Question: Federated search in Triple Store
2
gravatar for maorinphone
4.5 years ago by
maorinphone20
Japan
maorinphone20 wrote:

I converted data to RDF in our research institute. I use triple stores to search the RDF data such as Virtuoso, OWLIM-SE (GraphDB) and Fuseki.

I'd like to connect with many external databases on the fly by SPARQL endpoint. However I couldn't use more than one "SERVICE" query. Here is the sample query.

prefix b2r: <http://bio2rdf.org/>
prefix drgb: <http://bio2rdf.org/drugbank_vocabulary/>
prefix dbowl: <http://dbpedia.org/ontology/>
prefix orphan: <http://www.nibio.go.jp/orphanDrugTarget#>

select distinct ?title  ?protein_name
where {
?s dbowl:drugbank ?drugbank.
SERVICE <http://drugbank.bio2rdf.org/sparql>
 {?drugbank <http://purl.org/dc/terms/title> ?title;
                     <http://bio2rdf.org/drugbank_vocabulary:target> ?target.
   ?target  <http://bio2rdf.org/drugbank_vocabulary:x-uniprot> ?x_uniprot.
 BIND (SUBSTR(str(?x_uniprot),28) as ?uniprot_id)
 BIND (URI(CONCAT("http://purl.uniprot.org/uniprot/",?uniprot_id)) as ?uniprot)}
SERVICE <http://beta.sparql.uniprot.org/>
     {?uniprot <http://purl.uniprot.org/core/mnemonic> ?protein_name}}

Although I tried the query 3 triple stores, I failed to get results. I'd already tested one "SERVICE" query could work and these queries could work individual.

If you know how to solve the problem (I'd like to avoid that all data put into our triple store.),  please help me.

software error • 1.4k views
ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by maorinphone20
2
gravatar for me
4.5 years ago by
me690
Switzerland
me690 wrote:

The first issue is that the Virtuoso hosting the drugbank data does not support the URI() function only the IRI() function.

Then you run into a number of bugs in the Virtuoso hosting both bio2rdf and uniprot sparql implementation.

Opened issue at virtuoso's github, no we need to wait for a fix to this issue. Before your otherwise correct query will work,

 

 

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by me690

Thank you for your reply. (This post is almost the same for BioHackathon ML, sorry)
I installed Virtuoso 7. If it is caused by bug, it's a pity,

Kato-san told me in case of virtuoso, the change of settings have possibilities to solve the problem.
http://answers.semanticweb.com/questions/10360/virtuoso-federated-query
Although I could overcome an error, I couldn't get any results... 

It seems this Q and A semanticweb.com) includes some hints.
http://answers.semanticweb.com/search/?csrfmiddlewaretoken=599f1bddf88920d231c9236be45453cd&q=federated+query&Submit=search&t=question
#Still investigating...
We use OWLIM-SE too, I'd like to get more information about OWLIM-SE too. 

ADD REPLYlink written 4.5 years ago by maorinphone20
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