CaCORE Training: Using the UML Model Browser Course Number:1025 Duration: Self-paced Intended Audience: caDSR Users and Metadata Consumers Using UMLModels.

caCORE Training:

Using the UML Model Browser

Course Number: 1025Duration: Self-pacedIntended Audience: caDSR Users and

Metadata Consumers Using UML Models

Instructors: [email protected] NCI CBIIT Liaison: Dianne Reeves

[email protected]

mailto:[email protected]


Course Details: Using the UML Model Browser

Intended Audience

• This session targets learners who act in the following roles:• Application Developer Using API’s: https://wiki.nci.nih.gov/x/TYF8• caBIG® Developer: https://wiki.nci.nih.gov/x/Z4F8• caBIG® Model Owner: https://wiki.nci.nih.gov/x/zI_PAQ• Metadata Curator – Using UML Models: https://wiki.nci.nih.gov/x/mYF8• VCDE Mentor: https://wiki.nci.nih.gov/x/rIF8

• Select the link provided next to the role (while in slide show mode) to view a more detailed description of the tasks and responsibilities for that role.

https://wiki.nci.nih.gov/x/TYF8

https://wiki.nci.nih.gov/x/Z4F8

https://wiki.nci.nih.gov/x/zI_PAQ

https://wiki.nci.nih.gov/x/mYF8

https://wiki.nci.nih.gov/x/rIF8


Prerequisites for this Course

• In order to make the most of this training you should have completed the following:• Course 1000: Intro to caCORE and caDSR• Course 1010: Intro to Metadata in the caDSR• Course 1020: Using the CDE Browser

• All course materials are available through the caBIG® Learning Management System (LMS):• http://ncicbtraining.nci.nih.gov• Register for courses• Take quiz to receive credit for each course

http://ncicbtraining.nci.nih.gov/


Training Glossary

• Our training courses use terms and acronyms specific to the caBIG® community. To assist you with unfamiliar terms, a training glossary is available with definitions and additional information on our training wiki: https://wiki.nci.nih.gov/x/cCByAQ

• If you cannot find what you are looking for and would like to request a term be added to the glossary please send an email to: [email protected]

https://wiki.nci.nih.gov/x/cCByAQ



Course Outline

• This course is divided into six lessons. These lessons include:• Lesson 1: Introduction to UML Modeling• Lesson 2: Decomposing UML Class Diagrams into Metadata• Lesson 3: UML Model Browser Overview• Lesson 4: Search Options• Lesson 5: Search Results• Lesson 6: How to find your UML Model Metadata


Course Learning Objectives

• When you complete this course, you will be able to:• List four ways Unified Modeling Language (UML) represents the artifacts

of a software system• Identify the components of a UML Class Diagram• Analyze a UML class and determine the appropriate corresponding

caDSR Metadata• Determine how many Data Elements will be formed from a UML Class, its

attributes and data types• Access and navigate the UML Model Browser and change search

preferences to include test and training contexts• Search for UML Model Metadata with three different search options• Manipulate different variables to expand or narrow search results• Differentiate between a Class Search and Attribute Search• View your UML Model Metadata using the UML Model Browser

Lesson 1: Introduction to UML Modeling

• In this lesson, you will learn how to:• List four ways UML represents the artifacts of a software system• Identify the components of a UML Class Diagram• Identify the differences between a Class and an Object


Why Develop a Model?

• Modeling achieves four aims• Helps you visualize and understand a system by presenting a unified

vision of the system• Specifies the structure and behavior of a system prior to coding• Provides the template which guides you in constructing a system• Documents the decisions you have made


What is Unified Modeling Language (UML)?

• Definition: Unified Modeling Language (UML)

is a language used to • visualize • specify• construct • document

the artifacts of a software system.

• Remember UML is a way to express the different models of a system, but does not tell you HOW to develop the software.


UML: Documenting

• UML provides a standard way to document a system’s blueprint which can include:• System architecture• Individual features and requirements of the system• Test and Project Plans• How you are going to release or publish the software


UML: Visualizing

• UML is designed to promote communication using pictures rather than text ~”A picture is worth a thousand words.”

• Communicating conceptual models without standard vocabularies is error prone. UML offers symbols which represent well-defined semantics to combat this.

• Information about software systems cannot be understood unless models are build which transcend the textual programming language.


UML: Specifying

• UML is used to specify the components of a software system, primarily through the use of models.

