feat(NTO/Medical): 10 BioPortal namespace stubs + 25 MedCare-rs SQL transcodes#3
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Records D-OGIT-HEALTHCARE-BOOTSTRAP run: 14 TTL files (846 lines)
under NTO/Healthcare/{entities,enumerations}/, validation result
(rdflib 14/14 ok, 690 triples), out-of-scope deferrals.
…V1-4) agent-bioportal-stubs (Wave 2 of 12-agent palantir-cascade push) emitted 10 namespace stub TTL files under NTO/Medical/<NAMESPACE>/namespace.ttl. Source: AdaWorldAPI/MedCare-rs/releases/tag/bioportal-ontologies-2026-05-05 release manifest. Stubs ONLY — no data load. Full ingestion gated on the lance-graph-rdf-fma-snomed-v1 plan (lance-graph repo); each stub carries ogit:loaderStatus "stub" + ogit:loaderCrate "lance-graph-rdf" pointers. Per-stub shape: a ogit:Namespace + rdfs:label + rdfs:comment + ogit:contextIri (BioPortal canonical form) + ogit:contextId + dcterms:source + dcterms:license + ogit:fileSize + ogit:tripleCount + ogit:loaderCrate + ogit:loaderStatus. ContextId allocations (10..19) align with the lance-graph NamespaceRegistry::seed_defaults() reservation shipped in lance-graph commit 8366e70 (Wave 2 sibling agent-context-id): | Namespace | contextId | source filename | size | est triples | |---|---|---|---|---| | ICD10CM | 10 | ICD10CM.ttl | 51.6 MB | ~1.8M | | RxNorm | 11 | RXNORM.ttl | 218.8 MB | ~9M | | LOINC | 12 | LOINC.ttl | 739.2 MB | ~30M | | FMA | 13 | fma.owl | 266.2 MB | ~1.5M | | RadLex | 14 | RadLex.owl | 64.9 MB | ~600K | | SNOMED | 15 | SCTO.owl | 666 KB (partial) | ~50K | | MONDO | 16 | mondo-simple.owl | 215.5 MB | ~1.2M | | HPO | 17 | hp.obo | 10.7 MB | ~150K | | DRON | 18 | dron.owl | 701.7 MB | ~3M | | CHEBI | 19 | chebi.obo | 259.6 MB | ~1.5M | Directory labels stay human-readable (SNOMED, HPO); contextIri uses BioPortal canonical form (SNOMEDCT, HP). 10 files × 17 LOC = 170 LOC total. Under the 200-LOC envelope. Quality flags for downstream meta-2 validation: - SNOMED: SCTO.owl is 666 KB partial (full SNOMED CT is license-gated; the BioPortal release ships only the upper-level concept fragment). - DRON: derived from RxNorm + FDA per BioPortal metadata. - RadLex: rdfs:comment uses BioPortal's four-facet framing (modalities + anatomy + observations + procedures). Per AdaWorldAPI/lance-graph .claude/plans/lance-graph-ontology-v5.md ratification Q4: this OGIT fork never PRs back to almatoai/OGIT. https://claude.ai/code/session_01WevBiZ3jzVocu8fBpTY8sq
Wave 3 / agent-mysql-transcode of the 12-agent palantir-cascade push. Mirrors the top 25 tables from MedCare-rs/.MYSQL/Struktur.sql (104 total) as OGIT entity stubs. Stubs only — per-column rdfs:Property declarations deferred to a follow-on Wave-3.5 agent-medical-properties. Top-25 selection (per medcare-bridge projection relevance): praxis_* (10): praxis_addexamination, praxis_addtreatment, praxis_extpraxis, praxis_grund, praxis_lab_template_main, praxis_lab_template_values, praxis_licence, praxis_mitarbeiter, praxis_patient, praxis_waitingroom pat_* (4): pat_addexamination, pat_addtreatment, pat_medication, pat_specialist pf_* core (8): pf_alcohol, pf_allergy, pf_diagnosis, pf_drugs, pf_form_main, pf_inherit_disease, pf_laboratory_main, pf_laboratory_values glob_* (3): glob_mailsmtp, glob_user_right, glob_vital_mod Per-stub shape: a rdfs:Class + rdfs:subClassOf ogit:Entity + rdfs:label + rdfs:comment + dcterms:source "AdaWorldAPI/MedCare-rs/.MYSQL/Struktur.sql: <table>" + ogit:scope "NTO" + ogit:parent ogit:Node + ogit:loaderStatus "stub" + ogit:columnCount <N> + ogit:primaryKey "<col>" + ogit:mysqlTable "<table>". EntityName mapping: PascalCase of table_name preserving prefix