Appendix_C_-_Interactive_Training_Module_Outline_NIMS.pdf

NIMS Online Training Module Outline

NIMS Online Training Module

Outline

NIMS Online Training Module 2

Document Control

Change Record

Date Author Version Change Reference

23-Nov-12 Shashank B 1.0 First Version

17-Jan-13 Rajendra Pokle 1.1 Updated to meet 508 compliance requirements

Participants

Contributors

Name Representing Role

Shashank B PointCross Project Manager

Reviewers

Name Representing Role Review Date

Timothy Kropp FDA

NIMS Online Training Module 3

Contents

1 Introduction

2 Structure and Organization

3 Lesson Outline

3.1 About NIMS and Using the Interactive Module

3.2 Section 1: Accessing NIMS and Study Data

3.3 Section 2: ToxVision Setup

3.4 Section 3: Basic Reviewer Lessons

3.5 Section 4: Basic Search

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Outline for Interactive Module

1 Introduction The document outlines the structure, organization, and lessons available in the Interactive Training

Module for NIMS.

2 Structure and Organization

About NIMS and Using the Interactive Module

Section 1: Accessing NIMS and Study Data o Lesson 1: Login to NIMS o Lesson 2: Adding a study to My Workspace o Lesson 3: Study Activities View o Lesson 4: Adding study metadata

Section 2: ToxVision Setup o Lesson 1: Viewing a study in ToxVision o Lesson 2: Study data organization o Lesson 3: Viewing data for a selected data category o Lesson 4: View Group Summary Data for Body Weight o Lesson 5: View Individual Results for ECG Test Results o Lesson 6: View Individual Details for Organ Measurements o Lesson 7: Subject Profile View o Lesson8: Viewing group incidences for Clinical Observations o Lesson 9: Generating charts for Laboratory Test Results o Lesson 10: Exporting study data from Body Weight Gain

Section 3: Basic Reviewer Lessons o Lesson 1: Generating the Reviewer Template o Lesson 2: Working with Reviewer Panels o Lesson 3: Generating a z-transform box plot o Lesson 4: Consolidated Incidence View for treatment groups o Lesson 5: Export histopathology data to reviewer template o Lesson 6: View Individual Results for gross pathology data o Lesson 7: Tissue View o Lesson 8: Setting a treatment group as a baseline(reference group)

NIMS Online Training Module 5 o Lesson 9: Combine groups to create a new reviewer group o Lesson 10: Exclude subjects and recalculate group summary

Section 4: Basic Search o Lesson 1: Unstructured search o Lesson 2: Structured search with Clinical Pathology

3 Lesson Outline

3.1 About NIMS and Using the Interactive Module

The Nonclinical Information Management System (NIMS) is designed to provide nonclinical study data management, repository, data loading, analysis, search, and visualization functionalities needed by the FDA reviewers to conduct fast and efficient drug safety reviews.

The NIMS Online Training Module utilizes a procedural learning model approach. The instructional strategy employed in the procedural learning model can be described as a guided discovery learning approach used to develop skill in applying procedures. The intent is to allow the user to select a lesson from a menu and then place the user in a problem-solving environment that employs visual and functional simulation of the NIMS application. Users are expected to complete a specific lesson, which is an example of a range of similar specific lessons they will need to perform in the use of the NIMS application. The goal is not just to complete the example lesson, but also to learn the underlying procedure so as to apply it in future situations, where applicable.

The datasets used in the creation of the Online Training Module have been sanitized to remove all sensitive information and in some cases mock datasets have been created to enhance the instructional nature of the lesson.

3.2 Section 1: Accessing NIMS and Study Data

3.2.1 Lesson 1: Login to NIMS

Learning Objective: In this lesson, you will learn how to log into the NIMS application.

Steps:

1. Click the Internet Explorer icon to open Internet Explorer.

2. In the address bar click and type - https://nims.fda.gov

3. Press Enter. The FDA security disclaimer page opens.

4. In the FDA security disclaimer dialog box, click the OK button. The NIMS dashboard opens.

Conclusion: You have successfully logged in to NIMS. You can add the URL to the favorite links for subsequent access.

