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

BMC Genomics

Software

Krishna Palaniappan¹  I-Min A. Chen¹  Manoj Pillay¹  Victor M. Markowitz¹  Ken Chu¹  Anna Ratner¹  Jinghua Huang¹  Ernest Szeto¹  Marcel Huntemann²  Nikos C. Kyrpides²  Natalia N. Ivanova²  Michalis Hadjithomas²  Galina Ovchinnikova²  Natalia Mikhailova² 

[1] Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA;Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA;

关键词: Gene annotation;    Functional curation;    Manual curation;    IMG;    Metagenomics;    Microbial genomics;   

DOI  :  10.1186/s12864-016-2629-y

 received in 2016-02-02, accepted in 2016-04-16,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsHere, 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.ConclusionBy 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.

【 授权许可】

CC BY   
© Chen et al. 2016