Semanticscience Integrated Ontology (SIO)

SIO provides a simple, integrated ontology of types and relations for rich description of objects, processes, and their attributes. See the overview, design principles, design patterns, and the published paper.

Ontology

The OWL2 ontology is available at http://semanticscience.org/ontology/sio.owl

Subsets are available for modular import:

• Labels as SIO URIs
• All subsets (core, chemical, nlp, etc.)

Browse the ontology:

• BioPortal
• Ontobee
• AgroPortal
• AberOWL

SIO term resolution is handled by Ontobee:

• protein — SIO_010043
• dataset — SIO_000089
• data analysis — SIO_001051

Community

Questions: sio-ontology mailing list (sio-ontology@googlegroups.com)
Term requests: issue tracker

Projects using SIO:

• Bio2RDF — Linked Data for the Life Sciences
• SADI Semantic Web Services
• DisGeNET — gene-disease associations
• PubChem RDF (NCBI) — measurement values
• Gene Expression Atlas (EBI)
• Graph4Code
• IDSM — Integrated Database of Small Molecules

Development

Setup

Python 3.8+ is required.

python3 -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt

Scripts

scripts/bump_version.py — Increment the ontology version

Updates owl:versionInfo in ontology/sio.owl and sets dct:modified to today's date.

python3 scripts/bump_version.py            # bump minor version (default): 1.59 -> 1.60
python3 scripts/bump_version.py --major    # bump major version:           1.59 -> 2.0
python3 scripts/bump_version.py --patch    # bump patch version:           1.59 -> 1.59.1
python3 scripts/bump_version.py --set 2.0  # set an explicit version
python3 scripts/bump_version.py --dry-run  # preview without writing

scripts/generate_subsets.py — Generate subset OWL files

Reads ontology/sio.owl and writes subset files to ontology/sio/release/. Replaces ontology/generatesubsets.php.

python3 scripts/generate_subsets.py

Output files:

File	Description
sio-subset-<name>.owl	Per-subset ontology derived from sio:subset annotations
sio-subset-camelcase-label.owl	All terms with URIs derived from camelCase labels
sio-subset-dash-labels.owl	All terms with URIs derived from dash-separated labels
sio-subset-labels.owl	Copy of sio-subset-dash-labels.owl
sio-release.owl	Full versioned release with rdfs:isDefinedBy and owl:versionIRI

Subset membership is controlled by the sio:subset annotation property. The value supports suffix modifiers:

Suffix	Meaning
name	Include this term only
name+	Include this term and all descendants (transitive rdfs:subClassOf)
name++	Include this term, all descendants, and all ancestors
name-	Exclude this term and all descendants

scripts/diff_ontologies.py — Compare two ontology versions

Reports ontology-level annotation changes and added, removed, or modified classes, properties, and individuals between two OWL files.

python3 scripts/diff_ontologies.py <ontology1> <ontology2> [--format text|json]

• Inputs can be local file paths or URLs
• Default output is human-readable text; --format json produces machine-readable output
• Tracks: labels, definitions (dct:description), comments, deprecation, synonyms, subClassOf, equivalentClass, domain, range, inverseOf, disjointWith, and more

# Compare working file against a previous release
python3 scripts/diff_ontologies.py ontology/sio.owl ontology/sio/release/sio-release.owl

# Save diff as JSON
python3 scripts/diff_ontologies.py ontology/sio.owl ontology/sio-new.owl --format json > diff.json