EDAM Ontology Python Package

1.25.3 · active · verified Fri Apr 17

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.

Common errors

```
ModuleNotFoundError: No module named 'edam_ontology'
```
cause The `edam-ontology` package is not installed or the current Python environment does not have access to it.

fix Ensure the package is installed using `pip install edam-ontology` or activate the correct Python virtual environment where it is installed.
```
ImportError: cannot import name 'EDAM' from 'edam_ontology'
```
cause This usually indicates an older version of `edam-ontology` that does not expose the `EDAM` object directly, or a corrupted installation.

fix Upgrade to the latest version of the library using `pip install --upgrade edam-ontology`. If the problem persists, try a clean reinstall: `pip uninstall edam-ontology && pip install edam-ontology`.
```
TypeError: 'owlready2.entity.ThingClass' object is not callable
```
cause You are trying to call an EDAM class directly, expecting it to be a function or a constructor, instead of treating it as an `owlready2` class object.

fix When accessing EDAM entities like `EDAM.data` or `EDAM.tool`, these are `owlready2` class objects. Use their properties (e.g., `EDAM.data.label.first()`) or `owlready2` methods to query them, rather than attempting to call them like `EDAM.data()`.

Warnings

breaking Version 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.
gotcha The `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.
gotcha Loading 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.

Install

pip install edam-ontology Install latest version

Imports

EDAM
```
from edam_ontology import EDAM
```
EDAM is the primary entry point, an owlready2.World object.
EDAM_ONTOLOGY_VERSION
```
from edam_ontology import EDAM_ONTOLOGY_VERSION
```
Provides the semantic version string of the packaged EDAM ontology.

Quickstart

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.")

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