VICC normalization routines for diseases
Project description
Disease Normalizer
The Disease Normalizer resolves ambiguous references and descriptions of human diseases to consistently-structured, normalized terms. For concepts extracted from NCIt, Mondo Disease Ontology, The Human Disease Ontology, OMIM, and OncoTree, it designates a CURIE, and provides additional metadata like aliases and cross-references.
Documentation · Installation · API reference
Installation
The Disease Normalizer is available via PyPI:
python3 -m pip install disease-normalizer
See installation instructions in the documentation for a description of installation options and data setup requirements.
Examples
Use the live service to programmatically normalize disease terms, as in the following truncated example:
$ curl -s 'https://normalize.cancervariants.org/disease/normalize?q=liver%20cancer' | python -m json.tool
{
"query": "liver cancer",
"warnings": null,
"match_type": 80,
"normalized_id": "ncit:C34803",
"disease": {
"type": "Disease",
"id": "normalize.disease:liver%20cancer",
"label": "Primary Malignant Liver Neoplasm",
# ...
}
}
Or utilize the Python API for fast local access:
>>> from disease.query import QueryHandler
>>> from disease.database import create_db
>>> q = QueryHandler(create_db())
>>> result = q.normalize("NSCLC")
>>> result.normalized_id
'ncit:C2926'
Feedback and contributing
We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The documentation contains guidance for submitting feedback and contributing new code.
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