[Tdwg-guid] LSIDs for PubMed, GenBank, and NCBI Taxonomy

[Benjamin H Szekely]

Hi Rod,
     We have implementations of NCBI Pubmed, Genbank, Protein, and OMIM. 
Gene is on the way.  I'm in the process of updating our implementations 
since the NCBI upgraded their web service to 1.4.  I have created OWL 
ontologies for the various databases that you might find useful in your 
implementation.  They will be posted online soon but I could send them to 
you if you like.

- Ben

tdwg-guid-bounces at mailman.nhm.ku.edu wrote on 05/06/2006 06:12:13 AM:

> The web server that hosts most of my LSID work (including the Taxonomy 
> Search Engine) got hacked recently. Rebuilding it is taking time, but 
> one positive outcome is I'm trying to clean up some LSID stuff.
> 
> I've rebuilt the LSID authority for PubMed, GenBank, and NCBI taxonomy 
> (by hacking Roger Hyam's PHP code - IBM's Perl stack is giving me grief 
> on a Fedora Core 4 box). These are, of course, experimental, but 
> hopefully the RDF will be of interest. I've tried to use standard 
> vocabularies, and link  between records wherever possible (e.g., a 
> PubMed record for a paper will list sequences referred to in that 
> paper, a sequence will link back to the paper in which it was 
> published, etc.). I've set this up partly to support my attempt to 
> build a triple store for ants (see 
> http://iphylo.blogspot.com/2006/05/ants-rdf-and-triple-stores.html), 
> which I hope to have running in time for GUID2.
> 
> You can try out the LSIDs, which have the form
> 
> urn:lsid:ncbi.nlm.nih.gov.lsid.zoology.gla.ac.uk:   pubmed or gi or 
> taxon : id
> 
> e.g.
> 
> urn:lsid:ncbi.nlm.nih.gov.lsid.zoology.gla.ac.uk:pubmed:16601190
> 
> urn:lsid:ncbi.nlm.nih.gov.lsid.zoology.gla.ac.uk:gi:87047074
> 
> urn:lsid:ncbi.nlm.nih.gov.lsid.zoology.gla.ac.uk:taxon:369204
> 
> There's a lot more which could be added to the metadata, but I hope 
> this is of interest.
> 
> Regards
> 
> Rod
> 
> 
> ------------------------------------------------------------------------ 

> ----------------------------------------
> Professor Roderic D. M. Page
> Editor, Systematic Biology
> DEEB, IBLS
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QP
> United Kingdom
> 
> Phone:    +44 141 330 4778
> Fax:      +44 141 330 2792
> email:    r.page at bio.gla.ac.uk
> web:      http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html
> 
> Subscribe to Systematic Biology through the Society of Systematic
> Biologists Website:  http://systematicbiology.org
> Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/
> Find out what we know about a species: http://ispecies.org
> Rod's rants on phyloinformatics: http://iphylo.blogspot.com
> 
> 
> 
> 
> 
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