1. caCORE Training: UML-based Metadata Curation Session 1 Course Number:1071 Date:September 15, 2009 Duration: 90 Minutes Trainer: Becky Angeles bangeles@scenpro.com NCICB Liaison:Dianne Reeves reevesd@mail.nih.gov

2. Session Details: UML-based Metadata Session 1 Online Training Environment: Centra… Use these buttons (or choose from the Actions menu) to communicate with the trainer and other attendees. Example: Raise your hand to ask a question.

3. Session Details: UML-based Metadata Session 1 Online Training Environment: Centra You can adjust what you see on screen by choosing from the View menu or by scrolling.

4. Session Details: UML-based Metadata Session 1 Online Training Etiquette Be an active learner Ask lots of questions Avoid the temptation to multi-task Please keep your phone on MUTE Please do not put your phone on HOLD - disconnect from the teleconference to take another call Please state your name when asking a question or making a comment

5. Session Details: UML-based Metadata Session 1 Audience This session is targeted for: Application Developers caBIG Developers VCDE Mentors Compatibility Reviewers Metadata Curators - curating from a UML-based perspective caBIG caDSR

6. Session Details: UML Derived Metadata Part 1 Course Outline Learning Objectives Lesson 1: Introduction to UML Modeling Lesson 2: Decomposing UML Class Diagrams into Metadata Lesson 3: Semantic Integration and caBIG Compatibility Lesson 4: caCORE Build Process Workflow Lesson 5: Using the Semantic Integration Workbench (SIW)

7. Session Details: UML Derived Metadata Part 1 Learning Objectives When you complete this training, you will be able to: Discuss the benefits of UML modeling Identify three components of a UML Class Diagram Decompose a UML class and its attributes into caDSR metadata List the seven User Modes (Options) of the Semantic Integration Workbench (SIW) List the major steps in the UML Model Semantic Integration and caDSR loading process

8. Lesson 1: Introduction to Unified Modeling Language (UML) When you complete Lesson 1 you will be able to: Define the 4 ways UML represents the artifacts of a software system Discuss the role UML plays within the caDSR Identify 3 components of a UML Class Diagram Discuss the difference between a Class and an Object

9. Lesson 1: Introduction to UML Modeling What is UML? Definition: Unified Modeling Language (UML) is a language used to visualize, specify, construct and document the artifacts of a software system. Visualize Use the same language to facilitate communication about the software system Reveals previously unknown details about the software system Specify Models are precise, unambiguous and complete Many UML Diagram Types caCORE SDK uses only the UML Class Diagram Construct Supports many programming languages. (Java, C++, Visual Basic, etc.) Permits forward and reverse engineering Document UML allows you to document the system architecture, requirements, tests, project planning, and release management

10. Lesson 1: Introduction to UML Modeling UML Roles Role of UML in the caDSR A UML Class Diagram is used to transform the classes and attributes of a software system or data set into caDSR metadata. This process is called “Semantic Integration” Role of UML in the caCORE Build Process The same UML Class Diagram used for “Semantic Integration” is also used to generate code for a complete software system This process is called “Code Generation”