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3.2.2 Lesson 2: Adding a study to My Workspace

Learning Objective: In this lesson, you will learn how to add a study to My Workspace from the NIMS dashboard.

Steps:

1. Ensure you are looking at the “All Studies” view in the NIMS dashboard

2. From the ‘Study ID’ options in the drop-down, filter the desired study

3. Click the check-box to select the study

4. Click “Add to My Workspace" button

5. View the study that is added to My Workspace

Conclusion: You have now added the study that is chosen for review to My Workspace. Note that once a study is added to My Workspace, subsequent login to NIMS will direct you to My Workspace

3.2.3 Lesson 3: Study Activities View

Learning Objective: In this lesson, you will learn how to review a list of key activities and events for a study on a time scale and show you how to pull up the Study Activities View

Steps:

1. In the NIMS dashboard pause over the down arrow for the desired study. Click Study Activities

View.

2. Click Body Weights under Activities.

3. Click Body Weight under Body Weights.

4. Click Control under Activities.

5. Click Female under Control.

Conclusion: You have successfully learnt how to review a list of key activities and events for a study over a time scale by drilling down to the Study Activities View

3.2.4 Lesson 4: Adding study metadata

Learning Objective: In this lesson, you will learn how to add and save study-level metadata for a given study.

Steps:

1. Choose the study from the dashboard and go to the study level options from the drop down menu

2. Click “Edit” option

3. Type a value for Pharmacological Class

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4. Type free text comment in the Comments field

5. Add a Drug Substance by selecting the generic name from the drop-down selection

6. Click ‘Save’

Conclusion: You have learned how to edit (add, modify, and delete) study-level metadata for the selected study and save the changes in the Edit form for future reference.

3.3 Section 2: ToxVision Setup

3.3.1 Lesson 1: Viewing a study in ToxVision

Learning Objective: In this lesson you will learn how to open a selected study for viewing in ToxVision

1. From the NIMS dashboard, click on the hyperlinked study identifier under the Study ID column for the selected study

2. View data in ToxVision for the selected study in a new browser window

3. By default the Trial Summary data for the study is loaded in the right-hand pane.

Conclusion: The selected study data is available for review and analysis

3.3.2 Lesson 2: Study data organization

Learning Objective: In this lesson you will understand organization of study data categories in ToxVision.

1. In the left-hand pane of the ToxVision window, click the arrow beside the Trial Design Domains under Study/Trial Definition to expand the tree.

2. Under the Study/Trial Definition, click Trial Design Domains to expand and view data categories in this section for the study

3. Click Laboratory Test Results to expand the tree and display all the test names available for the study

4. Click the ‘Expand All’ button to view all the tests performed in the study

Conclusion: You have successfully learned how the study data categories are organized in ToxVision.

3.3.3 Lesson 3: Viewing data for a selected data category

Learning Objective: In this lesson, you will learn how to search and filter for a selected test name and view the data in ToxVision

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1. Under the Special-Purpose Domains, click Demographics

2. In the search box under Study Definition/Findings, type ‘hemoglobin’

3. View the navigation panel, filtered for Hemoglobin under Hematology

4. Double click Hemoglobin to view the data loaded for hemoglobin in the data grid

5. Under the Laboratory Test Results click “Hematocrit”

6. Click “Add to table” to add the parameter to the existing data table

7. Click ”Bilirubin” under Laboratory Test Results and select Add as new table to add data for

Bilirubin as a new data table

Conclusion: You have added data for the selected parameter into the ToxVision data panel.

3.3.4 Lesson 4: Viewing Group Summary Data for Body Weight

Learning Objective: In this lesson, you will learn how to work with group summary results for a parameter. The Body Weight parameter has been used as an example to demonstrate this.

Steps:

1. Open ToxVision for the selected study

2. From the navigation panel, double click Body Weight

3. In the right-hand data pane click the down arrow in the View dropdown beside Parameters as

Columns.

