1 eccf training computationally independent model (cim) eccf training working group march 2011

1

ECCF Training

Computationally Independent Model

(CIM)

ECCF Training Working Group

March 2011

Translation

"conceptual perspective" = the specification

formerly known as "Computationally Independent Model" (CIM)

To maintain consistency between this training material and its source documentation and other references, the original term "CIM" will be used in

this module to refer to what is know known as the "CP"

the specification

formerly known as "Computationally

Independent Model" (CIM)

"Conceptual Perspective" =

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Outline

• Introduction

• Review of ECCF

• What is a CIM?

• Viewpoints for a CIM

• Development of a CIM

• CIM Template and Example

• Review and Relationship to PIM

• References

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ECCF

• ECCF combines:

• The Model-Driven Architecture (MDA) layered approach to software design

• Viewpoints defined by the Reference Model for Open Distributed Processing (RM-ODP)

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What is a CIM?

• Computationally Independent Model (CIM)

• The most abstract MDA layer (conceptual)

• CIM specification

• Detailed analysis document that specifies a given business capability• Documents both "what" and "why"

• Contains:• Service capabilities• Traceability to requirements• Service information model• Service behavioral semantics

• Structured to address each of the RM-ODP viewpoints• Enterprise• Information• Computational/Behavioral• Engineering/Implementation

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RM-ODP Viewpoints for the CIM

• Enterprise Viewpoint

• Scope and vision

• Business objectives and policies

• Use cases and storyboards

• Core functional and non-functional requirements

• Service capabilities

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RM-ODP Viewpoints for the CIM

• Information Viewpoint

• Information model describing the entities used by the service

• Constrained domain analysis model (DAM)

• Includes classes, attributes, datatypes, and value sets

• Dynamic schema (state diagrams for entities)

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RM-ODP Viewpoints for the CIM

• Computational/Behavioral Viewpoint

• Service capabilities and constraints• Including roles and functional profiles

(aggregate service capabilities)

• Interactions with and dependencies on other services

• Describes the role of a system in overall business interactions

• Activity, sequence, or state diagrams

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RM-ODP Viewpoints for the CIM

• Engineering/Implementation Viewpoint

• Populated as needed

• Functions required to support the computational components

• Software platforms and environments

• Deployment/architecture requirements and constraints

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CIM Development

• Based on artifacts developed during the requirements analysis phase

• Examples include (but are not limited to):• Vision/Scope Document• Business Case Document• Use Case Model• Analysis Model• Design Model• Information Model• Architectural Diagrams/Document/Models• User Interface Model• Conformance Statements• Standards Documents• Glossaries

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CIM Development

• CIM development is iterative

• Artifacts are refined during development

• Top-down (business model) or bottom-up (implementations)

• NCI CBIIT created a template for CIM specifications

• Contains all required/optional components

• Viewpoints are built-in

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Outline

• Introduction

• CIM Template and Example

• In-class exercises

• Review and Relationship to PIM

• References

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NCI CBIIT CIM Template

• Contains all required/optional components

• Viewpoints are built-in

• http://tinyurl.com/NESdocs

Table of Contents

1. Overview and business case

2. Business storyboards

3. Detailed functional model

4. Profiles

5. System implementation details

6. Conformance and compliance

7. Appendix A: Relevant standards

8. Appendix B: References

9. Appendix C: Glossary

10. Appendix D: Cross reference tables

• Contains all required/optional components

• Viewpoints are built-in

• http://tinyurl.com/NESdocs

CIM Specification Training

• Walk through the CBIIT CIM template

• Discuss contents, purpose, intent of each section

• http://tinyurl.com/NESdocs• "CIM Service Specification Template"

• Study an example

• Molecular Annotation (MA) CIM

• http://tinyurl.com/CIMfiles• CIMSS_Molecular_Annotation_Service.doc

• Hands-on exercises

• Subject Registration (SR) CIM

• http://tinyurl.com/CIMfiles• Questions: CIM_Subject_Registration_Service_021811_4training.doc• Answers: CIM_Subject_Registration_Service_021811.doc

1. Overview and Business Case

• Service description and purpose

• Description of the service

• Business purpose of the specification

• Description of the functional capabilities in business terms

• Potential value to stakeholders and consumers

• Scope

• Overall potential scope of the service• Including specific exclusions

• Assumptions

• Related to scope

Overview and Business CaseExample: MA Service

• Service description and purpose

…Annotations providing detailed information on the molecular origin, biological process, and genetic alterations of associated experiment data can provide important insight on experimental outcomes. The Molecular Annotation Service provides a standardized set of interfaces for querying molecular (e.g. genomic, pathway) annotations.