11. Lesson 1: Introduction to UML Modeling UML Diagram Types Actor A Use Case 1 Use Case 2 Use Case 3 Actor B Sequence Diagram user mainWndfileMgr : FileMgr repositorydocument : Document gFile 1: Doc view request ( ) 2: fetchDoc( ) 3: create ( ) 4: create ( ) 5: readDoc ( ) 6: fillDocument ( ) 7: readFile ( ) 8: fillFile ( ) 9: sortByName ( ) ƯÁ¤¹®¼­¿¡ ´ëÇÑ º¸±â¸¦ »ç¿ëÀÚ°¡ ¿äûÇÑ´Ù. È­ÀÏ°ü¸®ÀÚ´Â Àоî¿Â ¹®¼­ÀÇ Á¤º¸¸¦ ÇØ´ç ¹®¼­ °´Ã¼¿¡ ¼³Á¤À» ¿äûÇÑ´Ù. È­¸é °´Ã¼´Â ÀоîµéÀÎ °´Ã¼µé¿¡ ´ëÇØ À̸§º°·Î Á¤·ÄÀ» ½ÃÄÑ È­¸é¿¡ º¸¿©ÁØ´Ù. Deployment Diagram Window95 ¹®¼­°ü¸® Ŭ¶óÀ̾ðÆ®.EXE Windows NT ¹®¼­°ü¸® ¿£Áø.EXE Windows NT Windows95 Solaris ÀÀ¿ë¼­¹ö.EXE Alpha UNIX IBM Mainframe µ¥ÀÌŸº£À̽º¼­¹ö Windows95 ¹®¼­°ü¸® ¾ÖÇø´ ºÐ»ê ȯ°æÀÇ Çϵå¿þ¾î¹× ³×Æ®¿÷À¸·ÎÀÇ Á¤º¸ ½Ã½ºÅÛ ¿¬°á ¸ðµ¨ - À©µµ¿ì 95 : Ŭ¶óÀ̾ðÆ® - À©µµ¿ì NT: ÀÀ¿ë¼­¹ö - À¯´Ð½º ¸Ó½Å: ÀÀ¿ë ¼­¹ö ¹× µ¥ÀÌŸ ¼­¹ö, Åë½Å ¼­¹ö - IBM ¸ÞÀÎÇÁ·¹ÀÓ: µ¥ÀÌŸ ¼­¹ö, Åë½Å ¼­¹ö Class Diagram Use Case Diagram

12. Lesson 1: Introduction to UML Modeling UML Class Diagram A Class Diagram depicts a logical grouping of classes Example: Simple Class Diagram 2 Classes 1 association (“relationship”) Course - name: String - location: String - daysOffered: String - creditHours: Integer - startDate: Date - endDate: Date Student - name: String - address: String - studentID: Integer - dateOfBirth: Date Add Student () Drop Student () Provide list of Courses taken () 1..*0..*

13. Lesson 1: Introduction to UML Modeling UML Class Diagram A Class Diagram depicts a logical grouping of classes Example: Simple Class Diagram 2 Classes 1 association (“relationship”) Course - name: String - location: String - daysOffered: String - creditHours: Integer - startDate: Date - endDate: Date Student - name: String - address: String - studentID: Integer - dateOfBirth: Date Add Student () Drop Student () Provide list of Courses taken () 1..*0..* class association (“relationship”)

14. Lesson 1: Introduction to UML Modeling UML Class A class is a description of a set of objects that share the same attributes, operations, relationships, and semantics Course - name: String - location: String - daysOffered: String - creditHours: Integer - startDate: Date - endDate: Date Student - name: String - address: String - studentID: Integer - dateOfBirth: Date Add Student () Drop Student () Provide list of Courses taken () 1..*0..* class class name attributes methods/ operations association (“relationship”) data type

15. Lesson 1: Introduction to UML Modeling Class Attribute An attribute is a property of a class Attributes are named Attributes describe the range of values that instances of the property may hold. A class may have any number of attributes Course - name: String - location: String - daysOffered: String - creditHours: Integer - startTime: Date - endTime: Date Student - name: String - address: String - studentID: Integer - dateOfBirth: Date Add Student () Drop Student () Provide list of Courses taken () 1..*0..* attributes

16. Lesson 1: Introduction to UML Modeling Attribute Data Types Each attribute has a datatype (or “representation”) Course - name: String - location: String - daysOffered: String - creditHours: Integer - startTime: Date - endTime: Date Student - name: String - address: String - studentID: Integer - dateOfBirth: Date Add Student () Drop Student () Provide list of Courses taken () 1..*0..* attribute data type

17. Lesson 1: Introduction to UML Modeling Classes and Objects - Clarification Classes and Objects are not the same thing An Object is an instance of a Class :Course - name = “Introduction to UML” - location = “online” - daysOffered = “Tuesday” - creditHours = “1” - startDate = “02/12/2008” - endDate = “03/04/2008” object Course - name: String - location: String - daysOffered: String - creditHours: Integer - startDate: Date - endDate: Date Add Student () Drop Student () class ≠

