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SAP Connected Health PlatformDocument Version: 1.0 – 2016-12-13

SAP Connected Health Platform Application Help

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Content

1 Getting Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31.1 What is SAP Connected Health Platform?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31.2 About This Document. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41.3 Applications Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41.4 Setting Your Language. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51.5 Personalization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51.6 Adjusting the Color Contrast. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

2 My Profile. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

3 Cohorts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83.1 Patient List. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93.2 Cohort Details. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103.3 Notes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .103.4 Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

4 Search. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

5 Patient Summary. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155.1 Timeline. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Chart Lanes in the Timeline. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .185.2 Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205.3 Related Documents. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205.4 Variant Browser. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Circular Plot View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22Chromosome View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24Categorizing Variants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

5.5 Configuration Selection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .28

6 Glossary. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .30

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1 Getting Started

Related Information

What is SAP Connected Health Platform? [page 3]About This Document [page 4]Applications Overview [page 4]Setting Your Language [page 5]Personalization [page 5]Adjusting the Color Contrast [page 6]

1.1 What is SAP Connected Health Platform?

SAP Connected Health platform, which is powered by SAP HANA, serves as a platform for precision-medicine applications. SAP Connected Health enables the processing and real-time analysis of big medical data from various sources in a single system.

The platform represents a foundation for diverse health-associated applications by providing:

● A flexible and extensible clinical data warehouse model● A common database schema● Functional libraries and algorithms● Industry-aware data integration management● Real-time analytics on large-scale structured and unstructured data (text)● A secure platform for solutions targeting genomics, patients cohort building, patient trial matching and

further care collaboration

In addition, the platform provides user interfaces for monitoring and administering various aspects of the platform, such as data integration and the clinical data warehouse. All user interfaces are included in the SAP Connected Health UI, which is built as an SAP HANA Fiori launchpad and serves as the central entry point for all applications running on the platform.

Regulatory Disclaimer

This software gives instant access to information from multiple sources and allows visualizing and analyzing complex data sets in real-time. The software is not intended to be used for diagnostic or

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therapeutic purposes. In particular and without limitation, the software is not intended to be used for (i) final selection of patients for a clinical study, or (ii) the detection, prevention, surveillance, treatment or relief of diseases, (iii) the detection, surveillance, treatment, relief or compensation of injuries and handicaps, or (iv) the examination, substitution or change of the anatomical structure or a physiological process of a human being.

1.2 About This Document

This guide describes how to use the various applications provided with SAP Connected Health.

1.3 Applications Overview

SAP Connected Health serves not only as a platform for health applications, but it also delivers several standard applications that provide features you can use in conjunction with the health applications.

In general, these standard applications can either appear as stand-alone tiles on the SAP Fiori launchpad or they can be integrated into health applications.

RememberYou can access these application from the SAP Fiori launchpad for SAP Connected Health, which is availabe at: http://<WebServerHost>:80<SAPHANAinstance>/sap/hana/uis/clients/ushell-app/shells/fiori/FioriLaunchpad.html?siteId=sap.hc.hph.flp|hph#.

Related Information

My Profile [page 7]Cohorts [page 8]Search [page 13]Patient Summary [page 15]

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1.4 Setting Your Language

Context

Before using any applications, we recommend setting your display language. This language setting is applied to all standard applications included with SAP Connected Health, as well as any additional applications running on top of the platform.

SAP Connected Health supports the following languages:

● English (default)● German● French

Procedure

1. Go to the SAP Fiori launchpad for SAP Connected Health.

The SAP Fiori launchpad is available at the following URL: http://<WebServerHost>:80<SAPHANAinstance>/sap/hana/uis/clients/ushell-app/shells/fiori/FioriLaunchpad.html?siteId=sap.hc.hph.flp|hph#

2. Open the My Profile application.

3. Follow the link under User Information User Preferences .

4. Under Preferences Locale , select your language.

NoteThe drop-down list contains all languages available for SAP HANA. However, not all languages are supported by SAP Connected Health.

