Enumerate pathway with efmtools (10.1093/bioinformatics/btn401). Compute Elementaray Flux Modes (EFMs) on the whole stoichiometry matrix, then retain reaction containing includeNodes. This parameter filter nodes based on the value of the id property. The schema needs to respect this following:

(s1:Species)-[HAS_SUBSTRATE]-(r:Reaction)-[HAS_PRODUCT]-(s2:Species)

The property stoichiometry embedded by Species is used to set the stoichiometry of the reaction (default: "1"). The property reversible embedded by Reaction is also used (default: false)

The procedure adds a new property on the nodes Species, Reaction with the name defined by the argument labelPathwayPrefix with a value of a list of integers indidicated which nodes are implied in the pathway ID.

Note: this plugin is used in a Desktop Neo4j instance.

Download JAR file from Release, then copy the JAR file into the plugin directory of a Neo4j instance.

In Neo4j browser:

CALL brsynth.enumeratePathway('includeNodes=List[str], labelPathwayPrefix=str')

Alphabetic order

• efmtool - Compute Elementary Flux Modes
• neo4j - Graphs for Everyone
• neo4j-apoc - Procedures on Cypher Neo4j