4. Concept Editor

Content of this section

The authoring tools allows browsing the terminology and performing unstructured edits. The Concept Editor will show two main panels that are described in the following sections.

4.1 Left Panel

4.1.1 Taxonomy tab

This tab shows SNOMED CT’s taxonomy view. Free browsing through parent-child hierarchies is allowed by clicking when clicking ‘greater than’ icon. Clicking on any concept will select it on the right panel. Also, selecting any orange circle in the taxonomy and dragging it into the right panel (concept area will become yellow when dragging a concept into it) will display it in the right panel.

4.1.1.1 Selecting concepts in the Taxonomy

Step-by-step guide

1. Click a concept text in the taxonomy view to display it on the right panel

Otherwise:

1. Click the orange circle in the taxonomy view
2. Drag it into the right panel until the description field turns yellow

4.1.2 Search tab

This tab allows searching terms containing specific words or parts of words. Search results may be exported to the briefcase.

Search modes

There are three search modes available:

1. Search mode by full text match: Terms that exactly match the search string are retrieved (e.g. the search string ‘appendic’ will retrieve all the descriptions that contain the search string only)
2. Partial matching search mode: Only terms that match the search string within any term are retrieved (e.g. the search string ‘append’ will retrieve all the descriptions that contain appendicitis, appendix, appendage, etc.)
3. Regular expressions search mode: regular terms are used for searching.

Grouping by concept will show the most exact match with the search string, i.e, only one description for each match; otherwise, all the descriptions for a given match are shown, which may result in extensive lists of matches.

Also, matches may be grouped by semantic tag, to show only concepts of the same hierarchy, by language to select descriptions in a given language, by module and/or by refset to improve search specificity.

4.1.2.1 Using search filters

To select search by semantic tag, click the link disorder in the Semantic Tag section of the Search tab. Only disorders with the search terms will be automatically displayed.

4.1.3 Favorites tab

The Favorites list is useful, for example, when there is a need for comparing concepts. 

 In the Concept Details panel, on the right, the Concept Summary tab shows a star. When it is selected, the concept is automatically added to the Favorites tab on the left. The list of favorites is Specific for each browser.

Step-by-step guide

1. Click the star in the concept details panel on the right. The concept will be automatically added to the Favorites list.
2. Click the delete icon besides the concept id to remove a concept from the list
3. Open Export results menu to select a destination (the briefcase or an Excel file.

4.1.4. Activities tab

This tab shows a list of changes done by concept, concept ID, author and time. List members may be ordered alphabetically or chronologically. Specific concepts may be retrieved using the filter option. Complete or partial words may be used for searching in the Activities tab.

4.1.4.1         Ordering activities 

Step-by-step guide

1. Click Order icon in Term cell to order activities alphabetically:

2. Click Order icon in Time cell to order activities chronologically:

3. Write a search term in the Filter window to retrieve text matches:

4.1.5 Concept walker tab

This tab is identical to the Summary tab on the right. It may be used for concept comparisons (e.g. comparing relationships, supertypes, etc.).

Step-by-step guide

1. Select or search for a concept in the Taxonomy tab or in the Search tab
2. Open the Walker tab, click the orange circle in the Concept Details tab and drag the selected concept  into the concept walker text (the area should turn into yellow)

3. Repeat step 1 and select another concept.

4. Open the Walker again. Both concepts are displayed

4.1.6 Classifier tab

Terminology classification is defined as a process that generates a logically consistent subtype classification by applying description logics rules to the stated definitions of a set of concepts. The stated view of a concept definition consists of the relationships directly edited by terminology authors. It consists of the stated subtype relationships plus the defining relationships that exist prior to running a description logic classifier. When classification is applied, inferences are derived by applying a consistent set of logical rules to the definition taking account of the definitions of related concepts. The result is the inferred view.

The classifier is a software tool that applies description logics rules to a set of data to make inferences about the relationships between sets of concepts.

4.1.6.1  Classifying the terminology

Step-by-step guide

1. In the Concept Editor, click Classifier to see previous classifier runs, specifying path name, request time, start time, as well as run duration and status
2. Press Schedule a run to run a new classification.

3. Click more info to see total numbers and lists of new and inactivated 'Is_a', new and inactivated attribute relationships, cycles and equivalent concepts, which are displayed in a modal window.

4. Click Show New 'IS_A' to see new supertype-subtype relationships (idem for 'Inactivated IS_A', 'New attributes', 'Inactivated attributes', 'Cycles detected', and ' Equivalents detected'.

