[Biophp-dev] Interface to LocusLink and Ensemble

[S Clark]

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Sorry about the delay, just got back from another ~2500km drive for busines=
s.
There's got to be an easier way to make a living...

Actually, if it's JUST the ID numbers that you are looking for,=20
you MAY be able to get what you need with ESearch(possibly followed by an
ESummary call) - the modules for those in CVS SHOULD be working (when last I
tested it with a few different types of searches it seemed to be working,
anyway - this was unfortunately several months ago).

The "problem" with EFetch is that unlike ESearch and ESummary, there is
actually a large difference in the fields that each type of records uses,
so whereas with ESummary and ESearch it's reasonably feasible to use
the same parser for all queries involving all data types, it looks like
it's going to require writing a separate parser for each type of ESearch
record (pubmed, sequence, taxonomy, etc.).  I noticed when I looked into the
structure of the EFetch results record for sequences that there are (or at
least were) some quirks in the format that'll need to be worked around (e.g.
'double-nested' date fields).

It occurs to me that I've never gotten around to posting the EFetch/Esummary
(as well as the BLAST frontends and parser) outside of the bioinformatics.o=
rg
CVS server - I'll see if I can put those up somewhere 'normal' tomorrow.

If you haven't already run into it, the URL for the Entrez Utilities
("EUtils") information at NCBI is:

http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html

On Thursday 26 February 2004 12:30 am, Serge Gregorio wrote:
> Hi Nico!  Belcome wack!  =3D)
>
> How's life treating you?
>
> Ah querying... that shuld be EFetch though I'm not too sure what its stat=
us
> at the moment.  Paging, Sean...
>
> Regards,
>
> Serge
>
> --------- Original Message ---------
>
> DATE: Wed, 25 Feb 2004 14:40:30
> From: Nico Stuurman <nicos@itsa.ucsf.edu>
> To: biophp-dev@bioinformatics.org
>
> Cc:
> >Hello all,
> >
> >Here I am again!  I got involved in setting up a simple database that
> >includes IDs from Genbank, LocuLink, Ensemble and Swissprot.  We
> >basically want to get all the relevant IDs (given just a single one).
> >
> >I never looked at the eFetch module, would that help in querying these
> >databases?
> >
> >Anyone knows of any other php code that would help?
> >
> >If I write some code, what format should I use so that it will be more
> > widely usuable?
> >
> >Best,
> >
> >Nico
>
> Need a new email address that people can remember
> Check out the new EudoraMail at
> http://www.eudoramail.com
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