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ECCF Training 2.0

Guidance for the Platform Independent

Model (PIM)

ECCF Training Working Group

January 2011

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Outline

• What is the PIM?• Looking through the viewpoints• Detailed look at artifacts by viewpoint

• Explanation• Example• Exercise

• Other Artifacts

What is the PIM?

• From analysis in CIM to logical model in PIM• Independent of technology stack• Typically one PIM for one CIM

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Looking through the viewpoints

• Enterprise Viewpoint• Minimal focus for the PIM (optional artifacts)• Mostly traceability to CIM

• Information Viewpoint• Constrained Local Information Model

• Computational / Behavioral• Service Contract

• Engineering / Implementation• Deployment Considerations

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Artifacts by Viewpoint

Information Viewpoint

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Information Model

• Add constraints and localizations to information model work begun in the CIM

• Artifacts:• Primary Information Object Types

• State Model

• Error Information Model

• Control Data Types

• Value Set Definitions

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Primary Information Object Types

• What are the Primary Information Objects?• Represent the main functionality• Other objects are associated with primary objects• Generally form the input and output• State is controlled by functionality of the service• There can be more than one primary object type

• How do we define them?• Object Model• State Transition Model• Traceability to referenced models

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MA Gene Object Model

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MA Gene State Model

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MA Gene Model Reference UML

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MA Gene Model Traceability

Trace Attribute Name Type Description

LSPIM Symbol ST The official symbol for the gene based on an organism-specific database of gene symbols, such as HUGO, MGI or RGD

New fullName ST The title of the gene.

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Gene

Error Information Model

• Defines the types for all the errors that the service may throw

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MA Exception Model

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Control Data Type Definitions

• What are control data types?• Search Criteria• Exception Conditions• Input Criteria• Result Sets

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MA – Search Criteria Types

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Value Set Definitions

• Attributes whose values are controlled by a list of valid values• Error Codes• Status Codes

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MA – Error Codes

Error Code Error Condition Description

MAE00000 Fatal Remote system error

MAE10001 Error Gene does not exist

MAE10002 Error Specified microarray is not supported

MAE10003 Error Reporter not found

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Artifacts by Viewpoint

Computational / Behavioral Viewpoint

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Interface Model

• Provides a logical grouping for service implementers

• Artifacts:• UML model of interfaces• List of operations• Detailed operation behavior descriptions

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MA – Interface Model

Interface No Interface Name Interface Description

MA-INF1 MAGeneAnnotationQuery Includes all of the operations for retrieving gene annotations

MA-INF2 MAFreestyleSearch Includes all of the operations for Freestyle Search

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MA – Interface Model UML

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MA – List of Operations (Truncated)

Operation No.

Operation Name Interface Name Operation Description

MA-INF1-OP1 getGenesBySymbol MAGeneAnnotationQuery Returns the genes named by the specified gene symbols and/or gene aliases

MA-INF1-OP2 getCellularLocations MAGeneAnnotationQuery Returns annotations describing a gene’s location within a cell

MA-INF2-OP1 freestyleSummarySearch MAFreestyleSearchProfile Returns a summary result for a given keyword or keywords

MA-INF2-OP2 freestyleSearch MAFreestyleSearchProfile Returns a list of results matching the given keyword or keywords

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Operation Behavior Description

• Detailed description of the behavior of each interface operation

• Grouped by interface

• Includes:

• Description

• Pre-Conditions

• Security Conditions

• Inputs

• Outputs

• Post-Conditions

• Exception Conditions

• Additional Implementation Details

• Notes

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MA - getGenesByMicroArrayReporter

Behavior Description • Client supplies a ReporterSearchCriteria instance with a reporter name and a microarray design to search within

• The case of the reporter name is ignored• If the Microarray is null then all Microarrays are

searched• The system returns the matching Gene object(s), if any

Pre-Conditions None

Security Pre-Conditions

None

Inputs ReporterSearchCriteria

Outputs Fully-populated instance(s) of Gene

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MA - getGenesByMicroArrayReporter (cont.)

Post-Conditions None

Alternate Conditions No matching genes found

Exception Conditions • Specified microarray is not supported• Reporter not found

Additional Details None

Notes None

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Dynamic Model

• Describe the interactions of the service with sequence diagrams or collaboration diagrams

• Includes relationships with other services

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MA – External Service Relationships

Service / System / Actor’s Name

Relationship Data Description

Integrative Translational Research System

Depends Molecular Annotations

Integrative Translational Research Systems such as caIntegrator depend on Molecular Annotations for looking up annotations for microarray reporters used in experiments being analyzed.

Gene Expression Analysis Tool

Depends Molecular Annotations

Gene Expression Analysis Tools such as GEWorkbench depend on a Molecular Annotations for putting expression data in context of a genome.

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