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[bioontology-support] BioPortal sparql

manuelso manuelso at stanford.edu
Wed Dec 19 18:59:21 PST 2012


Hi Nikolina,

The triple store has now the latest data. Can you run your queries again and let me know if the issue is still there.

Manuel


On Dec 17, 2012, at 12:28 PM, manuelso <manuelso at stanford.edu> wrote:

> Hi Nikolina,
> 
> Thanks a lot for the detailed feedback. I have looked into some the ontologies you just mentioned and it seems that they have been updated very recently. We have a bug in the process that syncs the triple store so the data you are querying is out of date. We are fixing this today. I will contact you later today or tomorrow to ask you to rerun your experiments with the most updated data.
> 
> Apologies for the inconvenience.
> 
> Best,
> 
> Manuel
> 
> On Dec 15, 2012, at 1:46 AM, Nikolina Koleva <nikolina.koleva19 at yahoo.de> wrote:
> 
>> 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
>>> 
>> 
> 
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