Pathway Commons

Repositories

• factoid

  A project to capture biological pathway data from academic papers
  JavaScript 7 15 7 0 Updated Sep 25, 2020

• app-ui

  Web UI for accessing Pathway Commons data
  JavaScript MIT 14 0 12 1 Updated Sep 10, 2020

• cpath2

  Biological pathway data integration and access platform (Pathway Commons)
  Java MIT 4 3 10 0 Updated Sep 3, 2020

• factoid-converters

  Forked from metincansiper/factoid-to-biopax-server

  Web services for Factoid project to convert between JSON, BioPAX, SBGN data formats
  Java MIT 2 1 0 0 Updated Aug 24, 2020

• grounding-search

  A biological entity grounding search service
  JavaScript MIT 3 3 5 0 Updated Aug 21, 2020

• semantic-search

  A simple semantic search engine for scientific papers.

  natural-language-processing transformers semantic-search
  Python MIT 0 3 1 0 Updated Aug 12, 2020

• sifgraph-server

  Pathway Commons binary SIF graph web service
  Java MIT 1 1 1 0 Updated Apr 25, 2020

• chibe

  Pathway visualization and analysis tool for Pathway Commons and other BioPAX data
  Java EPL-1.0 9 5 11 1 Updated Mar 9, 2020

• cytoscape-sbgn-stylesheet

  View biological networks via Cytoscape.js and sbgn-ml

  javascript svg science es6 graph biology graphs
  JavaScript MIT 10 17 13 1 Updated Jan 28, 2020

• rethinkdb-docker

  A Docker image that provides a RethinkDB database
  Dockerfile 0 0 0 0 Updated Jan 9, 2020

• about

  Pathway Commons Home Page (/about/)
  CSS 2 3 2 0 Updated Oct 29, 2019

• sifgraph

  Modeling and querying support for SIF graphs
  Java MIT 0 1 1 0 Updated Oct 14, 2019

• pcviz

  Pathway Commons Bio Network Visualizer
  JavaScript 3 6 8 0 Updated Sep 12, 2019

• ctd-to-biopax

  Comparative Toxicogenomics Database (CTD) to BioPAX Level3 data converter.
  Java 0 1 0 0 Updated Sep 2, 2019

• drugbank-to-biopax

  DrugBank to BioPAX Level3 data converter.
  Java 0 1 0 0 Updated Sep 1, 2019

• guide

  Resource for pathway analysis and Pathway Commons
  HTML 0 4 0 0 Updated Mar 14, 2019

• cpath2-client
  Java MIT 1 0 0 0 Updated Feb 10, 2019

• CyPath2

  Cytoscape 3 app that connects to PC2 (cpath2) and imports BioPAX sub-networks into Cytoscape 3 for analysis.
  Java LGPL-2.1 5 1 3 0 Updated Nov 7, 2018

• pcapi Archived

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

• sbgnml-to-cytoscape

  An npm module that converts xml based SBGN files to JSON for Cytoscape.js
  JavaScript MIT 1 1 5 0 Updated Jun 19, 2018

• reach-docker

  A docker version of the clulab/reach webservices
  Shell 0 0 1 1 Updated May 29, 2018

• pathway-commons-client

  A library to facilitate access to the Pathway Commons 2 API
  JavaScript MIT 1 2 6 0 Updated May 23, 2018

• pathway-cards

  Forked from onursumer/oncosign
  Java LGPL-3.0 3 3 2 (1 issue needs help) 0 Updated Apr 8, 2018

• reconx-to-biopax

  SBML to BioPAX Level3 converter, specific to the Recon2 data.
  Java 0 0 0 0 Updated Apr 4, 2018

• pathways-search Archived

  A web app to search pathways in Pathway Commons
  JavaScript MIT 4 2 0 0 Updated Jan 22, 2018

• csndb-to-biopax
  0 0 0 0 Updated Nov 2, 2017

• msigdb-to-biopax

  MSigDB (human C3 TFT motif gene sets only) to BioPAX Level3 data converter.
  Java 0 0 0 0 Updated Nov 1, 2017

• transfac-to-biopax

  To convert from TRANSFAC GSEA/GMT format - transcription factors and their predicted targets - to BioPAX L3.
  0 0 0 0 Updated Oct 19, 2017

• student-tutorial
  JavaScript MIT 0 0 0 0 Updated Sep 13, 2017

• networks Archived

  A web app to search sub-networks in Pathway Commons
  JavaScript MIT 0 0 0 0 Updated Aug 21, 2017