ArticleBMC genomics2016
Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
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- De novo cholesterol biosynthesis in bacteria.Nature communications · 2023Article
- Genotype-phenotype correlations within theFrontiers in microbiology · 2022Article
- Draft genome ofPeerJ · 2020Article
- MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data.Briefings in bioinformatics · 2019Article
- Galactitol catabolism in Sinorhizobium meliloti is dependent on a chromosomally encoded sorbitol dehydrogenase and a pSymB-encoded operon necessary for tagatose catabolism.Molecular genetics and genomics : MGG · 2019Article
- Complete Genome Sequence of Serratia quinivorans Strain 124R, a Facultative Anaerobe Isolated on Organosolv Lignin as a Sole Carbon Source.Microbiology resource announcements · 2019Article
- Complete Genome Sequence forMicrobiology resource announcements · 2019Article
- IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes.Nucleic acids research · 2019Article
- Genomic Characterization of a Mercury ResistantFrontiers in microbiology · 2019Article
- High-quality draft genome sequences ofAccess microbiology · 2019Article
- Bacterial Metabolites Produced Under Iron Limitation Kill Pinewood Nematode and AttractFrontiers in microbiology · 2019Article
- C-4 sterol demethylation enzymes distinguish bacterial and eukaryotic sterol synthesis.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- GROOLS: reactive graph reasoning for genome annotation through biological processes.BMC bioinformatics · 2018Article
- Draft Genome Sequences of Three Strains of a NovelGenome announcements · 2018Article
- Genome Sequence ofGenome announcements · 2018Article
- Complete Genome Sequence ofGenome announcements · 2018Article
- Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.