Case Definitions Now Available in Open Syndrome Format #

We are excited to announce a significant milestone in public health surveillance: the first case definitions are now available in the Open Syndrome format. This development marks a crucial step forward in standardizing disease surveillance.

What’s in the dataset #

The bundle covers 40 case definitions from a range of public health threats, countries, and health organizations, in both human- and machine-readable formats:

• JSON — Open Syndrome format (v1), machine-readable
• TXT — extracted text, one file per definition
• PDF — original source documents

File names follow <public-health-threat>_<provenance-or-organization>, so each definition is traceable to its source.

Each Open Syndrome JSON includes:

• Standardized clinical criteria
• Logical operators for combining symptoms and signs
• Version control for tracking updates
• Machine-readable thresholds and measurements

Two ways to access the definitions #

There are two sources, and they serve different needs.

1. Paper snapshot on Hugging Face (frozen bundle) #

The exact bundle used in the Open Syndrome paper — The Open Syndrome Definition as a Machine-Readable Standard for Public Health, forthcoming in the Journal of Medical Internet Research (preprint on arXiv) — is published on Hugging Face with a citable DOI:

• Repository: opensyndrome/case-definitions
• Size: ~62 MB · License: MIT · DOI: 10.57967/hf/6635

Structure:

.
├── human_readable/
│   ├── pdf/   # Original PDF documents
│   └── txt/   # Extracted text, one file per definition
└── machine_readable/
    └── json/  # Open Syndrome format (v1)

Browser, no tools required. Open the Files tab on Hugging Face and download files or folders directly — no account needed.

A single file by URL. Every file resolves at a stable URL, which makes scripting trivial:

curl -LO https://huggingface.co/datasets/opensyndrome/case-definitions/resolve/main/machine_readable/json/acuteflaccidparalysis_kenya.json

Whole bundle via the Hugging Face CLI:

pip install -U "huggingface_hub[cli]"
hf download opensyndrome/case-definitions --repo-type dataset --local-dir ./case-definitions

Whole bundle in Python:

from huggingface_hub import snapshot_download

path = snapshot_download(
    repo_id="opensyndrome/case-definitions",
    repo_type="dataset",
)
print(path)  # local cache directory containing all files

Or with git (requires git-lfs):

git lfs install
git clone https://huggingface.co/datasets/opensyndrome/case-definitions

2. Continuously updated definitions on GitHub #

If you want the current machine-readable definitions — including fixes and additions made after the paper — pull them from the GitHub repository, where every change is validated by CI against the Open Syndrome schema:

• Repository: OpenSyndrome/definitions

JSONs live under definitions/v1/, organized alphabetically. Grab a single file directly:

curl -LO https://raw.githubusercontent.com/OpenSyndrome/definitions/main/definitions/v1/d/diarrhea_pacificislands.json

Or clone the whole repo:

git clone https://github.com/OpenSyndrome/definitions.git

Which one should I use? Use the Hugging Face bundle to reproduce or cite the paper exactly. Use the GitHub repo when you want the freshest definitions for tooling and production.

What’s next #

This release is just the beginning. We are working on additional case definitions from other major health organizations, a UI to help on converting existing definitions to Open Syndrome format (already available in our Python library) and more!

Join the community #

We invite public health professionals, developers, and researchers to contribute to this initiative. Open an issue or pull request on the GitHub repository to suggest improvements or add a definition, and please cite us as described in our citation guide.

Together, we’re building a more standardized and efficient global disease surveillance system.