TY - JOUR
T1 - ORegAnno
T2 - An open-access community-driven resource for regulatory annotation
AU - Griffith, Obi L.
AU - Montgomery, Stephen B.
AU - Bernier, Bridget
AU - Chu, Bryan
AU - Kasaian, Katayoon
AU - Aerts, Stein
AU - Mahony, Shaun
AU - Sleumer, Monica C.
AU - Bilenky, Mikhail
AU - Haeussler, Maximilian
AU - Griffith, Malachi
AU - Gallo, Steven M.
AU - Giardine, Belinda
AU - Hooghe, Bart
AU - Van loo, Peter
AU - Blanco, Enrique
AU - Ticoll, Amy
AU - Lithwick, Stuart
AU - Portales-Casamar, Elodie
AU - Donaldson, Ian J.
AU - Robertson, Gordon
AU - Wadelius, Claes
AU - De bleser, Pieter
AU - Vlieghe, Dominique
AU - Halfon, Marc S.
AU - Wasserman, Wyeth
AU - Hardison, Ross
AU - Bergman, Casey M.
AU - Jones, Steven J.M.
N1 - Funding Information:
We thank the Open Regulatory Annotation Consortium for their continuing efforts to improve this resource through manual curation and record validation. We also thank the owners of regulatory sequence databases that made their data available for inclusion in ORegAnno. This work was funded by British Columbia Cancer Foundation; Genome Canada; Genome British Columbia; European Network of Excellence (ENFIN); BioSapiens Network of Excellence; Research Foundation – Flanders (FWO); The Pleiades Promoter Project; Michael Smith Foundation for Health Research to O.L.G., M.C.S., M.G. and S.J.M.J.; Canadian Institutes of Health Research to O.L.G.; European Molecular Biology Laboratory to S.B.M.; Marie Curie Early Stage Research Training Fellowship (MEST-CT-2004-504854) to M.H.; Natural Sciences and Engineering Research Council to S.B.M., and M.G.; Research Foundation – Flanders (FWO) to P.V.L.; Swedish Research Council to C.W. Funding to pay the Open Access publication charges for this article was provided by Genome Canada and Genome British Columbia.
PY - 2008/1
Y1 - 2008/1
N2 - 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.
AB - 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.
UR - https://www.scopus.com/pages/publications/38549087902
U2 - 10.1093/nar/gkm967
DO - 10.1093/nar/gkm967
M3 - Article
C2 - 18006570
AN - SCOPUS:38549087902
SN - 0305-1048
VL - 36
SP - D107-D113
JO - Nucleic acids research
JF - Nucleic acids research
IS - SUPPL. 1
ER -