Thanks, I like this proposal, Larry. You are right - it works now and
satisfies the requirement.
I amend my proposal to be:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=
DATABASE_GOES_HERE>&<IDENTIFIER_GOES_HERE
e.g.
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=596
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?
db=protein&id=NP_000624
RDF tools might not present this too prettily, but they can be fixed.
-Alan
On May 9, 2006, at 1:12 PM, Mark Wilkinson wrote:
I stand corrected :-)
Are there limits on the number of retrievals that can be done in a day
on these URLs? i.e. will my domain get blacklisted if I pull in 100K
records every hour?
Yes. Don't do that. (you don't need to for the purposes I outlined).
M
On Tue, 2006-05-09 at 10:58 -0600, Larry Hunter wrote:
On Tue, 2006-05-09 at 09:16 -0700, Mark Wilkinson wrote:
Hmmmm.... yeah, that's true... but my "gut" does a back-flip when
I am
forced to use a URI that refers to a web page, complete with
fancy NCBI
decorations and menu's
You're mistaken about that. If you don't want the decorations,
then use
the efetch URL:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?
which just brings back the raw data. Details here:
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html
Format the query to return XML or ASN.1, and there you are.
Look, I don't think these are very pretty interfaces, either, but
it is
possible to do what Alan wanted to do with no additional work.
Larry
--
--
Mark Wilkinson
Asst. Professor, Dept. of Medical Genetics
University of British Columbia
PI in Bioinformatics, iCAPTURE Centre
St. Paul's Hospital, Rm. 166, 1081 Burrard St.
Vancouver, BC, V6Z 1Y6
tel: 604 682 2344 x62129
fax: 604 806 9274
"For most of this century we have viewed communications as a conduit,
a pipe between physical locations on the planet.
What's happened now is that the conduit has become so big and
interesting
that communication has become more than a conduit,
it has become a destination in its own right..."
Paul Saffo - Director, Institute for the Future