5. Click Show Log to display any messages generated during classification.

4.2 Right panel

This panel contains two tabs for editing functions: Concept Details – for existing concepts – and New Concept, used for creating new concepts. Concept Details tab, in turn, contains ten tabs for editing functions, which will be explained separately.

Concept details bar

This bar is visible with any tab selected and consists in the following:

Eye icon – Shows a list of logged authors when two or more authors are editing the same concept. Also, offers a chat option to interchange messages.

Clock icon – The clock will open the history of concepts selected in the current session.

Refresh icon – Will refresh any open tab 

Options icon will open a modal window displaying different parameters for visualizing concept components that may be selected by the user

4.2.1 Summary tab

Concept details panel opens with the Summary tab, which shows the selected concept with its descriptions and concept ID, its parents and children. Also, any attribute relationships are shown in the light blue box besides the concept. The number of children is shown in brackets, but the list of subtypes (if any) is shown by clicking on Children. Also, clicking on greater than symbols will display the hierarchy. Visualizing stated or inferred views may also be chosen in this tab.

A selected concept may be replaced by one of its children (or parents) by dragging the orange circle from a concept in the hierarchy to the selected concept (the area will turn yellow when the concept is changed). Likewise, parent concepts may also be dragged in the same way into the selection area.

Clicking the star will include the concept in the Favorites list table (see 2.1.3 Favorites tab)

Copy icon enables smart copying. Any selected options will be copied to the clipboard and pasted into other applications.

4.2.2 Details tab

This tab shows the concept with its concept ID, definition status, descriptions with their acceptabilities in the selected language refset and relationships. In this tab concept edition can take place, mainly with two buttons: Edit concept and Clone concept.

Clicking Edit concept button will show the available editing options for existing concepts: selecting any of the listed links will enable creating a new Fully Specified Name (FSN), synonym(s), text definitions or relationships (both IS_As and attribute relationships). Also, a concept may be inactivated from here.

Clone concept will create a new identical concept that can.be further refined. This tool is mainly mainly used for authoring purposes when creating new concepts to ensure that subtypes share defining relationships with their supertypes.

4.2.3 New concept

This tab allows creating new concepts. It is worth mentioning that with this tool only IS_A relationships are created an id used for placing the new concept in a SNOMED CT hierarchy. The creation of synonyms, text definitions and attribute relationships are further described in the following sections.

4.2.3.1  Creating new concepts - Step-by-step guide

1. Type a text for the FSN (it is not necessary to write the semantic tag). A synonym identical to the FSN will be automatically created.
2. Drag a parent concept from the taxonomy or from the Search tab. This will automatically create a semantic tag in the new concept. More than one parent concept can be dragged into the field.

3. Click Create concept. The result is shown in the taxonomy with the flag of the extension that is creating the new concept. A FSN-like synonym without the semantic tag will be automatically created, with ‘Preferred’ acceptability. IS_A relationships are generated in this way and the new concepts are placed under their parent concepts.

4.2.4 Designation

This tab is used for editing descriptions, either fully specified names, synonyms or text definitions. All descriptions of a given concept are shown, i.e. in the local language refset, the EN-US language refset, as well as descriptions not belonging to any of them and retired descriptions. New descriptions may be added and descriptions from user's own language refset may be changed (acceptability, case sensitivity) or retired. Also, descriptions from other language refsets may be changed to acceptable in the user's language refset.

Synonyms, Fully Specified Names and Text definitions may be created by selecting one of these options from Add menu.

An empty field for free text writing is created upon selecting any of these options.

4.2.4.1 Creating synonyms and test definitions - Step-by-step guide

1. Write a description text
2. Click the green checkmark. An asterisk remains after clicking the green checkmark. This means that the description has not been saved yet.
3. Click Save changes to save the new description/text definition and display it in the user’s language refset, where it belongs.
4. The blue button on the right will offer additional options (i.e. to inactivate a description, to change the text of an unpublished description, and/or its case sensitivity and acceptability).

5. Select Inactivate option: The description is removed upon saving and shown in red under Inactive descriptions.

 6. Select Change text option: Only unpublished descriptions can be changed. Already published descriptions must be inactivated to be removed. However, only descriptions of the own extension can be inactivated/changed. Descriptions from core concepts cannot be changed. Only their acceptability for the user’s language may be modified (from preferred to acceptable and vice versa)

7. Select Not Acceptable option. The description is removed from the user’s language refset and is shown as an active description that is not acceptable for the user’s language refset.

