Java Configuration

Get undirected graph

Get directed graph

Configuration file

Program execution

Variable	Default value	Type	Description
allProteome	false	Boolean	If set to true, the set of vertices for the result graph will be the set of proteins in SwissProt. If set to false, an input list is requested.
inputListFile	./input.txt	String	Path to the input file.
maxNumVertices	21000	Integer	The graph will contain at most this number of vertices. If the input list has more proteins than this number, only the first maxNumVertices are used.
ignoreMisformattedRows	true	Boolean	If set to true, the misformatted rows of the input are ignored and continues to the other rows. If set to false, the execution of the program stops completely when a misformatted row appears.
verboseConsole	true	Boolean	If set to true, the console shows more messages along the process.
configFile	./Config.txt	String	Path to, and name of, the configuration file. This is not a variable that you can change in the configuration file itself. It looks for the file in that path, unless another path is specified using command line arguments.
outputGraphFile	./output.sif	String	Output file name with path.

Neo4j database access

Variable	Default value	Type	Description
host	bolt://localhost	String	The url where Neo4j is accessible with Reactome knowledgebase loaded.
username	neo4j	String	The username to access the database.
password	neo4j	String	The password associated to the username specified.

Graph

Variable	Default value	Type	Description
onlyNeighborsInList	true	Boolean	Output graph will only contain proteins(vertices) in the input list.
onlyOrderedEdges	true	Boolean	For the edges indicating a set or complex neighbour, output each pair of proteins only once.
showMissingProteins	true	Boolean	If set to true, the output graph will include the proteins contained in the input file but not are not present in Reactome.
showIsolatedVertices	true	Boolean	If set to true, the output graph will include the proteins contained in the input file but do not have connections.
cn	true	Boolean	Show edges indicating complex neighbours.
ds	true	Boolean	Show edges indicating defined set neighbours.
os	true	Boolean	Show edges indicating open set neighbours.
cs	true	Boolean	Show edges indicating candidate set neighbours.
io	true	Boolean	Show edges indicating two proteins participate in the same reaction, having the first one as input and the other as output.
oi	true	Boolean	Show edges indicating two proteins participate in the same reaction, having the first one as output and the other as input.
ci	true	Boolean	Show edges indicating two proteins participate in the same reaction, having the first one as catalyst and the other as input.
co	true	Boolean	Show edges indicating two proteins participate in the same reaction, having the first one as catalyst and the other as output.
oc	true	Boolean	Show edges indicating two proteins participate in the same reaction, having the first one as output and the other as catalyst.
ri	true	Boolean	Show edges indicating two proteins participate in the same reaction, having the first one as regulator and the other as input.
ro	true	Boolean	Show edges indicating two proteins participate in the same reaction, having the first one as regulator and the other as output.
or	true	Boolean	Show edges indicating two proteins participate in the same reaction, having the first one as output and the other as regulator.