use another database (UCSC) with biomaRt

Question

[iddir.yasmine]

Hello every body :-)

I need your help :'( I'm trying to use biomaRt with another database then Ensembl (UCSC), but I failed. Did some one sucess to use biomaRt with another database? is it possible, or only Ensemble is available?

Thanks for your answers :-)

[GenoMax]

While not the same thing, you can access data from UCSC database using their public MySQL server.

[Denise CS]

Can you give us some specifics please? Which data you are interested in?

Answer 1

[WouterDeCoster]

BiomaRt/Biomart is from Ensembl, so it makes sense that it's "just" for Ensembl data as well.

[Denise CS]

There is biomart.org for other databases (not only Ensembl and Ensembl Genomes) e.g. COSMIC, InterPro, VEGA, WormBase Parasite plus many others...The functionality within BioMart can change slightly from one database to the other and WormBase Parasite is a good example for that. The Ensembl BioMart will have other datasets such as UCSC genes too which can be used as filters or attributes e.g. (in xml):

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >

    <Dataset name = "hsapiens_gene_ensembl" interface = "default" >
        <Filter name = "with_ucsc" excluded = "0"/>
        <Filter name = "chromosome_name" value = "22"/>
        <Attribute name = "ensembl_gene_id" />
        <Attribute name = "ensembl_transcript_id" />
        <Attribute name = "ucsc" />
    </Dataset>
</Query>