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[bioontology-support] SPARQL Endpoint not showing certain relationships for OBO data

Darren Weber dlweber at stanford.edu
Tue Apr 29 23:10:21 PDT 2014


Thanks for pointing this out.  Manuel may be able to comment on the 
processing of MA for the triple store and the most effective SPARQL for 
this particular query.

Bear in mind that the SPARQL endpoint does not contain the same data 
available in the REST API.  The most current data is available in the 
REST API.  There is a plan to update and/or synchronize the data in the 
SPARQL endpoint with the REST API data.  Perhaps Manuel can comment on 
specific details.

Hope that helps,
Darren



On 4/29/14, 7:48 PM, Hok Hei Tam wrote:
>
> Dear Bioontology Support,
>
> I am a new user, and was testing out the SPARQL endpoint for 
> Bioportal. I find that some of the relationships in some ontologies 
> are missing from the SPARQL view.
>
> Using the Adult  Mouse Anatomy (MA) ontology from OBO, I used the query
>
> PREFIX MA:<http://purl.obolibrary.org/obo/MA_>
>
> SELECT DISTINCT ?o ?p WHERE {
>
>   MA:0002419 ?p ?o
>
> }
>
> I do not find any entries linking it to MA:0000127, which it should 
> from the obo file.
>
> id: MA:0002419
>
> name: pancreatic islet core
>
> synonym: "beta cell islet" RELATED []
>
> xref: EMAPS:3565328
>
> relationship: part_of MA:0000127 ! pancreatic islet
>
> It only shows a subClassOf relationship to
>
> http://bioportal.bioontology.org/.well-known/genid/33a788b7-3805-4d08-ac1b-7a77008c8926/695a2010000001a
>
> What is this object and is this an error or am I querying incorrectly?
>
> Thank you,
>
> Hok Hei Tam
>
>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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