mygene

What it is and what it does

Mygene is a thin Python wrapper around the MyGene.Info REST web service, which provides gene annotation data. Since v3.1.0, it has been built on top of biothings-client, a universal client for BioThings APIs. The package lets you query gene information by ID (Entrez, Ensembl, etc.), retrieve specific fields, and search across multiple species. Results can be returned as dictionaries or as pandas DataFrames.

The package is designed for bioinformatics workflows where you need to look up or cross-reference gene identifiers and their associated metadata. It handles both single-gene queries and batch operations, making it suitable for annotation pipelines and exploratory analysis. The underlying REST API is remote, so network access is required.

Use it for:

• Map gene IDs between different identifier systems (Entrez, Ensembl, gene symbol) for annotation pipelines.
• Retrieve gene metadata such as names, RefSeq accessions, and protein sequences for a list of gene identifiers.
• Search for genes by symbol or name across multiple species to identify orthologs or related genes.
• Export gene annotation results as a pandas DataFrame for downstream analysis or reporting.
• Integrate gene data lookup into bioinformatics workflows without maintaining a local gene database.

Worth the install?

AI-flagged interpretation of the facts on this page — verify before relying

Mygene is a Python wrapper for the MyGene.Info REST API that retrieves and queries gene annotation data, including symbols, names, and cross-references across multiple species.

Yes, if you need to query gene annotations and can tolerate dormant maintenance. The package is stable and has low install friction, but verify that the remote MyGene.Info API remains compatible with your use case. For active development, consider using biothings-client directly, which mygene wraps.

Install

mygene on PyPI

pip install mygene

uv add mygene

poetry add mygene

Installing mygene

Before you install

Low install friction with a single runtime dependency. Maintenance is dormant—the latest release was in April 2021—but the repository remains active with recent commits and the package is marked Production/Stable.

License in practice

BSD license is permissive, allowing use in both open-source and proprietary projects with minimal restrictions.

Quickstart

pip install mygene

import mygene
mg = mygene.MyGeneInfo()
result = mg.getgene(1017, fields='name,symbol')
print(result)

Verify before relying

• Whether the package continues to work reliably against the current MyGene.Info API despite dormant maintenance status.
• Current compatibility with Python versions beyond 3.9, given classifiers only list up to 3.9 and no recent releases.

Package facts

Evidence: mygene-3.2.2-py2.py3-none-any.whl

Keywords: biology, gene, annotation, web, service, client, api

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