Future Plans

The following updates are planned for upcoming releases of Ensembl.

Please note that we have no fixed timeline for most of these items

Gene annotation

  • Genebuilds in progress: Prairie vole (GCA_000317375.1), mouse lemur (GCA_000165445.2)
  • Upcoming genebuilds: Crab-eating macaque (GCA_000364345.1) and Atlantic salmon (GCA_000233375.3)
  • Please note: We are in the process of moving our gene annotation methods into the eHive system. We’ll write a blog post about this in 2016
  • Ensembl release 83 (expected December 2015):
    • Updated gene set for human – GENCODE 24
    • Updated gene set for mouse – GENCODE M8
    • Updated gene set for rat
    • Updated RefSeq imports for human and mouse: RefSeq annotation will be tagged when the RefSeq mRNA or protein does not match the sequence that is transcribed or translated from the reference genome
  • Ensembl release 84 (expected April 2016)
    • Updated gene set for mouse – GENCODE M9
    • Updated gene set for zebrafish
  • Ensembl release 85 (expected June/July 2016)
    • Updated gene set for human – GENCODE 25
    • Updated gene set for mouse – GENCODE M10
    • Updated gene set for rat
  • Regular updates
    • Minor assembly updates for human and mouse:  incorporation of new alternate sequence provided by the GRC, with basic gene annotation. The Primary Assembly coordinates remain unchanged when patches are added.
    • Planned updates to human, mouse, rat and zebrafish gene sets:  incorporation of HAVANA manual annotation. For mouse, the gene set is updated every release. For human and zebrafish, the gene sets are updated every second release.
    • CCDS: all CCDS models are included in the human (GENCODE) and mouse gene sets

Comparative Genomics

  • Incorporate an HMM-based classification of protein sequences for the Gene Trees and Families pipelines
  • Improved detection of partial / split genes
  • Annotate the orthologs with support / confidence values

Variation updates

  • Continue to import new variation data from dbSNP and DGVa where available.
  • Improve variation annotation using publicly available variant, phenotype and disease data.
  • Continue to import genome wide association study phenotypes for variants from the EBI-NHGRI Catalog, and variants and phenotypes from OMIM, Orphanet, OMIA and other sources.
  • Include phenotype data for structural variants.

Core API and schema

  • Switchable adaptors to serve data from sources other than MySQL databases
  • Megabase sized feature density tracks
  • Support for cigar and vulgar alignments
  • More efficient external reference assignment pipeline
  • FTP web tool for customisable file download
  • Transcript archive to retrieve sequence for retired features
  • TrackHub registry server

Regulation

  • Nearest gene/feature tool
  • Many more cell types (Roadmap Epigenomics, Blueprint, HipSci…)
  • Attach regulatory elements to genes via eQTLs, chromatin conformation data, etc.
  • Development of DNA methylation tracks i.e. high level summaries and differentially and variably methylated regions
  • Integrating RNA-seq data with regulatory element annotation
  • Web display developments:
    • Further refinements of wiggle track config/display including track highlighting
    • MotifFeature view incorporating variation consequences
  • Incorporate DNase1 footprinting and sequence conservation in to TFBS identification
  • Incorporating ChIP-seq data from further species for possible
    additional regulatory builds e.g. Schmidt et al (PMID: 20378774)
  • Investigate regulatory feature orthologs and/or comparative views

New web features

  • Complete the rework of Export / Download functionality
  • New view to display motif features
  • Redesign TrackHub attachment user interface and add support for the upcoming TrackHub registry
  • Redesign Protein Summary View
  • Extend Genoverse to support TrackHubs and uploaded user data
  • Replace Jalview with Wasabi
  • Review variation views to cope with even more data

Biomart

  • Investigate ways to improve scalability and retrievability of the data from the various marts.
  • Continue to incorporate new filters and attributes to the marts as new data is added to the Ensembl schemas.