Repositories list

• cpath2

  Public
  Biological pathway data integration and access platform (Pathway Commons)

  Java

  •

  MIT License

  •5•6•7•1•Updated Jul 12, 2025Jul 12, 2025

• app-ui

  Public
  Web UI for accessing Pathway Commons data

  JavaScript

  •

  MIT License

  •17•4•12•3•Updated Apr 24, 2025Apr 24, 2025

• factoid

  Public
  A project to capture biological pathway data from academic papers

  JavaScript

  •

  MIT License

  •7•29•31•4•Updated Mar 24, 2025Mar 24, 2025

• grounding-search

  Public
  A biological entity grounding search service

  searchidentifiersbiological-entities+ 1

  searchidentifiersbiological-entitiesgrounding

  JavaScript

  •

  MIT License

  •5•8•6•0•Updated Jan 6, 2025Jan 6, 2025

• hyper-recent

  Public
  Hyper-recent article feed

  JavaScript

  •

  MIT License

  •0•1•2•0•Updated Oct 15, 2024Oct 15, 2024

• about

  Public
  Pathway Commons Home Page (/about/)

  SCSS

  •2•3•2•0•Updated Aug 22, 2024Aug 22, 2024

• factoid-converters

  Public

  PathwayCommons/factoid-converters’s past year of commit activity
  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

  PathwayCommons/ctd-to-biopax’s past year of commit activity
  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-search+ 1

  natural-language-processingtransformerssemantic-searchdeclutr

  Python

  •

  MIT License

  •0•28•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

  •9•14•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

  javascriptsvgscience+ 13

  javascriptsvgsciencees6graphbiologygraphslabuoftcytoscape+ 6

  JavaScript

  •

  MIT License

  •31•69•14•2•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

  •3•5•5•0•Updated Jun 19, 2018Jun 19, 2018