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    • Pathway Commons binary SIF graph web service
      Java
      MIT License
      1120Updated Apr 10, 2026Apr 10, 2026
    • cpath2

      Public
      Biological pathway data integration and access platform (Pathway Commons)
      Java
      MIT License
      5671Updated Jul 12, 2025Jul 12, 2025
    • app-ui

      Public
      Web UI for accessing Pathway Commons data
      JavaScript
      MIT License
      174123Updated Apr 24, 2025Apr 24, 2025
    • factoid

      Public
      A project to capture biological pathway data from academic papers
      JavaScript
      MIT License
      729314Updated Mar 24, 2025Mar 24, 2025
    • A biological entity grounding search service
      JavaScript
      MIT License
      5860Updated Jan 6, 2025Jan 6, 2025
    • Hyper-recent article feed
      JavaScript
      MIT License
      0120Updated Oct 15, 2024Oct 15, 2024
    • about

      Public
      Pathway Commons Home Page (/about/)
      SCSS
      2320Updated Aug 22, 2024Aug 22, 2024
    • Web services for Factoid project to convert between JSON, BioPAX, SBGN data formats
      Java
      MIT License
      2250Updated Jun 24, 2024Jun 24, 2024
    • guide

      Public
      Resource for pathway analysis and Pathway Commons
      HTML
      0400Updated Apr 11, 2024Apr 11, 2024
    • Comparative Toxicogenomics Database (CTD) to BioPAX Level3 data converter.
      Java
      0101Updated Mar 10, 2024Mar 10, 2024
    • SBML to BioPAX Level3 converter, specific to the Recon2 data.
      Java
      0000Updated Feb 20, 2024Feb 20, 2024
    • DrugBank to BioPAX Level3 data converter.
      Java
      0200Updated Feb 20, 2024Feb 20, 2024
    • Java
      MIT License
      0000Updated Feb 11, 2024Feb 11, 2024
    • MSigDB (human C3 TFT motif gene sets only) to BioPAX Level3 data converter.
      Java
      0000Updated Feb 4, 2024Feb 4, 2024
    • MiRTarBase to BioPAX Level3 data converter.
      Java
      0010Updated Jan 27, 2024Jan 27, 2024
    • CyPath2

      Public
      Cytoscape 3 app that connects to PC2 (cpath2) and imports BioPAX sub-networks into Cytoscape 3 for analysis.
      Java
      GNU Lesser General Public License v2.1
      4240Updated Nov 19, 2023Nov 19, 2023
    • A Docker image that provides a RethinkDB database
      Dockerfile
      0010Updated Nov 1, 2023Nov 1, 2023
    • A simple semantic search engine for scientific papers.
      Python
      MIT License
      02874Updated Sep 14, 2023Sep 14, 2023
    • Chisio Layout (ChiLay) graph layout framework for SBGN
      Java
      3000Updated Aug 5, 2023Aug 5, 2023
    • A workflow for classifying articles
      Python
      MIT License
      0020Updated May 30, 2023May 30, 2023
    • ncbiutils

      Public
      A wrapper for retrieving records from PubMed
      Python
      MIT License
      0200Updated Feb 23, 2023Feb 23, 2023
    • A tool to classify journal abstracts with pathway content.
      Jupyter Notebook
      MIT License
      1010Updated Jan 4, 2023Jan 4, 2023
    • sifgraph

      Public
      Modeling and querying support for SIF graphs
      Java
      MIT License
      0110Updated Oct 29, 2022Oct 29, 2022
    • chibe

      Public
      Pathway visualization and analysis tool for Pathway Commons and other BioPAX data
      Java
      Eclipse Public License 1.0
      914131Updated May 25, 2022May 25, 2022
    • Enables a client to dump and retrieve data from a RethinkDB instance
      JavaScript
      MIT License
      0000Updated Jan 12, 2022Jan 12, 2022
    • pubmed-dl

      Public
      Python
      MIT License
      0010Updated Feb 10, 2021Feb 10, 2021
    • View biological networks via Cytoscape.js and sbgn-ml
      JavaScript
      MIT License
      3270142Updated Feb 9, 2021Feb 9, 2021
    • pcviz

      Public
      Pathway Commons Bio Network Visualizer
      JavaScript
      MIT License
      3890Updated Sep 12, 2019Sep 12, 2019
    • pcapi

      Public archive
      The Web API Docs App
      JavaScript
      0000Updated Sep 8, 2018Sep 8, 2018
    • An npm module that converts xml based SBGN files to JSON for Cytoscape.js
      JavaScript
      MIT License
      4550Updated Jun 19, 2018Jun 19, 2018
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