18. Lesson 1: Introduction to UML Modeling Review What You’ve Learned UML is used to visualize, specify, construct and document the artifacts of a software system. The role of UML in the caDSR is to transform the classes and attributes of a software system or data set into caDSR metadata (semantic integration) A Class Diagram is a logical grouping of classes A Class is the description of a set of objects that share the same attributes, operations, relationships, and semantics Classes contain attributes that describe the properties of the class Each attribute has a data type that specifies how that piece of information should be represented

19. Lesson 1: Introduction to UML Modeling Apply What You’ve Learned What is the name of this class? What is the name of the attribute used to describe a person’s address information? What is the data type for the “name” attribute? Person - birthDate: Date - educationLevel: Character - ethnicGroup: Character - gender: Character - maritalStatus: Character - name: String - postalAddress: String Example Class

20. Lesson 1: Introduction to UML Modeling Apply What You’ve Learned What is the name of this class? Answer: Person What is the name of the attribute used to describe a person’s address information? Answer: postalAddress What is the data type for the “name” attribute? Answer: String Person - birthDate: Date - educationLevel: Character - ethnicGroup: Character - gender: Character - maritalStatus: Character - name: String - postalAddress: String Example Class

21. Lesson 2: Decomposing UML Class Diagrams into Metadata When you complete Lesson 2, you will be able to: Compare a class diagram to caDSR Metadata Determine how many Data Elements will be formed from a UML Class, its attributes and data types

22. Lesson 2: Decomposing UML Class Diagrams into Metadata Where we are in the caCORE Build Process

23. Creating your UML Model is the first step in the caCORE Build Process 1.Design system and draw model (with a UML tool) 2.Perform Semantic Integration (with the SIW – Semantic Integration Workbench) 3.Register Metadata (with the UML Loader) 4.Generate Code (with the Code Generator) 5.Silver Level Compatibility Review and Deploy caGrid Service

24. UML Class Diagrams form the basis for creating and registering caDSR metadata In the caDSR, a Data Element corresponds to the combination of a class, a single attribute, and its data type. UML ClasscaDSR Data Element ClassObject Class AttributeProperty Datatype (of the attribute)Representation Term Data Element Concept Value Domain Lesson 2: Decomposing UML Class Diagrams into Metadata Class Diagram to Data Element

25. Class Name - attribute: Data type Lesson 2: Decomposing UML Class Diagrams into Metadata Class Diagram to Data Element Data Element Data Element Concept Value Domain Property Object Class Representation UML ClasscaDSR Data Element

26. Lesson 2: Decomposing UML Class Diagrams into Metadata Class Diagram to Data Element Data Element Data Element Concept Value Domain Property Object Class Representation Example UML Class caDSR Data Element Person - name: String

27. Person - name: String Lesson 2: Decomposing UML Class Diagrams into Metadata Class Diagram to Data Element Person Name java.lang.String Person Name java.lang.String Name Person String Example UML Class caDSR Data Element

28. Lesson 2: Decomposing UML Class Diagrams into Metadata Apply What You’ve Learned How many attributes does this class have? How many Data Elements are created from this one class? Person - birthDate: Date - educationLevel: Character - ethnicGroup: Character - gender: Character - maritalStatus: Character - name: String - postalAddress: String Example Class

29. Lesson 2: Decomposing UML Class Diagrams into Metadata Apply What You’ve Learned How many attributes does this class have? Answer: 7 How many Data Elements can be created from this one class? Answer: 7 Person - birthDate: Date - educationLevel: Character - ethnicGroup: Character - gender: Character - maritalStatus: Character - name: String - postalAddress: String Example Class

