Setting Up Data Collection in Oracle Clinical

To use TMS with Oracle Clinical, you must define two types of questions and associate them with DCM question groups:

• A parent question to collect data (called source terms in TMS) at an Oracle Clinical patient visit
• A derived question to receive each piece of information you want to retrieve from TMS

In addition, you must define one or more question sets. A question set is a reusable structure that:

• Specifies the TMS dictionary against which to classify the parent question response (TMS verbatim term)
• Includes variables that specify the information you want to retrieve from TMS

During definition of the parent question you:

• Link the parent question to a question set
• Link a derived question to each question set variable

The diagram shows the definitional links between Oracle Clinical and TMS. In the Oracle Clinical Global Library, you define parent and derived questions and questions sets, which specify questions' relation to dictionary data, and link parent and derived questions. In Oracle Clinical studies, you include parent and derived questions in the study definition and link the study to TMS domain/dictionary combinations. In TMS, you define valid dictionary/TMS domain combinations.

For more information, see:

• Defining and Using Question Sets
  
• Defining Questions
  
• Using a Derived Question as a Parent Question
  
• Associating Child Questions with Question Set Variables
  
• Associating Questions with Question Groups and DCMs
  

Defining and Using Question Sets

A question set defines the TMS information to be sent to Oracle Clinical in relation to a question response collected in Oracle Clinical. A question set definition has two parts:

• Defining a Question Set. General information about the question set: its name, description, and TMS dictionary against which question responses are to be classified.

• Defining Question Set Variables. Variables that specify the dictionary level and data to be derived (such as term, ID, or code; see Defining Question Set Variables for a complete list of derivable data).

  Alternatively, question set variables can derive Informative Notes from TMS to Oracle Clinical derived questions.

When you define a parent question (a question whose response is to be to a TMS dictionary term) you assign a question set to the parent question. Then, in the Details section of the parent question definition, you assign a derived question to each question set variable. Thus, the question set is the link between the parent question that collects Oracle Clinical data at a patient visit and the derived questions that contain information from TMS related to the response/verbatim term's classification in TMS.

You can assign the same question set to many different parent questions to collect the same TMS information for each parent question.

Note:

Define the question set completely before assigning it to a parent question. You cannot make changes to the question set after it is assigned to a parent question.

For more information, see:

• Defining a Question Set
  
• Defining Question Set Variables
  

Defining a Question Set

To define the question set:

1. In Oracle Clinical, from the Glib menu, select Question Sets, then choose Question Sets.
2. In the QS Name field, enter a unique name assigned to this question set. It can be up to 20 alphanumeric characters.
3. In the Description field, enter a description for the question set of up to 60 alphanumeric characters.
4. In the QS Type Code field, choose TMS Q SET from the list of values. The code entered in this field determines which of the Parameter 1…5 fields must be completed. None are required for TMS.
5. In the TMS Dictionary field, from the list of values choose the TMS dictionary to be accessed by this question set. You can use only strong dictionaries.
6. Leave the Parameter 1…5 fields blank. These fields are not used in this context.
7. Set the Review before TMS? box. Leave deselected to handle the initial review of thesaurus omissions in TMS.

   To handle the initial review in Oracle Clinical you must select this option and also set the short value FIRST_REVIEW in the local reference codelist TMS_OPTIONS to Yes (see Managing the TMS/Oracle Clinical Workflow).

8. Proceed to Defining Question Set Variables to complete the question set.

Defining Question Set Variables

Question set variables link child questions to the parent question and specify the information to be sent to and retrieved from TMS.

When you define a parent question to collect a drug name or medical condition to be classified in TMS, you associate it with a question set. The system populates the parent question's Details window with the question set variables. You must associate each variable with a child question that either sends additional information to TMS or holds information derived from TMS.

You define question set variables in the lower part of the Question Sets window. Each row defines one variable.

