| Oracle® Life Sciences Data Hub User's Guide Release 2.2 Part Number E22747-02 |
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| Oracle® Life Sciences Data Hub User's Guide Release 2.2 Part Number E22747-02 |
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View PDF |
This section contains information on the following topics:
The Oracle Life Sciences Data Hub (Oracle LSH) allows your company to gather data from many other systems such as clinical data management systems, clinical trial management systems, adverse event reporting systems, even financial or other nonclinical systems, together in one data repository where you can analyze data from all these sources together as necessary.
For example, your company can create programs to compare data from different trials in the same therapeutic area, compare adverse events reported for different drugs, or compare data from a current trial with data from a closed trial.
Oracle LSH allows your company to develop large sets of reports executed together and produced as a single- or multi-volume PDF output with a table of contents, page numbering, and hyperlinks. You can develop custom templates for use in these Report Sets.
Oracle LSH helps you remain in compliance with regulatory requirements by supporting the validation of all programs and other defined objects that handle data in Oracle LSH, and auditing changes to data over time. You can create and label snapshots of data at a particular point in time and later run the version of a program that was current at that time on that data to recreate your original results.
Each time you generate a report on data, you can generate a coversheet that traces the history of the reported data in Oracle LSH: when and from where the data was loaded into Oracle LSH, what programs and other objects manipulated the data in Oracle LSH, and whether those objects have been validated.
Your security privileges determine what reports you can see and what you can do in Oracle LSH. Depending on your privileges, you may be able to do the following:
View reports that have already been generated on Oracle LSH data. See Chapter 4, "Viewing Reports and Other Outputs" and Chapter 3, "Searching" for more information.
Create onscreen visualizations of Oracle LSH data. See Chapter 6, "Creating Data Visualizations" for more information.
Generate reports on the latest data, or on a data snapshot. See Chapter 5, "Generating Reports and Running Other Jobs" for more information.
Load data into Oracle LSH. See Chapter 5, "Generating Reports and Running Other Jobs" for more information.
Create Data Marts for export out of Oracle LSH. See Chapter 5, "Generating Reports and Running Other Jobs" for more information.
Run and view reports on sensitive, blinded data during the course of a trial. See Chapter 5, "Generating Reports and Running Other Jobs" for more information.
For information on creating the programs and other defined objects required to load data and to produce reports, data visualizations, and data marts, see the Oracle Life Sciences Data Hub Application Developer's Guide.
For information on developing a custom Oracle LSH implementation design for your company, see the Oracle Life Sciences Data Hub Implementation Guide.
For information on administrative tasks, see the Oracle Life Sciences Data Hub System Administrator's Guide.
For instruction on installing Oracle LSH, see the Oracle Life Sciences Data Hub Installation Guide.
To log in to Oracle LSH, you must have a browser on your computer and a URL, username and password provided by your company:
Open your internet browser.
Enter the URL provided by your company.
Enter your Oracle LSH username and password, as provided by your company.
Note:
After you have logged in for the first time you should change your password. See "Change Password".Press Enter or click the Login button. The Oracle Applications Navigator screen opens.
Click the Life Sciences Data Hub hyperlink. The system displays all the screens to which you have security access as hyperlinks.
Click on one of the hyperlinks; for example, My Home or Outputs. The system opens the corresponding Oracle LSH screen.
You can specify your preferences for some aspects of Oracle LSH's display and behavior.
There are general preferences that are the same for many Oracle applications, including:
There are other preferences developed especially for Oracle LSH, including:
Note:
You must click Preferences from an Oracle LSH screen such as My Home to see the Oracle LSH-specific preferences. If you still cannot see some of these preferences, your company's policy may be to set them for you.To set your preferences:
Click the Preferences link in the upper right corner of the My Home screen.
Click the link in the panel on the left side of the screen to display the preferences you want to set.
Enter your preferences.
Click Apply.
Details for each type of preference are displayed in the following sections.
Display preferences affect the way information is displayed for you in Oracle LSH.
American English is the only option in Oracle LSH Release 2.2. for both language preferences:
There is one Accessibility preference:
Accessibility Features Choose one of these settings:
Standard Accessibility. Renders Oracle LSH screens accessible to users using assistive technologies.