30. Lesson 2: Decomposing UML Class Diagrams into Metadata Apply What You’ve Learned 1.A UML Class corresponds to a _____________ in caDSR Metadata 2.A UML Attribute corresponds to a ______________ in caDSR Metadata 3.A UML Datatype corresponds to a ______________ in caDSR Metadata

31. Lesson 2: Decomposing UML Class Diagrams into Metadata Apply What You’ve Learned 1.A UML Class corresponds to a Object Class in caDSR Metadata 2.A UML Attribute corresponds to a Property in caDSR Metadata 3.A UML Data type corresponds to a Representation Term in caDSR Metadata

32. Lesson 3: Semantic Integration and caBIG ® Compatibility When you finish Lesson 3, you will be able to: Discuss the definition and importance of Semantic Integration List the 3 levels of caBIG ® Compatibility Discuss the requirements for caBIG ® Silver Level Compatibility

33. Lesson 3: Semantic Integration and caBIG ® Compatibility Where we are in the caCORE Build Process Semantic integration is the second step in the caCORE Build Process 1.Design system and draw model (with a UML tool) 2.Perform Semantic Integration (with the SIW – Semantic Integration Workbench) 3.Register Metadata (with the UML Loader) 4.Generate Code (with the Code Generator) 5.Silver Level Compatibility Review and Deploy caGrid Service

34. Semantic Integration is the series of steps taken to map UML classes and attributes to EVS concept codes These concepts are used to build caDSR Data Elements Goal: Semantic Interoperability This association between metadata and controlled vocabularies permits unambiguous interpretation of UML model objects and mapping between those objects in different domains. Resulting metadata is more sharable and interoperable. For example, the UML Class named Agent is mapped to C1708 (Agent) – if other models with an Agent class are mapped to C1708, semantic integration is achieved – both classes mean the same thing Lesson 3: Semantic Integration and caBIG ® Compatibility Semantic Integration Overview

35. Share Metadata Expose Data Share Data on Grid Participant wants to… Manual Process caCORE Build Process Manual Process caCORE Build Process UML Model Semantic Integration Bronze SilverGold Lesson 3: Semantic Integration and caBIG ® Compatibility Achieving Semantic Interoperability Manual Process caCORE Build Process Manual System Generation UML Model Semantic Integration Curation UML Model Semantic Integration Code Generation Curation “caCORE-like” System Manual System Generation Custom GRID Adapter UML Model Semantic Integration Curation UML Model GRID Node Semantic Integration Code Generation Curation

36. Absolute: Data Element metadata is recorded in the caDSR Data Elements are associated with a unique pairing of a Data Element Concept and Value Domain Data Elements MUST have names, definitions, and data types Data Element Concepts (DECs) and Value Domains (VDs) must be built from EVS concepts DECs are associated with a Conceptual Domain and have Object Class and Property assigned from EVS Value Domains have data types Enumerated Value Domains have a representation assigned from EVS If Permissible Values are used, there must be actual values in the value name and paired with a value meaning or reference a repository Lesson 3: Semantic Integration and caBIG ® Compatibility Achieving caBIG ® Silver-Level Compatibility (Absolute)

37. Required: No unexplained errors should be seen in the SIW Data Systems should use publicly accessible controlled vocabularies as well as local terminologies Reuse existing CDEs All Data Elements names, definitions, data types, and permissible values have unambiguous meanings (concepts) Permissible Value enumerations should be listed in the UML model Suggested: If Permissible Values are used, the value meaning should have an attached concept code and value meaning definition Lesson 3: Semantic Integration and caBIG ® Compatibility Achieving caBIG ® Silver-Level Compatibility (Required/Suggested)

38. Lesson 3: Semantic Integration and caBIG ® Compatibility Review What You’ve Learned In Lesson 3, you have learned: Semantic Integration is the series of steps taken to map UML classes and attributes to EVS concept codes The association between metadata and controlled vocabularies permits unambiguous interpretation of UML model objects - therefore making data more re-usable and sharable

39. Lesson 3: Semantic Integration and caBIG ® Compatibility Apply What You’ve Learned 1.There are _________ levels of caBIG ® Compatibility. 2._______________ ________________ is the series of steps taken to map UML classes and attributes to EVS concept codes. 3.Data Element Concepts and Value Domains must be built from EVS ____________ for caBIG Silver-Level Compatibility.