• UML allows you to build models that are precise, unambiguous and complete.

• There are many UML diagram types- we will focus of the UML Class Diagram. It is the only diagram utilized by Cancer Common Ontologic Representation Environment (caCORE) at this time.


UML: Constructing

• UML models can be directly connected to a variety of programming languages• Maps to Java, C++, Visual Basic, etc…

• Allows for mapping from a model in UML to a programming language or to a database• If the model is best expressed graphically, the UML model is utilized• If the model is best expressed textually, the programming language is

utilized• Permits forward engineering- the generation of code from a UML model• Permits reverse engineering- the construction of a model from existing

program source code


Example UML Diagram Types

NOTE: The Class Diagram is the only diagram recognized by the caCORE environment at this time.


UML Class

• A class is a representation of a generalized thing.• Classes are created in UML class diagrams.• A UML class is represented using a rectangle with three compartments

• Class Name• Attributes -will be discussed later in this lesson• Operations – functionality and/or behaviors of the class


Classes and Objects - Clarification

• Classes and Objects are not the same thing.• An Object is an instance of a Class.

• In UML, an object is represented as a rectangle with an underlined name.


Object/ Class Relationship

• A class is the static description of an object.• It defines the structure and behavior of each object in the class.• It serves as a template for creating objects.

• An object is the run-time instance of the class.• Modeling is from real-world objects.• Software objects are based on the real-world objects, but exist only in the

context of the system.

• Classes are used as templates within an executing software system to create software objects which represent the real-world objects you started with.

NOTE: Some classes/objects may be defined that don't represent real-world objects. They are there to support the design and are "software only.”


UML Class Diagram

• A Class Diagram depicts a logical grouping of classes related to one another.

• Example: Simple Class Diagram• 2 Classes: Course & Student• 1 Association (relationship)- We will discuss associations shortly.


Class Attribute

• An attribute is a named property of a class that describes the range of values that instances of the property may hold.• A class may have any number of attributes.

NOTE: UML best practices state that attributes should be named using camel-casing whereas the first letter of the first word is in small caps, all subsequent words in that attribute name are in big caps.

NOTE: UML best practices state that attributes should be named using camel-casing whereas the first letter of the first word is in small caps, all subsequent words in that attribute name are in big caps.


Attribute Data Types

• Attributes should have a data type or representation in order to be fully defined and semantically unambiguous.

• Data Types are added after the attribute name followed by a colon. (see the example below)

• Example: For the attribute “name”, string is the data type


UML Associations

• An association identifies a relationship.• Represented with a connecting line.• Identifies the classes that are involved in a relationship.

• Each side of the association should be named. • Best practice indicates all associations should be named and names

should use camel-casing format.


UML Multiplicity

• Multiplicity further specifies or defines association.• Displayed at the end of the relationship/association line.• In this diagram, the annotations (the 1 * and 0*) mean that for every one

course, there can be zero to many students enrolled and there is always at least one course. This means that our system needs the ability to search between courses and students.

NOTE: To view a complete list of annotations and their meanings, see Appendix A located at the end of this course.

NOTE: To view a complete list of annotations and their meanings, see Appendix A located at the end of this course.


Review

1. What is the name of this class?

2. What is the name of the attribute used to describe a person’s address information?

3. What is the data type for the “name” attribute?


Answers

1. What is the name of this class? • Person (correct answer)

2. What is the name of the attribute used to describe a person’s address information? • postalAddress (correct

answer)

3. What is the data type for the “name” attribute? • String (correct answer)


Recap

• Now that you have completed this lesson, you should be able to:• List the 4 ways UML represents the artifacts of a software system• Identify the components of a UML Class Diagram• Identify the differences between a Class and an Object

Lesson 2: Decomposing UML Class Diagrams into Metadata

• In this lesson, you will learn how to:• Identify the role UML plays within the caDSR• List the components of a Common Data Element• Analyze a UML class and determine the appropriate corresponding


attributes and data types


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”.

• The same UML Class Diagram can also be used to generate code for a complete software system.• This process is called “Code Generation”.


Data Element Review

• Before we begin analyzing our UML Model Metadata, let’s take a moment to review a data element:

• UML Class Diagrams form the basis for creating and registering semantically unambiguous caDSR metadata. The caDSR is made up of Data Elements.

• In the caDSR, a Data Element corresponds to the combination of a class, a single attribute and its data type.

