Appendix_F_-_NIMS_User_Guide.pdf

User Guide

NIMS User Guide

Table of Contents

1 NIMS Overview

2 Accessing NIMS

2.1 Logging into NIMS

2.2 Accessing the NIMS dashboard

2.3 About the Dashboard

2.3.1 All Studies

2.3.2 Accessing My Workspace

2.4 Dashboard Controls

2.4.1 Sorting

2.4.2 Filtering Studies

2.4.3 Rearranging columns

2.4.4 Hiding columns

2.5 Study Level Controls

2.5.1 Adding and removing multiple studies from My Workspace

2.5.2 Study Activities View

2.5.3 Edit Form (Editing/Adding study-level metadata)

2.5.4 Opening a Study in ToxVision

2.5.5 Exporting to SEND format

2.6 Advanced Search

2.7 Using Support and I Wish

3 Accessing ToxVision

3.1 Navigation Panel

3.1.1 Study/Trial Definition

3.1.2 Test Findings

3.1.3 Grouping by Study Definition/FindingsS

3.1.4 Search Parameter

3.1.5 Expand/Collapse

3.1.6 Adding data to the data panel

3.2 Data panel

3.2.1 Data Views

3.2.2 Data Panel Controls—Viewing Options

3.3 Clubbing Groups

3.4 Setting a Baseline Group

3.5 Exclude Treatment Groups

3.6 Recalculation of Group Summary (Include/Exclude Subjects)

3.7 Data Export

3.7.1 Checklist

3.7.2 Exporting a Study Summary to the Reviewer Template

3.7.3 Exporting to MS Word

3.7.4 Exporting as Excel as View

3.7.5 Exporting to MS Excel

3.7.6 Exporting to CSV

3.7.7 Exporting to XPT

3.7.8 Exporting to Prism

3.8 Graphs

3.8.1 Checklist

3.8.2 Viewing the X-Bar Graph

3.8.3 Viewing the Whisker-Plot Graph

3.8.4 Viewing the Line Graph

3.8.5 Viewing the Bar Graph

3.8.6 Generating Correlation Heat Maps

3.9 Generating the z-Transformation (Box-Plots)

3.9.1 Viewing the Groups’ Legend

3.9.2 Rearranging the Parameter Display

3.9.3 Deleting a Parameter

3.9.4 Viewing Z-Scores Boxplots

3.9.5 Creating MyList

3.9.6 Deleting MyList

3.10 Consolidated View

3.11 Subject Profile

3.12 Tissue View

4 Study Data Integration and Search (SDIS)

4.1 SDIS Homepage

4.1.1 Downloading the User Guide and Viewing the Shortcut Keys

4.1.2 Setup Search Criteria

4.1.3 Viewing the Saved Search Criteria

4.2 Saved Search Criteria

4.2.1 Filtering Panel

4.2.2 Listing Panel

4.2.3 Details Panel

4.3 Setting up Search

4.3.1 Search Criteria Pane

4.3.2 Types of Search

4.3.3 Selecting the Search Scope

4.3.4 Edit and Save Search Criteria

4.3.5 Initiating Search

4.4 Search Results

4.4.1 Viewing Search Criteria

4.4.2 Results Cluster

5 Administration Settings

5.1 Enabling User Access

5.1.1 Accessing the Corporate Screen

5.1.2 Performing Search

5.1.3 Adding User to NIMS and Virtual Data Room (VDR)

5.1.4 Adding a New Study

5.1.5 Selecting a Different Data Profile

5.2 Archiving/Deleting a Study

5.2.1 Archiving a Study

5.2.2 Retrieving an Archived Study

5.2.3 Deleting a Study

5.2.4 Viewing the Deleted Study Log

5.3 Adding a Document to the VDR

5.4 Deleting a Document from the VDR

1 NIMS Overview

The Nonclinical Information Management System (NIMS) project 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. NIMS comprises of commercially available software tools provided by PointCross that consist of the following components - Nonclinical Study Data Repository (NSDR); Study Data Integration and Search System

(SDIS); ToxVision++, and XTEND.

2 Accessing NIMS NIMS is a web-based application which is integrated into the Orchestra platform. It is recommended that the Orchestra link be opened in the Internet Explorer (IE) browser. Point the Uniform Resource

Locator (URL) to: https://nims.dev.fda.gov in the Internet Explorer address bar. You may bookmark the address for future access.

2.1 Logging into NIMS

Figure 1: Disclaimer dialog box

1. Click OK to view the NIMS dashboard as shown in Figure 1: Disclaimer dialog box.

https://nims.dev.fda.gov/

2.2 Accessing the NIMS dashboard

Once you have logged into NIMS, you will be directed to the NIMS dashboard as shown in Figure 2:

NIMS Dashboard.

Figure 2: NIMS Dashboard

2.3 About the Dashboard

2.3.1 All Studies

The default page that you see after logging into NIMS is the NIMS dashboard or the All Studies page as shown in Figure 3: All Studies. All available studies in NIMS are displayed on this page.

Figure 3: All Studies

2.3.2 Accessing My Workspace

When you log into NIMS, you are taken to the All Studies page as shown in Figure 3: All Studies. To access My Workspace, you need to add a study or studies to My Workspace to view the My

Workspace page as shown in Figure 4: My Workspace. To know how to add a study to My

Workspace, see Adding and removing multiple studies from My Workspace.

Figure 4: My Workspace

2.4 Dashboard Controls

The NIMS dashboard allows you to sort, filter/search on the studies listed and also to rearrange the columns.

2.4.1 Sorting

You can perform sorting in either the ascending or the descending order for all the columns as shown in Figure 5: Sort Ascending. In this example, the Study ID column has been sorted in the ascending order.

Figure 5: Sort Ascending

To sort the Study ID column in the ascending order:

1. In the All Studies page, click the Study ID drop-down box.

2. Click Sort Ascending as shown in Figure 5: Sort Ascending.

The studies will be displayed in the ascending order as shown in Figure 6: Sorted Ascending. Similarly, you can sort the studies in the descending order.

