Re: URIs

[Nicolas Novere comments on part of a recent proposal for BioPAX to  
be presented tomorrow: http://mumble.net/~alanr/cshl/URICV.htm]

On Jun 19, 2006, at 5:45 AM, Nicolas Le Novere wrote:
> Regarding this problem, we should team-up because we already did
> it. We bumped into the same problems for quantitative modelling, and
> decided to use the same systems of unique URIs. See:

Yes, the problem pops up everywhere. See recent threads on public- 
semweb-lifesci

http://lists.w3.org/Archives/Public/public-semweb-lifesci/2006May/ 
0042.html
http://lists.w3.org/Archives/Public/public-semweb-lifesci/2006Jun/ 
0149.html

We are having a teleconference about this in (checks clock) 5  
minutes. Details
Here http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/ 
2006-06-19_Conference_Call

Do consider joining the conversation.

There is also LSID to consider.

Do you have a specification of your web service available?

We should indeed all work together on this!

-Alan

>
> Le Novère N., Finney A., Hucka M., Bhalla U., Campagne F., Collado- 
> Vides J., Crampin E., Halstead M., Klipp E., Mendes P., Nielsen P.,  
> Sauro H., Shapiro B., Snoep J.L., Spence H.D., Wanner B.L. (2005)  
> Minimum Information Requested In the Annotation of biochemical  
> Models (MIRIAM). Nature Biotechnology, 23: 1509-1515.
> http://dx.doi.org/10.1038/nbt1156
>
> The new version of SBML has a formal way of using those UIRs:
> http://sbml.org/wiki/sbml-level-2-version-2.pdf
> See section 6.
>
> Since then, we have been developing a database to store those standard
> URIs and all the related information (name, synonyms, URLs,
> regular-expression to parse accession, associated documentation etc.)
> We developed WebServices to access the database. Therefore when a tool
> will parse an SBML file, it will be able to transform the URIs into
> physical URLs etc. Conversely, a tool will be able to generate the
> correct URI using the name of a resource and an accession.
>
> The database is not publicly available yet, but we already use it for
> BioModels Database purpose. Our plan is to release the whole lot by
> the end of August. But we could put a demo online before that.
>
> My suggestion is for BioPAX to use MIRIAM URIs. I see two great
> advantages to that: 1) our aim being exactly the same, it would
> eliminate some redundant work. 2) SBML and BioPAX constituents would
> be annotated using the same URIs, making the conversion so easier.
>
> What do-you think?
>
> On Mon, 19 Jun 2006, Alan Ruttenberg wrote:
>
>> http://mumble.net/~alanr/cshl/URICV.htm
>>
>> It's subject to change, but any comments or questions are  
>> appreciated.
>>
>> Many thanks to quick, late night,  reviews by Andrea, Joanne,  
>> Matthias and Emek.
>>
>> Regards,
>> Alan
>>
>> _______________________________________________
>> BioPAX-discuss mailing list
>> BioPAX-discuss@cbio.mskcc.org
>> http://cbio.mskcc.org/mailman/listinfo/biopax-discuss
>
> -- 
> Nicolas LE NOVERE,  Computational Neurobiology,
> EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10  
> 1SD, UK
> Tel: +44(0)1223 494 521,  Fax: +44(0)1223 494 468,  Mob: +33(0) 
> 689218676
> http://www.ebi.ac.uk/~lenov                   AIM screen name:  
> nlenovere

Received on Monday, 19 June 2006 14:55:04 UTC