Re: Use of LSID's "in the wild"

Excellent!  Thanks Steve!

M


On Fri, 02 Jun 2006 18:34:19 -0700, Steve Chervitz  
<Steve_Chervitz@affymetrix.com> wrote:

>
>
> Hi Mark:
>
>> I'm writing a manuscript at the moment where I discuss LSIDs, and I'm
>> trying to get a sense of how many people are using them "in the wild".
>> I know that biopathways has set up a lot of "proxy" LSID resolvers, but
>> that's kinda cheating :-)  I'm wondering who is actually using the LSID
>> standard in a production environment.  I know that BioMOBY and
>> myGrid/Tverna both use LSIDs, but who else?
>
> Here's a paper that describes the use of LSIDs by three other early  
> adopters
> besides myGrid and BioMoby. It's co-authored by one of the authors of the
> LSID spec (Sean Martin):
>
> The impact of Life Science Identifiers on Informatics data
> http://www.broad.mit.edu/cgi-bin/cancer/publications/pub_paper.cgi?mode=view
> &paper_id=126
>
> When you ask, "who is using the LSID standard?" you might want to
> differentiate between organizations who have adopted LSID syntax vs those
> who are also hosting and maintaining LSID resolution services. The  
> latter is
> a much bigger cookie to swallow, but the former is still a step forward.
>
> If the only thing that comes from the LSID spec is a notion of an  
> identifier
> syntax that becomes widely adopted by bioinformatics data providers, it
> would be a huge success, which was also noted in the conclusion of an IBM
> article you may have seen:
> http://www-128.ibm.com/developerworks/webservices/library/os-lsid2/
>
> Another useful distinction to make when considering who is using LSIDs is
> whether they are data providers or application providers (or both).  
> Ideally,
> you'd like to see the application providers using LSIDs that are created  
> and
> managed by the data providers, rather than used only internally within  
> the
> application.
>
> Here are some LSID users that would fall into the data provider category:
>
> * The HapMap project. I don't know if they provide a resolution service.
> Search for 'LSID' on this page:
> http://www.hapmap.org/downloads/index.html.en
>
> * Affymetrix uses an LSID-like syntax in its MAGE-ML formatted files
> containing NetAffx annotations of the sequences used in array designs.
> Here's a snippet from one such file:
>
> <BioSequence_package>
>   <BioSequence_assnlist>
>     <BioSequence  
> identifier="Affymetrix.com:Transcript:HG-U133A.1007_s_at"
>          ....
>
> It's not a true LSID since it doesn't begin with 'urn:lsid'. Affy doesn't
> host an LSID resolver or provide any sort of lookup service using these  
> ids.
> I summarized some of the issues we ran into here (see the section titled
> 'LSIDs and Content Negotiation' in particular):
>
> http://lists.w3.org/Archives/Public/public-swls-ws/2004Nov/att-0000/Affy_Sem
> Web-LifeSci_position_paper.pdf
>
> * Pseudogene.org. Don't know if they offer a resolution service:
> http://www.pseudogene.org/cgi-bin/set-results.cgi?tax_id=9606&all=View+All+S
> ets&criterion0=&operator0=&searchValue0=&sort=0&output=html
>
> The following would fall in the application provider category of LSID  
> users.
> While these may not fully qualify as "in the wild", one could ask: How
> widely are these apps being used by other parties, either in an R&D or
> production setting?
>
> * BioPathways Consortium (as you mention above).
> http://lsid.biopathways.org/authorities.shtml
>
> * Intellidimensions's RDF Gateway and Eric Jain's UniProt RDF project:
> http://labs.intellidimension.com/uniprot/query.rsp?q=10
> http://expasy3.isb-sib.ch/~ejain//rdf/migration.html
>
> * KIM. See Sean Martin's presentation from the W3C meeting. It describes  
> a
> system that makes extensive use of LSIDs:
> http://www.w3.org/2004/10/swls/w3c_slrp_presentation_Sean_Martin_IBM.pdf
>
> * GBIF. Looks like they are still at an early stage of development.
> http://wiki.gbif.org/dadiwiki/wikka.php?wakka=col2005lsid
>
> There may be others out there. This is not necessarily an exhaustive
> listing.
>
> Cheers,
> Steve
>
>

Received on Saturday, 3 June 2006 01:41:49 UTC