Figure 6: Sorted Ascending

2.4.2 Filtering Studies

You can filter studies based on various attributes (study ID, study title, study type, etc) using Filters as shown in Figure 7: Filtering Studies. In this example, the studies have been filtered using the study identification (ID) criteria “PC2345G” which is a study identifier.

Figure 7: Filtering Studies

To filter studies using the Study ID criterion:

1. In the Study ID column drop-down box, pause on Filters and enter the Study ID “PC2345G.”

2. Select the Filters check box.

All the studies with ID “PC2345G” will be displayed as shown in Figure 8: Filtered Studies.

Figure 8: Filtered Studies

2.4.3 Rearranging columns

You can rearrange any of the desired columns using the “drag-and-drop” function as shown in Figure

9: Rearranging columns. In this example, the Study ID column has been moved to the right of Study

Title column.

Figure 9: Rearranging columns

To move the Study ID column:

1. Click Study ID column title and drag it to the right of Study Title.

2. Release the mouse when the Study ID column is to the right of the Study Title.

The rearranged columns are displayed in Figure 10: Rearranged Columns.

Figure 10: Rearranged Columns

2.4.4 Hiding columns

You can clear the check boxes to hide the columns you want as shown in Figure 11: Hiding columns.

In this example, the Study ID column has been hidden from view.

Figure 11: Hiding columns

To hide the Study ID column:

1. Click the Study ID column and pause over Columns.

2. Clear the Study ID check box.

The Study ID column gets hidden from view as shown in Figure 12: Hidden Column. Similarly, you can hide as many columns as you want from the list that is displayed in the drop-down check box.

Figure 12: Hidden Column

2.5 Study Level Controls

Every study comes with the study-level controls, which can be used to customize and display the results the way you want them.

2.5.1 Adding and removing multiple studies from My Workspace

You can add or remove one or more studies from My Workspace as shown in Figure 13: Adding a

Study to My Workspace.

Figure 13: Adding a Study to My Workspace

To add a study:

1. Select the check box against the study that you want to add.

2. Pause over the down arrow next to the study check box.

3. From the menu, click Add to My Workspace.

The study gets added to My Workspace as the first record, and the My Workspace page opens as shown in Figure 14: Added a Study to My Workspace.

Figure 14: Added a Study to My Workspace

You can remove a study from your workspace as shown in Figure 15: Removing a Study from My

Workspace.

Figure 15: Removing a Study from My Workspace

1. In the My Workspace page, select the check box against the study that you want to remove.

2. Pause over the drop-down arrow next to the study check box.

3. Click Remove from My Workspace from the menu to remove the study.

Figure 16: Removing Multiple Studies from My Workspace

1. In the My Workspace page, select the check box against the studies that you want to remove.

2. Click Remove from My Workspace as shown in Figure 16: Removing Multiple Studies from My

Workspace.

Multiple studies are removed from My Workspace.

2.5.2 Study Activities View

The study activity view provides a high-level view of the key activities and events on the timeline of the study in Gantt format. The list of activities conducted as a part of the study (both in-life and post-necropsy activities) is listed in the left pane of the study activities view page. You can drill down/expand any of the activities listed in the submenu to view the additional components/details defining the particular activity. Example, list of tests conducted as a part of the activity, treatment/dose groups as well as the subjects which experienced the listed event/activity as shown in Figure 17: Study Activities View.

Figure 17: Study Activities View

To look up study activities view:

1. Select a study and pause over the down arrow next to the study check box.

2. Click the Study Activities View as shown in Figure 17: Study Activities View.

The Study Activities View window opens up as shown in Figure 18: Study Activities View Window.

3. Click any of the activity type in the Activities bar to drill down further. In this example, Body Weights has been drilled down further to display the group Control for females. The drill-down path is: Body

Weights > Control >Female>All subjects within this particular group and sex as shown in Figure 20:

Control—Female.

Figure 18: Study Activities View Window

Figure 19: Study Activities—Control

Figure 20: Control—Female (Day)

Figure 21: Control--Female (Week)

You can view the study activity epoch week by clicking the “+” radio button as shown in Figure 21:

Control--Female (Week).

2.5.3 Edit Form (Editing/Adding study-level metadata)

You can edit or add the study level metadata by clicking Edit from the study level controls option as shown in Figure 22: Editing/Adding study-level metadata.

Figure 22: Editing/Adding study-level metadata

To edit/add study-level metadata:

1. Select a study.

2. Pause over the down arrow and click Edit.

The Adding/Editing study-level metadata window opens up as shown in Figure 23: Adding/Editing study-level metadata window. Make your edits in this window.

Figure 23: Adding/Editing study-level metadata window

Figure 24: Metadata Window Edited

Figure 25: Edited Study

The changes are updated in the study list as shown in Figure 25: Edited Study.

2.5.4 Opening a Study in ToxVision

You can open a study in ToxVision by clicking the Study ID hyperlink as shown in Figure 26: Opening

ToxVision.

Figure 26: Opening ToxVision

To open a study in ToxVision:

1. Click the study hyperlink as shown in Figure 26: Opening ToxVision.

The study opens in the ToxVision window as shown in Figure 27: ToxVision Window.

Figure 27: ToxVision Window

Figure 28: Opening ToxVision--Alternative Method

Alternatively, you can open a study in ToxVision:

1. Select the study and pause over the down arrow next to the study check box.

2. In the study level control, click ToxVision.

The study opens in the ToxVision window as shown in Figure 27: ToxVision Window.

2.5.5 Exporting to SEND format

You can export a study to SEND format by clicking Export in the submenu as shown in Figure 29:

Exporting a Study to SEND format.

Figure 29: Exporting a Study to SEND format

To export a study to SEND format:

1. Select the study check box and pause over the down arrow.

2. Pause over Export and click To SEND Format.

The File Download dialog box opens as shown in Figure 30: SEND Format Dialog Box.

3. Click Save to download the study, unzip, and view the files in SEND format.

Figure 30: SEND Format Dialog Box

2.6 Advanced Search

You can do an advanced search by clicking the Advanced Search button on the NIMS dashboard as shown in Figure 31: Advanced search.

