The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns.

Prefix

encode

Keywords

biological regulation cage chip-seq assay chromatin binding chromatin interaction analysis by paired-end tag sequencing assay dna methylation dna sequence epigenetics functional genomics genome annotation histone nucleic acid sequence regulatory region rna-binding protein target sites rna-seq assay transcript analysis by paired-end tag sequencing assay transcription factor

Links

Homepage

Publications

2020 Expanded encyclopaedias of DNA elements in the human and mouse genomes

2020 Perspectives on ENCODE

2019 The ENCODE Portal as an Epigenomics Resource

2020 New developments on the Encyclopedia of DNA Elements (ENCODE) data portal

2018 The Encyclopedia of DNA elements (ENCODE): data portal update

2017 SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata

2016 Principles of metadata organization at the ENCODE data coordination center

2015 ENCODE data at the ENCODE portal

2015 Ontology application and use at the ENCODE DCC

2012 ENCODE data in the UCSC Genome Browser: year 5 update

2011 ENCODE whole-genome data in the UCSC Genome Browser: update 2012

2010 ENCODE whole-genome data in the UCSC genome browser (2011 update)

2009 ENCODE whole-genome data in the UCSC Genome Browser

2006 The ENCODE Project at UC Santa Cruz

2004 The ENCODE (ENCyclopedia Of DNA Elements) Project

Pattern for Local Unique Identifiers

Local identifiers in Encyclopedia of DNA Elements should match this regular expression:
^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$

Example Local Unique Identifier

ENCSR163RYW   Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from Encyclopedia of DNA Elements should match this regular expression:
^encode:ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$

Example CURIE

encode:ENCSR163RYW

Contact

Idan Gabdank   0000-0001-5025-5886

Mappings from records in Bioregistry to external registries comprises the metaregistry. This resource has 6 mappings to external registries with 3 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 ENCSR163RYW is used to demonstrate the providers available for Encyclopedia of DNA Elements. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.