5. Choose Save.6. Return to the homepage and refresh your browser.

1.5 Personalization

Within certain applications, you can change how information is presented to you. Generally, this means you can sort, filter, and hide specific types of information.

When a list of items, such as patients or documents, appears in a table, the attributes of that type of item are shown as columns. You can specify how you want to sort and filter these attributes, as well as which attributes are shown and which are hidden.

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Table 1:

Icon Description

Specify whether attributes are sorted ascending or de­scending.

This setting is specific to your current session; it isn't saved for future use.

Specify filters for attributes to include or exclude specific values.

This setting is specific to your current session; it isn't saved for future use.

Specify which attributes appear as columns in the table.

The system saves this setting and applies it to your future sessions.

1.6 Adjusting the Color Contrast

If you are visually impaired or have difficulties with the contrast between user interface elements, you can adjust the color contrast by applying the SAP High Contrast Black theme.

Context

The SAP High Contrast Black theme is intended for visually impaired users and provides the following:

● The background of the user interface is primarily black.● The foreground elements of user interfaces are primarily white.

The SAP High Contrast Black theme can be used both by users who are extremely light-sensitive and by users with severe visual impairments as it can help them to see text and UI elements better and faster.

Procedure

1. Go to the SAP Fiori launchpad for SAP Connected Health.

The SAP Fiori launchpad is available at the following URL: http://<WebServerHost>:80<SAPHANAinstance>/sap/hana/uis/clients/ushell-app/shells/fiori/FioriLaunchpad.html?siteId=sap.hc.hph.flp|hph#

2. Open the user options menu at the top-right of your screen and choose User Preferences.3. Under Theme, select SAP High Contrast Black and save your changes.

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2 My Profile

The My Profile application gives you an overview of your user, including which organizational units you belong to and what roles you have.

You can edit the attributes of your user account, for example, your first or last name. However, you can't change your assignments to organizational units or business roles.

NoteFor more information about the user attributes shown or your organizational and role assignments, contact your system administrator.

You can also change the standard SAP HANA user settings by choosing User Preferences. With these preferences, you can do the following:

● Change your password● Specify how the time and date are shown● Change the display language for your apps

SAP Connected Health supports English, German, and French as display languages.

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3 Cohorts

You use the Cohorts application to save and review groups of related patients and share these with colleagues.

In your clinical research or analysis, if you identify a group of patients that you want to save for further study or to share with colleagues, you can add these patients to an existing cohort or create a new cohort. After you add patients to a cohort, you can review the patients against the inclusion and exclusion criteria for the cohort and determine whether the patients should remain in the cohort. You can also save the cohort as a tile in the SAP Fiori launchpad.

You add patients to a cohort from other applications running on SAP Connected Health, such as Search.

RememberRegardless of the cohort or your contributor role, the patient data you see is always restricted based on your organization's security policy.

From the Cohorts Overview, you can view a list of all available cohorts and create or delete cohorts. You can also share selected cohorts with colleagues by choosing Add Contributors.

Cohort Overview Settings

Cohorts appear in the overview together with their relevant attributes, such as when they were created or how many patients are in the cohort. You can specify how you want to sort and filter these attributes, as well as which attributes appear as columns in the table.

Table 2:

Icon Description

Specify whether attributes are sorted ascending or de­scending.

This setting is specific to your current session; it isn't saved for future use.

Specify filters for attributes to include or exclude specific values.

This setting is specific to your current session; it isn't saved for future use.

Specify which attributes appear as columns in the table.

The system saves this setting and applies it to your future sessions.

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Related Information

Patient List [page 9]Cohort Details [page 10]Notes [page 10]Contributors [page 11]

3.1 Patient List

In the Cohorts application, on the Patient List tab, you can review the patients added to the cohort and specify whether they meet the inclusion or exclusion criteria.

