[FEATURE] Ontology Alignment

[KaifAhmad1]

Map and connect different ontologies together so Semantica can unify data across systems, standards, and domains.

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Modules and Folders Involved

• Alignment logic builds on:
  • semantica/ontology/ (public APIs, namespace handling, reuse).
  • semantica/triplet_store/ (storage of alignment triples and queries).
• Tests should be added to:
  • tests/ontology/
  • tests/triplet_store/
• Use only the existing semantica/ and tests/ directories; no new top‑level folders.

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Feature Behaviour

• Represents alignments between ontology entities (classes, properties, concepts) using standard predicates.
• Stores alignments as RDF triples in the existing triplet store.
• Exposes APIs to create, list, and query alignments.
• Allows query and validation engines to optionally use alignment information when reasoning over data.

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Why Alignment Matters

• Enables cross‑system interoperability and semantic integration.
• Lets a single semantic layer span multiple standards (e.g. internal model + industry models).
• Supports multi‑domain knowledge graphs where different ontologies must co‑exist.
• Critical for complex enterprise environments with many data sources and schemas.

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Existing Code and Tests

• Ontology
  • semantica/ontology/engine.py
  • semantica/ontology/namespace_manager.py
  • semantica/ontology/module_manager.py
  • semantica/ontology/reuse_manager.py
• Triplet store
  • semantica/triplet_store/triplet_store.py
  • semantica/triplet_store/query_engine.py
• Docs and tests
  • docs/reference/ontology.md
  • docs/reference/triplet_store.md
  • tests/ontology/test_ontology_advanced.py
  • tests/triplet_store/test_triplet_store.py

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New Functionality to Add

• Alignment representation
  • Use owl:equivalentClass, owl:equivalentProperty, skos:exactMatch, etc., stored as triples in TripletStore.
• Namespace support
  • In semantica/ontology/namespace_manager.py:
    • Confirm OWL and SKOS namespaces, and expose helpers if helpful.
• Alignment APIs
  • In semantica/ontology/engine.py (or a small helper inside ontology package):
    • Implement create_alignment, get_alignments, list_alignments methods that call TripletStore.
• Import‑time alignment suggestions
  • In semantica/ontology/reuse_manager.py:
    • Optionally compute suggested alignments when importing external ontologies.
• Alignment‑aware queries
  • In semantica/triplet_store/query_engine.py:
    • Add helpers to expand entity URIs to include aligned entities when use_alignments=True.
• Documentation and tests
  • Extend the docs and tests listed above with:
    • Examples of alignment creation.
    • Queries that use alignments to retrieve cross‑ontology results.

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Implementation Walkthrough

1. Alignment representation in RDF

   • Use standard predicates such as:
     • owl:equivalentClass
     • owl:equivalentProperty
     • skos:exactMatch, skos:closeMatch
   • In ontology/namespace_manager.py:
     • Confirm namespaces are defined for OWL and SKOS.

2. Alignment management API

   • In ontology/engine.py (or a small helper within the ontology package):
     • Implement public methods:
       • create_alignment(source_uri: str, target_uri: str, predicate: str) -> None
       • get_alignments(entity_uri: str) -> List[Dict[str, Any]]
       • list_alignments(ontology_uri: Optional[str] = None) -> List[Dict[str, Any]]
     • These methods should:
       • Use TripletStore APIs to write and read alignment triples.

3. Integration with reuse_manager

   • In ontology/reuse_manager.py:
     • When importing external ontologies or mapping them into a project:
       • Optionally create suggested alignments (e.g. based on identical URIs, labels, or provided mapping configs).

4. Query helpers using alignments

   • In triplet_store/query_engine.py:
     • Add helper functions that:
       • Given an entity URI, expand it into a set including aligned entities when a flag use_alignments=True is passed.
       • Allow higher‑level components to build queries that respect alignments.

5. Documentation

   • In docs/reference/ontology.md:
     • Add “Ontology Alignment” section demonstrating:
       • Creating alignments between two ontologies.
       • Running a query or validation that uses alignments.
   • Link from docs/reference/triplet_store.md where SPARQL helpers are documented.

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Finished When

• Contributors can programmatically:
  • Create alignments between ontology entities.
  • List and query alignments for a given entity or ontology.
• Triplet store helpers can expand queries using alignment information when requested.
• Tests cover:
  • Creating and retrieving alignment triples.
  • Using alignment‑aware queries to retrieve instances across aligned classes.
• Documentation makes it clear how ontology alignment fits into Semantica’s data integration story.