Hakuna
  • Version: Snow Owl v2.8
  • Start date: 15 July 2013
  • End date: 23 August 2013
  • Code name / adopted animal: Hakuna, a gorilla at the Budapest Zoo

Import new version of automap file

Import and compare automap file

When importing a new version of a spreadsheet, it can now be compared to a previous version. Changes or new items will be listed in the wizard. The new feature can be invoked by clicking Open import and compare with file dialog in the toolbar of the automap editor.

To start the comparison

  • Select the automap file (version 1) in the Project Explorer, and double-click it to open the automap editor.
  • Click the compare button in the toolbar to invoke the wizard.
  • Select the new version (version 2) of the spreadsheet that you want to import. Click Next.

Selecting a file for comparison

Now you can review a list of differences between the two versions. Select the ones you want to import by checking the boxes, and click Finish.

Compare wizard showing differences between two versions of an automap spreadsheet

The automap file has been updated with the new version. You can see that the newly imported items have not been mapped yet. Save the file, and click automap to map the new items.

Automap file after update

Updating reference sets from automap file

When you made changes to an automap file, for example by importing a newer version of a spreadsheet, you can now easily update the corresponding reference set. During the update new members will be added to the reference set. Members that were removed will be inactivated or deleted (if the reference set hasn’t been published yet). If the label changes (ID remains the same), the old mapping is inactivated (deleted) and a new one is created.

  • Open the updated automap file in the editor. Make sure that you approved the mappings.
  • Click the button in the editor’s toolbar to invoke the wizard
  • Check “Update existing complex type map reference set”
  • Existing reference set description: Select the reference set that you want to update from the drop-down menu.
  • Map target ID column: Make sure this column corresponds with your selection in the previous reference set.

Click OK to start the update.

Updating existing reference set

A dialog informs you about redundant members that were ignored at the update. Click OK to complete the update.

List of redundant members

Value domain improvements

Importing a value domain

From spreadsheet

To import a value domain from a spreadsheet

  • Go to File > Import > Snow Owl > Value Domains from Excel spreadsheet’, click ”Next.
  • Browse for the file you want to import, click Finish to proceed.
  • A warning will inform you that the import will overwrite all existing value domains. Click Yes to start the import.

Importing a value domain from an Excel spreadsheet

From SVS format

Snow Owl now supports importing value domain in the Sharing Value Sets (SVS) format. This allows importing value sets produced by the United States National Library of Medicine’s Value Set Authority Center (VSAC) that make use of the Unified Medical Language System (UMLS). These resources are available at https://vsac.nlm.nih.gov/#download-tab ; please choose the SVS (xml) format for the download.

To import the SVS file in Snow Owl

  • Go to File > Import > Snow Owl > Value Domains from UMLS SVS XML format, click Next.
  • Browse for the file you want to import, click Finish to proceed.
  • A warning will inform you that the import will overwrite all existing value domains. Click Yes to start the import.

Exporting a value domain

To export a value domain to an Excel file

  • Go to File > Export > Snow Owl > Value Domains to Excel file, click Next.
  • Specify the file and name and the location you want to export to, click Finish to complete the export.

Exporting a value domain to an Excel file

Hierarchical display in value domain editor

Members of the Value Domain are displayed in a hierarchy, which is similar to the tree view in the concept navigators. Click on the nodes to expand or collapse the tree. Double-clicking a concept will open the editor.

Terminologies are organized in separate folders, they can be easily distinguished by their icons.

Hierarchical display in value domain editor

Note: The question mark icon represent codes that are not imported (ICD-10CM and ICD-9CM), it’s not possible to open them in the editor.

Organizing value domains in the navigator

Value domains can be organized in folders and subfolders.

  • To create a new top-level folder, use the button in the toolbar.
  • To create a new subfolder, right-click on the parent folder and chose Add new folder from the context menu.

You can also use the context menu to remove and rename folders. If you want to move a value domain simply drag and drop it from one folder to another.

Adding a new subfolder in the value domain navigator

Browsing and searching Value Domains

Value domains are now supported by quick search.

Quick search displaying results in value domains

Value domains can be filtered in the value domain view.

Value domain view with filter search

Value domain search was integrated in the advanced search function. Searches can be performed for code (ID) or label (name).

Value domain search

Results of the query are displayed in the search view.

