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News: Ensembl GRCh37 release 79 data update
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gravatar for Thomas Maurel
2.6 years ago by
Thomas Maurel700
United Kingdom
Thomas Maurel700 wrote:

We are pleased to announce that the first Ensembl data update for human GRCh37 (e!79) has been released on http://grch37.ensembl.org/index.html.

We've made the following BioMart changes: 

  • Ensembl Genes 79
    • Split up the id list and id list limit filters to separate external references from probes filters
      • Renamed "Limit to genes..." to "Limit to genes (external references)..." and "Limit to genes (microarray probes/probesets)..."

      • Renamed "ID list limit  [Max 500 advised]" to "Input external references ID list [Max 500 advised]" and "Input microarray probes/probesets ID list [Max 500 advised]"

    • Separated the Variation page into Variation (Germline) and Variation (Somatic)
      • Renamed "chromosome_location" internal name to "chromosome_start" and added a new attribute called "chromosome_end" in the Variation (Germline) page
      • Renamed "somatic_chromosome_location" internal name to "somatic_chromosome_start" and added a new attribute called "somatic_chromosome_end" in the Variation (Somatic) page
      • Renamed "Chromosome Location (bp)" attribute to "Chromosome position start (bp)" in both Variation (Germline) and Variation (Somatic) pages
    • Renamed "external_transcript_id" attribute internal name to "external_transcript_name"
    • Added "Transcript length" in the Features, Structures and Sequences pages of the attribute section
    • Added "Transcription start site" in the Features, Structures and Sequences pages of the attribute section
    • Added "GENCODE basic annotation" to the attribute section
  • Ensembl Variation 79
    • Removed the "_20137" from all the variation_citation attributes internal names
    • Removed all the "_20126" from all the regulatory feature attributes internal names and prefixed all the internal names with "reg_"
    • Removed all the "_20125"  from all the motif feature attributes internal names and prefixed all the internal names with "motif_" 
    • Added clinical significance filter and attribute to the structural variation template
    • Added copy number attribute to the structural variation template
  • Ensembl Regulation 79
    • Brand new Regulation mart, faster, easier to use and packed with new features. Feature set has been split up into 6 sections.
    • Added Band Start and End filter
    • Added Marker Start and End filter
    • Added Encode region filter
    • Added SO name and accessions for the 6 Regulation sections
    • Added EFO Term accessions for Regulatory evidence, Regulatory features and Regulatory segments.
    • Added  "Has evidence" data to the Regulatory features section
    • Added Strand and "Evidence" to the miRNA Target Regions section.
  • Vega 59
    • Renamed "ID list limit  [Max 500 advised]" to "Input external references ID list [Max 500 advised]"

    • Renamed "external_transcript_id" attribute internal name to "external_transcript_name"

For the full details of the release please refer to http://grch37.ensembl.org/info/website/news.html

Best Regards,

Thomas

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