[Biophp-dev] Can I EFetch PubMed?

Serge Gregorio biophp-dev@bioinformatics.org
Sat, 14 Feb 2004 11:31:02 +0800

Hi Sean!

The reason I'm asking re: EFetching PubMed is that I've been asked to compile a comprehensive list of bioinformatics software and databases in existence today.  

I somehow managed to get my hands on an electronic database of Journal Titles from PubMed which describe these software/databases but that database does not contain other relevent information like Author(s), Citation(s), PubMed ID, Email address of Author(s), etc. but which can be found in the ABSTRACT viewable through the PubMed site.

Anyhow, it's a bit late in the day.  I've already submitted my draft to Rome (where a conference will be held that will use my output) yesterday evening.

Oh by the way, if you don't mind, I added an entry for BioPHP which acknowledges "S. Clark" as one of the authors/proponents.  Should you have any problems with that, just holler, and I'll email Rome about it.

Thanks and good luck with your studies/work.  =) 



You wrote:


--------- Original Message ---------

DATE: Thu, 12 Feb 2004 10:00:33
From: S Clark <mail-lists+biophpdev@dogphilosophy.net>
To: biophp-dev@bioinformatics.org

>Hash: SHA1
>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 
>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 I
>> have an MS Access table full of titles of articles (e.g. "A superfast BLAST
>> 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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