Screen Reader Optimized. Optimizes screens for screen readers. This option may degrade the output for sighted readers.
None. If you choose this option, some Oracle LSH screens may include features that are not accessible to some users.
There are several regional preferences:
Territory This setting has no effect in Oracle LSH Release 2.2.
Date Format From the drop-down list, select the way you want Oracle LSH to display dates.
Timezone From the drop-down list, select your time zone.
Number Format From the drop-down list, select the way you want Oracle LSH to display numbers.
Currency This setting has no effect in Oracle LSH Release 2.2.
Client Character Encoding This setting is used when uploading and downloading files to and from your computer through your browser. If you use non-English characters in source code, object names, or data, Oracle recommends that you change this setting to Unicode (UTF8) to ensure that these characters are displayed correctly in Oracle LSH.
Use this section to change the password you use to log on to Oracle LSH.
Known As Enter your name as you would like it to appear in the welcome banner onscreen.
Old Password Enter your current password.
These settings determine the screen that opens when you log in to Oracle LSH.
Responsibility Select Oracle LSH Responsibility to access the Oracle LSH user interface.
Page Select the tab you want to see when Oracle LSH opens; for example, My Home.
If you are unable to access part of the Oracle LSH user interface or perform a function that you feel you need to do, you can request increased privileges.
To request additional access:
Click the Preferences button.
Click Access Requests in the Preferences tab. The system displays your current roles.
Click the Help button and follow instructions there.
The following user preferences are specific to Oracle LSH. You can change the following settings:
When you log in to Oracle LSH, Oracle LSH will automatically open the Domain whose name you enter here. You can click the Search icon to see a list of Domains and select one. If you type all or the beginning of the Domain name and then click the Search icon, you see only the Domains that match what you entered.
You can change Domains in the Application Development screen as necessary.
Preferred Validation Status for Simple Search and Browse
Check the box if you prefer to see only objects and outputs whose validation status is Production when you conduct a Simple Search or browse the Reports or Applications tab. (You can request to see objects or outputs of any validation status when you use Advanced Search regardless of this setting.)
This setting is recommended for people who only need to view production data and reports in Oracle LSH. It is not recommended for people who are developing Oracle LSH applications.
Use this preference to change the password for your database user account.
Database Account Name The system displays your database user account name, if you have a database account.
Old Password Enter your current password.
New Password Enter your new password.
Confirm Password Enter your new password again.
This preference applies only to application developers who will work in SAS to create or upload programs to run on Oracle LSH data.
Oracle LSH handles data access from SAS as an integrated development environment (IDE) differently, depending on the connection mode you specify here:
Connected Mode. When you launch SAS from an Oracle LSH Program instance, Oracle LSH downloads views based on the Table Descriptors defined in the Program. You can see the current data in Oracle LSH while you work in SAS. If your program writes data to data sets, when you execute the program in the SAS IDE you pull data from Oracle LSH over the network and write to local data sets.
Your PC must have SAS Access to Oracle as well as the SAS client installed and must be connected to the Oracle LSH database through a network.
Disconnected Mode. When you launch SAS from an Oracle LSH Program instance, Oracle LSH downloads data sets with the same structure as the Program's Table Descriptors to your PC. In addition, Oracle LSH downloads the actual data contained in the Table instances to which the Table Descriptors are mapped. You can write your program working on the downloaded data.
Your PC must have the SAS client installed and must be connected to the Oracle LSH database through a network. SAS Access to Oracle is not required.
SAS Connected Mode with Work Area Data. This mode is the same as Connected mode except that it connects to the Work Area schema in the database. From SAS, you can browse views of current data in all Table instances in the Work Area, not just the Table instances linked to Table Descriptors of the Program.
You must use the SAS Access to Oracle tool to connect to Oracle LSH.
This preference applies only to application developers who will work in SAS to create or upload programs to run on Oracle LSH data. This setting determines the SAS client that is used when you launch a SAS integrated development environment (IDE) session. Your company may have removed this preference or added options.
