KG: consistent knowledge-graph schema + consistency validation #386

Goal

Generate a consistent BBQS knowledge graph and validate that no part contradicts another. Consistency ≠ completeness — missing per-project detail is out of scope for now. OWL = schema logic; SHACL = validation.

Decisions

• Source of truth: kg/bbqs.linkml.yaml (LinkML → gen-owl OWL + gen-shacl SHACL). Now v0.3 (keep-list cherry-picked from KG schema: SOSA device alignment, OOPS pitfall fixes, device-usage modeling #397; title/DANDI kept, device/SOSA deferred).
• Node spine: exporter over Supabase resources (resources.id = IRI, resource_type = rdf:type).
• Project is the one node — "Grant" is only NIH terminology (DB resource_type stays grant; exporter joins grants ⋈ projects).
• Validation engine: SHACL-first (pyshacl), OWL reasoner (robot/HermiT) second.
• Alignments: schema.org + PROV-O + NCBITaxon + Bioschemas/Croissant + reserved neuro hooks (NBO/UBERON/OBI/CogAtlas).

Phase status

• 0 — Foundations & decisions
• 1 — Schema authored — kg/bbqs.linkml.yaml v0.3, DB-grounded, Marr stubbed
• 2 — Consistency invariants — 13-row catalogue; RED/GREEN fixtures; schema↔DB drift guard
• 3 — Exporter (A) — resources spine → TTL; grants⋈projects; reified ProjectRole; species_aliases resolver; held_by bug fixed (resolves via resources.id, guarded by HeldByResolvesShape)
• 4 — Generate OWL + boilerplate SHACL (B) — bbqs.owl.ttl (3,165 triples) + bbqs.shapes.gen.ttl (22 NodeShapes)
• 5 — Backfill migration (C) — extend resource_type + add resource_id (species/devices/working-groups/funding/events/orgs/pubs) ← next
• 6 — Full-access export + OWL reasoning — light up shapes Move the AG-Grid column #5/SS-7: Design concepts of NeuroMCP #12; robot/HermiT; also owl:disjointWith (didn't emit via gen-owl)
• 7 — CI gate (D) Turn BBQS-KG into a class object programatically. #401 related to this to streamline CI gate
• 8 — Publish /schema + retire old surfaces (E) — in progress: /schema admin-gated + WIP banner done; tree regen + retire of old /schema + /data-model pending
• 9 — Spec artifacts in ../bbqs-agent/specs/ (F)

Consistency status (live)

5 SHACL contradiction shapes + the held_by referential shape + the enum-parity guard are enforced. On the anon export the real graph validates to 9 dangling study_species (#7); role-token (#4) and mechanism (#9) conform. Full catalogue + per-invariant status in kg/README.md.

Related

PR #397 (@Sulstice) reviewed → keep-list cherry-picked to dev (092e5a2); PR closed as superseded. Device-usage + SOSA to return as a focused PR.

Open modeling questions

Tool vs software boundary; Event source (new table vs Announcement subtype). (Algorithm resolved — promoted to its own resource_type.)