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Title: The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize

Abstract

As metabolic pathway resources become more commonly available, researchers have unprecedented access to information about their organism of interest. Despite efforts to ensure consistency between various resources, information content and quality can vary widely. Two maize metabolic pathway resources for the B73 inbred line, CornCyc 4.0 and MaizeCyc 2.2, are based on the same gene model set and were developed using Pathway Tools software. These resources differ in their initial enzymatic function assignments and in the extent of manual curation. Here, we present an in-depth comparison between CornCyc and MaizeCyc to demonstrate the effect of initial computational enzymatic function assignments on the quality and content of metabolic pathway resources.

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Donald Danforth Plant Science Center, St. Louis, MO (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Science Foundation (NSF); National Institutes of Health (NIH), Bethesda, MD (United States); Agricultural Research Service (ARS)
OSTI Identifier:
1618913
Alternate Identifier(s):
OSTI ID: 1423883
Grant/Contract Number:  
SC0008769; EEC-0813570; ABI-1062546; U01 GM110699
Resource Type:
Published Article
Journal Name:
BMC Systems Biology
Additional Journal Information:
Journal Name: BMC Systems Biology Journal Volume: 10 Journal Issue: 1; Journal ID: ISSN 1752-0509
Publisher:
Springer Science + Business Media
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Metabolic pathway databases; BioCyc; CornCyc; Database comparison; MaizeCyc; JavaCycO

Citation Formats

Walsh, Jesse R., Schaeffer, Mary L., Zhang, Peifen, Rhee, Seung Y., Dickerson, Julie A., and Sen, Taner Z. The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize. United Kingdom: N. p., 2016. Web. doi:10.1186/s12918-016-0369-x.
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Walsh, Jesse R., Schaeffer, Mary L., Zhang, Peifen, Rhee, Seung Y., Dickerson, Julie A., & Sen, Taner Z. The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize. United Kingdom. https://doi.org/10.1186/s12918-016-0369-x
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Walsh, Jesse R., Schaeffer, Mary L., Zhang, Peifen, Rhee, Seung Y., Dickerson, Julie A., and Sen, Taner Z. Tue . "The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize". United Kingdom. https://doi.org/10.1186/s12918-016-0369-x.
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@article{osti_1618913,
title = {The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize},
author = {Walsh, Jesse R. and Schaeffer, Mary L. and Zhang, Peifen and Rhee, Seung Y. and Dickerson, Julie A. and Sen, Taner Z.},
abstractNote = {As metabolic pathway resources become more commonly available, researchers have unprecedented access to information about their organism of interest. Despite efforts to ensure consistency between various resources, information content and quality can vary widely. Two maize metabolic pathway resources for the B73 inbred line, CornCyc 4.0 and MaizeCyc 2.2, are based on the same gene model set and were developed using Pathway Tools software. These resources differ in their initial enzymatic function assignments and in the extent of manual curation. Here, we present an in-depth comparison between CornCyc and MaizeCyc to demonstrate the effect of initial computational enzymatic function assignments on the quality and content of metabolic pathway resources.},
doi = {10.1186/s12918-016-0369-x},
journal = {BMC Systems Biology},
number = 1,
volume = 10,
place = {United Kingdom},
year = {Tue Nov 29 00:00:00 EST 2016},
month = {Tue Nov 29 00:00:00 EST 2016}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1186/s12918-016-0369-x
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Citation Metrics:
Cited by: 7 works
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Figures / Tables:

Fig. 1 Fig. 1: Overview of the pipelines used to create CornCyc 4.0 and MaizeCyc 2.2. Green represents common components, and orange and blue CornCyc- and MaizeCyc-specific components respectively. CornCyc andMaizeCyc were both based on the B73 RefGen_v2 gene model. They mainly differed in different functional annotation prediction methods incorporated into theirmore » respective pipelines. Both databases used Pathway Tools and MetaCyc for their reaction and pathway inference. Since both databases were created at different times, they used different versions of MetaCyc. Finally, manual curation has been applied to both databases. In order to account for differences at the pathway and reaction inference steps as well as at the manual curation step, we propagated updates from the same version of MetaCyc to both databases and allowed the propagation utility to remove manually curated data« less
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    Works referencing / citing this record:

    The MetaCyc database of metabolic pathways and enzymes
    journal, October 2017

    • Caspi, Ron; Billington, Richard; Fulcher, Carol A.
    • Nucleic Acids Research, Vol. 46, Issue D1
    • DOI: 10.1093/nar/gkx935

    MaizeGDB 2018: the maize multi-genome genetics and genomics database
    journal, November 2018

    • Portwood, John L.; Woodhouse, Margaret R.; Cannon, Ethalinda K.
    • Nucleic Acids Research, Vol. 47, Issue D1
    • DOI: 10.1093/nar/gky1046

    The MetaCyc database of metabolic pathways and enzymes - a 2019 update
    journal, October 2019

    • Caspi, Ron; Billington, Richard; Keseler, Ingrid M.
    • Nucleic Acids Research, Vol. 48, Issue D1
    • DOI: 10.1093/nar/gkz862
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