Fülike
  • Version: Snow Owl v3.0
  • Start date: 30 September 2013
  • End date: 08 November 2013
  • Code name / adopted animal: Fülike, an aardvark at the Budapest Zoo

Module dependency

Snow Owl now supports the import, automatic update and publication of the IHTSDO module dependency reference set. Validating for missing module dependencies have never been so easy!

Validate dependencies based on module dependency refset during import

When importing new components into the tool, Snow Owl validates if all the module dependencies are satisfied. This way, invalid import attempts can be detected and fixed easily.

Update module dependency refset when modules are updated

When creating a new module, the module dependency reference set is automatically updated. The new module will surely have dependencies for the IHTSDO model component module, as the model components are required for the concept definition. Additional dependencies are calculated based on the components created under this module.

Dependencies calculated for a new module

Module dependencies are not manually editable. The module dependency reference set is a structural reference set, that is updated behind the scenes.

Structural reference sets

Export module dependency refset

When selecting a particular module to export, the export wizard now supports the addition of the dependent modules. By adding the dependencies the export output will be universally valid, and can be used in other systems.

Adding the required dependencies to the export file

Mapping sets

Mapping set export

It’s now possible to export a mapping set as an Excel file. Go to File > Export > Snow Owl > Mapping sets to Excel file, click Next.

Exporting mapping sets as Excel file

Specify the file path, and the publication date, click Next to start the export.

Specifying publication date

After the export, you can choose to update the mapping set with the effective date. This will update all unpublished mappings to the date you set as target time. If you don’t check the box, the mappings will not be updated, they will remain unpublished.

Updating the effective date

Mapping set editor preferences

It is now possible to select the desired columns of the Mapping set editor’s table. The preferences can be access from the standard Snow Owl Preferencessupport, or from the mapping set editor by right-clicking on the table header. Note: after setting the preferences, the editor needs to be reopened to take effect.

Table preferences

Collaborative authoring for mapping sets

Snow Owl now supports mapping set authoring. The following use case, describes mapping set authoring with one author and one reviewer.

Creating a task for mapping set authoring

To invoke the task wizard, click the button NewTaskWizard.png in the Task view. On the first page of the wizard you are prompted to select

  • Repository: Select a repository from the drop-down editor. If you have not set up a repository, this function will be disabled.
  • Product: Chose a product from the drop-down menu.
  • Artifact Type: Select Mapping set authoring
  • Task Name: Enter a name for the task here. It will be used in the task view and in the title of the editor.

Hit Next to continue.

Creating a mapping set authoring task

On the next page, you can either modify an existing mapping set or create a new one. If you want to modify an existing value domain, select this option and enter the name of the value domain. For the new mapping set you have to specify the following mandatory text fields:

  • Name: Enter the name of the mapping set.
  • Definition: Enter a definition of the mapping set.
  • Purpose: Enter information about the objective here.
  • Version: Enter a version number.
  • Source: Enter the name of the source (e.g. your organisation).
  • Existing folders: This shows the MS existing folders. If you want the new MS to be located in this folder, you can select the destination folder here.

Specifying the mapping set

Select a scenario, specify the team members that will be working on the task, and add a task summary. Click Finish to complete the task generation.

Specifying team members for mapping set task

Working on a task

When activating the task, a mapping set will be automatically generated for your branch. Open the mapping set, add members, and save. You can review the mappings on the context page of the task editor. Once you are done working, synchronize, set task status to RESOLVED AS FIXED, and submit. This will hand the task over to the reviewer.

Reviewing mappings on the context tab

Reviewing and promoting changes

To accept or deny a mapping, click on the respective cell in the table. Only mappings that were accepted will be submitted for promotion. Members that were denied or not reviewed will be excluded. It’s also possible to write a comment, e.g. reason for denial, suggestion for different mapping.

Once the review is completed, make sure you save your review, set the status to Mark as VERIFIED, and submit. The status will change from RESOLVED to VERIFIED.

If you are not happy with the work performed, the task can be reopened and handed back to the author. Alternatively, a different author can be assigned by entering the user name of a new team member in the People section. The status will change from RESOLVED to REOPENED.

After a task reached the VERIFIED state it is ready to be promoted and committed into the main repository.

Go to the context page of the editor, and click Promote changeset . If it is disabled that means that the task has not been reviewed and verified, or that there were changes on the main repository that aren’t reflected on the task and you need to synchronize first.

After a successful promotion the status of the task changes from VERIFIED to CLOSED, the task is automatically inactivated. The new mapping set is added to the main repository.

