spec/spec.md

THIRAWAT-mapper-demo

End-to-end demo of THIRAWAT-mapper, a tool for mapping concepts from non-standard terminologies to standard terminologies in OHDSI/OMOP CDM.

Key steps

1. Turn the vocab set downloaded from Athena into DuckDB format using pip install athena2duckdb [https://pypi.org/project/athena2duckdb/]
2. Follow instructions in THIRAWAT-mapper
3. Use [https://huggingface.co/cambridgeltl/SapBERT-UMLS-2020AB-all-lang-from-XLMR] for retrieval with CLS pooling and [https://huggingface.co/sidataplus/THIRAWAT-SapBERT] for ColBERT reranker
4. Build a complete gradio app, see prelim example [spec/example.py]
5. Package everything into a Hugging Face Space [https://huggingface.co/spaces/sidataplus/THIRAWAT-mapper-demo]