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ORION-VIRCAT: a tool for mapping ICTV and NCBI taxonomies
Willy Valdivia-Granda1, Francis Larson
1Orion Integrated Biosciences Inc., New Rochelle, NY, 10805, USA.
Database : the Journal of Biological Databases and Curation
|February 17, 2010
Summary
ORION-VIRCAT is a new database that integrates viral taxonomy from the International Committee on the Taxonomy of Viruses (ICTV) and the National Center for Biotechnology Information Viral Genomes Resource (NCBI-VGR). This tool addresses discrepancies and improves viral classification accuracy.
Area of Science:
- Virology
- Bioinformatics
- Database Development
Background:
- Viruses, viroids, and prions are minuscule infectious agents reliant on host replication.
- The International Committee on the Taxonomy of Viruses (ICTV) has classified approximately 4379 virus species.
- The National Center for Biotechnology Information Viral Genomes Resource (NCBI-VGR) contains over 617,705 viral proteins.
Purpose of the Study:
- To develop an automated approach for mapping the ICTV's virus naming conventions to the NCBI-VGR's taxonomic classifications.
- To create a scalable and interoperable database resource for integrating and verifying viral taxonomic data.
- To address the growing challenge of classifying new viral species identified through metagenomic sequencing.
Main Methods:
- Developed ORION-VIRCAT, a scalable object-relational database implemented in PostgreSQL and extended to other platforms (Oracle, MySQL, SyBase).
- Automatically mapped and joined 617,705 entries from the NCBI-VGR to the ICTV's viral nomenclature.
- Analyzed discrepancies between the ICTV and NCBI-VGR classification schemas.
Main Results:
- Successfully mapped 399,095 NCBI-VGR entries to the ICTV classification.
- Identified 1 Order, 10 families, 35 genera, and 503 species with differing classifications between ICTV and NCBI-VGR.
- Corrected several discrepancies by mapping an additional 234,000 entries.
Conclusions:
- ORION-VIRCAT provides a crucial resource for harmonizing viral taxonomy between major databases.
- The database facilitates accurate classification of viral sequences, essential for managing the increasing volume of data from metagenomic studies.
- Automated cross-referencing and discrepancy resolution enhance the reliability of viral classification systems.
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