[Biophp-dev] bibliographic database

[mel list_php]

Sorry my mistake, the ncbi tool you suggested works fine, it's because I was 
using the sequence related publication id from uniprot to find related 
publications that it was giving only that kind of answer.

So if I can manage to find a few interesting publications for each of my 
targets (argh, 500...) I should be able to retrieve the files using elink 
and then to parse them to insert the information into mysql.
And maybe try their soap implementation as well!

Thank you very much.

Melanie



>From: "mel list_php" <list_php at hotmail.co.uk>
>Reply-To: Bioinformatics for PHP <biophp-dev at bioinformatics.org>
>To: biophp-dev at bioinformatics.org
>Subject: RE: [Biophp-dev] bibliographic database
>Date: Tue, 15 Mar 2005 14:26:06 +0000
>
>Hi,
>
>Thanks for the answer!!
>I tried the ncbi tools for a previous project to retrieve the publications 
>id, the problem is that it is only sequence-related publications and we 
>would like to retrieve more the one regarding expression, purification....
>I used http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html 
>(ELink)
>
>I tried Uniprot but same things they only provide sequence-related 
>publications.
>
>I will have a look at the Cabio project, I didn't know it.(seems huge, I'm 
>a bit lost!!)
>I'm interested in your Soap client, I found a pear package about soap, is 
>it related? Is it working with "old" (4.3.2) php? I was trying to find 
>help/doc for soap/php and perl/php( I saw a pecl extension for that), 
>because openBQS also uses soap, and I was playing a bit with bioperl and 
>wondering if there is an other way to use it than with system calls.
>Anyway I would like to see how you implemented yours it if you don't mind.
>
>About openBQS I met the guy who implemented it and he told me that he 
>hasn't been updating the website for a while. He is leaving EBI this year, 
>so it won't be maintained anymore. In addition it covers medline and not 
>pubmed.
>
>Actually I was hoping to find a tool like the one from the NCBI but 
>covering a wider range of publications.
>
>
>As you can see I have a lot of current questions and several things to try, 
>but I'll let you know if I manage to have something working....:-)
>
>Thanks a lot,
>Melanie
>
>
>
>
>
>>From: <Frederic.Fleche at sanofi-aventis.com>
>>Reply-To: Bioinformatics for PHP <biophp-dev at bioinformatics.org>
>>To: <biophp-dev at bioinformatics.org>
>>Subject: RE: [Biophp-dev] bibliographic database
>>Date: Tue, 15 Mar 2005 14:28:23 +0100
>>
>>Hi Mélanie,
>>
>>
>>First, sorry for the delay of the reply.
>>
>>I think you should also have a look at the ENTREZ GENE 
>>(http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene):
>>In the download section you will wertainly find information to do the 
>>following actions.
>>  - For each gene you will get the isoforms.
>>  - For each gene you will associate all the synonyms.
>>  - For each gene you will associate some interesting pubmid.
>>......
>>
>>You should also have a look at Cabio project at NCI 
>>(http://cabio.nci.nih.gov/) :
>>You will certainly find informations concerning gene expression.
>>If you need a php script for SOAP client service to Cabio do not hesitate 
>>to ask, I have one in my computer.
>>
>>Concerning openBQS I never use it. But you should check if is regularly 
>>updated.
>>
>>
>>Hope this helps a little.
>>
>>If more questions do not hesitate to ask.
>>
>>Fred
>>
>>
>>-----Message d'origine-----
>>De : biophp-dev-bounces+frederic.fleche=aventis.com at bioinformatics.org
>>[mailto:biophp-dev-bounces+frederic.fleche=aventis.com at bioinformatics.or
>>g]De la part de mel list_php
>>Envoyé : mercredi 9 mars 2005 11:20
>>À : biophp-dev at bioinformatics.org
>>Objet : [Biophp-dev] bibliographic database
>>
>>
>>Hi,
>>
>>I'm working on a database following experimental results on targets.
>>I'd like to include bibliographic information regarding these targets, if
>>possible classified by experimental step (sequence/expression/structure 
>>for
>>example).
>>
>>I was wondering if somebody here already made that kind of thing and would
>>have any suggestion on how to start?
>>I was thinking about using openBQS (http://industry.ebi.ac.uk/openBQS/) 
>>but
>>this is more a general query page, my ideal goal is to have something like 
>>a
>>page presenting the information on my targets at each step and next to it 
>>an
>>hyperlink "relevant publications".
>>My second idea was to retrieve synonyms of my targets names and using that
>>querying automatically SRS, retrieving pmid/title for each target and
>>storing that in a mysql table.
>>
>>As you see I'm in early stage of reflexion, so any idea wellcome!!
>>
>>Melanie
>>
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