[BioMart Users] Automating mart generation

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[BioMart Users] Automating mart generation

anu jagtap
Hello,

I am using Biomart 0.7.   To create new marts currently I use the martBuilder and martRunner tool.

I am wondering if we can perform these steps through script, making this whole process transparent to the end user.

I am tryign to build and interface where user can upload a file or mention database where he has the data and then run these steps at the background and make the mart available to the user. 

Any thoughts on this, if its feasible or not?

Thanks,
Anu





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Re: [BioMart Users] Automating mart generation

Arek Kasprzyk
Hi Anu,
i guess this is feasible but i am not sure if this is going to be very helpful. Configuring a mart is an interactive process (you can try different datasets, mask a few tables etc until you are happy) and it is best done through GUI. However once it is configured, the repetitive tasks such e.g an update are probably better done programmatically. Is it what you have in mind?

a

On Sun, Dec 18, 2011 at 10:01 PM, anu jagtap <[hidden email]> wrote:
Hello,

I am using Biomart 0.7.   To create new marts currently I use the martBuilder and martRunner tool.

I am wondering if we can perform these steps through script, making this whole process transparent to the end user.

I am tryign to build and interface where user can upload a file or mention database where he has the data and then run these steps at the background and make the mart available to the user. 

Any thoughts on this, if its feasible or not?

Thanks,
Anu





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Re: [BioMart Users] Automating mart generation

anu jagtap
Arek,

I have not yet fixed on the design. I wanted to know if it would be easier to build marts programmatically. But as you pointed out,I agree its easier to try different datasets and fix the final tables through GUI. As you mentioned we can update the datasets programmatically.

Can you please guide me on what I can use for updating the marts? 

Thanks,
Anu



On Mon, Dec 19, 2011 at 4:29 PM, Arek Kasprzyk <[hidden email]> wrote:
Hi Anu,
i guess this is feasible but i am not sure if this is going to be very helpful. Configuring a mart is an interactive process (you can try different datasets, mask a few tables etc until you are happy) and it is best done through GUI. However once it is configured, the repetitive tasks such e.g an update are probably better done programmatically. Is it what you have in mind?

a

On Sun, Dec 18, 2011 at 10:01 PM, anu jagtap <[hidden email]> wrote:
Hello,

I am using Biomart 0.7.   To create new marts currently I use the martBuilder and martRunner tool.

I am wondering if we can perform these steps through script, making this whole process transparent to the end user.

I am tryign to build and interface where user can upload a file or mention database where he has the data and then run these steps at the background and make the mart available to the user. 

Any thoughts on this, if its feasible or not?

Thanks,
Anu





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Re: [BioMart Users] Automating mart generation

Joachim Baran-2
Hi!

On 2011-12-20, at 12:34 AM, anu jagtap wrote:
[…] I wanted to know if it would be easier to build marts programmatically. […]
  There has been a rudimentary approach made for building and extending Ensembl marts: http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0024716

  The source code and necessary scripts are available publicly on GitHub: https://github.com/pubmed2ensembl/MartScript

  Perhaps this helps you or even enables you to build your own customized version.

Best Wishes,
Joachim

Joachim Baran, PhD
Database Programmer/Technical Analyst, Informatics and Bio-computing

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

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