Semantic WikiPathways Andra Waagmeester

Department of Bioinformatics - BiGCaT 2 Overview Introduction to WikiPathways GPML Pathway to RDF conversion Vocabularies used Obtaining identifiers URIs pathways and pathway elements Example queries Identifier mapping

Department of Bioinformatics - BiGCaT 3 WikiPathways Curated by the community Built on top of Mediawiki framework Live demo

Department of Bioinformatics - BiGCaT 4 GPML - GenMAPP Pathway Markup Language XML-based format. XML representation of GenMAPP MAPP format Recognised by WikiPathways, Pathvisio and Cytoscape

Department of Bioinformatics - BiGCaT 5

6 Pathway to RDF conversion

Department of Bioinformatics - BiGCaT 7 WP to RDF conversion

Department of Bioinformatics - BiGCaT 8 Vocabularies used Internal (vocabularies.wikipathways.org) –GPML –WP External –Biopax3 –Bibo –Foaf –tbd

Department of Bioinformatics - BiGCaT 9 Identifiers.org Providing resolvable persistent URIs. Based on Miriam ( Textual Pathway identifiers (xrefs) converted to identifiers.org uri through the miriam api

Department of Bioinformatics - BiGCaT 10 Example query (1) List pathways and their species SELECT DISTINCT ?organism ?label WHERE { ?concept wp:organism ?organism. ?organism rdfs:label ?label. }

Department of Bioinformatics - BiGCaT 11 Example query (2) List all datasource currently captured in WikiPathways and count the number of entries per data source: SELECT DISTINCT ?datasource count(?datasource) as ?numberEntries WHERE { ?concept dc:source ?datasource. } ORDER BY DESC(?numberEntries)

Department of Bioinformatics - BiGCaT 12 Example query (3) Extract the amount of pathways edited per contributor SELECT DISTINCT ?contributor COUNT(?pathway) as ?pathwaysEdited WHERE { ?pathway dc:contributor ?contributor } ORDER BY DESC(?pathwaysEdited)

Department of Bioinformatics - BiGCaT 13 Example query n Extracting Inchi out of ChEMBL SELECT ?concept ?inchi ?pathway ?identifier WHERE { ?concept dcterms:isPartOf ?pathway. ?concept dc:source "ChEMBL compound"^^xsd:string. ?concept dc:identifier ?identifier. SERVICE { ?s rdfs:label ?chidentifier. ?s ?inchi.} FILTER (xsd:string(?chidentifier)= xsd:string(?identifier)). }

Department of Bioinformatics - BiGCaT 14 Federated query Required unified URIs Identifier mapping

Department of Bioinformatics - BiGCaT 15 Identifier mapping Data enrichment Query expansion Unified identifier conversion

Department of Bioinformatics - BiGCaT 16 Data enrichment

Department of Bioinformatics - BiGCaT 17 Unified Identifiers

Department of Bioinformatics - BiGCaT 18 Query expansion

Department of Bioinformatics - BiGCaT 19 Acknowledgements the Innovative Medicines Initiative Joint (n°115191, FP7/ ) The NIH National Institute for General Medical Sciences (R01-GM100039)

Department of Bioinformatics - BiGCaT 20 Acknowledgement Gladstone Institute Alex Pico Maastricht University Martina Kutmon Egon Willighagen Chris Evelo Manchester University Alasdair Gray Christian BreninkMeijer

Department of Bioinformatics - BiGCaT 21 Resources: WikiPathways: Pathvisio: RDF: rdf.wikipathways.orgrdf.wikipathways.org SPARQL: sparql.wikipathways.orgsparql.wikipathways.org Vocabularies:vocabularies.wikipathways.orgvocabularies.wikipathways.org BridgeDb: IMS: ondex2.cs.man.ac.uk:9090/QueryExpander/)