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1. biomapper2 biomapper2 Public

   Map biomedical entities to KG nodes (entity linking and resolution)

   Python 1 1

2. biovector-eval biovector-eval Public

   A framework for optimizing vector databases in biological/biomedical domains. Evaluates embedding models, quantization strategies, and index configurations for metabolites, proteins, clinical tests…

   Jupyter Notebook

3. ddharmon ddharmon Public

   Data Dictionary Harmonization Tool: cluster equivalent variables across studies and anchor each to a Common Data Element (CDE), routed to expert review — library, notebooks, and CLI. (Web GUI on th…

   Python

4. PortFlow PortFlow Public

   A small toolkit for model portability. Includes conditional normalizing flows for fast imputation, transfer lasso for transfer learning of linear models, and PortFlow which combines both into a sin…

   Python

5. biomapper biomapper Public

   Python

6. ddharmon-ui ddharmon-ui Public

   Web GUI for ddharmon — upload data dictionaries, run the harmonization pipeline with live progress, review recommendations, export the review queue. Built on the Phenome-Health/ddharmon library.

   TypeScript