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[bioontology-support] [BioPortal] Feedback from brycemecum

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


That's an interesting result, apologies for the problem. I'm not an expert, but I've written it up as ticket 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

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<> (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.


    <owl:Class rdf:about="">
        <rdfs:subClassOf rdf:resource=""/>
                <owl:onProperty rdf:resource=""/>
                <owl:allValuesFrom rdf:resource=""/>
        <obo:IAO_0000115>Total carbon content of the living biomass (leaves+roots+wood)</obo:IAO_0000115>
        <dc:creator rdf:resource=""/>
        <dc:description>Biomass is organic matter derived from living organisms.</dc:description>
        <skos:prefLabel>Total Living Biomass MOV</skos:prefLabel>
        <owl:annotatedSource rdf:resource=""/>
        <owl:annotatedProperty rdf:resource=""/>
        <rdfs:comment>accessed 2015-03-25</rdfs:comment>

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

Name: brycemecum

Email: mecum at<mailto:mecum at>



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:

The RDF/XML for this term can be found in this diff:

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?

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

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

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