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@SCAI-BIO Fraunhofer SCAI Biomedical Data Intelligence Unit

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    Repositories list

    55 repositories

    • internal-mcp-server

      Public
      Turn any OpenAPI into an internal Model Context Protocol (MCP) server, making existing services accessible to AI assistants and agents.
      internal-toolsmcpapi-wrapper
      internal-toolsmcpapi-wrapperdeveloper-toolsapi-integrationmodel-context-protocolmcp-server
      Python
      •
      Apache License 2.0
      •0•0•0•2•Updated Oct 30, 2026Oct 30, 2026

    • kitsune

      Public
      A data stewardship tool for semi-automatic semantic mapping and harmonization of data dictionaries using standardized vocabularies and ontologies.
      ontologybiomedical-informaticsdata-dictionary
      ontologybiomedical-informaticsdata-dictionarycontrolled-vocabulariessemantic-searchhuman-in-the-loopdata-harmonizationsemantic-mappingsemantic-interoperabilitydata-stewardship
      TypeScript
      •
      Apache License 2.0
      •1•3•9•3•Updated Oct 30, 2026Oct 30, 2026

    • syndat

      Public
      Synthetic data quality evaluation & visualization
      pythonbioinformaticsdata-visualization
      pythonbioinformaticsdata-visualizationdata-qualitysynthetic-data
      Python
      •
      MIT License
      •1•14•15•0•Updated Oct 28, 2026Oct 28, 2026

    • PDataViewer

      Public
      A web application for visualizing the landscape of Parkinson’s disease cohorts.
      data-visualizationbiomedical-informaticslongitudinal-data
      data-visualizationbiomedical-informaticslongitudinal-datadata-explorationparkinsons-diseaseclinical-datacohort-selectioncohort-studiesresearch-software
      TypeScript
      •
      Apache License 2.0
      •0•3•2•0•Updated Oct 28, 2026Oct 28, 2026

    • psychstrata-dashboard

      Public
      Dashboard for Shared Decision Making on Treatment Resistance (TR) in Major Depressive Disorder (MDD)
      dashboardpsychiatrymajor-depressive-disorder
      dashboardpsychiatrymajor-depressive-disordertreatment-response
      TypeScript
      •
      Apache License 2.0
      •1•1•10•1•Updated Oct 28, 2026Oct 28, 2026

    • MultiNSDE

      Public
      Official code implementation for the MultiNSDE paper.
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 28, 2026Oct 28, 2026

    • ADHTEB

      Public
      ADHTEB - Alzheimers Disease Harmonization Text Embedding Benchmark
      benchmarkalzheimers-diseasedata-harmonization
      benchmarkalzheimers-diseasedata-harmonizationllms
      Python
      •
      Apache License 2.0
      •0•10•2•0•Updated Oct 26, 2026Oct 26, 2026

    • pytmle

      Public
      A Flexible Python Implementation of Targeted Estimation for Survival and Competing Risks Analysis
      Python
      •
      Apache License 2.0
      •1•3•0•1•Updated Oct 26, 2026Oct 26, 2026

    • datastew

      Public
      Python library for intelligent data stewardship using Large Language Model (LLM) embeddings
      data-harmonizationdata-stewardshiplarge-language-models
      data-harmonizationdata-stewardshiplarge-language-models
      Python
      •
      Apache License 2.0
      •0•14•8•0•Updated Oct 26, 2026Oct 26, 2026

    • tausurv

      Public
      A complete survival analysis library for Python
      Python
      •
      MIT License
      •0•5•2•2•Updated Oct 22, 2026Oct 22, 2026

    • commute-tmle

      Public
      Code accompanying the paper "Documented SARS-CoV-2 infection and risk of neurodegenerative disease diagnosis: a target trial emulation across three real-world c…
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 21, 2026Oct 21, 2026

    • dg-msm

      Public
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated Sep 23, 2026Sep 23, 2026

