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The Pathway Tools Schema

The Pathway Tools Schema. Motivations for Understanding Schema. Pathway Tools visualizations and analyses depend upon the software being able to find precise information in precise places within a Pathway/Genome DB

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The Pathway Tools Schema

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  1. The Pathway Tools Schema

  2. Motivations for Understanding Schema • Pathway Tools visualizations and analyses depend upon the software being able to find precise information in precise places within a Pathway/Genome DB • A Pathway/Genome Database is a web of interconnected objects; each object represents a biological entity

  3. Motivations for UnderstandingPathway Tools Schema • When writing complex queries to PGDBs, those queries must refer to classes and slots within the schema • Queries using Lisp, Perl, Java APIs • Queries using Query Page • Queries using Structured Advanced Query Form

  4. References • Pathway Tools User’s Guide • Appendix A: Guide to the Pathway Tools Schema • Ontology Papers section of http://biocyc.org/publications.shtml • “The outcomes of pathway database computations depend on pathway ontology” • "An Evidence Ontology for use in Pathway/Genome Databases," • "An ontology for biological function based on molecular interactions," • "Representations of metabolic knowledge: Pathways," • "Representations of metabolic knowledge,"

  5. Pathway Tools Ontology / Schema • Ontology classes: 1621 • Many datatypes from genomes to pathways • Classification schemes for pathways, chemical compounds, enzymatic reactions (EC system) • Cell Component Ontology • Protein Feature ontology • Comprehensive set of 221 attributes and relationships • Evidence codes, supporting citations

  6. Root Classes in the Pathway ToolsOntology • Chemicals -- All molecules • Polymer-Segments -- Regions of polymers • Protein-Features -- Features on proteins • Paralogous-Gene-Groups • Organisms • Enzymatic-Reactions -- Link enzymes to reactions they catalyze • Generalized-Reactions -- Reactions and pathways • Regulation -- Defines regulatory interactions • CCO -- Cell Component Ontology • Evidence -- Evidence ontology • Notes -- Timestamped, person-stamped notes • Organizations • People • Publications

  7. Principle Classes • Class names are capitalized, plural, separated by dashes • Genetic-Elements, with subclasses: • Chromosomes • Plasmids • Genes • Transcription-Units • RNAs • rRNAs, snRNAs, tRNAs, Charged-tRNAs, Regulatory-RNAs • Proteins, with subclasses: • Polypeptides • Protein-Complexes

  8. Principle Classes • Reactions, with subclasses: • Transport-Reactions • Enzymatic-Reactions • Pathways • Compounds-And-Elements

  9. Web of Relationships for One Enzyme Succinate + FAD = fumarate + FADH2 Enzymatic-reaction Succinate dehydrogenase Sdh-flavo Sdh-Fe-S Sdh-membrane-1 Sdh-membrane-2 sdhC sdhD sdhA sdhB TCA Cycle

  10. Representation of Function EC# Keq Succinate + FAD = fumarate + FADH2 Cofactors Enzymatic-reaction Molecular-Weight-Seq Molecular-Weight-Exp pI Succinate dehydrogenase Sdh-flavo Sdh-Fe-S Sdh-membrane-1 Sdh-membrane-2 sdhC sdhD sdhA sdhB TCA Cycle Left-end-position

  11. Monofunctional Monomer Pathway Reaction Enzymatic-reaction Monomer Gene

  12. Bifunctional Monomer Pathway Reaction Reaction Enzymatic-reaction Enzymatic-reaction Monomer Gene

  13. Monofunctional Multimer Pathway Reaction Enzymatic-reaction Multimer Monomer Monomer Monomer Monomer Gene Gene Gene Gene

  14. Pathway and Substrates Reactant-1 Pathway left in-pathway Reactant-2 Reaction Reaction Reaction Reaction Product-1 right Product-2

  15. Regulation • Reorganization and expansion of regulation under way in Pathway Tools • Initial application to EcoCyc • Class Regulation with subclasses that describe different biochemical mechanisms of regulation • Slots: • Regulator • Regulated-Entity • Mode • Mechanism

  16. Regulation of Enzyme Activity • Class Regulation-of-Enzyme-Activity • Each instance of the class describes one regulatory interaction • Slots: • Regulator -- usually a small molecule • Regulated-Entity -- an Enzymatic-Reaction • Mechanism -- One of: • Competitive, Uncompetitive, Noncompetitive, Irreversible, Allosteric, Unkmech, Other • Mode -- One of: + , -

  17. Transcription Initiation • Class Regulation-of-Transcription-Initiation • Slots: • Regulator -- instance of Proteins or Complexes (a transcription-factor) • Regulated-Entity -- instance of Promoters or Transcription-Units or Genes • Mode -- One of: + , -

  18. Attenuation • Class Transcriptional-Attenuation • Several subclasses depending on type of attenuation • Slots common to all: • Regulator -- Depends on subtype of attenuation • Regulated-Entity -- instance of Terminators or Genes or Transcription-Units • Mode -- One of: + , -

  19. Attenuation Subtypes • Small-Molecule-Mediated-Attenuation • Regulator = A small molecule • Leader transcript binds small molecule and determines formation of terminator or antiterminator • RNA-Polymerase-Modification • Regulator = instance of Proteins or Complexes • Regulatory protein binds to site in transcription unit and interacts with RNA polymerase to determine termination • RNA-Mediated-Attenuation • Ribosome-Mediated-Attenuation • Rho-Blocking-Antitermination • Protein-Mediated-Attenuation

  20. Frame IDs of Instances • Instance frame ID conventions have evolved over time • Examples: • Pathways • TRPSYN-PWY, P23-PWY • Genes • AG10045 • Monomers • TRPA-MONOMER, AG10045-MONOMER

  21. Slots in Multiple Classes • Common-Name • Synonyms • Names (computed as union of Common-Name, Synonyms) • Comment • Citations • DB-Links

  22. Genes Slots • Component-Of (links to replicon, transcription unit) • Left-End-Position • Right-End-Position • Transcription-Direction • Product

  23. Proteins Slots • Molecular-Weight-Seq • Molecular-Weight-Exp • pI • Locations • Modified-Form • Unmodified-Form • Component-Of

  24. Polypeptides Slots • Slots inherited from Proteins • Gene

  25. Protein-Complexes Slots • Slots inherited from Proteins • Components

  26. Reactions Slots • EC-Number • Left, Right • DeltaG0 • Keq • Spontaneous?

  27. Enzymatic-Reactions Slots • Enzyme • Reaction • Cofactors • Prosthetic-Groups • Alternative-Substrates

  28. Pathways Slots • Reaction-List • Predecessors • Primaries

  29. Inspecting PGDB Instance Frames • Right-click on object handles to find frame-id • Show menu allows printing of frames

  30. Inspecting PGDB Schema • Invoke GKB Editor Taxonomy Browser: • (gkb) or • Right-click: Edit  Ontology Editor • Invoke GKB Editor frame editor: • Right-click: Edit  Frame Editor • Information about GKB Editor: • User Guide: http://www.ai.sri.com/~gkb/user-man.html • Publication: http://www.ai.sri.com/pkarp/pubs/97gkb.ps

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