The source code to generate and analyze the network is available in the source code repository.
We make PhenomeNET available in two formats:
pre-filtered (similarity score >0.1) as list of node pairs and similarity score (Warning: 2.1GB). The file can be explored using grep and sort or similar tools to investigate associations between nodes in PhenomeNET. The file can be used as input for Cytoscape.
adjacency matrix (upper right half only) (Warning: 11GB). This file contains the column labels of the matrix. The file is intended for programmatic access to the raw data and requires additional software. See KeggEval.groovy, line 287ff, for example code.