Concept Management Apps

Concept Management Apps

Intern: Jenn Parise

Mentor: Darius Jazayeri

Link to the Concept Management Apps Wiki

Concept Management Apps

What we accomplished

First phase (100% Complete): Help implementors map their OpenMRS dictionaries to the SNOMED concept terminology (Deals with information that exists in OpenMRS now or that is user supplied information)

Second phase (100% Complete): Import the SNOMED concept terminology from the official release (Gets new data from SNOMED)

Third phase (90% Complete*): Give users new tools to browse the data from phase one and two, create a browser to view hierarchies

*On the third phase we have created a tool but didn't yet get to share it and iterate on the design

Concept Management Apps

The Concept Management Apps run in the new Reference Application

Concept Management Apps

The Concept Management Apps

To accomplish our goals we have created six new applications

Concept Management Apps

Download Concepts With Missing Mappings

Ability to download a spreadsheet with missing mappings

Choose which concept reference source to use for searching for missing mappings

Choose a default map type (pre-populates the “map type” column to make it easier to fill out the spreadsheet)

Choose which classes to include in the search for concepts missing mappings

Concept Management Apps

Once the source codes and map types have been filled in on the spreadsheet you can upload the data into the system

123

SAME-AS

2234

4455

3344

Concept Management Apps

Import SNOMED CT Terms and Relationships

Configuration:

The configuration section is where the user inputs the path to the SNOMED CT International Release files on the local server.

Because each local server can have the SNOMED CT source information stored in a different way, we ask for the user to verify which of the concept reference sources in the drop down represents SNOMED CT

The files for importing the data were too large to upload through the UI so, the user needs to point to them on the local server and then Lucene was used to index them.

Concept Management Apps

Import SNOMED CT Terms and Relationships

Import SNOMED CT Content

Add Names

Add Ancestors

Add Relationships

The tasks can take a long time to run so we give the option of canceling even after starting a task such as adding relationships

Concept Management Apps

Import SNOMED CT Terms and Relationships

Add Names:

Add names to the existing SNOMED CT reference terms in the database. For instance, looks in the SNOMED data files to see if there is a name to match concept reference terms that only have codes

Concept Management Apps

Import SNOMED CT Terms and Relationships

Add ancestors: Finds parents, grandparents, etc, for the concept reference terms that have a SNOMED CT source in the database and adds them as a new concept reference term if they do not exist

Concept Management Apps

Import SNOMED CT Terms and Relationships

Add relationships:

Shows the concept reference term mappings between the SNOMED CT concept reference terms

This task took many hours before switching to use Lucene. It now takes about about an hour and a half to create 54,000 mappings

Concept Management Apps

Browse Concept Reference Terms

Ability to browse through all the concept reference terms in the database

The old UI lets you search for reference terms by code/name, but doesn't let you browse them

Filter and display reference terms by concept reference source

Auto complete text for searching by name or source code

Sortable columns

Concept Management Apps

Add A Concept Reference Term

A tool for entering in a new concept reference term

Concept Management Apps

Choose Concept By Hierarchy

Traverses up and down through the concepts in the dictionary

Parents: If you choose a parent it gives a more general view of the concepts.

Children: If you choose a child then it is possible to see more specifically the terms related to the selected concept.

This make it so if a doctor looks up Diabetes they may find that Brittle Diabetes Mellitus is more precise than what they were initially looking for and if they select that they will see there is brittle type 1 diabetes which maps to the Unstable Type 1 Diabetes concept

We want to package this as a reusable concept search widget, but still want to iterate on the UI.

Concept Management Apps

Choose Concept By Hierarchy

Concept Management Apps

Questions

Concept Management Apps

Thank you