OMOP Processed Vocabularies

Repository for pre-processed vocabularies for working with the OMOP CDM at UCLH.

You can download these files directly or follow the local development instructions to use git to clone the files

Downloading versions

You can download a specific tagged version using https. in this format, replacing the curly braced values:

https://github.com/SAFEHR-data/omop-vocabs-processed/raw/refs/tags/{tag}/{relative_path}

For example for v4 data file for the data/version.txt:

R

tag = "v4"
relative_path = "data/concept.parquet"
download_url = glue::glue("https://github.com/SAFEHR-data/omop-vocabs-processed/raw/refs/tags/{tag}/{relative_path}")
download.file(download_url,
              destfile = "concept.parquet",
              mode = "wb")

Python

import urllib.request

tag = "v4"
relative_path = "data/concept.parquet"
download_url = f"https://github.com/SAFEHR-data/omop-vocabs-processed/raw/refs/tags/{tag}/{relative_path}"
local_filename = "concept.parquet"

urllib.request.urlretrieve(download_url, local_filename)

Shell

export OMOP_METADATA_VERSION=v4
export OMOP_METADATA_PATH=data/concept.parquet
curl -L -o concept.parquet "https://github.com/SAFEHR-data/omop-vocabs-processed/raw/refs/tags/${OMOP_METADATA_VERSION}/${OMOP_METADATA_PATH}"

Local development

If you haven't already set up git lfs with your git user account:

1. Download and install git lfs using their instructions
2. Set up git LFS with your git account

   git lfs install

Clone this repository:

git clone https://github.com/SAFEHR-data/omop-vocabs-processed.git

Release procedure

1. Update the vocabulary
2. Update the data/version.txt file with this version. For backwards compatibility, also copy this to data/metadata_version.txt, we will eventually not maintain this file.
3. Tag the release, replacing ${version} with your version, e.g. v4

   git tag ${version}

4. Push the tag for a release

   git push --tags origin