opencog-neo4j
Google Summer of Code 2015 Proposal to implement Neo4j Graph Backing Store as described in http://wiki.opencog.org/w/Neo4j_Backing_Store
Bio scheme files
We'll use the OpenCog Bio knowledge base
(dataset in separate repo at [email protected]:opencog-bio/bio-data.git), a moderately sized dataset about 212 MiB in size, to test performance.
mmc4.scm patch
mmc4.scm must be patched as follows due to typo and ConceptNode name mismatch:
(define count (count-all))
(define message (string-append " Atoms loaded " "\n"))
(display count)
(display message)
(define start_time (current-time))
(InheritanceLink
(ConceptNode "Aging-Mythelation_GeneSet")
(ConceptNode "Geneset")
)
(EvaluationLink
(PredicateNode "organism_of"
(ListLink
(ConceptNode "Aging-Mythelation_GeneSet")
(ConceptNode "Homo sapiens"))
)
)
(EvaluationLink
(PredicateNode "source_PubMedID"
(ListLink
(ConceptNode "Aging-Mythelation_GeneSet")
(NumberNode "#23177740"))
)
)
(EvaluationLink
(PredicateNode "brief_description_of"
(ListLink
(ConceptNode "Aging-Mythelation_GeneSet")
(PhraseNode "Genes Associated with Aging in Both the Methylome and th Transcript."))
)
)
Generating the Neo4j Database
After running OpenCogNeo4jGraphBackingStoreApplication, a Neo4j database will be created
at ~/tmp/opencog-neo4j. You can inspect it by running:
neo4j-shell -path ~/tmp/opencog-neo4j
If you want to use the Neo4j Web UI, first make it writable by Neo4j:
sudo adduser neo4j ceefour
chmod -Rc ug+rw ~/tmp/opencog-neo4j
Edit /etc/neo4j/neo4j-server.properties and comment:
org.neo4j.server.database.location=data/graph.db
then add:
org.neo4j.server.database.location=/home/ceefour/tmp/opencog-neo4j
then restart:
sudo service neo4j-service restart
Now you can access at http://localhost:7474/
Use this query:
MATCH (g:opencog_Gene), (c:opencog_Concept), (l:opencog_EvaluationLink)--(x) RETURN g, c, l, x LIMIT 75
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