Context descriptions (eg. to be used by medical specialties or "patient friendly" terminologies) can also be created. See Creating synonyms for specific uses.

4.2.5 Definition tab

Each concept in SNOMED CT is logically defined through its relationships to other concepts. Every active SNOMED CT concept (except the SNOMED CT root concept) has at least one | is a | relationship to a supertype concept. | Is a | relationships and defining attribute relationships are known as the defining characteristics of SNOMED CT concepts. They are considered defining because they are used to logically represent a concept by establishing its relationships with other concepts. This is accomplished by establishing | Is a | relationships with one or more defining concepts (called supertypes) and modeling the difference with those supertypes through defining attributes.

This tab is used for editing relationships, either supertype-subtype relationships and attribute relationships upon selecting an option from Add menu:

This tab shows inheritable relationships, i.e. the relationships that the concept inherited from its supertype(s) which can be further refined to more specific ones.

4.2.5.1 Creating new attribute relationships - Step-by-step guide

1. Select Add supertype to select a new parent concept. A modal window is opened displaying the taxonomy. Otherwise, a customized search may be done. The new parent will be created upon selecting a parent concept.

2. Select Add attribute to open a modal window where the allowed attributes are displayed.

3. Click Select to display the allowed values for the selected attribute.

4. An asterisk remains after adding an attribute. This means that the relationship has not been saved yet. Click Save changes to save the new relationship.

Also, in order to prevent cross-overs, a useful option is provided:

5. In Inheritable relationships click the arrow on the left to copy the existing descriptions to the new concept. The copied relationships will be shown as attributes of the new concept.

6. The blue button on the right will offer additional options (i.e. to inactivate a relationship, to change the type of an unpublished description or its destination, to refine destination, to group / ungroup a relationship or to inactivate a whole relationship group).

7. Selecting Refine destination will open a modal window where the available refinability options (if any) are shown. Search option is enabled to perform a customized search, too.

An asterisk remains after selecting refinability options. This means that the relationship has not been saved yet.

8. Press Save changes.

9. Select Group to create a relationship group (the selected relationship will remain with a yellow background, while other relationships will be highlighted with a yellow background.

10. Click on a highlighted relationship to group it with the selected one.

11. Finally, select Logical definition menu to change from Primitive to Sufficiently defined if defining characteristics are sufficient to define the concept relative to its immediate supertype(s).

4.2.6 Diagram tab

This tab shows a standardized representation of concept definitions in accordance with SNOMED CT Diagramming Standard. This consists of:

• the concept whose definition is being shown at the top left
• connected to a series of one or more relatinal operators to an expression

Diagram elements

Concepts: Concepts are represented by a rectangle containing concept name.

 represents primitive concepts  

 represents suficiently defined concepts
 

Relationships or attributes are represented using a rectangle with rounded ends and a double line border:

Is_a  (subtype) relationships are represented with an open-headed arrow:

Equivalent to:

Attribute groups are represented with a circle:

A conjunction is represented with a black “dot” (black filled small circle). It is only
necessary when two or more attributes are being joined in a diagram. It is optional when
attaching a single attribute:

An arrow is used to connect related elements where the connection is unidirectional. Connecting arrows always have an arrow head at one end, and therefore have an explicit direction from one element to another the direction the diagram should be read:

A line is used to connect elements in the diagram where the connection is bi-directional:

According to this diagramming standard, a complete concept definition is represented as:

4.2.7 Expressions tab

SNOMED CT expressions are a structured combination of one or more concept identifiers used to express an instance of a clinical idea. A single concept value is the simplest type of expression, which is referred to as a precoordinated expression.

Notations used in this tab:

Sufficiently defined concept

Primitive concept

4.2.8 Refsets tab

This tab lists refset(s) to which a concept belongs and its value(s).

4.2.9 Members tab

This tab shows a list of refset members. The selected concept should be a subtype of 900000000000455006| Reference set (foundation metadata concept) |

4.2.10 References tab

This tab shows a list of how many times a given concept is referenced, either in super type/subtype (IS_As) or attribute relationships. In the example, concept 54944003 |Dural sinus (body structure)| is referenced as:

• The parent of 4 concepts (i.e. it is linked to four children concepts by IS_A relationships)
• The finding site value of 2 concepts
• The procedure site – direct value of 14 concepts, and
• The procedure site – indirect of 9 concepts

Clicking Greater than symbols will display the list of concepts referencing the selected concept.

