[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bit flaky, and I think the DNS SRV record is out of date.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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------------------------------------------------------------------------ 
----------------------------------------
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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