Formats
Drug2ways handles the following formats:
CSV (.csv)
TSV (.tsv)
GraphML (.graphml or .xml)
GML (.gml or .xml)
BEL (.bel)
Pickle (.pickle). BELGraph object from PyBEL 0.13.2
Node-Link JSON (.json)
The GraphML, GML, EdgeList and Node-Link JSON readers of drug2ways rely on NetworkX. BEL and Pickle files rely on PyBEL. The two easiest format to work with drug2ways are a triple-based file represented as the file below (tsv/csv). The file must contain three columns: source, relation and target (order is not relevant) and the only condition is that the relation column contains 1 and -1 to indicate the direction of the relation (increase/decrease).
source |
target |
relation |
---|---|---|
Drug1 |
Protein1 |
-1 |
Protein1 |
Protein2 |
1 |
Protein2 |
Protein3 |
-1 |
Protein3 |
Disease1 |
1 |