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Nucleic Acids Research 2005 33(17):5691-5702; doi:10.1093/nar/gki866
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Published online 7 October 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes

Ross Overbeek1, Tadhg Begley16, Ralph M. Butler10, Jomuna V. Choudhuri3, Han-Yu Chuang17, Matthew Cohoon12, Valérie de Crécy-Lagard13, Naryttza Diaz3, Terry Disz12, Robert Edwards1,7,8, Michael Fonstein1,18, Ed D. Frank2, Svetlana Gerdes1, Elizabeth M. Glass2, Alexander Goesmann3, Andrew Hanson14, Dirk Iwata-Reuyl15, Roy Jensen5, Neema Jamshidi17, Lutz Krause3, Michael Kubal12, Niels Larsen11, Burkhard Linke3, Alice C. McHardy3, Folker Meyer3, Heiko Neuweger3, Gary Olsen9, Robert Olson12, Andrei Osterman1,8, Vasiliy Portnoy17, Gordon D. Pusch1, Dmitry A. Rodionov6, Christian Rückert4, Jason Steiner17, Rick Stevens2,12, Ines Thiele17, Olga Vassieva1, Yuzhen Ye8, Olga Zagnitko1 and Veronika Vonstein1,*

1Fellowship for Interpretation of Genomes 15W155 81st Street, Burr Ridge, IL 60527, USA 2Mathematics and Computer Science Division, Argonne National Laboratory Argonne, IL 60439, USA 3Center for Biotechnology, Institute for Genome Research, Bielefeld University 33594 Bielefeld, Germany, USA 4International NRW Graduate School in Bioinformatics & Genome Research, Institute for Genome Research, Bielefeld University 33594 Bielefeld, Germany, USA 5Emerson Hall, University of Florida PO Box 14425, Gainesville, FL 32604, USA 6Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia 7Center for Microbial Sciences, San Diego State University San Diego, CA 92813, USA 8The Burnham Institute San Diego CA 92037, USA 9Department of Microbiology, University of Illinois at Urbana-Champaign Urbana, IL 61801 10Computer Science Dept, Middle Tennessee State University Murfreesboro, TN 37132, USA 11Danish Genome Institute Gustav Wieds vej 10 C, DK-8000 Aarhus C, Denmark 12Computation Institute, University of Chicago Chicago, IL 60637, USA 13Departments of Microbiology and Cell Science, University of Florida Gainesville, FL 32611, USA 14Department of Horticultural Science, University of Florida Gainesville, FL 32611, USA 15Department of Chemistry, Portland State University Portland, OR 97207, USA 16Department of Chemistry and Chemical Biology, Cornell University Ithaca, NY14853, USA 17University of California San Diego, CA 92093, USA 18Cleveland BioLabs, Inc. Cleveland, OH 44106, USA

*To whom correspondence should be addressed. Tel: +1 630 325 4178; Fax: +1 630 325 4179; Email: Veronika{at}theFIG.info

Received June 9, 2005. Revised September 8, 2005. Accepted September 8, 2005.

The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms.


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