W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > October 2006

Prototype URL to Life Science Identifier (LSID) gateway now available

From: Sean Martin <sjmm@us.ibm.com>
Date: Thu, 12 Oct 2006 17:51:05 -0400
To: public-semweb-lifesci@w3.org
Cc: Lsid-developer@lists.sourceforge.net
Message-ID: <OF1B337842.BEA002A5-ON85257205.0060CC92-85257205.007805D9@us.ibm.com>
Hello all,
A little while back the W3C's HCLS BioRDF group (in the form of Susie 
Stephens) asked if I would look into establishing a prototype of a gateway 
service that allows the mapping of  LSIDs to URLs. The initial suggestion 
came from Henry Thompson who asked that we take at look at how the ARK 
system does something similar.  He and members of the W3C TAG, as well as 
others on the public-semweb-lifesci list have indicated how important they 
feel it is that one should be able to derefence URIs using the HTTP URI 
scheme and I believe this prototype succeeds in doing just that for LSIDs. 
You can read that conversation in the archives of the mail-list [1].

The OMG were both interested and willing to cooperate with this effort and 
they have established a new DNS domain lsid-info.org for the purpose. I am 
pleased to announce that the prototype gateway is now operational. [2]

 Here is our first stab at the syntax of the mapping. To form your LSID 
access URL, replace the string <LSID> with an actual resolvable LSID.

To retrieve the named bytes use http://lsid-info.org/<LSID> 
        Example: 
http://lsid-info.org/urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:genbank:30350027

To retrieve the RDF metadata (effectively a named graph) for the named 
bytes or concept use http://lsid-info.org/<LSID>? 
        Example: 
http://lsid-info.org/urn:lsid:gdb.org:GenomicSegment:GDB132938?

To retrieve and format the RDF metadata for the named bytes or concept as 
human-readable HTML use http://lsid-info.org/rdf2html/<LSID> 
        Example: 
http://lsid-info.org/rdf2html/urn:lsid:gene.ucl.ac.uk.lsid.biopathways.org:hugo:MVP

To retrieve information about the authority for the named bytes or concept 
use http://lsid-info.org/host/<LSID> 
        Example: 
http://lsid-info.org/host/urn:lsid:gdb.org:GenomicSegment:GDB132938

Obviously this syntax can be evolved so we would like feed back.

I hope that others will find this gateway as useful as I believe we will. 
It may be that early work of this group should focus on establishing 
recommendations for and possibly even implementations of how to bridge 
useful information that is provided using standards created by non-W3C 
organizations and communities to the Semantic Web.  It seems to me that 
perhaps we are going to need a number of similar gateways to be 
established permanently for other URI schemes like Handle DOIs[3], Oasis 
XRIs[4] as well as non-URI  based identifier schemes which provide named 
bytes and metadata that is or can be transformed to RDF.  In particular a 
gateway to the DOI system would be useful to us at this time because it is 
widely adopted in the scientific publishing community and we need a means 
to uniquely identify a paper (and indeed an offset into that paper) for 
the purposes of annotations stored  in our RDF backed systems.

Kindest regards, Sean


[1] 
http://lists.w3.org/Archives/Public/public-semweb-lifesci/2006Jul/0213.html
[2] http://lsid-info.org/
[3] http://www.doi.org/
[4] http://en.wikipedia.org/wiki/Extensible_Resource_Identifier
=

--
Sean Martin
IBM Corp
Received on Thursday, 12 October 2006 21:51:20 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:00:45 GMT