• In the table below, the UML Class attributes and the corresponding data element administered items are listed side by side:


Class Diagram to Data Element


Class Diagram to Data Element Illustration

NOTE: EVS is tied to caDSR to provide concepts for metadata. Object Class, Property and Representation are the EVS touch points in caDSR.

NOTE: EVS is tied to caDSR to provide concepts for metadata. Object Class, Property and Representation are the EVS touch points in caDSR.

NOTE: Java.lang.String is an example of a generic Value Domain specifically created for UML models.


Example: Class Diagram to Data Element

NOTE: Java.lang.String is an example of a generic Value Domain specifically created for UML models.


Importance of Decomposition

• Semantic Integration is the series of steps taken to map UML classes and attributes to EVS concept codes. • Remember, EVS concept codes are assigned to Object Classes,

Properties, and Representation Terms.• These concepts are used to build caDSR Data Elements. • Goal: Semantic Interoperability

• The 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.


Exercise

1. How many attributes does this class have?

2. How many Data Elements are created from this one class?


Exercise Answers

1. How many attributes does this class have?• 7 (correct answer)

2. How many Data Elements can be created from this one class? • 7 (correct answer)


Review

1. A UML Class corresponds to a _____________ in caDSR Metadata.

2. A UML Attribute corresponds to a ______________ in caDSR Metadata.

3. A UML Data type corresponds to a ______________ in caDSR Metadata.


Answers

1. A UML Class corresponds to a Object Class (correct answer) in caDSR Metadata.

2. A UML Attribute corresponds to a Property (correct answer) in caDSR Metadata.

3. A UML Data type corresponds to a Value Domain (correct answer) in caDSR Metadata.


Recap

• Now that you have completed this lesson, you should be able to:• Identify the role UML plays within the caDSR• List the components of a Common Data Element• Analyze a UML class and determine the appropriate corresponding


attributes and data types

Lesson 3: UML Model Browser Overview

• In this lesson, you will learn how to:• Navigate to the UML Model Browser Main Page• Utilize the links on the UML Model Browser home page to access the

appropriate tools• Access the UML Model Browser Home Page and Online Help• Include and exclude test and/or training contexts from your search results


What is the UML Model Browser?

• Web-based caDSR Tool • http://umlmodelbrowser.nci.nih.gov• Supports browsers Internet Explorer v7.0+ and Mozilla Firefox v3.0+

• Designed for UML model owners to search for and view UML-based metadata in the caDSR• Classes• Class Attributes• Associations (between classes and attributes)• ISO Components (metadata) related to those classes and attributes

NOTE: The UML Model Browser accesses the same metadata in the caDSR as the CDE Browser, but displays the information in a way that UML Model developers and/or owners can relate to (class/attribute/association structure).

NOTE: The UML Model Browser accesses the same metadata in the caDSR as the CDE Browser, but displays the information in a way that UML Model developers and/or owners can relate to (class/attribute/association structure).

http://umlmodelbrowser.nci.nih.gov/


Roles and Use Cases

• The following are a list of roles and uses cases applicable to the UML Model Browser.

• Roles• Application Developer Using APIs• caBIG® Developer• caBIG® Model Owner• Metadata Curator Using UML Models

• Use Cases• Verify/ find your UML Model Metadata in the caDSR• Search and View UML Model components loaded into the caDSR

• UML Classes• Attributes• Related metadata


Home Page

• http://umlmodelbrowser.nci.nih.gov



Useful Links Menu

• CDE Browser: designed to let users search for, view, and export data elements (DEs) from the Cancer Data Standards Repository (caDSR)

• FormBuilder: used by curators to create, update, and maintain forms and templates using the data elements maintained in the caDSR

• Admin Tool: (caDSR Administration Tool):allows user to administer data privileges and make specialized edits to content in the caDSR

• Curation Tool : users can search for CDEs by their administered items and create or edit data elements

• NCI Metathesaurus: allows users to search the NCI Metathesaurus • NCI Terminology Server: navigates to the NCI Term Browser which

allows users to search the NCI Thesaurus and other controlled vocabularies

• Sentinel Tool: users can watch for changes to data elements and receive alerts


Navigation Icons

• Navigation icons accessible at any time from the UML Model Browser• Home: Return to the UML Model Browser Main page • Online Help: Access help tutorials and additional UML Model Browser

instruction


Key Search Features

• Class/ Attribute Search: search by class name, attribute name, or select a specific project, subproject, or package from the drop down lists provided

• Tree Search: search across Contexts or within a specific Context, Project, Subproject, Package, Class

(Both search features will be discussed in detail later in this course)

• Search Preferences: allows for exclusion/inclusion of specific Contexts

1. Select Search Preferences link from the UML Model Browser Home Page.

1.