To create or run Load Sets to load data into Oracle LSH from an external Oracle system, you must have an account on the external system that allows you to access the data you are loading. Enter information about your external Oracle system accounts so that when you create or run a Load Set, Oracle LSH can log on to the external system using your account to perform the data load. No other Oracle LSH user can use your connections.
To add a user connection for yourself, do the following:
From the Adapter Name drop-down list, select the adapter name that corresponds to the type of data you want to load: one of the Oracle Clinical adapters or Oracle Tables and Views for any Oracle-based system. Adapters correspond to Load Set types. For further information, see "Defining Load Sets" in the Oracle Life Sciences Data Hub Application Developer's Guide.
Note:
You must create a different User Connection for each Oracle Clinical adapter you use, even for the same Oracle Clinical instance. You can use the same Oracle Clinical username and password for each.From the Remote Location drop-down list, select the external database from which you need to load data.
Click Add User Connection. The Create Connection screen opens.
Enter values for the following fields:
Name. Enter a meaningful name for the connection. For example, OC Randomization from location_x.
Description. Enter a meaningful description of the connection to help you determine later on that this is the connection you need to use.
User Name. Enter your username in the external system. Oracle LSH will use this information to log on to the external system.
Password. Enter your password in the external system. Oracle LSH will use this information to log on to the external system.
Classify the Connection to help you find it. Choose an appropriate hierarchy and level; for example, the project and study for which you need the connection.
Click Apply. Oracle LSH returns you to the User Connections screen.
The tabs you see in the Oracle LSH user interface depend on your security access. You should be able to see the My Home tab and the Reports tab.
If you are an administrator or a programmer you may see additional tabs. Information about the Classifications, Security, and Administration tabs is included in the Oracle Life Sciences Data Hub System Administrator's Guide and for the Applications tab in Oracle Life Sciences Data Hub Application Developer's Guide.
The My Home screen has two sections, one above the other: Notifications and Job Executions.
Notifications If you click on the My Home tab you see a section on Notifications. These are messages sent to you within Oracle LSH. They may require action on your part or simply provide information. For further information on Notifications, see Chapter 2, "Using Notifications."
Job Executions If you scroll down the page you see a section on Job Executions. Every time you run a job—for example, run a report on fresh data, or load data from an external system—the system displays information on the progress of the job on this screen. For further information, see Chapter 7, "Tracking Job Execution."
If you click on the Reports tab, you see two subtabs: Outputs and Visualizations.
Outputs The Outputs subtab has two purposes: to display existing reports, Report Sets, and Data Marts; and to display the submission screen for reports, Report Sets, and Data Marts as well as Workflows and Load Sets so that you can run the same job on fresh data as necessary. For further information, see Chapter 4, "Viewing Reports and Other Outputs" and Chapter 5, "Generating Reports and Running Other Jobs."
Visualizations In the Visualizations subtab you can see Business Areas that you can use to create visualizations—graphical or tabular displays of Oracle LSH data—in Oracle Business Intelligence Enterprise Edition. Business Areas consist of a set of views of Oracle LSH tables and their data, with joins and hierarchies defined to allow you to best compare and analyze the data. For further information, see Chapter 6, "Creating Data Visualizations."
You can get context-sensitive online help for any screen in Oracle LSH (except pop-up windows) by clicking the Help link in the upper right corner of every screen.
The information you see in online help is taken from one of the following Oracle LSH user manuals, depending on the topic:
Oracle Life Sciences Data Hub User's Guide (this book)
Oracle Life Sciences Data Hub Application Developer's Guide
Oracle Life Sciences Data Hub System Administrator's Guide
In addition, you can see these books and the Oracle Life Sciences Data Hub Implementation Guide under Health Sciences in the navigation tree on the left side of the help screen.
Many Oracle LSH screens display the icons and buttons described in the following sections:
The following button functions are the same throughout Oracle LSH application development.
Apply Oracle LSH applies changes you have made on the current screen to the database and opens a new screen. Always paired with Cancel.
Cancel Oracle LSH discards any work you have done in the current screen and returns you to the previous screen. Always paired with Apply.
