Active Entity Ontology for Science (AEOS)

AEOS is a portable ontology for modeling active and informational entities, their roles, affordances, states, and interaction motifs in scientific ecosystems. The repository is designed to be forked, edited, validated, and consumed without access to an external application.

Canonical surfaces

Path	Purpose
data/aeos.yaml	Canonical human-editable ontology source.
aeos.json	Deterministic machine-readable export.
schema/aeos.schema.json	Structural data contract.
releases.json	Release and provenance manifest.
docs/	Model, data, fork, curation, and publication guidance.
paper/	Maintained publication source and artifact notes.
archive/	Preserved 2022/v2 source artifacts.

The interactive reference is AEOS on Coda. The published paper is An Active Inference Ontology for Decentralized Science.

Quick start

Requires Python 3.10 or newer.

python3 -m venv .venv
.venv/bin/python -m pip install -e '.[test]'
.venv/bin/aeos validate
.venv/bin/aeos build
.venv/bin/pytest
.venv/bin/ruff check src tests scripts

pytest runs with the coverage gate (--cov=src --cov-fail-under=90), so the suite must stay at 90% or higher. The core commands are local and deterministic:

aeos validate --input data/aeos.yaml --schema schema/aeos.schema.json
aeos build --input data/aeos.yaml --output aeos.json
aeos build --check
aeos build --check --format json
aeos report --format json
aeos diff OLD.json NEW.json --format json

Use --input, --output, and --schema to work with a fork or a separate ontology file. The validator checks structure, IDs, references, roles, affordances, states, relationships, and motif steps. The export includes a derived graph for downstream search and visualization. The same commands are available as python -m aeos ...; see the command-line reference for all options, defaults, and exit codes.

Contributing

Edit data/aeos.yaml, run the validation and test commands, review the JSON diff, and document any release-level change in releases.json. See docs/forking.md, docs/data-contract.md, docs/contributing.md, docs/model.md, and docs/publication.md.

License and attribution

Repository content is released under CC BY 4.0. Please preserve the Active Inference Institute attribution, the ontology version, and the source publication when redistributing or adapting AEOS.