The Pathway Tools Schema

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The Pathway Tools Schema
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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
• When writing complex queries to PGDBs, those
  queries must name classes and slots within the
  schema
• A Pathway/Genome Database is a web of
  interconnected objects each object represents a
  biological entity

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Reference

• Pathway Tools Users Guide, Volume I
• Appendix A Guide to the Pathway Tools Schema

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Web of Relationships for One Enzyme
TCA Cycle
5
Frame Data Model

• Frame Data Model -- organizational structure for
  a PGDB
• Knowledge base (KB, Database, DB)
• Frames
• Slots
• Facets
• Annotations

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Knowledge Base

• Collection of frames and their associated slots,
  values, facets, and annotations
• AKA Database, PGDB
• Can be stored within
• An Oracle or MySQL DB
• A disk file
• Pathway Tools binary program

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Frames

• Entities with which facts are associated
• Kinds of frames
• Classes Genes, Pathways, Biosynthetic Pathways
• Instances (objects) trpA, TCA cycle
• Classes
• Superclass(es)
• Subclass(es)
• Instance(s)
• A symbolic frame name (id, key) uniquely
  identifies each frame

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Slots

• Encode attributes/properties of a frame
• Integer, real number, string
• Represent relationships between frames
• The value of a slot is the identifier of another
  frame
• Every slot is described by a slot frame in a KB
  that defines meta information about that slot

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Slot Links
TCA Cycle
in-pathway
reaction
catalyzes
component-of
product
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Slots

• Number of values
• Single valued
• Multivalued sets, bags
• Slot values
• Any LISP object Integer, real, string, symbol
  (frame name)
• Slotunits define properties of slots datatypes,
  classes, constraints
• Two slots are inverses if they encode opposite
  relationships
• Slot Product in class Genes
• Slot Gene in class Polypeptides

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Representation of Function
TCA Cycle
Left-end-position
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Monofunctional Monomer
Pathway
Reaction
Enzymatic-reaction
Monomer
Gene
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Bifunctional Monomer
Pathway
Reaction
Reaction
Enzymatic-reaction
Enzymatic-reaction
Monomer
Gene
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Monofunctional Multimer
Pathway
Reaction
Enzymatic-reaction
Multimer
Monomer
Monomer
Monomer
Monomer
Gene
Gene
Gene
Gene
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Pathway and Substrates
Reactant-1
Pathway
left
in-pathway
Reactant-2
Reaction
Reaction
Reaction
Reaction
Product-1
right
Product-2
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Transcriptional Regulation
trp
Int005
apoTrpR
TrpRtrp
Int001
site001
pro001
Int003
RpoSig70
trpL
trpLEDCBA
trpE
trpD
trpC
trpB
trpA
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Annotations

• Encode information about individual slot values
• Used to attach comments and citations to slot
  values
• Example
• Frame tryptophan-synthetase has a slot called
  Molecular-Weight with a value of 28
• Attached to that value is an annotation whose
  label is Citation and whose value is 3444332

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Facets

• Encode information about slots
• Allow association between a slot and
• comments
• citations
• Example Comment attached to Inhibitors of EnzRxn
• Allow access to schema information

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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
• Proteins, with subclasses
• Polypeptides
• Protein-Complexes

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Principle Classes

• Reactions, with subclasses
• Transport-Reactions
• Enzymatic-Reactions
• Pathways
• Compounds-And-Elements

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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

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Slots in Multiple Classes

• Common-Name
• Synonyms
• Names (computed as union of Common-Name,
  Synonyms)
• Comment
• Citations
• DB-Links

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Genes Slots

• Component-Of (links to replicon, transcription
  unit)
• Left-End-Position
• Right-End-Position
• Centisome-Position
• Transcription-Direction
• Product

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Proteins Slots

• Molecular-Weight-Seq
• Molecular-Weight-Exp
• pI
• Locations
• Modified-Form
• Unmodified-Form
• Component-Of

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Polypeptides Slots

• Gene

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Protein-Complexes Slots

• Components

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Reactions Slots

• EC-Number
• Left, Right
• Substrates (computed as union of Left, Right)
• DeltaG0
• Keq
• Spontaneous?

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Enzymatic-Reactions Slots

• Enzyme
• Reaction
• Activators
• Inhibitors
• Physiologically-Relevant
• Cofactors
• Prosthetic-Groups
• Alternative-Substrates
• Alternative-Cofactors

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Pathways Slots

• Reaction-List
• Predecessors
• Primaries