Querying individual mart instances
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@laurent-gatto-5645
Last seen 15 days ago
Belgium

Dear all,

With the prolonged downtime and uncertainty about the central biomart portal, I will need to query individual biomart instance. biomaRt package problem answers described how to do this for the main Ensemble instance, but there are many more out there. I struggled a bit to discover the details of other marts which I rely on, such as

> library("biomaRt")
> listMarts(mart = NULL, host="plants.ensembl.org", path="/biomart/martservice")
            biomart              version
1       plants_mart           Plant Mart
2 plants_variations Plant Variation Mart
> listMarts(mart = NULL, host="fungi.ensembl.org", path="/biomart/martservice")
            biomart               version
1       fungal_mart           Fungal Mart
2 fungal_variations Fungal Variation Mart
> listMarts(mart = NULL, host="metazoa.ensembl.org", path="/biomart/martservice")
             biomart                version
1       metazoa_mart           Metazoa Mart
2 metazoa_variations Metazoa Variation Mart
> listMarts(mart = NULL, host="www.ebi.ac.uk", path="/uniprot/biomart/martservice")
               biomart                  version
1              unimart         UNIPROT (EBI UK)
2 ENSEMBL_MART_ENSEMBL ENSEMBL GENES 80(EBI UK)

Is anyone aware of a way to discover these more efficiently than trial and error, or, better, if these URLs are already available somewhere in Bioconductor?

Thank you very much in advance.

Laurent

biomart • 1.2k views
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1
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Thomas Maurel ▴ 800
@thomas-maurel-5295
Last seen 16 months ago
United Kingdom

Dear Laurent,

As far as I know, the easiest way at the moment is to do the following:

If you are interested in the non vertebrate Ensembl marts, you can get a full list of the available marts on the following page: http://ensemblgenomes.org/info/access/biomart

Hope this helps,

Regards,

Thomas

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@laurent-gatto-5645
Last seen 15 days ago
Belgium

Dear all,

I have tried to test all Biomart instances systematically to infer the host and path values to be passed to biomaRt::listMarts. For example, to query the Pancreatic Expression Database:

> host <- "pancreasexpression.org"
> path <- "/biomart/martservice"
> listMarts(mart=NULL, host, path)

##            biomart                        version
## 1       Pancreas63 Pancreatic Expression Database
## 2         REACTOME             REACTOME (CSHL US)
## 3       CosmicMart             COSMIC (SANGER UK)
## 4          unimart               UNIPROT (EBI UK)
## 5 prod-intermart_1                       InterPro
## 6            pride                          PRIDE

 

Some are failing, probably because I got the wrong argument values. Feel free to update if you can correct some of the failing examples: https://github.com/lgatto/marts.

Best wishes,

Laurent

 

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