VICC normalization routines for diseases

These details have not been verified by PyPI

Project links

Documentation

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.

Project details

These details have not been verified by PyPI

Project links

Documentation

Release history Release notifications | RSS feed

This version

0.6.0

Nov 29, 2024

0.5.0

Jul 15, 2024

0.4.0.dev4 pre-release

Jun 7, 2024

0.4.0.dev3 pre-release

Dec 20, 2023

0.4.0.dev2 pre-release

Dec 4, 2023

0.4.0.dev1 pre-release

Nov 28, 2023

0.4.0.dev0 pre-release

Oct 25, 2023

0.3.1

Jan 11, 2023

0.3.0

Nov 2, 2022

0.2.21.dev0 pre-release

May 12, 2023

0.2.20

May 7, 2023

0.2.19

Jan 11, 2023

0.2.18

Jan 10, 2023

0.2.17

Jan 6, 2023

0.2.16

Nov 2, 2022

0.2.15

Oct 31, 2022

0.2.14

Sep 23, 2022

0.2.13

Aug 24, 2022

0.2.12

Jan 24, 2022

0.2.11

Nov 18, 2021

0.2.10

Sep 7, 2021

0.2.9

Sep 7, 2021

0.2.7

Apr 15, 2021

0.2.4

Mar 31, 2021

0.2.3

Mar 30, 2021

0.2.2

Mar 29, 2021

0.2.1

Mar 29, 2021

0.2.0

Mar 12, 2021

0.1.1

Mar 3, 2021

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

disease_normalizer-0.6.0.tar.gz (290.3 kB view details)

Uploaded Nov 29, 2024 Source

Built Distribution

disease_normalizer-0.6.0-py3-none-any.whl (50.8 kB view details)

Uploaded Nov 29, 2024 Python 3

File details

Details for the file disease_normalizer-0.6.0.tar.gz.

File metadata

Download URL: disease_normalizer-0.6.0.tar.gz
Upload date: Nov 29, 2024
Size: 290.3 kB
Tags: Source
Uploaded using Trusted Publishing? Yes
Uploaded via: twine/5.1.1 CPython/3.12.7

File hashes

Hashes for disease_normalizer-0.6.0.tar.gz
Algorithm	Hash digest
SHA256	`fb2d900f7e0008b167aa60bcfa2d8bd70cf1b026465d7be236186dcf4e6e284a`
MD5	`3ab629b15293da54f2e3aca83410d673`
BLAKE2b-256	`a9bdd35422286b1cec9dc9f87d38c84a0125f2808f5b4c2b20bf8999e6705d19`

See more details on using hashes here.

Provenance

The following attestation bundles were made for disease_normalizer-0.6.0.tar.gz:

Publisher: release.yml on cancervariants/disease-normalization

Attestations:

Statement type: https://in-toto.io/Statement/v1
- Predicate type: https://docs.pypi.org/attestations/publish/v1
- Subject name: disease_normalizer-0.6.0.tar.gz
- Subject digest: fb2d900f7e0008b167aa60bcfa2d8bd70cf1b026465d7be236186dcf4e6e284a
- Sigstore transparency entry: 152488915
- Sigstore integration time: Nov 29, 2024