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

[Sean Martin]

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
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Sean Martin
IBM Corp