kempersc 554fe520ea Add comprehensive rules for LinkML schema management and ontology mapping

- Introduced Rule 42: No Ontology Prefixes in Slot Names to enforce clean naming conventions.
- Established Rule: No Rough Edits in Schema Files to ensure structural integrity during modifications.
- Implemented Rule: No Version Indicators in Names to maintain stable semantic naming.
- Created Rule: Ontology Detection vs Heuristics to emphasize the importance of verifying ontology definitions.
- Defined Rule 50: Ontology-to-LinkML Mapping Convention to standardize mapping practices.
- Added Rule: Polished Slot Storage Location to specify directory structure for polished slot files.
- Enforced Rule: Preserve Bespoke Slots Until Refactoring to prevent unintended migrations during slot updates.
- Instituted Rule 56: Semantic Consistency Over Simplicity to mandate execution of revisions in slot_fixes.yaml.
- Added new Genealogy Archives Registry Enrichment class with multilingual support and structured aliases.

2026-02-15 19:20:09 +01:00

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Exact Mapping Predicate/Class Distinction Rule

🚨 CRITICAL: The exact_mappings property implies semantic equivalence. Equivalence can only exist between elements of the same ontological category.

The Rule

Slots (Predicates) MUST ONLY have exact_mappings to ontology predicates (properties).
- ❌ INVALID: Slot analyze maps to schema:object (a Class).
- ✅ VALID: Slot analyze maps to crm:P129_is_about (a Property).
Classes (Entities) MUST ONLY have exact_mappings to ontology classes (entities).
- ❌ INVALID: Class Person maps to foaf:name (a Property).
- ✅ VALID: Class Person maps to foaf:Person (a Class).
When true equivalence exists and is verified, exact mapping is preferred.
- ✅ VALID: Class Acquisition maps to crm:E8_Acquisition.
- ✅ VALID: Slot mapped to an actually equivalent ontology property.
- ❗ Do not avoid exact_mappings by default; avoid only when scope is broader/narrower/similar-but-not-equal.

Rationale

Mapping a slot (which defines a relationship or attribute) to a class (which defines a type of entity) is a category error. schema:object represents the class of objects, not the relationship of "having an object" or "analyzing an object".

Verification Checklist

When adding or reviewing exact_mappings:

Is the LinkML element a Class or a Slot?
Did you verify the target term type in the ontology definition files (do not rely on naming heuristics)?
Do they match? (Class↔Class, Slot↔Property)
If the target ontology uses opaque IDs (like CIDOC-CRM E55_Type), verify the type definition in the ontology file.
If semantic scope is truly equivalent, use exact_mappings (not close/broad as a conservative fallback).

Common Pitfalls to Fix

Mapping slots to schema:Object or schema:Thing.
Mapping slots to skos:Concept.
Mapping classes to schema:name or dc:title.

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