File formats

All SPRAS file formats are tab-separated values.

Node file

Node files include a header row and rows providing attributes for each node. One column is for the node identifier and must have the header value NODEID. All other columns specify additional node attributes such as prizes. Any nodes that are listed in a node file but are not present in one or more edges in the edge file will be removed. For example:

NODEID	prize	sources	targets	active	dummy
A	1.0		True	True	True
B	3.3	True		True
C	2.5		True	True
D	1.9	True	True	True

A secondary format provides only a list of node identifiers and uses the filename as the node attribute, as in the example sources.txt. This format may be deprecated.

Edge file

Edge files do not include a header row. Each row lists the two nodes that are connected with an edge, the weight for that edge, and, optionally, a directionality column to indicate whether the edge is directed or undirected. The directionality values are either a ‘U’ for an undirected edge or a ‘D’ for a directed edge. If the directionality column is not included, SPRAS will assume that the file’s edges are entirely undirected. The weights are typically in the range [0,1] with 1 being the highest confidence for the edge.

For example:

A	B	0.98	U
B	C	0.77	D

or

A	B	0.98
B	C	0.77

Gold Standard

Nodes

Gold standard node files are txt files and do not include a header row.

Each row in the file represents a single node identifier. The file is structured as a single column with one node per line. These nodes typically correspond to gene or protein identifiers that are relevant to the biological pathway of interest.

For example:

A
B
C

Pathway output format

Output pathway files in the standard SPRAS format include a header row and rows providing attributes for each edge. The header row is Node1    Node2   Rank    Direction. Each row lists the two nodes that are connected with an edge, the rank for that edge, and a directionality column to indicate whether the edge is directed or undirected. The directionality values are either a ‘U’ for an undirected edge or a ‘D’ for a directed edge, where the direction is from Node1 to Node2. Pathways that do not contain ranked edges can output all 1s in the Rank column.

For example:

Node1	Node2	Rank	Direction
A	B	1	D
B	C	1	D
B	D	2	U
D	A	3	U