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

Dear Laurent,

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

• Get the biomart host argument for the mart that you are interested in from the DATABASE column from the following page: http://www.biomart.org/community.html
• The path argument should be "/biomart/martservice" for most of the marts but If you want more information regarding a mart, you can replace "martview" in the following URL "http://www.ebi.ac.uk/uniprot/biomart/martview" by "martservice?type=registry" which will give you the following URL "http://www.ebi.ac.uk/uniprot/biomart/martservice?type=registry". This will help you find the path and mart name.

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

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