1. Under Question Set Questions, click in the first available row.
2. Specify a Sequence Number for the variable. This number represents the display order you want to appear in parent question's Details window, relative to the other variables in the question set. Sequence numbers can be up to three digits.
3. Enter any value you want, from 1 to 30 alphanumeric characters, in the Parameter Name field. This field must be completed and each Parameter Name must be unique within the Question Set, but is not used by the system.
4. In the Display Prompt field, enter the text that you want to appear as the variable name in the Details window of the parent question. This field will be mapped to a derived question. Consider using a naming convention to make it easy to decide which question you should associate with which variable; for example, dictionary level_type of information. See the possible types of information at Step 8 below. Up to 15 alphanumeric characters.

   Note:

   The reportable levels of the dictionary specified for this question set are listed in the Parameter Name 1 list of values.

5. Choose a Data Type of CHAR.
6. Len. Enter a length for the question set variable. It must be long enough to handle the data that will be returned from TMS. The largest amount allowed is 200. This is the recommended size.

   Note:

   You set the display length for the Data Entry form in the Len field in the DCM Questions window.

7. Question Type. Select one:

   • OUTPUT if the variable is for information derived from TMS, such as a Preferred Term or ATC. Questions defined for this purpose must be defined as derived.

   • INPUT if the variable is to send auxiliary information to TMS in a dictionary with nonunique terms in the coding level, such as WHO-Drug Format C. You can use questions to collect auxiliary information such as Country, Pharmaceutical Form, and Strength in order to classify terms to nonunique dictionary terms.

   • INDICATION if the variable is to send information to TMS about the indication for which a drug was taken. For example, WHO-Drug supports classifying different occurrences of the same source term to different ATC terms depending on the indication. See Classifying Indication Omissions.

   • ROUTE if the variable is to send information to TMS about the route of administration for which how a drug was taken. Typically, it is identified along with the Indication.

     Note:

     The ROUTE variable is added for the TMS 5.3 release.

8. Parameter Name 1. The list of values varies depending on the question type:

   • For INPUT question types, all auxiliary information sublevels defined for the dictionary are listed.

   • For INDICATION question types, there is no list of values. Leave blank.

   • For OUTPUT question types, the list of values includes all dictionary levels and Info Note. Select one dictionary level from which to derive the term related to the parent question term. Alternatively, use Informative Notes to send additional information from TMS to Oracle Clinical. See Defining Informative Note Attributes for information about Informative Notes.

     Note:

     Do not enter the name of a group level here. To derive information from a dictionary level that is contained in a group level, you must enter the sublevel here, not the group level.

     If you have a Primary Link required to a group level, but a particular term's Primary Link is to any of the sublevels in the group level, you must create a variable for each sublevel.

9. Parameter Name 2. The information you enter here depends on whether you chose a dictionary level or Informative Note in the Parameter Name 1 field and applies only to OUTPUT question types.

   Dictionary Level. If you specify a dictionary level in the Parameter Name 1 field, TMS returns information about the parent term's related term in that level. In the Parameter Name 2 field you must specify the type of data you want to derive from TMS.

   For example, if the verbatim term "Headache" is classified to Preferred Term "Head Discomfort," whose related High Level Term is "Neurological Signs and Symptoms NEC," and you specify High Level Term for the dictionary level in Parameter Name 1 and Term Upper for Parameter Name 2; if the question response value was "Headache," TMS would return the value "NEUROLOGICAL SIGNS AND SYMPTOMS NEC" as the value for the derived question specified in the parent question Details window for this variable.

   The list of values displays the following derivable data:

   • CATEGORY. Optional field used to by some dictionaries to further categorize terms; MedDRA supplies Diagnose, Adverse Event, or Undefined as categories for its terms.

   • COMMENT_TEXT. User-defined comment entered by the term's creator about the term.

   • DICTIONARY VERSION. The version of the dictionary, as defined by an Informative Note (see Defining Informative Note Attributes).

