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README.md
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A MCP server for extracting and normalizing domain-specific entities from biomedical text. We leverage OpenAI LLMs to identify entities and match them to standardized terminology.
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## Installation
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This project uses `uv` from Astral for dependency management. Follow these steps to set up the project:
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- `target_entity`: Type of entity to extract ("Disease", "Tissue", or "Cell Type")
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and returns a list of normalized entities.
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A MCP server for extracting and normalizing domain-specific entities from biomedical text. We leverage OpenAI LLMs to identify entities and match them to standardized terminology.
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## Motivation
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Biomedical text normalization addresses a critical challenge in healthcare informatics: approximately 80% of electronic health record (EHR) data exists as unstructured medical text. Such text often contains abbreviations, misspellings, and non-standardized terminology, creating barriers to effective data utilization. This variability hinders leveraging clinical narratives for:
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- **Clinical decision support** at the point of care
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- **Patient comprehension** of their own medical records
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- **Biomedical research** including cohort identification and pharmacovigilance
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By implementing named entity recognition and normalization to controlled vocabularies like SNOMED-CT, our MCP server enables downstream applications to process biomedical text with greater accuracy, bridging the gap between natural clinical language and structured data requirements of modern healthcare systems.
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## Installation
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This project uses `uv` from Astral for dependency management. Follow these steps to set up the project:
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- `target_entity`: Type of entity to extract ("Disease", "Tissue", or "Cell Type")
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and returns a list of normalized entities.
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## Future Improvements
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Our biomedical text normalization MCP server can be enhanced in several ways:
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- Expanded Entity Coverage: Extend beyond the current entity types (Disease, Tissue, Cell Type) to include medications, procedures, laboratory tests, and genomic entities.
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- User Feedback Loop: Implement a mechanism for users to correct normalization errors, creating a dataset for continuous model improvement.
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- Multilingual Support: Expand capabilities to handle medical text in languages beyond English.
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