title: ORegAnno: an open-access community-driven resource for regulatory annotation.
abstract: ORegAnno is an open-source, open-access database and literature curation system for community-based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. The current release comprises 30 145 records curated from 922 publications and describing regulatory sequences for over 3853 genes and 465 transcription factors from 19 species. A new feature called the 'publication queue' allows users to input relevant papers from scientific literature as targets for annotation. The queue contains 4438 gene regulation papers entered by experts and another 54 351 identified by text-mining methods. Users can enter or 'check out' papers from the queue for manual curation using a series of user-friendly annotation pages. A typical record entry consists of species, sequence type, sequence, target gene, binding factor, experimental outcome and one or more lines of experimental evidence. An evidence ontology was developed to describe and categorize these experiments. Records are cross-referenced to Ensembl or Entrez gene identifiers, PubMed and dbSNP and can be visualized in the Ensembl or UCSC genome browsers. All data are freely available through search pages, XML data dumps or web services at: http://www.oreganno.org.
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada. obig@bcgsc.ca
authors.forename: Obi L
authors.initials: OL
authors.lastname: Griffith
authors.forename: Stephen B
authors.initials: SB
authors.lastname: Montgomery
authors.forename: Bridget
authors.initials: B
authors.lastname: Bernier
authors.forename: Bryan
authors.initials: B
authors.lastname: Chu
authors.forename: Katayoon
authors.initials: K
authors.lastname: Kasaian
authors.forename: Stein
authors.initials: S
authors.lastname: Aerts
authors.forename: Shaun
authors.initials: S
authors.lastname: Mahony
authors.forename: Monica C
authors.initials: MC
authors.lastname: Sleumer
authors.forename: Mikhail
authors.initials: M
authors.lastname: Bilenky
authors.forename: Maximilian
authors.initials: M
authors.lastname: Haeussler
authors.forename: Malachi
authors.initials: M
authors.lastname: Griffith
authors.forename: Steven M
authors.initials: SM
authors.lastname: Gallo
authors.forename: Belinda
authors.initials: B
authors.lastname: Giardine
authors.forename: Bart
authors.initials: B
authors.lastname: Hooghe
authors.forename: Peter
authors.initials: P
authors.lastname: Van Loo
authors.forename: Enrique
authors.initials: E
authors.lastname: Blanco
authors.forename: Amy
authors.initials: A
authors.lastname: Ticoll
authors.forename: Stuart
authors.initials: S
authors.lastname: Lithwick
authors.forename: Elodie
authors.initials: E
authors.lastname: Portales-Casamar
authors.forename: Ian J
authors.initials: IJ
authors.lastname: Donaldson
authors.forename: Gordon
authors.initials: G
authors.lastname: Robertson
authors.forename: Claes
authors.initials: C
authors.lastname: Wadelius
authors.forename: Pieter
authors.initials: P
authors.lastname: De Bleser
authors.forename: Dominique
authors.initials: D
authors.lastname: Vlieghe
authors.forename: Marc S
authors.initials: MS
authors.lastname: Halfon
authors.forename: Wyeth
authors.initials: W
authors.lastname: Wasserman
authors.forename: Ross
authors.initials: R
authors.lastname: Hardison
authors.forename: Casey M
authors.initials: CM
authors.lastname: Bergman
authors.forename: Steven J M
authors.initials: SJ
authors.lastname: Jones
mesh_terms: D022126:Access to Information; D000818:Animals; D001665:Binding Sites; D030561:Databases, Nucleic Acid; D006801:Humans; D020407:Internet; D050436:Regulatory Elements, Transcriptional; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors