Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] BioPortal sparql

Nikolina Koleva nikolina.koleva19 at yahoo.de
Sat Dec 15 01:46:01 PST 2012


Dear Manuel,

thank you very much for the quick and helpful response!

I tried this query and it works. Capitalizing the ontology abbreviations reduced the number of "no results" from 27 to 15 which is almost 50% and that is great.

However, for the following examples "no results" are returned, although the ontology abbreviation is actually capitalized:

PR	http://purl.obolibrary.org/obo/snap#_MaterialEntity
BASIC-VERTEBRATE-GROSS-ANATOMY	http://www.co-ode.org/ontologies/basic-bio/top-self-standing.owl#Non_material_entity
SOPHARM	http://obi.sourceforge.net/ontology/OBI.owl#OBI_255
NMR	http://obi.sourceforge.net/ontology/OBI.owl#OBI_255
EMO	http://www.ifomis.org/bfo/1.1/snap#MaterialEntity
NIF	http://purl.obolibrary.org/obo/snap_MaterialEntity
OAE	http://purl.obolibrary.org/obo/BFO_0000040
OMIT	http://www.ifomis.org/bfo/1.1/snap#MaterialEntity
AERO	http://www.ifomis.org/bfo/1.1/snap#MaterialEntity
CCO	http://purl.obolibrary.org/obo/SIO_000004
PCO	http://purl.obolibrary.org/obo/BFO_0000040
GEXO	http://purl.obolibrary.org/obo/SIO_000004
REXO	http://purl.obolibrary.org/obo/SIO_000004
RETO	http://purl.obolibrary.org/obo/SIO_000004
IDODEN	http://purl.obolibrary.org/obo/BFO_0000040

Best,
Nikolina
 
 
On Dec 14, 2012, at 7:09 PM, manuelso <manuelso at stanford.edu> wrote:

> Hi Nikolina,
> 
> The IRIs for graphs use acronyms capitalized. You need to ONTODM instead of OntoDM. The following query should give the results you expect:
> 
> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
> 
> SELECT * WHERE {
> GRAPH <http://bioportal.bioontology.org/ontologies/ONTODM> {
> 
>   <http://www.ifomis.org/bfo/1.1/snap#MaterialEntity> rdfs:subClassOf ?parent.
>       OPTIONAL {?parent rdfs:label ?label}.
>       } 
>   }
> 
> Best,
> 
> Manuel
> 
> 
> On Dec 14, 2012, at 6:29 AM, Nikolina Koleva <nikolina.koleva19 at yahoo.de> wrote:
> 
>> 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
>> 
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20121215/b5695f5c/attachment.html>


More information about the bioontology-support mailing list