Check In Oracle LSH saves the new version of the object definition in the database and allows other Definers to check out the object, according to normal security limitations. Only the person who checked the object out can check it in (except for Report Set definitions, which have shared editing; see "Concurrent Editing" in the Oracle Life Sciences Data Hub Application Developer's Guide).
Check Out To modify an existing object definition, you must check it out first. See "Understanding Object Versions and Checkin/Checkout" in the Oracle Life Sciences Data Hub Application Developer's Guide for further information.
Continue Used for processes that require a series of screens. Oracle LSH saves your work temporarily and displays the next screen in the process. If you cancel before the Save or Apply operation at the end of the process, which saves your work in the database, the system discards the temporarily saved work.
Copy Creates a copy of each selected object definition or instance that you can paste into a new location. The original object remains unchanged. To copy, you must first select the item(s) you want to copy and click the Copy button. Then go to the location into which you want to paste the copy, and click Paste. The system prevents you from doing anything else until you either cancel or paste. You can copy multiple objects from the same container at the same time. When you click Paste, the system pastes all the objects into the new location. See "Copying Objects" in the Oracle Life Sciences Data Hub Application Developer's Guide.
Move Moves each selected objects to a different location without breaking any links; use Paste to complete the operation. See "Moving Objects" in the Oracle Life Sciences Data Hub Application Developer's Guide.
Paste Places one or more object(s) into a single Oracle LSH location to complete the Copy or Move operation.
Uncheck Oracle LSH discards the new version of the object you checked out. Only the person who checked the object out can uncheck it. The previous version continues to function as before.
Oracle LSH uses icons for actions and to represent object types. See:
The following icons appear on the main Application Development screen. Some appear on many other screens as well.
You must check out object definitions to modify them.
You must check in object definitions to install and use them.
Cloning is an option only for Work Areas. See "Cloning Work Areas for Testing and Production" in the Oracle Life Sciences Data Hub Application Developer's Guide
When Oracle LSH displays the Collapse icon, the child objects are displayed, but you can click the icon to hide them.
Click Create Child to create a new object that is a child of the row object. The type of object you can create as a child varies depending on the parent.
For an Application Area, Work Area is the only child you can create in this way. To create definitions of primary objects, either click Manage Definitions or create an instance and a definition in a Work Area within the Application Area. Oracle LSH automatically creates the new definition in the Application Area that contains the Work Area.
For a Work Area, you can create any primary object type: Business Area, Data Mart, Load Set, Program, Report Set, Table, or Workflow. Oracle LSH automatically creates the new definition in the Application Area that contains the Work Area, and an instance of it in the Work Area.
Oracle LSH displays either the Expand or the Collapse icon to the left of every object that owns one or more objects. When Oracle LSH displays the Expand icon, the child objects are hidden, but you can click the icon to show them.
Use the Focus icon to move your selected container to the top of the tree and expand all its branches.
Click this icon to create or modify the definitions contained in the Domain or Application Area.
Click this icon to open the Mapping screen and map Table instances to Table Descriptors inside Program instances or other Oracle LSH executable objects.
Use the Move operation to remove an object from its current location and paste it into a new location.
Click Reorder to rearrange the display of objects on this screen.
There are two kinds of icons to select objects in Oracle LSH.
Square. The square checkbox allows you to select multiple objects.
Circle. The circular radio button allows you to select only one object.
Select the required objects. Then click a button in the toolbar immediately above, such as Copy to copy all selected objects or Remove to remove all selected objects.
Click this icon to see the version history of the object.
Each Oracle LSH object type has its own icon, shown below.
Notification With Approval Request
There are two ways to navigate around Oracle LSH screens and invoke actions:
Point to the field or button you want to use. Left-click to select a field or invoke the action of the button.
To enter text in a field, select it and then type the text.
Use the Tab and arrow keys (up, down, left and right) to navigate around the screen. The active onscreen item is outlined with a dotted line. If an enterable field is active, anything you type appears in the field.
To move from one frame of the screen to another, press Ctrl+Tab.
Press Enter to invoke the action of a button when the button is active.
Press the spacebar to select a radio button or checkbox.
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