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    42 repositories

    • biochatter

      Public
      Backend library for conversational AI in biomedicine
      chatbotknowledge-graphvector-databasellmretrieval-augmented-generationbiocypher
      Jupyter Notebook
      •
      MIT License
      •46•168•103•9•Updated Jun 18, 2025Jun 18, 2025

    • tcr-epitope

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•4•0•Updated Jun 18, 2025Jun 18, 2025

    • documentation

      Public
      This is the unified documentation of BioCypher ecosystem libraries
      2•0•0•0•Updated Jun 17, 2025Jun 17, 2025

    • biocage

      Public
      Fast, secure, and practical Python sandbox designed specifically for safely executing code generated by LLMs
      Python
      •
      MIT License
      •0•1•0•0•Updated Jun 11, 2025Jun 11, 2025

    • biocypher

      Public
      A unifying framework for biomedical research knowledge graphs
      bioinformaticsframeworksqlneo4jrdfpostgresqlontologyknowledge-graphbiomedicalrdfs
      Python
      •
      MIT License
      •38•255•181•1•Updated Jun 10, 2025Jun 10, 2025

    • omnipath-secondary-adapter

      Public
      BioCypher adapter to retrieve data from Omnipath database (Networks, Intercell, Complexes, EnzymePTM and Annotations).
      neo4jknowledge-graphbiological-networksbiocypherontoweaver
      Jupyter Notebook
      •
      MIT License
      •3•0•6•0•Updated Jun 10, 2025Jun 10, 2025

    • biochatter-light

      Public
      The light frontend for BioChatter, in pure Python
      Python
      •
      MIT License
      •14•54•19•2•Updated Jun 7, 2025Jun 7, 2025

    • project-template

      Public template
      Template for creating a BioCypher-driven knowledge graph
      Python
      •
      MIT License
      •8•12•1•0•Updated Jun 2, 2025Jun 2, 2025

    • biotope

      Public
      The repository for creating a command line integration for biocypher software components
      Python
      •
      MIT License
      •0•1•0•0•Updated May 16, 2025May 16, 2025

    • open-targets

      Public
      Python
      •
      MIT License
      •5•15•8•0•Updated May 7, 2025May 7, 2025

    • biogather

      Public
      Placeholder
      Python
      •
      MIT License
      •1•0•0•0•Updated Feb 26, 2025Feb 26, 2025

    • metalinks

      Public
      Python
      •
      GNU General Public License v3.0
      •2•6•5•0•Updated Feb 7, 2025Feb 7, 2025

    • .github

      Public
      0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

    • DFG528753569

      Public
      Home of the software sustainability project under No. DFG 528753569
      0•0•11•0•Updated Jan 22, 2025Jan 22, 2025

    • biochatter-next

      Public
      The advanced implementation for BioChatter, using Next.js
      TypeScript
      •
      MIT License
      •9•13•10•1•Updated Jan 17, 2025Jan 17, 2025

    • biochatter-server

      Public
      FastAPI server for BioChatter integration into web apps
      Python
      •
      MIT License
      •10•3•2•0•Updated Jan 14, 2025Jan 14, 2025

    • scverse-x-biochatter

      Public
      Repository for collecting code generated in the 2024 de.NBI BioHackathon 3 that does not clearly belong somewhere else
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •2•3•0•0•Updated Dec 13, 2024Dec 13, 2024

    • project-planning

      Public
      Demo use case for BioChatter: scheduling of project work
      Python
      •
      MIT License
      •0•0•11•0•Updated Dec 9, 2024Dec 9, 2024

    • pole

      Public
      Demo data repository (crime statistics)
      Python
      •
      MIT License
      •3•4•2•0•Updated Dec 6, 2024Dec 6, 2024

    • issues

      Public
      This is a special repository that contains only issues that go beyond a single package and rather affect the whole ecosystem and its management.
      0•0•4•0•Updated Dec 4, 2024Dec 4, 2024

    • collectri

      Public
      Python
      •
      MIT License
      •3•1•0•1•Updated Dec 3, 2024Dec 3, 2024

    • biocypher-paper

      Public
      HTML
      •
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • scirpy-collaboration

      Public
      Repository for organising the scirpy-biocypher collaboration
      0•0•13•0•Updated Nov 11, 2024Nov 11, 2024

    • meta-graph

      Public
      A meta-graph of BioCypher modular adapters, created by a BioCypher pipeline
      Python
      •
      MIT License
      •1•4•5•0•Updated Nov 8, 2024Nov 8, 2024

    • igvf-catalog

      Public
      Catalog API for the IGVF project (fork from the original at IGVF-DACC)
      Python
      •
      MIT License
      •4•0•0•0•Updated Nov 8, 2024Nov 8, 2024

    • OTAR3088

      Public
      Project management for the BioCypher parts of OTAR3088
      0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • patient-kg

      Public
      BioCypher Knowledge Graph for clinical patient data (ICD10, Snomed CT, Loinc, german OPS)
      Jupyter Notebook
      •
      MIT License
      •0•5•0•0•Updated Oct 11, 2024Oct 11, 2024

    • decider-genetics

      Public
      Python
      •
      MIT License
      •4•1•3•0•Updated Aug 26, 2024Aug 26, 2024

    • graphpack

      Public
      A Python tool to perform graph compression and visualization
      Python
      •
      MIT License
      •0•1•1•0•Updated Aug 2, 2024Aug 2, 2024

    • biomedical-resource-ontology

      Public
      A repository to store our version of the BRO
      MIT License
      •2•0•0•1•Updated Jul 31, 2024Jul 31, 2024
    0