OHDSI Home | Forums | Wiki | Github

Ohdsi hades

Hello Everyone,

I am Mounika. I am performing research analysis on COVID data which is a OMOP CDM. I need some help finding the right package and functions in HADES to answer basic questions (shown below) characterizing the population and writing them to any output file like a CSV file.

  • What is the total count of individuals?
  • What is the gender breakdown of individuals?
  • What is the ethnicity breakdown of individuals?
  • What is the age breakdown (5 year increments) of individuals?
  • What is the distribution of conditions/diagnoses?

I know we can view some of these results in ATLAS, but I am trying to see if we can answer these questions using HADES and write the results to output file to view them.

Did anyone tried to answer such questions using HADES? if so please suggest me the packages and functions that I can use. And also please suggest if there are any documentations or relevant community call videos that could help me.

@schuemie, could you please provide any guidance to help me get started on this?

Thank you

Hi @Mounika_Thakkallapal , you want to use the FeatureExtraction package to your cohorts of interest, that’ll give you everything you are looking for. Here’s the link to the documentation: Generating Features for a Cohort • FeatureExtraction

Hey @Mounika_Thakkallapal , if you’d be wiling to use something outside HADES but does exactly what you are looking for (the distribution point has not been added but I could add the functionality), please checkout a package we developed at GTRI called OMOPCDMCohortCreator.jl. It depends on having Julia installed on your system instead of Java. It works alongside the rest of the tidyverse quite well in my experience. More than happy to support you if you want to give it a try!

1 Like

Thank you @Patrick_Ryan.

Hey @TheCedarPrince,

Thank you for recommending OMOPCDMCohortCreator.jl. I will try it out and let you know if I need any help with it.

1 Like

Certainly! The pure Julia tutorial for it is also here: Beginner Tutorial 🐣 · OMOPCDMCohortCreator.jl

Would love to hear how it works out! Thanks!