transformation of protégé ontologies into the eclipse ... · 1 transformation of protégé...

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Transformation of ProtégéOntologies into the Eclipse

Modeling Framework

Deepak SharmaDivision 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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EMF XML Schema

UML Java

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• 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 Frameworkhttp://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 workModel Representation

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XML Schema

UML

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XML Schema

UML

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EMF at workModel Representation (XSD)

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EMF at workModel Representation (XSD)

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EMF at workCreate an EMF Project

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EMF at workEMF Project Components

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CORE

GENMODEL

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EMF at workEMF CORE Component

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EMF at workEMF CORE Component

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EMF at workEMF GENMODEL Component

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EMF at workEMF GENMODEL Component

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EMF at workGenerate Implementation

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EMF at workGenerate Implementation

Generates Implementation

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EMF at workImplementation

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EMF at workImplementation

Generated Implementation

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EMF at workXML Schema Snapshot

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EMF at workGenerated Implementation

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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 &

objects used in LexGrid tooling• Supports non-semantic entities (from

the toolkit perspective) as name/value pair

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LexGrid ModelInformation Model (partial)

cd codingSchemes

describable

codingScheme

concepts::conceptsdescribable

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 ModelCoding Scheme Node

cd codingSchemes

describable

codingScheme



describable



associatableElement




concepts::property

concepts::comment




1..*+association

0..*+sourceConcept

0..*+targetConcept

1..*+concept

0..*+property

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cd codingSchemes

describable

codingScheme



describable



associatableElement




concepts::property

concepts::comment




1..*+association

0..*+sourceConcept

0..*+targetConcept

1..*+concept

0..*+property

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LexGrid ModelCoded Entry

cd codingSchemes

describable

codingScheme



describable



associatableElement




concepts::property

concepts::comment




1..*+association

0..*+sourceConcept

0..*+targetConcept

1..*+concept

0..*+property

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cd codingSchemes

describable

codingScheme



describable



associatableElement




concepts::property

concepts::comment




1..*+association

0..*+sourceConcept

0..*+targetConcept

1..*+concept

0..*+property

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LexGrid ModelConcept Property

cd codingSchemes

describable

codingScheme



describable



associatableElement




concepts::property

concepts::comment




1..*+association

0..*+sourceConcept

0..*+targetConcept

1..*+concept

0..*+property

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LexGrid ModelCodedEntry Node

Concept Code

Concept Name

Property Name

Property Value

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LexGrid ModelAssociation 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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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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Body (has regional parts)HeadNeckUpper limbRight Upper limbLeft Upper limbLower limbRight Lower limbLeft Lower limbTrunk

Targets

Source

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LexGrid Modelhttp://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 ProtégéInstance 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 MappingClasses and Instances

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PropertyString with other values

PresentationString with values “Preferred name”, “name”, “Synonyms”, “Eng-Equivalent”

LexGridSlot type in FMASlot Type decides Category

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PropertyOtherProperty {true | false}Boolean

AssociationProtégé CLS or Instance

Comment:Documentation

Definition“definition”LexGridSlot type in FMA

Slot Type decides Category

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Presentation or its attributes

“Authority”“Source”“Language”“TA ID”“Eponym”, …

LexGridSlot 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 output file

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EMF at workGenerated Implementation Classes

Generated Implementation

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EMF at workFactory Classes

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EMF at workCreate Coding Scheme

Creates Coding Scheme

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EMF at workCreate Concept

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EMF at workCreate Relation

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EMF at workXML Serialization

These classes are from ECORE frameworke.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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CONCEPTS

BASICS

RELATIONS

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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 StatusEMF 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

output 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://informatics.mayo.edu

Deepak SharmaDivision of Biomedical InformaticsMayo [email protected]

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