Transformation of Protg Ontologies into the Eclipse Modeling - - PowerPoint PPT Presentation

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Transformation of Protg Ontologies into the Eclipse Modeling - - PowerPoint PPT Presentation

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Transformation of Protg Ontologies into the Eclipse Modeling Framework Deepak Sharma Division of Biomedical Informatics Mayo Clinic 1 Outline Motivation Eclipse Modeling Framework (EMF) EMF at work LexGrid Model & FMA

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Transformation of Protégé Ontologies into the Eclipse Modeling Framework

Deepak Sharma Division of Biomedical Informatics Mayo Clinic

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Outline

  • Motivation
  • Eclipse Modeling Framework (EMF)
  • EMF at work
  • LexGrid Model & FMA Mapping
  • FMA Transformation Example
  • Conclusion
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Outline

  • Motivation
  • Eclipse Modeling Framework (EMF)
  • EMF at work
  • LexGrid Model & FMA Mapping
  • FMA Transformation Example
  • Conclusion
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Outline

Lots of things to talk about in short time

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Outline

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Motivation

Why do a transformation?

  • Native form of FMA cannot be readily integrated

into grid, databases and other terminologies

  • Need to transform content into a format and

structure that is readily accessible via:

  • Standard API’s
  • SQL
  • …
  • The Mayo LexGrid model is one such candidate
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Motivation

Why EMF ?

  • Easy & Simple to:
  • Use EMF Transformation
  • Integrate EMF with Protégé
  • Use EMF as a hub
  • Successful FMA transformation
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What is EMF ?

Eclipse Modeling Framework

  • Framework & Code Generation

tool

  • Available with Eclipse
  • Modeling EMF Programming
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Eclipse Modeling Framework

EMF XML Schema UML Java

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Eclipse Modeling Framework

  • Model in XMI (XML Metadata

Interchange) format

  • EMF Project
  • ECORE
  • GENMODEL
  • Generated Code can be customized
  • Easy to Update & Regenerate
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EMF

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Eclipse Modeling Framework

http://www.eclipse.org/emf/

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EMF at work

  • Output
  • Mapping
  • Protégé Content
  • Model &

Representation

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EMF at work

  • Output
  • Mapping
  • Protégé Content
  • Model &

Representation LexGrid XML Document

  • FMA to LexGrid Model
  • FMA
  • LexGrid Model in XML

Schema

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EMF at work

Model Representation

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EMF at work

Model Representation

XML Schema UML

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EMF at work

Model Representation

XML Schema UML

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EMF at work

Model Representation (XSD)

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EMF at work

Model Representation (XSD)

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EMF at work

Create an EMF Project

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EMF at work

Create an EMF Project

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EMF at work

Create an EMF Project

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EMF at work

Create an EMF Project

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EMF at work

Create an EMF Project

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EMF at work

EMF Project Components

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EMF at work

EMF Project Components

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EMF at work

EMF Project Components

CORE GENMODEL

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EMF at work

EMF CORE Component

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EMF at work

EMF CORE Component

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EMF at work

EMF GENMODEL Component

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EMF at work

EMF GENMODEL Component

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EMF at work

Generate Implementation

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EMF at work

Generate Implementation

Generates Implementation

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EMF at work

Implementation

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EMF at work

Implementation Generated Implementation

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EMF at work

XML Schema Snapshot

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EMF at work

Generated Implementation

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EMF at work

Generated Implementation

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EMF at work

Generated Implementation More implementation classes snapshots Later in this presentation

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EMF at work

  • Customize the implementation
  • Before & After Generation
  • Make EMF implementation available

by either :

  • Create and include as an Archive
  • Application dependent on EMF

implementation classes.

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EMF at work

  • Customize the implementation
  • Before & After Generation
  • Make EMF implementation available

by either :

  • Create and include as an Archive
  • Application dependent on EMF

implementation classes.

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EMF at work

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EMF at work

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LexGrid Model

  • Developed by Mayo Biomedical

Informatics Group

  • Formal model of terminology
  • Explicit definition of entities &
  • bjects used in LexGrid tooling
  • Supports non-semantic entities (from

the toolkit perspective) as name/value pair

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LexGrid Model

Information Model (partial)

cd codingSchemes describable

codingScheme concepts::concepts

describable

relations::relations

describable

relations::association relations:: associationInstance

associatableElement

relations::associationTarget

versionableAndDescribable

concepts::codedEntry concepts::property concepts::comment concepts::definition concepts::presentation

0..1 +concepts 0..* +relations 1..* +association 0..* +sourceConcept 0..* +targetConcept 1..* +concept 0..* +property

