Using the MetaCyc Pathway Database and the BioCyc Database Collection

Ron Caspi1, Peter D. Karp1

1 SRI International, Menlo Park, California
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.17
DOI:  10.1002/0471250953.bi0117s20
Online Posting Date:  December, 2007
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

Abstract

The MetaCyc database (http://metacyc.org) is a collection of more than a thousand metabolic pathways from a wide variety of organisms, collected from the literature by manual curation. BioCyc contains more than 370 Pathway/Genome Databases, each of which describes the genome and predicted metabolic pathways of a single organism, as computationally predicted from the annotated genomes, using MetaCyc data as a reference. The protocols in this unit introduce the user to the extensive data content available in MetaCyc and BioCyc, and to mechanisms for querying, visualizing, and analyzing these data using the Pathway Tools software. Curr. Protoc. Bioinform. 20:1.17.1‐1.17.51. © 2007 by John Wiley & Sons, Inc.

Keywords: metabolism; pathways; omics viewer; expression analysis tools; pathway comparison; genomics

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Introduction
  • Basic Protocol 1: The MetaCyc Pathway Database Home Page
  • Basic Protocol 2: Browsing the Database
  • Basic Protocol 3: Searching Using the Query Page Through the Web Server
  • Alternate Protocol 1: Searching the Database Using the Desktop Version
  • Basic Protocol 4: Searching the Database Using the Advanced Query Form
  • Basic Protocol 5: Finding Information About Enzymes
  • Basic Protocol 6: Finding Information About Pathways
  • Basic Protocol 7: Using the Genome Browser
  • Basic Protocol 8: Performing a Cross‐Species Pathway and Gene Comparison
  • Basic Protocol 9: Using the Cellular Overview Diagram Through the Web Server
  • Alternate Protocol 2: Using the Cellular Overview in the Desktop Version of Pathway Tools
  • Basic Protocol 10: Using the Regulatory Overview in the Desktop Version
  • Basic Protocol 11: Using the Genome Overview in the Desktop Version
  • Basic Protocol 12: Using the Cellular Omics Viewer Through the Web Server
  • Alternate Protocol 3: Using the Cellular Omics Viewer in the Desktop Version of Pathway Tools
  • Basic Protocol 13: Generating Posters from PGDBs
  • Basic Protocol 14: Downloading PGDBs from the PGDB Registry
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

   Caspi, R., Foerster, H., Fulcher, C.A., Hopkinson, R., Ingraham, J., Kaipa, P., Krummenacker, M., Paley, S., Pick, J., Rhee, S.Y., Tissier, C., Zhang, P., and Karp, P.D. 2006. MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 34:D1‐D6.
   Green, M.L. and Karp, P.D. 2004. A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 5:76.
   Karp, P.D., Ouzounis, C.A., Moore‐Kochlacs, C., Goldovsky, L., Kaipa, P., Ahrén, D., Tsoka, S., Darzentas, N., Kunin, V., and López‐Bigas, N. 2005. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 33:6083‐6089.
   Karp, P.D., Paley, S., and Romero, P. 2002. The Pathway Tools software. Bioinformatics 18;S225‐S232.
   Krieger, C.J., Zhang, P., Mueller, L.A., Wang, A., Paley, S., Arnaud, M., Pick, J., Rhee, S.Y., and Karp, P.D. 2004. MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 32:D438‐D442.
   Paley, S.M. and Karp, P.D. 2006. The Pathway Tools cellular overview diagram and Omics Viewer Nucleic Acids Res. 34:3771‐3778.
Internet Resources
   http:/metacyc.org
  MetaCyc home page
   http:/biocyc.org
  BioCyc home page
   http:/ecocyc.org
  EcoCyc home page
   http:/humancyc.org
  HumanCyc home page
   http://bioinformatics.ai.sri.com/ptools/
  Pathway Tools information site
   http://biocyc.org/biocyc‐pgdb‐list.shtml
  List of all BioCyc Pathway/Genome Databases
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library