CellNOpt Documentation Center (CNODocs) (0.1.6)

2.1. SIF FormatΒΆ

Section author: Thomas Cokelaer, 2013

The SIF format (simple interaction format) is a cytoscape compatible format, which is just a space separated value format. It is convenient for building a graph from a list of interactions. It also makes it easy to combine different interaction sets into a larger network, or add new interactions to an existing data set.

The advantage resides in its simplicity:

specy1 1 specy2
specy1 1 specy3

with the disadvantage that this format does not include any layout information. Each line in a SIF file represent an interaction between a source and one or more target nodes:

nodeA relationship nodeB
nodeC relationship nodeA
nodeD relationship nodeE nodeF nodeB

The SIF format used in CellNOpt is actually a subset of the official SIF format:

#. Generally there is only one target
#. The relationship can be only the number 1 or -1 (for inhibitor)
#. Duplicate entries are not ignored.

Delimiters can be spaces or tabs (mixed).

Duplicated entries are ignored. Multiple edges between the same nodes must have different edge types.

Self loops are also possible:

A 1 A

In cytoscape, the relationship type can be any string. However, in CellNOptR we are limited to the values 1 and -1 that correspond to activation or inhibition.