40. Lesson 3: Semantic Integration and caBIG Compatibility Apply What You’ve Learned (Answers) 1.There are 3 levels of caBIG ® Compatibility. 2.Semantic Integration is the series of steps taken to map UML classes and attributes to EVS concept codes. 3.Data Element Concepts and Value Domains must be built from EVS concepts for caBIG ® Silver-Level Compatibility.

41. Lesson 4: caCORE Build Process Workflow Overview When you complete this Lesson, you will be able to: Identify the 5 steps involved in the caCORE Build Process Workflow Name the tool used to perform semantic integration within the caCORE Build Process Workflow Discuss the format in which to export a UML model before the model is loaded to caDSR

42. Lesson 4: caCORE Build Process Workflow Overview caCORE Build Process 1.Design system and draw model (with a UML tool) 2.Perform Semantic Integration (with the SIW – Semantic Integration Workbench) 3.Register Metadata (with the UML Loader) 4.Generate Code (with the Code Generator) 5.Pass Silver Level Compatibility Review and Deploy caGrid Service

43. Lesson 4: caCORE Build Process Workflow Overview caCORE Build Process Workflow 1.Design System & Draw Model a.Export the Class Diagram as an XMI file (Enterprise Architect) or save as a UML file (ArgoUML v0.24 or v0.26 only) 2.Perform Semantic Integration a.Use the Semantic Integration Workbench (SIW) tool b.Annotate every class and attribute in XMI/UML file (class diagram) with vocabulary identifiers 3.Register Metadata a.NCI CBIIT loads XMI file (class diagram) into the caDSR Sandbox database b.Review metadata in the caDSR Sandbox database c.NCI CBIIT loads reviewed XMI file (class diagram) into the caDSR Production database 4.Generate Code a.Use the SDK Code Generator 5.Silver Level Compatibility Review and Deploy caGrid Service a.Pass the Compatibility Review b.Use caGrid Introduce Toolkit to deploy caGrid Service

44. Lesson 4: caCORE Build Process Workflow Overview 1. Design System & Draw Model Create your system/project model in UML “Logical View” model describes your domain Includes classes, attributes, data types, relationships Use Recommended Naming Conventions Conform to Java naming conventions and terminology standards Use clear Package, Class and Attribute names Use Standard Vocabulary (EVS) Class/attribute need at least one concept from a vocabulary Create Class and Attribute Definitions as Tagged Values Class and attribute tagged value = “CADSR_Description” Class Associations Must be named with associated class names Multiplicity and direction must be defined Attribute Data Types must already exist in caDSR

45. Lesson 4: caCORE Build Process Workflow Overview caCORE Tools Modeling Constraints Ignored UML Elements – operations and methods Attribute Types – each attribute must have a type (Java primitive data type or Java wrapper class defined in model) Recognized Relationships – associations and generalizations(inheritance); aggregations and compositions are treated as simple associations Association End Role Names –source and a target (class name) defined Association End Multiplicity – must be specified at both ends Association End Navigability (directionality) – must be specified Packages and the Logical Model – model should be placed in the Logical Model package of a modeling tool. Classes should be placed in a “domain” package in the “Logical Model” package. Package names must conform to java package limitations. UML Descriptions – all classes and attributes must have a “CADSR_Description” tag containing a concise definition Java Limitations – avoid using Java reserved words as class/attribute names – avoid hyphens, angle brackets or other reserved characters

46. Lesson 4: caCORE Build Process Workflow Overview 1. Design System & Draw Model – prior to Export Class and Attribute names, definitions and data types must be frozen caBIG participants should work with their VCDE metadata mentors throughout this process Export the UML Class Diagram to an XMI file (EA) or.uml (ArgoUML) using the guidelines described in the caCORE SIW and UML Loader Technical Guide Export from the top package “Logical View” Right click to export from this package Includes model for API Review (caBIG Compatibility) Includes model for VCDE Review (caBIG Compatibility)

47. Lesson 4: caCORE Build Process Workflow Overview 1. Design System & Draw Model – Export (EA only) Recommended settings in Enterprise Architect when you export your UML model as an XMI file: Enable full EA Roundtrip XMI version 1.1 and UML version 1.3 Ensure “Use DTD” is NOT CHECKED For those using ArgoUML – save model as a.uml file.