After you add patients to a cohort from another application running on SAP Connected Health, such as Patient Search, those patients appear in the Cohort application in the patient list. For the patient list, patients are grouped into the following categories and shown on different tabs:

● PendingWhen patients are added to a cohort from another application, they initially appear under Pending. An editor or owner then needs to evaluate them against the inclusion criteria.

● IncludedPatients that fullfill the inclusion criteria, as determined by an editor or owner.

● ExcludedPatients that don't fullfill the inclusion criteria, as determined by an editor or owner.

You can specify to which category a patient belongs by selecting the patient and choosing Include or Exclude. If you want, you can also add the patient to another cohort in addition to the current cohort.

From the patient list, you can also go to more information about the patient or their related documents.

You can export a list of the patients to a .CSV file. To do so, choose the (Actions) icon in the bottom right corner of the screen and then choose Export Contact List.

To save the cohort as a tile in the SAP Fiori launchpad, choose (Actions) and choose Save as Tile.

NoteIn the patient list, you can view only those patients for whom you have access permission. This means, you might not see the complete list of patients assigned to the cohort.

Patient List Settings

Patients appear in the patient list together with their available attributes, such as vital status or how many cohorts they are assigned to. You can specify how you want to sort and filter these attributes, as well as which attributes appear as columns in the table.

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Table 3:

Icon Description

Specify whether attributes are sorted ascending or de­scending.

This setting is specific to your current session; it isn't saved for future use.

Specify filters for attributes to include or exclude specific values.

This setting is specific to your current session; it isn't saved for future use.

Specify which attributes appear as columns in the table.

The system saves this setting and applies it to your future sessions.

3.2 Cohort Details

In the Cohorts application, on the Cohort Details tab, you can edit the title and description of the cohort if you are assigned as either an editor or an owner.

You can use the Description field to record information about the specific aim or purpose of the cohort and you can list the criteria you use to determine whether a patient should be included or excluded.

3.3 Notes

In the Cohorts application, on the Notes tab, you can add and view notes regarding the cohort.

All editors and owners of the cohort can enter comments or provide additional information by creating a note. In addition, if changes are made to the cohort details or contributors list this information is also recorded as a note.

If the list of notes is long, you can search for specific notes or filter the notes by their type:

● User notesContributors (editors and owners) can create notes to add comments or share additional information with other users who can view the cohort.If you include a pending patient request to a cohort or exclude a patient from the cohort, you provide notes to describe the change in the cohort status. These user notes are not translated.

● System notesThe system automatically generates notes in the follwoing scenarios:○ When contributors make any change to the cohort, for example, adds a patient or changes the cohort

description.

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○ When patients are added to a new or exsiting cohort either from Patients Search or Patient Analytics application.

○ When contributors move patient in a cohort, for example, from Pending to Excluded or from Included to Excluded.

System notes are always translated. It is displayed in the Language tab using the current locale.

NoteIf you exclude a patient from the cohort, you must specify a reason, which is recorded as a note. However, this note is patient-specific and does not appear on the Notes tab. You can access this note from the Notes column on the Patient List tab.

3.4 Contributors

In the Cohorts application, on the Contributors tab, you can share a cohort with colleagues by adding them as contributors and assigning them a role.

To do so, you can search for a specific active user, add them as a contributor, and define what role they should have for the cohort. If you created the cohort, you are automatically assigned the owner role.

Table 4:

Role Description

Reader Users can view the cohort details, notes, the list of contribu­tors, and the list of patients currently in the cohort. How­ever, users can't make any changes or assign contributors.

Editor Users can view and edit the cohort details, add notes, add readers or editors, and include or exclude patients from the existing patient list.

Owner Users can view and edit the cohort details, add notes, add all types of contributors, and include or exclude patients from the existing patient list. These users can also delete the co­hort.

A cohort can have multiple owners.

NoteRegardless of role, a user can only view patients to whom they have access privileges. This means your contributors might all see a different number of patients in the cohort.

