[BiO BB] Know how to use sort in NCBI Entrez web services ESearch?

Peter Andrews Peter.Andrews at Dartmouth.EDU
Fri May 19 09:05:47 EDT 2006


I received a prompt reply from the Entrez help desk.

Unfortunately the answer was not what i hoped for:

>Dear NCBI user:
>
>Sort parameter is not available for Entrez Gene eutilities calls.
>Currently it works for Pubmed database only.
>
>Best regards,
>
>A. Gabrielian
>NCBI Help desk

My project is to create a backend database for use in a microarray visual
analysis tool described here:
http://helix-web.stanford.edu/psb05/abstracts/p296.html

I need a backend db because of performance considerations -- Entrez's web
service and 3 second inter-call limits would be too slow for my needs.

-------------------------------------------
Peter Andrews
Software Engineer
Dartmouth Medical School
Computational Genetics
Rubin 708
(603) 653-6017
Peter.Andrews at dartmouth.edu <mailto:Peter.Andrews at dartmouth.edu>



> -----Original Message-----
> From:
> bio_bulletin_board-bounces+peter.andrews=dartmouth.edu at bioinformatics.or
> g
> [mailto:bio_bulletin_board-bounces+peter.andrews=dartmouth.edu at bioinform
> atics.org]On Behalf Of Mike Marchywka
> Sent: Wednesday, May 17, 2006 6:10 PM
> To: The general forum at Bioinformatics.Org
> Subject: RE: [BiO BB] Know how to use sort in NCBI Entrez web services
> ESearch?
>
>
> I think I have accused them of not supporting just about
> everything but they keep
> answering my questions. The eutil help desk is very responsive- I
> would suggest trying
> them and get back to us with the answer or a link to whatever you
> are talking about.
>
> I used to do all this stuff with java until a linux guy got me
> hooked on scripts.
> So far, I haven't found any text processing that isn't easier
> using the simple
> search/fetch in a perl or bash script. Do you have a link
> describing what you are using
> and what it is supposed to do?
>
> One complaint I have with perl under cygwin is that I quickly end up with
> hash tables thrashing through VM. I could probably fix this with
> c++ or java but generally
> it is just an annoyance rather than a barrier.
>
>
>
> *************************************************************************
> Mike Marchywka
> EyeWonder
> Instant Streaming, Infinite Results
>
> 1447 Peachtree Street
> 9th Floor
> Atlanta, GA 30309
>
> w.678-891-2033
> c.
> h.770-565-8101
> mmarchywka at eyewonder.com
> alt: marchywka at hotmail.com
> Instant Streaming, Intelligent results.
> *************************************************************************
>
>
>
> -----Original Message-----
> From:
> bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformatics
> .org
[mailto:bio_bulletin_board-bounces+mmarchywka=eyewonder.com at bioinformatics.o
rg]On Behalf Of Peter Andrews
Sent: WednesdayMay-17-2006 05:35 PM
To: bio_bulletin_board at bioinformatics.org
Subject: [BiO BB] Know how to use sort in NCBI Entrez web services ESearch?


I am using the Entrez web service from java. I am having difficulty finding
documentation or examples on how to control the sort order of results for
esearch queries.

Any help will be appreciated.

Thank you,

Peter
-------------------------------------------
Peter Andrews
Software Engineer
Dartmouth Medical School
Computational Genetics
Rubin 708
(603) 653-6017
Peter.Andrews at dartmouth.edu
_______________________________________________
Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bio_bulletin_board





More information about the BBB mailing list