[Biophp-dev] bibliographic database

Wed Mar 16 07:50:51 EST 2005

Hi Melanie,

Still sorry for the delay of my responses. Indeed I like when people answer my question quickly.
So I did two scripts soap-client : one for NCI and one for NCBI I didn't send it to Biophp cause it is not yet bipophp formated.
You will find my script in the nusaop mailing list. In fact I use nusoap and it is very convenient to do soap request with it.

you will find my two scripts at the following address :
for NCI  : http://sourceforge.net/mailarchive/message.php?msg_id=6906282
for NCBI : http://sourceforge.net/mailarchive/message.php?msg_id=9706347
           http://sourceforge.net/mailarchive/message.php?msg_id=9708245

Good websites about nusoap : http://www.getluky.net/archives/000155.html
I recommend the link to Scott Nichols website. This guy is a very active developer of nusoap.

Hope this helps,

Do not hesitate to let me know if you increased my code ;-)(I am sure you will).

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 : mardi 15 mars 2005 15:26
À : biophp-dev at bioinformatics.org
Objet : RE: [Biophp-dev] bibliographic database

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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