1. Semantic WikiPathways Andra Waagmeester

2. 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

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

4. 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

5. Department of Bioinformatics - BiGCaT 5

6. 6 Pathway to RDF conversion

7. Department of Bioinformatics - BiGCaT 7 WP to RDF conversion

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

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

10. 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. } http://sparqlbin.com/#4f91f23a032a87cc46c5a526a6da673a

11. 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) http://sparqlbin.com/#a86569fa8a5ae4b004fdf2432b3ce98c

12. 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)

13. 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)). }

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

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

16. Department of Bioinformatics - BiGCaT 16 Data enrichment

17. Department of Bioinformatics - BiGCaT 17 Unified Identifiers

18. Department of Bioinformatics - BiGCaT 18 Query expansion

19. Department of Bioinformatics - BiGCaT 19 Acknowledgements the Innovative Medicines Initiative Joint (n°115191, FP7/2007-2013) The NIH National Institute for General Medical Sciences (R01-GM100039)

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

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