   • DICT_CONTENT_ALT_CODE. Optional, user-defined, indexed, unique ID for a term. Designed to provide a link to another thesaurus system.

   • DICT_CONTENT_CODE. Optional field designed to serve as the primary key within a dictionary. TMS does not require that the dict content code be unique.

   • DICT_CONTENT_ID. Unique ID across TMS for this term; the primary key in TMS.

   • TERM. A term as entered or loaded (uppercase, lowercase, or mixed case).

   • TERM_UPPER. A term, all uppercase.

   • VALUE_1…4. Optional. Data defined by the user for a dictionary level. See Defining Level Details.

   Dictionary Informative Notes. If you entered "Dictionary Informative Notes" in the Parameter Name 1 field, in the Parameter Name 2 field the list of values displays all the derivable Informative Note Attributes defined in this installation.

   For example, you can derive an Informative Note of type URL containing a link to information about the dictionary term.

   See Defining Informative Note Attributes for information about Informative Notes. For information about the particular Informative Note Attributes that have been defined for this TMS installation, from the Definition menu, select Define Informative Notes Attributes in TMS.

10. Info Note? The system populates this field depending on the setting of the Parameter Name 2.
11. Save.

Defining Questions

Two types of questions are used by TMS: parent questions are used to collect responses at patient visits; and child questions, derived questions that receive the information specified by question set variables from TMS. Use the standard Oracle Clinical question definition process for both parent and child questions, with the TMS-specific settings below.

Parent questions can also be derived questions in special cases; see Using a Derived Question as a Parent Question.

You cannot convert an active, non-TMS question set question for processing in TMS. You must define a new question with a question type of Question Set and the name of its question set as part of the definition. You may want to model your TMS parent questions on your standard Glib questions, changing their names using a convention such as suffix _TMS.

Note:

A particular derived or parent question can be used only once within a question group: a particular question cannot be used in more than one question set, and can be used only once in a single question set.

This section includes:

• Defining a Parent Question
  
• Defining a Child Question
  

Defining a Parent Question

The parent question collects the verbatim term (clinical data, question response) during an Oracle Clinical visit.

To define a parent question and link it to a question set:

1. In Oracle Clinical, from the Glib menu, select Questions, then choose Questions.
2. Complete the definition fields as usual in Oracle Clinical (see Oracle Clinical Creating a Study in the Oracle Clinical documentation set), completing these fields as follows:

   • Question Type. You must set this field to QUESTION_SET. This value activates the Question Set Name field.

   • Question Data Type. You must set this field to CHAR.

   • Question Set Name. Enter the name of the question set to which you want to link this parent question.

   • Derived? Normally you should leave this box deselected. However, there are some cases where you may want a derived parent question; see Using a Derived Question as a Parent Question.

   • Display Prompt. This text becomes the display prompt in the Data Entry form.

3. Save.

   Note:

   You can either activate the question now by setting the status to A, or leave it provisional so you can change it if necessary. You must activate it and save your work before you can link the question to a question group and use it in a study.

4. Click the Details button to associate derived questions with question set variables. You must define the derived questions before you can do this step. See Defining a Child Question and Associating Child Questions with Question Set Variables for instructions.

Defining a Child Question

Create a child derived question for each variable of the question set. Consider using a naming convention to make it easy to remember which question you should associate with which variable; for example, dictionary level_type of information.

To define a child derived question:

1. In the Oracle Clinical Glib menu, select Questions, then choose Questions.
2. Complete the definition fields as usual in Oracle Clinical (see Oracle Clinical Creating a Study in the Oracle Clinical documentation set), completing these fields as follows:

   • Question Type. Set this field to THES VALIDATED.

   • Data Type. Set this field to CHAR.

   • Len (length) Enter a length at least as long as the question set variable it is being associated with (see below); the maximum setting, 200 characters, is recommended.

