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Semantic WikiPathways

Semantic WikiPathways. Andra Waagmeester. Overview. Introduction to WikiPathways GPML Pathway to RDF conversion Vocabularies used Obtaining identifiers URIs pathways and pathway elements Example queries Identifier mapping. WikiPathways. Curated by the community

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Semantic WikiPathways

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  1. Semantic WikiPathways Andra Waagmeester

  2. Overview • Introduction to WikiPathways • GPML • Pathway to RDF conversion • Vocabularies used • Obtaining identifiers URIs pathways and pathway elements • Example queries • Identifier mapping

  3. WikiPathways • Curated by the community • Built on top of Mediawiki framework • Live demo

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

  5. Pathway to RDF conversion

  6. WP to RDF conversion

  7. Vocabularies used • Internal (vocabularies.wikipathways.org) • GPML • WP • External • Biopax3 • Bibo • Foaf • tbd

  8. Identifiers.org • Providing resolvable persistent URIs. • Based on Miriam (http://www.ebi.ac.uk/miriam) • Textual Pathway identifiers (xrefs) converted to identifiers.org uri through the miriam api

  9. 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

  10. 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

  11. 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)

  12. 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 <http://rdf.farmbio.uu.se/chembl/sparql>{ ?s rdfs:label ?chidentifier . ?s <http://www.blueobelisk.org/chemistryblogs/inchi> ?inchi .} FILTER (xsd:string(?chidentifier)= xsd:string(?identifier)) . }

  13. Federated query • Required unified URIs • Identifier mapping

  14. Identifier mapping • Data enrichment • Query expansion • Unified identifier conversion

  15. Data enrichment

  16. Unified Identifiers

  17. Query expansion

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

  19. Acknowledgement Gladstone Institute • Alex Pico Maastricht University • Martina Kutmon • EgonWillighagen • Chris Evelo Manchester University • Alasdair Gray • Christian BreninkMeijer

  20. Resources: • WikiPathways: www.wikipathways.org • Pathvisio: www.pathvisio.org • RDF: rdf.wikipathways.org • SPARQL: sparql.wikipathways.org • Vocabularies:vocabularies.wikipathways.org • BridgeDb: www.bridgeDb.org • IMS: ondex2.cs.man.ac.uk:9090/QueryExpander/)

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