4. Select “Days as Columns” from the “View” drop down, to view data displayed in the study days as columns fashion.

Conclusion: You have successfully learned how to add the group summary data for the Body Weight parameter in the data panel with the toggled view displayed.

3.3.5 Lesson 5: View Individual Results for Electrocardiogram Test Results

Learning Objective: In this lesson, you will learn how to navigate to the Individual Results section for a parameter. We will use summary (Mean) Heart Rate to demonstrate this.

Steps:

1. Open ToxVision for the selected study

2. From the navigation panel, double click Summary(Mean) Heart Rate under Electrocardiogram

Test Results

3. From the data panel showing Group Summary results by default, click Individual Results tab

4. View results displayed for each subject for all the treatment groups

5. From the column header ‘Group’, click on drop-down for additional options

6. Go to “Filters” and select the check-box against “3:GROUP 3”

7. Click Apply Filter and view the filtered results for the selected group

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Conclusion You have successfully learned how to view results for the selected parameter at the individual subject level and use the filter feature.

3.3.6 Lesson 6: View Individual Details for Organ Measurements

Learning Objective: In this task, you will learn how to view individual details for organ measurements as submitted by the sponsor. Liver weight has been used to demonstrate this.

Steps:

1. For the selected study in ToxVision, expand Organ Measurements from the navigation panel

2. Under “Weight” double-click “LIVER” to view the summary data loaded in the data panel by default.

3. Click “Individual Details” tab and view the data for LIVER as submitted by the sponsor.

4. From the column header ‘Phase’, click the drop-down for additional options

5. Click Sort Descending to sort values in this field in descending order

Conclusion: You have successfully learned how to view the data for individual subjects in detail for all fields that are submitted in the source files.

3.3.7 Lesson 7: Subject Profile View

Learning Objective: In this lesson, you will learn how to look at the Individual Subject Profile by navigating from the Vital Signs domain.

Steps:

1. For the selected study in ToxVision, expand Vital Signs from the navigation panel.

2. Double click “Temperature” to view summary data loaded in the data panel by default

3. Click “Individual Results” tab and view results at the individual subject level

4. From the “Unique Subject identifier” column, click the hyperlinked subject ID “USB 751”

5. The subject profile spanning all the data domains where observations are captured for the individual subject is displayed.

6. Click Body Weights from the navigation panel from this view to load individual subject details for the subject

7. View the Control and treatment group mean and SD for the subject

Conclusion: You have successfully learnt how to pull up the individual subject profile for the selected subject.

3.3.8 Lesson 7: Viewing group incidences for Clinical Observations

Learning Objective: In this lesson you will learn how to view and navigate through the group incidence view for Clinical Observations

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1. From the navigation panel under Clinical Observations, double click Behavior.

2. View incidence values loaded up under Group Summary and pause over the 3/1 incidence value to display the number of subjects and occurrences

3. Click incidence value to further drill-down open the detailed view

4. View the subjects that contributed to the incidence and the day on which the occurrence happened

Conclusion: You are now able to view and navigate through the incidence tables for Clinical

Observations.

3.3.9 Lesson 8: Generating charts for Laboratory Test Results

Learning Objective: In this lesson you will learn how to compare group mean values for Laboratory Test

Results across treatment groups with a line graph

Steps:

1. Open ToxVision for the selected study

2. From the navigation panel, select ‘Basophils’ under Laboratory Test Results and load the data in the right-hand pane.

3. View group summary data for Basophils

4. Use check boxes to select Basophils and the desired treatment groups

5. From the “Menu” button on the top right click “Graph” and then “Line Graph”

6. View the Group Mean values plotted using line graph

Conclusion: You are now able to generate line graph for the selected parameter. Similarly you can export the data as Bar, X-bar and box-whisker charts.

