What’s coming in Ensembl release 74

Ensembl 74 is scheduled for release in December 2013. Highlights for the coming release include:

Updated gene sets
  • Human GENCODE release 19 and mouse GENCODE release M2: manual annotation from Havana will be updated and merged with Ensembl automatic annotation to produce the next gene sets for GENCODE
  • ArmadilloAssembly patches will be added and annotated for human (GRCh37.p13) and mouse (GRCm38.p2)
  • Armadillo assembly will be updated to Dasnov3.0 and include RNAseq data
Variation data imports and updates
  • The latest sequence variants from dbSNP build 138 for human, mouse and cow will be imported.
  • COSMIC version 67 will be imported and COSMIC structural variants will be updated.
  • Mouse phenotype data from IMPC (International Mouse Phenotyping Consortium) will be imported.
  • Variation data for Sheep from dbSNP build 128 and available genotyping chips will be imported.
  • Variation citations will be updated and include, for the first time, data mined by UCSC.
New species (all with RNASeq data)
  • SheepSheep (Oar_v3.1)
  • Cave fish (AstMex102)
  • Spotted gar (LepOcu1)
New web features
  • The Ensembl species list page will contain an exportable table with sortable columns
  • Secondary structure of RNAs will be on the Gene Summary page
  • The gene phenotype view will show phenotypes associated with orthologues of the current gene.

For more details on the declared intentions, please visit our Ensembl admin site. Please note that these are intentions and are not guaranteed to make it into the release.

2 thoughts on “What’s coming in Ensembl release 74

  1. Hey guys,

    I love to see the COSMIC 67 update – Can you expand on the plans for the Ensembl REST server ? I’m interested in fetching the clinical annotation and publication data from the variation database via REST. I was thinking about something like:

    For the publications:

    http://beta.rest.ensembl.org/vep/human/id/rs116035550/publication?content-type=application/json

    Also the access to the variation.clinical_significance, variation.evidence and access to the ClinVar RCV ID’s would be a plus.

    Any chance you publish a short tutorial on how to extend the current API to write your own services ?

  2. Hi Jan,

    Happy to answer any questions about the REST API and direction. At the moment we are trying to improve our batch processing with POST requests and improving our VEP integration. It’s also fair to say that variation data has progressed significantly (such as publication data and phenotypes) since our first API release last year. It has not received much attention since then. We will discuss internally what’s the best way to access these new data sets and schedule them for development.

    As for the short tutorial we have no experience of extending the API but I believe it is possible the same way you would extend a Catalyst application. This kind of documentation is on our to do list but is lower priority than quite a few other features.

    Hope this helps