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Re: Accession Numbers - Linking Strategies

From: juty <juty@ebi.ac.uk>
Date: Tue, 26 Jun 2012 15:41:09 +0100
Message-ID: <4FE9CA05.4090205@ebi.ac.uk>
To: Michel Dumontier <michel.dumontier@gmail.com>
CC: "Hammond, Tony" <t.hammond@nature.com>, "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>, bio2rdf <bio2rdf@googlegroups.com>, IdOrg-board@googlegroups.com
Hi Tony,

Just to echo what Michel says, we are working on incorporating Bio2RDF 
namespaces into the MIRIAM Registry, to make them available through the 
Identifiers.org resolving system. This is in progress, but if anyone has 
datasets that they would like to have made available through this system 
more immediately, then please feel free to submit information about that 
dataset here: http://www.ebi.ac.uk/miriam/main/mdb?section=submit
(Note: you do not need to complete the entire form, but please please 
please give us something we can follow up on).

You can find more information on Identifiers.org and the MIRIAM Registry 
here: http://identifiers.org/pubmed/22140103



(MIRIAM Registry curator)

On 26/06/12 15:21, Michel Dumontier wrote:
> Hi Tony,
>   The complete list of Bio2RDF namespaces is at freebase:
> http://www.freebase.com/view/base/bio2rdf/bm/-/base/bio2rdf
> Please note that we have submitted our list of datasets and namespaces 
> to http://identifiers.org, and we are awaiting their incorporation 
> into the MIRIAM registry. You can submit individual datasets at 
> identifiers.org <http://identifiers.org>, if you need to :)
> Best,
> m.
> On Tue, Jun 26, 2012 at 9:55 AM, Hammond, Tony <t.hammond@nature.com 
> <mailto:t.hammond@nature.com>> wrote:
>     Hi:
>     This is probably a very simplistic question but I was wondering if
>     there were any best practices for linking based on accession
>     numbers for RDF documents. There seem to be different service
>     based type mechanisms for each individual registry which may not
>     provide the most stable means of linking. Correspondingly using
>     lingua francas such as Bio2RDF namespacing [1] can also be
>     problematic in that not all the namespaces of interest appear to
>     be represented  and these also (as I understand it) provide no
>     guarantee for dereference but rather a common URI template.
>     So just what is the best policy for linking accession numbers? Or
>     should one avoid this.
>     Thanks,
>     Tony
>     [1]
>     http://sourceforge.net/apps/mediawiki/bio2rdf/index.php?title=Namespace
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> Michel Dumontier
> Associate Professor of Bioinformatics, Carleton University
> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest 
> Group
> http://dumontierlab.com

Nick Juty
Database Curator
European Bioinformatics Institute
Cambridge, United Kingdom
Received on Thursday, 28 June 2012 09:51:21 UTC

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