1. Overview of the Pathway Tools Software and Pathway/Genome Databases
© 2013 SRI International

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Founded by Stanford University in 1946
Independent in 1970; changed name from Stanford Research Institute to SRI International in 1977
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OPPORTUNITIES
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3. Tutorial Overview Mix of lectures and lab sessions
Questions encouraged at any time

4. MetaCyc Family of Pathway/Genome Databases
20,000+ databases from many institutions
All domains of life with microbial emphasis
Genomes plus predicted metabolic pathways
DBs derived from MetaCyc via computational pathway prediction
Common schema
Common controlled vocabularies
Managed using Pathway Tools software
MetaCyc Family
20,000+
BioCyc.org
11,000
Archives of Toxicology 85:

5. Highly Curated Pathway/Genome Databases
Organism
Organization
Publications Curated From
MetaCyc
Multiorganism
SRI
51,000
EcoCyc
E. coli
33,000
BsubCyc
B. subtilis
4,000
HumanCyc
H. sapiens
AraCyc
A. thaliana
TAIR/Carnegie Institution
4,100
YeastCyc
S. cerevisiae
SGD/SRI
980
MouseCyc
M. musculus
MGD/Jackson Laboratory

6. Pathway Tools Enables Multi-Use Metabolic Databases
Metabolic Model
Encyclopedia
Queryable Database
Mention that all of these five usage facets are validated.
Zoomable Metabolic Map
Omics Data
Analysis

7. + Annotated PathoLogic Genome MetaCyc Pathway/Genome Pathway/Genome
Database
Pathway/Genome
Navigator
MetaFlux
Pathway/Genome
Editors
Briefings in Bioinformatics 11:
Licensed by 8,000+ Groups

8. Pathway/Genome Navigator Omics Viewers SmartTables
Outline for Tutorial
Introduction
Pathway/Genome Navigator
Omics Viewers
SmartTables

9. MetaCyc: Curated Metabolic Database
MetaCyc v
KEGG
2017
SEED
2015
Citations
51,000
Pathways
2,500
316
Modules
583
Subsystems
Reactions
13,800
10,411
Metabolites
13,400
17,883
Mini-reviews (textbook pages)
7,500
MetaCyc is free and open, contains computed atom mappings
“A Systematic Comparison of the MetaCyc and KEGG Pathway Databases
BMC Bioinformatics (1):112

10. Information Sources -- Publications
Primary Pathway Tools citation:
"Pathway Tools version 19.0: Integrated Software for Pathway/Genome Informatics and Systems Biology," Briefings in Bioinformatics 2015.
Pathway Tools overview publication:
"Pathway Tools version 19.0: Integrated Software for Pathway/Genome Informatics and Systems Biology", 2015,
Primary BioCyc/MetaCyc citation:
"The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases", Nucleic Acids Res, 44:D471-80, 2016.

11. Information Sources BioCyc Web site: Help Menu Basic Help Search Help
BioCyc Glossary
Publications
Website User Guide
PGDB Concepts
Guide to EcoCyc
Guide to MetaCyc