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

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Experimental identification of DNA regulatory regions, transcription factor binding sites, and regulatory variants is crucial for understanding gene regulation.
• Existing databases may lack comprehensive, community-curated data on these elements.
• Efficient literature curation systems are needed to keep pace with the growing body of research.

Purpose of the Study:

• To present ORegAnno, an open-source, open-access database and literature curation system.
• To facilitate community-based annotation of experimentally identified regulatory elements.
• To provide a centralized resource for gene regulation data.

Main Methods:

• Development of a literature curation system with a 'publication queue' for user input and manual annotation.
• Creation of user-friendly annotation pages for data entry.
• Implementation of an evidence ontology for categorizing experimental data.
• Cross-referencing records with external databases (Ensembl, Entrez, PubMed, dbSNP).

Main Results:

• The database contains 30,145 records curated from 922 publications, covering regulatory sequences for 3,853 genes and 465 transcription factors across 19 species.
• The 'publication queue' includes 4,438 expert-entered and 54,351 text-mined gene regulation papers.
• Records are cross-referenced and can be visualized in genome browsers.

Conclusions:

• ORegAnno provides a valuable, freely accessible resource for researchers studying gene regulation.
• The community-based approach enhances data curation and coverage.
• The system supports data integration and visualization for broader accessibility.