Dear all,

We are pleased to announce that the new Ensembl marts for release 80 are now live on www.ensembl.org.

If you are using biomaRt, you can change your host to access our most recent data (With R 2.2 and Bioconductor version 3.1)

ensembl_mart_80 <- useEnsembl(biomart=“ensembl")

• Ensembl Genes 80
  • Added Protein domains start and end attributes (protein-based coordinate)
  • Renamed "ENCODE region" filter to "ENCODE Pilot Regions", added a link to the publication (http://www.genome.gov/26525202) 
  •  Renamed the following Uniprot filters and attributes
    • "UniProt/Swissprot ID" to "UniProt/Swissprot Accession"
    • "UniProt/TrEMBL ID" to "UniProt/Swissprot Accession"
    • "UniProt Genename ID" to "UniProt Gene Name"
    • "Uniprot Genename Transcript Name" to "Uniprot Transcript Name"
  • Updated rat (Rnor_6.0) and zebrafish (GRCz10) assemblies
  • New Phenotype source filter in the "Phenotype" filter section
  • Renamed "APPRIS principal isoform annotation" filter and attributes to "APPRIS annotation"
• Ensembl Variation 80
  • New Phenotype source filter in the "General variation" filter section
  • Updated rat (Rnor_6.0) and zebrafish (GRCz10) assemblies
• Ensembl Regulation 80
  • Renamed "ENCODE region" filter to "ENCODE Pilot Regions", added a link to the publication (http://www.genome.gov/26525202) 
• Vega 60
  • Updated rat (Rnor_6.0) and zebrafish (GRCz10) assemblies
  • Added Protein domains start and end attributes (protein-based coordinate)

A complete list of the changes in release 80 can be found at http://www.ensembl.org/info/website/news.html

Best Regards,

Thomas 

We have added the GTF files from Ensembl's release-80 to Bioconductor (Bioc version 3.1 and 3.2) . You can access  them : 

> library(AnnotationHub)
> ah = AnnotationHub()
> gtf = query(ah , c("gtf", "80", "Ensembl", "rattus"))  

> gtf  # access  the record information
AnnotationHub with 1 record
# snapshotDate(): 2015-05-22 
# names(): AH47095
# $dataprovider: Ensembl
# $species: Rattus norvegicus
# $rdataclass: GRanges
# $title: Rattus_norvegicus.Rnor_6.0.80.gtf
# $description: Gene Annotation for Rattus norvegicus
# $taxonomyid: 10116
# $genome: Rnor_6.0
# $sourcetype: GTF
# $sourceurl: ftp://ftp.ensembl.org/pub/release-80/gtf/rattus_norvegicus/Rat...
# $sourcelastmodifieddate: 2015-05-01
# $sourcesize: 11465361
# $tags: GTF, ensembl, Gene, Transcript, Annotation 
# retrieve record with 'object[["AH47095"]]' 
> gr <- gtf[[1]]   # download the file as an GRanges object. 
require(“GenomicRanges”)
retrieving 1 resource
  |======================================================================| 100%

Optionally, create a transcript data base

> txdb <- GenomicFeatures::makeTxDbFromGRanges(gr)
> txdb
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Genome: Rnor_6.0
# transcript_nrow: 39595
# exon_nrow: 243102
# cds_nrow: 207962
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2015-05-23 08:58:20 -0700 (Sat, 23 May 2015)
# GenomicFeatures version at creation time: 1.21.5
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1

Sonali.