Search Preferences

• Test and Training Contexts are excluded by default.

2. De-select the contexts you want to include in your search results (removing the checkmark means they WILL be included).

3. Select the Reset to default search preferences link to exclude Test and Training contexts.

4. Select Save to retain your selected search preferences.

5. Select Back to return to the UML Model Browser Main Page.

NOTE: Changes to Search Preferences persist only for the current UML Model Browser session. When you exit the browser and re-enter, the preferences return to the default.

NOTE: Changes to Search Preferences persist only for the current UML Model Browser session. When you exit the browser and re-enter, the preferences return to the default.


Review

1. __________ and ___________ contexts are excluded from search results by default.

2. TRUE or FALSE: The Home Page and Online help can be accessed at ANY time from the UML Model Browser.

3. Which caDSR tool is accessible from the UML Model Home Page?

A. Admin Tool

B. CDE Browser

C. NCI Term Browser

D. All of the above


Answers

1. Test (correct answer) and Training (correct answer) contexts are excluded from search results by default.

2. TRUE or FALSE: The Home Page and Online help can be accessed at ANY time from the UML Model Browser.• TRUE (correct answer)

3. Which caDSR tool is accessible from the UML Model Home Page?

A. Admin Tool

B. CDE Browser

C. NCI Term Browser

D. All of the above (correct answer)


Recap

• Now that you have completed this lesson, you should be able to:• Navigate to the UML Model Browser Main Page• Utilize the links on the UML Model Browser home page to access the tools• Access the UML Model Browser Home Page and Online Help from any

page in the UML Model Browser• Include and exclude test and/or training contexts from your search results

Lesson 4: Search Options

• In this lesson, you will learn how to:• Search for UML Model Metadata utilizing three search options

1. Tree Search

2. Class/ Attribute Search

3. Combination Tree & Class/ Attribute Search• Expand search results using the wildcard “*” character• Perform an Attribute Search against a Class Name search term


UML Model Browser Search Options

• Tree Search• Lists the different contexts in caDSR and displays the groups of UML

models within each context.• Class/ Attribute Search

• A straightforward search interface, allowing users to enter a class or attribute search term.

• Combination Tree & Class/ Attribute Search • Users can select a context to refine a specified class/ attribute search.


Tree Search

• UML Model Browser has a Tree Search very similar to the CDE Browser.

• Displays current caDSR Contexts at the top level.

• For each caDSR Context, the Tree Search• Lists all UML classes• Is grouped by project, subproject

(optional) and package• Search for classes by navigating the

tree and selecting a Context project, subproject (optional) or package.

• Search for attributes by selecting a class.

• NOTE: Packages have the package icon next to the package name.

NOTE: Packages have the package icon next to the package name.


Narrowing/ Widening Search Results

• Selecting a link returns all of the class elements associated with the selected level.• Context• Project• Subproject• Package

• The number of elements will depend on the level of the node you select from the tree (Example: Selecting the caBIG® context will display far more elements than BRIDG 1.0 project).


Tree Search Crumb Trail

• When you expand the tree and make your selections, your tree search path is displayed in the crumb trail.• Hint: Hovering over acronyms in the tree will display the full name.

• Search terms are entered in either the Class Name or Attribute Name fields.

• The Browser searches for exact matches for the term entered in the search field.

• Searches can be narrowed by (optional)• UML Project Name• Sub Project Name• Package Name• Version


Basic Class/ Attribute Search


Wildcard (*) Supported

• Class Name, Attribute Name and Version support the wildcard (*).• An asterisk (*) is the wildcard character.• Use wildcards to broaden your search.• Wildcards can be used more than once in a search term or phrase.

• Examples

1. You want to search for model elements which contain the term patient in either the Class Name or Attribute Name field• Enter *patient*

2. To search for model elements that begin with the term patient• Enter patient*

3. Wildcards can be used to bridge words. To search for patient name • Enter *patient*name*

NOTE: UML Model Browser searches are NOT case sensitive.NOTE: UML Model Browser searches are NOT case sensitive.


