The EcoCyc and MetaCyc Pathway/Genome Databases

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The EcoCyc and MetaCyc Pathway/Genome Databases

• Peter D. Karp, Ph.D.
• Bioinformatics Research Group
• SRI International
• pkarp_at_ai.sri.com
• http//www.ai.sri.com/pkarp/
• http//EcoCyc.org/

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Overview

• Motivations and terminology
• Pathway/genome databases
• BioCyc collection
• EcoCyc, MetaCyc
• Pathway Tools software
• Bioinformatics Database Warehouse project

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What to do When Theories BecomeLarger than Minds
can Grasp?

• Example E. coli metabolic network
• 160 pathways involving 744 reactions and 791
  substrates
• Example E. coli genetic network
• Control by 97 transcription factors of 1174 genes
  in 630 transcription units
• Past solutions
• Partition theories across multiple minds
• Encode theories in natural-language text
• We cannot compute with theories in those forms
• Evaluate theories for consistency with new data
  microarrays
• Refine theories with respect to new data
• Compare theories describing different organisms

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Solution Biological Knowledge Bases

• Store biological knowledge and theories in
  computers in a declarative form
• Amenable to computational analysis and generative
  user interfaces
• Establish ongoing efforts to curate (maintain,
  refine, embellish) these knowledge bases
• Accepted to store data in computers, but not
  knowledge
• Such knowledge bases are an integral part of the
  scientific enterprise

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Pathway Definition

• Chemical reactions interconvert chemical
  compounds
• An enzyme is a protein that accelerates chemical
  reactions
• A pathway is a linked set of reactions
• Often regulated as a unit
• A conceptual unit of cells biochemical machine

A B C D
A C E
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Terminology

• Model Organism Database (MOD) DB describing
  genome and other information about an organism
• Pathway/Genome Database (PGDB) MOD that
  combines information about
• Pathways, reactions, substrates
• Enzymes, transporters
• Genes, replicons
• Transcription factors, promoters, operons, DNA
  binding sites
• BioCyc Collection of 15 PGDBs at BioCyc.org
• EcoCyc, AgroCyc, YeastCyc

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BioCyc Collection ofPathway/Genome DBs

• Computationally Derived Datasets
• Agrobacterium tumefaciens
• Caulobacter crescentus
• Chlamydia trachomatis
• Bacillus subtilis
• Helicobacter pylori
• Haemophilus influenzae
• Mycobacterium tuberculosis RvH37
• Mycobacterium tuberculosis CDC1551
• Mycoplasma pneumonia
• Pseudomonas aeruginosa
• Saccharomyces cerevisiae
• Treponema pallidum
• Vibrio cholerae
• Yellow Open Database

• Literature-based Datasets
• MetaCyc
• Escherichia coli (EcoCyc)

http//BioCyc.org/
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Terminology Pathway Tools Software

• PathoLogic
• Prediction of metabolic network from genome
• Computational creation of new Pathway/Genome
  Databases
• Pathway/Genome Editors
• Distributed curation of PGDBs
• Distributed object database system, interactive
  editing tools
• Pathway/Genome Navigator
• WWW publishing of PGDBs
• Querying, visualization of pathways, chromosomes,
  operons
• Analysis operations
• Pathway visualization of gene-expression data
• Global comparisons of metabolic networks
• Bioinformatics 18S225 2002

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Pathway Tools Algorithms

• Query, visualization and editing tools for these
  datatypes
• Full Metabolic Map
• Paint gene expression data on metabolic network
  compare metabolic networks
• Pathways
• Pathway prediction
• Reactions
• Balance checker
• Compounds
• Chemical substructure comparison
• Enzymes, Transporters, Transcription Factors
• Genes Blast search
• Chromosomes
• Operons
• Operon prediction