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Contributor List Settings

Contributors appear in the list together with their relevant attributes, such as name or e-mail address. You can specify how you want to sort and filter these attributes, as well as which attributes appear as columns in the table.

Table 5:

Icon Description

Specify which attributes appear as columns in the table.

The system saves this setting and applies it to your future sessions.

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4 Search

You use the Search application to find patients and documents currently available in SAP Connected Health. This application appears as both a tile on the Fiori launchpad and a search bar at the top of every screen.

To find a specific patient or document, you can search by the following:

● Patient first name or last name● Patient ID● City where the patient lives● Clinical terms that may appear in documents related to the patient● Document metadata, such as document title or author● Codes (and their related texts) used in interaction details, such as primary diagnosis

By default, the application uses fuzzy search, a fault-tolerant search feature that returns patients even if the name, date, or clinical term that you enter is missing characters or is entered incorrectly.

Search Results

Search results are shown on different tabs based on the related entity, such as Patients or Documents.

NoteBy default, these entities are Patients and Documents; however, the entities used in your system may differ based on your data sources and configuration.

In the search results table for each entity, results are shown together with their relevant attributes. You can

specify which attributes appear as columns in the table by choosing .

Patient Search Results

From the Patients view, you can perform the following actions:

● View further details by clicking the patient's name, which opens the Timeline view in the Patient Summary app..

● View a list of related documents for the patient by clicking the number shown in the Related Documents column.

● Add the patient to a cohort by choosing the Add to Cohort button for an individual patient, or select multiple patients and choose the Add to Cohort button above the patient table.

If you search by clinical terms used in the patients' documents, the search results table has a Document Preview column, in which you see text passages from the documents that contain the clinical terms. You can view these documents by clicking View More in the Document Preview column.

Document Search Results

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From the Documents view, you can perform the following actions:

● Open a plain text version of the document by clicking on the document title.● View details on the related patient by clicking the patient name.● Add the patients relating to the documents to a cohort by selecting one or more documents and choosing

the Add to Cohort button.● Download the original version of the document by clicking the download icon.

Search Tips

When you enter your search terms in the search field, by default, the search returns only records that contain all of the terms you enter.

To further define or control your search, you can use the following search operators:

Operator Description

Wildcard (*) Use an asterisk (*) to represent one or more characters in a string.

Exclude words (-) Use a hyphen (-) before a word to exclude records that contain the word.

Exact phrase ("") Surround a phrase with quotation marks ("") to return only records that contain the exact phrase. Note that fuzzy search and synonyms also work on words within quotation marks.

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5 Patient Summary

You view patient details by clicking on the patient's name from any application running on SAP Connected Health.

In the Patient Summary application, you can view basic data about the patient and specific information about their interactions with medical professionals. Within the available tab views, interactions are grouped into color-coded categories, such as diagnostics or treatments. The number of interactions a patient has had in each category is also shown.

NoteThe standard Patient Summary tabs provided by the system are the Timeline, Overview and Related Document tabs. The tabs you see in your system can differ based on your configuration and whether additional custom tabs have been implemented.

NoteWhen you view a patient, the views and content visible to you depends on the configuration assigned to you. For more information, contact your system administrator.

In the Patient Summary application, you can create an SAP Fiori launchpad tile for a patient by choosing Save as Tile in the bottom right corner of the screen. You see the tile in the My Home area of the SAP Fiori launchpad. By choosing the tile, you can open the Patient Summary application for this patient directly from the launchpad.

Related Information

Timeline [page 16]Overview [page 20]Related Documents [page 20]Variant Browser [page 22]Configuration Selection [page 28]

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5.1 Timeline

In the Patient Summary application, on the Timeline tab, you can view the interactions between the patient and medical professionals in chronological order.

Interactions

In the timeline, interactions are grouped by category and each category is shown as a separate tile lane.

