the-ontology-project

Pre-Core legacy archive

The artifacts in this directory predate TOP Core — the three-layer architecture (1 root, 8 categories, 28 leaves) that landed via ADRs 0012–0014 and shipped in core/v1/ and taxonomy/taxonomy.ttl. They are preserved for historical reference and to keep the reasoning that produced them queryable.

Do not load these against current Core. The namespaces, shapes, and design assumptions conflict with the current architecture. They will not validate against core/v1/shapes.ttl. They should not be referenced from new specs.

What’s here

Path	What it was	Why archived
reference-graphs/clinical-trials/	The pre-Core clinical-research work — Sponsor / Study / Site / Participant / Recruit / Visit / OversightBody / InvestigationalProduct / Event lifts across PRs #1–#14. Includes spec HTMLs, planning MDs, the v0.7.0-strawman JSON intermediate, SHACL shapes, worked examples, verification histories.	Authored before Core landed; uses pre-Core namespaces (topc: mixed with top: for clinical-research) and pre-rename file paths. Bo’s call: “all the clinical work we did, it’s trash with the new core — we have to refactor the entire reference graph.” The clinical-research workflow rebuilds from scratch against Core.
onto/clinical/v1/, onto/commons/v1/	The published mirrors at top.scientix.ai/onto/... from before the /onto/ path was dropped (ADR-0014).	Superseded by core/v1/.
clinical-research-owl-classes.ttl	An early draft of clinical-research workflow OWL classes (formerly clinical-research/source/owl-classes.ttl).	Uses stale topc: prefix, references the old commons/source/core.ttl path that no longer exists. Predates the namespace collapse.
tools/	The JSON-intermediate translator scaffold — build_context.py and build_shacl.py. Consumed top-strawman.json and emitted JSON-LD @context + SHACL Turtle.	Tied to the pre-Core authoring pattern (JSON intermediate → emitted artifacts). The new pattern authors OWL/SHACL directly in core/v1/shapes.ttl. The translator may revive in some form if the clinical-research rebuild adopts a similar intermediate; that decision rides with the rebuild.

What’s valuable here

The shape of these artifacts is wrong; the reasoning isn’t. Specifically:

• Operator-vocabulary work. The spec HTMLs name entities, attributes, and enums in the language operators actually use. That naming is durable — the rebuild against Core preserves the names and re-roots them as workflow-extension subclasses of Core leaves.
• Lifecycle insights. Participant’s 11-state lifecycle, Visit’s template-vs-occurrence split, Site’s operational hierarchy (Site → StudySite → Study → Protocol → SOA), Event’s discriminator-not-class pattern — all surfaced from real operational scenarios and remain useful design references.
• Cross-walks. FHIR / SDTM / CDASH / USDM / OMOP mappings in each spec doc document what projection adapters will emit. The mappings themselves don’t change because Core changed; they get reattached to the rebuilt classes.
• Audit + dependency work. cdisc-dependency-pipeline.md, cdisc-ecosystem-alignment.md, usdm-ingest-audit.md, temporal-prov-native.md — discipline that informs how the clinical-research workflow will handle upstream-standard churn.

What’s stale and should not be carried forward

• The OWL/SHACL artifacts (shapes.ttl, the JSON intermediate, the @context.jsonld) — wrong namespaces, wrong inheritance, wrong shape.
• The boolean flags on Sponsor (isSponsorOfRecord, hasRegulatoryResponsibility, …) — per ADR-0015 these reify to top:Attestation instances. The rebuild does not carry forward the flags.
• The OOUX-locked-9 framing — superseded by the 12-functional-area framing (Bo’s reframe, 2026-05-11; not yet documented as an ADR but it’s how the rebuild will be organized).
• The verification questions left open against Sponsor (8 closed; 0 open), Site/StudySite (14 pending), Study (12 pending) — moot under the rebuild. The conversations that produced them are still in the spec HTMLs for reference.

Cross-references repaired

Cross-references from index.html, README.md, roadmap.md, roadmap.html, and first-principles.md that pointed at these artifacts have been updated to either point here under legacy/, drop the link entirely, or replace with a current-state reference. Anchor links inside the archived HTMLs still work within this directory.

Provenance

Archived 2026-05-12 per ADR (the cleanup PR introducing this directory). The git history retains the original paths and the move commits; git log --follow against any archived file reaches back to its original lift commit.

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