Java Configuration

The configuration of the program is specified in the Command line and in a configuration file. Command line has priority over the configuration file. If none of them are specified, default values are taken.

Command line arguments

Input and Output

Argument	Description
-i,--input <file>	Input file path and name
-o,--output <file>	Output file path and name
-c,--conf <file>	Configuration file path and name

Neo4j database access

Argument	Description
-h,--host <url>	Url of the Neo4j database
-u,--username <user>	Username to access Neo4j with Reactome
-p,--password <pass>	Password to access Neo4j with Reactome

Graph vertices

Argument	Description
-n,--maxNumVertices <number>	Use only the first n proteins
-l,--onlyProteinsInList	Only use as vertices the proteins in input list
-i,--showDisconnectedProteins	Add to graph proteins without interactions in Reactome
-y,--year <year>	Only proteins participant in reactions with first publication before/at year

By default, the program will use all proteins in the list, and show also neighbours of the proteins even when they are not part of the input. This means, an input with n proteins, can result in a graph with more than n vertices.

Note that not all Human proteins reviewed in Uniprot are annotated in Reactome. When those proteins do not appear, they will be isolated vertices in the graph, which means no arc start or end in those vertices. By default all disconnected vertices, are not shown in the graph.

Graph arcs

By default, all types of arcs are included in the result graph. If at least one of the edge type arguments is set, then only the specified types will be included in the result graph.

• Reaction participants: When two proteins P1 and P2 are members of the same reaction, they have unidirectional interactions represented by one arc P1 to P2, where P1 has the first role, and P2 has the second role.

Argument
-io,--InputToOutput
-ci,--CatalystToInput
-co,--CatalystToOutput
-ri,--RegulatorToInput
-ro,--RegulatorToOutput
-oc,--OutputToInput
-oc,--OutputToCatalyst
-or,--OutputToRegulator

• Set or complex members: When two proteins P1 and P2 are members of the same complex or set, the resulting graph will contain one arc from P1 to P2 and one from P2 to P1.

Argument
-cn,--ComplexNeighbour
-ds,--DefinedSetNeighbour
-os,--OpenSetNeighbour
-cs,--CandidateSetNeighbour
-es,--EntitySetNeighbour

Configuration file

The configuration file is optional. By default, the program will try to read the file "./Config.txt" in the same directory of the executable "jar". If the file, is not there, then it continues with the execution. The path and name of the configuration file can be modified using the command line arguments.

All the command line arguments listed above can be specified in the configuration file without the "-" or "--" in front of the argument names. The arguments can be in any random order, one each line, in the following format:

<arg_name>=<value>
<arg_name2>=<value>
//Optional Comment
<arg_nam3>=<value>
<arg_nam4>=<value>

Alternatively, for the flag arguments which do not require a value, it suffices to write the name of the argument to set its value to true:

<arg_name>
<arg_name2>