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

  • Please note: In January 2017, we have moved to a new system of gene annotation which we call ‘clade annotation’. This means that we plan to annotate a batch of closely related assemblies at the same time, and then move on to the next batch.
  • Regular updates
    • Minor assembly updates for human and mouse:  incorporation of new alternate sequence provided by the GRC, with basic gene annotation.
    • 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.

Comparative Genomics

  • Improved detection of partial / split genes

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


  • Integrate more cell types (Roadmap Epigenomics, HipSci…)
  • Integrate more TFBS PWMs (e.g. SELEX, UniProbe…)
  • 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
  • Annotate epigenomic markers of phenotype or differentiation
  • Web display developments:
    • Further refinements of wiggle track config/display including track highlighting
    • MotifFeature view incorporating variation consequences
  • Incorporating ChIP-seq data from further species for possible additional regulatory builds.
  • Investigate regulatory feature orthologs and/or comparative views

New web features

  • Complete the rework of Export / Download functionality
  • Redesign Protein Summary View
  • Extend Genoverse to support TrackHubs and uploaded user data


  • 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.