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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:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [2];  [2];  [2];  [2];  [2]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biosciences Computing
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Prokaryotic Super Program
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1379303
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 17; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 60 APPLIED LIFE SCIENCES; Gene annotation; Functional curation; Manual curation; IMG; Metagenomics; Microbial genomics

Citation Formats

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., and Kyrpides, Nikos C. Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system. United States: N. p., 2016. Web. doi:10.1186/s12864-016-2629-y.
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. Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system. United States. doi:10.1186/s12864-016-2629-y.
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., and Kyrpides, Nikos C. Tue . "Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system". United States. doi:10.1186/s12864-016-2629-y. https://www.osti.gov/servlets/purl/1379303.
@article{osti_1379303,
title = {Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system},
author = {Chen, I-Min A. and Markowitz, Victor M. and Palaniappan, Krishna and Szeto, Ernest and Chu, Ken and Huang, Jinghua and Ratner, Anna and Pillay, Manoj and Hadjithomas, Michalis and Huntemann, Marcel and Mikhailova, Natalia and Ovchinnikova, Galina and Ivanova, Natalia N. and Kyrpides, Nikos C.},
abstractNote = {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 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.},
doi = {10.1186/s12864-016-2629-y},
journal = {BMC Genomics},
number = 1,
volume = 17,
place = {United States},
year = {2016},
month = {4}
}

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Works referenced in this record:

The COG database: an updated version includes eukaryotes
journal, January 2003

  • Tatusov, Roman L.; Fedorova, Natalie D.; Jackson, John D.
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