3.3.10 Lesson 9: Exporting study data from Body Weight Gain

Learning Objective: In this lesson you will learn how to export study data to standard template formats

1. From the navigation panel in ToxVision, select “Body Weight Gain” under Laboratory Test

Results and load the data in the right-hand panel

2. Use check boxes to select the parameter and desired treatment groups

3. From the “Menu” button on the top right click “Export To” followed by “Excel”

4. The selected data is exported to the predefined Excel template

Conclusion: You are now able to export the selected data to the Excel format. Similarly you can export data to other formats like CSV, XML, XPT, and Prism.

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3.4 Section 3: Basic Reviewer Lessons

3.4.1 Lesson 1: Exporting Study Parameter data to the Reviewer Template

Learning Objective: In this lesson, you will learn how to export Trial Summary data into Reviewer

Template (in Word format) to get a complete overview of the study under review.

Steps:

1. Open ToxVision for the selected study

2. View Trial Summary

3. Click the “Menu” button on the top right

4. Click “Export To Reviewer Template”

5. View the data in the Reviewer Template(Rich Text File Format) and save the file for future reference

Conclusion: You have successfully exported the summary data for the selected study into the Reviewer

Template for sharing, reporting and/or further analysis

3.4.2 Lesson 2: Working with Reviewer Panels

Learning Objective: In this lesson you will learn how to group parameters using standard reviewer panels to identify an effect or marker.

Steps:

1. Open study in ToxVision for the selected study

2. From the navigation panel click Group By drop-down

3. From the pick list select ‘Reviewer Panel’

4. Double click ‘Liver/hepatobiliary’ to load the parameters within the panel into the ToxVision data tables

Conclusion: You are now able to group the parameters based on standard panels and load the data in

ToxVision. Similarly you can group the clinical pathology data by standard Biomarker Panels

3.4.3 Lesson 3: Generating the z-transform box plot

Learning Objective: In this lesson you will be able to generate the z-transform box plot to review and compare clinical pathology data.

Steps:

1. From the navigation panel on the left hand side, click the down arrow beside “Laboratory Test

Results.”

2. Select z-Transformation(Box-Plot) from the drop down menu

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3. From the “z-transformation (Box-Plot) Setup” dialog box click the Group By drop down.

4. In the Group By drop down, select the Biomarker Panel.

5. Select Plasma for the Sample Type parameter and female for the sex parameter.

6. Click OK

7. View clinical pathology parameters plotted as a z-transform box plot

Conclusion: You have successfully learned how to generate the z-Transformation (Box-Plot) to review and compare the clinical pathology data.

3.4.4 Lesson 4: Consolidated Incidence View for treatment groups

Learning Objective: In this lesson you will learn how to view incidence values for all the observations categorized by tissues across study days and treatment groups

Steps:

1. From the navigation panel on the left hand side click the consolidated view icon next to the

Microscopic Findings

2. Scroll to the right to view the group incidence values for all observations categorized by tissues across study days and treatment groups loaded up in the data panel

3. Click the first hyperlink to view the Subject List.

Conclusion: You have learned how to pull up the Consolidated View and drill down to the subject level.

3.4.5 Lesson 5: Export histopathology data to reviewer template

Learning Objective: In this lesson you will learn how to export histopathology data to a reviewer template into MS Word.

Steps:

1. In the left-hand pane, click the consolidated view icon for Microscopic Findings.l

2. In the Consolidated View – Microscopic Findings tab, click Menu to view the dropdown.

3. In the dropdown menu, mouse over “Export To” to view the submenu.

4. In the submenu, click Word to view the histopathology data in the Word template.

Conclusion: You have successfully learned how to navigate through the consolidated view and export the histopathology data to the MS Word reviewer template.

3.4.6 Lesson 6: View Individual Results for gross pathology data

Learning Objective: In this lesson you will learn how to view Individual Results for Gross Pathology Data

1. From the navigation panel for a selected study expand Macroscopic Findings

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2. Double click the parameter Liver to load the data in the data tables

3. Click “Individual Results” tab to view incidences at the individual subject level

Conclusion: You have successfully learned how to view consolidated incidences for all subjects across treatment groups and study days.

