Document Detail


Data mining in the MetaCyc family of pathway databases.
MedLine Citation:
PMID:  23192547     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Pathway databases collect the bioreactions and molecular interactions that define the processes of life. The MetaCyc family of pathway databases consists of thousands of databases that were derived through computational inference of metabolic pathways from the MetaCyc pathway/genome database (PGDB). In some cases, these DBs underwent subsequent manual curation. Curated pathway DBs are now available for most of the major model organisms. Databases in the MetaCyc family are managed using the Pathway Tools software. This chapter presents methods for performing data mining on the MetaCyc family of pathway DBs. We discuss the major data access mechanisms for the family, which include data files in multiple formats; application programming interfaces (APIs) for the Lisp, Java, and Perl languages; and web services. We present an overview of the Pathway Tools schema, an understanding of which is needed to query the DBs. The chapter also presents several interactive data mining tools within Pathway Tools for performing omics data analysis.
Authors:
Peter D Karp; Suzanne Paley; Tomer Altman
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural    
Journal Detail:
Title:  Methods in molecular biology (Clifton, N.J.)     Volume:  939     ISSN:  1940-6029     ISO Abbreviation:  Methods Mol. Biol.     Publication Date:  2013  
Date Detail:
Created Date:  2012-11-29     Completed Date:  2013-06-06     Revised Date:  2014-01-10    
Medline Journal Info:
Nlm Unique ID:  9214969     Medline TA:  Methods Mol Biol     Country:  United States    
Other Details:
Languages:  eng     Pagination:  183-200     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Animals
Arabidopsis / genetics
Computational Biology / methods*
Data Mining / methods*
Databases, Genetic*
Escherichia coli / genetics
Gene Expression
Gene Regulatory Networks
Genome, Bacterial
Genome, Fungal
Genome, Human
Genome, Plant
Humans
Internet
Metabolic Networks and Pathways*
Mice
Microarray Analysis
Saccharomyces cerevisiae / genetics
Software*
Grant Support
ID/Acronym/Agency:
GM077678/GM/NIGMS NIH HHS; GM080746/GM/NIGMS NIH HHS; GM75742/GM/NIGMS NIH HHS; R01 GM080746/GM/NIGMS NIH HHS
Comments/Corrections

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