Dr. Howsun Jow,
Yes you are right, the attributes UniProtKB/SwissProt Accession, and UniProtKB/TrEMBL Accession are not available in the latest Ensembl Plants Mart release 9. For information on why it was not included, please contact Ensembl helpdesk at [email protected]<https://lists.biomart.org/mailman/listinfo/users> Thank you, Elena From: Howsun Jow <[email protected]<mailto:[email protected]>> Date: Thu, 2 Jun 2011 19:27:53 -0400 To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [BioMart Users] Ensembl Plants biomart - Changes between version 8 and version 9 Hello, A few months ago I wrote an R script that used the Ensembl Plants biomart (version 8 and dataset Arabidopsis Thaliana) to get the corresponding uniprot identifiers for a list of refseq_dna identifiers e.g. Arabidopsis = useMart("plant_mart_9", dataset="athaliana_eg_gene") x<- getBM(attributes = c("refseq_dna","uniprot_swissprot_accession"), values=c("NM_122767"), mart=Arabidopsis, filters = c("refseq_dna")) This, however, no longer works for version 9 of the database as "uniprot_swissprot_accession" and "uniprot_sptrembl" attributes no longer exist in version 9 of the biomart. Is this a deliberate omission and if so can version 8 of the Ensembl Plant biomart be accessed elsewhere? Thank you. Dr. Howsun Jow.
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