    • radar-ad-rmt-analysis

      Public
      Python
      •0•0•0•0•Updated Aug 28, 2026Aug 28, 2026

    • tau-kg-benchmarking-GPT

      Public
      Benchmarking the performance of GPT-based LLMs against human curated Tau KG from Human Brain Pharmacome (HBP)
      Jupyter Notebook
      •
      Apache License 2.0
      •1•1•0•0•Updated Aug 13, 2026Aug 13, 2026

    • apta

      Public
      Text-to-Graph Framework for Post-Covid Mechanisms & Therapeutic Targeting
      HTML
      •0•0•0•0•Updated Jun 11, 2026Jun 11, 2026

    • primekg-rag

      Public
      RAG-based method for mapping variables to PrimeKG subgraphs with textual graph descriptions.
      knowledge-graphragllm
      knowledge-graphragllmprimekggraph-retrieval
      Python
      •
      Apache License 2.0
      •0•3•0•0•Updated Jun 10, 2026Jun 10, 2026

    • Guidelines_Store_Agent

      Public
      This repository contains the implementation of a constrained clinical reasoning agent for evidence-grounded question answering over a partially harmonized biome…
      Python
      •
      MIT License
      •0•0•0•0•Updated May 13, 2026May 13, 2026

    • covid-NDD-comorbidity-NLP

      Public
      This work aims to integrate diverse, curated biological databases with a comprehensive analysis of the growing body of literature on the potential long-term ne…
      Jupyter Notebook
      •1•4•0•0•Updated Apr 17, 2026Apr 17, 2026

    • tau-kg-extension-nlp

      Public
      Extending the Tau subgraph within the pharmacome using NLP.
      Jupyter Notebook
      •0•0•0•0•Updated Mar 6, 2026Mar 6, 2026

    • CGEx

      Public
      CGEx (Cypher Generating Expert), a system that enables users to interact with a COVID-NDD comorbidity knowledge graph using simple natural language questions. C…
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 23, 2025Dec 23, 2025

    • ollama-docker

      Public
      Pre-build docker containers for different LLMs using Ollama
      dockerllmollama
      dockerllmollama
      Shell
      •
      Apache License 2.0
      •0•1•0•0•Updated Nov 19, 2025Nov 19, 2025

    • covid-NDD-image-based-information-extraction

      Public
      Extracting structured knowledge from biomedical images using LLMs, focusing on COVID-19 and neurodegeneration. Leverages GPT-4o for image analysis and semantic …
      Jupyter Notebook
      •1•0•0•1•Updated Nov 6, 2025Nov 6, 2025

    • MultiNODEs

      Public
      Python
      •
      MIT License
      •2•10•0•0•Updated Sep 5, 2025Sep 5, 2025

    • SEEDS

      Public
      SEEDS (Similarity based Expert Embedding Decision System) is a Retrieval-Augmented Generation (RAG) based agricultural question-answering (QA) system. It is bui…
      Python
      •
      Apache License 2.0
      •1•2•0•0•Updated Aug 21, 2025Aug 21, 2025

    • BiomarkerOntology

      Public
      The Biomarker Ontology
      0•0•1•0•Updated Jul 31, 2025Jul 31, 2025

    • CBM-Comorbidity-KG

      Public
      a manually curated, comorbidity-centric knowledge graph linking COVID-19 to neurodegenerative diseases
      Cypher
      •
      Apache License 2.0
      •1•0•0•0•Updated Jun 12, 2025Jun 12, 2025

    • cv-extraction

      Public
      Web-Tool for LLM based CV extraction
      text-miningresume-parserllm
      text-miningresume-parserllm
      Python
      •
      Apache License 2.0
      •0•1•2•0•Updated May 5, 2025May 5, 2025

    • PD-diagnostic-delay

      Public
      Parkinson's disease diagnostic delay analysis
      0•1•0•0•Updated Mar 31, 2025Mar 31, 2025

    • causal-npi-effects

      Public
      A causal machine learning framework to assess effects of non-pharmaceutical interventions on pandemic disease spread.
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 18, 2025Mar 18, 2025

    • MMPK-SciML

      Public
      Official implementation of the paper Scientific Machine learning for predicting plasma concentrations in anti-cancer therapy
      Python
      •
      MIT License
      •0•4•0•0•Updated Mar 11, 2025Mar 11, 2025
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