دورية أكاديمية
أعرض في EDS

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

التفاصيل البيبلوغرافية
العنوان: Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system.
المؤلفون: Chen IM; Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA. imachen@lbl.gov., Markowitz VM; Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA., Palaniappan K; Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA., Szeto E; Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA., Chu K; Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA., Huang J; Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA., Ratner A; Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA., Pillay M; Biosciences Computing, Computational Research Division, Lawrence Berkeley, National Laboratory, Berkeley, California, USA., Hadjithomas M; Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA., Huntemann M; Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA., Mikhailova N; Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA., Ovchinnikova G; Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA., Ivanova NN; Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA., Kyrpides NC; Prokaryotic Super Program, DOE Joint Genome Institute, Walnut Creek, California, USA.
المصدر: BMC genomics [BMC Genomics] 2016 Apr 26; Vol. 17, pp. 307. Date of Electronic Publication: 2016 Apr 26.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : BioMed Central, [2000-
مواضيع طبية MeSH: Genome, Microbial* , Software*, Computational Biology/*methods , Genomics/*methods , Molecular Sequence Annotation/*methods, Cooperative Behavior ; Data Accuracy ; Information Dissemination ; Internet ; User-Computer Interface
مستخلص: 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.
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فهرسة مساهمة: Keywords: Functional curation; Gene annotation; IMG; Manual curation; Metagenomics; Microbial genomics
تواريخ الأحداث: Date Created: 20160428 Date Completed: 20161109 Latest Revision: 20181113
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC4847265
DOI: 10.1186/s12864-016-2629-y
PMID: 27118214
قاعدة البيانات: MEDLINE
الوصف
تدمد:1471-2164
DOI:10.1186/s12864-016-2629-y