Since release 81, Ensembl has provided the gene annotations in GFF3 files alongside the already existing GTF ones. While GTF uses its own controlled vocabulary to classify features, GFF3 takes advantage of sequence ontology. In the initial release, we attempted to map all existing Ensembl biotypes to equivalent SO terms.

This has proven unsatisfactory for several reasons:

  • not all biotypes have an equivalent SO term
  • there are too many levels of granularity, with 25 terms for genes and another 25 for transcripts
  • some SO mappings do not respect the parent-child relationship expected between gene and transcript SO terms
  • some SO mappings are inaccurate, missing or wrong
  • it is mostly redundant with the biotypes which are also provided as an attribute
  • there can be confusion when most features have identical values in the third column (the SO term) and the biotype attribute, yet a handful do not

For all these reasons, our SO term mapping has undergone a major overhaul to take advantage of the functionality sequence ontologies offer. This new mapping, which will be used from release 90 onwards, attempts to provide general biotype groupings that match the ones used on the website. As a result, all gene biotypes are mapped to one of these three groups, coding, non-coding or pseudogene. Meanwhile, transcript biotypes are mapped to one of five main groups: mRNA, pseudogenic_transcript, long non coding RNAs, short non coding RNAs and IG biotypes.

Additionally, the groupings remove some of the previous granularity that can still be explored via the biotype and the assigned terms respect the gene-transcript relationship where possible.

To see the full extent of those changes, as they will be reflected in the GFF3 files provided from release 90 onwards, please check these files on the FTP.
We hope this improvement will help our users take better advantage of the GFF3 format.

We are pleased to announce that Ensembl Genomes 36 has now been released, which includes new and updated genome assemblies and gene annotation as well as updated variation data and comparative genomics analyses. Find out more below:

  • Ensembl Bacteria includes an additional 142 genomes from release 35 together with an update to gene families.
  • Ensembl Fungi has added gene symbols for 1-to-1 orthologues from S. cerevisiae to Botrytis cinerea and includes updated PHI-base 4.3 annotations.
  • Ensembl Metazoa now has automated RNA gene annotation for 37 species (i.e. all species that have not been imported from FlyBase, VectorBase or WormBase) and alignment of Rfam 12.2 covariance models for all species. There are also updated protein features, which now includes features from new sources (CDD, MobiDB and SFLD).
  • Ensembl Protists now has new automatic ncRNA alignments across all protist species as well as updated PHI-base 4.3 annotations.
  • Ensembl Plants now includes the new genome assembly for Hordeum vulgare (barley), the biggest diploid yet sequenced, which is included in updated comparative peptide analyses for all species. There are also new ncRNA gene annotations and new plant reactome cross references across all plant species. New and updated variation data has also been included in this release for both Oryza sativa and Arabidopsis thaliana. Last, but not least, 80829 variation markers from the iSelect 90k array and 13.8 million Inter-Homoeologous Variants (IHVs) have been added to the wheat assembly, along with chloroplast and mitochondrial components (including gene annotations) imported from ENA.

Please see the release notes for full details of the updates.

Ensembl 90 is scheduled for August 2017 and it’s set to be our biggest release ever in terms of new genome annotation. Here’s what you can look forward to:

New assemblies, gene sets and annotations

  • Annotation of 15 rodent genomes, including three updates to old genomes:
    • Brazilian guinea pig
    • Chinese hamster
    • Damara mole rat
    • Degu
    • Golden Hamster
    • Guinea Pig (update)
    • Kangaroo rat (update)
    • Lesser Egyptian jerboa
    • Long-tailed chinchilla
    • Naked mole-rat – we have two different assemblies for naked mole-rat so you can keep working with your preferred genome
    • Northern American deer mouse
    • Prairie vole
    • Squirrel (update)
    • Upper Galilee mountains blind mole rat
  • Bringing in annotation of the well-used rodent cell-line, Chinese Hamster Ovary, and two mouse species, Ryukyu mouse and Shrew mouse.
  • Annotation on the latest Pig genome assembly, Sscrofa11.1
  • Updating the Human gene set to GENCODE 27.
  • Updating the Mouse gene set to GENCODE M15.
  • Adding transcript models from RNA-seq to the gene database and pri-miRNAs to the otherfeatures database in Zebrafish.

Other updates and highlights

  • Updating our human variation database with:
    • COSMIC 81 somatic variants
    • HGMD 2016.4
    • dbSNP 150
    • DGVa structural variants
    • TopMed in GRCh37
    • Phenotypes from NHGRI-EBI GWAS, OMIM, ClinVar, UniProt, Cosmic Gene Census, DDG2P, MIM Morbid and Orphanet
  • In other species we also have variation updates as follows:
    • DGVa in Cow, Dog and Mouse
    • Phenotype updates from relevant databases in Cat, Chicken, Chimpanzee, Cow, Dog, Horse, Macaque, Mouse, Pig, Rat, Sheep, Turkey and Zebrafish
  • Updating our microarray probe mappings in:
    • C.intestinalis
    • Caenorhabditis elegans
    • Chicken
    • Chimpanzee
    • Cow
    • Dog
    • Fruitfly
    • Human
    • Macaque
    • Mouse
    • Mouse 129S1/SvImJ
    • Mouse A/J
    • Mouse AKR/J
    • Mouse BALB/cJ
    • Mouse C3H/HeJ
    • Mouse C57BL/6NJ
    • Mouse CAST/EiJ
    • Mouse CBA/J
    • Mouse DBA/2J
    • Mouse FVB/NJ
    • Mouse LP/J
    • Mouse NOD/ShiLtJ
    • Mouse NZO/HlLtJ
    • Mouse PWK/PhJ
    • Mouse SPRET/EiJ
    • Mouse WSB/EiJ
    • Pig
    • Platypus
    • Rabbit
    • Rat
    • Saccharomyces cerevisiae
    • Xenopus
    • Zebrafish

For more details on the declared intentions, please visit our Ensembl admin site. Please note that these are intentions and are not guaranteed to make it into the release.

Ensembl transcripts have two identifiers, the versioned ENST, which is stable through time and can be tracked from release to release, and a separate identifier that incorporates a gene symbol. The latter have changed in e!89; read on for more details.Continue reading