48. Lesson 4: caCORE Build Process Workflow Overview 2. Perform Semantic Integration - SIW Start the Semantic Integration Workbench (SIW) http://cadsrsiw.nci.nih.gov Review your Un-Annotated Model (SIW Step 1) Run the “Semantic Connector Report” (SIW Step 3) Send the Model Submission Package to NCICB Application Support: ncicb@pop.nci.nih.govncicb@pop.nci.nih.gov submission package info: https://gforge.nci.nih.gov/docman/index.php?gr oup_id=64&selected_doc_group_id=184&langu age_id=1 Work with NCI’s terminology experts as they annotate every class and attribute in your XMI file (class diagram) with vocabulary identifiers Verify all annotations by checking the “Model Owner Verified” box (SIW Step 5)

49. Lesson 4: caCORE Build Process Workflow Overview 3. Load and Review Model NCICB uses the UML Loader to load (“transform”) the XMI file into caDSR metadata Review your caDSR Metadata in the caDSR Sandbox database Once reviewed, NCICB will load the model into the caDSR Production database Work with your preceptor or VCDE mentor to make any necessary edits to the metadata

50. Lesson 4: caCORE Build Process Workflow Overview 4. Generate Code Generate Code Code Generator creates the caCORE- compatible software system. Generates Java-beans Generates the Object Managers and Data Access Objects Generates an XML Schema and corresponding Castor XML Mapping files Creates a Web Services Deployment Descriptor (WSDD) file

51. Lesson 4: caCORE Build Process Workflow Overview 5. Silver Review / Deploy caGrid Service Pass the Silver Level Compatibility Review Assemble Project and Institution Information Deploy caGrid Service Use the caGrid Introduce Toolkit Index Service Global Model Exchange

52. Lesson 4: caCORE Build Process Workflow Overview Apply What You’ve Learned 1.In what format do you export your UML Class Diagram so that it can be used in the Semantic Integration process? 2.What is the name of the tool where you perform Semantic Integration (mapping individual classes and attributes to standard vocabulary concepts)?

53. Lesson 4: caCORE Build Process Workflow Overview Review Questions 1.In what format do you export your UML Class Diagram so that it can be used in the Semantic Integration process? Answer: XMI 2.What is the name of the tool where you perform Semantic Integration (mapping individual classes and attributes to standard vocabulary concepts)? Answer: SIW (Semantic Integration Workbench)

54. Lesson 5: Overview of the Semantic Integration Workbench (SIW) When you complete Lesson 5, you will be able to: Identify at least 3 benefits of using the Semantic Integration Workbench (SIW) List the seven (7) modes of the SIW Identify which SIW mode is NOT performed by the model owner Discuss validations that the SIW performs in relation to the UML Model

55. Lesson 5: Overview of the SIW Details of the SIW Use: Perform the tasks associated with semantic annotation and review for loading of UML Models into caDSR Audience: UML Model developers/users performing semantic annotation Technology: Java application - downloaded and installed on user’s desktop Benefits: Facilitates the semantic integration process Removes the requirement that users should understand ISO/IEC 11179 and the mapping between ISO and caDSR Users select NCI Thesaurus concepts for model annotation Simplifies editing, eliminates ‘cut and paste’ and typographical errors Identifies and facilitates correction of missing data and data type errors Provides the ability to generate and remove default GME tags

56. Lesson 5: Overview of the SIW Launching the SIW To Launch the SIW for the first time: Download Java JRE: (http://java.sun.com/javase/downloads/index.jsp)http://java.sun.com/javase/downloads/index.jsp Open the SIW URL (http://cadsrsiw.nci.nih.gov/)http://cadsrsiw.nci.nih.gov/ Once Java SE is downloaded to your machine, you only need to navigate to the SIW URL to start the tool

57. Lesson 5: Overview of the SIW SIW User Modes The SIW Welcome panel includes seven (7) options for SIW use, listed in the order of their use in the SIW Workflow.