Figure 31: Advanced search

To do an advanced search:

1. Click the Advanced Search button on the NIMS dashboard.

The study opens in the SDIS window as shown in Figure 32: Advanced Search Window.

Figure 32: Advanced Search Window

2.7 Using Support and I Wish

You can click the I Wish… button to suggest new features, functionalities, request changes, or improvements to the product; and the Support button to ask for assistance. When you click the buttons, an email is populated with the Support or the I Wish … IDs as the case may be.

Figure 33: Support and I Wish

3 Accessing ToxVision

You can select a study from NIMS dashboard to view the study data in ToxVision by clicking the study identifier link as shown in Figure 26: Opening ToxVision. To see a study opened in ToxVision window see Figure 27: ToxVision Window.

3.1 Navigation Panel

The navigation panel contains all the submitted domains for a particular study categorized/classified under the Study/Trial Definitions and Test Findings.

3.1.1 Study/Trial Definition

The navigation pane for Study/Trial Definition clusters all SEND domains by Trial Design Domains, Special Purpose Domains, and Interventions. On further expanding the options, the system provides the ability to view each of these SEND categories as submitted for review as shown in Figure 34:

Study/Trial definition. It has to be noted that the Trial Summary details are loaded by default.

Figure 34: Study/Trial definition

3.1.2 Test Findings

The test finding panel contains all the findings and event-related domains submitted for the study as per the SEND model.

Figure 35: Test findings

3.1.3 Grouping by Study Definition/FindingsS

Parameters under Study Definition/Findings are grouped/categorized as a complete Parameter listing (by laboratory test categories), biomarker panels (laboratory test parameters classified as renal, hepatic, cardiac biomarkers, etc.), and reviewer panels (cross-domain panels categorized organ wise). You can select the Parameter from the Group By drop-down as shown in Figure 36:

Parameter to view the parameters.

Figure 36: Parameter

Biomarker Panel

You can select the Biomarker Panel from the Group By drop down in the navigation panel as shown in Figure 37: Biomarker Panel to view the biomarker panels. You can drill down further to view the parameters under each panel. A set of pre-defined parameters indicating particular effect/markers are grouped together as biomarker panels.

Figure 37: Biomarker Panel

Reviewer Panel

You can select the Reviewer Panel from the Group By drop down as shown in Figure 38: Reviewer

Panel to view the reviewer panels for this particular study.

Figure 38: Reviewer Panel

3.1.4 Search Parameter

You can type the name of an existing parameter to be displayed in the left-hand pane as shown in

Figure 39: Search Parameter.

Figure 39: Search Parameter

3.1.5 Expand/Collapse

You can expand or collapse the parameter tree in the left-hand pane by clicking the Expand

All/Collapse All icons as shown in Figure 40: Expand/Collapse.

Figure 40: Expand/Collapse

3.1.6 Adding data to the data panel

Adding a New Table

1. Click the desired parameter to open the submenu.

2. Click Add as new table to add the selected parameter to a new table.

The selected parameter will be added as a new table in the data grid as shown in Figure 41: Add as new table.

Note: You can double click on a parameter to load data directly in the right-hand pane (grid).

Figure 41: Add as new table

Adding to a Table

1. Click the desired parameter to open the submenu.

2. Click Add to table to add the selected parameter to an existing table.

The selected parameter will be added to the already existing data grid by clicking the Add to table submenu as shown in Figure 42: Add to table.

Figure 42: Add to table

3.2 Data panel

The data panel enables data visualization for the selected parameters in three views, namely, group summary, individual results, and individual details.

3.2.1 Data Views

Group Summary

The Group Summary tab displays the summary level details of the selected parameter at the group level like mean, SD and % Difference within a study as shown in Figure 43: Group Summary.

Figure 43: Group Summary

To view the Group Summary tab:

1. In the ToxVision window select a Parameter in left-hand pane.

In this example, Activated Partial Thromboplastin Time parameter has been selected under Test

Findings- Laboratory Test Results.

2. Click Activated Partial Thromboplastin Time to display the table menu.

3. In the table menu click Add as new table.

The Group Summary gets populated in the new table and opens in the right-hand pane. Click

Individual Results and Individual Details tabs to view the respective details.

Individual Results

The Individual Results tab displays group wise subject level details of the selected parameter for a selected study as shown in Figure 44: Individual Results.

Figure 44: Individual Results

Individual Details

The Individual Details tab displays data for the selected parameter at the individual animal level for a selected study which includes comments, flags, and remarks made for every subject observation as shown in Figure 45: Individual Details. The order of the variables here is as per SENDIG. The structure of the data displayed under this tab is according to the domain structure in SEND (variable labels, order, and values as submitted by the sponsor).

Figure 45: Individual Details

3.2.2 Data Panel Controls—Viewing Options

Parameter as columns

You can view the data in Parameter as Columns and compare interrelationship among the parameters as shown in Figure 46: Parameter as columns.

Figure 46: Parameter as columns

Days as columns

You can view the data in Days as Columns for a given parameter as shown in Figure 47: Days as columns.

Figure 47: Days as columns

Incidence with groups as columns

You can view data in Incidence with groups as columns for MI and MA domains as shown in Figure

48: Incidence with group as columns.

Figure 48: Incidence with group as columns

Incidence with days as columns

You can view data in Incidence with days as columns for MI and MA as shown in Figure 49: Incidence with days as columns.

Figure 49: Incidence with days as columns

Sort and Filter

You can rearrange or filter the study data (group, sex, and parameter) using the Sort and Filter feature to select or deselect data columns for display as shown in Figure 50: Sort and filter.

Figure 50: Sort and filter

To filter a group by negative control:

1. Click the Group drop down and pause over Filters.

2. Select Negative Control and click Apply Filter.

The group gets filtered for negative control as shown in Figure 51: Filtered View. You may apply the filter for more items in the same column or across columns.

3. To clear filters for a single column, click Clear Filter.

4. To clear filters across multiple columns, click Clear All Filters.

Figure 51: Filtered View

Graph

Available graphical views are shown in Figure 52: Viewing Graph.

