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@PathwayCommons Pathway Commons

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    45 repositories

    • factoid

      Public
      A project to capture biological pathway data from academic papers
      JavaScript
      •
      MIT License
      •7•28•26•4•Updated Nov 9, 2024Nov 9, 2024

    • hyper-recent

      Public
      Hyper-recent article feed
      JavaScript
      •
      MIT License
      •0•1•2•0•Updated Oct 15, 2024Oct 15, 2024

    • app-ui

      Public
      Web UI for accessing Pathway Commons data
      JavaScript
      •
      MIT License
      •16•2•13•2•Updated Sep 23, 2024Sep 23, 2024

    • about

      Public
      Pathway Commons Home Page (/about/)
      SCSS
      •2•3•2•0•Updated Aug 22, 2024Aug 22, 2024

    • grounding-search

      Public
      A biological entity grounding search service
      searchidentifiersbiological-entitiesgrounding
      JavaScript
      •
      MIT License
      •5•8•9•0•Updated Aug 6, 2024Aug 6, 2024

    • cpath2

      Public
      Biological pathway data integration and access platform (Pathway Commons)
      Java
      •
      MIT License
      •5•6•7•0•Updated Jul 12, 2024Jul 12, 2024

    • factoid-converters

      Public
      Web services for Factoid project to convert between JSON, BioPAX, SBGN data formats
      Java
      •
      MIT License
      •2•2•5•0•Updated Jun 24, 2024Jun 24, 2024

    • sifgraph-server

      Public
      Pathway Commons binary SIF graph web service
      Java
      •
      MIT License
      •0•1•2•0•Updated Jun 24, 2024Jun 24, 2024

    • guide

      Public
      Resource for pathway analysis and Pathway Commons
      HTML
      •0•4•0•0•Updated Apr 11, 2024Apr 11, 2024

    • ctd-to-biopax

      Public
      Comparative Toxicogenomics Database (CTD) to BioPAX Level3 data converter.
      Java
      •0•1•0•1•Updated Mar 10, 2024Mar 10, 2024

    • reconx-to-biopax

      Public
      SBML to BioPAX Level3 converter, specific to the Recon2 data.
      Java
      •0•0•0•0•Updated Feb 20, 2024Feb 20, 2024

    • drugbank-to-biopax

      Public
      DrugBank to BioPAX Level3 data converter.
      Java
      •0•2•0•0•Updated Feb 20, 2024Feb 20, 2024

    • cpath2-client

      Public
      Java
      •
      MIT License
      •0•0•0•0•Updated Feb 11, 2024Feb 11, 2024

    • msigdb-to-biopax

      Public
      MSigDB (human C3 TFT motif gene sets only) to BioPAX Level3 data converter.
      Java
      •0•0•0•0•Updated Feb 4, 2024Feb 4, 2024

    • mirtarbase-to-biopax

      Public
      MiRTarBase to BioPAX Level3 data converter.
      Java
      •0•0•1•0•Updated 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
      •4•2•4•0•Updated Nov 19, 2023Nov 19, 2023

    • rethinkdb-docker

      Public
      A Docker image that provides a RethinkDB database
      Dockerfile
      •0•0•1•0•Updated Nov 1, 2023Nov 1, 2023

    • semantic-search

      Public
      A simple semantic search engine for scientific papers.
      natural-language-processingtransformerssemantic-searchdeclutr
      Python
      •
      MIT License
      •0•27•7•4•Updated Sep 14, 2023Sep 14, 2023

    • chilay-sbgn

      Public
      Chisio Layout (ChiLay) graph layout framework for SBGN
      Java
      •3•0•0•0•Updated Aug 5, 2023Aug 5, 2023

    • classifier-pipeline

      Public
      A workflow for classifying articles
      Python
      •
      MIT License
      •0•0•2•0•Updated May 30, 2023May 30, 2023

    • ncbiutils

      Public
      A wrapper for retrieving records from PubMed
      Python
      •
      MIT License
      •0•2•0•0•Updated Feb 23, 2023Feb 23, 2023

    • pathway-abstract-classifier

      Public
      A tool to classify journal abstracts with pathway content.
      Jupyter Notebook
      •
      MIT License
      •1•0•1•0•Updated Jan 4, 2023Jan 4, 2023

    • sifgraph

      Public
      Modeling and querying support for SIF graphs
      Java
      •
      MIT License
      •0•1•1•0•Updated 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
      •10•13•13•1•Updated May 25, 2022May 25, 2022

    • rethinkdb-backup

      Public
      Enables a client to dump and retrieve data from a RethinkDB instance
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Jan 12, 2022Jan 12, 2022

    • pubmed-dl

      Public
      Python
      •
      MIT License
      •0•0•1•0•Updated Feb 10, 2021Feb 10, 2021

    • cytoscape-sbgn-stylesheet

      Public
      View biological networks via Cytoscape.js and sbgn-ml
      javascriptsvgsciencees6biologygraphslabuoftnetworksbader
      JavaScript
      •
      MIT License
      •31•61•14•1•Updated Feb 9, 2021Feb 9, 2021

    • pcviz

      Public
      Pathway Commons Bio Network Visualizer
      JavaScript
      •
      MIT License
      •3•8•9•0•Updated Sep 12, 2019Sep 12, 2019

    • pcapi

      Public archive
      The Web API Docs App
      JavaScript
      •0•0•0•0•Updated Sep 8, 2018Sep 8, 2018

    • sbgnml-to-cytoscape

      Public
      An npm module that converts xml based SBGN files to JSON for Cytoscape.js
      JavaScript
      •
      MIT License
      •2•5•5•0•Updated Jun 19, 2018Jun 19, 2018