Planning Strong Dictionary Structure

TMS provides flexibility in designing dictionaries, including those supplied by vendors. You can design the dictionary structure, ranking levels hierarchically and/or creating levels at the same rank. You can define the cardinality and optionality of level relations, and specify a Primary Link or Primary Path Link between levels.

Basic strategies for organizing dictionary structure include:

• Ranking levels in a vertical hierarchy so that terms become more general and fewer in each higher level of the hierarchy, effectively organizing lower-level terms into categories.

• Adding levels horizontally, at the same rank, to provide supplementary information about terms, such as preferred names or indications.

• Assigning levels to group levels to promote efficiency and enforce Primary Links to more than one level (see Requiring a Primary Link to a Group Level).

• Defining the classification level as a group level that includes both the conventional classification level and a synonym level with a many-to-one relation to the classification level. In this case, TMS searches in both sublevels for a match to a verbatim term. If it finds a match in the synonym level, it creates the VTA to link directly to the related conventional classification level term. Because of this behavior, using group levels as classification levels greatly increases the likelihood that a match will be found without increasing the number of terms in the conventional classification level.

Review each of the remaining sections in this chapter to consider your dictionary needs before defining a TMS dictionary or writing load scripts.

For more information, see:

• Uniqueness of Terms
  
• Defining Relationships Between Dictionary Levels
  
• Grouping Levels
  
• Deriving Terms
  
• Enforcing the Structure
  
• Strong Dictionary Structure in Other Forms
  

Uniqueness of Terms

In addition to the flexibility with which many internal and vendor-supplied dictionaries define their hierarchies and relationships, dictionaries can also differ in the manner in which they handle a term's uniqueness. You can specify that terms be unique throughout a level or group level in a dictionary, throughout all levels of a dictionary, or choose not to enforce uniqueness of terms at all for a particular dictionary.

If you plan to use a dictionary for classification of verbatim terms, you must enforce uniqueness on the classification level. For other internal or vendor-supplied dictionaries, choose the degree of uniqueness based on how duplicate terms exist within the dictionary.

TMS evaluates uniqueness based on the "term upper" version of a dictionary term, in which TMS converts the dictionary term to all uppercase letters and removes all extraneous spaces.

Defining Relationships Between Dictionary Levels

To create strong dictionary relations in TMS, so that you can link terms in one level to terms in another, you must define relations between the levels in the dictionary structure.

During Activation, TMS checks all terms and relations against the relations defined for their dictionary levels. Terms and relations whose definitions conflict with the defined level relations cannot be activated. For example, if you have defined relations to more than one term in a level with a Single cardinality relation, the Activation job activates the first relation it processes and rejects the rest.

You must define the following attributes for relations between levels within a strong dictionary: Mandatory Relations and Cardinality. For relations with Many cardinality defined, you can also define a Primary Link if the dictionary includes a group level (a primary path), or you may also define the level with Indication.

The relations you define between levels create the derivation path for verbatim terms associated with the dictionary. A valid derivation path enables TMS to derive one and only one term from each level above the verbatim term level, and send the derived terms to an external system such as Oracle Clinical (see Derivation Path). If Single cardinality is defined from the lower to the higher level, no Primary Link is required because a term in the lower level can be related to only one term in the higher level, and TMS can derive that term. If Many cardinality is defined, so that a term in the lower level can be related to multiple terms in the higher level, you must require a Primary Link to identify which related term in the higher level is derived. See Primary Links and Primary Path Links.

In this section:

• Mandatory Relations
  
• Cardinality
  
• Primary Links and Primary Path Links
  
• Indication
  

Mandatory Relations

For each level relation you can require that a term in each level have a relation with a term in the other level, or define the relation as optional in either direction. For example:

The Relation Is Mandatory in One Direction but Optional in the Other

Terms in Level A must have a relation to a term in Level B, but terms in Level B may or may not have a relation to a term in Level A.

