Handover Document: Dynamic Ontology Feature

Progress Summary

Tasks Completed This Session

1. Feature Gates Implementation

   • Added feature gates to terraphim_types/Cargo.toml: ontology (default), medical, hgnc
   • Made EntityType/RelationshipType enums feature-gated with #[cfg(feature = "medical")]
   • Changed ExtractedEntity.entity_type and ExtractedRelationship.relationship_type to String-based types for cross-domain use
   • Feature-gated HgncNormalizer module with #[cfg(feature = "hgnc")]

2. Knowledge Graph Normalization Example

   • Created crates/terraphim_types/examples/kg_normalization.rs
   • Loads markdown documents from knowledge corpus
   • Builds ontology with extracted terms
   • Extracts entities with confidence scores
   • Computes coverage signals
   • Exports thesaurus for Terraphim automata

3. Verification

   • Tested with and without hgnc feature
   • Verified extraction works: 1013 documents, 4090 terms extracted
   • Domain concepts correctly identified: knowledge graphs, ontology, schema, inference, entity, relationship

4. Documentation

   • Created docs/src/dynamic-ontology.md (technical docs)
   • Created docs/blog/dynamic-ontology-launch.md (blog post)
   • Created docs/blog/announcement-dynamic-ontology.md (announcement templates)
   • Updated docs/src/SUMMARY.md

5. Release

   • Committed: a3a8c152
   • Tagged: v1.9.0
   • Pushed to remote

Current Implementation State

All Dynamic Ontology feature gates implemented and functional:

• Core generic types (GroundingMetadata, CoverageSignal, SchemaSignal) available by default
• Medical-specific types gated behind medical feature
• HGNC gene normalization gated behind hgnc feature
• Examples demonstrate both string-based and enum-based usage

What's Working

• Feature gates compile with all feature combinations
• kg_normalization example extracts domain concepts correctly
• Coverage signals compute quality governance
• No vector embeddings required - uses existing automata

What's Blocked

Nothing blocked. Feature is complete and pushed to remote.

Technical Context

# Current branch
main

# Recent commits
a3a8c152 docs: add Dynamic Ontology documentation and blog posts
48214f51 feat(terraphim_types): add knowledge graph normalization example
0f443e27 feat(terraphim_types): implement dynamic ontology feature gates

# Modified files
docs/src/dynamic-ontology.md (new)
docs/blog/dynamic-ontology-launch.md (new)
docs/blog/announcement-dynamic-ontology.md (new)
docs/src/SUMMARY.md (modified)

Key Files

| File | Purpose | |------|---------| | crates/terraphim_types/Cargo.toml | Feature gate definitions | | crates/terraphim_types/src/lib.rs | Core types with feature gates | | crates/terraphim_types/examples/kg_normalization.rs | Demo example | | docs/src/dynamic-ontology.md | Technical documentation |

How to Test

# Run without hgnc feature
cargo run --example kg_normalization -p terraphim_types

# Run with hgnc feature
cargo run --example ontology_usage -p terraphim_types --features hgnc

Next Steps (If Continuing)

1. Automatic ontology expansion based on coverage gaps
2. Integration with external ontologies (UniProt, ChEBI)
3. Batch processing for large document sets