How can I download data from plants.ensembl.org using wget in biomart?
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Entering edit mode
3.4 years ago
utsafar ▴ 80

using commands like this:

wget -O result.txt 'http://www.ensembl.org/biomart/martservice?query=<Query virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6"><Dataset name="hsapiens_gene_ensembl" interface="default"><Filter name="ensembl_gene_id" value="ENSG00000139618"/><Attribute name="ensembl_gene_id"/><Attribute name="ensembl_transcript_id"/><Attribute name="hgnc_symbol"/><Attribute name="uniprotswissprot"/></Dataset></Query>'

I can easily download data from ensembl.org, but when I try to use the same commands for plants.ensembl.org I just go to http://plants.ensembl.org/index.html.

How can I solve my problem?

ensembl wget biomart • 2.2k views
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Entering edit mode

Mike and Astrid, thanks to your helps I found my mistakes:

This is my wrong command:

wget -O result.txt 'http://www.plants.ensembl.org/biomart/martview/martservice?query=<Query virtualSchemaName="plants_mart" formatter="CSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6"><Dataset name="atauschii_eg_gene" interface="default"><Attribute name="ensembl_peptide_id"/></Dataset></Query>'

First mistake: I forgot to remove 'www.' from my url

2nd mistake: '/martview' will be removed

So this is the example correct command to get aegilops tauschii gene IDs from plants.ensembl.org:

wget -O result.txt 'http://plants.ensembl.org/biomart/martservice?query=<Query virtualSchemaName="plants_mart" formatter="CSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6"><Dataset name="atauschii_eg_gene" interface="default"><Attribute name="ensembl_gene_id"/></Dataset></Query>'
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3
Entering edit mode
3.4 years ago
Mike Smith ★ 1.9k

This is a pretty unusual way to query Ensembl, typically people use the Perl API or biomaRt R-package, which should make constructing queries a lot easier, but if this suits your workflow then great.

I don't know how this is different from what you're trying, but this works for me:

wget -O result.txt 'http://plants.ensembl.org/biomart/martservice?query=<Query virtualSchemaName="plants_mart" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6">     
<Dataset name="athaliana_eg_gene" interface="default">
    <Filter name="ensembl_gene_id" value="AT1G01010"/>
    <Attribute name="ensembl_gene_id"/>
    <Attribute name="ensembl_transcript_id"/>
    <Attribute name="external_gene_name"/>
</Dataset>
</Query>'

You can paste the URL into a browser to check its working, and here's the contents of the output file:

% cat result.txt 
AT1G01010   AT1G01010.1 NAC001
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3
Entering edit mode
3.4 years ago

You could also look into the Ensembl Genomes REST API as an alternative: http://rest.ensemblgenomes.org

E.g. this endpoint: http://rest.ensemblgenomes.org/documentation/info/lookup rest.ensemblgenomes.org/lookup/id/AT1G01010?content-type=application/json;expand=1

The endpoint documentation includes wget examples.

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