Title: Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system

Abstract

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. Conclusion: By incorporating annotation operations into IMG, we providemore » 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.« less

Authors:

Chen, I-Min A.; Markowitz, Victor M.; Palaniappan, Krishna; Szeto, Ernest; Chu, Ken; Huang, Jinghua; Ratner, Anna; Pillay, Manoj; Hadjithomas, Michalis; Huntemann, Marcel; Mikhailova, Natalia; Ovchinnikova, Galina; Ivanova, Natalia N.; Kyrpides, Nikos C.

Publication Date:

Tue Apr 26 00:00:00 EDT 2016

Research Org.:

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:

1618545

Alternate Identifier(s):

OSTI ID: 1379303

Grant/Contract Number:  

AC02-05CH11231

Resource Type:

Published Article

Journal Name:

BMC Genomics

Additional Journal Information:

Journal Name: BMC Genomics Journal Volume: 17 Journal Issue: 1; Journal ID: ISSN 1471-2164

Publisher:

Springer Science + Business Media

Country of Publication:

United Kingdom

Language:

English

Subject:

97 MATHEMATICS AND COMPUTING; 60 APPLIED LIFE SCIENCES; Gene annotation; Functional curation; Manual curation; IMG; Metagenomics; Microbial genomics