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: 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
- 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
- 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
- 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
- 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.