This is a test version of Biostars. For the public version, visit https://www.biostars.org.
use another database (UCSC) with biomaRt

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 :-)

r
• 3,376 views • link
updated by WouterDeCoster WouterDeCoster • written by iddir.yasmine • iddir.yasmine

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

• 0 views • link
written by Denise CS Denise CS

1 answer

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

• 0 views • link
written by WouterDeCoster WouterDeCoster

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>
• 0 views • link
updated by GenoMax GenoMax • written by Denise CS Denise CS

Log in to answer this question.

More posts like this