Question: use another database (UCSC) with biomaRt
0
gravatar for iddir.yasmine
3.8 years ago by
iddir.yasmine0 wrote:

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 • 1.6k views
ADD COMMENTlink modified 3.8 years ago by WouterDeCoster44k • written 3.8 years ago by iddir.yasmine0

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

ADD REPLYlink written 3.8 years ago by genomax91k

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

ADD REPLYlink written 3.8 years ago by Denise CS5.1k
0
gravatar for WouterDeCoster
3.8 years ago by
Belgium
WouterDeCoster44k wrote:

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

ADD COMMENTlink written 3.8 years ago by WouterDeCoster44k
2

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>
ADD REPLYlink modified 3.8 years ago by genomax91k • written 3.8 years ago by Denise CS5.1k
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