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[bioontology-support] BioPortal sparql

manuelso manuelso at stanford.edu
Mon Dec 17 12:28:21 PST 2012


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 We have a bug in the process that syncs the triple store so the data you are querying is out of date.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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