优化许多neo4j节点之间的关系建立

Question

I have a database containing two particular node types: GenomicRange and GeneModel . The GenomicRange node set contains ~80 million nodes while GeneModel contains ~45,000 nodes.

The GenomicRange nodes contain a property posStart which is stored as an integer. The GeneModel node contains two particular integer properties geneStart and geneEnd . These coordinates are found on a chromosome property found in both node types (eg 1 through 10 ).

What I would like to do is to efficiently create relationships (eg [:RANGE_WITHIN] ) between these two nodes if (1) Their chromosome properties match, (2) if the posStart value in GenomicRange falls within range of the geneStart and geneEnd properties on the GeneModel node.

My problem I am currently having is that my querying/building process is incredibly slow. Is there a way to optimize this code?

Thanks for your help!

MATCH (model:GeneModel)
WITH model
MATCH (range:GenomicRange)
WHERE range.chromosome = model.chromosome AND range.posStart >= model.geneStart AND range.posStart <= model.geneEnd
CREATE (range)-[:RANGE_WITHIN]->(model)

Answer 1

Few suggestions:

Add index on the properties you are using for comparison.

Here: posStart, chromosome, geneEnd, geneStart.

`CREATE INDEX ON :GenomicRange(chromosome)`

Increase Heap Memory: Creating index increases memory usage so increase heap size up to 50% of your memory. You can configure this in neo4j.conf file.

Increase page cache: more the cache size more the data cached in memory, It will help avoid costly disk access.

Read more about memory configuration here .

PS If you still get out of memory error after increasing heap size, swap GenomicRange and GeneModel on line 1 and 3 OR use APOC plugin to create relationships periodically.