The following updates are planned for upcoming releases of Ensembl.
Please note that we have no fixed timeline for most of these items
- Genebuilds in progress:
- Upcoming genebuilds:
- 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 2017
- Ensembl release 87 (expected December 2016):
- New lincRNA annotation for Nile tilapia, spotted gar, opossum and platypus
- Updated gene sets for mouse (GENCODE M12), chicken and zebrafish
- New RNA-seq models for zebrafish, for 18 stages of embryonic development
- Ensembl release 88 (expected March 2017)
- Updates to human and mouse GENCODE gene sets
- Ensembl release 89 (expected May 2017)
- Pig Sscrofa11
- Several new rodent assemblies
- 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.
- Incorporate an HMM-based classification of protein sequences for the Protein-Trees pipeline
- Improved detection of partial / split genes
- 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
- 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
- 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.