Figure 52: Viewing Graphs

Printing

The Print option allows you to print the study data as shown in Figure 53: Printing.

Figure 53: Printing

Figure 54: Print View

Exporting

You can export the selected group(s) to different export formats as shown in Figure 55: Exporting the Study Data.

Figure 55: Exporting the Study Data

Maximizing the Screen

You can maximize the screen by clicking the maximize icon as shown in Figure 56: Maximizing the

Screen.

Figure 56: Maximizing the Screen

Figure 57: Maximized Screen

3.3 Clubbing Groups

You can select two or more groups/sets from Trial Sets domain and combine them into a single virtual group for analysis as shown in Figure 58: Clubbed Baseline Group.

Figure 58: Clubbed Baseline Group

Figure 59: Baseline Group

To club groups and to set up a baseline group:

1. Click Trial Sets from Trial Design Domains.

2. Select two or more groups and click Club Groups as shown in Figure 58: Clubbed Baseline Group.

The club group dialog box opens.

3. Type in the Group Name, Description, and select Set as baseline in the dialog box and click Save.

The baseline clubbed group is created.

4. Click Reset to undo changes.

3.4 Setting a Baseline Group

You can set the baseline for any available group to perform intergroup comparison as shown in

Figure 60: Setting a Baseline Group.

Figure 60: Setting a Baseline Group

3.5 Exclude Treatment Groups

The treatment groups for a given study can be excluded from analysis in ToxVision.

Figure 61: Exclude treatment group from analysis

To exclude treatment group

1. Click Trial Sets from Trial Design Domains

2. Click the check box against the group to be excluded

3. Go to Menu and click Exclude

4. Click Reset to undo changes

Figure 62: Excluded Treatment Groups from Analysis

The excluded treatment groups are not available for analysis.

3.6 Recalculation of Group Summary (Include/Exclude Subjects)

The group summary (Means and SD) can be recalculated by excluding a finding for a subject within a treatment group.

Figure 63: Include/Exclude subjects

To exclude a value-

1. Click Individual Results or Individual Details.

2. Click the value to strike off and exclude from group summary calculation.

3. Click Recalculate button.

Figure 64: Recalculated Group Summary

The recalculated group summary values will appear as a dialog box. The changed values will be highlighted in Blue. On pause-over the old value will appear.

3.7 Data Export

3.7.1 Checklist

Findings Group Summary Individual Results Individual Details

Body Weight Gain Body Weights

Clinical Observations

Death Diagnosis

Events Electrocardiogram Test Results

Laboratory Test Results Macroscopic Findings

Microscopic Findings Organ Measurements Pharmacokinetics Concentrations

Pharmacokinetics Parameters

Vital Signs

The checklist explains the data export for the given findings:

Example: Data can be exported for body weight gain under group summary, individual results, and individual details; however, for death diagnosis data cannot be exported under group summary and individual results but only under individual details.

3.7.2 Exporting a Study Summary to the Reviewer Template

You can export the Trial Summary details for a particular study to the reviewer template as shown in

Figure 65: Exporting a Study to the Reviewer Template.

Figure 65: Exporting a Study to the Reviewer Template

To export a study to the reviewer template:

1. In the ToxVision window click the Menu drop down and pause over Export to.

2. In the submenu, click Reviewer Template.

The study gets populated in the reviewer template as shown in Figure 66: A Study in the Reviewer

Template.

Figure 66: A Study in the Reviewer Template

3.7.3 Exporting to MS Word

You can export the qualitative data to an MS Word template under the macroscopic and microscopic findings as shown in Figure 67: Exporting to MS Word.

Figure 67: Exporting to MS Word

3.7.4 Exporting as Excel as View

You can export the selected study data to Excel as View as shown in Figure 68: Exporting to Excel as

View.

Figure 68: Exporting to Excel as View

The option allows you to export the data in the selected tables to an excel in the same format as displayed in the ToxVision view.

3.7.5 Exporting to MS Excel

You can export the selected study data to MS Excel in a pre-defined structured template as shown in

Figure 69: Exporting to MS Excel.

Figure 69: Exporting to MS Excel

3.7.6 Exporting to CSV

You can export the selected study data to the comma separated values (CSV) format as shown in

Figure 70: Exporting to CSV.

Figure 70: Exporting to CSV

3.7.7 Exporting to XPT

You can export the selected study data to external page table (XPT) as shown in Figure 71: Exporting to XPT.

Figure 71: Exporting to XPT

3.7.8 Exporting to Prism

You can export the selected study data to prism file format (.pzfx) as shown in Figure 72: Exporting to Prism.

Figure 72: Exporting to Prism

3.8 Graphs

3.8.1 Checklist

You can view the checklist for graphs in table as shown below.

Test Findings Group Summary Individual Results Individual Details

Body Weight Gain

Body Weights Clinical Observations Death Diagnosis

Events Electrocardiogram Test Results

Laboratory Test Results

Macroscopic Findings

Microscopic Findings Organ Measurements

Concentrations

Parameters

Vital Signs

The checklist explains that you can view graphs for the given findings:

Example: For body weight gain, you can view the graphs under group summary and individual results but not under individual details. For clinical observations, you cannot view any graph under group summary, individual results, or individual details.

3.8.2 Viewing the X-Bar Graph

You can view the X-Bar graph under the Menu as shown in Figure 73: Viewing the X-Bar Graph.

Figure 73: Viewing the X-Bar Graph

To view the results in a graphical presentation for a given parameter and subject/group:

1. Select at least one parameter and one subject/group as shown in Figure 73: Viewing the X-Bar Graph.

2. Click the Menu drop-down and pause over Graph.

3. Click the desired graph from the graph list: X-bar graph, whisker-plot graph, line graph, and bar graph.

Figure 74: X-Bar Graph

3.8.3 Viewing the Whisker-Plot Graph

You can view the whisker-plot graph for the selected study under the drop-down menu as shown in

Figure 75: Viewing the Whisker-Plot Graph.

