ORegAnno: an open-access community-driven resource for regulatory annotation.
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.
Griffith
Obi L
OL
Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada. obig@bcgsc.ca
Montgomery
Stephen B
SB
Bernier
Bridget
B
Chu
Bryan
B
Kasaian
Katayoon
K
Aerts
Stein
S
Mahony
Shaun
S
Sleumer
Monica C
MC
Bilenky
Mikhail
M
Haeussler
Maximilian
M
Griffith
Malachi
M
Gallo
Steven M
SM
Giardine
Belinda
B
Hooghe
Bart
B
Van Loo
Peter
P
Blanco
Enrique
E
Ticoll
Amy
A
Lithwick
Stuart
S
Portales-Casamar
Elodie
E
Donaldson
Ian J
IJ
Robertson
Gordon
G
Wadelius
Claes
C
De Bleser
Pieter
P
Vlieghe
Dominique
D
Halfon
Marc S
MS
Wasserman
Wyeth
W
Hardison
Ross
R
Bergman
Casey M
CM
Jones
Steven J M
SJ
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
D014157:Transcription Factors