[Biophp-dev] Can I EFetch PubMed?

S Clark biophp-dev@bioinformatics.org
Thu, 12 Feb 2004 10:00:33 -0700

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Welcome back!

EFetch is not currently done at all, but ESearch and ESummary SHOULD
work, to the extent that those two interfaces return the information you
are looking for (you could use ESearch to fetch the ID's of other
publications for an author, for example, and then conceivably use ESummary
to fetch summaries of all of them).

They haven't been extensively tested yet, but what I've used of=20
them seem to work okay.

Right now I have both school and full-time work (thankfully) again, and
I also need to make absolutely certain any BioPHP stuff I continue
to develop doesn't fall under one of those "we own anything you ever do
or think" clauses in the employment contract, but I haven't given up on

Right now what little BioPHP time I have (very little at the moment
unfortunately) is being used to try to figure out some way of determining
why Mr. Aniba can't get the BLAST frontend to return any results
under Windows.  Somewhat baffling.   I think the next thing to try is
to artificially construct a "known" database and query that I KNOW
what result should come out, so that I can test it.

However, if you'll actually have a use for EFetch-pubmed soon, I will
try to move it up on the schedule to work on it.  (I think pubmed records
might be a little simpler to parse than sequence records, the way NCBI
structures them.  Of course, I could be wrong...)

On Thursday 12 February 2004 04:31 am, Serge Gregorio wrote:
> Hello everyone!  I'm back from my little vacation!
> Hey Sean, can I use your EFetch etc. modules to get PubMed data?  Suppose=
> have an MS Access table full of titles of articles (e.g. "A superfast BLA=
> variant that uses the Clarkian algorithm.").
> Can I write a script that fetches other related information such as the
> Author(s), the citation ("Nucleic Acids Res. Vol. 10, No 2: pp. 68-76"),
> and even the author's email address ("Contact: sean@dogphilosophy.net")...
> and stores them into my SQL table?
> Just wondering...
> Regards,
> Serge
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