Figure 75: Viewing the Whisker-Plot Graph

Figure 76: Whisker-Plot Graph

3.8.4 Viewing the Line Graph

You can view the line graph for the selected study as shown in Figure 77: Viewing the Line Graph.

Figure 77: Viewing the Line Graph

Figure 78: Line Graph

3.8.5 Viewing the Bar Graph

You can view the bar graph for the selected study as shown in Figure 79: Viewing the Bar Graph.

Figure 79: Viewing the Bar Graph

Figure 80: Bar Graph

3.8.6 Generating Correlation Heat Maps

You can generate heat maps for a parameter by clicking the icon and selecting Correlation Analysis-

Heat Map as shown in Figure 81: Generating Correlation Heat Maps.

Figure 81: Generating Correlation Heat Maps

To generate a correlation heat map:

1. Click the down arrow for Laboratory test results to open the menu.

2. Click the Correlation Analysis-Heat Map.

The Setup Correlation Analysis—Heat Map dialog box opens as shown in Figure 82: Setup Correlation

Analysis dialog box.

3. Fill out the required fields and click OK.

The correlation heat map is generated as shown in Figure 83: Correlation analysis heat map.

Clicking the Correlation Analysis Heat Map will make the pop-up appear where you can select the criteria for generating the Heat Map as shown in Figure 82: Setup Correlation Analysis dialog box.

Figure 82: Setup Correlation Analysis dialog box

Correlation Analysis Heat Map has been shown in Figure 83: Correlation analysis heat map.

Figure 83: Correlation analysis heat map

3.9 Generating the z-Transformation (Box-Plots)

You can generate the z-Transformation (Box-Plots) for a parameter by clicking the down arrow and selecting the z-Transformation (Box-Plot) as shown in Figure 84: Generating the z-Transformation

(Box-Plot).

Figure 84: Generating the z-Transformation (Box-Plot)

To generate the z-Transformation (Box-Plot):

1. Click the down arrow for Laboratory test results to open the menu.

2. Click the z-Transformation (Box-Plot).

The z-Transformation (Box-Plot) panel opens in a new window as shown in.Figure 85: z-

Transformation (Box-Plot) Panel.

3. Click the desired panels in the left-hand pane. You may toggle between the male/female tabs in the right-hand pane.

The z-Transformation (Box-Plot) is generated as shown in Figure 86: z-Transformation (Box-Plot).

Figure 85: z-Transformation (Box-Plot) Panel z-Transformation (Box-Plot) has been shown in Figure 86: z-Transformation (Box-Plot).

Figure 86: z-Transformation (Box-Plot)

3.9.1 Viewing the Groups’ Legend

You can view the Groups’ legend by clicking on Groups as show in Figure 87: Groups Legend.

Figure 87: Groups Legend

3.9.2 Rearranging the Parameter Display

You can rearrange the parameter display by clicking the up arrow beside the parameter.

Figure 88: Rearranging Parameter Display

Example, click the up arrow beside the parameter Cholesterol as shown in Figure 88: Rearranging

Parameter Display.

Figure 89: Rearranged Parameter Display

The Cholesterol parameter moves to the top of the list as shown in Figure 89: Rearranged Parameter

Display.

3.9.3 Deleting a Parameter

You can delete a parameter from the display by clicking the delete button beside the parameter.

Figure 90: Deleting a Parameter

Example, the Cholesterol parameter has been deleted by clicking the delete button as shown in

Figure 90: Deleting a Parameter and Figure 91: Deleted Parameter.

Figure 91: Deleted Parameter

3.9.4 Viewing Z-Scores Boxplots

You can view the Z-scores boxplots that show actual data scales in standard units, and can make a male/female data comparison by clicking the respective tabs.

Note: The Z-Score and standard units by default are displayed for the male.

Figure 92: Opening a Panel

Example, click the Triglycerides panel for Day 14 to view the Z scores.

Figure 93: Boxplots for z-scores for males change titles accordingly for the rest

Figure 94: Standard Units

Click the Standard Units tab to view the standard units as shown in Figure 94: Standard Units.

Figure 95: Male-Female Comparison

Figure 96: Male-Female Standard Units

You can view data for males/females in a single display for the standard units and z-scores by clicking the arrow beside Female as shown in Figure 95: Male-Female Comparison.

3.9.5 Creating MyList

You can create a customized list by adding the desired list of parameters to MyList.

Figure 97: Creating MyLIst

To create MyList:

1. In the left-hand pane, click the MyList button to create the customized list.

The New Panel window opens.

2. Click the New Panel button and type your MyList name in the text box as shown in Figure 99: My

Panel Text Box and press Enter.

3. Select the desired profile and the desired parameters and click Done.

The selected parameters are added to MyList as shown in Figure 102: Added Parameters.

Figure 98: New Panel Window

Figure 99: My Panel Text Box

Figure 100: Adding Parameters to MyList

Figure 101: Adding Parameters--Done button

Figure 102: Added Parameters

3.9.6 Deleting MyList

You can delete the customized list that you have created by clicking the Edit button followed by the delete button as shown in Figure 103: Deleting MyList-Edit Button and Figure 104: Deleting MyList-

Delete Button. Click OK when prompted to delete the MyList. Differentiate between editing the parameter list that exists under the newly created panel vs. delete the whole panel.

Figure 103: Deleting MyList-Edit Button

Figure 104: Deleting MyList-Delete Button

3.10 Consolidated View

You can click the icon on the left-hand pane to view the consolidated view as shown in Figure 105:

Consolidated View.

Figure 105: Consolidated View

To view the consolidated view:

1. Click the icon in the left-hand pane as shown in Figure 105: Consolidated View.

The consolidated view is displayed in the right-hand pane.

3.11 Subject Profile

The Individual Results and Individual Details tab shows individual subject-level data. You can view the Subject Profile for a selected subject by clicking the unique subject identifier as shown in Figure

106: Subject Profile.

Figure 106: Subject Profile

To view the subject profile:

1. Click the Unique Subject Identifier in the Individual Results or the Individual Details tab.

The subject profile opens in a new window with data for Demographics for the particular subject being displayed in the right-hand pane as shown in Figure 107: Subject Profile Window. Click on any parameter from the left hand pane to load data into additional tables.

