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

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:
 [1] ;  [2] ;  [3] ;  [3] ;  [4] ;  [5]
  1. Iowa State Univ., Ames, IA (United States). Bioinformatics and Computational Biology Program, Electrical and Computer Engineering Dept. and USDA-ARS Corn Insects and Crop Genetics Research Unit
  2. Univ. of Missouri, Columbia, MO (United States). USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences
  3. Carnegie Inst. of Science, Stanford, CA (United States). Dept. of Plant Biology
  4. Iowa State Univ., Ames, IA (United States). Bioinformatics and Computational Biology Program and Electrical and Computer Engineering Dept.
  5. Iowa State Univ., Ames, IA (United States). Bioinformatics and Computational Biology Program, USDA-ARS Corn Insects and Crop Genetics Research Unit and Dept. of Genetics, Development and Cell Biology; USDA-ARS Crop Improvement and Genetics Research Unit, Albany, CA (United States)
Publication Date:
Grant/Contract Number:
sc0008769; EEC-0813570; ABI-1062546; U01 GM110699
Type:
Accepted Manuscript
Journal Name:
BMC Systems Biology
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1752-0509
Publisher:
BioMed Central
Research Org:
Donald Danforth Plant Science Center, St. Louis, MO (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23). Biological Systems Science Division; National Science Foundation (NSF); National Institutes of Health (NIH), Bethesda, MD (United States); Agricultural Research Service (ARS)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Metabolic pathway databases; BioCyc; CornCyc; Database comparison; MaizeCyc; JavaCycO
OSTI Identifier:
1423883