ORegAnno: an open-access community-driven resource for regulatory annotation
| Autor: | Mikhail Bilenky, Obi L. Griffith, Claes Wadelius, Shaun Mahony, Maximilian Haeussler, Ian J. Donaldson, D. Vlieghe, Stein Aerts, Stephen B. Montgomery, Pieter De Bleser, Elodie Portales-Casamar, Enrique Blanco, Casey M. Bergman, Belinda Giardine, Bart Hooghe, Ross C. Hardison, Wyeth W. Wasserman, Katayoon Kasaian, Steven M. Gallo, Peter Van Loo, Stuart Lithwick, Amy Ticoll, Malachi Griffith, Steven J.M. Jones, Bryan Chu, Marc S. Halfon, Monica C. Sleumer, Bridget Bernier, Gordon Robertson |
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| Rok vydání: | 2007 |
| Předmět: |
dbSNP
computer.internet_protocol Biology Ontology (information science) Bioinformatics computer.software_genre Access to Information User-Computer Interface 03 medical and health sciences Annotation 0302 clinical medicine Genetics Animals Humans Ensembl Regulatory Elements Transcriptional Queue 030304 developmental biology Internet 0303 health sciences Binding Sites Information retrieval Entrez Gene Articles Web service Databases Nucleic Acid computer 030217 neurology & neurosurgery XML Transcription Factors |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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