JOT: a Protg Scripting Environment for Creating and Managing - - PowerPoint PPT Presentation

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JOT: a Protg Scripting Environment for Creating and Managing - - PowerPoint PPT Presentation

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JOT: a Protg Scripting Environment for Creating and Managing Ontologies Olivier Dameron SMI - Stanford University Protg Conference 2004 Context / Problems 1. Repetitive tasks ex: creation of lateralized concepts and their

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JOT: a Protégé Scripting Environment for Creating and Managing Ontologies

Olivier Dameron

Protégé Conference 2004

SMI - Stanford University

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Context / Problems

  • 1. Repetitive tasks

ex: creation of lateralized concepts and their relationships

  • 2. Enumerations

ex: Ribs

  • 3. Dependancies between concepts or

relationships ex: Thorax / Skin of Thorax

  • 4. Ontology maintenance

require adhoc detection and fixing

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Objective:

Scripting environment for Protégé

  • 1. Create macros
  • 1. repetitive and error-prone tasks
  • 2. formalism for handling intrinsic complexity
  • 3. towards more abstraction
  • 2. Code reuse
  • 3. User-friendly and powerfull
  • 1. simple and intuitive syntax
  • 2. well formalised
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Architecture

  • 1. Principle
  • 1. Python interpreter in Java: Jython
  • 2. Thread (share address space with Protégé)
  • 2. Shared variable: kb
  • 3. Compatibility with frames and OWL
  • 1. instance of KnowledgeBase (Frames)
  • 2. instance of OWLKnowledgeBase (OWL)
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Architecture

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SLIDE 6

Architecture

  • 1. Python Code
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SLIDE 7

Architecture

  • 1. Python Code
  • 2. Python Console
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SLIDE 8

Architecture

  • 1. Python Code
  • 2. Python Console
  • 3. Jython
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SLIDE 9

Architecture

  • 1. Python Code
  • 2. Python Console
  • 3. Jython

JOT

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SLIDE 10

Architecture

  • 1. Python Code
  • 2. Python Console
  • 3. Jython
  • 4. Protégé

JOT

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SLIDE 11

Architecture

  • 1. Python Code
  • 2. Python Console
  • 3. Jython
  • 4. Protégé

kb

JOT

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Frames

  • 1. Get frame's attributes
  • 2. Create frame
  • 3. Create instances
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Frames

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Frames

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Frames

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Frames

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Frames

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OWL

  • 1. Get classes' attributes
  • 2. Create class
  • 3. Create relations
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OWL

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OWL

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OWL

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OWL

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Repetitive tasks

Creation of a lateralized anatomical concept: Hand

  • create Hand
  • create subconcepts LeftHand and

RightHand

  • define LeftHand = Hand on the LeftSide
  • Hand: either LeftHand or RightHand
  • LeftHand and RightHand are disjoint
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Repetitive tasks

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Repetitive tasks

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Repetitive tasks

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Repetitive tasks

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Repetitive tasks

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Repetitive tasks

createLateralizedConcept(“Hand”, “Anat”):

c = createConcept(“Hand”, “AnatomicalConcept”) lc = createConcept(“LeftHand”, “Hand”) rc = createConcept(“RightHand”, “Hand”) define c = lc or rc define lc = c and LeftAnatomicalConcept define rc = c and RightAnatomicalConcept make lc and rc disjoint

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Repetitive tasks

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Repetitive tasks

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Repetitive tasks

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Repetitive tasks

After classification:

  • LeftThumb
  • LeftIndex
  • LeftMiddleFinger
  • LeftRingFinger
  • LeftLittleFinger

... are LeftFinger

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Enumerations

  • 1. Vertebrae
  • 2. Ribs (lateralized !)
  • 3. Muscles
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Enumerations

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Enumerations

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Enumerations

Coverage (automatically generated)

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Dependencies

  • 1. Ex: Wall of Heart

Heart = WallOfHeart, Septum, 4 cavities Heart = LeftAtrium, RightAtrium, LeftVentricle, RightVentricle

  • 2. WallOfLeftAtrium

constitutionalPartOf LeftAtrium regionalPartOf WallOfHeart

  • 3. Epicardium, Myocardium, Endocardium

constitutionalPartOf WallOfLeftAtrium regionalPartOf Epicardium

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Dependencies

16 composed concepts 32 relations of direct composition You are lucky if you don't forget one If you do, enjoy the debuging Not scalable

no neighborhood relationships {anterior, posterior, lateral} + {inferior, superior} parts of LeftAtrium

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Ontology maintenance

  • 1. Make specific functions on the fly
  • 2. Reuse functions
  • 3. Dynamically insert / remove java listeners
  • 4. Take advantage of all the existing Java

libraries (web services, ...)

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Lessons learned

JOT is usefull :-)

higher level functions from extensional to intensional description

Domain-independant but language-specific macros Domain-dependant but language independent functions (reuse functions from 1 according to the language)

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Conclusion

  • 1. Direct calls to the Protégé API => no

limitations

  • 2. Jython => power of Python + Java
  • 3. Code reuse allow to hide the low-level

Protégé API