[BioMart Users] Useful information about Ensembl release 63 mart databases

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[BioMart Users] Useful information about Ensembl release 63 mart databases

Rhoda Kinsella
The new Ensembl marts for release 63 are live on www.ensembl.org and
www.biomart.org. The following improvements and modifications have been

Ensembl Genes 63:

Updated to new Microbat assembly Myoluc2.0
Updated to new Yeast assembly EF3
Added a new Exon ID filter to the GENE->Limit to genes filter. 
Reinstated the protein allele attribute in the Variation->GERMLINE
VARIATION INFORMATION attribute section.
The PRIDE team have collaborated with us to reinstate the linking between the Ensembl Gene mart and the PRIDE mart.
The Exon ID was removed from the Transcript Event attribute section as this was misleading.
The text (bp) was removed from the GO attributes.
Gene and transcript biotype attributes have been added to the Sequence attribute section.
The HGNC symbol link has been updated.
The following external references are now stored on gene IDs: EntrezGene, WikiGene, RFAM, MIM, MIM_GENE, MIM_MORBID, miRBase, UniGene, Uniprot_genename, DBASS3, DBASS5

Ensembl Variation 63:

Updated mouse to dbSNP 132
Phenotypes in the GENERAL VARIATION FILTERS->Phenotype filter drop down have had all commas removed as this caused problems for the biomart code which resulted in incorrect filtering.
Peptide shift attribute has been reinstated in the Variation->GENE ASSOCIATED INFORMATION attribute section.
The Variation->SEQUENCE VARIATION->Variation annotation attribute section has been renamed Phenotype annotation
Variation ID attribute has been renamed Variation Name

Ensembl Regulation 63:

"Is projected" attribute added to the Regulatory features.
Annotated features have now been renamed to Regulatory Evidence
Useful text information on how to use the filters and attributes for this mart has been added to the top of the filter panel and the top of the attribute panel on the interface. 

Vega 43:

Human and Danio manual annotation has been updated to represent the annotation presented in Vega release 43. 


Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus, 
Cambridge CB10 1SD,

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