How To Set Registry File To Access A Online Db Like Cosmic Or Ensembl

Question

[Manjulapra]

Hi all, I am very new both to perl and BioMart. I am stuck with the configuration or the registry file. Can anyone help me by telling me how to set the configuration or the Registry file to point to a database like COSMIC? I am wondering about these things;

■ Is there any reading material on creating the registry file?

■ For online databases, how do we get the host address? Is it the same MartView address of the database?

■ What is the difference between MartURLLocation, MartDBLocation, RegistryDBPointer, RegistryURLPointer, RegistryDBPointer tags? How and when should we use them? Should they be in different files or can they reside in the same file?

Any help is appreciated!

Thanking in advance,

Manjula Dharmawardhana

[Joachim]

Unless you have to use the old Perl-based BioMart, I would encourage you to use the new Java-based BioMart 0.8. You can find installation instructions and the like here: http://www.biomart.org/rc6_documentation.pdf

Answer 1

[Chris Evelo]

It might be easiest to look at the provided examples:

The registry file refers to the connection parameters to the data sources (i.e., marts) you would like to include. This could be your own database (mart) or a publicly available mart. Several example registry files (*.xml) are available under the directory:

/home/gmod/software/biomart/biomart-perl/conf/

This is from http://gmod.org/wiki/BioMart_Tutorial#Setting_the_Registry where you can also find an extended tutorial.