Timeline and Mouse Navigation

You can move backward or forward in the timeline by clicking and dragging the timeline area to the left or right. You can also change the time scale and zoom in and out by scrolling with your mouse wheel.

To view an interaction in more detail, simply click the interaction to display the details.

Timeline and Keyboard Navigation

You can also use the Tab key on your keyboard to navigate to the timeline area. Once you have selected the timeline area, you can change the time scale and zoom in and out by pressing the Up arrow or Down arrow keys. You can move backward or forward in the timeline by pressing the Left arrow or Right arrow keys.

You can tab further to navigate through the interactions. To view an interaction in more detail, you select it by tabbing to it and then press Enter .

Orientation and Advanced Navigation

When you're viewing interactions, there are various features to help you with orientation and navigation and to provide a clearer overview of your patient data:

Table 6:

Feature Description

Fullscreen mode When you enter the patient timeline from the Search or Cohorts applications, you can enter and exit fullscreen

mode by choosing the (Enter Fullscreen) icon or (Exit Fullscreen) icon at the top right of the Patient Summary screen.

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Feature Description

Line for current day The vertical blue line in the timeline indicates the current day.

Date of birth (DOB)

Date of death (DOD)

The date of birth (DOB) and, where applicable, the date of death (DOD) of a patient are delimited by the vertical black lines in the timeline. The white area between these lines indi­cates the period in which the patient is living. The gray areas outside these lines indicate periods prior to the birth or fol­lowing the death of the patient.

Dateless interactions If there are interactions in your system for which date infor­mation is missing, these interactions are docked to the left of the timeline and stacked within their respective tile lanes.

Navigation lane You can use the navigation lane below the main timeline area to navigate within the timeline.

TipThe white area in the navigation lane represents the time range and indicates the area in focus in the timeline.

In the navigation lane, you can use your mouse to navigate in three different ways:

● Navigate to the left or right in the timelineYou select the time range of the navigation lane and slide it to the left or right.

● Zoom in or out of the timelineYou drag the left or right border of the time range to ex­tend or reduce the area of focus. This allows you to ad­just your zoom level.

● Specify the range you want to view in the timelineYou specify an area outside the current time range that you want to view in the timeline. You do this by select­ing a gray area using a click, hold, drag, and release mo­tion with your mouse.

TipIn the navigation lane, you can also see small colored boxes that represent the interactions on the timeline. You can use these as a means of orientation when you use the navigation lane to navigate.

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Related Information

Chart Lanes in the Timeline [page 18]

Variant Browser [page 22]

5.1.1 Chart Lanes in the Timeline

In the Patient Summary application, some data displayed in the lanes of the Timeline tab can be better visualized when you plot this data as a chart rather than as tiles in the timeline tile lanes.

In the timeline, you may want to see the development of higher frequency data over time. This would allow you to identify tendencies and trends and see how a patient has responded to treatment, for example. Or you might want to see how weight or medication values develop over time. In addition to the tile lanes available in the Patient Summary timeline, you can also display chart lanes for certain attributes of the interactions displayed in tile lanes. You can choose which attributes you want to display as charts. Each chart is displayed in a separate chart lane. You can also choose whether you want to visualize the data for an attribute as a line chart or as a dotted chart.

Table 7:

Option Function Description

Minimize a tile lane You can use this option to minimize a tile lane. If a lane of tiles in your timeline contains higher frequency data, such as lab results or medica­tion data, for example, you might want to minimize this tile lane to re­move this information from your timeline.

Restore a tile lane If you decide you do want to examine data in tiles in a tile lane that is minimized, you can simply restore the display for this tile lane.

Add a chart lane Chart lanes are not initially displayed by default so you need to add your own chart lanes manually. Your system configuration determines what data you can choose to plot in a chart lane. In the tile lanes displayed, you only see the icon to add a chart lane if an attribute from an interac­tion in this lane has been configured as a plottable attribute.