The purpose of this service is to provide a set of capabilities for retrieving molecular annotations… There are a variety of molecular annotations…

The development of a common, reusable set of interfaces provided by this service will facilitate standardization, integration, and interoperability between various systems that provide and consume of molecular annotations.

This service specification provides a key infrastructure component for NCI to support molecular annotations originating from other systems. This service serves as a main platform for integrating molecular annotations among all heterogeneous systems/components independent of platform within the integrative cancer research domain.

…Annotations providing detailed information on the molecular origin, biological process, and genetic alterations of associated experiment data can provide important insight on experimental outcomes. The Molecular Annotation Service provides a standardized set of interfaces for querying molecular (e.g. genomic, pathway) annotations.

The purpose of this service is to provide a set of capabilities for retrieving molecular annotations… There are a variety of molecular annotations…

The development of a common, reusable set of interfaces provided by this service will facilitate standardization, integration, and interoperability between various systems that provide and consume of molecular annotations.

This service specification provides a key infrastructure component for NCI to support molecular annotations originating from other systems. This service serves as a main platform for integrating molecular annotations among all heterogeneous systems/components independent of platform within the integrative cancer research domain.

Overview and Business CaseExample: MA Service

• In Scope

• Molecular annotations, including lexical search

• Functional associations, cellular locations, biological processes, genetic variations, diseases, and agents associated with a gene

• Physical location of a gene

• Homologous genes

• Genomic annotations by microarray reporter

• Out of Scope

• Other types of annotations, including those for miRNAs, proteins, pathways, and other associations

• Assumptions

• Annotations will be retrieved using standard identifiers

• No security constraints

2. Business Storyboards

• Define a set of business scenarios in which the service will be used

• Should be sufficient but not exhaustive

• Provide an overview of the business scenario

• Provide a list of actors

• People (roles)

• System

Business StoryboardsExample: MA Service

•Overview

…The storyboards provided here cover two individuals looking for annotations for their specific data, as well as two external systems which would like to fully integrate with a molecular annotation service.

•Actors

Person Role Notes

Researcher Usually an investigator associated with a study working in conjunction with the bioinformatics developer

Bioinformatics Developer An IT developer with expertise in using Application Programming Interfaces (APIs)

System Actor Notes

Integrative Translational Research System (e.g. caIntegrator2)

Leverages MA service to retrieve information on genes; may be associated with a microarray reporter

Gene Expression Analysis Tool (e.g. geWorkbench)

Leverages molecular annotations service to retrieve information on genes

Business StoryboardsExample: MA Service

• MA-SB1 – Researcher Initiated Molecular Annotations

Outline Researcher wants to obtain a list of Single Nucleotide Polymorphisms (SNPs) associated with a gene and information on where that gene lies on the chromosome

Detail Jane Doe is a researcher studying the CHEK2 gene for links to breast cancer. She needs a complete list of known SNPs located on this gene. She decides to use an integrative translational research system to call the NCI’s molecular annotation service in order to retrieve this information. She queries for the “CHEK2” gene and uses the User Interface (UI) to retrieve structural variations. The translational research system calls “Get Structural Variations” on her behalf, and provides the gene symbol “CHEK2” as her initial input. The molecular annotation service processes the query and returns a list of SNPs which she can use to continue her analysis.

