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A Strategy for Sensitive, Large Scale Quantitative Metabolomics
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Computational Metabolomics Operations at BioCyc.org.

Peter D Karp1, Richard Billington2, Timothy A Holland3

  • 1Bioinformatics Research Group, SRI International, 333 Ravenswood Ave AE206, Menlo Park, CA 94025, USA. pkarp@ai.sri.com.

Metabolites
|May 27, 2015
PubMed
Summary
This summary is machine-generated.

BioCyc.org is a comprehensive web portal for genome and metabolic pathway data, featuring over 5500 organisms. It offers advanced tools for metabolomics data analysis, including enrichment analysis and data visualization.

Keywords:
metabolic databasemetabolic pathwaysmetabolomics data analysis

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Area of Science:

  • Bioinformatics
  • Metabolomics
  • Systems Biology

Background:

  • BioCyc.org is a web portal offering genome and metabolic pathway data for over 5500 organisms.
  • It includes organism-specific databases with varying curation levels, such as the highly curated EcoCyc for Escherichia coli.
  • The MetaCyc database provides a universal view of metabolic pathways, reactions, enzymes, and metabolites across all domains of life.

Purpose of the Study:

  • To provide a comprehensive resource for exploring genomic and metabolic pathway information.
  • To offer computational tools for the analysis and visualization of metabolomics data.
  • To facilitate the storage, manipulation, and enrichment analysis of metabolite lists.

Main Methods:

  • Data integration from 5500 organism-specific databases.
  • Development of computational operations for metabolomics data analysis.
  • Implementation of features like SmartTables for metabolite list management and enrichment analysis.
  • Provision of interactive and programmatic web services for data access and analysis.

Main Results:

  • BioCyc.org serves as a central hub for diverse biological data.
  • The platform enables advanced metabolomics data analysis, including metabolite identification and enrichment.
  • Users can visualize metabolomics data on pathway and metabolic map diagrams.
  • Programmatic access to data and analysis tools is available.

Conclusions:

  • BioCyc.org is a valuable resource for researchers studying metabolism and genomics.
  • The portal's tools enhance the analysis and interpretation of metabolomics data.
  • Its comprehensive nature and accessibility support a wide range of biological research applications.