[bioontology-support] [BioPortal] Feedback from Peter Karp

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[bioontology-support] [BioPortal] Feedback from Peter Karp

support

Name: Peter Karp

Email: [hidden email]

Location: https%3A%2F%2Fbioportal.bioontology.org%2Fsearch


Feedback:

Hi, I'm trying to find term RO:0002327 in the Relations Ontology using BioPortal.
This would seem straightforward, but when I go to your home page and enter RO:0002327 in the Search field, the results do not include this term in the top results.


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Re: [bioontology-support] [BioPortal] Feedback from Peter Karp

John Graybeal-2
Hello Peter,

Thank you for your question, you are correct that this *should* be straightforward. The reason you are not finding it with your searches is that BioPortal's search function only searches for classes, and RO_0002327 is an ObjectProperty (details below). BioPortal doesn't provide a search capability for properties, an omission we hope to fix with our next award.

I had to navigate the tree to find it, but can't give you a link directly to the term, I'm sorry.

These improvements have been added to ticket https://github.com/ncbo/bioportal-project/issues/130, feel free to review or comment on that ticket.

John



    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002327">
        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002215"/>
        <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002333"/>
        <owl:propertyChainAxiom rdf:parseType="Collection">
            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327"/>
            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
        </owl:propertyChainAxiom>
        <owl:propertyChainAxiom rdf:parseType="Collection">
            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327"/>
            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002017"/>
        </owl:propertyChainAxiom>
        <obo:IAO_0000112>a particular instances of akt-2 enables some instance of protein kinase activity</obo:IAO_0000112>
        <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
        <obo:IAO_0000118>catalyzes</obo:IAO_0000118>
        <obo:IAO_0000118>executes</obo:IAO_0000118>
        <obo:IAO_0000118>has</obo:IAO_0000118>
        <obo:IAO_0000118>is catalyzing</obo:IAO_0000118>
        <obo:IAO_0000118>is executing</obo:IAO_0000118>
        <obo:IAO_0000232>This relation differs from the parent relation &apos;capable of&apos; in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.</obo:IAO_0000232>
        <obo:IAO_0000232>This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.</obo:IAO_0000232>
        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
        <rdfs:label xml:lang="en">enables</rdfs:label>
    </owl:ObjectProperty>

On Mar 18, 2021, at 4:44 PM, [hidden email] wrote:

Name: Peter Karp

[hidden email]

Location: https%3A%2F%2Fbioportal.bioontology.org%2Fsearch


Feedback:

Hi, I'm trying to find term RO:0002327 in the Relations Ontology using BioPortal.
This would seem straightforward, but when I go to your home page and enter RO:0002327 in the Search field, the results do not include this term in the top results.


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360




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Re: [bioontology-support] [BioPortal] Feedback from Peter Karp

Peter Karp

Thanks John, I had a feeling that might be the reason...


On 3/23/21 3:51 PM, John Graybeal wrote:
Hello Peter,

Thank you for your question, you are correct that this *should* be straightforward. The reason you are not finding it with your searches is that BioPortal's search function only searches for classes, and RO_0002327 is an ObjectProperty (details below). BioPortal doesn't provide a search capability for properties, an omission we hope to fix with our next award.

I had to navigate the tree to find it, but can't give you a link directly to the term, I'm sorry.

These improvements have been added to ticket https://github.com/ncbo/bioportal-project/issues/130, feel free to review or comment on that ticket.

John



    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002327">
        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002215"/>
        <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002333"/>
        <owl:propertyChainAxiom rdf:parseType="Collection">
            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327"/>
            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
        </owl:propertyChainAxiom>
        <owl:propertyChainAxiom rdf:parseType="Collection">
            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327"/>
            <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002017"/>
        </owl:propertyChainAxiom>
        <obo:IAO_0000112>a particular instances of akt-2 enables some instance of protein kinase activity</obo:IAO_0000112>
        <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
        <obo:IAO_0000118>catalyzes</obo:IAO_0000118>
        <obo:IAO_0000118>executes</obo:IAO_0000118>
        <obo:IAO_0000118>has</obo:IAO_0000118>
        <obo:IAO_0000118>is catalyzing</obo:IAO_0000118>
        <obo:IAO_0000118>is executing</obo:IAO_0000118>
        <obo:IAO_0000232>This relation differs from the parent relation &apos;capable of&apos; in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.</obo:IAO_0000232>
        <obo:IAO_0000232>This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.</obo:IAO_0000232>
        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term"/>
        <rdfs:label xml:lang="en">enables</rdfs:label>
    </owl:ObjectProperty>

On Mar 18, 2021, at 4:44 PM, [hidden email] wrote:

Name: Peter Karp

[hidden email]

Location: https%3A%2F%2Fbioportal.bioontology.org%2Fsearch


Feedback:

Hi, I'm trying to find term RO:0002327 in the Relations Ontology using BioPortal.
This would seem straightforward, but when I go to your home page and enter RO:0002327 in the Search field, the results do not include this term in the top results.


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360




_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support