Improving microbial genome annotations in an integrated database context.
Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that all...
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Public Library of Science (PLoS)
2013
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oai:doaj.org-article:04f77dd709824ada9d00d4faf5a0d2042021-11-18T07:57:59ZImproving microbial genome annotations in an integrated database context.1932-620310.1371/journal.pone.0054859https://doaj.org/article/04f77dd709824ada9d00d4faf5a0d2042013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23424620/?tool=EBIhttps://doaj.org/toc/1932-6203Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG) family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/.I-Min A ChenVictor M MarkowitzKen ChuIain AndersonKonstantinos MavromatisNikos C KyrpidesNatalia N IvanovaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 2, p e54859 (2013) |
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Medicine R Science Q I-Min A Chen Victor M Markowitz Ken Chu Iain Anderson Konstantinos Mavromatis Nikos C Kyrpides Natalia N Ivanova Improving microbial genome annotations in an integrated database context. |
description |
Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG) family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/. |
format |
article |
author |
I-Min A Chen Victor M Markowitz Ken Chu Iain Anderson Konstantinos Mavromatis Nikos C Kyrpides Natalia N Ivanova |
author_facet |
I-Min A Chen Victor M Markowitz Ken Chu Iain Anderson Konstantinos Mavromatis Nikos C Kyrpides Natalia N Ivanova |
author_sort |
I-Min A Chen |
title |
Improving microbial genome annotations in an integrated database context. |
title_short |
Improving microbial genome annotations in an integrated database context. |
title_full |
Improving microbial genome annotations in an integrated database context. |
title_fullStr |
Improving microbial genome annotations in an integrated database context. |
title_full_unstemmed |
Improving microbial genome annotations in an integrated database context. |
title_sort |
improving microbial genome annotations in an integrated database context. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2013 |
url |
https://doaj.org/article/04f77dd709824ada9d00d4faf5a0d204 |
work_keys_str_mv |
AT iminachen improvingmicrobialgenomeannotationsinanintegrateddatabasecontext AT victormmarkowitz improvingmicrobialgenomeannotationsinanintegrateddatabasecontext AT kenchu improvingmicrobialgenomeannotationsinanintegrateddatabasecontext AT iainanderson improvingmicrobialgenomeannotationsinanintegrateddatabasecontext AT konstantinosmavromatis improvingmicrobialgenomeannotationsinanintegrateddatabasecontext AT nikosckyrpides improvingmicrobialgenomeannotationsinanintegrateddatabasecontext AT natalianivanova improvingmicrobialgenomeannotationsinanintegrateddatabasecontext |
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1718422707849134080 |