3. Detailed Functional Model

• Structure of the Service

• List of capabilities

• Detail of the Capabilities

• Description

• Pre- and Post-Conditions

• Security

• Inputs and Outputs

• Exception Conditions

• Aspects Left for Technical Bindings

Detailed Functional ModelExample: MA Service

[M] = Mandatory, [O] = Optional

Name [M] Get Structural Variations

Description [M] Returns variations which are located on a given gene

Pre-Conditions [M] None

Security Pre-Conditions [M] None

Inputs [M] Gene Symbol or Alias Organism Identifier

Outputs [M] Collection of Genetic Variations

Post-Conditions [O] None

Alternate Conditions No Variations found

Exception Conditions [M] Gene does not exist

Aspects left for Technical Bindings [O]

NA

Notes [O] NA

Exercise

• Refer to the Subject Registration CIM

• http://tinyurl.com/CIMfiles• CIM_Subject_Registration_Service_021811_4training.doc

• Review background information

• Note: Focus on the yellow-highlighted sections

• Section 1: Overview and business cases

• Section 2: Business storyboards

• Section 3.1: List of capabilities

Exercise

• Fill in the blanks for the following capabilities

• Initiate Subject Registration (page 22)

• Enroll Subject (page 25)

• Take Subject Off Study (page 28)

• Query Subject Registration (page 31)

• Discuss as a group

• http://tinyurl.com/CIMfiles• Answers: CIM_Subject_Registration_Service_021811.doc

4. Profiles

• Functional Profiles

• Groupings of similar or related capabilities• Defined from the perspective of the consumer of the operations

• Semantic Profiles

• Constrained information models• Derived from standard models (e.g., HL7 RIM, BRIDG)

• Define objects that are used by the service capabilities

• Conformance Profiles

• Combinations of functional and semantic profiles• 1 or more functional profiles + exactly 1 semantic profile

• Defines a set of coherent capabilities against which conformance can be claimed

Functional ProfilesExample: MA Service

• Groupings of similar or related capabilities

Functional Profile No.

Functional Profile Name

Functional Profile Description

Capability Name

MA-FP1 Gene Annotation Query Profile

Contains all the capabilities for retrieving gene annotations

Get Genes By Symbol or Alias Get Genes By Microarray Reporter Get Functional AssociationsGet Cellular LocationsGet Biological ProcessesGet Disease AssociationsGet Agent AssociationsGet Structural VariationsGet Homologous Gene

Semantic ProfilesExample: MA Service• Constrained information models

• Objects that are used by the service capabilities

• "The MA service binds to and complies with the semantics of the LSDAM v1.1 information model."

Sequence Annotation

SNP

Gene

Sequence

OrganismBRIDG::Drug

Location

Gene ID

Constrained from LS DAM 1.1

Conformance ProfilesExample: MA Service

• Combinations of functional and semantic profiles

• 1 or more functional profiles + exactly 1 semantic profile

Conformance No MA-CP1

Conformance Name

LSDAM-based Gene Annotation Conformance Profile

Description This conformance profile defines the functionality for the Gene Annotation Service using LSDAM semantics

Usage Context This profile would be used by a researcher wishing to access gene annotations

Mandatory Yes

Functional Profile(s)

MA-FP1: Gene Annotation Query ProfileMA-FP2: Freestyle Search ProfileMA-FP3: Database Release Query Profile

Semantic Profile(s) MA-SP1: LSDAM v1.1

Exercise

• Refer to the Subject Registration CIM

• http://tinyurl.com/CIMfiles• CIM_Subject_Registration_Service_021811_4training.doc

• Review background information

• Section 4.1: Functional profiles

• Section 4.2: Semantic profiles

• Complete Section 4.3 (conformance profiles)

• The first one is done for you

• Discuss as a group

5. System Implementation Details

• Runtime interaction details

• Define complex sets of interactions or dependencies

• Illustrate business scenarios that use multiple operations of the service in specific sequences

• May use UML activity or sequence diagrams

• Implementation/deployment considerations

• May include dependencies on existing infrastructure

System Implementation DetailsExample: MA Service

• No runtime interactions

• Implementation considerations

• The specification does not specify the behavior of the objects• e.g., lazy loading, eager loading

• Deployment considerations

• The MA service could be deployed on the same system as the caBIO database, which may be used by the MA service

6. Conformance and Compliance

• Testable, verifiable statements

• Made in the context of a single RM-ODP viewpoint

• May have hierarchical relationships within a given viewpoint

• At the CIM level, statements may refer to compliance of artifacts at the PIM and PSM levels

• Examples of conformance statements

• http://tinyurl.com/NESdocs

Conformance and ComplianceExample: MA Service

Name Type Viewpoint Description Test method

Multiple Jurisdic-tions

Obligation Enterprise The MA service will span jurisdictional boundaries and will need to support a federated data model.

