---
id: prefixcommons
version: "0.1.12"
license: unclear
license_treatment: permissive
maintenance: dormant
---

# prefixcommons — A python API for working with ID prefixes

License: permissive · Maintenance: dormant · Downloads: 307.2K/mo

## What it is and what it does

prefixcommons is a Python library that converts between compact identifier notation (CURIEs) and their full Uniform Resource Identifiers (URIs) using JSON-LD context files. It ships with standard contexts that map biomedical ontology prefixes to their canonical URIs—for example, GO:0008150 expands to http://purl.obolibrary.org/obo/GO_0008150. The core functions are expand_uri (CURIE to URI) and contract_uri (URI to CURIE), and you can supply your own context maps as dictionaries if the built-in ones don't fit your use case.

The package is designed for workflows where you need to normalize identifier formats across biomedical ontologies. It depends on requests, click, pytest-logging, and PyYAML. The codebase is dormant (last release 2022-07-19), though the repository remains active, so it is not abandoned but not actively developed.

Use it for:

- Normalize biomedical ontology identifiers in data pipelines by converting CURIEs to full URIs.
- Batch expand or contract identifiers when integrating data from multiple ontology sources.
- Define custom prefix-to-URI mappings for domain-specific identifier schemes.
- Validate and standardize identifier formats in bioinformatics ETL workflows.

## Worth the install?

AI-flagged interpretation of the facts above — verify before relying.

Converts between CURIEs (compact URI identifiers like GO:0008150) and full URIs using JSON-LD contexts.

Yes, if you work with biomedical ontologies or need CURIE-to-URI conversion. The package is stable, has no known vulnerabilities, and low install friction. The dormant maintenance status is a minor concern for a specialized tool—monitor the repository if you depend on current ontology prefix definitions, but core functionality is unlikely to break.

## Install

pip install prefixcommons
uv add prefixcommons
poetry add prefixcommons

## Installing prefixcommons

Before you install: Low friction: pure Python wheel with four common runtime dependencies (requests, click, pytest-logging, PyYAML). Maintenance is dormant—last release 2022-07-19, though repository has recent commits.

License in practice: Licensed under BSD (permissive), so you can use and modify the package freely in most contexts without restriction.

Quickstart:

pip install prefixcommons
from prefixcommons import expand_uri, contract_uri
print(expand_uri('GO:0008150'))
print(contract_uri('http://purl.obolibrary.org/obo/GO_0008150'))

Verify before relying:

- Whether the standard JSON-LD context files are kept current with latest ontology prefix definitions.
- Performance characteristics when expanding or contracting large batches of identifiers.
- Whether custom context maps support the full JSON-LD specification or a subset.

## Package facts

- License: not declared (permissive)
- Python support: supports_current
- Install friction: low
- Maintenance: dormant
- Downloads: 307.2K/month (top 15,000 on PyPI)
- Known vulnerabilities: none known

## Tags

CURIE to URI conversion, ontology identifier expansion, prefix commons, JSON-LD context resolution, OBO identifier mapping, ontology-identifiers, biomedical-data, semantic-web

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