[BioC] Gramene now available via biomaRt

Steffen Durinck durincks at mail.nih.gov
Tue Feb 20 20:51:16 CET 2007

Dear biomaRt users,

I would like to notify you that the Gramene database has recently been 
added to the BioMart central service which makes this database available 
to us through biomaRt.
Gramene (www.gramene.org), is a resource for comparative grass genomics 
and includes Maize, Rice and also Arabidopsis.

Here is a short example using Gramene:

 > library(biomaRt)
 > listMarts()
                          name                                 version
1                      ensembl                ENSEMBL 42 GENE (SANGER)
2     compara_mart_homology_42            ENSEMBL 42 HOMOLOGY (SANGER)
3  compara_mart_pairwise_ga_42 ENSEMBL 42 PAIRWISE ALIGNMENTS (SANGER)
4                          snp          ENSEMBL 42 VARIATION  (SANGER)
5                         vega                       VEGA 21  (SANGER)
6                      uniprot                 UNIPROT PROTOTYPE (EBI)
7                          msd                     MSD PROTOTYPE (EBI)
8             wormbase_current                     WORMBASE 167 (CSHL)
9         ENSEMBL_MART_ENSEMBL                          GRAMENE (CSHL)
10                       dicty                DICTYBASE (NORTHWESTERN)

 > gramene = useMart('ENSEMBL_MART_ENSEMBL')
 > listDatasets(gramene)
                 dataset                         description version
1            osativa_snp           Rice Polymorphisms (SNPs)
2 athaliana_gene_ensembl     Arabidopsis Gene Models (TAIR6)   TAIR6
3   osativa_gene_ensembl           Rice Gene Models (TIGRv4)    TIGR
4     zmays_gene_ensembl Maize Gene Models (Gramene FGENESH)   BAC01
gramene = useMart('ENSEMBL_MART_ENSEMBL', dataset='athaliana_gene_ensembl')

 > ath1 = c("261578_at","257476_at","257524_at","259129_at")
 > result = 
filters="affy_ath1", values=ath1, mart=gramene)
 > result[9,]
    affy_ath1_id          tair_id chromosome_name start_position
9    259129_at AT3G02150.1-TAIR               3         391098
9 PTF1 (PLASTID TRANSCRIPTION FACTOR 1); transcription factor; a 
chloroplast trans-acting factor of the psbD light-responsive promoter.


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