When you add a chart lane, you specify one attribute for each chart lane that you add. You do this by either entering the name of the attribute in the search field or selecting the attribute directly from the list of inter­actions and their attributes displayed. You can only add chart lines for those attributes that are displayed.

Remove a chart lane If you no longer want to view the data for your attribute in a chart lane, you can simply use this option to remove the chart lane.

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Option Function Description

Specify the type of chart vis­ualization

You use this option to specify how you want to visualize your data in the chart lane. There are two options:

●To visualize your data as a line chart

●To visualize your data as a dotted chart with data points only

Individual data points in chart

Display information for chart data points

If you want to display the information for any data point in your chart, you can hover over the data point to display more detailed information. If you select or click the data point, the data for all the interaction attrib­utes is displayed in a pop-up. The data displayed is similar to the data displayed when you select the corresponding tile in the tile lane.

NoteThe values you see displayed to the left at the start of each lane are the most recent values recorded for the attribute plotted in that chart lane.

TipIf you want to adjust the order in which your tile lanes appear, you can do this by selecting the title area to the left of your tile lane and dragging the lane to its new position. This moves the tile lane as well as any associated chart lanes you've added.

Similarly, you can also adjust the order in which your chart lanes appear by selecting the title area of your chart lane and dragging the lane to its new position below the tile lane.

TipYou can choose which lanes you want to show by selecting or deselecting the category checkboxes above the timeline.

Saving Your Settings

The settings you choose for your tile lanes and chart lanes are stored for the following combination of specifics:

● The user you used to log on● The browser you're using● The configuration assigned to you by your administrator

The information stored includes the order and visibility of lanes, which lanes are minimized, which chart lanes you’ve added, and the visualization options you selected for your chart lanes. So if you log on using a different browser or with a different user, this information can't be retrieved and applied.

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Restoring to Default Settings

You can use the Reset to Default option to restore the system default lanes and selections on the Timeline and Overview tabs. On the Timeline tab, this also removes all chart lanes and restores all tile lanes to their original state. The tile lanes are restored in the order specified in your system configuration. Tile lanes are only restored if they haven't been explicitly hidden by your system configuration.

NoteWhen you use the Reset to Default option, any previous settings saved for your user are lost and can't be retrieved.

5.2 Overview

In the Patient Summary application, on the Overview tab, you can view a vertical list of interactions between the patient and medical professionals in reverse chronological order.

You can choose which interaction categories to show by selecting or deselecting the category checkboxes at the top of the list.

5.3 Related Documents

In the Patient Summary application, on the Related Documents tab, you can view a list of documents associated with the patient, such as doctor's letters.

This list of documents is only intended as an overview or reference. To view an actual document, you click the document title to see a preview of the document or download a copy and open it outside of the application.

For information about how documents are associated with specific patients or information about which documents in your organization are available in the application, please contact your system administrator.

NoteBased on your privileges, you might see only a restricted number of documents, even if more are available in the system.

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Search

For patients with multiple related documents, you can find specific documents by searching based on the following:

● Metadata, such as the file name or document type● Clinical terms used in the documents

If you search by clinical terms, the search results table has a Preview column, in which you see short text passages from the documents that contain the clinical terms.

TipAs part of your search, you can also use the document list settings to set filters to include or exclude documents based on, for example, the document type or author.

Document List Settings

Documents appear in the list together with their relevant attributes, such as title or document type. You can specify how you want to sort and filter these attributes, as well as which attributes appear as columns in the table.

Table 8:

Icon Description

Specify whether attributes are sorted ascending or de­scending.

This setting is specific to your current session; it isn't saved for future use.

Specify filters for attributes to include or exclude specific values.

This setting is specific to your current session; it isn't saved for future use.

Specify which attributes appear as columns in the table.

The system saves this setting and applies it to your future sessions.

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5.4 Variant Browser

The Variant Browser visually guides you through the genetic variants of a patient's genomic sample. It does this by showing how many variants a patient has in specific regions of genes.

