[Tdwg-guid] LSIDs for PubMed, GenBank, and NCBI Taxonomy
Roderic Page
r.page at bio.gla.ac.uk
Sat May 6 12:12:13 CEST 2006
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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