Git Product home page Git Product logo

omocl's Introduction

OMOCL

Note

OMOCL is the result of a research project. To support our research, please cite one of our papers instead of referencing our github in scientific articles. You can find an overview of papers about OMOCL here. If you are not sure which paper to cite, we recommend this one:

Severin Kohler, Diego Boscá, Florian Kärcher, Birger Haarbrandt, Manuel Prinz, Michael Marschollek, Roland Eils, Eos and OMOCL: Towards a seamless integration of openEHR records into the OMOP Common Data Model, Journal of Biomedical Informatics, Volume 144, 2023 (Link)

Thanks!

Introduction

The OMOP Conversion Language is a declerative mappings language for openEHR archetype-to-CDM mappings. It is based on yaml. For more info check our wiki.

For a engine to execute the mappings see Eos

mapping coverage

10.5% ███▒▒▒▒▒▒▒

counting published archetypes from the international ckm

omocl's People

Contributors

sevkohler avatar yampeku avatar

Stargazers

avatar avatar avatar avatar

Watchers

avatar

Forkers

yampeku bjornna

omocl's Issues

Multiple events on OBSERVATION

This is good work on a great concept!

I have a question related to how you will deal with multiple EVENT on an OBSERVATION.

I am working on ETL for openEHR data. To extract i.e. Body Temperature I use the following AQL. The example illustrates how I query for only POINT_EVENT and also support for multiple versions of the archetype.

The latter, versions of archetype, could be done safer to only allow specific versions. Currently there are v1 and v2 published over the years.

select
   pe/time/value as 'time',
   pe/data[at0001]/items[at0004]/value/magnitude as 'value',
   pe/data[at0001]/items[at0004]/value/units as 'unit',
   temp/data[at0002]/origin/value as 'origin',
   temp/protocol[at0020]/items[at0021]/value/value AS 'location_of_measurement',
   temp/data[at0002]/events[at0003]/state[at0029]/items[at0030]/value/value AS 'body_exposure',
   c/name/value as 'composition_name',
   c/context/start_time/value as 'start_time',
   c/context/end_time/value as 'end_time',
   temp/archetype_details/archetype_id/value as 'archetype_id'
from
   composition c
      contains observation temp[openEHR-EHR-OBSERVATION.body_temperature.v*]
         contains POINT_EVENT pe
order by
   temp/data[at0002]/origin/value desc,
   pe/time/value desc

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.