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[bioontology-support] BioPortal sparql

Nikolina Koleva nikolina.koleva19 at yahoo.de
Fri Dec 14 06:29:28 PST 2012


Dear all,

I have a question about the BioPortal sparql.  
For a list of hits found in the BioPortal by searching for the term "material entity", I try to get the parent concept and ask for its label (optionally). 
I am running the following query in a loop as long as I get a parent and in each iteration I set the parent to the value of the term:

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
    
    SELECT * WHERE {
    GRAPH <http://bioportal.bioontology.org/ontologies/SWO> {
        
        <http://www.ifomis.org/bfo/1.1/snap#MaterialEntity> rdfs:subClassOf ?parent.
            OPTIONAL {?parent rdfs:label ?label}.
            } 
        }

thereby:

1. http://bioportal.bioontology.org/ontologies/SWO is the ontology in which I found the term

2. http://www.ifomis.org/bfo/1.1/snap#MaterialEntity is the full id of the term 

Well, this works and returns results but unfortunately not for every hit I got. I have tested it on 70 of the hits for the term "material entity" and in 27 of the cases I got no results.

For
1. http://bioportal.bioontology.org/ontologies/OGMS
2. http://www.ifomis.org/bfo/1.1/snap#MaterialEntity 

I do get results 
but 
for 
1. http://bioportal.bioontology.org/ontologies/OntoDM
2. http://www.ifomis.org/bfo/1.1/snap#MaterialEntity

no results are retrieved although the id of the term is the same.


When I checked both entries in BioPortal web interface they both have the subClassOf property ...

It would be great if you have any ideas why this happens. 


Best regards,
Nikolina
 


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