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

LexGrid Model Association Node cd relations describable relations +association 1..* 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] Source concept +sourceConcept 0..* associationInstance + «XSDattribute» sourceCodingScheme [0..1]: localName [0..1] + «XSDattribute» sourceConcept: conceptCode Target +targetConcept 0..* associatableElement associationTarget (concept / Data) + «XSDattribute» targetCodingScheme [0..1]: localName [0..1] + «XSDattribute» targetConcept: conceptCode 53

54 Association Node LexGrid Model

LexGrid Model Association Node Source Body (has regional parts) Head Neck Upper limb Right Upper limb Targets Left Upper limb Lower limb Right Lower limb Left Lower limb Trunk 55

LexGrid Model http://informatics.mayo.edu 56

57 FMA (Protégé)

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 58

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 59

60 Classes and Instances FMA Mapping

FMA Mapping to LexGrid Slot Type decides Category Slot type in FMA LexGrid String with values Presentation “Preferred name”, “name”, “Synonyms”, “Eng-Equivalent” String with other Property values 61

FMA Mapping to LexGrid Slot Type decides Category Slot type in FMA LexGrid “definition” Definition :Documentation Comment Protégé CLS or Association Instance Boolean Property {true | false} Other Property 62

FMA Mapping to LexGrid Slot Type decides Category Slot type in FMA LexGrid (Instances of ‘Concept name’) “Authority” Presentation or its attributes “Source” “Language” “TA ID” “Eponym”, … 63

64 EMF at work

65 EMF at work

EMF at work NOW Create objects using Generated EMF Classes AND Generate XML output file 66

EMF at work Generated Implementation Classes Generated Implementation 67

68 Generated Implementation Classes EMF at work

69 Generated Implementation Classes EMF at work

70 Generated Implementation Classes EMF at work

71 Factory Classes EMF at work

EMF at work Create Coding Scheme Creates Coding Scheme 72

73 Create Concept EMF at work

74 Create Relation EMF at work

EMF at work XML Serialization These classes are from ECORE framework e.g. package org.eclipse.emf.ecore.xmi.impl 75

76 EMF at work

77 FMA (LexGrid XML Snapshot)

78 FMA (LexGrid XML Snapshot)

Transformation Example • Concept “Body” • LexGrid Editor tool (Mayo) • Observe Mappings: • FMA Content with Protégé • Transformed LexGrid content with LexGrid Editor 79

80 Concept “Body” (FMA)

81 “Body” (FMA) - Attributes

82 Concept “Body” (LexGrid)

83 Concept “Body” (LexGrid)

84 Concept “Body” (LexGrid)

85 RELATIONS BASICS Concept “Body” (LexGrid) CONCEPTS

86 Concept “Body” (LexGrid)

87 “Body” (FMA) - Attributes

88 “Body” (FMA) - Attributes

89 “Body” (FMA) - Attributes

90 “Body” (FMA) - Attributes

91 “Body” (LexGrid) - Attributes

92 “Body” (LexGrid) - Attributes

93 “Body” (FMA) - Relations

94 “Body” (LexGrid) - Relations

95 “Body” (LexGrid) - Relations

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 96

97 EMF at work

98 EMF at work

Current Status EMF as a Hub Available at http://informatics.mayo.edu 99

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 100