Class Search vs. Attribute Search

• To conduct a Class Search • Enter a search term in the Class Name field and select Class Search

• To conduct an Attribute Search • Enter a search term in the Attribute Name field and select Attribute Name

• Let’s look at an example on the next slide….


Class Search Example

1. Enter the search term protein in the Class Name field.

2. Select Class Search.

3. Results returned are a list of classes (16 results) with protein in the class name.


Attribute Search Example

1. Enter the search term protein in the Attribute Name field.

2. Select Attribute Search.

3. Results returned are a list of attributes (6 results) with protein found in the attribute name.


Attribute Search against Class Name

• The UML Model Browser also allows users to enter search criteria in the Class Name field and perform an Attribute Search.

• Results display a list of attributes that match the search parameters entered.

• Let’s look at an example on the next slide…NOTE: KNOWN ISSUE: The UML Model Browser does not display accurate results if users

conduct a Class Search against Attribute Name criteria. This is a known issue and will be resolved in the future.

NOTE: KNOWN ISSUE: The UML Model Browser does not display accurate results if users conduct a Class Search against Attribute Name criteria. This is a known issue and will be resolved in the future.


Attribute Search Against Class Name Example1. Enter a search term person* in the Class Name field.

2. Select Attribute Search.

3. Results returned are a list of Attributes with the term Person* in the Class Name.


Combined Search Methods

• Users may combine a Class or Attribute Search within a specified context, project, subproject or package.

• The selected level will display in the search field.

• Let’s walk through an example• Search criteria: You are interested in all

the attributes in the BRIDG 2.1 project

which contain the term “name” (Hint: you

already know the project is located under

the caBIG® context)

1. Navigate to the search tree and expand

(select the plus “+” sign) the caBIG context

2. Expand (select the plus “+” sign) BRIDG 2.1

project

3. Select the package link for the project

gov.nih.nci.BRIDG.domain


Combined Search Methods cont…

• Once the package link is selected, the UML Project Name and Package Name fields are automatically populated.

4. Verify the correct field populations to constrain your search

5. Enter *name* in the Attribute Name search text box

6. Select Attribute Search

7. Evaluate Results


Review

1. Which of the following is NOT a search option available in the UML Model Browser

A. Class Search

B. Tree Search

C. Tree Search Combined with a Class Search

D. Concept Search

2. You conducted a Class search for “Person” and only returned one result. What option is available in the UML Model Browser to possibly expand your search results?

A. Select the Bioconductor link from the Search Tree and conduct your search again.

B. Change your search term to people. Certainly more than one person would give you more results.

C. Use the wildcard character “*” both before and after your search term.


Answers

1. Which of the following is NOT a search option available in the UML Model Browser

A. Class Search

B. Tree Search

C. Tree Search Combined with a Class Search

D. Concept Search (correct answer)

2. You conducted a Class search for “Person” and only returned one result. What option is available in the UML Model Browser to possibly expand your search results?

A. Select the Bioconductor link from the Search Tree and conduct your search again.

B. Change your search term to people. Certainly more than one person would give you more results.

C. Use the wildcard character “*” both before and after your search term (correct answer)


Exercise

• Navigate to the UML Model Browser (http://umlmodelbrowser.nci.nih.gov/) to answer the questions.

1. How many classes are in the Clinical Trials Lab Model (Hint: the Project is located in the caBIG® context?

A. Less than five

B. Five to 100

C. More than 100

2. How many results do you get when you perform a Class Search for “gene”?

A. Zero

B. One to 250

C. Over 5000



Exercise Solution

• Navigate to the UML Model Browser (http://umlmodelbrowser.nci.nih.gov/) to answer the following questions.

1. How many classes are in the Clinical Trials Lab Model? (Hint: the Project is located in the caBIG® context.)

A. Less than five

B. Five to 100 (correct answer)

C. More than 100

2. How many results do you get when you perform a Class Search for “gene”?

A. Zero

B. One to 250 (correct answer)

C. Over 5000



Recap

• Now that you have completed this lesson, you should be able to:• Search for UML Model Metadata utilizing three search options

1. Tree Search

2. Class/ Attribute Search

3. Combination Tree & Class/ Attribute Search• Expand search results using the wildcard “*” character• Perform an Attribute Search against a Class Name search term

Lesson 5: Search Results

• In this lesson, you will learn how to:• Navigate the Classes tab and the Attributes tab to locate information

pertaining to a specific project’s UML Model Metadata• Access the CDE Browser from the Classes and Attributes tabs to assess

associated caDSR metadata• Manipulate the search results table by performing different sorts • Locate project information from a list of search results


Viewing Search Results

• UML model elements that match your search results criteria appear in the search results table.


