Question: Ensembl mart release 53: Useful information for BiomaRt users
9.0 years ago by
Rhoda Kinsella • 660
Rhoda Kinsella • 660 wrote:
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.
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