Nucleic Acids Research

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

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Published online 7 October 2005

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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 Edwards^1,7,8, Michael Fonstein^1,18, 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 Osterman^1,8, Vasiliy Portnoy¹⁷, Gordon D. Pusch¹, Dmitry A. Rodionov⁶, Christian Rückert⁴, Jason Steiner¹⁷, Rick Stevens^2,12, Ines Thiele¹⁷, Olga Vassieva¹, Yuzhen Ye⁸, Olga Zagnitko¹ and Veronika Vonstein^1,*

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 1000^th 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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