Classes/ Attributes Tabs

• The Classes and Attributes Tabs are available for all searches in the UML Model Browser.• Class Search displays the Classes tab• Attribute Search displays the Attributes tab

• Selecting the Attributes tab AFTER conducting a Class Search will display the same search results as entering a Class Name search term and selecting the Attributes Search button.

NOTE: KNOWN ISSUE: The UML Model Browser does not display accurate results if users conduct an Attribute Search and select the Classes tab from the search results table. This is a known issue and will be resolved in the future.NOTE: KNOWN ISSUE: The UML Model Browser does not display accurate results if users

conduct an Attribute Search and select the Classes tab from the search results table. This is a known issue and will be resolved in the future.


Sorting Results

• By default, the UML Model Browser sorts search results by Class Name or Attribute (depends on the type of search conducted).

• Sort Order can be changed by selecting the desired column heading.• The initial sort order is ascending. Selecting the column heading again

displays descending sort order.


Classes Tab

• Classes Tab displays when a class search is conducted.• Selecting the Classes tab when conducting an Attribute Search displays

all Classes that match the search criteria entered.• Classes Tab active links

• Class Name• Project Name• Class Details


Class Name Link (Classes Tab)

1. Select the Class Name link to display all of the attributes for the project’s use of the class element.


Project Name Link (Classes Tab)

1. Select the Project Name Link to view information about the project.


Class Details Link (Classes Tab)

1. Selecting the Class Details link opens the CDE Browser in a separate window.

• The Class Details column displays the public ID of the caDSR Object Class to which the model element is mapped.

1


Object Class Tab


Attributes Tab

• Attributes Tab displays when an attribute search is conducted.• Attributes Tab active links:

• DE Name• Project Name- identical to the Project Name link in the Classes Tab


DE Name Link (Attributes Tab)

• The DE Name column link displays the full name of the data element (DE or CDE) to which the attribute is mapped in the caDSR for the selected project.

• Selecting the link opens the CDE Browser data element details in a separate window.• For more information on data element details refer to course 1020: Using

the CDE Browser.


Review

1. The _________ tab displays after conducting a Class Search and the __________ tab displays after conducting an Attribute Search.

2. Additional details about a project can be found by selecting:

A. Project Name Link

B. DE Name Link

C. Class Details Link

D. Class Name Link

3. Which links open the CDE Browser from the search results table? (Hint: there is more than one correct answer)


B. DE Name Link


D. Class Name Link


Answers

1. The Classes (correct answer) tab displays after conducting a Class Search and the Attributes (correct answer) tab displays after conducting an Attribute Search.

2. Additional details about a project can be found by selecting:

A. Project Name Link (correct answer)

B. DE Name Link


D. Class Name Link

3. Which links open the CDE Browser from the search results table? (Hint: there is more than one correct answer)


B. DE Name Link (correct answer)

C. Class Details Link (correct answer)

D. Class Name Link


Exercise

• Navigate to the UML Model Browser (http://umlmodelbrowser.nci.nih.gov/) to answer the following questions.

• Perform the following search• Enter person in the Class Name search field• Select Class Search

1. How many attributes are associated with the BRIDG 1.0 (public ID- 2236731) Person Class?

A. One to Five

B. Five to 100

C. Greater than 250

2. Which DE Name is associated with the address Attribute Name?

A. Person Address java.lang.long

B. Person Address java.lang.String

C. There is no address attribute for the class name person



Exercise Solution

1. How many attributes are associated with the BRIDG 1.0 (public ID- 2236731) Person Class?

A. One to Five

B. Five to 100 (correct answer) – locate the BRIDG 1.0 project from the list of results and select the Person link to display the list of attributes this project uses for the person class

C. Greater than 250

2. Which DE Name is associated with the address Attribute Name?

A. Person Address java.lang.long

B. Person Address java.lang.String (correct answer) - Select the Attributes Tab from the list of search results. Locate the address attribute along with the data element name (DE Name)