Test cases include multiple domain scenarios.

Semantic Model

Obligation Informa-tional

The MA service must provide traceability to classes in the LSDAM where applicable.

Design Review

Data Types

Obligation Informa-tional

The MA service must conform to NCI’s constrained list of ISO 21090 data types.

Design Review

Functional Profiles

Obligation Computa-tional

Functional Profiles shall be deployed as functional wholes. Ignoring or omitting functional behavior defined within a functional profile is not permitted, nor is diverging from the detailed functional specifications provided in Section 4.

1.Design Review2.Test cases

7-10. Appendices A-D

• Appendix A: Relevant Standards

• List of potentially relevant standards• Relationship to the specification• Implications of deployment in environments that use alternative standards

• Appendix B: References

• Appendix C: Glossary

• Appendix D: Cross Reference Tables

• List of storyboards

• Mapping of capabilities to storyboards

• Operations used by actors

7-10. Appendices A-DExample: MA Service

• Appendix A: Relevant Standards

• LS DAM

• BRIDG

• LS BAM

• HUGO gene nomenclature

• Appendix B: References

• MA service scope and description document

• Appendix C: Glossary

• Domain-specific (rather than enterprise-wide) terms

• Appendix D: Cross Reference Tables

• List of storyboards

• Mapping of capabilities to storyboards

• Operations used by actors

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NCI CBIIT CIM Template

• Contains all required/optional components

• Viewpoints are built-in

• http://tinyurl.com/NESdocs

Table of Contents

1. Overview and business case

2. Business storyboards

3. Detailed functional model

4. Profiles

5. System implementation details

6. Conformance and compliance

7. Appendix A: Relevant standards

8. Appendix B: References

9. Appendix C: Glossary

10. Appendix D: Cross reference tables

• Contains all required/optional components

• Viewpoints are built-in

• http://tinyurl.com/NESdocs

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Outline

• Introduction

• CIM Template and Example

• Review and Relationship to PIM

• References

38

Review of the CIM

• Computationally Independent Model (CIM)

• The most abstract MDA layer (conceptual)

• CIM specification

• Detailed analysis document that specifies a given business capability• Documents both "what" and "why"

• Contains:• Service capabilities• Traceability to requirements• Service information model• Service behavioral semantics

• Structured to address each of the RM-ODP viewpoints• Enterprise• Information• Computational/Behavioral• Engineering/Implementation

RM-ODP Viewpoints for the CIM

• Enterprise Viewpoint• Scope and vision• Business objectives and policies• Use cases and storyboards• Core functional and non-functional requirements• Service capabilities

• Computational/Behavioral Viewpoint• Service capabilities and constraints

• Including roles and functional profiles (aggregate service capabilities)

• Interactions with and dependencies on other services• Describes the role of a system in overall business interactions

• Activity, sequence, or state diagrams

• Information Viewpoint• Information model describing the entities used by the

service• Constrained domain analysis model (DAM)• Includes classes, attributes, datatypes, and value sets

• Dynamic schema (state diagrams for entities)

• Engineering/Implementation Viewpoint• Populated as needed• Functions required to support the computational

components• Software platforms and environments• Deployment/architecture requirements and constraints

39

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NCI CBIIT CIM Template

• Contains all required/optional components

• Viewpoints are built-in

• http://tinyurl.com/NESdocs

Table of Contents

1. Overview and business case

2. Business storyboards

3. Detailed functional model

4. Profiles

5. System implementation details

6. Conformance and compliance

7. Appendix A: Relevant standards

8. Appendix B: References

9. Appendix C: Glossary

10. Appendix D: Cross reference tables

• Contains all required/optional components

• Viewpoints are built-in

• http://tinyurl.com/NESdocs

41

Outline

• Introduction

• CIM Template and Example

• Review and Relationship to PIM

• References

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References

• NCI SAIF IG

• NCI CBIIT CIM Template

• NCI CBIIT SAIF Best Practices, Policies, and Patterns

• Molecular Annotation CIM Specification

• Subject Registration CIM Specification