[biomart-users] How can I get datasets in a "RESTful" way on ensembl.org?

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[biomart-users] How can I get datasets in a "RESTful" way on ensembl.org?

Kenta Sato
Hi all,

I'm very new to BioMart and working on developing a client to interact with BioMart servers.

I read the docs of BioMart (http://www.biomart.org/other/biomart_0.9_0_documentation.pdf) and found a way to get datasets using REST APIs (page 77). I tried some queries below to get a list of datasets but nothing succeeded:

curl "http://www.ensembl.org/martservice/datasets?config=ENSEMBL_MART_ENSEMBL"
curl "http://www.ensembl.org/biomart/martservice/datasets?config=ENSEMBL_MART_ENSEMBL"

I guess, say, http://www.ensembl.org/biomart/martservice?type=datasets&mart=ENSEMBL_MART_ENSEMBL returns a table-like list of datasets but I want to get results in XML formats because it is more consistent. How can I access metadata on ensembl.org in a RESTful way as described in the docs?

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Re: [biomart-users] How can I get datasets in a "RESTful" way on ensembl.org?

Thomas Maurel
Hello,

I am afraid that the Ensembl marts are still using BioMart version 0.7 so the 0.9 commands from the documentation won’t work.
You can get the list of datasets using the following URL: http://www.ensembl.org/biomart/martservice?type=datasets&mart=ENSEMBL_MART_ENSEMBL
More informations at the bottom of the following page: http://www.ensembl.org/biomart/martservice
As far as I know, you cannot get a list of datasets in xml format, but you can query a mart using XML, see following page for more information: http://www.ensembl.org/info/data/biomart/biomart_restful.html

Hope this helps,
Kind Regards,
Thomas
On 4 Feb 2017, at 07:17, Kenta Sato <[hidden email]> wrote:

Hi all,

I'm very new to BioMart and working on developing a client to interact with BioMart servers.

I read the docs of BioMart (http://www.biomart.org/other/biomart_0.9_0_documentation.pdf) and found a way to get datasets using REST APIs (page 77). I tried some queries below to get a list of datasets but nothing succeeded:


I guess, say, http://www.ensembl.org/biomart/martservice?type=datasets&mart=ENSEMBL_MART_ENSEMBL returns a table-like list of datasets but I want to get results in XML formats because it is more consistent. How can I access metadata on ensembl.org in a RESTful way as described in the docs?

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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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