Modeling for Semantic Interoperability

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Modeling for Semantic Interoperability

• Vocabularies and Common Data ElementsCross-cuttin
  g WorkspaceFace-to-Face Meeting
• June 16-17, 2005
• Nafis Zebarjadi zebarjadin_at_saic.com

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Agenda

• Creating the Logical Model
• Naming Best Practices
• Semantic Connector

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Learning Objectives

• Upon completion of this session, you will be able
  to
• Explain modeling constraints imposed by caCORE
  SDK tools
• Analyze a UML model and correct potential
  problems
• Apply best practices for naming domain
  objects/attributes
• Generate a valid XMI file for use by SDK tools
• Describe the semantic connector workflow
• Discuss the various parts of a semantic connector
  report

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Creating the Logical Model
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Creating the Logical Model

• Class diagram models target domain
• Logical model is basis for semantic integration
• Also used to generate caCORE-like system
• Focus on attributes and relationships of domain
  objects

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Creating the Logical Model

• caCORE framework does NOT constrain domain
  modeling
• Constraints are imposed by SDK transformation
  tools
• User must specify desired packages for code
  generation
• Provides flexibility in modeling
• Enables evolutionary development
• Constraints ensure
• Completeness of model
• Correct code generation
• Ability to perform semantic integration

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Creating the Logical Model

• Constraint 1 Allowable UML Elements
• Model can contain any element, BUT
• Only class elements recognized by SDK tools
• Classes may contain both attributes and
  operations
• Operations will be disregarded
• Attributes should be typed

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Creating the Logical Model

• Constraint 2 Allowable Relationships
• UML Loader registers
• association relationships
• inheritance relationships (generalizations)
• Aggregations and compositions
• allowed in model
• treated same as simple associations

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Creating the Logical Model

• Constraint 3 Attribute Types
• Attribute types must be Java primitive data types
• Complex types should be modeled as associations
• Enumerated lists not supported by UML Loader
• Recommendation
• Define Java primitives in model
• Note enumerated value domains

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Creating the Logical Model

• Constraint 3 Attribute Types (continued)

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Creating the Logical Model

• Constraint 4 Association End Role Names
• Association ends must be given a role name
• Indicates role of objects on either end
• Also used to generate method names by SDK
• Naming convention
• Use associated class name
• If multiplicity gt 1, append Collection
• What is best practice?

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Creating the Logical Model

• Constraint 5 Association End Multiplicity
• Multiplicity must be explicitly defined
• Determines use of collections as necessary
• Constraint 6 Association End Navigability
• Direction of association must be explicitly
  defined
• Determines visibility of related objects

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Creating the Logical Model

• Example Associations (Constraints 4, 5, 6)

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Creating the Logical Model

• Constraint 7 Description
• ALL classes and attributes need description
• Good practice
• Required for semantic interoperability
• Method of description varies with modeling tool

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Creating the Logical Model

• Constraint 8 Logical Model Package
• Elements must reside in Logical Model package
• Semantic Connector will ignore all other packages

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Creating the Logical Model

• Review SDK Modeling Constraints
• Only UML class
• Associations generalizations
• Attribute types must be Java primitive data types
• Each association end must be given a name
• Association end multiplicity
• Association end navigability
• Each class and attribute must have a description
• Model must exist in Logical Model

• Review SDK Modeling Constraints
• Only UML ____ elements are recognized
• __________ and ____________ are registered by
  UML Loader
• Attribute types must be ____________________
• Each association end must be given a _____
• Association end ________ must be specified
• Association end _________ must be specified
• Each class and attribute must have a _________
• Model must exist in ____________ package

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Naming Best Practices
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Naming Best Practices

• Be Consistent!
• Choose a convention and use it throughout your
  models and, if possible, across the entire
  organization.

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Naming Best Practices

• Adopt a case convention
• For example
• UpperCamelCase for ClassNamelowerCamelCase for
  attributeNameUNDERLINED_CAPS for CONSTANT_NAME

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Naming Best Practices

• Avoid using class identifiers in attribute names
• Use id, name instead of geneId, chromosomeName

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Naming Best Practices

• Avoid using abbreviations and acronyms
• Use DatabaseReference instead of DbRef
• BUT its okay to use id instead of
  identifier,SNP instead of SingleNucleotidePolymor
  phism
• (Be smart!)

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Naming Best Practices

• Avoid technical jargon
• Use Microarray instead of Chip

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Naming Best Practices

• Use Singular/Plural Names as Appropriate
• Class and attribute names are ALWAYS
  singularGene instead of Genes, location instead
  of locations
• Add Collection to association end names when
  multiplicity gt 10..1 location, gene0..
  taxonCollection

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Naming Best Practices

• Review
• ___________
• Adopt a ____ convention
• Avoid using ____ identifiers in attribute ______
• ___________ and ________ should be avoided
• Avoid technical _____
• _____ pluralize class and attribute names
• Add _________ to association ends with
  multiplicity gt 1

• Review
• Be consistent!
• Adopt a case
• Avoid using class
  names
• Abbreviations acronyms
• Avoid technical jargon
• Never
• Add Collection

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Semantic Connection
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Running the Semantic Connector

• Submit the annotated XMI file to NCICB
• To NCICB_at_pop.nci.nih.gov
• Include For semantic connection in the subject
  line
• Your model will be run through the Semantic
  Connector
• A semantic connector report will be generated
• Comma-separated file (CSV)
• Relates terms from diagram to EVS concepts
• Report will be curated, verified and sent to you
  for approval and submission for loading

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Semantic Connector Workflow
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Generating XMI for Semantic Interoperability

• Requirements for XMI file
• XMI 1.1
• UML 1.3
• Unisys/Rose extensions
• Export tagged values
• Include Logical Model package
• Exclude diagrams

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Semantic Connector Workflow
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Semantic Connector Report

• Semantic Connector Report BEFORE Human
  Verification

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Semantic Connector Report

• Semantic Connector Report AFTER Human
  Verification

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Annotated Model
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Questions?
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Further Reading

• caCORE SDK Programmers Guide
• ftp//ftp1.nci.nih.gov/pub/cacore/SDK/caCORE_SDK1.
  0_Programmers_Guide.pdf
• Chapter 5 Generating a caCORE-like System
• XMI Page at Object Management Group (OMG)
• http//www.omg.org/technology/documents/formal/xmi
  .htm
• Introduction to XMI
• Official specifications