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Model Organism Databases

• DBs that describe the genome and other
  information about an organism
• Every sequenced organism with an active
  experimental community requires a MOD
• Integrate genome data with information about the
  biochemical and genetic network of the organism
• MODs are platforms for global analyses of an
  organism
• Interpret gene expression data in a pathway
  context
• Characterize systems properties of metabolic and
  genetic networks
• Determine consistency of metabolic and transport
  networks
• In silico prediction of essential genes

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EcoCyc Project EcoCyc.org

• E. coli Encyclopedia
• Model-Organism Database for E. coli
• Computational symbolic theory of E. coli
• Electronic review article for E. coli over 3500
  literature citations
• Tracks the evolving annotation of the E. coli
  genome
• Collaborative development via Internet
• Karp (SRI) -- Bioinformatics architect
• John Ingraham -- Advisor
• (SRI) Metabolic pathways
• Saier (UCSD) and Paulsen (TIGR)-- Transport
• Collado (UNAM)-- Regulation of gene expression
• Database content 18,000 objects

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EcoCyc E.coli Dataset
Pathway/Genome Navigator
Pathways 165
Reactions 2,760
Compounds 774
Enzymes 914 Transporters 162 Promoters
812 TransFac Sites 956 Citations 3,508
Proteins 4,273
Transcription Units 724 Factors 110
Genes 4,393
http//EcoCyc.org/
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EcoCyc Procedures

• All DB updates by 5 staff curators
• Information gathered from biomedical literature
• Corrections solicited from E. coli researchers
• Review-level database
• Four releases per year
• Available through WWW site, as data files, as
  downloadable application
• Quality assurance of data and software
• Evaluate database consistency constraints
• Perform element balancing of reactions
• Run other checking programs
• Display every DB object

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MetaCyc Metabolic Encyclopedia

• Nonredundant metabolic pathway database
• Describe a representative sample of every
  experimentally determined metabolic pathway
• Literature-based DB with extensive references and
  commentary
• Pathways, reactions, enzymes, substrates
• 460 pathways, 1267 enzymes, 4294 reactions
• 172 E. coli pathways, 2735 citations
• Nucleic Acids Research 3059-61 2002.
• Jointly developed by SRI and Carnegie Institution
• New focus on plant pathways

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Family of Pathway/GenomeDatabases
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Pathway Tools Implementation Details

• Allegro Common Lisp
• Sun and PC platforms
• Ocelot object database
• 250,000 lines of code
• Lisp-based WWW server at BioCyc.org
• Manages 15 PGDBs

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Pathway Tools Architecture
Pathway Genome Navigator
Object DBMS
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Ocelot Knowledge Server Architecture

• Frame data model
• Classes, instances, inheritance
• Frames have slots that define their properties,
  attributes, relationships
• A slot has one or more values
• Each value can be any Lisp datatype
• Slotunits define metadata about slots
• Domain, range, inverse
• Collection type, number of values, value
  constraints
• Transaction logging facility
• Schema evolution

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Ocelot Storage System Architecture

• Persistent storage via disk files, Oracle DBMS
• Concurrent development Oracle
• Single-user development disk files
• Read-only delivery bundle data into binary
  program
• Oracle storage
• DBMS is submerged within Ocelot, invisible to
  users
• Relational schema is domain independent, supports
  multiple KBs simultaneously
• Frames transferred from DBMS to Ocelot
• On demand
• By background prefetcher
• Memory cache
• Persistent disk cache to speed performance via
  Internet

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The Common Lisp ProgrammingEnvironment

• Gatt studied Lisp and Java implementation of 16
  programs by 14 programmers (Intelligence 1121
  2000)

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EcoCyc WWW Server
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Pathway/Genome DBs Created byExternal Users

• Plasmodium falciparum, Stanford University
• plasmocyc.stanford.edu
• Mycobacterium tuberculosis, Stanford University
• BioCyc.org
• Arabidopsis thaliana and Synechosistis, Carnegie
  Institution of Washington
• Arabidopsis.org1555
• Methanococcus janaschii, EBI
• Maine.ebi.ac.uk1555
• Other PGDBs in progress by 24 other users
• Software freely available
• Each PGDB owned by its creator