grouping. praxis_patient -> PraxisPatient. pf_diagnosis -> PfDiagnosis. pat_medication -> PatMedication. glob_vital_mod -> GlobVitalMod. Spot-check (3 tables) confirms columnCount accuracy: - PraxisPatient: 29 cols (matches programmatic SQL extraction) - PfDiagnosis: 17 cols - GlobVitalMod: 42 cols (1 id + 8 v*_name + 8 v*_unit + 8 v*_mask + 8 v*_active + 4 chklist_* + 1 office_right + 4 header_* = 42) Validation: rdflib parses all 25 cleanly. LOC: 25 files × ~18 lines = 450 total. Above the META-NUDGE-6 tightened envelope of 150 (3.0×) — agent appended a BLOCKER per META-NUDGE-5 discipline. Main-thread arbitration: ACCEPT. Cause is structural (per-file Turtle @Prefix blocks cannot be shared across files; the 11-predicate spec floor × 25 files = ~18 lines/file = 450 LOC minimum). Consolidating into fewer files would damage per-table addressability — the whole point of Pillar 3 of the v1 cascade plan. The 150 envelope was a discipline target, not a floor-feasibility target. rdfs:comment quality flags for downstream meta-3 validation: - PfDrugs: interpreted as recreational/illicit-drug snapshot (combo_drugs references suggest substance lookup). Could alternatively be Rx-listing. - PraxisGrund: "Grund" translated as German "base/foundation"; 13 columns (name/address/contact/customer-id) match a base clinic-profile interpretation. - GlobMailsmtp: assumed clinic-wide (not per-tenant) SMTP per glob_ prefix. Per AdaWorldAPI/lance-graph .claude/plans/lance-graph-ontology-v5.md ratification Q4: never PR back to almatoai/OGIT. https://claude.ai/code/session_01WevBiZ3jzVocu8fBpTY8sq
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| @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . | ||
| @prefix dcterms: <http://purl.org/dc/terms/> . | ||
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| ogit.Medical:HPO |
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The pull_request validation workflow runs ./validate.sh; with these new namespace stubs it exits before parsing the rest because the validator derives the resource name from this subject and rejects NTO/Medical/HPO/namespace.ttl as File Name mismatch: namespace.ttl does not match with name: HPO and Directory mismatch ... should be under directory Medical. The same namespace.ttl layout is used for all 10 BioPortal stubs, so any PR including them will fail CI unless the files/IRIs are arranged the way the OGIT validator expects.
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| ogit.Medical:PraxisPatient | ||
| a rdfs:Class ; | ||
| rdfs:subClassOf ogit:Entity ; |
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These SQL mirror classes are declared as rdfs:subClassOf ogit:Entity, but they omit the required OGIT entity fields used throughout the repo (dcterms:description, dcterms:valid, dcterms:creator, ogit:mandatory-attributes, ogit:optional-attributes, and ogit:allowed). Running java -jar bin/ogit-validator.jar NTO/Medical/sql_mirror/PraxisPatient.ttl reports exactly those missing properties, so after the namespace path issue is fixed the same CI validation will still reject all of these entity stubs.
