Registry / data / prefixcommons

prefixcommons

library0.1.12pypypi✓ verified 87d ago

PrefixCommons is a Python API designed for working with ID prefixes, enabling the canonicalization, expansion, and contraction of CURIEs (Compact URIs). It is currently at version 0.1.12 and maintains an infrequent release cadence, often aligned with specific project requirements such as those from the Alliance of Genome Resources.

data serialization

pip install prefixcommons

github ↗package ↗

INSTALL

IMPORT

SIG · PREFIXCOMMONS

prefixcommons

datapythonv0.1.12

Install

4.4s avg

Import

592ms

Disk

37MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v0.1.12 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.910 runs

installs and imports cleanly · install 0.0s · import 0.613s · 38.6MB

glibc

py 3.10–3.910 runs

installs and imports cleanly · install 4.4s · import 0.571s · 40MB

37MB installed

● package 37MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

expand_uri

✓ from prefixcommons.curie_util import expand_uri

✗ from prefixcommons import expand_uri

Core utility functions like expand_uri and contract_uri reside in the `curie_util` submodule, not directly under the top-level package.

contract_uri

✓ from prefixcommons.curie_util import contract_uri

✗ from prefixcommons import contract_uri

Core utility functions like expand_uri and contract_uri reside in the `curie_util` submodule, not directly under the top-level package.

read_biocontext

✓ from prefixcommons.curie_util import read_biocontext

Helper function to load a common set of biomedical prefixes.

This quickstart demonstrates how to expand and contract CURIEs using the default prefix map provided by the library, as well as how to supply a custom prefix map or load a pre-defined biomedical context map for more specific use cases.

from prefixcommons.curie_util import expand_uri, contract_uri, read_biocontext # Using the default prefix map expanded_go = expand_uri('GO:0008150') print(f"Expanded GO: {expanded_go}") contracted_go = contract_uri('http://purl.obolibrary.org/obo/GO_0008150') print(f"Contracted GO: {contracted_go}\n") # Using a custom prefix map custom_map = {'EXAMPLE': 'http://example.org/myterms/'} expanded_custom = expand_uri('EXAMPLE:001', prefix_map=custom_map) print(f"Expanded custom: {expanded_custom}") # Loading a biomedical context map bio_context = read_biocontext() expanded_ncbi = expand_uri('NCBIGENE:12345', prefix_map=bio_context) print(f"Expanded NCBIGENE from bio_context: {expanded_ncbi}")

Debug

Known issues

gotchaThe default prefix map, loaded internally from `resources/prefixcommons.jsonld`, may not be exhaustive for all domains or may become stale over time. For robust applications, relying solely on this default map for critical or very specific prefixes is not recommended.

fix

Consider explicitly loading domain-specific context maps using functions like `prefixcommons.curie_util.read_biocontext()` or provide your own custom `prefix_map` dictionary to functions like `expand_uri` and `contract_uri`.

affects: All versions

gotchaPrefixCommons has an infrequent release cadence, often tied to specific project needs. While stable, this means that updates to its default prefix maps for very new or niche identifiers might not be as frequent as external data sources.

fix

For applications requiring the absolute latest or highly specialized prefix definitions, it is advisable to rely on custom-maintained prefix maps or external services rather than solely on the library's built-in defaults. Monitor the GitHub repository for updates.

affects: All versions

Errors

Common errors & fixes

ModuleNotFoundError: No module named 'prefixcommons.curie_util'

Attempting to import core utility functions directly from the top-level `prefixcommons` package instead of their specific submodule `curie_util`.

fix

Change your import statement from `from prefixcommons import expand_uri` (or similar) to `from prefixcommons.curie_util import expand_uri, contract_uri`.

KeyError: 'UNKNOWN_PREFIX'

The CURIE prefix (e.g., 'MYAPP' in 'MYAPP:123') is not found in the currently active prefix map when attempting to expand or contract a URI.

fix

Ensure that the `prefix_map` supplied to `expand_uri` or `contract_uri` (or the default map being used) contains the required prefix. You can load specific contexts using `prefixcommons.curie_util.read_biocontext()` or pass a custom dictionary: `expand_uri('MYAPP:123', prefix_map={'MYAPP': 'http://example.com/myapp/'})`.

Upgrade

Version history

0.1.12latest on PyPI · released Jul 19, 2022

Audit

Dependencies

requestsrequiredUsed for fetching external resources and context maps, although core functionality doesn't strictly depend on it for local maps.

Agent activity

2 hits · last 30 days

node

Resources

githubhttps://github.com/prefixcommons/prefixcommons-py ↗

packagehttps://pypi.org/project/prefixcommons/ ↗