[Biojava-l] Bibliographic objects & NCBI's Pubmed

[Michael Driscoll]

The citation model developed at the National Library of Medicine, which is fairly
robust and has been in use for many years in Medline, has been implemented and
extended in NCBI's Pubmed. (http://www.ncbi.nlm.nih.gov/pubmed .)

Resource links of interest:

NLM's current DTD:
 http://www.ncbi.nlm.nih.gov:80/entrez/query/static/PubMed.dtd
An example XML file:
 http://www.ncbi.nlm.nih.gov:80/entrez/query/static/spec.html#ExampleXMLfile
Another entry -- to see XML select "View As XML" in toolbar:
 http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=2231712&dopt=Abstract



Mike

Ingenieur Logiciel
GENSET SA
24 rue Royale
75008 Paris FRANCE


> Message: 10
> Date: Wed, 17 Jan 2001 16:17:08 +0000
> From: Thomas Down <td2@sanger.ac.uk>
> To: Tom Oinn <tmo@ebi.ac.uk>
> Cc: biojava-l@biojava.org
> Subject: Re: [Biojava-l] Bibliographic objects
> Organization: This tangled web on which I'm laid intwined
>
> On Wed, Jan 17, 2001 at 04:13:14PM +0000, Tom Oinn wrote:
> >
> > > Is there any demand for this?
> >
> > Yes. We (in this case We -> Interpro programmers) are also thinking
> > about this, as we have what is tending towards a unified model for
> > references within EMBL, SWISSPROT and InterPro. We found the following
> > problems....
> >
> > 1. The databases that we ideally want to be able to model citations in
> > are not very good from the point of view of consistancy. We find many
> > mis-spellings, etc.
>
> Yes *sigh*.  On the other hand, I'm not sure this should have
> any effect on the actual Reference, Author, etc. interfaces.
> I'd rather cope with ambiguities and typos by having external
> classes for performing fuzzy comparisons between objects.
>
> > Would any of the Sanger people have time to call round to the EBI? I
> > can attempt to arrange all the interested people at this end, probably
> > in a few weeks. Suggestions?
>
> I'd be happy to drop round pretty much any time that's convenient.
> Matthew has expressed an interest, too -- he'll be along if he can.
>
> Thanks,
>     Thomas.