The Pathway Tools Schema - PowerPoint PPT Presentation

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The Pathway Tools Schema

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Bioinformatics. Motivations for Understanding Schema ... Bioinformatics. Frame Data Model. Frame Data Model ... Bioinformatics. Knowledge Base ... – PowerPoint PPT presentation

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Title: The Pathway Tools Schema


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
  • 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

3
Reference
  • Pathway Tools Users Guide, Volume I
  • Appendix A Guide to the Pathway Tools Schema

4
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

6
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

7
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

8
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

9
Slot Links
TCA Cycle
in-pathway
reaction
catalyzes
component-of
product
10
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

11
Representation of Function
TCA Cycle
Left-end-position
12
Monofunctional Monomer
Pathway
Reaction
Enzymatic-reaction
Monomer
Gene
13
Bifunctional Monomer
Pathway
Reaction
Reaction
Enzymatic-reaction
Enzymatic-reaction
Monomer
Gene
14
Monofunctional Multimer
Pathway
Reaction
Enzymatic-reaction
Multimer
Monomer
Monomer
Monomer
Monomer
Gene
Gene
Gene
Gene
15
Pathway and Substrates
Reactant-1
Pathway
left
in-pathway
Reactant-2
Reaction
Reaction
Reaction
Reaction
Product-1
right
Product-2
16
Transcriptional Regulation
trp
Int005
apoTrpR
TrpRtrp
Int001
site001
pro001
Int003
RpoSig70
trpL
trpLEDCBA
trpE
trpD
trpC
trpB
trpA
17
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

18
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

19
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

20
Principle Classes
  • Reactions, with subclasses
  • Transport-Reactions
  • Enzymatic-Reactions
  • Pathways
  • Compounds-And-Elements

21
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

22
Slots in Multiple Classes
  • Common-Name
  • Synonyms
  • Names (computed as union of Common-Name,
    Synonyms)
  • Comment
  • Citations
  • DB-Links

23
Genes Slots
  • Component-Of (links to replicon, transcription
    unit)
  • Left-End-Position
  • Right-End-Position
  • Centisome-Position
  • Transcription-Direction
  • Product

24
Proteins Slots
  • Molecular-Weight-Seq
  • Molecular-Weight-Exp
  • pI
  • Locations
  • Modified-Form
  • Unmodified-Form
  • Component-Of

25
Polypeptides Slots
  • Gene

26
Protein-Complexes Slots
  • Components

27
Reactions Slots
  • EC-Number
  • Left, Right
  • Substrates (computed as union of Left, Right)
  • DeltaG0
  • Keq
  • Spontaneous?

28
Enzymatic-Reactions Slots
  • Enzyme
  • Reaction
  • Activators
  • Inhibitors
  • Physiologically-Relevant
  • Cofactors
  • Prosthetic-Groups
  • Alternative-Substrates
  • Alternative-Cofactors

29
Pathways Slots
  • Reaction-List
  • Predecessors
  • Primaries
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