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FAIRdom / JERMOntology

The JERM Ontology is an application ontology designed to describe the items in SEEK and the relationships between them (for example, data, models, experiment descriptions, results, samples, protocols, standard operating procedures and publications); and to enable these relationships to be expressed with formal semantics.
http://jermontology.org
BSD 3-Clause "New" or "Revised" License
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Map JERM's ISA model to linkedISA vocabulary? #5

Open stain opened 6 years ago

stain commented 6 years ago

(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 commented 6 years ago

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