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license: apache-2.0
language:
- en
tags:
- ontology
- knowledge-graphs
- embeddings
---
# 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
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:
- `ontologies`
- `classes`
- `synonyms`
- `labels`
- `parents`
## 🔎 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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