TVB-O Ontology Specification

The Virtual Brain Ontology — formal vocabulary, dynamical-systems axioms, and per-model briefs

The TVB-O ontology is the formal, machine-readable backbone of the TVB-O data model. It provides the shared vocabulary and axioms used by the Python package, the Odoo platform, and every external interoperability target (NeuroML, openMINDS, BIDS).

Browse the specification

The interactive Widoco specification (with WebVOWL visualisation) lives at ./spec/. It is regenerated on every release directly from the LinkML schema and the hand-authored axiom layer.

Stable identifiers

Every term resolves through the W3ID redirector:

https://w3id.org/tvbo/                # this page (HTML) / the OWL file (RDF)
https://w3id.org/tvbo/tvbo.owl        # the merged OWL artefact
https://w3id.org/tvbo/JansenRit       # term-level dereferencing

Content negotiation routes browsers to the HTML spec and RDF clients to the Turtle/OWL representation. Do not link to the GitHub Pages URL directly: the W3ID redirect is the persistent identifier.

Downloads

Artefact Format What it is
tvbo.owl OWL/XML Merged T-box + axioms + A-box, ELK-materialised
tvb-o-axioms.ttl Turtle Hand-authored axiom layer (technical, biological, dynamical)
tvb-o.shacl.ttl Turtle (SHACL) Validation shapes generated from the LinkML schema

The structural T-box (tvb-o-struct.owl) and the A-box (tvb-o-data.ttl) ship inside the tvbo Python package under tvbo/data/ontology/ and are also available as GitHub release assets.

How the specification is built

The pipeline is fully reproducible from the LinkML schema:

make gen-owl       # tvb-o-struct.owl  (T-box from LinkML)
make gen-shacl     # tvb-o.shacl.ttl   (validation shapes)
make gen-abox      # tvb-o-data.ttl    (A-box from YAML database)
make gen-merged    # tvbo.owl          (ROBOT merge + ELK reasoner)
make gen-widoco    # docs/ontology/spec/ (Widoco HTML + WebVOWL)

The hand-authored axiom layer (ontology/tvb-o-axioms.ttl) extends the generated T-box with categories that cannot be expressed in LinkML alone:

  1. Technical axioms — backends, capabilities, tasks, requirements.
  2. Biological axioms — anatomical, cellular, and neurotransmitter substrate grounding via UBERON/CL/GO/CHEBI/MESH cross-references.
  3. Dynamical axioms — qualitative regimes, bifurcations, attractors, stochasticity character, model features.
  4. Per-model briefs — for each canonical mean-field model, a concise set of axioms summarising its biological substrate, phase-space dimensionality, and dynamical repertoire.

See the methods chapter for the full ontological-engineering rationale and the restructuring plan for the active development roadmap.

Citing TVB-O

Please cite the ontology by its persistent identifier:

TVB-O — The Virtual Brain Ontology. https://w3id.org/tvbo/

A formal citation accompanies the manuscript currently in preparation.