Including Co-referent URIs in a SPARQL Query
Christian Y A Brenninkmeijer, Carole Goble, Alasdair J G Gray, Paul Groth,
Antonis Loizou, and Steve Pettifer
www.openphacts.org [email protected]@open_phacts @gray_alasdair
Multiple Identities
Andy Law's Third Law“The number of unique identifiers assigned to an individual is never less than the number of Institutions involved in the study”
http://bioinformatics.roslin.ac.uk/lawslaws.html
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P12047X31045P120
47
GB:29384RS_
2353
Are these the same thing?
Gleevec® = Imatinib Mesylate
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DrugbankChemSpider PubChem
Imatinib
MesylateImatinib MesylateYLMAHDNUQAMNNX-UHFFFAOYSA-N
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Multiple Links: Different Reasons
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Link: skos:closeMatchReason: non-salt form
Link: skos:exactMatchReason: drug name
Strict Relaxed
Analysing Browsing
Dynamic Equality
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skos:exactMatch(InChI)
Strict Relaxed
Analysing Browsing
Dynamic Equality
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skos:closeMatch(Drug Name)
skos:closeMatch(Drug Name)
skos:exactMatch(InChI)
Open PHACTS Discovery Platform
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Drug Discovery Platform
Apps
Domain API
Interactive responses
Production qualityintegration platform
MethodCalls
Integration Approach
• Data kept in original model• Data cached in central triple store• API call translated to SPARQL query• Query expressed in terms of original data
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OPS Discovery Platform
RDFNanopub
Db
VoID
Data Cache (Virtuoso Triple Store)
Semantic Workflow Engine
Linked Data API (RDF/XML, TTL, JSON)DomainSpecificServices
Identity Resolution
Service
Chemistry RegistrationNormalisation & Q/C
IdentifierManagement
Service
Indexing
Cor
e Pl
atfo
rm
P12374EC2.43.4
CS4532
“Adenosine receptor 2a”
RDF
VoID
Db
RDFNanopub
Db
VoID
RDF
Db
VoID
RDFNanopub
VoID
Public Content Commercial
Public Ontologies
User Annotations
Apps
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Platform Interaction
1. Resolve user input: – User enters search text– Resolve to a URI for concept
2. Request data for URI– Expand URI to equivalent for each dataset– Run resulting SPARQL query
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?iri cheminf:logd ?logd .FILTER (?iri = cw:979b545d-f9a9 || ?iri = cs:2157 || ?iri = chembl:1280 || ?iri = db:db00945 )
cw:979b545d-f9a9 cheminf:logd ?logd .GRAPH <http://rdf.chemspider.com> {
}
cw:979b545d-f9a9 cheminf:logd ?logd .
Query Expansion
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Identity Mapping Service
(BridgeDB)
Query Expander Service
Profiles
Mappings
Q, L1 Q’
[cw:979b545d-f9a9,cs:2157, chembl:1280,db:db00945]
cw:979b545d-f9a9, L1
Can also be achieved through UNION
Experiment
Is it feasible to use a stand-off mapping service?• Base lines (no external call):
– “Perfect” URIs– Linked data querying
• Expansion approaches (external service call):– FILTER by Graph– UNION by Graph
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“Perfect” URI BaselineWHERE { GRAPH <chemspider> { cs:2157 cheminf:logp ?logp . } GRAPH <chembl> { chembl_mol:m1280 cheminf:mw ?mw . }}
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Linked Data BaselineWHERE { GRAPH <chemspider> { cs:2157 cheminf:logp ?logp . } GRAPH <chembl> { ?chemblid cheminf:mw ?mw . } cs:2157 skos:exactMatch ?chemblid .}
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Queries
Drawn from Open PHACTS API:1. Simple compound information (1)2. Compound information (1)3. Compound pharmacology (M)4. Simple target information (1)5. Target information (1)6. Target pharmacology (M)
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Queries
Drawn from Open PHACTS API:1. Simple compound information (1)2. Compound information (1)3. Compound pharmacology (M)4. Simple target information (1)5. Target information (1)6. Target pharmacology (M)
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Data:167,783,592 triples
Mappings:2,114,584 triples
Lenses:1
Datasets and Links
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Average execution times
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Average execution times
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0.01
8
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Conclusions
• Query expansion slower in general– Due to separate service call– Difference below human perception– UNION faster than FILTER on Virtuoso
• Stand-off mappings feasible• Infrastructure can support lenses
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Strict Relaxed
Analysing Browsing
