validate-schema: extend term-label validation to slots and classes (slot_uri, class_uri, *_mappings)

[cmungall]

Summary

validate-schema currently validates the meaning field of enum permissible values only. It would be valuable to apply the same ontology-label consistency check to slots and classes — i.e. slot_uri, class_uri, and the mapping slots (exact_mappings, close_mappings, related_mappings, narrow_mappings, broad_mappings).

Current behavior (v0.3.0)

EnumValidator.validate_schema() iterates enums only:

all_enums = schema_view.all_enums()
for enum_name in all_enums:
    ...
    issues = self.validate_enum(enum_def, enum_name)

validate_enum then checks, for each PV with a meaning, that the ontology term's label matches one of the PV's own strings (text / title / description / aliases / annotations).

There is no equivalent for slots or classes. A schema can map a slot via slot_uri: ENVO:00001998 or exact_mappings: [MIXS:0000011], or a class via class_uri, and those CURIEs are never checked — they could be nonexistent, obsolete, or label-inconsistent with the element name, and validate-schema stays green.

Why it matters

We generate per-study LinkML "data dictionary" profiles in which every slot carries slot_uri / exact_mappings to MIxS / BERVO / ENVO terms, while only categorical levels become enums. validate-schema vets the enum-PV groundings beautifully — it caught a real mis-grounding for us (meaning: NCBITaxon:62324, which is Anopheles funestus, not Miscanthus). But the much larger set of slot-level mappings is entirely unvetted, so the strongest correctness signal doesn't cover most of the schema.

Proposed enhancement

In validate-schema, additionally iterate schema_view.all_slots() and schema_view.all_classes() and validate:

• slot_uri / class_uri
• exact_mappings, close_mappings, related_mappings, narrow_mappings, broad_mappings

For each, confirm the CURIE resolves in a configured ontology. A label-vs-name check is reasonable but should probably be looser than for enum PVs, since a mapping isn't an exact identity. Suggested defaults:

• error on unresolvable / obsolete CURIEs for configured prefixes (mirrors the enum behavior),
• warn / info on label mismatch (configurable, off by default for related/narrow/broad).

Related observation (matching is element-side only)

For PVs, the match is: ontology primary label ∈ {PV text, title, description, aliases, structured_aliases, select annotations}. The ontology term's own synonyms are not consulted, so a legitimate common-name grounding fails unless the user adds the ontology label as a PV alias — e.g. switchgrass → NCBITaxon:38727 ("Panicum virgatum") fails until Panicum virgatum is added as an alias. Optionally consulting the adapter's exact/related synonyms would reduce that friction. Mentioning here for context; happy to split into a separate issue.

Environment: linkml-term-validator 0.3.0.

[github-actions]

Issue Summary & Analysis

What this issue asks for

Extend validate-schema to check ontology term groundings in slots and classes — specifically slot_uri, class_uri, and the five mapping slots (exact_mappings, close_mappings, related_mappings, narrow_mappings, broad_mappings) — applying the same CURIE-resolution and label-consistency checks that currently apply only to enum meaning fields.

Motivating real-world use case: Per-study LinkML "data dictionary" profiles where every slot carries slot_uri/exact_mappings to MIxS/BERVO/ENVO terms, but only categorical levels become enums. The enum-PV validator catches mis-groundings (e.g. NCBITaxon:62324 = Anopheles funestus, not Miscanthus), but the much larger set of slot-level mappings is completely unvetted.

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Current code architecture

The validation machinery is split across two layers:

Layer	File	Iterates
Legacy validator	validator.py → EnumValidator.validate_schema()	schema_view.all_enums() only
Plugin (validate-schema CLI)	plugins/permissible_value_plugin.py → PermissibleValueMeaningPlugin.process()	schema_view.all_enums() only

Both stop at enums. Slot and class definitions — with their slot_uri, class_uri, and *_mappings attributes — are never visited.

The key building block is already in place: BaseOntologyPlugin.get_ontology_label(curie) (in plugins/base.py) provides multi-level cached label lookup via OAK and can be reused directly.

