search

AIDAVA-DEV / AIDAVA-Reference-Ontology

AIDAVA Reference Ontology
1 stars 0 forks source link

hasCode in Procedure #99

Open SarehAghaei opened 2 months ago

SarehAghaei commented 2 months ago

In MUG data, there are free-text columns such as therapy or procedure that cannot be coded to a specific code. Since the cardinality of 'hasCode' is 1..1 with SNOMED ID ranges, which SNOMED code should be chosen? We have opted to use the most general code, which is 71388002 |Procedure (procedure)|.

However, if validation rules require more specific codes, could you please provide a solution for finding the code for a free-text entry?

rcelebi commented 2 months ago

Any free text column that need to be mapped to SNOMED codes should first be tagged in OpenRefine. Once the column is tagged with 'Entity Linking' label, the pipeline will return a code for each text entry. Can you provide an example of free text for the procedure? @ensaremirerol can help you perhaps?

SarehAghaei commented 2 months ago

Sure! It would be great to code texts using OpenRefine! An example:

"Plan lt. CCU:

ensaremirerol commented 2 months ago

Hey @SarehAghaei,

To get started, update or begin using the OpenRefine instance by following this link: AIDAVA OpenRefine.

Or as an alternative, if you have installed OpenRefine using official web site. You can install following extension to get the functionality. This instance is equipped with all the necessary extensions for AIDAVA.

Extension How to install extensions to OpenRefine

I recommend the first option as it is easier.

Once updated, you'll notice two new buttons under the Edit Column Menu: "Tag with NLP" and "Tag with Entity Linking." Utilize these buttons to tag the required columns for NLP or Entity Linking workflow.

It's important to note that these operations won't change your data. They simply add special entries to the Operation History. In the Ingestion workflow, we use these entries to identify which columns require Entity Linking or NLP.