Datasets:

opensyndrome
/

case-definitions

Error code:   FeaturesError
Exception:    ArrowInvalid
Message:      Schema at index 1 was different: 
title: string
description: string
scope: string
category: string
version: string
open_syndrome_version: string
published_in: string
published_at: timestamp[s]
published_by: list<item: string>
location: string
language: string
organization: string
authors: list<item: string>
inclusion_criteria: list<item: struct<type: string, logical_operator: string, values: list<item: struct<type: string, name: string, values: list<item: struct<type: string, name: string, description: string, attribute: string, operator: string, value: int64, unit: string>>, description: string>>>>
references: list<item: struct<url: string>>
status: string
human_readable_definition: string
target_public_health_threats: list<item: string>
keywords: list<item: string>
definition_type: string
vs
title: string
description: string
scope: string
category: string
version: string
open_syndrome_version: string
published_in: string
published_at: timestamp[s]
published_by: list<item: string>
location: string
language: string
organization: string
authors: list<item: string>
inclusion_criteria: list<item: struct<type: string, logical_operator: string, values: list<item: struct<type: string, name: string, description: string>>, code: struct<system: string, code: string>>>
references: list<item: struct<title: string, url: string>>
notes: list<item: string>
status: string
human_readable_definition: string
target_public_health_threats: list<item: string>
keywords: list<item: string>
definition_type: string
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/split/first_rows.py", line 228, in compute_first_rows_from_streaming_response
                  iterable_dataset = iterable_dataset._resolve_features()
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/iterable_dataset.py", line 3422, in _resolve_features
                  features = _infer_features_from_batch(self.with_format(None)._head())
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/iterable_dataset.py", line 2187, in _head
                  return next(iter(self.iter(batch_size=n)))
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/iterable_dataset.py", line 2391, in iter
                  for key, example in iterator:
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/iterable_dataset.py", line 1882, in __iter__
                  for key, pa_table in self._iter_arrow():
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/iterable_dataset.py", line 1904, in _iter_arrow
                  yield from self.ex_iterable._iter_arrow()
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/iterable_dataset.py", line 527, in _iter_arrow
                  yield new_key, pa.Table.from_batches(chunks_buffer)
                File "pyarrow/table.pxi", line 4116, in pyarrow.lib.Table.from_batches
                File "pyarrow/error.pxi", line 154, in pyarrow.lib.pyarrow_internal_check_status
                File "pyarrow/error.pxi", line 91, in pyarrow.lib.check_status
              pyarrow.lib.ArrowInvalid: Schema at index 1 was different: 
              title: string
              description: string
              scope: string
              category: string
              version: string
              open_syndrome_version: string
              published_in: string
              published_at: timestamp[s]
              published_by: list<item: string>
              location: string
              language: string
              organization: string
              authors: list<item: string>
              inclusion_criteria: list<item: struct<type: string, logical_operator: string, values: list<item: struct<type: string, name: string, values: list<item: struct<type: string, name: string, description: string, attribute: string, operator: string, value: int64, unit: string>>, description: string>>>>
              references: list<item: struct<url: string>>
              status: string
              human_readable_definition: string
              target_public_health_threats: list<item: string>
              keywords: list<item: string>
              definition_type: string
              vs
              title: string
              description: string
              scope: string
              category: string
              version: string
              open_syndrome_version: string
              published_in: string
              published_at: timestamp[s]
              published_by: list<item: string>
              location: string
              language: string
              organization: string
              authors: list<item: string>
              inclusion_criteria: list<item: struct<type: string, logical_operator: string, values: list<item: struct<type: string, name: string, description: string>>, code: struct<system: string, code: string>>>
              references: list<item: struct<title: string, url: string>>
              notes: list<item: string>
              status: string
              human_readable_definition: string
              target_public_health_threats: list<item: string>
              keywords: list<item: string>
              definition_type: string

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Open Syndrome Dataset

The first dataset of case definitions in both human- and machine-readable formats.

It comprises 40 case definitions from various public health threats, countries, and health organizations.

Read more about the Open Syndrome Definition (machine-readable format) here.

How is the dataset organised?

The file names follow the pattern <public-health-threat>_<provenance-or-organization>.

In the human-readable folder, in the PDF folder, you will find the original PDFs collected during the initial phase. These PDFs may contain multiple case definitions, depending on the organization. The TXT folder contains the text used for the case definition in question.

In the machine-readable folder, you will find the case definition in the Open Syndrome Definition format in the JSON folder.

.
├── human_readable
│   ├── pdf
└── ├──txt
└── machine_readable
    └── json

Citing & Authors

If you find this repository helpful, feel free to cite our publication: The Open Syndrome Definition

@misc{ferreira2025opensyndromedefinition,
      title={The Open Syndrome Definition},
      author={Ana Paula Gomes Ferreira and Aleksandar Anžel and Izabel Oliva Marcilio de Souza and Helen Hughes and Alex J Elliot and Jude Dzevela Kong and Madlen Schranz and Alexander Ullrich and Georges Hattab},
      year={2025},
      eprint={2509.25434},
      archivePrefix={arXiv},
      primaryClass={cs.AI},
      url={https://arxiv.org/abs/2509.25434},
}

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