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Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation

Updating genome databases to reflect newly published molecular findings for an organism was hard enough when only a single strain of a given organism had been sequenced. With multiple sequenced strains now available for many organisms, the challenge has grown significantly because of the still-limit...

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Autores principales: Paley, Suzanne, Keseler, Ingrid M., Krummenacker, Markus, Karp, Peter D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7982652/
https://www.ncbi.nlm.nih.gov/pubmed/33763039
http://dx.doi.org/10.3389/fmicb.2021.614355
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author Paley, Suzanne
Keseler, Ingrid M.
Krummenacker, Markus
Karp, Peter D.
author_facet Paley, Suzanne
Keseler, Ingrid M.
Krummenacker, Markus
Karp, Peter D.
author_sort Paley, Suzanne
collection PubMed
description Updating genome databases to reflect newly published molecular findings for an organism was hard enough when only a single strain of a given organism had been sequenced. With multiple sequenced strains now available for many organisms, the challenge has grown significantly because of the still-limited resources available for the manual curation that corrects errors and captures new knowledge. We have developed a method to automatically propagate multiple types of curated knowledge from genes and proteins in one genome database to their orthologs in uncurated databases for related strains, imposing several quality-control filters to reduce the chances of introducing errors. We have applied this method to propagate information from the highly curated EcoCyc database for Escherichia coli K–12 to databases for 480 other Escherichia coli strains in the BioCyc database collection. The increase in value and utility of the target databases after propagation is considerable. Target databases received updates for an average of 2,535 proteins each. In addition to widespread addition and regularization of gene and protein names, 97% of the target databases were improved by the addition of at least 200 new protein complexes, at least 800 new or updated reaction assignments, and at least 2,400 sets of GO annotations.
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spelling pubmed-79826522021-03-23 Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation Paley, Suzanne Keseler, Ingrid M. Krummenacker, Markus Karp, Peter D. Front Microbiol Microbiology Updating genome databases to reflect newly published molecular findings for an organism was hard enough when only a single strain of a given organism had been sequenced. With multiple sequenced strains now available for many organisms, the challenge has grown significantly because of the still-limited resources available for the manual curation that corrects errors and captures new knowledge. We have developed a method to automatically propagate multiple types of curated knowledge from genes and proteins in one genome database to their orthologs in uncurated databases for related strains, imposing several quality-control filters to reduce the chances of introducing errors. We have applied this method to propagate information from the highly curated EcoCyc database for Escherichia coli K–12 to databases for 480 other Escherichia coli strains in the BioCyc database collection. The increase in value and utility of the target databases after propagation is considerable. Target databases received updates for an average of 2,535 proteins each. In addition to widespread addition and regularization of gene and protein names, 97% of the target databases were improved by the addition of at least 200 new protein complexes, at least 800 new or updated reaction assignments, and at least 2,400 sets of GO annotations. Frontiers Media S.A. 2021-03-08 /pmc/articles/PMC7982652/ /pubmed/33763039 http://dx.doi.org/10.3389/fmicb.2021.614355 Text en Copyright © 2021 Paley, Keseler, Krummenacker and Karp. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Paley, Suzanne
Keseler, Ingrid M.
Krummenacker, Markus
Karp, Peter D.
Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation
title Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation
title_full Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation
title_fullStr Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation
title_full_unstemmed Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation
title_short Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation
title_sort leveraging curation among escherichia coli pathway/genome databases using ortholog-based annotation propagation
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7982652/
https://www.ncbi.nlm.nih.gov/pubmed/33763039
http://dx.doi.org/10.3389/fmicb.2021.614355
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