Both Relations Are Mandatory

Terms in Level B must have a relation to a term in Level A, and terms in Level A must have a relation to a term in Level B.

Both Relations Are Optional

Terms in Level B may or may not have a relation to a term in Level A, and terms in Level A may or may not have a relation to a term in Level B.

Cardinality

The cardinality of a level relation controls the ratio allowed between terms in two levels and must be defined in both directions:

• Can a single term in Level A be linked to more than one term in Level B?

• Can a single term in Level B be linked to more than one term in Level A?

You can define a level relation as many-to-many, one-to-many in either direction, or one-to-one.

Primary Links and Primary Path Links

If you define a relation where a term in Lower Level B can be linked to many terms in Higher Level A (Many cardinality), you can specify that each term in Lower Level B must have a Primary Link to a single term in Higher Level A. If the relation is on the derivation path—levels from which TMS can derive terms to be sent to an external system—you must require a Primary Link. Otherwise, TMS cannot activate the dictionary.

When a Primary Link is required, it is possible to create a Domain Primary Link for a particular term to override its Global Primary Link within a particular domain.

When you define a group level, you can define primary relations from terms outside (and below) the group level to the group level in two different ways:

• Primary Link. If you define a Primary Link to the group level, and Many cardinality is defined on the higher side of level relations, the lower-level term can have links to multiple terms on multiple levels in the group level, but only one link can be the Primary Link. The Primary Link can be between the lower-level term and a single term on any level within the group level.
• Primary Path Link. If you define a Primary Path Link to the group level, a term in the lower level can have links to multiple terms in multiple levels within the group level, but it must have a Primary Link to a term in the lowest level within the group, and to a related term in the next highest level, all the way to the top level.

  You must load or define the Primary Link for each lower-level term to a term in each of the group levels from the bottom up. TMS restricts your choices at each level to terms that are related to the Primary Link term in the immediately lower level. Thus, different lower-level terms can have a Primary Link to the same term in the lowest group level but different terms in the higher group levels (see the figure below).

  Primary Path Links are designed to accommodate MedDRA's structure.

See Grouping Levels for background information on group levels.

The figure below shows derivation paths using Primary Link (on the left) and a primary path (on the right). In these examples, all relations between levels are many-to-many, so Primary Links are required for each relation in the derivation path.

• The example on the left shows a dictionary structure without a group level, where a Primary Link is required between each level and the next higher level. Terms PT1 and PT2 are both defined with a Primary Link to the same term—HLT1—in the next higher level. Their derivation path is the same because the rest of the derivation path depends on the Primary Links defined for the higher-level terms: HLT1 has a single Primary Link to HLGT1, which has a single Primary Link to SOC1.
• The example on the right shows a dictionary structure where the HLT, HLGT, and SOC levels are all included in a group level, but a primary path is defined between the PT level and the group level. In this case, terms PT1 and PT2 can be linked to the same term in the HLT level and yet be linked to different terms in the two higher levels. This model conforms to MedDRA's structure.

Note:

Note that there is a third possible structure. If you defined the same group level as in the example on the right—containing the SOC, HLGT, and HLT levels—and defined a Primary Link from the PT level to the group level instead of a Primary Path Link, then the terms PT1 and PT2 would each link to HLT1 but, if Many cardinality were defined from the HLT to the HLGT and from the HLGT to the SOC, their derivation path would end there. No higher level terms could be derived because no other Primary Links or primary paths would exist.

If Single cardinality were defined from the HLT to the HLGT and from the HLGT to the SOC, and those levels were defined as reportable and their relations as derivable, the derivation path would continue all the way to the SOC level.

Figure 6-2 Figure 6-2 Derivation Path Examples for MedDRA

Indication

Note:

In TMS 5.3 release, you can specify the term with an Indication at the Level Relations.

If you do not define a primary link when a term has multiple higher level terms, you can specify the term with an Indication at the Level Relations. By assigning an Indication at the term level, TMS will derive from receiving an indication and route of administration the classified Indication Assignment to the external system.

