1. 1 ECCF Training 2.0 Guidance for the Platform Independent Model (PIM) ECCF Training Working Group January 2011

2. 2 Outline What is the PIM? Looking through the viewpoints Detailed look at artifacts by viewpoint Explanation Example Exercise Other Artifacts

3. What is the PIM? From analysis in CIM to logical model in PIM Independent of technology stack Typically one PIM for one CIM 3

4. 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 4

5. Artifacts by Viewpoint Information Viewpoint 5

6. 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 6

7. 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 7

8. MA Gene Object Model 8

9. MA Gene State Model 9

10. MA Gene Model Reference UML 10

11. MA Gene Model Traceability TraceAttribute NameTypeDescription LSPIMSymbolSTThe official symbol for the gene based on an organism-specific database of gene symbols, such as HUGO, MGI or RGD NewfullNameSTThe title of the gene. 11 Gene

12. Error Information Model Defines the types for all the errors that the service may throw 12

13. MA Exception Model 13

14. Control Data Type Definitions What are control data types? Search Criteria Exception Conditions Input Criteria Result Sets 14

15. MA – Search Criteria Types 15

16. Value Set Definitions Attributes whose values are controlled by a list of valid values Error Codes Status Codes 16

17. MA – Error Codes Error CodeError ConditionDescription MAE00000FatalRemote system error MAE10001ErrorGene does not exist MAE10002ErrorSpecified microarray is not supported MAE10003ErrorReporter not found 17

18. Artifacts by Viewpoint Computational / Behavioral Viewpoint 18

19. Interface Model Provides a logical grouping for service implementers Artifacts: UML model of interfaces List of operations Detailed operation behavior descriptions 19

20. MA – Interface Model Interface NoInterface NameInterface Description MA-INF1MAGeneAnnotationQueryIncludes all of the operations for retrieving gene annotations MA-INF2MAFreestyleSearchIncludes all of the operations for Freestyle Search 20

21. MA – Interface Model UML 21

22. MA – List of Operations (Truncated) Operation No. Operation NameInterface NameOperation Description MA-INF1-OP1getGenesBySymbolMAGeneAnnotationQueryReturns the genes named by the specified gene symbols and/or gene aliases MA-INF1-OP2getCellularLocationsMAGeneAnnotationQueryReturns annotations describing a gene’s location within a cell MA-INF2-OP1freestyleSummarySearchMAFreestyleSearchProfileReturns a summary result for a given keyword or keywords MA-INF2-OP2freestyleSearchMAFreestyleSearchProfileReturns a list of results matching the given keyword or keywords 22

23. 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 23

24. MA - getGenesByMicroArrayReporter Behavior DescriptionClient 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-ConditionsNone Security Pre- Conditions None InputsReporterSearchCriteria OutputsFully-populated instance(s) of Gene 24

25. MA - getGenesByMicroArrayReporter (cont.) Post-ConditionsNone Alternate ConditionsNo matching genes found Exception ConditionsSpecified microarray is not supported Reporter not found Additional DetailsNone NotesNone 25

26. Dynamic Model Describe the interactions of the service with sequence diagrams or collaboration diagrams Includes relationships with other services 26

27. MA – External Service Relationships Service / System / Actor’s Name RelationshipDataDescription Integrative Translational Research System DependsMolecular 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 DependsMolecular Annotations Gene Expression Analysis Tools such as GEWorkbench depend on a Molecular Annotations for putting expression data in context of a genome. 27