URL: | http://www.oreganno.org/ |
Full name: | Open Regulatory Annotation |
Description: | 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. |
Year founded: | 2006 |
Last update: | 2015-11-17 |
Version: | v3.0 |
Accessibility: | |
Country/Region: | United States |
Data type: | |
Data object: |
NA
|
Database category: | |
Major species: |
NA
|
Keywords: |
University/Institution: | University of Washington |
Address: | St. Louis, MO 63108, USA |
City: | St. Louis |
Province/State: | MO |
Country/Region: | United States |
Contact name (PI/Team): | Obi L. Griffith |
Contact email (PI/Helpdesk): | obig@bcgsc.ca |
ORegAnno 3.0: a community-driven resource for curated regulatory annotation. [PMID: 26578589]
The Open Regulatory Annotation database (ORegAnno) is a resource for curated regulatory annotation. It contains information about regulatory regions, transcription factor binding sites, RNA binding sites, regulatory variants, haplotypes, and other regulatory elements. ORegAnno differentiates itself from other regulatory resources by facilitating crowd-sourced interpretation and annotation of regulatory observations from the literature and highly curated resources. It contains a comprehensive annotation scheme that aims to describe both the elements and outcomes of regulatory events. Moreover, ORegAnno assembles these disparate data sources and annotations into a single, high quality catalogue of curated regulatory information. The current release is an update of the database previously featured in the NAR Database Issue, and now contains 1 948 307 records, across 18 species, with a combined coverage of 334 215 080 bp. Complete records, annotation, and other associated data are available for browsing and download at http://www.oreganno.org/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. |
ORegAnno: an open-access community-driven resource for regulatory annotation. [PMID: 18006570]
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. |
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. [PMID: 16397004]
MOTIVATION: Our understanding of gene regulation is currently limited by our ability to collectively synthesize and catalogue transcriptional regulatory elements stored in scientific literature. Over the past decade, this task has become increasingly challenging as the accrual of biologically validated regulatory sequences has accelerated. To meet this challenge, novel community-based approaches to regulatory element annotation are required. |