If a genome sample exists for a patient, you can explore genetic variants of the patient by opening the Variant Browser from the Timeline tab in the Patient Summary application. Simply choose an interaction that has genetic information associated with it.

NoteThe Variant Browser can also be integrated into other applications running on SAP Connected Health platform. For information about accessing the Variant Browser from another application, see the corresponding Application Help for that product.

Related Information

Circular Plot View [page 22]Chromosome View [page 24]Categorizing Variants [page 28]

5.4.1 Circular Plot View

The circular plot view of the Variant Browser provides a visual overview of genetic variants of all chromosomes for the patient.

The inner circle represents the Variant Density track. Peaks in the Variant Density track indicate areas of the genome with many variants.

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To navigate from the circular plot to the genetic variants of a specific chromosome in the chromosome view, you simply choose a chromosome from the circular plot.

To examine a specific gene or location on the genome, choose the icon and enter the name of the gene or a chromosome number and position range, for example chr3:1822-1938 for the position range 1822 to 1938 on chromosome 3.

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5.4.2 Chromosome View

The chromosome view in the Variant Browser enables you to visually examine chromosomes, genes, gene variants, and translations in more detail.

Overview

In the chromosome view, you see an ideogram of the chromosome with position numbers and a number of horizontal tracks with the following visualizations:

Chromosome View Tracks

Table 9:

Track Description

Reference Displays the DNA bases of the reference genome when you zoom into an area of the chromo­some.

Variant Density Peaks in this track indicate areas with a high number of variants. You can zoom into these areas to separate aggregated variants up to the single-base level where the differences between pa­tient and reference genome become visible.

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Track Description

Variants As an additional visualization, this track uses an icon that resembles a lollipop to denote specific locations on the gene with variants:

This icon appears regardless of how much you zoom in or out, making it easier to identify areas of interest as soon as you open the chromosome view.

● Color:By default, the color assigned to a lollipop matches the color assigned automatically to the track. However, you can configure the meaning of the color of lollipops based on the cate­gory colors of the variants they represent. You configure these colors in the Categorize

Variant Data feature, which you can access by choosing the icon in the lower-right side of the screen. These colors are then reflected in the lollipop head, giving it a pie-chart ap­pearance when there are multiple variants of different colors at the same location.

● Stem width:The width of the lollipop represents the range of variants that have been aggregated to­gether into one lollipop. So if the stem has a significant width, this indicates there are multi­ple variants that are aggregated into one lollipop. The stem of aggregated lollipops spans from the smallest to the largest chromosome positions of these variants. This aggregation is only required when you are zoomed out. The lollipop splits up into more lollipops when you zoom in further. So the stem width is used simply for aggregation purposes and is re­quired when there are too many variants on the screen.

Genes Indicates all genes on the chromosome with their names and an arrow at one of the ends of each gene to denote the reading direction of that particular gene.

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Track Description

Translations Visualizes the translations of DNA into proteins. When you zoom in, you see the sequence of amino acids.

There are three main elements that are used to visualize the individual transcripts in the Translations track: labels, blocks (gray and orange), and zig-zag lines:

● Labels:The labels are always located at the beginning of every transcript. So you see them to the right or left of each transcript, depending on the reading direction of the gene. They indi­cate the transcript with the name of the protein in parentheses, such as NM_000546.5 (NP_000537.3). The exact notation of these labels depends on the GFF3 file that was loaded into your system. If there are multiple proteins for the same transcript, you see each of these listed here.

● Blocks:The orange and gray blocks represent exons (the protein-coding sections of the DNA).○ Gray blocks:

The gray blocks represent untranslated regions (UTRs) of exons. So you typically see these gray blocks at the start and end of each gene, with the 5' UTR at the start of the gene and the 3' UTR at the end of the gene. Whether a strand is a forward or reverse strand therefore determines whether you see the 5' UTR and 3' UTR to the right or left in your translation. Since 5' UTRs and 3' UTRs can either span an entire exon, multiple exons, or just be part of an exon, this is what determines how much gray coloring you see for the exons.

