Ontology: add Uberon, NCIT, EDAM, IAO, STATO and SchemaOrg providers #98

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1. stevevanhooser

   added 6 commits that reference this issue on Sep 2, 2026

   Run ndi-ontology-matlab's own case table against the port

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   485e031

   Return bare ids from NDIC, NCIm and PubChem, as MATLAB does

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   25cc743

   Fix CHEBI id lookups and the EMPTY ontology URL

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   1aeb5f7

   Stop caching empty lookups, and retry them in the shared case table

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   90724c6

   Fail the shared-case job when the live cases could not run

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   b761f46

   Raise NDIOntologyLookupError instead of returning an empty result

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   66ff9f9
2. stevevanhooser commented on Sep 3, 2026

   

   stevevanhooser

   on Sep 3, 2026 – with Claude

   ContributorAuthor

   More actions

   Done, and closing. The work landed in ndi-ontology-python rather than here, so GitHub never linked it — closing keywords don't cross repositories.

   Where it went

   The ontology namespace was split out into Waltham-Data-Science/ndi-ontology-python, the companion to ndi-ontology-matlab (which is the source of truth — NDI-matlab has no +ndi/ontology.m). NDI-python re-exports it at src/ndi/ontology.py, so every call site here still reads from ndi.ontology import lookup and nothing downstream changed shape.

   The distribution is top-level ndi_ontology rather than ndi.ontology, because a second distribution cannot add a subpackage to a regular package — MATLAB merges the ndi namespace across path entries for free and Python does not. That divergence is recorded in the bridge contract's decision_log.

   The three items, in the order this issue suggested

   1. Single-source the prefix map — the 14-entry literal _PREFIX_MAP is gone; _load_prefix_map() reads ontology_list.json alone (22 prefixes) and raises on an empty registry. Registering an ontology is now one edit, which was the point.

   2. Alphanumeric OLS ids + synonyms — worth checking, as you suspected, and it was broken. OLSProvider was calling term.zfill(7), so CHEBI:15377 went out as CHEBI:0015377 and every CHEBI lookup-by-id returned empty. MATLAB's preprocessLookupInput (ontology.m:395) pads nothing. The id is now sent verbatim, which is also what makes alphanumeric ids work — OM:Temperature and OM:Acidity resolve live. Synonyms are carried through: OntologyResult.__slots__ is ("id", "name", "prefix", "definition", "synonyms", "short_name"), matching MATLAB's declaration order at ontology.m:125, and unpacking derives from __slots__ so the order cannot drift.

   3. The six providers — Uberon, NCIT, EDAM, IAO, STATO, SchemaOrg. Only three turned out to be OLS-backed; EDAM and IAO download and parse OWL, and SchemaOrg walks a JSON-LD @graph. PROVIDER_REGISTRY now has 19.

   Verification

   Rather than per-provider unit tests, parity is checked against ndi-ontology-matlab's own fixture — ontology_lookup_tests.json, 66 cases across 15 ontologies, each naming the exact expected_id and expected_name. The file is read directly, never vendored, so it cannot drift the way ontology_list.json had (17 registered prefixes against 22). CI checks out ndi-ontology-matlab and points NDI_ONTOLOGY_MATLAB_DIR at it.

   Latest run on main: 84 passed in 95.54s, zero skipped — including the new providers live (EDAM:1929, format:FASTA, IAO:document, schema:Person, STATO:p-value, UBERON:heart) and every should_succeed: false case.

   The fixture earned its keep. It caught six port defects, four of which had been invisible because an empty result was indistinguishable from a real answer:

   NDIC / NCIm / PubChem	returned prefixed ids where MATLAB returns bare
   CHEBI	the zfill above
   EMPTY	a 404'd data source, whose three failure cases were passing vacuously
   the lookup cache	a transient failure cached as though it were a fact

   lookup() now raises NDIOntologyLookupError instead of returning an empty result, matching MATLAB, which errors on every failure and whose own test asserts verifyError(funcToTest, ?MException). Every call site here already sat inside except Exception, and this repo's suite was unchanged across that switch.

   One thing this issue asked for that is shipped but unverified

   NCIT has no test case. It is implemented and registered, but ontology_lookup_tests.json has no NCIT entry, so it has never been checked against a real lookup in either language. The same is true of SNOMED, EFO and WBStrain, which predate this work. Filed upstream as Waltham-Data-Science/ndi-ontology-matlab#8; until cases exist there, test_case_table_covers_every_ported_provider carries them in a known_gaps set so the omission stays visible rather than silent.

   Everything else this issue named is covered by live parity cases that pass.

   Merged in ndi-ontology-python: #3 (providers + prefix registry), #4 (lookup() raises), #5 (live-test gate).

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   Generated by Claude Code
3. stevevanhooser

   closed this as completedon Sep 3, 2026