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 A.J.G.Gray@hw.ac.uk@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

Questions

A.J.G.Gray@hw.ac.ukwww.macs.hw.ac.uk/~ajg33@gray_alasdair

Open PHACTS Project

pmu@openphacts.orgwww.openphacts.org@open_phacts