Question: biomart xml queries: where do you specify the genome build (or ensembl version) you want to use?
1
gravatar for Pablo Marin-Garcia
4.6 years ago by
Spain
Pablo Marin-Garcia1.8k wrote:

I have a biomart xml query and I am going to obtain the data with curl and the RESTfull de biomart. 

In the dataset it is defined the specie and ensembl but not the version of ensembl to use.

​<?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 = "hgnc_symbol" value = "LDLR"/>
    <Attribute name = "external_gene_db" />
    <Attribute name = "ensembl_gene_id" />
    <Attribute name = "chromosome_name" />
    <Attribute name = "start_position" />
    <Attribute name = "end_position" />
    <Attribute name = "strand" />
    <Attribute name = "ensembl_transcript_id" />
    <Attribute name = "ensembl_exon_id" />
    <Attribute name = "rank" />
    <Attribute name = "exon_chrom_start" />
    <Attribute name = "exon_chrom_end" />
    <Attribute name = "genomic_coding_start" />
    <Attribute name = "genomic_coding_end" />
</Dataset>
</Query>

question: where I specify the build?

biomart ensembl • 2.0k views
ADD COMMENTlink modified 4.6 years ago by Pierre Lindenbaum119k • written 4.6 years ago by Pablo Marin-Garcia1.8k
2
gravatar for Pierre Lindenbaum
4.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

I think you have to select the correct host for your data: http://grch37.ensembl.org/biomart/martview

 

 

ADD COMMENTlink written 4.6 years ago by Pierre Lindenbaum119k

Thanks Pierre, I have just seen that in ensembl-dev mailing list there was a similar question this week but using the biomart perl API and the answer was the same. Thanks.

ADD REPLYlink written 4.6 years ago by Pablo Marin-Garcia1.8k
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