Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms.

Prefix

ensembl

Alternative Prefixes

Ensembl

Keywords

genome genome annotation databases genome/gene sequence

License

http://www.ebi.ac.uk/Information/termsofuse.html

Links

Homepage @ensembl@genomic.social

Publications

2025 DIGGER 2.0: digging into the functional impact of differential splicing on human and mouse disorders

2022 Ensembl 2022

2020 Ensembl 2020

2019 Ensembl 2019

https://bioregistry.io/pubmed:28365736

2016 Ensembl 2017

2016 The Ensembl gene annotation system

2016 The Ensembl Variant Effect Predictor

2016 Ensembl comparative genomics resources

2016 ncRNA orthologies in the vertebrate lineage

2016 Ensembl comparative genomics resources

2016 Ensembl regulation resources

2015 Ensembl 2016

2015 The ensembl regulatory build

2014 Ensembl 2015

2014 The Ensembl REST API: Ensembl Data for Any Language

2013 WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis

2013 Ensembl 2014

2012 Ensembl 2013

2012 GENCODE: the reference human genome annotation for The ENCODE Project

2012 Incorporating RNA-seq data into the zebrafish Ensembl genebuild

2011 Ensembl 2012

2011 Ensembl BioMarts: a hub for data retrieval across taxonomic space

2011 Disease and phenotype data at Ensembl

2010 Ensembl 2011

2010 Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

2010 eHive: an artificial intelligence workflow system for genomic analysis

2010 A database and API for variation, dense genotyping and resequencing data

2010 Touring Ensembl: a practical guide to genome browsing

2010 Ensembl variation resources

2009 Ensembl's 10th year

2008 Ensembl 2009

2008 EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

2008 Genome-wide nucleotide-level mammalian ancestor reconstruction

2007 Ensembl 2008

2007 Genome browsing with Ensembl: a practical overview

2006 Ensembl 2007

2006 TranscriptSNPView: a genome-wide catalog of mouse coding variation

2006 Ensembl 2006

2005 Ensembl 2005

2004 Genome information resources - developments at Ensembl

2004 ESTGenes: alternative splicing from ESTs in Ensembl

2004 The Ensembl computing architecture

2004 The Ensembl Web site: mechanics of a genome browser

2004 The Ensembl automatic gene annotation system

2004 The Ensembl analysis pipeline

2004 The Ensembl core software libraries

2003 Ensembl 2002: accommodating comparative genomics

2002 The Ensembl genome database project

Pattern for Local Unique Identifiers

Local identifiers in Ensembl Gene should match this regular expression:
^((ENS[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$

Example Local Unique Identifiers

ENSG00000139618   Resolve
ENSG00000049246.14   Resolve
ENSG00000109819.9   Resolve
ENSG00000132326.12   Resolve
ENSG00000179094.16   Resolve
ENST00000264867.7   Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from Ensembl Gene should match this regular expression:
^ensembl:((ENS[FPTG]\d{11}(\.\d+)?)|(FB\w{2}\d{7})|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?)|([A-Z_a-z0-9]+(\.)?(t)?(\d+)?([a-z])?))$

Example CURIEs

ensembl:ENSG00000139618
ensembl:ENSG00000049246.14
ensembl:ENSG00000109819.9
ensembl:ENSG00000132326.12
ensembl:ENSG00000179094.16
ensembl:ENST00000264867.7

Pattern for RDF URIs

http://rdf.ebi.ac.uk/resource/ensembl/$1

Example RDF URI

http://rdf.ebi.ac.uk/resource/ensembl/ENSG00000139618

Contact

Paul Flicek   0000-0002-3897-7955

A summary of the relations in the Bioregistry schema can be found here.

Provided By

astd ratmap

In Collection (3)

FHIR External Terminologies Global Biodata Coalition - Global Core Biodata Resources Synapse.org external links

Mappings from records in Bioregistry to external registries comprises the metaregistry. This resource has 12 mappings to external registries with 7 unique external prefixes.

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier ENSG00000139618 is used to demonstrate the providers available for Ensembl Gene. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.

Additional providers curated in the Bioregistry are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.