Introduction
This book is a worked example: building an ontology from nothing to a validated artifact, one step at a time, following Noy & McGuinness’s Ontology Development 101 (2001 — “N&M”) adapted to LinkML. There is one chapter per N&M step. The schema grows incrementally, and each chapter embeds a frozen listing of the schema as it stood at that point, so editing the schema later can’t silently change what an earlier chapter shows.
The ontology is grounded in BFO 2020 (ISO/IEC 21838-2:2020) and the Common
Core Ontologies (CCO). Grounding is by URI: each class is referenced through
subclass_of and the prefixes, not pulled in with LinkML imports: (which
is reserved for other LinkML schemas).
BFO (the Basic Formal Ontology, ISO/IEC 21838-2:2020) is a small top-level ontology of the most general categories: objects, qualities, processes, and the like. CCO (the Common Core Ontologies) is a mid-level layer built on top of BFO. We ground the ontology in them by pointing its terms at BFO/CCO IRIs instead of inventing categories from scratch.
The domain
The domain is food and wine, N&M’s own running example: wines, foods, and the pairings between them, expressed in LinkML and grounded in BFO/CCO rather than the OWL/RDFS of the 2001 paper. Where N&M’s choices don’t sit cleanly on a BFO foundation, the chapter that makes the change says so.
The generated schema documentation (class diagrams, the interactive class
graph, and RDF) is published next to this book under
schema/.
Using this as a template
This repository is also the template the book describes. To build your own
ontology with the same workflow, clone it (or use GitHub’s “Use this
template”), then run the setup-ontology skill: it resets the showcase
back to a blank scaffold, renames the placeholder to your schema’s name,
and hands off to advance-step, which walks one N&M step per chapter. The
README covers the toolchain and the setup sequence.