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[bioontology-support] sparql issue

manuelso manuelso at stanford.edu
Thu May 9 21:16:07 PDT 2013


Hi Maxwell,

It is a bug in our system I believe. The query:

SELECT DISTINCT (COUNT(?s) as ?c)
FROM <http://bioportal.bioontology.org/ontologies/SEMPHYSKB-HUMAN>
WHERE {
	?s a owl:Class .
} 

returns a much smaller count than the actual number shown in the BioPortal UI/Rest  (388 vs 5937). That ontology is not complete in the triple store and we need to fix that. I have reported the issue and we will address it soon.

Do you need to use this ontology in combination with SPARQL ? To retrieve standard predicates like labels, synonyms, subClassOf, etc.  the REST endpoint fits perfectly.

http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses

Thanks for reporting this issue,

Manuel




On May 9, 2013, at 10:47 AM, Maxwell Neal <mneal at u.washington.edu> wrote:

> Hi all,
> 
> I've been trying to send queries over the SemPhysKB-Human ontology using BioPortal SPARQL and have run into a snag.  I have been trying to run a test query that should return the two subclasses of semsim:SemSim_component but I get no results. (Please see attached image showing the two subclasses of this term in the BioPortal tree view.) Here is the query:
> 
> *********************************************************************************
> PREFIX semsim: <http://www.bhi.washington.edu/SemSim#>
> PREFIX opb: <http://bhi.washington.edu/OPB#>
> 
> SELECT DISTINCT *
> FROM <http://bioportal.bioontology.org/ontologies/SEMPHYSKB-HUMAN>
> WHERE {
> 	?x ?p semsim:SemSim_component .
> }  
> *********************************************************************************
> 
> When I perform a similar query that should return all the subclasses of semsim:Reference_physical_property, I get the expected results; a set of OPB physical property classes. Here is the query that appears to be working. Is it the same as the one above, except for the object in the WHERE statement.
> 
> *********************************************************************************
> PREFIX semsim: <http://www.bhi.washington.edu/SemSim#>
> PREFIX opb: <http://bhi.washington.edu/OPB#>
> 
> SELECT DISTINCT *
> FROM <http://bioportal.bioontology.org/ontologies/SEMPHYSKB-HUMAN>
> WHERE {
> 	?x ?p semsim:Reference_physical_property .
> }
> *********************************************************************************
> 
> 
> My deepest apologies if I am making a rookie mistake here with SPARQL, but my spider sense tells me something's afoot.
> 
> Many thanks for your time,
> 
> M 
> 
> 
> <Screen shot 2013-05-09 at 10.31.25 AM.png>
> 
> 
> ---------------------------------
> Maxwell Neal
> 
> Post-doctoral researcher
> Department of Bioengineering
> University of Washington
> mneal at uw.edu
> ---------------------------------_______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support



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