Figure 107: Subject Profile Window

You can add additional parameters to the data grid from the left-hand pane by clicking on them individually.

3.12 Tissue View

The navigation panel allows you to view all the group summary data of the study for a selected tissue in a single view by accessing the Tissue View as shown in Figure 108: Navigating to Tissue

View.

Figure 108: Navigating to Tissue View

Figure 109: Tissue View

To view the tissue view:

1. Click Tissue View from the menu as shown in Figure 108: Navigating to Tissue View.

The group summary data for the selected tissue is displayed in a new window.

4 Study Data Integration and Search (SDIS)

4.1 SDIS Homepage

You can view the SDIS home screen as shown in Figure 110: SDIS Homepage.

To navigate to the SDIS homepage:

NIMS>Click Advanced Search>SDIS homepage. The default tab is the Setup Search Criteria. Click

Saved Search Criteria to view the saved search criteria details as shown in Figure 111: Saved Search

Criteria.

Figure 110: SDIS Homepage

Figure 111: Saved Search Criteria

4.1.1 Downloading the User Guide and Viewing the Shortcut Keys You can download/access the SDIS user guide by clicking the Help icon as shown in Figure 112:

Downloading the User Guide.

Figure 112: Downloading the User Guide

To download the user guide:

1. Click the Help icon in the SDIS homepage to view the menu.

2. Click User Guide to download the user guide.

3. Click Shortcut Keys to view the list of shortcut keys as shown in Figure 113: Viewing the Shortcut

Keys.

Figure 113: Viewing the Shortcut Keys

4.1.2 Setup Search Criteria

You can perform two types of search, namely, structured search and unstructured search. You can create a structured search using parameters from the search parameter panel and unstructured search using the free text search option under the Setup Search Criteria.

Figure 114: Setup Search Criteria

4.1.3 Viewing the Saved Search Criteria

You can view the saved search criteria on the SDIS homepage by clicking Saved Search Criteria as shown in Figure 115: Viewing the Saved Search Criteria.

Figure 115: Viewing the Saved Search Criteria

Parameters for structured search.

Textbox for unstructured search.

4.2 Saved Search Criteria

4.2.1 Filtering Panel

In the left pane, you can view all the saved search criteria which have been categorized as personal, published, and history as shown in Figure 116: Filtering Panel.

Figure 116: Filtering Panel

Personal Search

All your personal saved search criteria are available under this section. Following are the options available to you:

o Edit: You can edit the search criteria saved in the personal category.

o Load: You can load the selected personal criteria in the Setup Search Criteria.

o Publish: You can publish the personal search criteria to all the SDIS users.

Figure 117: Saved Search Criteria Dialog Box

To create a personal search:

1. Select the study details in the Setup Search Criteria and click Save Criteria.

The Save Search Criteria dialog box opens.

2. Fill out the required fields and click Save.

The personal search gets saved as shown in Figure 118: Personal Search Details.

Figure 118: Personal Search Details

Published

All the published search criteria are saved under Published. The following option is available to you under published:

Load: Displays the selected Published criteria in Setup Search Criteria.

History

This category saves the entire search that you have performed. Following are the options available to you:

o Edit: You can edit the title and description in the saved personal criteria along with the option to save it in personal or published category.

o Load: Displays the selected Published criteria in Setup Search Criteria o Delete: You can delete a particular search criterion.

4.2.2 Listing Panel

You can view the summary of the entire search under the saved search tab. It displays the summary information about the saved search performed by the different users.

4.2.3 Details Panel

Allows you to view details of the selected search such as description, search criteria, scope, and the user who has performed that search. You can also edit, delete, or load saved searches and publish a saved search to all the SDIS users.

4.3 Setting up Search

4.3.1 Search Criteria Pane

You can perform two types of search namely, structured search and unstructured search. You can create a structured search using parameters from the search parameter panel in the left-hand side and unstructured search by typing in the text search box in the right-hand side as shown in Figure

119: Search Criteria Pane.

Figure 119: Search Criteria Pane

Parameters for structured search.

Textbox for unstructured search.

4.3.2 Types of Search

There are two types of search present in SDIS, namely, structured and unstructured search.

Structured Search

You can narrow down the search criteria and perform specific search using the compound, study, groups, subjects, and test findings.

o Selecting Search on Attribute Data

In the structured search by default, the AND condition is applied between multiple search criteria. This data type includes the attribute types --study, test materials, treatment groups and subjects as shown in Figure 120: Selecting Search on Attribute Data.

Figure 120: Selecting Search on Attribute Data o Selecting Search on Qualitative Data

Qualitative data type parameters include study observations recorded from the test findings such as clinical observations, palpable masses, organ microscopy, and organ gross observations as shown in

Figure 121: Selecting Search on Qualitative Data.

Figure 121: Selecting Search on Qualitative Data o Selecting Search on Quantitative Data

Quantitative data type parameters include numerical measurements from the test findings such as body weights, food and water consumption, clinical pathology data, organ weights, and PK/TK parameters.

Figure 122: Selecting Search on Quantitative Data

Unstructured Search

You can perform search using the free text search option. You can enter values related to study title, study ID, compound ID, compound name, species, strain, parameter name, findings to search, and it will display the matched values for the specified parameters as shown in Figure

124: Show Search Results Window.

Figure 123: Unstructured Search

Figure 124: Show Search Results Window

4.3.3 Selecting the Search Scope

You can select the search scope from the Scope drop down as shown in Figure 125: Selecting the

Search Scope.

Figure 125: Selecting the Search Scope

4.3.4 Edit and Save Search Criteria

Use the Edit Criteria option to revise the existing search criteria. You can choose AND, OR, and NOT operators by clicking Edit Criteria as shown in Figure 126: Edit and Save Search Criteria.

Figure 126: Edit and Save Search Criteria

You can use the Save Search Criteria option to save search criteria and share the search criteria by selecting the Publish option while saving the Save Search Criteria as shown in Figure 127: Save

Search Criteria.