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LexGrid Model

Coding Scheme Node

cd codingSchemes describable

codingScheme concepts::concepts

describable

relations::relations

describable

relations::association relations:: associationInstance

associatableElement

relations::associationTarget

versionableAndDescribable

concepts::codedEntry concepts::property concepts::comment concepts::definition concepts::presentation

0..1 +concepts 0..* +relations 1..* +association 0..* +sourceConcept 0..* +targetConcept 1..* +concept 0..* +property

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LexGrid Model

Information Model (partial)

cd codingSchemes describable

codingScheme concepts::concepts

describable

relations::relations

describable

relations::association relations:: associationInstance

associatableElement

relations::associationTarget

versionableAndDescribable

concepts::codedEntry concepts::property concepts::comment concepts::definition concepts::presentation

0..1 +concepts 0..* +relations 1..* +association 0..* +sourceConcept 0..* +targetConcept 1..* +concept 0..* +property

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LexGrid Model

Coded Entry

cd codingSchemes describable

codingScheme concepts::concepts

describable

relations::relations

describable

relations::association relations:: associationInstance

associatableElement

relations::associationTarget

versionableAndDescribable

concepts::codedEntry concepts::property concepts::comment concepts::definition concepts::presentation

0..1 +concepts 0..* +relations 1..* +association 0..* +sourceConcept 0..* +targetConcept 1..* +concept 0..* +property

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LexGrid Model

Information Model (partial)

cd codingSchemes describable

codingScheme concepts::concepts

describable

relations::relations

describable

relations::association relations:: associationInstance

associatableElement

relations::associationTarget

versionableAndDescribable

concepts::codedEntry concepts::property concepts::comment concepts::definition concepts::presentation

0..1 +concepts 0..* +relations 1..* +association 0..* +sourceConcept 0..* +targetConcept 1..* +concept 0..* +property

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LexGrid Model

Concept Property

cd codingSchemes describable

codingScheme concepts::concepts

describable

relations::relations

describable

relations::association relations:: associationInstance

associatableElement

relations::associationTarget

versionableAndDescribable

concepts::codedEntry concepts::property concepts::comment concepts::definition concepts::presentation

0..1 +concepts 0..* +relations 1..* +association 0..* +sourceConcept 0..* +targetConcept 1..* +concept 0..* +property

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LexGrid Model

CodedEntry Node

Concept Code Concept Name Property Name Property Value

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LexGrid Model

Association Node

cd relations describable

association + «XSDattribute» association: localName + «XSDattribute» forwardName: tsCaseIgnoreIA5String + «XSDattribute» isAntiReflexive [0..1]: tsBoolean [0..1] + «XSDattribute» isAntiSymmetric [0..1]: tsBoolean [0..1] + «XSDattribute» isAntiTransitive [0..1]: tsBoolean [0..1] + «XSDattribute» isFunctional [0..1]: tsBoolean [0..1] + «XSDattribute» isReflexive [0..1]: tsBoolean [0..1] + «XSDattribute» isReverseFunctional [0..1]: tsBoolean [0..1] + «XSDattribute» isSymmetric [0..1]: tsBoolean [0..1] + «XSDattribute» isTransitive [0..1]: tsBoolean [0..1] + «XSDattribute» isTranslationAssociation [0..1]: tsBoolean [0..1] + «XSDattribute» reverseName: tsCaseIgnoreIA5String + «XSDattribute» targetCodingScheme [0..1]: localName [0..1] associationInstance + «XSDattribute» sourceCodingScheme [0..1]: localName [0..1] + «XSDattribute» sourceConcept: conceptCode

associatableElement

associationTarget + «XSDattribute» targetCodingScheme [0..1]: localName [0..1] + «XSDattribute» targetConcept: conceptCode

describable

relations

0..* +sourceConcept 0..* +targetConcept 1..* +association

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LexGrid Model

Association Node

cd relations describable

association + «XSDattribute» association: localName + «XSDattribute» forwardName: tsCaseIgnoreIA5String + «XSDattribute» isAntiReflexive [0..1]: tsBoolean [0..1] + «XSDattribute» isAntiSymmetric [0..1]: tsBoolean [0..1] + «XSDattribute» isAntiTransitive [0..1]: tsBoolean [0..1] + «XSDattribute» isFunctional [0..1]: tsBoolean [0..1] + «XSDattribute» isReflexive [0..1]: tsBoolean [0..1] + «XSDattribute» isReverseFunctional [0..1]: tsBoolean [0..1] + «XSDattribute» isSymmetric [0..1]: tsBoolean [0..1] + «XSDattribute» isTransitive [0..1]: tsBoolean [0..1] + «XSDattribute» isTranslationAssociation [0..1]: tsBoolean [0..1] + «XSDattribute» reverseName: tsCaseIgnoreIA5String + «XSDattribute» targetCodingScheme [0..1]: localName [0..1] associationInstance + «XSDattribute» sourceCodingScheme [0..1]: localName [0..1] + «XSDattribute» sourceConcept: conceptCode

associatableElement

associationTarget + «XSDattribute» targetCodingScheme [0..1]: localName [0..1] + «XSDattribute» targetConcept: conceptCode

describable

relations

0..* +sourceConcept 0..* +targetConcept 1..* +association

Source concept Target (concept / Data)

