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Criteria2Query concept sets

#1

I’ve discovered this superb tool that is Criteria2Query, which is quite impressive. However, the export to Atlas function does not really work as the video tutorial implies it should work. I’ve only managed to get empty concept sets in the exported json, which when imported into atlas give problems because concept set id is 0.

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Every other criteria except from the concept sets seems to be working perfectly

In addition to that, here go two additional questions:
Does Criteria2Query need to be linked to an actual Atlas instance?
How does it know which vocabulary to use?

#2

Pinging @Patrick_Ryan and @Cong_Liu as they can probably point me in the right direction

#3

Hi @Diego_Bosca_Tomas @Patrick_Ryan ,

Sorry for the confusion.

Hi Diego,

You used the first version of Criteria2Query, which has issues with concept sets. Our latest version of Criteria2Query is accessible here: http://34.70.212.14:8080/criteria2query_box/. This new version made the following changes to the earlier version:

    1. It no longer relies on Atlas and can directly and automatically translate free-text eligibility criteria into executable cohort definition SQL query in any dataset formatted in the OMOP Common Data Model. We provide two example datasets (i.e., SynPUF1k and SynPUF5% datasets) for the SQL query execution result display. All files, including eligibility criteria representation in JSON format, cohort definition SQL query, and example cohort characteristics table, are accessible.
    1. Users can use the modification functions to modify or refine the automatically extracted criteria and their mapped concepts and generate a more promising and accurate cohort definition. Functions include annotating an unextracted medical term with or without concept, updating the semantic type or code for the mapping results, removing one or more annotated medical terms, selecting the eligibility criteria text paragraphs whose information will be included in the cohort definition. The concept searching function is supported by ATHENA.

Here is a screenshot of the new editable user interface.

Graphical user interface, text, application Description automatically generated

1 Like
#4

Thank you very much, I’ll try this one!

It works like a charm, great work!

#5

Hi @chunhua

I would really like to run the latest version of Criteria2Query locally, but I’m not sure if the version you are running under http://34.70.212.14:8080 is updated in the github repo.

I’ll really appreciate if you can provide more info about how I can clone the latest version.

Thanks!

Omri.

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