   • Derived. Select this box.

   • Default Prompt. Enter text to become the label for the derived question in the Data Entry form.

3. Save.

   Note:

   You can either activate the question now by setting the status to A, or leave it provisional so you can change it if necessary. You can associate a provisional derived question with a parent question, but you must activate it and save your work before you can link the question to a question group and use it in a study.

Using a Derived Question as a Parent Question

Batch Validation can run its TMS process twice, once before and once after deriving question responses with Oracle Clinical derivation procedures (see Batch Validation Execution Order), and allows parent questions to be defined as derived, making it possible to do either of the following during a single Batch Validation job:

• Derive a value to an Oracle Clinical question in TMS, run an Oracle Clinical derivation procedure to take that value and use it to populate the value of a (derived) parent question, and send the derived parent question value to TMS to derive additional Oracle Clinical question set question values.

• Run an Oracle Clinical derivation procedure to populate the value of a (derived) parent question as necessary, and send the derived parent question value to TMS to derive additional Oracle Clinical question set question values.

Note:

Oracle supports only the amount of derivation that can be accomplished within a single Batch Validation. Oracle does not support using an Oracle Clinical derivation procedure to populate the value of another derived parent question with the value of the original derived parent question.

Also, Batch Validation runs the TMS portion twice only if a derived parent question exists and requires processing.

For more information, see:

• Examples
  

Examples

Deriving a parent question may be useful in the following situations:

Deriving Data from Two Dictionaries for One Verbatim Term

To classify a single verbatim term to two different dictionaries, and derive information from both dictionaries into Oracle Clinical, you can do so by defining two question sets, as follows:

• The first question set references the first dictionary and includes a (non-derived) parent question to collect a response during data entry and derived child questions to receive TMS values from the first dictionary as specified by the question set variables (a standard Oracle Clinical TMS question set).

• The second question set references the second dictionary and includes a parent question defined as a derived question and derived child questions to receive TMS values from the second dictionary as specified by the question set variables.

To populate the value of the derived parent question, you must write a derivation procedure in Oracle Clinical that propagates the value collected for the first parent question to the second (derived) parent question.

During Batch Validation, the system first derives values from TMS (from the first dictionary) for the first set of derived questions, then processes the derivation procedure that populates the second parent question value, and finally derives values from TMS (from the second dictionary) for the second set of derived questions.

Classifying a Term Substituted for the Original Question Response

If many of the originally collected question responses are inconsistent with current terminology—for example, in a historic study or a study conducted by a company your company has acquired—you can leave the original data and thesaurus derivations, if any, intact but add current information by doing the following:

1. Define a new question for each original question whose responses may be outdated.

2. Examine each response to the original question and manually enter an appropriate value in current terminology for each corresponding new question.

3. Define a new derived parent question also corresponding to each original question whose responses may be outdated. Associate the parent question with a question set and child derived questions to define and receive the related information you want to derive from TMS.

4. Write a derivation procedure that compares the values of the original question and the new non-derived question, and populates the new derived parent question with the value of the new non-derived question if it has a value; otherwise with the original response.

5. Run Batch Validation. TMS processes the value of the new derived parent question and returns the data specified in its question set.

Classifying Previously Unclassified Terms

Add derived parent terms to legacy studies to derive TMS information for question responses that previously had no derived thesaurus information.

1. Define a new derived parent question for each original question for which you want to derive thesaurus values. Associate the parent question with a question set and child questions to define and receive the related information you want to derive from TMS.
2. Write a derivation procedure to populate the value of the new derived parent question with the original question's value.
3. Run Batch Validation. Oracle Clinical runs the derivation procedure to populate the value of the new derived parent question, and TMS returns the data specified in the question set.

Associating Child Questions with Question Set Variables

After you have created a question set, a parent question to collect data, and all the child questions you need for the parent question, you must assign one child question to each variable of the question set associated with the parent question. If it is unclear what information should be associated with each variable, look up the question set definition from the Glib menu, by selecting Question Sets, and then Question Sets.