3.4.7 Lesson 7: Tissue View

Learning Objective: In this lesson you will learn how to view group summary information for the BRAIN parameter across data domains in a single view.

Steps:

1. Open ToxVision for the selected study

2. From the navigation panel, expand the tree for Microscopic Findings

3. Click BRAIN

4. Select ‘Tissue View’ from the drop down list.

5. View the group summary data for BRAIN from all the data categories where there are findings reported for BRAIN

Conclusion: You have successfully learned how to pull up and view Tissue View.

3.4.8 Lesson 8: Setting a treatment group as a baseline (reference group)

Learning Objective: In this lesson you will learn how to set a treatment group as a baseline for comparison.

Steps:

1. Open ToxVision for selected study

2. Click “Trial Sets” under “Trial Design Domains” from the navigation panel to view treatment groups

3. Load Terminal Body Weight data and compare group summary results across treatment groups

4. In the Trial Sets view, select a new baseline group by clicking ”No” in the Baseline column for

SET02, Negative Control

5. Compare the group summary results with % Difference calculated for the new baseline group in the BG table

Conclusion: You have successfully learned how to change the reference group for comparison and set a new baseline group.

3.4.9 Lesson 9: Combine groups to create a new reviewer group

Learning Objective: In this lesson you will learn how to combine available treatment groups to create new reviewer group for analysis.

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1. Open ToxVision for the selected study

2. Click ”Trial Sets” under “Trial Design Domains” from the navigation panel to view treatment groups

3. Load Terminal Body Weight data in the data table

4. In the Trial Sets view select SET03 and SET04.

5. Click “Club Groups” to open a dialog box

6. Type Group Name as “SET03 and SET04”

7. Type Description as “Combined group.”

8. Click “Save” to create a new reviewer group

9. View data for Terminal Body Weight with the new reviewer group added

Conclusion: You have successfully learned how to combine available treatment groups to create a new reviewer group.

3.4.10 Lesson 10: Exclude subjects and recalculate group summary

Learning Objective: In this lesson you will learn how to exclude subjects from a treatment group and recalculate group summary.

Steps:

1. Load data for Body Weight into the data tables from the navigation panel

2. Click Individual Results tab

3. Exclude values under the results column. Do this by click the first three values.

4. Click “Recalculate”

5. A new pop-up box with the recalculated group summary is displayed.

6. Pause over the blue highlighted area to look at the previous value.

Conclusion: You have successfully learned how to exclude values for a given subject and recalculate group summary.

3.5 Section 4: Basic Search

3.5.1 Lesson 1: Unstructured search

Learning Objective: In this lesson you will learn how to open SDIS and exercise search using the free text search option.

Steps:

1. From the NIMS dashboard, click Advanced Search button

2. View the Study Data Integration and Search System(SDIS)

3. In the Setup Search Criteria tab, type the search text “mouse” in the search box

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4. Click Search or press the Enter key

5. Show Search Results tab will be displayed with the studies that matched the search criteria

Conclusion: You have successfully learned how to open SDIS and search for the desired value using free text search with the search results visible in the results screen.

3.5.2 Lesson 2: Structured search with Clinical Pathology parameters

Learning Objective: In this lesson you will learn how to setup structured search with Clinical Pathology parameters

Steps:

1. From the SDIS screen, click Laboratory Test Results from the navigation panel

2. Under the parameter field, type ‘Alanine Aminotransferase’ or select from pick list

3. Change the lower limit of the range slider value to “10.”

4. Setup another search criteria with Aspartate Aminotransferase in the Laboratory Test Results

5. Change the lower limit of the range slider value to “20.”

6. Click Search to view the studies that matched the search criteria

7. Click “Save Criteria” and type “Clinical Pathology” in the text box.

8. In the Description text box type “Increase in ALT and AST.”

9. Click the Save button.

10. Click the Saved Search Criteria tab to view the saved search criteria.

Conclusion: You have successfully learned how to setup complex search criteria using the structured search method.

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