[BioMart Users] Biomart question

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[BioMart Users] Biomart question

Drake Evans
My name is Andrew Evans and I am working in a lab at the Vanderbilt University Medical Center.  We are trying to install and use Biomart software to analyze gene sequences.  I'm having a little difficulty with understanding biomart.  Hoping that you can answer some of my questions and point me in the right direction. 

I am trying to use the Perl API to generate queries for Biomart databases.  I do not want to query my own data but the data of databases already using biomart (Ensembl etc.).  So my real questions are as follows:
- Do I need to have biomart-perl API installed on my computer in order to query other biomart databases? 
- How do I use the perl API to query biomart? 

I have been able to successfully query biomart using the web based martview at biomart.org but I would like to streamline the process using the perl API.  I can generate the Perl script using the Perl button but how do I activate and run the script query?

Any help would be greatly appreciated.

Andrew Evans
 

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Re: [BioMart Users] Biomart question

Joachim Baran-2
Hi!

On 3 February 2011 13:37, Drake Evans <[hidden email]> wrote:
> - Do I need to have biomart-perl API installed on my computer in order to
> query other biomart databases?
  Yes, because you will need to include some BioMart modules in your
Perl script that come with the API.

> - How do I use the perl API to query biomart?
> I can generate the Perl script using the Perl button but how do I
> activate and run the script query?
  Using the generated Perl scripts that are created by the "Perl
button" is a step in the right direction. You then only need to
execute the script. Lets say your script is called "martquery.pl",
then you can run it via the command "perl martquery.pl" on any
operating system.

Joachim
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Re: [BioMart Users] Biomart question

Syed Haider
Drake,

and that you dont have to use Perl API to get the data from BioMart
central portal. Alternatively, you can retrieve the same data over
webservices (XML button on MartView) and just send this XML to BioMart
Central portal. See section "(a) Querying BioMart " on this page:

http://www.biomart.org/martservice.html

HTH,
Syed

On 03/02/2011 19:01, Joachim Baran wrote:

> Hi!
>
> On 3 February 2011 13:37, Drake Evans<[hidden email]>  wrote:
>> - Do I need to have biomart-perl API installed on my computer in order to
>> query other biomart databases?
>    Yes, because you will need to include some BioMart modules in your
> Perl script that come with the API.
>
>> - How do I use the perl API to query biomart?
>> I can generate the Perl script using the Perl button but how do I
>> activate and run the script query?
>    Using the generated Perl scripts that are created by the "Perl
> button" is a step in the right direction. You then only need to
> execute the script. Lets say your script is called "martquery.pl",
> then you can run it via the command "perl martquery.pl" on any
> operating system.
>
> Joachim
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
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