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Map JERM's ISA model to linkedISA vocabulary? #5

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stain opened this issue Nov 20, 2017 · 1 comment
Open

Map JERM's ISA model to linkedISA vocabulary? #5

stain opened this issue Nov 20, 2017 · 1 comment

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@stain
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stain commented Nov 20, 2017

(As mentioned in #4): how can the JERM Ontology's ISA relations be aligned with the official http://isa-tools.github.io/linkedISA/ ?

Somehow their http://purl.org/isaterms is broken - but they are also at https://github.com/ISA-tools/linkedISA-ontologies

I was looking at Alejandra's https://doi.org/10.5524/100148 which has code like:

    <owl:NamedIndividual rdf:about="http://w3id.org/isa/soapdenovo2/investigation/2">
        <rdf:type rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
        <rdf:type rdf:resource="http://purl.org/isaterms/investigation"/>
        <rdf:type rdf:resource="http://www.w3.org/ns/prov#Activity"/>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SOAPdenovo2</rdfs:label>
        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://w3id.org/isa/soapdenovo2/investigation/2</rdfs:comment>
    </owl:NamedIndividual>

    <owl:NamedIndividual rdf:about="http://w3id.org/isa/soapdenovo2/study/3">
        <rdf:type rdf:resource="http://purl.obolibrary.org/obo/OBI_0000066"/>
        <rdf:type rdf:resource="http://purl.org/isaterms/study"/>
        <rdf:type rdf:resource="http://www.w3.org/ns/prov#Activity"/>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SOAPdenovo2</rdfs:label>
        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Experimental Metadata Licence: http://creativecommons.org/
publicdomain/zero/1.0/</rdfs:comment>
        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Study Funding Agency: State Key Development Program for Ba
sic Research of China-973 Program</rdfs:comment>
        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Study Grant Number: 2011CB809203</rdfs:comment>
        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://w3id.org/isa/soapdenovo2/study/3</rdfs:comment>
        <obo:BFO_0000050 rdf:resource="http://w3id.org/isa/soapdenovo2/investigation/2"/>
    </owl:NamedIndividual>

so presumably our http://jermontology.org/ontology/JERMOntology#hasPart is equivalent (or sub property) of the generic http://purl.obolibrary.org/obo/BFO_0000050 ("part of") and types like http://purl.org/isaterms/study and http://purl.org/isaterms/investigation (notice lowercase for some reason) are (somewhat) equivalent to our http://jermontology.org/ontology/JERMOntology#Study and http://jermontology.org/ontology/JERMOntology#Investigation

But I don't find any http://purl.org/isaterms mapping in https://github.com/FAIRdom/JERMOntology/blob/master/JERM.owl

Would a direct mapping be feasible - or is the linkedISA structure more complicated than the view we have in JERM?

@stain
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stain commented Nov 20, 2017

btw.. forget about BFO_0000050 - LinkedISA has it's own has_part

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