○ Orange blocks:The orange blocks represent the coding DNA sequences (CDSs), so these are the parts of the gene that are translated into amino acids. When you zoom into the tran­scripts, the letters you see in the orange blocks represent the amino acids. The end of the protein sequence is visually represented by a black dot for the stop codon as shown to the left in the following figure:

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Track Description

● Zig-zag lines:These represent introns (spliced out regions) and the zig zags symbolize the folding over of the pre-mRNA in splicing.

Navigating Within the Chromosome View

Within the chromosome view, you can navigate around in a number of ways, for example:

● To zoom in to see more details, you can scroll the mouse wheel or use the scrolling function of your touchpad. You can repeat this to zoom in further. You can also pan to the left or right.

● To examine a region of the displayed chromosome, you can drag and drop a region within the ideogram. Your selected region is then reflected by the blue slider under the ideogram. Alternatively, just below the ideogram where you see the chromosome position numbers, you can click and drag over a region to zoom in.

● To scroll down and view more information when a large number of tracks are displayed, click and hold your mouse in the tracks and drag upward.

● To examine another chromosome, choose the tab for the chromosome at the top of the view:

● To return to the circular plot choose next to the chromosome tabs.

You can also click a variant to see the chromosome number and cytogenetic location, the gene names as well as the allele frequency in the sample and in the reference genome. In the pop-up window, you can choose a gene name to find additional information on the gene in the NIH and ProteomicsDB databases or to search for patients with variants in this gene.

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5.4.3 Categorizing Variants

In the Variant Browser, to help visually distinguish between variants, you can create categories of variants and assign colors to them.

Context

To categorize variants, proceed as follows:

Procedure

1. In the Variant Browser, choose the icon in the lower-right side of the screen.2. Select the type of variant data that you want to based your category on, such as variants, variant alleles, or

variant annotations.3. Select an attribute of that type of variant data to base the category on.4. Enter a name for the category and choose Add Category.5. From the list of available variants in the default category, drag and drop variants into your new category.6. Click the color box next to the category name and select a color for the category.7. Activate the category by using the on/off toggle switch.8. Repeat these steps to add additional categories as required.9. Choose Save and Apply.

TipIf you just choose Apply, you can use your new category for your current session, but if you log off or close your Web browser, the category will be lost.

5.5 Configuration Selection

If more than one configuration for the Patient Summary application is assigned to you, you can select which configuration you want to work with.

If several configurations for the Patient Summary application are assigned to you, you have to select a configuration in the Configuration Selection dialog when you view a patient in the Patient Summary application.

When you select a configuration, you can specify that this configuration is to be saved as the default configuration. The next time when you view a patient, this default configuration is preselected.

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You can select a different configuration for the Patient Summary application when you view a patient from the Search or a Patient Summary tile on the SAP Fiori launchpad. To do so, choose the Options menu in the upper right corner and then choose Select Configuration.

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6 Glossary

attribute Characteristic that describes a patient, an interaction, or other clinical entity. You can use attributes to filter clinical data during search or analysis.

cohort A group of patients with similar characteristics who are identified as being commonly relevant for research purposes. You can inspect, evaluate, and share cohorts with other users.

interaction An instance of any form of communication between a patient and the health care provider, such as a diagnosis, treatment, or letter. Interaction is the central entity of the clinical data model. You can model most clinically relevant events as interactions. An interaction may occur at a specific time or across a span of time.

patient summary

A view that provides a chronological overview of the interactions contained in a single patient's medical record.

track A given sequence or property of a genome, such as variant density, visualized across a horizontal line.

variant A variation in a DNA sequence of a sample genome when compared to a reference genome.

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Important Disclaimers and Legal Information

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