1. BLAZING FAST PERFORMANCE
with Spring Cache, Lucene, GPars, RDF and Grails

2. WHAT’S A TRIPLE?
subject
predicate
object

3. WHAT’S A TRIPLE?
subject “Imatinib”
predicate type
object Pharmaceutical Drug

4. LINKING OPEN DRUG DATA
http://esw.w3.org/HCLSIG/LODD

5. WHAT’S A TRIPLE?
http://www4.wiwiss.fu-berlin.de/drugbank/page/drugs/DB00619
subject predicate object
DB00619 label “Imatinib”
DB00619 type drugbank:drugs
DB00619 brandName “Gleevec”
DB00619 drugbank:target targets:17

6. WHAT’S A TRIPLE?
http://www4.wiwiss.fu-berlin.de/drugbank/page/targets/17
subject predicate object
DB00619 drugbank:target targets/17
targets/17 type drugbank:drugs
“Proto-oncogene tyrosine-
targets/17 label protein kinase ABL1”
targets/17 geneName “ABL1”

7. RELATIONSHIPS
ABL1
Imatinib
target
Legend
associatedGene Gene
possibleDrug Disease
Compound
Predicate
Leukemia

8. PERFORMANCE
Type-ahead search

9. select id, label
from targets
where label like ‘%${queryValue}%’

10. select id, label
from targets
where label like ‘%${queryValue}%’
SELECT ?uri ?label WHERE {
?uri rdfs:label ?label .
?uri rdf:type drugbank:targets .
FILTER regex(?label, 'Q${queryValue}E', 'i')"
}

11. select id, label
from targets
where label like ‘%${queryValue}%’
SELECT ?uri ?label WHERE {
?uri rdfs:label ?label .
?uri rdf:type drugbank:targets .
FILTER regex(?label, 'Q${queryValue}E', 'i')"
}
40 million records

12. Index the data (up front performance hit)
Search (really really really really fast)
BuildConfig.groovy:
runtime 'org.apache.lucene:lucene-core:3.0.1'
-OR-
grails install-plugin searchable

13. DE-DUPE

14. Lucene Extension
Index the (RDF) data
Search (really really really really fast)

15. Understands Triples (or structured data)
subject predicate object
DB00619 label “Imatinib”
SirenTupleQuery tupleQuery = new SirenTupleQuery()
tupleQuery.add(createCellQuery(‘label’,
SirenTupleConstraintPosition.PREDICATE), SirenTupleClause.Occur.MUST)
tupleQuery.add(createCellQuery(‘imatinib’,
SirenTupleConstraintPosition.OBJECT), SirenTupleClause.Occur.MUST)

16. GRAILS SPRING CACHE
• grails install-plugin springcache
• Add @Cacheable (and or @CacheFlush) annotation to
services / controllers
@Cacheable('somecachename')
def slow(String name) {
log.info "resolving $name"
Thread.sleep(2000)
return "took a long time to resolve ${name}"
}

17. GPARS
• BuildConfig.groovy:
runtime 'org.codehaus.gpars:gpars:0.10'
runtime 'org.coconut.forkjoin.jsr166y:jsr166y:070108'
• http://www.gpars.org/guide/index.html
• Note:hibernate session is not available on GPars threads; you
need to get one yourself (use DomainClass.withTransaction)
• Data Parallelism
• Map-Reduce, Fork-Join, and many more...

18. GPARS
void resolve(scoreDocs){
scoreDocs.each {scoreDoc ->
//do something in single thread
}
}
void resolveWithPool(scoreDocs){
GParsPool.withPool {
scoreDocs.eachParallel {scoreDoc ->
//do something in parallel
}
}
}

19. OTHER HANDY TOOLS
• Grails Melody (Java Melody) (monitoring)
• Perf4j (logging performance)
• Solr (lucene search server)
• Grails Console Plugin (web based console)