ORegAnno: An open-access community-driven resource for regulatory annotation

Obi L. Griffith, Stephen B. Montgomery, Bridget Bernier, Bryan Chu, Katayoon Kasaian, Stein Aerts, Shaun Mahony, Monica C. Sleumer, Mikhail Bilenky, Maximilian Haeussler, Malachi Griffith, Steven M. Gallo, Belinda Giardine, Bart Hooghe, Peter Van loo, Enrique Blanco, Amy Ticoll, Stuart Lithwick, Elodie Portales-Casamar, Ian J. DonaldsonGordon Robertson, Claes Wadelius, Pieter De bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth Wasserman, Ross Hardison, Casey M. Bergman, Steven J.M. Jones

Research output: Contribution to journalArticle

173 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)D107-D113
JournalNucleic acids research
Volume36
Issue numberSUPPL. 1
DOIs
StatePublished - Jan 1 2008

All Science Journal Classification (ASJC) codes

  • Genetics

Fingerprint Dive into the research topics of 'ORegAnno: An open-access community-driven resource for regulatory annotation'. Together they form a unique fingerprint.

  • Cite this

    Griffith, O. L., Montgomery, S. B., Bernier, B., Chu, B., Kasaian, K., Aerts, S., Mahony, S., Sleumer, M. C., Bilenky, M., Haeussler, M., Griffith, M., Gallo, S. M., Giardine, B., Hooghe, B., Van loo, P., Blanco, E., Ticoll, A., Lithwick, S., Portales-Casamar, E., ... Jones, S. J. M. (2008). ORegAnno: An open-access community-driven resource for regulatory annotation. Nucleic acids research, 36(SUPPL. 1), D107-D113. https://doi.org/10.1093/nar/gkm967