Formats

Below is a list of graph formats supported by GraphIO.

SIF (.sif)

Simple format for building a graph from a list of interactions.

Each line in the file specifies a source node, an interaction type and one or more target nodes, separated by spaces.

nodeA interactionX nodeB
nodeB interactionY nodeC nodeD
nodeE

For more details see here.

XGMML (.xgmml)

XML format based on GML. Supported by Cytoscape. See specification.

LEDA (.gw, .leda)

See specification.

Tab-separated edge list (.tab, .txt)

Simple plain text format describing a graphs as a list of interactions. First line must contain a header. Each of the following lines contains two node labels separated by a tab character (\t). An edge label can optionally be specified as a third argument.

Example:

INTERACTOR_A	INTERACTOR_B	LABEL
nodeA	nodeB	edgeType1
nodeA	nodeC   edgeType2
nodeC	nodeD	edgeType1