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…yout) OGIT validator rejects namespace.ttl files in subdirectories: the file basename must match the subject IRI local name. Subject ogit.Medical:HPO requires file at NTO/Medical/HPO.ttl, not NTO/Medical/HPO/namespace.ttl. Renamed 10 BioPortal namespace stubs (git mv preserves history): NTO/Medical/ICD10CM/namespace.ttl -> NTO/Medical/ICD10CM.ttl NTO/Medical/RxNorm/namespace.ttl -> NTO/Medical/RxNorm.ttl NTO/Medical/LOINC/namespace.ttl -> NTO/Medical/LOINC.ttl NTO/Medical/FMA/namespace.ttl -> NTO/Medical/FMA.ttl NTO/Medical/RadLex/namespace.ttl -> NTO/Medical/RadLex.ttl NTO/Medical/SNOMED/namespace.ttl -> NTO/Medical/SNOMED.ttl NTO/Medical/MONDO/namespace.ttl -> NTO/Medical/MONDO.ttl NTO/Medical/HPO/namespace.ttl -> NTO/Medical/HPO.ttl NTO/Medical/DRON/namespace.ttl -> NTO/Medical/DRON.ttl NTO/Medical/CHEBI/namespace.ttl -> NTO/Medical/CHEBI.ttl TTL content unchanged: the subject IRI ogit.Medical:<NAME> was already correct; only the file location moves. The 10 now-empty parent directories will be cleaned up alongside the SQL-stub metadata fix in the follow-up commit. Sibling codex P1 (SQL stubs missing dcterms:description etc.) is in flight via agent-ogit-validator-fix and will land separately. Per AdaWorldAPI/lance-graph .claude/plans/lance-graph-ontology-v5.md ratification Q4: never PR back to almatoai/OGIT. https://claude.ai/code/session_01WevBiZ3jzVocu8fBpTY8sq
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…ch validator Follow-up to commit 13a8d3f. The codex-recommended flat depth-3 layout (NTO/Medical/<NAME>.ttl) passes single-file validator invocation (java -jar bin/ogit-validator.jar <one-file>) but FAILS batch invocation through ./validate.sh. agent-ogit-validator-fix empirically verified: validate.sh's xargs- batch pipeline triggers a path.subpath(2, getNameCount-1) extraction that requires >= 4 path components. Depth-3 fails with "Directory mismatch: <NAME>.ttl should be under directory Medical". Depth-4 (NTO/Medical/namespaces/<NAME>.ttl) yields "Validation successful". Moved the 10 BioPortal namespace stubs (git mv preserves history): NTO/Medical/ICD10CM.ttl -> NTO/Medical/namespaces/ICD10CM.ttl NTO/Medical/RxNorm.ttl -> NTO/Medical/namespaces/RxNorm.ttl NTO/Medical/LOINC.ttl -> NTO/Medical/namespaces/LOINC.ttl NTO/Medical/FMA.ttl -> NTO/Medical/namespaces/FMA.ttl NTO/Medical/RadLex.ttl -> NTO/Medical/namespaces/RadLex.ttl NTO/Medical/SNOMED.ttl -> NTO/Medical/namespaces/SNOMED.ttl NTO/Medical/MONDO.ttl -> NTO/Medical/namespaces/MONDO.ttl NTO/Medical/HPO.ttl -> NTO/Medical/namespaces/HPO.ttl NTO/Medical/DRON.ttl -> NTO/Medical/namespaces/DRON.ttl NTO/Medical/CHEBI.ttl -> NTO/Medical/namespaces/CHEBI.ttl The depth-4 layout still satisfies the codex P1 finding (file basename == subject IRI local name). The new `namespaces/` parent segment is canonical OGIT shape (mirrors `entities/`, `verbs/`, `enumerations/`). SQL stubs at NTO/Medical/sql_mirror/<NAME>.ttl are already at depth-4 (4 components: NTO + Medical + sql_mirror + file) and pass the batch validator after the metadata enrichment in commit fe551f0. Verification: - validate.sh on this checkout: ZERO errors mention Medical/ or sql_mirror/ - Other validate.sh errors (WorkOrder verbs Issued/HasPosition/ AccessesPortal/OwnsPasswords basename mismatch + Tenant.ttl missing dcterms:valid/dcterms:creator/ogit:allowed) are pre-existing in the v4-shipped WorkOrder namespace from prior OGIT PR #1 + PR #2 merges. Out of scope for this PR; tracked as separate cleanup work. Together with commits 13a8d3f (initial flat layout) and fe551f0 (SQL stub metadata enrichment), this closes both codex P1 findings on #3. https://claude.ai/code/session_01WevBiZ3jzVocu8fBpTY8sq
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…rate-gkuJG fix(NTO/Medical): codex P1 follow-ups on PR #3 (depth-4 namespaces + SQL entity metadata)
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Summary
OGIT-fork half of the 12-agent palantir-cascade implementation push. Two commits, 35 new TTL files, +620 LOC. Sibling lance-graph PR carries the Rust-side codec cascade column extension that consumes these stubs.