58. Lesson 5: Overview of the SIW Review Un-Annotated XMI File Performed by: Model Owner Do this step first Easy way to check for missing tags for classes and attributes Missing tags are flagged in the Errors tab Input: UML Model in XMI or UML format Output: UML Model in XMI or UML format

59. Lesson 5: Overview of the SIW Review Un-Annotated XMI File – Trouble-shooting Can’t find the.XMI files? Files are created in the same root directory as the input file Note the location of your.XMI input file Error message displays or first run does not complete Confirm your.XMI file is in the expected format Check.XMI export settings in EA Contact NCICB Application Support

60. Lesson 5: Overview of the SIW Perform XMI Roundtrip Performed by: Model Owner Annotates model with existing caDSR CDEs Launched by entering the Project Name, (Classification Scheme Long Name) and Version Input: XMI or UML file Output: Roundtrip XMI or UML file A partially annotated XMI file. The file is annotated with caDSR public IDs rather than EVS concepts. After performing this step, the model owner should review the mapping in the XMI Review mode (Step 5)

61. Lesson 5: Overview of the SIW Run Semantic Connector Performed by: Model Owner Performs an EVS search for each element in the UML Model and attaches one or more EVS concepts per element Input: UML Model in XMI or UML format (original or Roundtrip) Output: Saved XMI or UML files This file is sent to EVS curation team for review and insertion of new concepts to match the UML class and attribute entities

62. Lesson 5: Overview of the SIW Next Steps for Model Owner (1) If you want the EVS team to complete the concept mappings for you: Email NCICB Application Support (ncicb@pop.nci.nih.gov) with the following:ncicb@pop.nci.nih.gov Semantic Integration Submission Template located in the “Docs” section of the UML Model project on the NCICB GForge site: http://gforge.nci.nih.gov/docman/index.php?group_id=64&selected_doc_group_id=1 84&language_id=1 http://gforge.nci.nih.gov/docman/index.php?group_id=64&selected_doc_group_id=1 84&language_id=1.EAP or.UML file ${filename}.xmi or ${filename}.uml FirstPass_${filename}.xmi or FirstPass_${filename}.uml Documentation file from EA (or other UML Tool) NCICB Application Support will conduct a review of all files to verify completeness

63. Lesson 5: Overview of the SIW Next Steps (2) If you wish to map classes and attributes in your model to existing CDEs in caDSR AND NCIt concepts: 1.Run Option 2: Perform XMI Roundtrip to map CDEs (optional) 2.Run Option 3: Run Semantic Connector to map concepts to any classes and attributes not mapped to a CDE 3.Run Option 5: Review Annotated XMI File to edit the concept mappings in the classes and attributes for which you know the semantics 4.Check each class and attribute that you map as Model Owner Verified, to indicate to the EVS team that you have intentionally selected these concepts 5.Submit your model and required files to Application Support (ncicb@pop.nci.nih.gov) (ncicb@pop.nci.nih.gov)

64. Lesson 5: Overview of the SIW Curate XMI File Performed by: EVS Concept Curation Team EVS curation team adds and removes concepts and indicates recommended semantic mappings. Can be an iterative process New or existing EVS concepts can be utilized for annotating the model Input: First Pass XMI or UML file Output: Annotated First Pass XMI or UML file referred to as the “Curated XMI File” EVS Concept Curation Team will be in contact with the model owner if they have questions.