4.2.11 History tab

The upper part of this screen shows the Paths used for development. The path in use  shows the component versions:

The lower part shows the path in use displaying the changes done with change dates and times and an explanation of differences from previous versions.

Clicking on Timeline button will open a modal window displaying the changes done,which can be individually selected  and showing detailed views of every change done. The user may also choose to roll back to a previous version.

Clicking on Graph button will download the history of ordered versions:

4.2.12 Graph tab

Displays a graphic view of the concept with its primitive ancestors following SNOMED CT's Diagramming Standard. When Inheritance is selected, attribute relationships are displayed in different colors. This helps to identify where do inherited attribute relationships come from. In the example shown below, notice that the green attribute relationship |Occurrence (attribute)| in |Respiratory condition of fetus OR newborn (disorder)| is inherited from the ancestor |Disorder of fetus or newborn (disorder)|. This view is especially useful for identifying crossovers.

4.3. Inactivating concepts

Only concepts of the own language refset can be inactivated, i.e. someone working with the Denmark extension cannot inactivate a concept from the International Edition or from the Spanish extension. Therefore, the option Inactivate concept is shown for concepts of the own extension only.

Step-by-step guide

1. In the Concept Details panel, click Edit concept
2. Click Inactivate concept to open the inactivation interface
3. Select a reason for inactivating the concept in the drop-down (if no reason is selected, Reason not stated will be specified by default and no further actions are required).

4. After selecting “Ambiguous component” as reason for inactivation:

1. 1. Drag an equivalent concept into the association field:

5. After selecting “Component moved elsewhere” option:

a. Drag an extension namespace concept into the association field:

6. After selecting “Duplicate component” option:

a. Drag the duplicate active concept into the association field:

7. After selecting “Erroneous / Outdated component” option:

a. Drag the former proximal supertype into the ‘WAS A’ association field.

b. Drag the active replacement component into the ‘REPLACED BY’ association field.

8. After selecting “Limited component” option:

a. Drag the former proximal supertype into the ‘WAS A’ association field.

9. Click Inactivate.

4.4 Reactivating concepts

Only concepts of the own language refset can be reactivated, i.e. someone working with the Denmark extension cannot reactivate a concept from the International Edition or from the Spanish extension. Therefore, the option Activate concept is shown for concepts of the own extension only.

Step-by-step guide

1. In the Concept Details panel, click Edit concept
2. Click Activate concept to open the inactivation interface
3. Drop a concept from the taxonomy view into the field to create concept parents (inactive concepts do not have parents)

4. Press Reactivate concept to show the concept in the taxonomy again:

4.5 Changing concept relationships

Both the type and the target of unpublished relationships may be changed. This action is allowed for relationships of user’s own extension. Concepts from the International edition cannot be changed; therefore, their relationships cannot be edited.

Step-by-step guide

1. In the Concept Details panel, click Edit concept.
2. Click Activate concept to open the inactivation interface
3. In the Details tab, click the pencil on the right to open the interface that allows changing the attribute and the value of an existing relationship.
4. Open Type drop-down menu to see the allowed attributes

5. Click Select target to display the list of allowed target concepts.  Alternatively, a desired concept of the allowed range may be searched.

6. Click Select

7.  Select the Green checkmark to accept changes.

8. Click Save, otherwise any changes will be lost.

4.5.1 Inactivating relationships - Step-by step guide

Active relationships in the user’s extension may be inactivated and replaced by others. This action is only allowed for users own extensions. Concepts from the International Edition cannot be changed and therefore, their relationships cannot be edited.

1. Select a concept from your extension. In the Concept Editor, press Edit concept 
2. Click a relationship’s pencil icon to edit it.

3. Turn relationship Status from Active into Inactive.

4. Select the Green Checkmark to accept the new status.

 5. Click Save, otherwise Status will not change.

4.6 Adapting concepts of the International Edition to local use (localization)

There are cases where a concept has a description with preferred acceptability in one language refset and another description that is acceptable. However, these acceptabilities may not be suitable for other users. Therefore, acceptabilities may be changed in the local extension but linking the descriptions used in the source language:

Example: 58377000 has a description |Trash| with preferred acceptability and |Garbage| as an acceptable synonym in the International Edition.

In the example shown there are no descriptions for STID 58377000 in language refset SD. Therefore, they should be linked from source language and acceptability assigned accordingly:

1. Click Link from source to open drop-down displaying all existing descriptions for a given concept.

2. Select a description to open a modal window to specify acceptability.

3. Click Add to language refset with the desired acceptability.