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Drupal as a Semantic Web platform - ISWC 2012
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Drupal as a Semantic Web platform - ISWC 2012

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This presentation describes some use cases and deployments of Drupal for building bio-medical platforms powered by semantic web technologies such as RDF, SPARQL, JSON-LD.

This presentation describes some use cases and deployments of Drupal for building bio-medical platforms powered by semantic web technologies such as RDF, SPARQL, JSON-LD.

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  • 1. Drupal as a Semantic Web platformStéphane Corlosquet, Sudeshna Das, Emily Merrill, Paolo Ciccarese,and Tim ClarkMassachusetts General HospitalISWC 2012, Boston, USA – Nov 14th, 2012
  • 2. Drupal● Dries Buytaert - small news site in 2000● Open Source - 2001● Content Management System● LAMP stack● Non-developers can build sites and publish content● Control panels instead of code http://www.flickr.com/photos/funkyah/2400889778
  • 3. Who uses Drupal?
  • 4. Who uses Drupal?
  • 5. Who uses Drupal?
  • 6. Who uses Drupal?
  • 7. Who uses Drupal?
  • 8. Who uses Drupal?
  • 9. Who uses Drupal?
  • 10. Who uses Drupal?
  • 11. Who uses Drupal?
  • 12. Who uses Drupal? http://buytaert.net/tag/drupal-sites
  • 13. Drupal ● Open & modular architecture ● Extensible by modules ● Standards-based ● Low resource hosting ● Scalable http://drupal.org/getting-started/before/overview
  • 14. Building a Drupal site http://www.flickr.com/photos/toomuchdew/3792159077/
  • 15. Building a Drupal site● Create the content types you need Blog, article, wiki, forum, polls, image, video, podcast, e- commerce... (be creative) http://www.flickr.com/photos/georgivar/4795856532/
  • 16. Building a Drupal site● Enable the features you want Comments, tags, voting/rating, location, translations, revisions, search... http://www.flickr.com/photos/skip/42288941/
  • 17. Building a Drupal site
  • 18. Building a Drupal siteThousands of freecontributed modules● Google Analytics● Wysiwyg● Captcha● Calendar● XML sitemap● Five stars● Twitter● ... http://www.flickr.com/photos/kaptainkobold/1422600992/
  • 19. The Drupal Community http://www.flickr.com/photos/x-foto/4923221504/
  • 20. Use Case #1:Stem Cell Commons http://stemcellcommons.org
  • 21. Repository• New repository for stem cell data as part of Stem Cell Commons• Harvard Stem Cell Institute (HSCI): Blood and Cancer program system• Designed to incorporate - multiple stem cell types - multiple assay types - user requested features• Integrated with analytical tools• Enhanced search and browsing capabilities
  • 22. Content types
  • 23. Integrated with Analysis tools
  • 24. What about RDF?
  • 25. Drupal 7 default RDF Schema
  • 26. SCC RDF Schema
  • 27. Backend architecture
  • 28. Modules used● Contributed module for more features ● RDF Extensions ● Serialization formats: RDF/XML, Turtle, N-Triples ● SPARQL ● Expose Drupal RDF data in a SPARQL Endpoint ● Features and packaging ● Build distributions / deployment workflow
  • 29. SPARQL Endpoint● SPARQL Endpoint available at /sparql
  • 30. SPARQL Endpoint● Need to query Drupal data across different classes from R● Need a standard query language● SQL?● Query Drupal data with SPARQL
  • 31. Backend architecture (revisited)
  • 32. SPARQL queryPREFIX obo: <http://purl.obolibrary.org/obo/>PREFIX mged: <http://mged.sourceforge.net/ontologies/MGEDontology.php#>PREFIX dc: <http://purl.org/dc/terms/>SELECT ?bioassay_title WHERE { ?experiment obo:OBI_0000070 ?bioassay; dc:title ?bioassay_title . ?bioassay mged:LabelCompound <http://exframe-dev.sciencecollaboration.org/taxonomy/term/588> .}GROUP BY ?bioassay_titleORDER BY ASC(dc:date)
  • 33. Wrap up use case #1● Drupal is a good fit for building web frontends● Editing User Interfaces out of the box● Querying Data in SQL: ● not very friendly ● may not be appropriate / performant● Querying with SPARQL: ● Use the backend that match your needs ● ARC2 can be sufficient for prototyping and lightweight use cases
  • 34. Use Case #2: Data LayersDomeo + Drupal
  • 35. Domeo● Annotation Tool developed by MIND Informatics, Massachusetts General Hospital● Annotate HTML documents● Share annotations● Annotation Ontology (AO), provenance, ACL● JSON-LD Service to retrieve annotations● http://annotationframework.org/
  • 36. Domeo
  • 37. Domeo
  • 38. Domeo
  • 39. Domeo
  • 40. JSON-LD● JSON for Linked Data● Client side as well as server side friendly● Browser Scripting: – Native javascript format – RDFa API in the DOM● Data can be fetched from anywhere: – Cross-Origin Resource Sharing (CORS) required● Clients can mash data
  • 41. List of publications in Drupal
  • 42. Can we layer personal annotations on top?
  • 43. What do we have?● RDFa markup for each publication
  • 44. RDFa API● Extract structured data from RDFa documents● Green Turtle: RDFa 1.1 library in Javascriptdocument.getElementsByType(http://schema.org/ScholarlyArticle);
  • 45. RDFa API
  • 46. Domeo + Drupal● Data mash up from independent sources
  • 47. Domeo + Drupal
  • 48. Wrap up use case #2● Another use case for exposing data as RDFa● RDFa and JSON-LD fit well together ● HTML → RDFa ● JSON → JSON-LD● CORS support not yet available everywhere ● Grails didnt have it ● Use JSONP instead
  • 49. Thanks!● Stéphane Corlosquet ● scorlosquet@gmail.com ● @scorlosquet ● http://openspring.net/● MIND Informatics ● http://www.mindinformatics.org/