edam-ontology

What it is and what it does

This package bundles the EDAM ontology—a standardized vocabulary of bioinformatics operations, data types, identifiers, topics, and formats—as a Python distribution. EDAM is widely used in bioinformatics tools and workflows to annotate and describe computational tasks and data. The package exists primarily to let Python projects, especially Galaxy packages, access this ontology without requiring non-Python dependencies or external network calls.

The package is a direct Python port of the EDAM ontology maintained at edamontology.org. It carries no runtime dependencies, installs cleanly on Python 3.9 and later, and is actively maintained. The underlying ontology is published under CC BY-SA 4.0 and described in a peer-reviewed article (Ison et al., 2013).

Use it for:

• Annotate bioinformatics workflows or tool descriptions with standardized EDAM operation and data type terms
• Build Galaxy tool wrappers that reference EDAM vocabulary without external ontology lookups
• Validate or map bioinformatics tool inputs and outputs against a shared ontology standard
• Generate documentation or metadata for bioinformatics software using EDAM classifications

Worth the install?

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

Provides a Python-packaged version of the EDAM ontology, a standardized vocabulary for bioinformatics operations, data types, and formats.

Yes, if you work with bioinformatics tools or workflows that need to reference EDAM terms. The package has no dependencies, installs easily, and is actively maintained. If you don't need EDAM vocabulary, there's no reason to install it.

Install

edam-ontology on PyPI

pip install edam-ontology

uv add edam-ontology

poetry add edam-ontology

Installing edam-ontology

Before you install

Low install friction with no runtime dependencies. Actively maintained with recent commits and stable Python 3.9+ support across modern versions.

License in practice

MIT license permits unrestricted use, modification, and distribution in commercial and private projects with minimal obligations.

Quickstart

pip install edam-ontology

import edam_ontology
# Access EDAM ontology data as packaged Python objects

Verify before relying

• How the ontology data is exposed in the Python API (structure, access patterns, query methods)
• Whether the package includes tools for searching or filtering EDAM terms beyond raw data access
• Performance characteristics when working with the full ontology dataset

Package facts

Evidence: edam_ontology-1.25.3-py3-none-any.whl

Keywords: EDAM

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