IMG ER: a system for microbial genome annotation expert review and curation

IMG ER: a system for microbial genome annotation expert review and curation

2009 | Victor M. Markowitz, Konstantinos Mavromatis, Natalia N. Ivanova, I-Min A. Chen, Ken Chu and Nikos C. Kyropides
The paper introduces IMG ER, an expert review and curation system for microbial genome annotations. It aims to improve the accuracy and completeness of microbial genome annotations by providing tools for systematic and efficient revision. IMG ER supports the review and curation of annotations for both new and publicly available microbial genomes within the integrated genome framework of the Integrated Microbial Genomes (IMG) system. New genome datasets are included into IMG ER prior to their public release, either with their native annotations or with annotations generated by IMG ER's annotation pipeline. IMG ER allows addressing annotation problems detected with IMG's comparative analysis tools, such as genes missed by gene prediction pipelines or genes without an associated function. Over the past year, IMG ER was used for improving the annotations of about 150 microbial genomes. IMG ER provides support for enhanced metadata characterization of microbial genomes. Genomes in both IMG and IMG ER are characterized by metadata attributes, such as phenotype and habitat, which are based on the recommendations of the Genome Standards Consortium. Metadata attribute values are collected at the time of genome submission to IMG ER and subsequently shared with public genome project resources such as GOLD. Gene annotations that result from expert review and curation are captured in IMG ER as 'MyIMG' annotations associated with individual scientist or group accounts. Genomes curated with IMG ER are included into Genbank either as new submissions or as revisions of previously submitted datasets, thus contributing to a coordinated improvement of the public genome data resources. IMG ER is available at http://img.jgi.doe.gov/er and requires acquiring first an account at http://img.jgi.doe.gov/request. The paper discusses the methods used in IMG ER for genome annotation review, including comparative genome context, genome annotation review, and the use of various tools for identifying and curating missing genes and enzymes. The results show that IMG ER has been used to revise the annotations of about 20,500 genes across 380 genomes, with 9 of these genomes leading to publications. The discussion highlights the importance of IMG ER in improving the accuracy and completeness of microbial genome annotations and its potential for future development.The paper introduces IMG ER, an expert review and curation system for microbial genome annotations. It aims to improve the accuracy and completeness of microbial genome annotations by providing tools for systematic and efficient revision. IMG ER supports the review and curation of annotations for both new and publicly available microbial genomes within the integrated genome framework of the Integrated Microbial Genomes (IMG) system. New genome datasets are included into IMG ER prior to their public release, either with their native annotations or with annotations generated by IMG ER's annotation pipeline. IMG ER allows addressing annotation problems detected with IMG's comparative analysis tools, such as genes missed by gene prediction pipelines or genes without an associated function. Over the past year, IMG ER was used for improving the annotations of about 150 microbial genomes. IMG ER provides support for enhanced metadata characterization of microbial genomes. Genomes in both IMG and IMG ER are characterized by metadata attributes, such as phenotype and habitat, which are based on the recommendations of the Genome Standards Consortium. Metadata attribute values are collected at the time of genome submission to IMG ER and subsequently shared with public genome project resources such as GOLD. Gene annotations that result from expert review and curation are captured in IMG ER as 'MyIMG' annotations associated with individual scientist or group accounts. Genomes curated with IMG ER are included into Genbank either as new submissions or as revisions of previously submitted datasets, thus contributing to a coordinated improvement of the public genome data resources. IMG ER is available at http://img.jgi.doe.gov/er and requires acquiring first an account at http://img.jgi.doe.gov/request. The paper discusses the methods used in IMG ER for genome annotation review, including comparative genome context, genome annotation review, and the use of various tools for identifying and curating missing genes and enzymes. The results show that IMG ER has been used to revise the annotations of about 20,500 genes across 380 genomes, with 9 of these genomes leading to publications. The discussion highlights the importance of IMG ER in improving the accuracy and completeness of microbial genome annotations and its potential for future development.
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