1. 1 ECCF Training Computationally Independent Model (CIM) ECCF Training Working Group March 2011

2. Translation 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"=

3. 3 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

4. 4 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)

5. 5 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

6. 6 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

7. 7 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)

8. 8 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

9. 9 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

10. 10 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

11. 11 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

12. 12 Outline Introduction CIM Template and Example In-class exercises Review and Relationship to PIM References

13. 13 NCI CBIIT CIM Template 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

14. 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

15. 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

16. Overview and Business Case Example: 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.

17. Overview and Business Case Example: 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

18. 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

19. Business Storyboards Example: 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 RoleNotes ResearcherUsually an investigator associated with a study working in conjunction with the bioinformatics developer Bioinformatics DeveloperAn IT developer with expertise in using Application Programming Interfaces (APIs) System ActorNotes 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

20. Business Storyboards Example: MA Service MA-SB1 – Researcher Initiated Molecular Annotations OutlineResearcher wants to obtain a list of Single Nucleotide Polymorphisms (SNPs) associated with a gene and information on where that gene lies on the chromosome DetailJane 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.

21. 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

22. Detailed Functional Model Example: 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 ConditionsNo Variations found Exception Conditions [M]Gene does not exist Aspects left for Technical Bindings [O] NA Notes [O]NA

23. 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

24. 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

25. 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

26. Functional Profiles Example: MA Service Groupings of similar or related capabilities Functional Profile No. Functional Profile Name Functional Profile Description Capability Name MA-FP1Gene Annotation Query Profile Contains all the capabilities for retrieving gene annotations  Get Genes By Symbol or Alias  Get Genes By Microarray Reporter  Get Functional Associations  Get Cellular Locations  Get Biological Processes  Get Disease Associations  Get Agent Associations  Get Structural Variations  Get Homologous Gene

27. Semantic Profiles Example: 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 Organism BRIDG::Drug Location Gene ID Constrained from LS DAM 1.1

28. Conformance Profiles Example: MA Service Combinations of functional and semantic profiles 1 or more functional profiles + exactly 1 semantic profile Conformance NoMA-CP1 Conformance Name LSDAM-based Gene Annotation Conformance Profile DescriptionThis conformance profile defines the functionality for the Gene Annotation Service using LSDAM semantics Usage ContextThis profile would be used by a researcher wishing to access gene annotations MandatoryYes Functional Profile(s) MA-FP1: Gene Annotation Query Profile MA-FP2: Freestyle Search Profile MA-FP3: Database Release Query Profile Semantic Profile(s)MA-SP1: LSDAM v1.1

29. 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

30. 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

31. System Implementation Details Example: 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

32. 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

33. Conformance and Compliance Example: MA Service NameTypeViewpointDescriptionTest method Multiple Jurisdic- tions ObligationEnterpriseThe MA service will span jurisdictional boundaries and will need to support a federated data model. Test cases include multiple domain scenarios. Semantic Model ObligationInforma- tional The MA service must provide traceability to classes in the LSDAM where applicable. Design Review Data TypesObligationInforma- tional The MA service must conform to NCI ’ s constrained list of ISO 21090 data types. Design Review Functional Profiles ObligationComputa- 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 Review 2.Test cases

34. 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

35. 7-10. Appendices A-D Example: 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

36. 36 NCI CBIIT CIM Template 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

37. 37 Outline Introduction CIM Template and Example Review and Relationship to PIM References

38. 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

39. 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 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) 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 Engineering/Implementation Viewpoint Populated as needed Functions required to support the computational components Software platforms and environments Deployment/architecture requirements and constraints 39

40. 40 NCI CBIIT CIM Template 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. 41 Outline Introduction CIM Template and Example Review and Relationship to PIM References

42. 42 References NCI SAIF IG NCI CBIIT CIM Template NCI CBIIT SAIF Best Practices, Policies, and Patterns Molecular Annotation CIM Specification Subject Registration CIM Specification