Pathway Commons

factoid

A project to digitally capture biological data from academic papers

pcviz

Pathway Commons Bio Network Visualizer

grounding-search

A biological entity grounding search service

chibe

Pathway visualization and analysis tool for Pathway Commons and other BioPAX data

cytoscape-sbgn-stylesheet

View biological networks via Cytoscape.js and sbgn-ml

app-ui

Web UI for accessing Pathway Commons data

guide

Resource for pathway analysis and Pathway Commons

cpath2

Biological pathway data integration and access platform (Pathway Commons)

about

Pathway Commons Home Page (/about/)

cpath2-client

drugbank-to-biopax

DrugBank to BioPAX Level3 data converter.

sifgraph-server

Pathway Commons binary SIF graph web service

CyPath2

Cytoscape 3 app that connects to PC2 (cpath2) and imports BioPAX sub-networks into Cytoscape 3 for analysis.

sbgnml-to-cytoscape

An npm module that converts xml based SBGN files to JSON for Cytoscape.js

ctd-to-biopax

Comparative Toxicogenomics Database (CTD) to BioPAX Level3 data converter.

sifgraph

Modeling and querying support for SIF graphs

reach-docker

A docker version of the clulab/reach webservices

pathway-commons-client

A library to facilitate access to the Pathway Commons 2 API

reconx-to-biopax

SBML to BioPAX Level3 converter, specific to the Recon2 data.

csndb-to-biopax

msigdb-to-biopax

MSigDB (human C3 TFT motif gene sets only) to BioPAX Level3 data converter.

transfac-to-biopax

To convert from TRANSFAC GSEA/GMT format - transcription factors and their predicted targets - to BioPAX L3.

student-tutorial

path-stat

NodeJS Tool for scraping Pathway Commons for statistical analysis