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Implementation path

The cleanest approach is a new plugin (SlotClassMappingPlugin or similar) rather than extending PermissibleValueMeaningPlugin. This follows the existing composable plugin pattern and allows users to opt in/out independently.

The new plugin's process() would:

for slot_name, slot_def in self.schema_view.all_slots().items():
    for curie in [slot_def.slot_uri] + list(slot_def.exact_mappings or []) + ...:
        yield from self._validate_mapping(element="slot", name=slot_name, curie=curie, mapping_type="slot_uri")

for class_name, class_def in self.schema_view.all_classes().items():
    for curie in [class_def.class_uri] + list(class_def.exact_mappings or []) + ...:
        yield from self._validate_mapping(element="class", name=class_name, curie=curie, mapping_type="class_uri")

Severity recommendations (as proposed in the issue):

• slot_uri / class_uri unresolvable for configured prefix → ERROR
• exact_mappings unresolvable for configured prefix → ERROR
• Label mismatch on slot_uri/exact_mappings → WARN (configurable; loose matching appropriate since mapping ≠ identity)
• Label mismatch on related_/narrow_/broad_mappings → INFO or off by default
• Unconfigured prefix → INFO (mirrors current enum behavior in validate_enum())

The label-vs-name match for slots should use the slot's title, description, aliases, and name — analogous to extract_aliases() in PermissibleValueMeaningPlugin.

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Related open issues to be aware of

• _validate_label can crash on a non-string label value #38 – _validate_label can crash on non-string label values: any new code calling get_ontology_label() and then comparing the result should guard against this same bug. Fix _validate_label can crash on a non-string label value #38 first or in the same PR.
• Term validator silently passes when cache is missing for a prefix — should warn or fail #30 – Silent pass when cache is missing for a prefix: slot/class CURIEs from high-coverage ontologies like MIxS/ENVO will hit this gap. The same fix that addresses Term validator silently passes when cache is missing for a prefix — should warn or fail #30 for enum validation should apply here.
• Add option to include obsolete terms in reachable_from expansions #27 – Option to include obsolete terms in reachable_from: the issue explicitly mentions checking for obsolete CURIEs, which is the flip side of this — the new validator should flag them.

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Secondary observation: synonym matching is element-side only

The issue correctly notes that ontology synonyms are not consulted on the ontology side — the check is "does the ontology's primary label appear in the element's aliases?" not "does any of the ontology's synonyms match the element name?" This causes false positives, e.g. slot named switchgrass mapped to NCBITaxon:38727 ("Panicum virgatum") fails unless the user adds "Panicum virgatum" as an alias.

For slot/class mappings this friction will be even more pronounced, since slot names are often colloquial while slot_uri targets formal ontology labels. Consulting the OAK adapter's exact_synonyms() (or related_synonyms() for looser checks) in the match logic would substantially reduce false positives. This is a good candidate to address together with or just after this issue.

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@dragon-ai-agent suggestion

@dragon-ai-agent please implement a new SlotClassMappingPlugininsrc/linkml_term_validator/plugins/slot_class_mapping_plugin.py` that:

1. In pre_process(), captures context.schema_view
2. In process(), iterates schema_view.all_slots() and schema_view.all_classes(), checking slot_uri, class_uri, exact_mappings, close_mappings, related_mappings, narrow_mappings, broad_mappings for each
3. Calls self.get_ontology_label(curie) (inherited from BaseOntologyPlugin) to resolve each CURIE
4. Yields ValidationResult with ERROR for unresolvable CURIEs on configured prefixes, WARN for label mismatches (configurable, defaults to off for related/narrow/broad), INFO for unconfigured prefixes
5. Wires the new plugin into the validate-schema CLI subcommand in cli.py alongside the existing PermissibleValueMeaningPlugin
6. Adds unit tests using simpleobo:tests/data/test_ontology.obo following the pattern in tests/test_simple.py
   Also guard against the non-string label bug from _validate_label can crash on a non-string label value #38 in the new validation path.`