Hello Bioc users, I am having trouble in finding attribute "mirbase" in the biomaRt latest ensembl version. I can find it in the ensembl_mart_51 version but not in the latest version (ENSEMBL GENES 60). Is there any way to add that attribute so that the latest miRNA coordinates can be retrieved. Thank you, Neel Here is my session info. R version 2.11.1 (2010-05-31) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 [R.app GUI 1.34 (5589) i386-apple-darwin9.8.0] biomaRt 2.4.0 > library("biomaRt") > listMarts() biomart version 1 ensembl ENSEMBL GENES 60 (SANGER UK) 2 snp ENSEMBL VARIATION 60 (SANGER UK) 3 functional_genomics ENSEMBL FUNCTIONAL GENOMICS 60 (SANGER UK) 4 vega VEGA 40 (SANGER UK) > listMarts(archive=TRUE) biomart version 1 ensembl_mart_51 Ensembl 51 2 snp_mart_51 SNP 51 3 vega_mart_51 Vega 32 4 ensembl_mart_50 Ensembl 50 5 snp_mart_50 SNP 50 6 vega_mart_50 Vega 32 7 ensembl_mart_49 ENSEMBL GENES 49 (SANGER) > ensembl=useDataset("drerio_gene_ensembl", mart= ensembl) Checking attributes ... ok Checking filters ... ok > filters=listFilters(ensembl) > filters name description 24 with_mirbase with miRBase ID(s) 25 with_rfamR with Rfam ID(s) > attributes = listAttributes(ensembl) > attributes # I DO NOT FIND mirbase in this list. > miRNA = getBM(c("mirbase","ensembl_gene_id","start_position","chromo some_name"), filters=c("chromosome_name","with_mirbase"), values= list(13, TRUE), mart = ensembl) Error in getBM(c("mirbase", "ensembl_gene_id", "start_position", "chromosome_name"), : Invalid attribute(s): mirbase # When I change the database to ensembl_mart_51, mirbase appears. > ensembl = useMart("ensembl_mart_51", dataset = "drerio_gene_ensembl",archive=TRUE) Checking attributes ... ok Checking filters ... ok > listAttributes(ensembl) name description 34 mirbase miRBase Neel Aluru Postdoctoral Scholar Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543 USA 508-289-3607

Hi Neel This omission has also been reported by another Ensembl user and we will reinstate this attribute in the release 61 marts in January. Apologies for any inconvenience caused. Regards Rhoda On 14 Dec 2010, at 23:20, Neel Aluru wrote: > Hello Bioc users, > > I am having trouble in finding attribute "mirbase" in the biomaRt > latest ensembl version. I can find it in the ensembl_mart_51 version > but not in the latest version (ENSEMBL GENES 60). Is there any way > to add that attribute so that the latest miRNA coordinates can be > retrieved. > > Thank you, > > Neel > > > Here is my session info. > > R version 2.11.1 (2010-05-31) > Copyright (C) 2010 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > [R.app GUI 1.34 (5589) i386-apple-darwin9.8.0] > biomaRt 2.4.0 > >> library("biomaRt") >> listMarts() > > biomart version > 1 ensembl ENSEMBL > GENES 60 (SANGER UK) > 2 snp ENSEMBL > VARIATION 60 (SANGER UK) > 3 functional_genomics ENSEMBL FUNCTIONAL > GENOMICS 60 (SANGER UK) > 4 vega > VEGA 40 (SANGER UK) > >> listMarts(archive=TRUE) > biomart version > 1 ensembl_mart_51 Ensembl 51 > 2 snp_mart_51 SNP 51 > 3 vega_mart_51 Vega 32 > 4 ensembl_mart_50 Ensembl 50 > 5 snp_mart_50 SNP 50 > 6 vega_mart_50 Vega 32 > 7 ensembl_mart_49 ENSEMBL GENES 49 (SANGER) > >> ensembl=useDataset("drerio_gene_ensembl", mart= ensembl) > Checking attributes ... ok > Checking filters ... ok > >> filters=listFilters(ensembl) >> filters > > name description > 24 > with_mirbase with miRBase ID(s) > 25 > with_rfamR with Rfam ID(s) >> attributes = listAttributes(ensembl) >> attributes > # I DO NOT FIND mirbase in this list. >> miRNA = >> getBM >> (c("mirbase","ensembl_gene_id","start_position","chromosome_name"), >> filters=c("chromosome_name","with_mirbase"), values= list(13, >> TRUE), mart = ensembl) > Error in getBM(c("mirbase", "ensembl_gene_id", "start_position", > "chromosome_name"), : > Invalid attribute(s): mirbase > > # When I change the database to ensembl_mart_51, mirbase appears. >> ensembl = useMart("ensembl_mart_51", dataset = >> "drerio_gene_ensembl",archive=TRUE) > Checking attributes ... ok > Checking filters ... ok >> listAttributes(ensembl) > > name description > > 34 > mirbase miRBase > > > > > > > > Neel Aluru > Postdoctoral Scholar > Biology Department > Woods Hole Oceanographic Institution > Woods Hole, MA 02543 > USA > 508-289-3607 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.