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Re: bind results

From: Me <helenadeus@gmail.com>
Date: Thu, 14 Jun 2012 14:15:49 +0200
Cc: bio2rdf <bio2rdf@googlegroups.com>, W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Message-Id: <907227CC-501A-449C-B5B8-C39A5C506696@gmail.com>
To: Michel Dumontier <michel.dumontier@gmail.com>
Hi Michel, 

That's good to know :)

Thank you very much,

Lena


On Jun 13, 2012, at 7:10 PM, Michel Dumontier wrote:

> Helena,
>   the BIND endpoint refers to the BIND (Biomolecular Interaction Network Database) database, not BindingDB.
> 
> we should note that the BIND db is now deprecated, as we are parsing iRefIndex for all PPI from  BIND, BioGRID, CORUM, DIP, HPRD, InnateDB, IntAct, MatrixDB, MINT, MPact, MPIDB, MPPI and OPHID.
> 
> http://irefindex.uio.no/wiki/iRefIndex
> http://cu.irefindex.bio2rdf.org/sparql/
> 
> m.
> 
> On Wed, Jun 13, 2012 at 9:29 AM, Helena Deus <helenadeus@gmail.com> wrote:
> Hi there, 
> 
> I am running the following query in BIND through federated query:
> 
> select *
> where {
> 
> SERVICE <http://bind.bio2rdf.org/sparql> {
> ?protein1 <http://bio2rdf.org/ns/bio2rdf#xGI> ?protein2 .
> ?protein1 a <http://bio2rdf.org/ns/bind:MolType-protein> .
>  ?protein2  a <http://bio2rdf.org/ns/bind:MolType-protein> .
> filter ( ?protein1 !=  ?protein2 )
> }
> 
> }
> 
> This strange list of "protein associations" does not seem to make sense; 
> 
> Some of these associations, e.g.
> <http://bio2rdf.org/gi:9606>	 <http://bio2rdf.org/gi:33589859>
> 
> Appear to come from the BIND raw file "BDB_cid.txt ( 5.72 MB ) Mapping between BindingDB monomerid and PubChem cid"
> Which would mean that gi:9609 is a monomer and gi:33589859 is a pubchem cid, which is a compound (in this case, it goes by the very long name of tetra-O-benzyl-d-mannitol deriv. 1jj, D-Mannitol, 1,6-bis-O-[(2-fluorophenyl)methyl]-2,5-bis-O-[(4-fluorophenyl)methyl]-)
> 
> So, I think that a whole bunch of identifiers appear to be misclassified... Unless I am missing something... 
> 
> Any help with be greatly appreciated!
> Best,
> -- 
> Helena F. Deus
> Post-Doctoral Researcher at DERI/NUIG
> http://lenadeus.info/
> 
> 
> 
> 
> -- 
> Michel Dumontier
> Associate Professor of Bioinformatics, Carleton University
> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
> http://dumontierlab.com
> 
Received on Thursday, 14 June 2012 12:16:18 GMT

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