ERROR When Using Ensembl Plants Biomart Wget API
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7 weeks ago
Dora ▴ 10

I am going to use wget to download data from ensembl plants biomart

By following the instruction here: https://plants.ensembl.org/info/data/biomart/biomart_restful.html#biomartperlapi

I use this command:

wget -O result.txt 'http://www.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query virtualSchemaName = "plants_mart" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" ><Dataset name = "athaliana_eg_gene" interface = "default" ><Attribute name = "ensembl_gene_id" /><Attribute name = "external_gene_name" /><Attribute name = "chromosome_name" /><Attribute name = "go_id" /><Attribute name = "go_linkage_type" /><Attribute name = "entrezgene_id" /></Dataset></Query>'

I do get the result.txt, but here is what inside:

Query ERROR: caught BioMart::Exception::Usage: WITHIN Virtual Schema : plants_mart, Dataset athaliana_eg_gene NOT FOUND

here is my xml file

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

    <Dataset name = "athaliana_eg_gene" interface = "default" >
        <Attribute name = "ensembl_gene_id" />
        <Attribute name = "external_gene_name" />
        <Attribute name = "chromosome_name" />
        <Attribute name = "go_id" />
        <Attribute name = "go_linkage_type" />
        <Attribute name = "entrezgene_id" />
    </Dataset>
</Query>

I am so confused because I got this xml file as the image shows

enseml plant biomart

Does anyone could tell me what's wrong?

biomart plant ensembl • 391 views
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Entering edit mode
7 weeks ago
Ben_Ensembl ★ 2.4k

Hi Dora,

For plant species such as A. thalina, you should use the http://plants.ensembl.org/biomart service, so the start of your wget query should look like this:

wget -O result.txt 'http://plants.ensembl.org/biomart/martservice?query=

I hope this helps

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A couple of hours back using plants.ensembl.org was generating a 504 error but it seems to be working now.

 wget -O result.txt 'http://plants.ensembl.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE Query><Query  virtualSchemaName = "plants_mart" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" ><Dataset name = "athaliana_eg_gene" interface = "default" ><Attribute name = "ensembl_gene_id" /><Attribute name = "external_gene_name" /><Attribute name = "chromosome_name" /></Dataset></Query>'
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Thank you very much, that works perfectly :) ! Maybe someone needs to use a plant dataset as an example (instead of human dataset ) in the https://plants.ensembl.org/info/data/biomart/biomart_restful.html#biomartperlapi

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