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LexGrid Model

Association Node

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LexGrid Model

Association Node

Body (has regional parts) Head Neck Upper limb Right Upper limb Left Upper limb Lower limb Right Lower limb Left Lower limb Trunk

Targets Source

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LexGrid Model

http://informatics.mayo.edu

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FMA (Protégé)

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FMA (Protégé)

Root Nodes

  • Anatomical entity
  • Attribute entity
  • Anatomical transformation entity
  • Dimensional entity
  • Spatial association value
  • Miscellaneous term
  • Biological entity

“Concept name”

Has > 130,000 instances correspond to FMA concept names & add more information to them

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FMA Mapping to LexGrid

  • Both Protégé CLS and Protégé

Instance map to LexGrid Coded Entry

  • Meta-Class / CLS / Instance

distinction in FMA model is pragmatic decision – not “ontological”

  • Most FMA classes are both
  • Exception is “Concept name”,

which is strictly descriptive

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FMA Mapping

Classes and Instances

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FMA Mapping to LexGrid

Property String with other values Presentation String with values “Preferred name”, “name”, “Synonyms”, “Eng-Equivalent” LexGrid Slot type in FMA

Slot Type decides Category

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FMA Mapping to LexGrid

Property Other Property {true | false} Boolean Association Protégé CLS or Instance Comment :Documentation Definition “definition” LexGrid Slot type in FMA

Slot Type decides Category

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FMA Mapping to LexGrid

Presentation or its attributes “Authority” “Source” “Language” “TA ID” “Eponym”, … LexGrid Slot type in FMA (Instances of ‘Concept name’)

Slot Type decides Category

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EMF at work

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EMF at work

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EMF at work

NOW Create objects using Generated EMF Classes AND Generate XML

  • utput file
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EMF at work Generated Implementation Classes

Generated Implementation

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EMF at work Generated Implementation Classes

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EMF at work Generated Implementation Classes

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EMF at work Generated Implementation Classes

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EMF at work Factory Classes

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EMF at work Create Coding Scheme

Creates Coding Scheme

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EMF at work Create Concept

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EMF at work Create Relation

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EMF at work XML Serialization

These classes are from ECORE framework e.g. package org.eclipse.emf.ecore.xmi.impl

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EMF at work

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FMA (LexGrid XML Snapshot)

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FMA (LexGrid XML Snapshot)

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Transformation Example

  • Concept “Body”
  • LexGrid Editor tool (Mayo)
  • Observe Mappings:
  • FMA Content with Protégé
  • Transformed LexGrid content with

LexGrid Editor

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Concept “Body” (FMA)

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“Body” (FMA) - Attributes

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Concept “Body” (LexGrid)

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Concept “Body” (LexGrid)

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Concept “Body” (LexGrid)

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Concept “Body” (LexGrid)

CONCEPTS BASICS RELATIONS

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Concept “Body” (LexGrid)

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“Body” (FMA) - Attributes

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“Body” (FMA) - Attributes

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“Body” (FMA) - Attributes

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“Body” (FMA) - Attributes

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“Body” (LexGrid) - Attributes

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“Body” (LexGrid) - Attributes

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“Body” (FMA) - Relations

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“Body” (LexGrid) - Relations

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“Body” (LexGrid) - Relations

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Current Status

  • Transformation tool is a Java

application

  • Possible to make a Protégé plug-in
  • Need to Isolate “Mapping to LexGrid

Model” from EMF implementation

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EMF at work

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EMF at work

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Current Status

EMF as a Hub

Available at http://informatics.mayo.edu

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Conclusion

  • Easily used EMF to work with user

model and generate code

  • Successfully
  • Converted FMA content to LexGrid

Model

  • Used EMF to create LexGrid XML
  • utput document
  • EMF as a hub
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Thanks!

  • Harold Solbrig
  • Thomas Johnson
  • Dr. Christopher Chute
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Thanks!

Protégé Conference Organizers

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Questions ?

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Questions ?

http:/ / inform atics.m ayo.edu

Deepak Sharma Division of Biomedical Informatics Mayo Clinic sharma.deepak2@mayo.edu