Editing SNOMED CT content

If you want to expand the ontology, you can add a new concept that represents an entirely new clinical meaning, or refines the meaning of an existing concept with new descriptions or relationships. You are only allowed to edit a concept's core properties like status and definition status, its descriptions and source relationships. Destination relationships and reference set memberships are read only; you can use the reference set editors to add and remove reference set members. Editing is strongly limited for released components; the limitations will be described in more detail in the rest of this section.

Creating a new concept

Snow Owl provides full support for a concept model, which dramatically simplifies editing. When creating a new concept the valid relationships and description types for the concept are displayed in a form editor, so you simply have to enter any missing information.

Modeling method

Snow Owl enables selecting the preferred modeling method by using either the proximal parent, or the proximal primitive supertype for concept authoring.

Proximal primitive parent model selects the closest primitive parent (or parents) in the hierarchy to the concept being modeled. By using this modeling method, inferred attributes from the selected concept are automatically added to the new concept as stated attributes. After running the classifier, more accurate inferred parents will be indentified. This method is recommended by the IHTSDO, as it reduces the maintenance of parent relationships and increases the accuracy and breadth of supertypes and subtypes.

The other modeling method is Proximal parent (or parents) - here the direct parent is used, regardless of its definition status. Attributes are not copied over to the new concept, as the classifier will inherit them as needed.

Both modeling options are available when creating a new child or sibling concept. After selecting the modeling option and finishing the wizard, the new concept's editor is shown to allow modifications to the descriptions and attributes.

Choosing between proximal and proximal primitive parents in the new child concept wizard

Choosing between proximal and proximal primitive parents in the new sibling concept wizard

Creating a child concept

Before starting to model the new meaning, you need to decide where you want to place it in the hierarchy. Once you have established that, you can start creating the new concept directly from the SNOMED CT Concepts view.

SNOMED CT view context menu

Right-click on the desired parent concept and selecting Add new child concept. An editor for the new concept is opened after selecting the Modeling method. This action creates a child of the selected concept with identical SNOMED CT descriptions. This way, only differing information has to be entered in the editor. For the new concept, an IS A relationship to the parent concept is generated as well as unique concept ID. A warning message on the top of the editor informs you that the fully specified name is not unique.

Setting the editor to display the stated relationships and enable modeling

[[Image:ChildConcept.png|thumb|none|700px|SNOMED CT child concept of ' Body structure with identical descriptions]]

Enter a unique fully specified name and preferred term for the new concept. Hit Save, and enter a commit comment.

Entering unique fully specified name and preferred term

The new concept now appears in the SNOMED CT view. If you have not classified your newly added concept, it will only be visible in the stated form of the concept tree. You can toggle between the stated and the inferred view with the Authoring toggle button in the application toolbar.

SNOMED CT concept view with newly created child concept

Creating a sibling concept

Adding a sibling is similar to the process of creating a child concept described in the section above. Right-click on the desired sibling concept and selecting Add new sibling concept. This action will create a new concept after selecting the Modeling method as a sibling of the selected concept. The descriptions and properties will be copied from the selected concept to the new sibling concept. An IS A relationship to the parent concept is generated as well as unique concept ID.

Editing an existing concept

Adding a synonym

As an example for editing a concept, we will change the description of a concept by adding a synonym.

Click the add description icon to create new entry boxes in the description section. A small asterisk * next to the editor's title indicates that you have unsaved changes. An informational message appears at the top of the editor box (here: Concept contains unpublished changes), a small information symbol is also added to the top-level concept icon.

Text boxes for adding a description type and a description term

Type your description type (e.g. Synonym) in the text box on the left, and your new description term (e.g. Hantavirus) in the text box to the right. The autocomplete function described in the quick search section is also available.

Click the save button in the main toolbar to submit your changes the repository. Before the changes are saved, a dialog box will appear in which you may enter a comment describing your change.

Dialog for entering a commit comment

Once the changes have been saved, the new description appears in the editor. The box around the description term (here: Hantavirus) indicates an unpublished change. This means that the change has been saved in the repository but not been formally published yet. Once a concept has been published, only the text appears.

Box around new description term indicates unpublished change

Error, warning, and informational messages are displayed at the top of the concept editor. You can click on one of the messages to jump to this point in the concept editor.