For example: In the WHO-Drug B3 format dictionary, for the Trade name Abnal, the ATC can be derived to any of the following number:

• A01AD, OTHER AGENTS FOR LOCAL ORAL TREATMENT

• A06AG, ENEMAS

• A12CA, SODIUM

• B05BB, SOLUTIONS AFFECTING THE ELECTROLYTE BALANCE

• B05CB, SALT SOLUTIONS

• B05XA, ELECTROLYTE SOLUTIONS

• D03, PREPARATIONS FOR TREATMENT OF WOUNDS AND ULCERS

• D09A, MEDICATED DRESSINGS

• R01AX, OTHER NASAL PREPARATIONS

• R05CB, MUCOLYTICS

• S01XA, OTHER OPHTHALMOLOGICALS

• S02DC, INDIFFERENT PREPARATIONS

• V07AB, SOLVENTS AND DILUTING AGENTS, INCL. IRRIGATING SOLUTIONS

• V91, HOMEOPATHIC PREPARATION

If an Indication and Route of Administration are specified by the external system then in TMS the indication and route of administration can be classified to Abnal with Indication of Sinus Infection and Route of Administration of Nasal to R01AX Other Nasal Preparations.

Grouping Levels

You can arrange levels of a strong dictionary into a group level, and define other levels as having a relation with the group level rather than one or more of its sublevels. You can then define individual terms as having relations with terms in sublevels within the group level. This enhances efficiency and functionality by:

• Eliminating unnecessary duplication of terms in more than one level. By enforcing uniqueness of terms throughout the VTC group level in the figure below, for example, you can ensure that no duplicate terms exist between the PN and SYN levels.
• Allowing you to define a Primary Link requirement to the group level as a whole; when you define specific Primary Links for terms from outside the group level to the group level, you can choose to create the Primary Link to a term in any one of the group's sublevels.

For example, you could define WHO-Drug as shown in the figure below, with two group levels, ATC and classification level VTC:

Figure 6-3 Figure 6-3 Goup Levels in a Sample WHO-Drug Dictionary

This definition of WHO-Drug makes use of the Group Level feature as described in the following sections:

• Classifying Verbatim Terms to a Group Level
  
• Requiring a Primary Link to a Group Level
  
• Group Level Constraints
  
• Tree Structure Display of Group Levels
  

Classifying Verbatim Terms to a Group Level

By defining the classification level (the level in which TMS looks for a match to verbatim terms) as a group level, you can include more than one sublevel within the group for TMS to search. This increases the number of terms TMS can search without forcing the same terms to exist on multiple levels, which reduces the size of the dictionary. If you define a group level to be the classification level, you must specify that a term can exist in only one of the group's sublevels at a time. To enforce this structure, choose Level from the Term Uniqueness list when you define the group level.

In the WHO-Drug structure shown above, the classification level is defined as the group level called VTC, which contains as sublevels the Preferred Name level and the Synonym level. When TMS attempts to classify a verbatim term, it searches both sublevels, one after the other. Because TMS searches both levels to find a match, it is not necessary to include every preferred term in the Synonym level because TMS searches both levels to find a match.

Requiring a Primary Link to a Group Level

Grouping the dictionary's higher levels and requiring a Primary Link to the group level enables you to define a Primary Link for a specific term to any one of the group's sublevels. TMS derives the Primary Link term and related terms in any higher levels within the group if the following conditions apply:

• There is a many-to-one or one-to-one relation between each lower and higher level (Single cardinality is required at the higher end).

• The group level and all its sublevels are defined as reportable.

• The relations between the levels are defined as derivable.

Alternatively, you can define a primary path between the group level and a lower level. A primary path enables you to specify which terms to derive for each lower level term from each of the group sublevels (see Primary Links and Primary Path Links).

Note:

In addition, you must create structures in the external system to receive the derived values; in Oracle Clinical you need a question set variable and derived question for each sublevel that might contain the Primary Link term (see Setting Up Data Collection in Oracle Clinical).

