[Tdwg-guid] LSIDs for PubMed, GenBank, and NCBI Taxonomy
Roderic Page
r.page at bio.gla.ac.uk
Mon May 8 10:12:16 CEST 2006
Dear Ben,
Who do I contact regarding the lsid.biopathways.org resolver? It's a
bit flaky, and I think the DNS SRV record is out of date. My crude LSID
tester reports errors (e.g.,
http://linnaeus.zoology.gla.ac.uk/~rpage/lsid/tester/?
q=urn%3Alsid%3Ancbi.nlm.nih.gov.lsid.biopathways.org%3Apubmed%3A12441807
), which I suspect is because the SRV record states the resolver is on
port 9090, when it's actually on port 80 (at least, I get a WSDL from
http://lsid.biopathways.org:80/authority/ but not
http://lsid.biopathways.org:9090/authority/).
As an aside, I guess this is an interesting management issue -- how
does one discover who to complain to when an LSID authority is broken?
I've had a quick look at the PubMed stuff that I did manage to get out
of the Biopathways site. My concern about this is that it perhaps
models the PubMed record a little too closely (in the same way that a
lot of NCBI's XML is horrendous as it models the underlying ASN.1 -
yuck). If we're going to integrate this stuff with other providers
(e.g., RDF feeds from the publishing industry or projects like
Connotea) then I think we need to adopt generic vocabularies (such as
Dublin Core and PRISM), rather than object specific ones. I think the
last thing a user wants to do is have to learn a new vocabulary for
each data source. That rather defeats the dream of easy integration.
Regards
Rod
On 6 May 2006, at 15:43, Benjamin H Szekely wrote:
>
> 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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> >
> >
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>
------------------------------------------------------------------------
----------------------------------------
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
Send instant messages to your online friends http://uk.messenger.yahoo.com
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