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

[Juha Muilu]

Hi 
I am forwarding Martin Senger's reply, he is not on the list.

> 
> > 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 .)
> >
   The specification developed in the OMG Life Science Research group
(as
mentioned before by Mike Dickson) was designed after studying several
data
models, and one of them was the Pubmed. I believe (and even more, we are
now working on implementation of it) that the LSR specification can be
used to access "any" bibliographic repository and still provide data in
an
interoperable way. The details of the data model (and the spec itself)
can
be found at http://industry.ebi.ac.uk/~senger/BQS/ (which is only a
temporary URL - the right one later will be
http://industry.ebi.ac.uk/openBQS/), especially at
http://industry.ebi.ac.uk/~senger/BQS/web.

   Regards,
   Martin



Michael Driscoll wrote:
> 
> 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.
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l

-- 
 +--------------------------------------------------------------------+
 |Juha Muilu, Ph.D., EMBL Outstation| Email:  muilu@ebi.ac.uk         |
 |European Bioinformatics Institute | Phone:  +44 (0)1223 494 624     |
 |Wellcome Trust Genome Campus      | Fax:    +44 (0)1223 494 468     |
 |Hinxton, Cambridge CB10 1SD, UK   | http://industry.ebi.ac.uk/~muilu|
 +--------------------------------------------------------------------+