Value Domains

Exporting value domains in SVS

Value domains can now be exported in Sharing Value Sets (SVS) format. This allows exporting value sets that make use of the Unified Medical Language System (UMLS).

  • Go to File > Export > Snow Owl > Value domains to UMLS SVS XML file, click Next.
  • Specify the file path, and the publication date, click Next to start the export.
  • After the export, you can choose to update the value domain and the value domain members with the effective date. This will update all value domain members with the date you set as target time. If you don’t check the box, the value domain and its members will remain unpublished.

Updating the effective date

Local code systems

Adding members from context menu

The context menu of the local code systems view now allows to add codes to an active value domain. The function is similar to adding concepts to a reference set. You can either add only the selected code to a value domain, or the selected code and its descendants.

Adding codes to a value domain

Search for alternative terms

Filter search, quick search and advances search now considers alternative terms.

Advanced search for alternative terms in LCS

Validation rules

The deletion of local code systems or codes is not allowed when they are are referenced in Value Domains or Mapping Sets.

Validation for referenced components

Export/Import enhancements

Setting the effective time

After export, you can choose to update the effective date for the exported artefacts. This will update all unpublished artefacts to the date you set as target time. If you don’t check the box, the effective time will not be updated.

Metadata support

Support for importing and exporting metadata has been added to Local code sets, Value domains and Mapping sets. Metadata will be exported as additional rows under the mandatory properties in a format similar to mandatory properties as property/value pairs in the consecutive cells. In case of multiple keywords, multiple rows with the same property but different values are exported. In case of the import, the Source organisation field in Snow Owl will be automatically set to MOHH and the id is automatically generated.

Support for incremental import

The import for value domains, mapping sets and local code systems now allows to merge the content of the import file with the existing database. During the import, the existing data is compared to the content of the import file, so that only new components are added to the database. No merge is performed at the property level.

Local code systems

To import local code systems to an existing database

  • Go to File > Import > Local Code System from Excel file. Next.
  • Select your import file and check Merge components into existing database. Finish.

Merging imported components with existing database

The import wizard now summarises the imported content. A small blue plus decorator indicates that a component was added. The screenshot shows different local codes that were added as well as the local code system. When clicking on a component, the details are displayed in the bottom section (e.g. imported metadata of the local code system). The icons indicate the type of component (e.g. for metadata). The middle section contains details about the import (e.g. time, user name, date, file name).

Summary of imported content

When selecting the “Merging imported components with existing database” option, the following merge strategy is applied:

  • When a new local code set has been encountered -> the local code set is imported
  • When an existing local code set set is encountered (same Code System ID OR same Short name)
    • When an local code is encountered (same ID) -> it is skipped
    • When a new local code is encountered (different ID) -> local code is added to the existing local code system

Note: No merge is performed at the property level.

Value Domains

To import value domains into an existing database

  • Go to File > Import > Value Domains from Excel spreadsheet. Next.
  • Select your import file and check Merge components into existing database. Finish.

Merging imported components with existing database

The import wizard displays the imported content. Click on a component to see details in the bottom part. In the screenshot, you can see that a value domain (Occupation) was added. The bottom section displays different value domain members that were added as well as the meta data of the value domain. A small blue plus decorator indicates that a component was added. The icon indicates the type of component (e.g. for value domain members). The middle section contains details about the import (e.g. user name, date, file name).

Summary of imported value domain content

When selecting the “Merging imported components with existing database” option, the following merge strategy is applied:

  • When a new value domain has been encountered -> the new value domain is imported
  • When an existing value domain is encountered (same name)
    • When an existing member is encountered -> it is skipped
    • When a new member is encountered -> it is added to the existing value domain

Note: No merge is performed at the property level.

Mapping Sets

To import mapping sets into an existing database

  • Go to File > Import > Mapping Sets from Excel spreadsheet. Next.
  • Select your import file and check Merge components into existing database. Finish.

Merging imported mapping set components with existing database

The import wizard displays the imported content. Click on a component to see details in the bottom part. In the screenshot, you can see that two mapping sets were added. The bottom section displays different mappings as well as the metadata of the selected mapping set. For mappings, the source member is displayed in the “Changes” column. A small blue plus decorator indicates that a component was added. The middle section contains details about the import (e.g. user name, date, file name).

Summary of imported mapping set content

When selecting the “Merging imported components with existing database” option, the following merge strategy is applied:

  • When a new mapping set has been encountered -> the new mapping set is imported
  • When an existing mapping set is encountered (same name)
    • When an existing mapping is encountered (same source member) -> it is skipped
    • When a new mapping is encountered (different source member) -> mapping is added to the existing mapping set

Note: No merge is performed at the property level.