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

Peter Karp pkarp at AI.SRI.COM
Tue Mar 23 16:42:04 PDT 2021


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 
> <https://urldefense.us/v3/__https://github.com/ncbo/bioportal-project/issues/130__;!!Nv3xtKNH_4uope0!1DA1_fBbWBTDteV3hVbzqg0dE7t0PnqDyVOlHRIyEuxlZojghVYe_ozaZw6I$>, 
> feel free to review or comment on that ticket.
>
> John
>
>
>  <!-- http://purl.obolibrary.org/obo/RO_0002327 
> <https://urldefense.us/v3/__http://purl.obolibrary.org/obo/RO_0002327__;!!Nv3xtKNH_4uope0!1DA1_fBbWBTDteV3hVbzqg0dE7t0PnqDyVOlHRIyEuxlZojghVYe_to_e6om$> 
> -->
>
> <owl:ObjectProperty 
> rdf:about="http://purl.obolibrary.org/obo/RO_0002327 
> <https://urldefense.us/v3/__http://purl.obolibrary.org/obo/RO_0002327__;!!Nv3xtKNH_4uope0!1DA1_fBbWBTDteV3hVbzqg0dE7t0PnqDyVOlHRIyEuxlZojghVYe_to_e6om$>">
> <rdfs:subPropertyOf 
> rdf:resource="http://purl.obolibrary.org/obo/RO_0002215 
> <https://urldefense.us/v3/__http://purl.obolibrary.org/obo/RO_0002215__;!!Nv3xtKNH_4uope0!1DA1_fBbWBTDteV3hVbzqg0dE7t0PnqDyVOlHRIyEuxlZojghVYe_oc7b1Zm$>"/>
> <owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002333 
> <https://urldefense.us/v3/__http://purl.obolibrary.org/obo/RO_0002333__;!!Nv3xtKNH_4uope0!1DA1_fBbWBTDteV3hVbzqg0dE7t0PnqDyVOlHRIyEuxlZojghVYe_mUJYzWI$>"/>
> <owl:propertyChainAxiom rdf:parseType="Collection">
> <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327 
> <https://urldefense.us/v3/__http://purl.obolibrary.org/obo/RO_0002327__;!!Nv3xtKNH_4uope0!1DA1_fBbWBTDteV3hVbzqg0dE7t0PnqDyVOlHRIyEuxlZojghVYe_to_e6om$>"/>
> <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000051 
> <https://urldefense.us/v3/__http://purl.obolibrary.org/obo/BFO_0000051__;!!Nv3xtKNH_4uope0!1DA1_fBbWBTDteV3hVbzqg0dE7t0PnqDyVOlHRIyEuxlZojghVYe_plWqDBK$>"/>
> </owl:propertyChainAxiom>
> <owl:propertyChainAxiom rdf:parseType="Collection">
> <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002327 
> <https://urldefense.us/v3/__http://purl.obolibrary.org/obo/RO_0002327__;!!Nv3xtKNH_4uope0!1DA1_fBbWBTDteV3hVbzqg0dE7t0PnqDyVOlHRIyEuxlZojghVYe_to_e6om$>"/>
> <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002017 
> <https://urldefense.us/v3/__http://purl.obolibrary.org/obo/RO_0002017__;!!Nv3xtKNH_4uope0!1DA1_fBbWBTDteV3hVbzqg0dE7t0PnqDyVOlHRIyEuxlZojghVYe_vq3jVSj$>"/>
> </owl:propertyChainAxiom>
> <obo:IAO_0000112>a particular instances of akt-2 enables some instance 
> of protein kinase activity</obo:IAO_0000112>
> <obo:IAO_0000117>Chris Mungall</obo:IAO_0000117>
> <obo:IAO_0000118>catalyzes</obo:IAO_0000118>
> <obo:IAO_0000118>executes</obo:IAO_0000118>
> <obo:IAO_0000118>has</obo:IAO_0000118>
> <obo:IAO_0000118>is catalyzing</obo:IAO_0000118>
> <obo:IAO_0000118>is executing</obo:IAO_0000118>
> <obo:IAO_0000232>This relation differs from the parent relation 
> 'capable of' in that the parent is weaker and only expresses 
> a capability that may not be actually realized, whereas this relation 
> is always realized.</obo:IAO_0000232>
> <obo:IAO_0000232>This relation is currently used experimentally by the 
> Gene Ontology Consortium. It may not be stable and may be obsoleted at 
> some future time.</obo:IAO_0000232>
> <oboInOwl:inSubset 
> rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_gp2term 
> <https://urldefense.us/v3/__http://purl.obolibrary.org/obo/valid_for_go_gp2term__;!!Nv3xtKNH_4uope0!1DA1_fBbWBTDteV3hVbzqg0dE7t0PnqDyVOlHRIyEuxlZojghVYe_ko8dhGF$>"/>
> <rdfs:label xml:lang="en">enables</rdfs:label>
> </owl:ObjectProperty>
>
>> On Mar 18, 2021, at 4:44 PM, support at bioontology.org 
>> <mailto:support at bioontology.org> wrote:
>>
>> Name: Peter Karp
>>
>> Email: pkarp at ai.sri.com <mailto:pkarp at ai.sri.com>
>>
>> Location: https%3A%2F%2Fbioportal.bioontology.org 
>> <https://urldefense.us/v3/__http://2Fbioportal.bioontology.org__;!!Nv3xtKNH_4uope0!1DA1_fBbWBTDteV3hVbzqg0dE7t0PnqDyVOlHRIyEuxlZojghVYe_qtxwFh7$>%2Fsearch 
>>
>>
>>
>> *Feedback:*
>>
>> Hi, I'm trying to find term RO:0002327 in the Relations Ontology 
>> using BioPortal.
>> This would seem straightforward, but when I go to your home page and 
>> enter RO:0002327 in the Search field, the results do not include this 
>> term in the top results.
>>
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu 
>> <mailto:bioontology-support at lists.stanford.edu>
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support 
>> <https://urldefense.us/v3/__https://mailman.stanford.edu/mailman/listinfo/bioontology-support__;!!Nv3xtKNH_4uope0!1DA1_fBbWBTDteV3hVbzqg0dE7t0PnqDyVOlHRIyEuxlZojghVYe_g9QDgTR$>
>
> ========================
> 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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