Search view displaying results of value domain search

Validation rules for value domains

The following validation rules are enforced when creating a new value domain

Name, Version, Definition and Source fields are mandatory

Creating a new value domain

The following items have to be unique

  • Folder names within the same folder
  • Value domain name
  • Value domain members, the same concept cannot be added twice

Message about redundant value domain members

Members pointing to missing concepts are allowed with a warning. A small question mark decorator indicates that these concepts have not been imported.

Decorator indicating missing concepts

Value domain memberships of a code

The membership of a code is now displayed in the Value Set tab of the concept editor.

Value domain membership displayed on Value Sets tab

Local code system improvements

Import local code system

To import a local code system from an Excel file

  • Go to File > Import > Snow Owl > Local Code Systems from Excel file, click Next.
  • Specify the file and name and the location you want to import, click Finish to proceed.
  • A warning will inform you that the import will overwrite all existing local code systems. Click Yes to start the import.

You can review the newly imported Local Code System in the LCS view.

Export local code system

To export a local code system to an Excel file

  • Go to File > Export > Snow Owl > Local Code Systems to Excel file’, click ”Next.
  • Specify the file and name and the location you want to export to, click Finish to complete the export.

The Excel file will be automatically opened. Different code systems are filed in separate worksheets.

Exported Local Code System in Excel

Validation rules for Local Code Systems

The following validation rules are enforced when creating a local code system. Hovering over the red x icon will reveal more information about the error.

  • Name, short name, Code System OID, Code System Version fields are mandatory.
  • Code system OIDs are globally unique
  • Code system short name is globally unique

Validation for unique OID

The following validation rules are enforced when creating a local code

  • Code and term are mandatory
  • Code and term are unique within the same terminology
  • Alternative terms and main terms are unique

Validation for unique Term

Universal restrictions on the concept overview page

We now indicate that a relationship is a universal restriction directly on the concept overview page. This helps distinguish cases where a concept contains both existential and universal restrictions on the same relationship, as is common in pharmaceutical products that (e.g.) differentiate between products containing only paracetamol from those containing paracetamol and codeine.

Universal restriction

Managing publications: Update effective date on concepts and reference set members

Previously publication dates could only be assigned when a full publication was created (RF2 full export). Now, you can assign effective dates to unpublished components at the reference set publication as well (both during RF1/RF2 and spreadsheet export). The publication dates also apply for referenced components that are unpublished, so not only the reference set member is published, but also the referenced concept.

To export a reference set

  • Open the reference set and click the export button, and select Export reference set delimiter separated values format
  • Select the components you want to export.
  • Specify file path, delimiter, and the publication date (target effective time).

Specifying the publication date

You can now review the unpublished components, which will be exported and assigned the effective date. The update will affect the reference set concept itself, the reference set membership, and also the effective date of unpublished concepts. This means, if an unpublished concept is a member of the reference set, not only the date of the reference set membership will change but also its publication status. Concepts that were already published will keep their original publication date, only the reference set membership date will be updated.

Click Next to start the export.

Unpublished components

After the export, you can choose to update the concepts and the reference set with the effective date. This will update all components to the date you set as target time. If you don’t check the box, the components will not be updated, and there will be no changes to the effective time of the concepts and the reference set: They will remain unpublished.

Updating the effective date

If you open the reference set concept, you can see that the effective time changed from Unpublished to the date you set as target time. The effective time of the reference set membership can be reviewed by hovering over the members in the reference set editor.

Effective date after export

Collaborative Authoring: Value domain authoring

Snow Owl now supports creating value domain authoring tasks. To invoke the task wizard, click the button in the Task view. Alternatively you can use the main menu: File > New > Snow Owl > New Task.

Select “Value domain authoring” as the artifact type. Hit Next to continue.

Specifying a new value domain authoring task

Now specify if you want to create a new value domain, or modify an existing one.

If you chose to create a new value domain, you have to specify the Value domain display name. A new value domain will be created upon task activation. It will be visible in the value domain view when working on the branch, which means after the task has been activated.

Creating a new value domain in Task Wizard

If you chose to modify an existing value domain, you have to specify the value domain you want to work on. Enter the name of your value domain, the quick search function will automatically come up and display matching value domains.

Selecting an existing value domain from quick search