Figure 127: Save Search Criteria

4.3.5 Initiating Search

You can initiate search by one of the following ways:

You can build the criteria from the left panel as shown in Figure 128: Initiating Search and click the

Search button to initiate search.

Figure 128: Initiating Search

Use an existing saved search by clicking the Load button as shown in Figure 129: Existing saved search.

Figure 129: Existing saved search

4.4 Search Results

4.4.1 Viewing Search Criteria

The results view has three sections, namely, search results panel, search criteria panel, and the detailed view panel. You can view the summary of the search results against the title No. of Results in the right-hand pane as shown in Figure 130: Viewing Search Criteria.

Figure 130: Viewing Search Criteria

4.4.2 Results Cluster

The Results Cluster panel displays the count of all the studies that meet the search criteria as shown in Figure 131: Results Cluster. The counts of all the studies are clustered around predefined attributes.

Figure 131: Results Cluster

Search results panel

Search criteria panel

Detailed view panel

5 Administration Settings

5.1 Enabling User Access

5.1.1 Accessing the Corporate Screen

Figure 132: Enabling User Access

To enable the user access:

1. In the NIMS dashboard, click Switch To.

The Switch To menu opens.

2. In the Switch To menu, click Corporate.

The corporate screen opens as shown in Figure 133: Corporate Screen.

Figure 133: Corporate Screen

3. In the People tab click the drop-down menu and select Contacts.

5.1.2 Performing Search

Figure 134: Performing Search

1. Enter the user name in the Search text box and click Go.

2. The user is displayed under contacts as shown in Figure 135: User Displayed.

Figure 135: User Displayed

5.1.3 Adding User to NIMS and Virtual Data Room (VDR)

Figure 136: Adding User to NIMS

1. Right-click the user name and click Add as Orchestra User in the menu as shown in Figure 136: Adding

User to NIMS.

The Add User Details dialog box appears.

2. Type the user details, select the company from the Company drop down and click Save.

The user gets added to Orchestra and VDR as shown in Figure 138: Adding User to Orchestra and VDR.

Figure 137: Add User Details

Figure 138: Adding User to Orchestra and VDR

5.1.4 Adding a New Study

You can add a new study by clicking the Add New button as shown in Figure 139: Adding a New

Study.

Figure 139: Adding a New Study

Click Add New as shown in Figure 139: Adding a New Study to add a new study.

Entering Study Metadata

You can enter the study metadata as shown in Figure 140: Entering Study Metadata.

Figure 140: Entering Study Metadata

Selecting Data Profile

You can select the data profile under Study Source tab and click Save and Close as shown in Figure

141: Select Data Profile.

Figure 141: Select Data Profile

Import Study Data Manually

You can import the study data manually by clicking Submission Status as shown in Figure 142:

Import Study Data Manually.

Figure 142: Import Study Data Manually

To import the study data manually:

1. Click Submission Status in the selected study.

2. In the Study Report Summary page click Import.

3. In the Import Study Data, click Browse.

The Choose File to Upload dialog box opens.

4. Select the XPT file from your local drive to import the study manually.

Figure 143: Study Report Summary

Figure 144: Import Study Data

5.1.5 Selecting a Different Data Profile

Figure 145: Reimporting a Study

In case the study import for a particular data profile fails, you can choose to select a different data profile from the drop-down menu and click Save Changes to reimport the study.

5.2 Archiving/Deleting a Study

You can archive/delete a study by selecting the desired study from the NIMS dashboard and clicking the I Want To drop-down button as shown in Figure 146: Archiving/Deleting a Study.

Figure 146: Archiving/Deleting a Study

5.2.1 Archiving a Study

Select the desired study and click Archive in the I Want To drop-down menu. Click OK in the dialog box. The study gets filed away and is removed from the dashboard as shown in Figure 147: Archiving a Study.

Figure 147: Archiving a Study

5.2.2 Retrieving an Archived Study

Figure 148: Retrieving an Archived Study

To retrieve an archived study:

1. In the I Want To drop-down menu click Get Archived.

The archived study is displayed.

2. Select the archived study and click Activate in the I Want To drop-down menu.

The study activate dialog box opens.

3. In the study activate dialog box, click OK.

The study gets retrieved into the system.

4. To view the retrieved study, click Get Active in the I Want To drop-down menu.

5.2.3 Deleting a Study

Select the desired study and click Delete in the I Want To drop-down menu. Click OK in the delete study dialog box as shown in Figure 149: Deleting a Study. The study gets deleted from the system.

Note: A deleted study cannot be retrieved but only a log of the deleted study can be viewed.

Figure 149: Deleting a Study

5.2.4 Viewing the Deleted Study Log

You can view the deleted study log by clicking Get Deleted in the I Want To drop-down menu. The log is displayed as shown in Figure 150: Viewing the Deleted Study Log.

Figure 150: Viewing the Deleted Study Log

5.3 Adding a Document to the VDR

In the NIMS dashboard click Switch To to view the drop-down menu. In the drop-down menu, click

VDR as shown in Figure 151: Adding Documents to the VDR.

Figure 151: Adding Documents to the VDR

Figure 152: Uploading a Document to the VDR

Right-click the desired folder where you want to upload the document and click Upload. The Add

Documents dialog box appears as shown in Figure 153: Add Documents. You can either drag and drop your files in the dialog box or click the Select Files to Upload button to upload the files and click

Save.

Figure 153: Add Documents

5.4 Deleting a Document from the VDR

To delete an uploaded document to the VDR:

1. Click the down arrow beside the document to view the drop-down menu as shown in Figure 154:

Deleting a Document from the VDR.

2. In the drop-down menu, click Delete document.

The Delete document dialog box appears as shown in Figure 155: Delete Document Dialog Box.

3. Cite a reason for the document deletion and click Yes.

The document gets deleted from the VDR.

