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

biomedical science comparative genomics genome genomics

Links

Homepage @ensembl@genomic.social

Contact

Paul Flicek   0000-0002-3897-7955

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

Publications

• 2022 Ensembl 2022
• 2020 Ensembl 2020
• 2019 Ensembl 2019
• 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
• Ensembl 2015

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

Provided By

astd

Has Parts (bfo:0000051 )

ensembl.bacteria ensembl.fungi

In Collection

FHIR External Terminologies Global Biodata Coalition - Global Core Biodata Resources

The metaregistry provides mappings between the Bioregistry and other registries. There are 12 mappings to external registries for this resource with 7 unique external prefixes.

When using this resource in RDF, the following URI format should be used:

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

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. 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.