@article{0166b86b6da147c3b01d1a3d8132b200,
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.",
author = "Griffith, {Obi L.} and Montgomery, {Stephen B.} and Bridget Bernier and Bryan Chu and Katayoon Kasaian and Stein Aerts and Shaun Mahony and Sleumer, {Monica C.} and Mikhail Bilenky and Maximilian Haeussler and Malachi Griffith and Gallo, {Steven M.} and Belinda Giardine and Bart Hooghe and {Van loo}, Peter and Enrique Blanco and Amy Ticoll and Stuart Lithwick and Elodie Portales-Casamar and Donaldson, {Ian J.} and Gordon Robertson and Claes Wadelius and {De bleser}, Pieter and Dominique Vlieghe and Halfon, {Marc S.} and Wyeth Wasserman and Ross Hardison and Bergman, {Casey M.} and Jones, {Steven J.M.}",
note = "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.",
year = "2008",
month = jan,
doi = "10.1093/nar/gkm967",
language = "English (US)",
volume = "36",
pages = "D107--D113",
journal = "Nucleic acids research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "SUPPL. 1",
}