Registry / data / edam-ontology

edam-ontology

library1.25.3pypypiunverified

The edam-ontology library provides versioned, Python-packaged data for the EDAM ontology (http://edamontology.org/). It offers convenient access to the ontology as an `owlready2` World object, enabling programmatic querying and navigation. The current version is 1.25.3, with releases typically tied to new EDAM ontology versions and Python compatibility updates.

data serialization

pip install edam-ontology

github ↗package ↗homepage ↗

INSTALL

IMPORT

SIG · EDAM-ONTOLOGY

edam-ontology

datapythonv1.25.3

Install

1.6s avg

Import

—

Disk

18MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v1.25.3 · 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 0.000s · 19.7MB

glibc

py 3.10–3.910 runs

installs and imports cleanly · install 1.6s · import 0.000s · 20MB

18MB installed

● package 18MB

Code

Verified usage

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

EDAM

✓ from edam_ontology import EDAM

✗ from edam_ontology import EDAM

This quickstart demonstrates how to import the EDAM ontology and its version, and then perform a basic query to count entities and access a specific class using the `owlready2` API.

from edam_ontology import EDAM, EDAM_ONTOLOGY_VERSION print(f"EDAM Ontology version: {EDAM_ONTOLOGY_VERSION}") # EDAM is an OWLReady2 World object that can be queried. # For example, count all individuals (entities) in the ontology: num_entities = len(EDAM.individuals()) print(f"Number of EDAM entities: {num_entities}") # Accessing a specific class (e.g., 'data'): data_class = EDAM.data if data_class: print(f"Found EDAM class: {data_class.label.first()}") else: print("EDAM.data class not found.")

Debug

Known issues

breakingVersion 1.25.3 dropped support for Python 3.5-3.8. The library now requires Python 3.9 or newer.

fix

Upgrade your Python environment to version 3.9 or higher.

affects: 1.25.3 and later

gotchaThe `EDAM` object is an `owlready2.World` instance. Effective use of the ontology requires familiarity with `owlready2`'s API for querying, navigating, and manipulating OWL ontologies.

fix

Refer to the `owlready2` documentation (e.g., `owlready2.readthedocs.io`) to understand how to interact with OWL `World` objects, classes, properties, and individuals.

affects: All versions

gotchaLoading the full EDAM ontology into memory (via `edam_ontology.EDAM`) can consume significant RAM (several hundred MBs), especially in resource-constrained environments.

fix

Ensure sufficient memory is available. For very large-scale or resource-limited applications, consider designing your workflow to only load necessary parts or explore alternative methods like SPARQL queries against an external EDAM endpoint if applicable.

affects: All versions

Upgrade

Version history

1.25.3latest on PyPI · released Oct 30, 2025

Audit

Dependencies

owlready2requiredRequired to load and query the ontology data.

Agent activity

11 hits · last 30 days

node

Resources

githubhttps://github.com/edamontology/edam-ontology.py ↗

packagehttps://pypi.org/project/edam-ontology/ ↗

homepagehttp://edamontology.org ↗