Neo4j cypher query efficiency and syntax - neo4j

Question

I am attempting to query an ontology of health represented as an acyclic, directed graph in Neo4j v2.1.5. The database consists of 2 million nodes and 5 million edges/relationships. The following query identifies all nodes subsumed by a disease concept and caused by a particular bacteria or any of the bacteria subtypes as follows:
MATCH p = (a:ObjectConcept{disease}) <-[:ISA*]- (b:ObjectConcept),
q=(c:ObjectConcept{bacteria})<-[:ISA*]-(d:ObjectConcept)
WHERE NOT (b)-->()--(c) AND NOT (b)-->()-->(d)
RETURN distinct b.sctid, b.FSN
This query runs in < 1 second and returns the correct answers. However, adding one additional parameter adds substantial time (20 minutes). Example:
MATCH p = (a:ObjectConcept{disease}) <-[:ISA*]- (b:ObjectConcept),
q=(c:ObjectConcept{bacteria})<-[:ISA*]-(d:ObjectConcept),
t=(e:ObjectConcept{bacteria})<-[:ISA*]-(f:ObjectConcept),
WHERE NOT (b)-->()--(c)
AND NOT (b)-->()-->(d)
AND NOT (b)-->()-->(e)
AND NOT (b)-->()-->(f)
RETURN distinct b.sctid, b.FSN
I am new to cypher coding, but I have to imagine there is a better way to write this query to be more efficient. How would Collections improve this?
Thanks

Answer 1

I already answered that on the google group:
Hi Scott,
I presume you created indexes or constraints for :ObjectConcept(name) ?
I am working with an acyclic, directed graph (an ontology) that models
human health and am needing to identify certain diseases (example:
Pneumonia) that are infectious but NOT caused by certain bacteria
(staph or streptococcus). All concepts are Nodes defined as
ObjectConcepts. ObjectConcepts are connected by relationships such as
[ISA], [Pathological_process], [Causative_agent], etc.
The query requires:
a) Identification of all concepts subsumed by the concept Pneumonia as follows:
MATCH p = (a:ObjectConcept{Pneumonia}) <-[:ISA*]- (b:ObjectConcept)
this already returns a number of paths, potentially millions, can you check that with
MATCH p = (a:ObjectConcept{Pneumonia}) <-[:ISA*]- (b:ObjectConcept) return count(*)
b) Identification of all concepts subsumed by Genus Staph and Genus Strep (including the concept Genus Staph and Genus Strep) as follows. Note:
with b MATCH (b) q = (c:ObjectConcept{Strep})<-[:ISA*]-(d:ObjectConcept), h = (e:ObjectConcept{Staph})<-[:ISA*]-(f:ObjectConcept)
this is then the cross product of the paths from "p", "q" and "h", e.g. if all 3 of them return 1000 paths, you're at 1bn paths !!
c) Identify all nodes(p) that do not have a causative agent of Strep (i.e., nodes(q)) or Staph (nodes(h)) as follows:
with b,c,d,e,f MATCH (b),(c),(d),(e),(f) WHERE (b)--()-->(c) OR (b)-->()-->(d) OR (b)-->()-->(e) OR (b)-->()-->(f) RETURN distinct b.Name;
you don't need the WITH or even the MATCH (b),(c),(d),(e),(f)
what connections are there between b and the other nodes ? do you have concrete ones? for the first there is also missing one direction.
the where clause can be a problem, in general you want to show that perhaps this query is better reproduced by a UNION of simpler matches
e.g
MATCH (a:ObjectConcept{Pneumonia}) <-[:ISA*]- (b:ObjectConcept)-->()-->(c:ObjectConcept{name:Strep}) RETURN b.name
UNION
MATCH (a:ObjectConcept{Pneumonia}) <-[:ISA*]- (b:ObjectConcept)-->()-->(e:ObjectConcept{name:Staph}) RETURN b.name
UNION
MATCH (a:ObjectConcept{Pneumonia}) <-[:ISA*]- (b:ObjectConcept)-->()-->(d:ObjectConcept)-[:ISA*]->(c:ObjectConcept{name:Strep}) return b.name
UNION
MATCH (a:ObjectConcept{Pneumonia}) <-[:ISA*]- (b:ObjectConcept)-->()-->(d:ObjectConcept)-[:ISA*]->(c:ObjectConcept{name:Staph}) return b.name
another option would be to utilize the shortestPath() function to find one or all shortest path(s) between Pneumonia and the bacteria with certain rel-types and direction.
Perhaps you can share the dataset and the expected result.

Answer 2

The query was successfully accomplished using UNION functions as follows:
MATCH p = (a:ObjectConcept{sctid:233604007}) <-[:ISA*]- (b:ObjectConcept),
q = (c:ObjectConcept{sctid:58800005})<-[:ISA*]-(d:ObjectConcept)
WHERE NOT (b)-->()--(c) AND NOT (b)-->()-->(d)
RETURN distinct b
UNION
MATCH p = (a:ObjectConcept{sctid:233604007}) <-[:ISA*]- (b:ObjectConcept),
t = (e:ObjectConcept{sctid:65119002}) <-[:ISA*]- (f:ObjectConcept)
WHERE NOT (b)-->()-->(e) AND NOT (b)-->()-->(f)
RETURN distinct b
The query runs in sub 20 seconds vs. 20 minutes by reducing the cardinality of the objects being queried.