| | --- |
| | 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`) |
| | - **ChromaDB** → vector embeddings (see `bioportal_chroma`) for semantic retrieval |
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| | 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. |
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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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| |
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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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| |
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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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