The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
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.
Overbeek
Ross
R
Fellowship for Interpretation of Genomes, 15W155 81st Street, Burr Ridge, IL 60527, USA.
Begley
Tadhg
T
Butler
Ralph M
RM
Choudhuri
Jomuna V
JV
Chuang
Han-Yu
HY
Cohoon
Matthew
M
de Crécy-Lagard
Valérie
V
Diaz
Naryttza
N
Disz
Terry
T
Edwards
Robert
R
Fonstein
Michael
M
Frank
Ed D
ED
Gerdes
Svetlana
S
Glass
Elizabeth M
EM
Goesmann
Alexander
A
Hanson
Andrew
A
Iwata-Reuyl
Dirk
D
Jensen
Roy
R
Jamshidi
Neema
N
Krause
Lutz
L
Kubal
Michael
M
Larsen
Niels
N
Linke
Burkhard
B
McHardy
Alice C
AC
Meyer
Folker
F
Neuweger
Heiko
H
Olsen
Gary
G
Olson
Robert
R
Osterman
Andrei
A
Portnoy
Vasiliy
V
Pusch
Gordon D
GD
Rodionov
Dmitry A
DA
Rückert
Christian
C
Steiner
Jason
J
Stevens
Rick
R
Thiele
Ines
I
Vassieva
Olga
O
Ye
Yuzhen
Y
Zagnitko
Olga
O
Vonstein
Veronika
V
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
D000214:Acyl Coenzyme A; D012269:Ribosomal Proteins; C008047:3-hydroxy-3-methylglutaryl-coenzyme A; D007930:Leucine; D003065:Coenzyme A