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Ontology & Embedding Database
This repository provides the local ontology database to be used by StructSense (in general can be used for any other purpose), including both structured ontological data and precomputed vector embeddings for efficient semantic search.
Overview
- 3,925,124 classes
- 2,683,756 synonyms
- Data storage:
- SQLite → structured ontology data (
bioportal.db) - ChromaDB → vector embeddings (see
bioportal_chroma) for semantic retrieval
- SQLite → structured ontology data (
Vector embeddings (includes label + synonyms + alternative labels + definition) are generated using the BAAI/bge-large-en-v1.5 model to enable high-quality semantic similarity search.
Database Schema (Main Tables)
If you plan to extend or enrich the database, the primary tables include:
ontologiesclassessynonymslabelsparents
🔎 Search & Query
You can explore the ontology, perform semantic search, and run database queries via the Hugging Face Space:
👉 https://huggingface.co/spaces/sensein/demo-ontology-search
Data Source
The original ontology data is sourced from BioPortal, which aggregates biomedical ontologies from multiple authoritative providers.
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