Scientific lenses to support multiple views over linked Chemistry data

Alasdair J G GrayA.J.G.Gray@hw.ac.ukalasdairjggray.co.uk@gray_alasdair

Open PHACTS

pmu@openphacts.orgopenphacts.org@open_phacts

Multiple Identities

P12047X31045

P12047

GB:29384RS_2353

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Gleevec®: Imatinib Mesylate

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DrugbankChemSpider PubChem

Imatinib

MesylateImatinib MesylateYLMAHDNUQAMNNX-UHFFFAOYSA-N

Gleevec®: Imatinib Mesylate

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DrugbankChemSpider PubChem

Imatinib

MesylateImatinib MesylateYLMAHDNUQAMNNX-UHFFFAOYSA-N

Are these records the same?It depends upon your task!

Example Use Cases

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I need to perform an analysis, give me

details of the active compound in Gleevec.

Which targets are known to interact

with Gleevec?

Scientific Lenses – A. J. G. Gray 6

skos:exactMatch(InChI)

Strict Relaxed

Analysing Browsing

Structure Lens

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I need to perform an analysis, give me details of the active compound in

Gleevec.

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skos:closeMatch(Drug Name)

skos:closeMatch(Drug Name)

skos:exactMatch(InChI)

Strict Relaxed

Analysing Browsing

Name Lens

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Which targets are known to interact with Gleevec?

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What is a Scientific Lens?

A lens defines a conceptual view over the data Specifies operational equivalence conditions

Consists of: Identifier (URI) Title

(dct:title) Description

(dct:description) Documentation link

(dcat:landingPage) Creator

(pav:createdBy) Timestamp

(pav:createdOn) Equivalence rules

(bdb:linksetJustification)16 October 2014 Scientific Lenses – A. J. G. Gray

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Ibuprofen consists of two equally active stereoisomers.• Stereoisomers not always represented in dataUsers wish to retrieve information for any stereoisomer.

CHEMBL427526

CHEMBL521CHEMBL175

Lens Effects: Ibuprofen

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Default Lens

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Ibuprofen consists of two equally active stereoisomers.• Stereoisomers not always represented in dataUsers wish to retrieve information for any stereoisomer.

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Stereoisomer Lens

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Ibuprofen consists of two equally active stereoisomers.• Stereoisomers not always represented in dataUsers wish to retrieve information for any stereoisomer.

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Mapping Generation

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ops:OPS437281

✔

ops:OPS380297

has_stereoundefined_parent [ci:CHEMINF_000456]

ops:OPS380292

is_stereoisomer_of[ci:CHEMINF_000461] Other relationships

• has part• is tautomer of• uncharged counterpart• isotope…

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Explorer Screenshot

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Explorer Screenshot

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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

Co

re P

latf

orm

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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?iri cheminf:logd ?logd .FILTER (?iri = cw:979b545d-f9a9 || ?iri = cs:2157 || ?iri = chembl:1280 || ?iri = db:db00945 )

GRAPH <http://rdf.chemspider.com> {

}GRAPH <http://…

cw:979b545d-f9a9 cheminf:logd ?logd .

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

cw:979b545d-f9a9 cheminf:logd ?logd .

Lenses: Under the hood

• IMS call adds overhead• Call time below human perception [1]• Can also be achieved through UNION[1] C. Y. A. Brenninkmeijer, C. Goble, A. J. G. Gray, P. Groth, A. Loizou, and S. Pettifer, “Including Co-referent URIs in a SPARQL Query,” COLD2013, http://ceur-ws.org/Vol-1034/

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API Hits

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April 2013 – March 2014: 15.8mApril 2014 – Sept 2014: 14mTotal: 29.8 million

Conclusions

Scientific data is complex and messy

Requires flexibility in linking

Equivalence depends upon context

Lenses provide support for operational

equivalence

Chemical structures support automatic

computing of links with justification

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Co-authorsRoyal Society of Chemistry Colin Batchelor Karen Karapetyan Jon Steele Valery Tkachenko Antony Williams

University of Manchester Christian Brenninkmeijer Ian Dunlop Carole Goble Steve Pettifer Robert Stevens

Swiss Institute for Bioinformatics Christine Chichester

European Bioinformatics

Institute Mark Davies Anna Gaulton John Overington

University of Vienna Daniela Digles

Maastricht University Chris Evelo Andra Waagmeester Egon Willighagen

VU University of Amsterdam Paul Groth Antonis Loizou

Connected Discovery Lee Harland

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Questions

Alasdair J G GrayA.J.G.Gray@hw.ac.ukalasdairjggray.co.uk@gray_alasdair

Open PHACTSpmu@openphacts.orgopenphacts.org@open_phacts

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Demo at stall 33 this evening!

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Source Initial Records Triples Properties

ChEMBL 1,481,473 304,360,749 77

DrugBank 19,628 517,584 74

UniProt 564,246 405,473,138 82

ENZYME 6,187 73,838 2

ChEBI 40,575 1,673,863 2

GeneOntology 38,137 2,447,682 26

GOA 661,232 1,765,622,393 15

ChemSpider 1,361,568 215,193,441 23

ConceptWiki 2,828,966 4,291,131 1

WikiPathways 946 1,949,074 34

Over 2.7 billion

triples

Open PHACTS Data

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App EcosystemAn “App Store”?

http://www.openphactsfoundation.org/apps.html

Explorer Explorer2 ChemBioNavigator Target Dossier Pharmatrek Helium

MOE Collector Cytophacts Utopia Garfield SciBite

KNIME Mol. Data Sheets PipelinePilot scinav.it Taverna

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Discovery Platform

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Drug Discovery Platform

Apps

Domain API

Interactive responses

Production qualityintegration platform

MethodCalls

Linked Data API

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Drug

Disease (1.4)

PathwayTarget

https://dev.openphacts.org/