C. There is no address attribute for the class name person


Recap

• Now that you have completed this lesson, you should be able to:• Navigate the Classes tab and the Attributes tab to locate information

pertaining to a specific project’s UML Model Metadata• Access the CDE Browser from the Classes and Attributes tabs to assess

associated class and attribute caDSR metadata• Manipulate the search results table by performing different sorts • Locate project information from a list of search results

Lesson 6: How to Find Your UML Model Metadata

• In this lesson, you will learn how to:• Locate your UML Model Metadata in the caDSR and compare them to

your actual UML Model


Purpose

• Once your model is loaded into the caDSR, you will want to find your UML Model Metadata using the UML Model Browser. This lesson will walk you through the steps required to find your UML Model metadata.

• For this lesson, we have loaded a simple model called the BootCampModel under the training context. We will use this model for our exercises.

NOTE: Remember, Test and Training Contexts are not included by default in the UML Model Browser. Select the Search Preferences link and include these contexts for this lesson. Once you have saved your search preferences, navigate to the Search Tree and select the Refresh tree link to view the BootCampModel under the training context. This might take some time.

NOTE: Remember, Test and Training Contexts are not included by default in the UML Model Browser. Select the Search Preferences link and include these contexts for this lesson. Once you have saved your search preferences, navigate to the Search Tree and select the Refresh tree link to view the BootCampModel under the training context. This might take some time.


BootCampModel

• You will want to reference this slide to walk through the exercises in this lesson.


UML Model Components to Find

• Classification Schemes, Classification Scheme Items, and packages all exist as expected in the browser tree.

• Classes and attributes mapped to CDEs • CDE Alternate Names/ Definitions (if applicable)• Class/ Object Class and Attribute/Property mappings• Associations created as expected• Data types mapped to Value Domains• Permissible Values (if enumerated)

Lesson 6 : How to Find Your UML Model Metadata

Classification Scheme Verification

• Verify your model context, classification scheme (CS), classification scheme items (CSI), package location.

• Verify the all of the classes in your model my selecting the package from the search tree.


Classes


Attributes

• Verify the attributes listed for each class are correct. Select the Class Name to view all of the attributes (not shown).


Associations

1. Select the package link (gov.nih.nci.training.bootcamp.domain) to view a list of classes in the model. (not shown)

2. Select the Class Details (Protein) link to view the associations for the chosen class in the CDE Browser on the Associations tab.


Alternate Names/ Definitions (if applicable)• If you are reusing a CDE in your model and curated an alternate name/

alternate definition, you can verify this information from the Data Element Details> Data Element tab which displays after the DE Name link is selected.


Object Class and Property Concept Mappings

• Select Data Element Concept tab to view Object Class and Property Concepts from the Data Element Details. Data Element Details are viewed by selecting the DE Name link from the search results table in the UML Model Browser.


Object Class and Associations

1. Select the Class Details link (2223335) to view CDE Browser Object Class Details (contains more detail than Data Element Details> DEC tab) and Associations.


Object Class and Associations cont…


Value Domain / Data Type Mappings• VD Mappings are found in the Data Element Details > Value Domain Tab (CDE

Browser) which are accessed by selecting the DE NAME link from the UML Model Browser.


Permissible Values (if enumerated)


Review

• To answer the questions you will need to access the UML Model Browser in the Sandbox environment: http://umlmodelbrowser-sandbox.nci.nih.gov/ (don’t forget to change your Search Preferences)

1. How many classes are there in the BootCampModel (under the training context)?

2. How many attributes are loaded for this model? Does this match the UML Model?

3. What is the public ID of the Class Gene/ Object Class?

4. Does the Class Protein and Class Gene association appear as expected?

5. How many attributes are loaded into the caDSR for the Gene Class? Does this match our UML Model?

6. What is the Data Type for the Class - Gene Attribute – id loaded into the caDSR? Is this correct?

http://umlmodelbrowser-sandbox.nci.nih.gov/


Answers

1. How many classes are there in the BootCampModel (under the training context)?• 9 (correct answer)

2. How many attributes are loaded for this model? Does this match the UML Model?• 33 and Yes (correct answer)• Remember Children (ActiveSite & BindingSite inherit the parent attributes)

3. What is the public ID of the Class Gene/ Object Class?• 2223336 (correct answer)

4. Does the Class Protein and Class Gene association appear as expected?• Yes (correct answer)

5. How many attributes are loaded into the caDSR for the Gene Class? Does this match our UML Model?• 3 and Yes (correct answer)

