Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system
- PMID: 27118214
- PMCID: PMC4847265
- DOI: 10.1186/s12864-016-2629-y
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 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.
Keywords: Functional curation; Gene annotation; IMG; Manual curation; Metagenomics; Microbial genomics.
Figures
Similar articles
-
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes.Nucleic Acids Res. 2019 Jan 8;47(D1):D666-D677. doi: 10.1093/nar/gky901. Nucleic Acids Res. 2019. PMID: 30289528 Free PMC article.
-
IMG 4 version of the integrated microbial genomes comparative analysis system.Nucleic Acids Res. 2014 Jan;42(Database issue):D560-7. doi: 10.1093/nar/gkt963. Epub 2013 Oct 27. Nucleic Acids Res. 2014. PMID: 24165883 Free PMC article.
-
IMG/M: integrated genome and metagenome comparative data analysis system.Nucleic Acids Res. 2017 Jan 4;45(D1):D507-D516. doi: 10.1093/nar/gkw929. Epub 2016 Oct 13. Nucleic Acids Res. 2017. PMID: 27738135 Free PMC article.
-
Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities.Mol Genet Metab. 2015 Mar;114(3):388-96. doi: 10.1016/j.ymgme.2014.11.016. Epub 2014 Dec 4. Mol Genet Metab. 2015. PMID: 25542617 Free PMC article. Review.
-
Ten years of maintaining and expanding a microbial genome and metagenome analysis system.Trends Microbiol. 2015 Nov;23(11):730-741. doi: 10.1016/j.tim.2015.07.012. Epub 2015 Oct 14. Trends Microbiol. 2015. PMID: 26439299 Review.
Cited by
-
De novo cholesterol biosynthesis in bacteria.Nat Commun. 2023 May 22;14(1):2904. doi: 10.1038/s41467-023-38638-8. Nat Commun. 2023. PMID: 37217541 Free PMC article.
-
Genotype-phenotype correlations within the Geodermatophilaceae.Front Microbiol. 2022 Nov 10;13:975365. doi: 10.3389/fmicb.2022.975365. eCollection 2022. Front Microbiol. 2022. PMID: 36439792 Free PMC article.
-
High-quality draft genome sequences of Pseudomonas monteilii DSM 14164T, Pseudomonas mosselii DSM 17497T, Pseudomonas plecoglossicida DSM 15088T, Pseudomonas taiwanensis DSM 21245T and Pseudomonas vranovensis DSM 16006T: taxonomic considerations.Access Microbiol. 2019 Oct 29;1(10):e000067. doi: 10.1099/acmi.0.000067. eCollection 2019. Access Microbiol. 2019. PMID: 32974501 Free PMC article.
-
Draft genome of Rosenbergiella nectarea strain 8N4T provides insights into the potential role of this species in its plant host.PeerJ. 2020 Apr 6;8:e8822. doi: 10.7717/peerj.8822. eCollection 2020. PeerJ. 2020. PMID: 32292647 Free PMC article.
-
Genomic Characterization of a Mercury Resistant Arthrobacter sp. H-02-3 Reveals the Presence of Heavy Metal and Antibiotic Resistance Determinants.Front Microbiol. 2020 Jan 17;10:3039. doi: 10.3389/fmicb.2019.03039. eCollection 2019. Front Microbiol. 2020. PMID: 32010097 Free PMC article.
References
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources