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    105 repositories

    • OKN-WOBD

      Public
      Python
      •2•2•3•0•Updated Apr 24, 2026Apr 24, 2026

    • coPI.science

      Public
      Python
      •0•1•0•1•Updated Apr 24, 2026Apr 24, 2026

    • sulab.org

      Public
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •9•0•0•1•Updated Apr 16, 2026Apr 16, 2026

    • DrugMechDB

      Public
      A database of paths that represent the mechanism of action from a drug to a disease in an indication.
      ncats-translator
      ncats-translator
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •22•72•9•3•Updated Apr 13, 2026Apr 13, 2026

    • TSRI-CBB

      Public
      This is the Github repository for The Scripps Research Institute Computational Biology and Bioinformatics (CBB) community and affiliated core track for graduate…
      HTML
      •0•7•1•0•Updated Mar 23, 2026Mar 23, 2026

    • agentic-bte

      Public
      Biomedical research platform combining LLMs with BioThings Explorer knowledge graphs. Features MCP Server and LangGraph multi-agent workflows for drug discovery…
      Python
      •
      MIT License
      •1•0•0•0•Updated Jan 30, 2026Jan 30, 2026

    • DBR-X

      Public
      DBR-X: Drug-Based Reasoning Explainer
      Jupyter Notebook
      •0•3•0•0•Updated Jan 14, 2026Jan 14, 2026

    • Applied-Bioinformatics-2025

      Public
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 4, 2025Mar 4, 2025

    • KnowledgeGraphEmbedding

      Public
      Jupyter Notebook
      •
      MIT License
      •272•1•0•0•Updated Aug 9, 2024Aug 9, 2024

    • CBRonMRN

      Public
      Python
      •0•0•0•0•Updated Feb 21, 2024Feb 21, 2024

    • WikidataIntegrator

      Public
      A Wikidata Python module integrating the MediaWiki API and the Wikidata SPARQL endpoint
      Python
      •
      MIT License
      •46•259•11•0•Updated Nov 14, 2023Nov 14, 2023

    • DMDB_Analysis

      Public
      Jupyter Notebook
      •2•0•0•2•Updated Apr 20, 2023Apr 20, 2023

    • DrugMechDB-1

      Public
      A database of paths that represent the mechanism of action from a drug to a disease in an indication.
      Jupyter Notebook
      •
      MIT License
      •22•0•0•0•Updated Apr 13, 2023Apr 13, 2023

    • path_plots

      Public
      A simple repo to quickly plot paths in a newtorkx graph
      Python
      •3•0•0•0•Updated Mar 23, 2023Mar 23, 2023

    • scheduled-bots

      Public
      GeneWiki Scheduled Bots
      Jupyter Notebook
      •
      MIT License
      •15•9•15•2•Updated Feb 17, 2023Feb 17, 2023

    • GeneWikiCentral

      Public
      GeneWiki Organization
      JavaScript
      •
      MIT License
      •2•5•74•9•Updated Feb 2, 2023Feb 2, 2023

    • mark2cure

      Public
      Mark2Cure allows anyone that can read English, regardless of background, to help in the process of biomedical discovery.
      Python
      •8•14•35•50•Updated Jan 11, 2023Jan 11, 2023

    • Lit2Hybrid

      Public
      Vue
      •0•0•0•26•Updated Jan 6, 2023Jan 6, 2023

    • genewikiworld

      Public
      Generate a network of all items we care about, and some we don't....
      Jupyter Notebook
      •
      Apache License 2.0
      •2•6•2•6•Updated Dec 8, 2022Dec 8, 2022

    • Wikidata-phenomizer

      Public
      Incorporate wikidata statements into phenomizer
      Jupyter Notebook
      •
      MIT License
      •1•3•0•22•Updated Dec 8, 2022Dec 8, 2022

    • wikidata-translate

      Public
      Python
      •2•0•0•6•Updated Dec 8, 2022Dec 8, 2022

    • Krusty

      Public
      neo4j <-> wikibase import/export tool
      neo4jwikibaseimport-export
      neo4jwikibaseimport-export
      Python
      •2•2•9•4•Updated Dec 8, 2022Dec 8, 2022

    • garbanzo

      Public
      Wikidata Semantic Query API
      Python
      •6•2•1•7•Updated Dec 7, 2022Dec 7, 2022

    • bioshovel

      Public
      Biological text mining tool.
      Python
      •1•3•0•1•Updated Oct 20, 2022Oct 20, 2022

    • Applied-Bioinformatics

      Public
      Student course material for the Applied Bioinformatics course at Scripps Research
      Jupyter Notebook
      •32•38•2•0•Updated Oct 11, 2022Oct 11, 2022

    • dataset-repository-selector

      Public
      A tool to help biologists make their datasets more findable, accessible, and schema.org-compliant
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Sep 21, 2022Sep 21, 2022

    • Wikidata_Biomedical-Subgraph

      Public
      This is a follow-up effort from work done within Waagmeester et al 2020 eLife and Mayers et al 2022 Bioinformatics
      pythonjsonwikidata
      pythonjsonwikidataknowledge-graphdrug-repurposing
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •0•0•3•0•Updated Aug 26, 2022Aug 26, 2022

    • sparql_to_pandas

      Public
      Example for accessing SPARQL endpoints in Python with Pandas
      Jupyter Notebook
      •9•13•0•7•Updated Aug 23, 2022Aug 23, 2022

    • biogps_core

      Public
      JavaScript
      •
      GNU General Public License v3.0
      •0•0•50•3•Updated Jul 8, 2022Jul 8, 2022

    • niaid-data-portal

      Public
      NIAID Dataset Portal
      Python
      •
      MIT License
      •2•0•0•0•Updated May 18, 2022May 18, 2022
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