65. Lesson 5: Overview of the SIW Review Annotated XMI File Performed by: Model Owner or Reviewer SIW performs a number of validation checks to ensure the XMI file will be correctly transformed into caDSR metadata Users review concept mapping and association details between a specific class or attribute and EVS concept Input: Annotated First Pass XMI or UML file Output: Approved Annotated First Pass XMI or UML file

66. Lesson 5: Overview of the SIW Review Annotated XMI File - Validation For each UML Class and Attribute, SIW checks for the presence of at least one: Concept code Concept name Concept definition Concept definition source Valid data type Verifies that no two classes have identical concept mappings Verifies that no two attributes have the same concept annotations within a class Inheritance A child class cannot have attributes that are also defined in the parent class. Associations All associations should be present (not ‘unspecified’) All associations should have a role name

67. Lesson 5: Overview of the SIW Generate Default GME Tags Performed by: Model Owner or Reviewer Generates GME tags to model elements Can be run anytime throughout the semantic annotation process Input: XMI or UML file Output: GMEDefault XMI or UML file

68. Lesson 5: Overview of the SIW GME Cleanup Performed by: Model Owner Removes all GME tagged values from an XMI file Useful when an XMI file is fully annotated with GME tags, but the user wishes to replace those tags or let SIW regenerate default values. Input: GME Annotated XMI or UML file Output: GMECleanup XMI or UML file

69. Lesson 5: Overview of the SIW Review what you have Learned Benefits for using the SIW to perform semantic integration include: (Select the best answer) A.Simplifies editing B.Eliminates ‘cut and paste’ and typographical errors C.Removes the requirement that users should understand ISO/IEC 11179 D.All of the Above There are ___ user modes in the Semantic Integration Workbench A.3 B.4 C.7 As a model owner, you will only ever perform ____ of those modes A.3 B.2 C.4

70. Lesson 5: Overview of the SIW Review what you have Learned Benefits for using the SIW to perform semantic integration include: (Select the best answer) D.All of the Above There are ___ user modes in the Semantic Integration Workbench C.7 As a model owner, you will only ever perform ____ of the SIW modes C.4

71. Session Review Questions What is the only kind of UML diagram that the caCORE Build process supports? What naming conventions should you follow when naming your UML entities? What components of a Data Element do a UML Class and Attribute relate to? True or False: Proper semantic integration requires that each class and class attribute from your model be mapped to appropriate metadata.

72. Session Review Questions What is the only kind of UML diagram that the caCORE Build process supports? Class Diagram What naming conventions should you follow when naming your UML entities? Java What components of a Data Element do a UML Class and Attribute relate to? Object Class and Property True or False: Proper semantic integration requires that each class and class attribute from your model be mapped to appropriate metadata. True

73. Contact Information Contact: Becky Angeles (bangeles@scenpro.com) Jennifer Brush (jbrush@scenpro.com) Dianne Reeves (reevesd@mail.nih.gov)reevesd@mail.nih.gov caCORE SIW and UML Loader v4.0 Technical Guide: https://gforge.nci.nih.gov/docman/view.php/16/15449/caCORE_SIW- UMLLoader_v40_TechnicalGuide.pdf https://gforge.nci.nih.gov/docman/view.php/16/15449/caCORE_SIW- UMLLoader_v40_TechnicalGuide.pdf caCORE SDK v4.1 Programmer’s Guide: https://gforge.nci.nih.gov/docman/view.php/148/15067/caCore_SDK_v41_Pro grammersGuide.pdf caCORE SDK v4.0 Developer’s Guide: https://gforge.nci.nih.gov/docman/view.php/148/8650/caCORE%20SDK%204. 0%20Developer%27s%20Guide_101007.pdf caCORE Training Wiki: https://wiki.nci.nih.gov/x/OAFyhttps://wiki.nci.nih.gov/x/OAFy caCORE Training Home Page: http://ncicb.nci.nih.gov/NCICB/training/cadsr_training http://ncicb.nci.nih.gov/NCICB/training/cadsr_training caDSR Home Page: http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/cadsr