| --- |
| license: apache-2.0 |
| language: |
| - en |
| tags: |
| - ontology |
| - knowledge-graphs |
| - embeddings |
| --- |
| |
| # Ontology & Embedding Database |
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| 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. |
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| ## Overview |
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| - **3,925,124 classes** |
| - **2,683,756 synonyms** |
| - Data storage: |
| - **SQLite** → structured ontology data (`bioportal.db`) |
| - **Embeddings** → vector embeddings (to be uploaded) |
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| Vector embeddings (includes preferred label + definition + synonyms + alternative labels + parent labels + ontology context) are generated using the `BAAI/bge-small-en-v1.5` model to enable high-quality semantic similarity search. |
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| ## Database Schema (Main Tables) |
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| If you plan to extend or enrich the database, the primary tables include: |
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| - `ontologies` |
| - `classes` |
| - `synonyms` |
| - `labels` |
| - `parents` |
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| ## 🔎 Search & Query |
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| You can explore the ontology, perform semantic search, and run database queries via the Hugging Face Space: |
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| 👉 https://huggingface.co/spaces/sensein/demo-ontology-search |
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| ## Data Source |
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| The original ontology data is sourced from **BioPortal**, which aggregates biomedical ontologies from multiple authoritative providers. |
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