Group Level Constraints

TMS enforces the following additional constraints for group levels.

• A level can be linked to a group level or a sublevel within it, but not to both.

• If two group levels are linked, none of the sublevels can be linked directly to sublevels in the other group.

• A group level cannot be a child level because that might cause problems during derivation. However, a group level can be lower in the hierarchy than other levels if the top sublevel (not the group level itself) has the child relation with the parent level.

Tree Structure Display of Group Levels

Group levels do not fit easily into a standard tree structure display. TMS displays them as follows:

• If a group level exists below the top of the hierarchy, its sublevels are displayed twice: once below the group level, which is displayed as a sibling level to the level above (because it cannot be defined as a child level), and once directly under the higher level with the relation between the top sublevel and the higher level displayed.
• The Group Level icon is displayed to the left of the group level.
• The relation icons (lines, dotted lines, and branches) appear in color for all sublevels within a group except the topmost, which by definition cannot have a conventional relation defined to the group level.

This display is for a sample WHO-Drug dictionary as shown in the tree diagram below.

Figure 6-4 Figure 6-4 Sample WHO-Drug Dictionary in the TMS Navigator Tree

Deriving Terms

When TMS successfully maps a verbatim term to a dictionary term, it derives related terms or other user-defined information from the dictionary levels you specify when you set up the derived questions in Oracle Clinical question sets. See Defining Questions. When you use TMS with another external system, you must create the objects to receive the derived values and the mechanism to call for them. If TMS is fully integrated with the external system, it derives the values to the external system on demand.

In MedDRA, for example, you can classify the verbatim term secondary anemia to the classification level term secondary anaemia (LLT). In the dictionary definition, you can specify that the Preferred Term (PT) and System Organ Class (SOC) levels be derivable and reportable. If you have specified that TMS should derive a term, TMS returns the PT level term secondary anaemia and the SOC level term blood and lymphatic system disorders.

See the Oracle Thesaurus Management System Technical Reference Manual for more information on integrating TMS with external systems.

In this section:

• Derivation Path
  
• Setting Up Derivation Within a Dictionary
  

Derivation Path

In the TMS dictionary structure, you must define one and only one derivation path. A derivation path is a series of consecutively related levels defined as derivable that begins at the classification level and includes all levels from which you want to derive terms. There must be one and only one path from the verbatim term level to each derivable level.

Setting Up Derivation Within a Dictionary

Deriving terms from TMS into an external system such as Oracle Clinical requires setup activity in both TMS and the external system.

To set up derivation:

1. Select Report Value? in the Define Dictionary Level window to be able to derive terms from the level you are defining. The Report Value? setting is optionally used by the external system to display the levels available for reporting.
2. Select the Derivable? box in the Define Level Relations window for each level in the path of derivable levels. There must be one and only one pathway to derivable terms in any level from the classification level. All levels you define as reportable must also be derivable, but derivable levels do not necessarily have to be reportable.
3. Create objects to receive the derived values and the mechanism to call for them. This process varies according to the external system and the level of integration. For information on deriving terms for Oracle Clinical, see Integrating TMS with Oracle Clinical. For information on levels of integration, see Getting Started.

Enforcing the Structure

Each time TMS tries to activate a term, it runs several types of validation tests to ensure that the term and its relations conform to the dictionary structure you have defined. During this process, TMS:

• Checks if the term and its relations to terms in other levels do not violate the cardinality and optionality specifications you have defined between levels.

• Runs any additional validation code to enforce further rules and relations (see Step 8, Add Validation Code (Optional)).

• Prevents deletion of terms linked to a verbatim term assignment.

Strong Dictionary Structure in Other Forms

TMS reflects the structure you define in the way it displays the dictionary in the Maintain Repository Data and Browse Repository Data windows. See Using the Tree Structure for details on how TMS reflects dictionary structure in these windows.