Cypher queries to explore the data from STON in Neo4j

The queries below were launched in Neo4j to obtain the results shown in the paper. 


---------- Finding modules of IFNG in iNOS pathway ----------

The following query means to identify modules in the database by finding 
1) all nodes named “IFNG” 
2) all processes connected to them 
3) all nodes involved in those processes.
This query has been used to retrieve the module presented in Figure 2.

Query:
MATCH (n-->p), (x), (z)
WHERE n.Name = 'IFNG' AND x.NodeType <> 'process' AND z.NodeType <> 'process'
RETURN n-->p, p-[*1]->x, z-[*1..2]->p


The following query is meant to query the database through programmatic access, as a JSON format. 
First, the query is defined, then  parameters are given. It will give the same result as the previous query.
{
  “query” : “MATCH (n-->p), (x), (z)
             WHERE n.Name = {Entity} AND NOT(x.NodeType = {Reaction}) AND NOT(z.NodeType = {Reaction})
      	     RETURN n-->p, p-[*1]->x, z-[*1..2]->p”,
  “params” : {
    “Entity” : “IFNG”,
     “Reaction” : “process”
  }
} 



---------- Linking levels of granularity between two maps (PD and AF) ----------

In the following query, nodes are compared two by two. 
In order to create a link the compared nodes should have:
1) different SBGN language (one PD, one AF) and file name
2) same name, nodetype, compartment and unit of information
This query has been used to obtain the links between iNOS PD and iNOS AF map, presented in Figure 3.

Query:
MATCH (n1),(n2)
WHERE n1.ID <> n2.ID
AND n1.SbgnFileType = 'processdescription'
AND n2.SbgnFileType = 'activityflow'
AND n1.FileName <> n2.FileName
AND n1.Name = n2.Name
AND (n1.NodeType STARTS WITH n2.EntityType OR n1.NodeType ENDS WITH n2.EntityType)
AND n1.Compartment = n2.Compartment  AND n1.NodeType <> 'process'
AND (n1.UnitOfInformation STARTS WITH n2.EntityName OR n1.UnitOfInformation ENDS WITH n2.EntityName)
CREATE (n1-[r:PDtoAF]->n2)
RETURN r, n1, n2