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: Zebrafish (GCA_000002035.3) and Rat (GCA_000001895.4)
- Upcomong genebuilds: Crab-eating macaque (GCA_000364345.1) and Atlantic salmon (GCA_000233375.3).
- Ensembl release 79 (expected March 2015):
- Updated gene set for human – GENCODE 22
- Ensembl release 80 (expected June 2015):
- Zebrafish GRCz10 genebuild with manual annotation from HAVANA
- Rat Rnor_6.0 genebuild with manual annotation from HAVANA
- 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
- New widget for tree visualisation
- Incorporate an HMM-based classification of protein sequences for the Gene Trees and Families pipelines
- Improved detection of partial / split genes
- Annotate ohnologs
- Extend the EPO multiple alignment pipeline to all vertebrates
- Prediction of ancestral protein sequences
- Continue to import new variation data from dbSNP and DGVa where available
- Improve variation annotation using data from the 1000 Genomes Project once the phase 3 data is accessioned.
- Continue to import genome wide association study phenotypes for variants from the NHGRI catalog, and variants and phenotypes from OMIM, Orphanet and OMIA.
- Import variation changes of somatic origin (from COSMIC)
- Include phenotype data for structural variants
- Work with Locus-specific databases (LSDBs) to include genotype-phenotype data from these resources
Core API and schema
- Switchable adaptors to serve data from sources other than MySQL databases
- Megabase sized feature density tracks
- New implementation for the get nearest feature method
- More efficient external reference assignment pipeline
- New REST 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
- Motif feature display
- Mobile-friendly version of website (currently in beta testing at m.ensembl.org)
- Rework of Export / Download functionality to both update codebase and improve usability
- 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.