VICC normalization routines for genes

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Gene Normalizer

Overview

The Gene Normalizer provides tools for resolving ambiguous human gene references to consistently-structured, normalized terms. For gene concepts extracted from NCBI Gene, Ensembl, and HGNC, it designates a CURIE, and provides additional metadata like current and previously-used symbols, aliases, database cross-references and associations, and coordinates.

Live service

Documentation · Installation · Usage · API reference

Install

The Gene Normalizer is available on PyPI:

python3 -m pip install gene-normalizer

See installation instruction in the documentation for a description of installation options and data setup requirements.

Examples

Use the live service to programmatically normalize gene terms, as in the following truncated example:

$ curl 'https://normalize.cancervariants.org/gene/normalize?q=BRAF' | python -m json.tool
{
    "query": "BRAF",
    "match_type": 100,
    "gene": {
        "conceptType": "Gene",
        "id": "normalize.gene.hgnc:1097"
        "primaryCoding": {
            "id": "hgnc:1097",
            "code": "HGNC:1097",
            "system": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/",
        },
        "name": "BRAF",
        "extensions": [
            {
                "name": "aliases",
                "value": [
                    "BRAF1",
                    "B-RAF1",
                    "NS7",
                    "RAFB1",
                    "B-raf",
                    "BRAF-1"
                ]
            }
        ]
    }
    # ...
}

Or utilize the Python API for fast access:

>>> from gene.database import create_db
>>> from gene.query import QueryHandler
>>> q = QueryHandler(create_db())
>>> result = q.normalize("KRAS")
>>> result.gene.primaryCoding.id
'hgnc:6407'

See the usage and normalization entries in the documentation for more.

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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This version

0.11.1

Dec 30, 2025

0.11.0

Nov 4, 2025

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Aug 21, 2025

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Jul 21, 2025

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Jul 10, 2025

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Apr 22, 2025

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Jan 2, 2025

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Dec 30, 2024

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Jul 19, 2024

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Jul 15, 2024

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Jul 8, 2024

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Jul 2, 2024

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Apr 24, 2024

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Oct 20, 2023

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Oct 25, 2022

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Oct 24, 2022

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Oct 24, 2022

Reason this release was yanked:

Bug that doesn't allow package to be imported

0.2.3

Sep 28, 2022

0.2.2

Sep 23, 2022

0.2.1

Aug 26, 2022

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Aug 24, 2022

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Oct 5, 2023

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Jun 27, 2023

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Mar 31, 2023

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Aug 9, 2021

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Aug 6, 2021

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0.1.11

Aug 4, 2021

0.1.10

Jun 30, 2021

0.1.5

Mar 31, 2021

0.1.4

Mar 30, 2021

0.1.3

Mar 29, 2021

0.1.2

Mar 11, 2021

0.1.0

Mar 2, 2021

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