[BioC] Ensembl mart release 53: Useful information for BiomaRt users

[Rhoda Kinsella]

Hi,
The new Ensembl marts for release 53 are now live on www.ensembl.org.  
The following improvements and modifications have been made:

Mart Builds (all species)

Ensembl mart 53:

     * Modifications have been made to the registry so that BiomaRt  
users can now connect to host="www.ensembl.org/biomart/martservice"
     * Addition of three new species (zebra finch, anole lizard and  
sloth)
     * Updated the assembly names for Dasypus novemcinctus (dasNov2)  
and Loxodonta africana (loxAfr2)
     * Corrected biotype internal naming error (structure_biotype now  
points to gene_biotype), reported by BioConductor users
     * Corrected Refseq DNA predicted internal naming error  
(refseq_DNA_predicted attribute is now refseq_dna_predicted), reported  
by BioConductor users
     * Removed the consequence type (variation feature) attribute
     * Added Superfamily protein domain attribute
     * Added an RGD symbol filter and attribute

Vega mart 34:

     * Corrected biotype internal naming error (structure_biotype now  
points to gene_biotype), reported by BioConductor users

Ensembl variation mart 53:

     * Removed the consequence type (variation feature) attribute
     * Added new "with phenotype data" filter for the variation  
annotation information
     * Added new variation annotation attributes:
          1. Associated gene
          2. Associated variant risk allele
          3. Risk allele frequency in controls
          4. p value
          5. Associated variation names
          6. Study information

Addition of Reactome, WormBase and PRIDE databases.
Addition of martsoap (see http://www.biomart.org/martservice.html for  
more information)

Regards,
Rhoda


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