JuliaHealth / JuliaHealth/HealthSampleData.jl
[FEATURE] Create 10K OMOP CDM Patient Sample
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- Dominant language
- Julia
- Stars
- 2
- Forks
- 2
- PR merge metrics
- No merged PRs in 30d
Description
We need to create a 5K OMOP CDM patient sample for HealthSampleData. This is a rather complex process but can be accomplished in the following steps:
- Set-up a PostgreSQL DBMS on a server
- Generate Synthetic OMOP CDM Data using Synthea
- Install Java on a server
- Install Synthea v3.0.0
- Enable export to CSV (see this: https://github.com/synthetichealth/synthea/wiki/CSV-File-Data-Dictionary)
- Run synthea jar like `java -jar synthea -s 12345 -p 10000
- Extract
output/csvto directory for loading process
- Load synthetic OMOP CDM data into DBMS
- Install R on a server
- Install this package: https://github.com/NACHC-CAD/ETL-Synthea
- Download Athena vocabularies (see: https://athena.ohdsi.org/search-terms/start for downloading)
- Create zipped vocabularies into a directory called
vocabin the same directory asoutput/csv - Execute tutorial in https://github.com/NACHC-CAD/ETL-Synthea
- Export PostgreSQL database into SQLite
- Share SQLite export with @TheCedarPrince for hosting
That is the overall process but rather complex. Happy to support each step along the way.
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing the Synthea v3.0.0 CSV export instructions and the ETL-Synthea tutorial linked in the issue. Set up PostgreSQL, generate the requested synthetic patient data, load it with the Athena vocabularies, and export the result to SQLite. Done means the SQLite export is shared with @TheCedarPrince; resolve whether the target is 5K or 10K patients first.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- java, postgresql, r, sqlite
- Domain
- data, databases, devops, infrastructure
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100