---
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.