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[bioontology-support] [BioPortal] Feedback from brycemecum

John Graybeal jgraybeal at stanford.edu
Tue Sep 17 12:57:48 PDT 2019


Bryce,

That's an interesting result, apologies for the problem. I'm not an expert, but I've written it up as ticket https://github.com/ncbo/bioportal-project/issues/136 so that we can bring some more expertise to the question.

It seems BioPortal is not fully recognizing the pattern for citing source for a definition, though Protege does. (The pattern is documented in the OBO guidelines at http://www.obofoundry.org/principles/fp-006-textual-definitions.html).

I didn't have time to test this thoroughly, but examining the ECSO ontology, it seemed in some places to use another pattern from that guidance, as shown below for the concept http://bioportal.bioontology.org/ontologies/ECSO/?p=classes&conceptid=http%3A%2F%2Fpurl.dataone.org%2Fodo%2FECSO_00000043&jump_to_nav=true<http://bioportal.bioontology.org/ontologies/ECSO/?p=classes&conceptid=http://purl.dataone.org/odo/ECSO_00000043&jump_to_nav=true> (OWL shown below).

That seems to work OK in BioPortal—might that be a good workaround? Looks like there are 26 cases that would require changing.

John

    <owl:Class rdf:about="http://purl.dataone.org/odo/ECSO_00000043">
        <rdfs:subClassOf rdf:resource="http://purl.dataone.org/odo/ECSO_00000552"/>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#measuresUsingProtocol"/>
                <owl:allValuesFrom rdf:resource="http://purl.dataone.org/odo/ECSO_00000096"/>
            </owl:Restriction>
        </rdfs:subClassOf>
        <odo:ECSO_01000005>http://en.wikipedia.org/wiki/Biomass</odo:ECSO_01000005>
        <obo:IAO_0000115>Total carbon content of the living biomass (leaves+roots+wood)</obo:IAO_0000115>
        <obo:IAO_0000119>http://nacp.ornl.gov/MsTMIP_variables.shtml</obo:IAO_0000119>
        <dc:creator rdf:resource="http://orcid.org/0000-0002-8087-1775"/>
        <dc:description>Biomass is organic matter derived from living organisms.</dc:description>
        <rdfs:label>Total_Living_Biomass_MOV</rdfs:label>
        <skos:hiddenLabel>Total_Living_Biomass_MOV</skos:hiddenLabel>
        <skos:prefLabel>Total Living Biomass MOV</skos:prefLabel>
    </owl:Class>
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.dataone.org/odo/ECSO_00000043"/>
        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000119"/>
        <owl:annotatedTarget>http://nacp.ornl.gov/MsTMIP_variables.shtml</owl:annotatedTarget>
        <rdfs:comment>accessed 2015-03-25</rdfs:comment>
    </owl:Axiom>


On Sep 17, 2019, at 10:27 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: brycemecum

Email: mecum at nceas.ucsb.edu<mailto:mecum at nceas.ucsb.edu>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FECSO%2Fsubmissions%2F61%2Fedit

Feedback:

After making a change to our ontology and re-uploading to BioPortal, we're seeing our definition show up twice on our landing page for this term: http://bioportal.bioontology.org/ontologies/ECSO/?p=classes&conceptid=http%3A%2F%2Fpurl.dataone.org%2Fodo%2FECSO_00002092.

The RDF/XML for this term can be found in this diff: https://github.com/DataONEorg/sem-prov-ontologies/commit/694957803cf77f5723ddd6ff1b7c88e810cc8c75#diff-3aac6f836ca99404f3acabd594fa36d3L16842.

Our ontology isn't configured with a custom term URI For the definition field. This isn't really a huge deal but it would be nice to only show the definition once. Is there something we can do on our end to change this?

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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


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