6. What is the Data Type for the Class - Gene Attribute – id loaded into the caDSR? Is this correct?• Long and Yes (correct answer)


Recap

• Now that you have completed this lesson, you should be able to:• Locate your UML Model Metadata in the caDSR and compare them to

your actual UML Model

1025: Using the UML Model Browser

Course Recap

• Now that you have completed this course, you should be able to:• List four ways Unified Modeling Language (UML) represents the artifacts

of a software system• Identify the components of a UML Class Diagram• Analyze a UML class and determine the appropriate corresponding


attributes and data types• Access and navigate the UML Model Browser and change search

preferences to include test and training contexts• Search for UML Model Metadata with three different search options• Manipulate different variables to expand or narrow search results• Differentiate between a Class Search and Attribute Search• View your UML Model Metadata using the UML Model Browser


Appendix A

UML Multiplicity Table


Appendix A UML Multiplicity Table

• The following table lists multiplicity options that their associated meanings.

Indicator Meaning

0..1 Zero or one

1 One only

0..* Zero or more

1..* One or more

n Only n (where n > 1)

0..n Zero to n (where n > 1)

1..n One to n (where n > 1)

Multiplicity Table

caDSR Training Account Request

• If your role requires curator access to the caDSR, you will need to request a caDSR training account. A caDSR training account will allow you to practice curation on the caDSR sandbox server while you complete your training.

• If you are unsure if your role requires access, please send an email inquiry to Dianne Reeves: [email protected].

• See the next slide for training account request instructions…

NOTE: The caDSR Training Account is different from the LMS Training account you use to register for courses.

NOTE: The caDSR Training Account is different from the LMS Training account you use to register for courses.


Training Account Request Instructions

• Send an email to NCICB Application Support: [email protected] • Please copy/paste the following information into the email, filling in your

details where instructed.• First Name: <your first name here>

Last Name: <your last name here>Email address: <your email address here>Title: <your job title>Organization: <your organization or affiliation>Business Need: <provide a brief description of the business reason for requesting a caDSR Account.>Account Type: TRAININGContexts: Read/Write access for TEST and TRAINING on the Sandbox tier

• Once you have completed ALL of your required training, see Next Steps for Metadata Curators: https://wiki.nci.nih.gov/x/GAty.


https://wiki.nci.nih.gov/x/GAty

Training User Accounts – on Sandbox Server

• If your role will not require a curator account on caDSR production, a set of user names and passwords have been set up for you to access the tools on the caDSR sandbox server.

• CDE Browser: http://cdebrowser-sandbox.nci.nih.gov/• UML Model Browser: http://umlmodelbrowser-sandbox.nci.nih.gov/• CDE Curation Tool: htttp://cdecurate-sandbox.nci.nih.gov/• Sentinel Tool: http://cadsrsentinel-sandbox.nci.nih.gov• Admin Tool: http://cadsradmin-sandbox.nci.nih.gov/• User ID / Password: Trainee01 / Trainee01

• Trainee02 / Trainee02• …• Trainee09 / Trainee09• Trainee10 / Trainee10

http://cdebrowser-sandbox.nci.nih.gov/

http://umlmodelbrowser-sandbox.nci.nih.gov/

Course Quiz in the LMS

• In order to receive credit for mastery of this content, you will need to register for this course and complete the accompanying quiz in the caBIG ® Learning Management System.

• To register, go here:


1. Log in with your user name and password

2. Select My Training link located on the left side of the screen

3. Select the course from you list of courses in progress

4. Select the associated quiz located below the Course Materials link


Contact Information

• Training Team:• [email protected]

• NCI CBIIT Liaison: Dianne Reeves • ([email protected])

• NCI CBIIT Application Support• [email protected]

• caDSR Home Page• http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/cadsr

• caCORE Training Home Page• http://ncicb.nci.nih.gov/NCICB/training/cadsr_training

• caCORE Training Wiki• https://wiki.nci.nih.gov/x/OAFy



CaCORE Training: Using the UML Model Browser Course Number:1025 Duration: Self-paced Intended Audience: caDSR Users and Metadata Consumers Using UMLModels.

Documents

uml model metadata

uml model browserprerequisites

ways uml

uml modelinglesson

uml models

uml modelingwhy

uml modelingin

uml class diagramidentify