Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system.
BACKGROUND
The exponential growth of genomic data from next generation technologies renders traditional manual expert curation effort unsustainable. Many genomic systems have included community annotation tools to address the problem. Most of these systems adopted a "Wiki-based" approach to take advantage of existing wiki technologies, but encountered obstacles in issues such as usability, authorship recognition, information reliability and incentive for community participation.


RESULTS
Here, we present a different approach, relying on tightly integrated method rather than "Wiki-based" method, to support community annotation and user collaboration in the Integrated Microbial Genomes (IMG) system. The IMG approach allows users to use existing IMG data warehouse and analysis tools to add gene, pathway and biosynthetic cluster annotations, to analyze/reorganize contigs, genes and functions using workspace datasets, and to share private user annotations and workspace datasets with collaborators. We show that the annotation effort using IMG can be part of the research process to overcome the user incentive and authorship recognition problems thus fostering collaboration among domain experts. The usability and reliability issues are addressed by the integration of curated information and analysis tools in IMG, together with DOE Joint Genome Institute (JGI) expert review.


CONCLUSIONS
By incorporating annotation operations into IMG, we provide an integrated environment for users to perform deeper and extended data analysis and annotation in a single system that can lead to publications and community knowledge sharing as shown in the case studies.
Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA. imachen@lbl.gov.
I-Min A
IM
Chen
Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA.
Victor M
VM
Markowitz
Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA.
Krishna
K
Palaniappan
Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA.
Ernest
E
Szeto
Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA.
Ken
K
Chu
Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA.
Jinghua
J
Huang
Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA.
Anna
A
Ratner
Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA.
Manoj
M
Pillay
Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA.
Michalis
M
Hadjithomas
Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA.
Marcel
M
Huntemann
Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA.
Natalia
N
Mikhailova
Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA.
Galina
G
Ovchinnikova
Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA.
Natalia N
NN
Ivanova
Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA.
Nikos C
NC
Kyrpides
D019295:Computational Biology / Q000379:methods*; D003299:Cooperative Behavior; D000068598:Data Accuracy; D064349:Genome, Microbial; D023281:Genomics / Q000379:methods*; D033181:Information Dissemination; D020407:Internet; D058977:Molecular Sequence Annotation / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
Functional curation; Gene annotation; IMG; Manual curation; Metagenomics; Microbial genomics