c3b6a7b(Wave 2)AdaWorldAPI/MedCare-rs/releases/tag/bioportal-ontologies-2026-05-05release manifestNTO/Medical/{ICD10CM, RxNorm, LOINC, FMA, RadLex, SNOMED, MONDO, HPO, DRON, CHEBI}/namespace.ttl3baf5b9(Wave 3)AdaWorldAPI/MedCare-rs/.MYSQL/Struktur.sql(104 tables; this PR ships top 25)NTO/Medical/sql_mirror/<EntityName>.ttlDeliverables (2 D-ids)
D-CASCADE-V1-4 — BioPortal namespace stubs (Wave 2,
agent-bioportal-stubs)10 namespace stub TTL files, 170 LOC, under the 200-LOC envelope. Each declares
ogit:Namespace+ canonicalogit:contextIri+ogit:contextId+dcterms:source(citing the BioPortal release tag) +dcterms:license+ogit:fileSize+ogit:tripleCount+ogit:loaderCrate "lance-graph-rdf"+ogit:loaderStatus "stub".ICD10CM.ttlRXNORM.ttlLOINC.ttlfma.owlRadLex.owlSCTO.owlmondo-simple.owlhp.obodron.owlchebi.oboContextId allocations 10..19 byte-aligned with the lance-graph PR's
NamespaceRegistry::seed_defaults()(cross-verified: meta-2 confirmed perfect agreement, no runtime negotiation).D-CASCADE-V1-5 — MedCare-rs MySQL transcode (Wave 3,
agent-mysql-transcode)25 entity stubs, 450 LOC, mirroring the top tables from
Struktur.sql(104 total; the remaining 80 are deferred to a follow-up sweep). Each declaresrdfs:Class+rdfs:subClassOf ogit:Entity+dcterms:source "AdaWorldAPI/MedCare-rs/.MYSQL/Struktur.sql:<table>"+ogit:scope "NTO"+ogit:loaderStatus "stub"+ogit:columnCount <N>+ogit:primaryKey "<col>"+ogit:mysqlTable "<table>".Top-25 selection (per medcare-bridge projection relevance):
praxis_*(10):praxis_addexamination,praxis_addtreatment,praxis_extpraxis,praxis_grund,praxis_lab_template_main,praxis_lab_template_values,praxis_licence,praxis_mitarbeiter,praxis_patient,praxis_waitingroompat_*(4):pat_addexamination,pat_addtreatment,pat_medication,pat_specialistpf_*core (8):pf_alcohol,pf_allergy,pf_diagnosis,pf_drugs,pf_form_main,pf_inherit_disease,pf_laboratory_main,pf_laboratory_valuesglob_*(3):glob_mailsmtp,glob_user_right,glob_vital_modEntityName mapping: PascalCase preserving prefix grouping (e.g.
praxis_patient→PraxisPatient,pf_diagnosis→PfDiagnosis).LOC overshoot rationale: 25 files × ~18 LOC each = 450 LOC, against a 150-LOC envelope (3.0×). Cause is structural: per-file Turtle requires
@prefixblocks at top of each file (cannot share across files); the 11-predicate spec floor × 25 files = ~18 lines/file = 450 LOC structural minimum.agent-mysql-transcodeappended a BLOCKER per the orchestration's META-NUDGE-5 discipline; main-thread arbitration ACCEPTED — consolidating into fewer files would damage per-table addressability (the whole point of Pillar 3 of the v1 cascade plan). The 150 envelope was a discipline target, not a feasibility floor for this many files.Validation: rdflib parses all 25 cleanly. Spot-check ✓ on 3 tables:
PraxisPatient=29,PfDiagnosis=17,GlobVitalMod=42.Strengths (per meta-3)
seed_defaults()in the lance-graph sibling PR — cross-verified zero drift.Struktur.sql:<table>— every stub is a verifiable lineage entry.Struktur.sqlfor V1-5).Concerns (per meta-3 — all deferable)
combo_*enum lookups + auxiliary utilities).rdfs:commentquality flags unvalidated against BioPortal metadata: SNOMED (SCTO.owl partial framing), DRON (RxNorm + FDA derivation), RadLex (four-facet framing modalities + anatomy + observations + procedures).NTO/Medical/only —NTO/WorkOrder/was previously shipped (feat(NTO/WorkOrder): add WorkOrder namespace from AdaWorldAPI/WoA transcode (15 entities + 12 verbs) #1 + feat(NTO): WoA predicate fills + Healthcare clinical-workflow bootstrap #2);NTO/Healthcare/Network/SDF/SGOnot touched in this push.Test plan
@prefix+ entity declaration + 11+ predicates per stub).agent-mysql-transcode).PraxisPatient=29 cols (matchespraxis_patientSQL),PfDiagnosis=17 (matchespf_diagnosis),GlobVitalMod=42 (matchesglob_vital_mod).NamespaceRegistry::seed_defaults().rdfs:commentflags above.columnCountvalues from any of the 22 unspot-checked stubs.Per
lance-graph-ontology-v5.mdratification Q4This PR does not open an upstream PR to
almatoai/OGIT.AdaWorldAPI/OGITis the extension-fork-only target.Cross-references
AdaWorldAPI/lance-graphbranchclaude/create-graph-ontology-crate-gkuJG→main. Carries the Rust-side codec cascade column extension (Wave 3agent-cascade-colsshippedMappingRowwith cascade columns +thinking_style+attribute_sources) and the 9 other deliverables.NTO/WorkOrderpredicate fills +NTO/Healthcareclinical-workflow bootstrap)..claude/plans/ogit-cascade-supabase-callcenter-v1.md(in lance-graph) — Pillar 4 (BioPortal arsenal) + the SQL transcode design.https://claude.ai/code/session_01WevBiZ3jzVocu8fBpTY8sq
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