| Data Mining in the MetaCyc Family of Pathway Databases. | |
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MedLine Citation:
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PMID: 23192547 Owner: NLM Status: In-Data-Review |
Abstract/OtherAbstract:
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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. |
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Authors:
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Peter D Karp; Suzanne Paley; Tomer Altman |
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Publication Detail:
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Type: Journal Article |
Journal Detail:
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Title: Methods in molecular biology (Clifton, N.J.) Volume: 939 ISSN: 1940-6029 ISO Abbreviation: Methods Mol. Biol. Publication Date: 2013 |
Date Detail:
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Created Date: 2012-11-29 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 9214969 Medline TA: Methods Mol Biol Country: United States |
Other Details:
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Languages: eng Pagination: 183-200 Citation Subset: IM |
Affiliation:
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Bioinformatics Research Group, SRI International, Menlo Park, CA, USA, pkarp@ai.sri.com. |
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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