EV_CT_Pharmacokinetic_Data -->

<owl:Class rdf:about="http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/DIKB_evidence_ontology_v1.3.owl#EV_CT_Pharmacokinetic_Data"/>

<!-- http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/DIKB_evidence_ontology_v1.3.owl#EV_CT_Pharmacokinetic_Material -->

<owl:Class rdf:about="http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/DIKB_evidence_ontology_v1.3.owl#EV_CT_Pharmacokinetic_Material">
    <rdfs:subClassOf rdf:resource="&mp;Material"/>
</owl:Class>

I'd expect #EV_CT_Pharmacokinetic_Data to be a subClassOf mp:Data

jodischneider commented 8 years ago

For 1st problem: Need to update OWL from http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/just-inclusion-criteria/just-inclusion-criteria.html "[EV_CT_PK_Phenotype] A phenotyped pharmacokinetic clinical trial: A drug pharmacokinetics study whose population consists of at least two groups known to possess distinct drug metabolizing phenotypes" Remove mp:Data type & create new item for Data?

jodischneider commented 8 years ago

mp:Data part of the problem resolved with edit to https://github.com/dbmi-pitt/DIKB-Micropublication/blob/master/scripts/mp-scripts/dikbv1.2-to-MP-plus-OA.py

rkboyce commented 8 years ago

I created a web protege project and invited you all so we can begin to define the methods and data types. It seems the instances will all will be related by MP:Supports but I will need to add discussion of how the classes are related to the WG Standard Dev discussions

jodischneider commented 8 years ago

Next steps: added "Discuss data and materials taxonomy" to WG Standard Dev agenda Current draft: https://github.com/dbmi-pitt/DIKB-Evidence-analytics/blob/master/dikb-ontology/dikb-revision-ontologies-owl-REVISION-50/DIKB_evidence_ontology_sam_update.owl