concept management apps intern: jenn parise mentor: darius jazayeri link to the concept management...
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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
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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