title: The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
abstract: 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.
authors.affiliation: Fellowship for Interpretation of Genomes, 15W155 81st Street, Burr Ridge, IL 60527, USA.
authors.forename: Ross
authors.initials: R
authors.lastname: Overbeek
authors.forename: Tadhg
authors.initials: T
authors.lastname: Begley
authors.forename: Ralph M
authors.initials: RM
authors.lastname: Butler
authors.forename: Jomuna V
authors.initials: JV
authors.lastname: Choudhuri
authors.forename: Han-Yu
authors.initials: HY
authors.lastname: Chuang
authors.forename: Matthew
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authors.lastname: Cohoon
authors.forename: Valérie
authors.initials: V
authors.lastname: de Crécy-Lagard
authors.forename: Naryttza
authors.initials: N
authors.lastname: Diaz
authors.forename: Terry
authors.initials: T
authors.lastname: Disz
authors.forename: Robert
authors.initials: R
authors.lastname: Edwards
authors.forename: Michael
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authors.lastname: Fonstein
authors.forename: Ed D
authors.initials: ED
authors.lastname: Frank
authors.forename: Svetlana
authors.initials: S
authors.lastname: Gerdes
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Glass
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.forename: Andrew
authors.initials: A
authors.lastname: Hanson
authors.forename: Dirk
authors.initials: D
authors.lastname: Iwata-Reuyl
authors.forename: Roy
authors.initials: R
authors.lastname: Jensen
authors.forename: Neema
authors.initials: N
authors.lastname: Jamshidi
authors.forename: Lutz
authors.initials: L
authors.lastname: Krause
authors.forename: Michael
authors.initials: M
authors.lastname: Kubal
authors.forename: Niels
authors.initials: N
authors.lastname: Larsen
authors.forename: Burkhard
authors.initials: B
authors.lastname: Linke
authors.forename: Alice C
authors.initials: AC
authors.lastname: McHardy
authors.forename: Folker
authors.initials: F
authors.lastname: Meyer
authors.forename: Heiko
authors.initials: H
authors.lastname: Neuweger
authors.forename: Gary
authors.initials: G
authors.lastname: Olsen
authors.forename: Robert
authors.initials: R
authors.lastname: Olson
authors.forename: Andrei
authors.initials: A
authors.lastname: Osterman
authors.forename: Vasiliy
authors.initials: V
authors.lastname: Portnoy
authors.forename: Gordon D
authors.initials: GD
authors.lastname: Pusch
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Rodionov
authors.forename: Christian
authors.initials: C
authors.lastname: Rückert
authors.forename: Jason
authors.initials: J
authors.lastname: Steiner
authors.forename: Rick
authors.initials: R
authors.lastname: Stevens
authors.forename: Ines
authors.initials: I
authors.lastname: Thiele
authors.forename: Olga
authors.initials: O
authors.lastname: Vassieva
authors.forename: Yuzhen
authors.initials: Y
authors.lastname: Ye
authors.forename: Olga
authors.initials: O
authors.lastname: Zagnitko
authors.forename: Veronika
authors.initials: V
authors.lastname: Vonstein
mesh_terms: D000214:Acyl Coenzyme A / Q000378:metabolism; D003065:Coenzyme A / Q000096:biosynthesis; D019295:Computational Biology; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D020407:Internet; D007930:Leucine / Q000378:metabolism; D012269:Ribosomal Proteins / Q000145:classification; D012984:Software; D009626:Terminology as Topic; D018875:Vocabulary, Controlled
chemical_list: D000214:Acyl Coenzyme A; D012269:Ribosomal Proteins; C008047:3-hydroxy-3-methylglutaryl-coenzyme A; D007930:Leucine; D003065:Coenzyme A