Cargando…
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...
Autores principales: | , , , |
---|---|
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 |
_version_ | 1783667766948003840 |
---|---|
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. |
format | Online Article Text |
id | pubmed-7982652 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT paleysuzanne leveragingcurationamongescherichiacolipathwaygenomedatabasesusingorthologbasedannotationpropagation AT keseleringridm leveragingcurationamongescherichiacolipathwaygenomedatabasesusingorthologbasedannotationpropagation AT krummenackermarkus leveragingcurationamongescherichiacolipathwaygenomedatabasesusingorthologbasedannotationpropagation AT karppeterd leveragingcurationamongescherichiacolipathwaygenomedatabasesusingorthologbasedannotationpropagation |