Figure 154: Deleting a Document from the VDR

Figure 155: Delete Document Dialog Box

Table of Figures

Figure 1: Disclaimer dialog box

Figure 2: NIMS Dashboard

Figure 3: All Studies

Figure 4: My Workspace

Figure 5: Sort Ascending

Figure 6: Sorted Ascending

Figure 7: Filtering Studies

Figure 8: Filtered Studies

Figure 9: Rearranging columns

Figure 10: Rearranged Columns

Figure 11: Hiding columns

Figure 12: Hidden Column

Figure 13: Adding a Study to My Workspace

Figure 14: Added a Study to My Workspace

Figure 15: Removing a Study from My Workspace

Figure 16: Removing Multiple Studies from My Workspace

Figure 17: Study Activities View

Figure 18: Study Activities View Window

Figure 19: Study Activities—Control

Figure 20: Control—Female (Day)

Figure 21: Control--Female (Week)

Figure 22: Editing/Adding study-level metadata

Figure 23: Adding/Editing study-level metadata window

Figure 24: Metadata Window Edited

Figure 25: Edited Study

Figure 26: Opening ToxVision

Figure 27: ToxVision Window

Figure 28: Opening ToxVision--Alternative Method

Figure 29: Exporting a Study to SEND format

Figure 30: SEND Format Dialog Box

Figure 31: Advanced search

Figure 32: Advanced Search Window

Figure 33: Support and I Wish

Figure 34: Study/Trial definition

Figure 35: Test findings

Figure 36: Parameter

Figure 37: Biomarker Panel

Figure 38: Reviewer Panel

Figure 39: Search Parameter

Figure 40: Expand/Collapse

Figure 41: Add as new table

Figure 42: Add to table

Figure 43: Group Summary

Figure 44: Individual Results

Figure 45: Individual Details

Figure 46: Parameter as columns

Figure 47: Days as columns

Figure 48: Incidence with group as columns

Figure 49: Incidence with days as columns

Figure 50: Sort and filter

Figure 51: Filtered View

Figure 52: Viewing Graphs

Figure 53: Printing

Figure 54: Print View

Figure 55: Exporting the Study Data

Figure 56: Maximizing the Screen

Figure 57: Maximized Screen

Figure 58: Clubbed Baseline Group

Figure 59: Baseline Group

Figure 60: Setting a Baseline Group

Figure 61: Exclude treatment group from analysis

Figure 62: Excluded Treatment Groups from Analysis

Figure 63: Include/Exclude subjects

Figure 64: Recalculated Group Summary

Figure 65: Exporting a Study to the Reviewer Template

Figure 66: A Study in the Reviewer Template

Figure 67: Exporting to MS Word

Figure 68: Exporting to Excel as View

Figure 69: Exporting to MS Excel

Figure 70: Exporting to CSV

Figure 71: Exporting to XPT

Figure 72: Exporting to Prism

Figure 73: Viewing the X-Bar Graph

Figure 74: X-Bar Graph

Figure 75: Viewing the Whisker-Plot Graph

Figure 76: Whisker-Plot Graph

Figure 77: Viewing the Line Graph

Figure 78: Line Graph

Figure 79: Viewing the Bar Graph

Figure 80: Bar Graph

Figure 81: Generating Correlation Heat Maps

Figure 82: Setup Correlation Analysis dialog box

Figure 83: Correlation analysis heat map

Figure 84: Generating the z-Transformation (Box-Plot)

Figure 85: z-Transformation (Box-Plot) Panel

Figure 86: z-Transformation (Box-Plot)

Figure 87: Groups Legend

Figure 88: Rearranging Parameter Display

Figure 89: Rearranged Parameter Display

Figure 90: Deleting a Parameter

Figure 91: Deleted Parameter

Figure 92: Opening a Panel

Figure 93: Boxplots for z-scores for males change titles accordingly for the rest

Figure 94: Standard Units

Figure 95: Male-Female Comparison

Figure 96: Male-Female Standard Units

Figure 97: Creating MyLIst

Figure 98: New Panel Window

Figure 99: My Panel Text Box

Figure 100: Adding Parameters to MyList

Figure 101: Adding Parameters--Done button

Figure 102: Added Parameters

Figure 103: Deleting MyList-Edit Button

Figure 104: Deleting MyList-Delete Button

Figure 105: Consolidated View

Figure 106: Subject Profile

Figure 107: Subject Profile Window

Figure 108: Navigating to Tissue View

Figure 109: Tissue View

Figure 110: SDIS Homepage

Figure 111: Saved Search Criteria

Figure 112: Downloading the User Guide

Figure 113: Viewing the Shortcut Keys

Figure 114: Setup Search Criteria

Figure 115: Viewing the Saved Search Criteria

Figure 116: Filtering Panel

Figure 117: Saved Search Criteria Dialog Box

Figure 118: Personal Search Details

Figure 119: Search Criteria Pane

Figure 120: Selecting Search on Attribute Data

Figure 121: Selecting Search on Qualitative Data

Figure 122: Selecting Search on Quantitative Data

Figure 123: Unstructured Search

Figure 124: Show Search Results Window

Figure 125: Selecting the Search Scope

Figure 126: Edit and Save Search Criteria

Figure 127: Save Search Criteria

Figure 128: Initiating Search

Figure 129: Existing saved search

Figure 130: Viewing Search Criteria

Figure 131: Results Cluster

Figure 132: Enabling User Access

Figure 133: Corporate Screen

Figure 134: Performing Search

Figure 135: User Displayed

Figure 136: Adding User to NIMS

Figure 137: Add User Details

Figure 138: Adding User to Orchestra and VDR

Figure 139: Adding a New Study

Figure 140: Entering Study Metadata

Figure 141: Select Data Profile

Figure 142: Import Study Data Manually

Figure 143: Study Report Summary

Figure 144: Import Study Data

Figure 145: Reimporting a Study

Figure 146: Archiving/Deleting a Study

Figure 147: Archiving a Study

Figure 148: Retrieving an Archived Study

Figure 149: Deleting a Study

Figure 150: Viewing the Deleted Study Log

Figure 151: Adding Documents to the VDR

Figure 152: Uploading a Document to the VDR

Figure 153: Add Documents

Figure 154: Deleting a Document from the VDR

Figure 155: Delete Document Dialog Box