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

Hi Mark,

Just to add a bit to Steve's reply...

> > 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, ...

In the gene expression domain, best practice states that with-in MAGE-ML
documents that an LSID like syntax be used for identifiers.  Although it
is still ad hoc to resolve these, for well-know data sources such as
Affymetrix, Agilent, GenBank, ArrayExpress, etc., when parsing through a
MAGE document, one can at least decompose the NamingAuthority, Namespace
and ObjectID, and based on the NamingAuthority convert the information
into the 'native' URI for that NamingAuthority.

This has proved very useful to a number of consumers of MAGE-ML.

cheers,
Michael

Michael Miller
Lead Software Developer
Rosetta Biosoftware Business Unit
www.rosettabio.com

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org 
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of 
> Mark Wilkinson
> Sent: Friday, June 02, 2006 6:42 PM
> To: Steve Chervitz; public-semweb-lifesci@w3.org
> Subject: 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+A
ll+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 Monday, 5 June 2006 16:33:02 UTC