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[bioontology-support] sparql endpoint

manuelso manuelso at stanford.edu
Wed Mar 5 09:57:56 PST 2014


Sina,

Thanks for the clarifications. You need to use a library that knows how to handle SPARQL federation, not all of them do. Jena ARQ supports it. What are you using ?

Manuel 

On Mar 5, 2014, at 9:48 AM, Madani,Sina <AHMadani at mdanderson.org> wrote:

> Thank you Manuel,
> Yes, I understand your point for using SERVICE. I didn’t include the portion of the query that points to my local triple store where it makes a federated query.
> I wanted to make sure that from my local triple store (AllegroGraph) I can extract data from (remote) Bioportal sparql endpoint first and, if it is successful,  then connect Bioportal data (CUI) to my local CUIs to get the hierarchy/relationships between CUIs. I am not using Java.   Is this even possible?
>  
> Thanks!
> Sina
>  
> P.S Thanks for the filter replacement. In my original code I was using a list of 10 codes and that’s why I used Filter J
>  
> Sina
>  
> From: manuelso [mailto:manuelso at stanford.edu] 
> Sent: Wednesday, March 05, 2014 11:20 AM
> To: Madani,Sina
> Cc: support at bioontology.org Support
> Subject: Re: [bioontology-support] sparql endpoint
>  
> Hi Sina,
>  
> Your apikey seems to be fine.
>  
> I am not sure if you can combine FROM and SERVICE. But  you do not need to use a SERVICE query, SERVICE should be  used for federated resources and your query is targeting only one endpoint. Something like this would the job better and faster:
>  
> PREFIX xsd:  <http://www.w3.org/2001/XMLSchema#>
> PREFIX skos:  <http://www.w3.org/2004/02/skos/core#>
>  
> SELECT ?x ?label
> FROM <http://bioportal.bioontology.org/ontologies/SNOMEDCT>
> WHERE
> {
> ?x skos:notation '372030009'^^xsd:string;
> skos:prefLabel ?label.
> }
>  
> Notice how I replaced the filter.
>  
> If you are using Java, to run that query you can use, as a template, the code in here:
>  
> https://github.com/ncbo/sparql-code-examples/blob/master/java/src/org/ncbo/stanford/sparql/examples/JenaARQTest.java
>  
> Manuel
>  
> PS: I hope you don’t mind me cc-ing the support list so that this gets archived. I have removed your api key from the thread.
>  
> On Mar 5, 2014, at 7:48 AM, Madani,Sina <AHMadani at mdanderson.org> wrote:
> 
> 
> Thank you Manuel,
> One more question. I am trying to access your sparql endpoint from my local AllegroGraph store but am getting error (Executing query failed: bad request Remote server returned error code 403.
> ) while executing below query.
> Is it something wrong with my query or my apikey is not active? I want to link some of Bioportal SNOMED data to my local store data.
>  
> Thanks!
> Sina
>  
> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
> PREFIX snomed-term: <http://purl.bioontology.org/ontology/SNOMEDCT/?apikey=APIKEY>
> PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
>  
>  
> SELECT ?o ?label
> FROM <http://bioportal.bioontology.org/ontologies/SNOMEDCT>
> WHERE
> {
> SERVICE <http://sparql.bioontology.org/sparql/?apikey=APIKEY> { ?x skos:notation ?o;
>                                                                                                                                                                                                                 skos:prefLabel ?label.  
>                                                                                                                                                                                                                   FILTER (str(?o) in ('372030009'))  }    
> }
>  
>  
> Executing query failed: bad request Remote server returned error code 403.
>  
> From: manuelso [mailto:manuelso at stanford.edu] 
> Sent: Monday, March 03, 2014 5:59 PM
> To: Madani,Sina
> Cc: support at bioontology.org
> Subject: Re: [bioontology-support] sparql endpoint
>  
> Sina,
>  
> That is correct, those are different SNOMED versions. We are working on a new version of the SPARQL endpoint that will be updated regularly. This release will probably happen in late March or early April. 
>  
> Best,
>  
> Manuel
>  
>  
> On Mar 3, 2014, at 12:09 PM, Madani,Sina <AHMadani at mdanderson.org> wrote:
> 
> 
> 
> Hi
> I am using Bioportal’s  sparql endpoint to extract preLabel of some SNOMED concepts based on their codes or class names.
> However, for some of the concepts no data is returned. If I do a regular Bioportal search (non sparql) for those concept codes (like the one shown in the query below)  I do get a result though.
> Does this mean the sparql endpoint is pointing to a different version of SNOMED?
>  
>  
> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
> PREFIX snomed-term: <http://purl.bioontology.org/ontology/SNOMEDCT/>
> PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
> SELECT ?o ?label
> FROM <http://bioportal.bioontology.org/ontologies/SNOMEDCT>
> WHERE
> {
>     ?x skos:notation ?o;
>        skos:prefLabel ?label.  
> FILTER (str(?o) in ('450945008'))      
> }
>  
> [no results]
>  
>  
> <image001.png>
>  
> Thanks!
> Sina
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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