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Some IRefIndex geneid links are incorrect and should be to the symbol namespace
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Peter Ansell  
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 More options Jul 4 2012, 9:55 pm
From: Peter Ansell <ansell.pe...@gmail.com>
Date: Thu, 5 Jul 2012 11:55:39 +1000
Local: Wed, Jul 4 2012 9:55 pm
Subject: Some IRefIndex geneid links are incorrect and should be to the symbol namespace
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Some triples in the irefindex namespace are being generated to the
geneid namespace when they should be pointing at the symbol namespace.
The predicates in question are [1] and [2], for example on the uri
[3]. In the example, http://bio2rdf.org/geneid:MAGEA4 should be
http://bio2rdf.org/symbol:MAGEA4

The rdfiser script [4] assumes that irefindex will always have the
following mapping 'entrez gene/locuslink' => 'geneid', and that works
for the other predicates, but the irefindex database fails to
distinguish the numeric identifiers from the textual symbols that we
put in "symbol:", which is based mostly on HGNC.

I can write a sparql rule to fix the error dynamically in the webapp
if necessary, but it would be best to fix it in the rdfiser so that
users of the sparql endpoint are not confused about the difference
between the endpoint and the webapp.

Peter

[1] http://bio2rdf.org/irefindex_vocabulary:aliasa
[2] http://bio2rdf.org/irefindex_vocabulary:aliasb
[3] http://bio2rdf.org/irefindex:739540
[4] https://github.com/bio2rdf/bio2rdf-scripts/blob/master/irefindex/iref...


 
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Michel Dumontier  
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 More options Jul 5 2012, 4:38 pm
From: Michel Dumontier <michel.dumont...@gmail.com>
Date: Thu, 5 Jul 2012 16:38:55 -0400
Local: Thurs, Jul 5 2012 4:38 pm
Subject: Re: Some IRefIndex geneid links are incorrect and should be to the symbol namespace
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so, are we using the "symbol" or "hgnc" namespace?

m.

--
Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com

 
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Peter Ansell  
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 More options Jul 5 2012, 4:43 pm
From: Peter Ansell <ansell.pe...@gmail.com>
Date: Fri, 6 Jul 2012 06:43:33 +1000
Local: Thurs, Jul 5 2012 4:43 pm
Subject: Re: Some IRefIndex geneid links are incorrect and should be to the symbol namespace
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hgnc contains the numeric identifiers from hgnc and symbol has
contained the textual gene symbols.

Peter

On 6 July 2012 06:38, Michel Dumontier <michel.dumont...@gmail.com> wrote:


 
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Michel Dumontier  
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 More options Jul 5 2012, 5:10 pm
From: Michel Dumontier <michel.dumont...@gmail.com>
Date: Thu, 5 Jul 2012 17:10:43 -0400
Local: Thurs, Jul 5 2012 5:10 pm
Subject: Re: Some IRefIndex geneid links are incorrect and should be to the symbol namespace
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got it. ok, i will make the change.

m.

--
Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com

 
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Paul Boddie  
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 More options Jul 6 2012, 7:48 am
From: Paul Boddie <paul.bod...@biotek.uio.no>
Date: Fri, 6 Jul 2012 04:48:41 -0700 (PDT)
Local: Fri, Jul 6 2012 7:48 am
Subject: Re: Some IRefIndex geneid links are incorrect and should be to the symbol namespace
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On Thursday, 5 July 2012 03:55:39 UTC+2, Peter Ansell wrote:

> Some triples in the irefindex namespace are being generated to the
> geneid namespace when they should be pointing at the symbol namespace.
> The predicates in question are [1] and [2], for example on the uri
> [3]. In the example, http://bio2rdf.org/geneid:MAGEA4 should be
> http://bio2rdf.org/symbol:MAGEA4

I have to admit that I'm not following RDF-based work and I'm therefore not
familiar with the various namespaces in use, but as someone currently
responsible for the iRefIndex data, should I make sure that gene symbols
use the hgnc prefix corresponding to the MI:1095 controlled vocabulary term
in the PSI-MI TAB output?

Paul


 
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Michel Dumontier  
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 More options Jul 6 2012, 10:02 am
From: Michel Dumontier <michel.dumont...@gmail.com>
Date: Fri, 6 Jul 2012 10:02:33 -0400
Local: Fri, Jul 6 2012 10:02 am
Subject: Re: Some IRefIndex geneid links are incorrect and should be to the symbol namespace
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Paul, what does MI:1095 correspond to?

http://bioportal.bioontology.org/ontologies/39508/?p=terms&conceptid=...

m.

On Fri, Jul 6, 2012 at 7:48 AM, Paul Boddie <paul.bod...@biotek.uio.no>wrote:

--
Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com

 
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Paul Boddie  
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 More options Jul 6 2012, 10:12 am
From: Paul Boddie <paul.bod...@biotek.uio.no>
Date: Fri, 06 Jul 2012 16:12:59 +0200
Local: Fri, Jul 6 2012 10:12 am
Subject: Re: Some IRefIndex geneid links are incorrect and should be to the symbol namespace
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On 06/07/12 16:02, Michel Dumontier wrote:

I was thinking of this:

http://www.ebi.ac.uk/ontology-lookup/?termId=MI%3A1095

In the data we produce, that term won't actually get used, but the
symbols would be prefixed with hgnc as the "database name"
(corresponding to the "preferred name" in the ontology term entry) as
described in the PSI-MI TAB specification:

https://code.google.com/p/psicquic/wiki/MITAB26Format

Paul


 
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Michel Dumontier  
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 More options Jul 6 2012, 11:54 am
From: Michel Dumontier <michel.dumont...@gmail.com>
Date: Fri, 6 Jul 2012 11:54:59 -0400
Local: Fri, Jul 6 2012 11:54 am
Subject: Re: Some IRefIndex geneid links are incorrect and should be to the symbol namespace
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i think prefixing these terms with hgnc would be very useful!

m.

On Fri, Jul 6, 2012 at 10:12 AM, Paul Boddie <paul.bod...@biotek.uio.no>wrote:

--
Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com

 
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