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Global Consistency Checking of Biochemical
Network

• Given
• A PGDB for an organism
• A set of initial metabolites
• Infer
• What set of products can be synthesized by the
  small-molecule metabolism of the organism
• Can known growth medium yield known essential
  compounds?
• Pacific Symposium on Biocomputing p471 2001

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AlgorithmForward Propagation
Nutrient set
Products
PGDB reaction pool
Transport
Fire reactions
Metabolite set
Reactants
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Results

• Phase I Forward propagation
• 21 initial compounds yielded only half of 38
  essential compounds for E. coli
• Phase II Manually identify
• Bugs in EcoCyc (e.g., two objects for tryptophan)
• Missing initial protein substrates (e.g., ACP)
• Missing pathways in EcoCyc
• Phase III Forward propagation with 11 more
  initial metabolites
• Yielded all 38 essential compounds

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Nutrient-Related AnalysisValidation of the
EcoCyc Database

• Results on EcoCyc

• Phase I
• Essential compounds
• produced 19
• not produced 19
• Total compounds
• produced (28)
• Reactions
• Fired (31)

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Missing Essential Compounds Due To

• Bugs in EcoCyc
• Narrow conceptualization of the problem
• Protein substrates
• Incomplete biochemical knowledge

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Nutrient-Related AnalysisValidation of the
EcoCyc Database

• Results on EcoCyc

• Phase II (After adding 11 extra metabolites)
• Essential compounds
• produced 38
• not produced 0
• Total compounds
• produced (49)
• not produced (51)
• Reactions
• Fired (58)
• Not fired (42)

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Pathway Tools Misconceptions

• PathoLogic
• Does not re-annotate genomes
• Pathway Tools does not handle quantitative
  information
• Pathway/Genome Editors do not work through the
  web

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HumanCyc Human Metabolic PathwayDatabase
Consortium

• Construct DB of human metabolic pathways using
  PathoLogic
• Link to human genome web sites
• Hire one curator to refine and curate with
  respect to literature over a 2 year period
• Remove false-positive predictions
• Insert known pathways missed by PathoLogic
• Add comments and citations from pathways and
  enzymes to the literature
• Add enzyme activators, inhibitors, cofactors,
  tissue information
• Available as flatfiles and with Pathway/Genome
  Navigator
• New versions to be released every 6 months

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Summary

• Pathway/Genome Databases
• MetaCyc non-redundant DB of literature-derived
  pathways
• 14 organism-specific PGDBs available through SRI
  at BioCyc.org
• Computational theories of biochemical machinery
• Pathway Tools software
• Extract pathways from genomes
• Morph annotated genome into structured ontology
• Distributed curation tools for MODs
• Query, visualization, WWW publishing

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BioCyc and Pathway Tools Availability

• WWW BioCyc freely available to all
• BioCyc.org
• Six BioCyc DBs openly available to all
• BioCyc DBs freely available to non-profits
• Flatfiles downloadable from BioCyc.org
• Binary executable
• Sun UltraSparc-170 w/ 64MB memory
• PC, 400MHz CPU, 64MB memory, Windows-98 or newer
• PerlCyc API
• Pathway Tools freely available to non-profits

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Acknowledgements

• SRI
• Suzanne Paley, Pedro Romero, John Pick, Cindy
  Krieger, Martha Arnaud
• EcoCyc Project
• Julio Collado-Vides, Ian Paulsen, Monica Riley,
  Milton Saier
• MetaCyc Project
• Sue Rhee, Lukas Mueller, Peifen Zhang, Chris
  Somerville
• Stanford
• Gary Schoolnik, Harley McAdams, Lucy Shapiro,
  Russ Altman, Iwei Yeh

• Funding sources
• NIH National Center for Research Resources
• NIH National Institute of General Medical
  Sciences
• NIH National Human Genome Research Institute
• Department of Energy Microbial Cell Project
• DARPA BioSpice, UPC

BioCyc.org