Error message display

Changing the preferred term

The preferred term of a concept is indicated by a rosette icon .

As an example, we want to change the preferred term from Calcific tendinitis of shoulder to Milwaukee shoulder.

Preferred term indicated by rosette icon

Setting new preferred term

Preferred term indicated by rosette icon

Adding a relationship

You can add new relationships on the Overview page or on the Source relationships page. When creating a new relationship an identifier is automatically generated; it conforms to IHTSDO rules and uses the namespace configured in the application preferences. The source of the relationship is the concept that you are currently editing. Relationship type and target concepts can be selected by using the search dialog. The Source relationships page is advisable for more advanced users.

Adding a relationship on the Overview page

Relationship types that are conform with the concept model are automatically displayed in the Properties section of the Overview page. The value entry fields are empty.

Editor displaying relationships that conform with the MRCM

To define a relationship,

List of valid relationship values that conform with the MRCM

It is also possible to add a relationship that is not conform with the concept model.

The new relationship is now displayed on the Overview page and also on the Source relationship page. Please note that the values for Characteristic type, Union, Union group, Modifier, and Relationship negated are automatically set. You can see them if you hover over the relationship value. If you want to modify these settings, go to the Source relationship page of the editor.

Quick search displaying valid values for relationship type

Adding a relationship on the source relationship page

Defining relationships on the the Source relationship page is advisable for more advanced users with specific requirements since the New SNOMED CT relationship wizard allows defining any kind of relationship and modifying its settings. The values for Characteristic type, Union, Union group, Modifier, and Relationship negated can be manually modified.

To add a new relationship from the Source relationship page you need to bring up the New SNOMED CT relationship wizard.

New SNOMED CT Relationship wizard

The new relationship is now displayed in the table of the Source relationship page and also on the Overview page.

New SNOMED CT Relationship wizard on source relationships page

Adding descriptions

Descriptions can be added from the Overview page as described in the section about adding a synonym or alternatively from the Descriptions page.

New SNOMED CT Description wizard

The new description is now displayed in the table of the Description page and also in the Descriptions section of the Overview page.

Descriptions page with new SNOMED CT description

Removing components

There are two options for removing newly added components: Inactivation or deletion.

Inactivating a concept

You can inactivate a concept from the SNOMED CT view or directly in the editor

Inactivating a concept in editor

The inactivation plan shows which components will be affected by the inactivation. You can also specify the reason for inactivation (e.g. moved to) and a target component (e.g. the concept that the inactivated concept was replaced by).

Inactivation plan

If you return to the concept in the concept editor, you will see that the status has been changed to inactive and the effective time set to unpublished. The inactivity status and retirement target details were also updated.

Inactivated concept

Inactive concepts are not present in the SNOMED CT view or in the quick search. To find an inactive concept you need to use the advanced search dialog and open the concept editor from the search results.

Advanced search for inactive concept

Deleting a concept

Unpublished concepts can be deleted from the SNOMED CT view or from the editor.

Review the deletion plan and click finish to delete the concept.

Deletion plan dialog

In case you are trying to delete a published concept, a message will inform you that the requested component can not be deleted.

Published concepts can not be deleted only inactivated


Creating a concept from post-coordinated expression

Snow Owl supports the creation of post-coordinated expressions using the SNOMED CT compositional grammar. The expression authoring is similar to the Extended SNOMED CT Compositional Grammas expression authoring. To create a concept from a post-coordinated expression

Post-coordinated expression in editor

Click Create Concept from SCG expression button. The post-coordinated expression is now added as a pre-coordinated concept to SNOMED CT. You can see the editor for the new concept.

Post-coordinated concept in editor

Enter the Fully specified name and the Preferred term in the editor; all the other properties for the concept and its descriptions and relationships are set to default values. Save your work.

Generate normal form

Snow Owl supports decomposing a terminology concept or a post-coordinated expression into its normal form based on the rules provided by IHTSDO.

Concept in expression editor

You can see the normal form now in the expression editor.

Concept in its normal form

Test subsumption

Two selected post-coordinated expression can be tested to check whether one subsumes the other or they are equivalent with each other. Equivalence can occur if the expressions are in different state of decomposition. To start the subsumption test

The test result is displayed in the dialog.

Subsumption test dialog