1. In Oracle Clinical, from the Glib menu select Questions, then choose Questions.
2. Execute a query for the parent question.
3. Highlight the parent question name. This activates the Details button.
4. Press the Details button. The Details window displays the prompts for the variables of the question set linked to this parent question (see Defining and Using Question Sets).
5. In the row for each variable, use the LOV to enter the name of the question you created to collect it.
6. Save.

Associating Questions with Question Groups and DCMs

Before you can use parent or derived questions in a study you must associate them with a question group, DCM, DCI, and study as usual in Oracle Clinical (see the Oracle Clinical Creating a Study manual).

You do not have to use all the derived questions associated with a parent question in the Global Library. If you choose not to derive all the information defined in the question set, in the DCM question group you can simply not include the derived question mapped to the variable you do not need.

However, the parent question and all its derived questions you do need must be in the same question group.

All questions are visible in the data entry form, but only the parent question is enterable. When values are derived for the derived questions during Batch Validation, they are displayed in the data entry form. You can reference their values as you can any other question response values, in Oracle Clinical data extract and validation procedures.

You can associate the same question set with multiple parent questions in the same DCM.

For more information, see:

• Planning Question Groups and DCMs for RDC Special Listings
  
• Adding Derived Questions to an Ongoing Study
  

Planning Question Groups and DCMs for RDC Special Listings

If you are using Oracle Remote Data Capture (RDC) Release 4.5.3.10 or above, you can use Special Listings to display concomitant medications and adverse events by patient. (If you are using TMS to code any other type of data, you can display Special Listings for it too.)

If RDC detects that any question in a DCM is a mapped to a TMS dictionary (is a parent question) it displays an additional item in the drop-down list of actions a user can take in the Home and Casebooks pages. By default, this item's text is: Review TMS_dictionary_name/DCM_name. You can substitute other text (such as Adverse Events or ConMeds) for the dictionary name by defining a special type of Informative Note. This text appears on the Special Listings page as well; see RDC Action Informative Notes.

When a user selects a patient and selects a dictionary/DCM combination, the Special Listings page displays the patient's responses to all questions that are mapped to that dictionary in that DCM, in every visit and CRF where the DCM has been collected. In addition, the Auxiliary Information field displays the question name and the patient's response for every other question in the question group that is defined as Displayed and not as Derived.

In the figure below, the response to the parent question is displayed in the Verbatim Term column. In the Auxiliary Information column, the system displays all other nonderived, displayed questions in the same question group as the parent question; in this case, Start Date, End Date, and SAE (Yes/No).

To optimize Special Listings behavior, plan Question Groups and DCMs as follows:

• Question Groups. Include any questions related to the parent question that you would like to have displayed with it in RDC Special Listings, and do not include any questions you do not want displayed.
• DCMs. To enable viewing all adverse event or all concomitant medication data for a patient at the same time, use the same DCM to collect adverse event or conmed data in any DCI/CRF where you need to collect it.

Figure 4-1 Figure 4-2 RDC Special Listings Page

Adding Derived Questions to an Ongoing Study

If you initially do not include all the derived questions associated with a parent question and then decide midway through a study that you do want to derive that information, do the following:

1. Add the derived question to the DCM in the DCM's Question Group Questions window.
2. In Oracle Clinical, from the Plan menu, select TMS Domains. The Maintain Domain Elements window opens.
3. Select the project to which the DCM's study belongs, and click Studies. The Studies window opens.
4. Select the study to which the DCM belongs.
5. Click Domain Elements. The Domain Elements window opens.
6. Select the dictionary referenced by the parent question's question set.
7. Click Force Rederivation. During the next Batch Validation run, all the parent questions associated with the study will be reprocessed and the associated derived questions repopulated or, in the case of the new question, populated for the first time.