Drupal as a       Semantic Web platformStéphane Corlosquet, Sudeshna Das, Emily Merrill, Paolo Ciccarese,and Tim ClarkMass...
Drupal●   Dries Buytaert - small news site in 2000●   Open Source - 2001●   Content Management System●   LAMP stack●   Non...
Who uses Drupal?
Who uses Drupal?
Who uses Drupal?
Who uses Drupal?
Who uses Drupal?
Who uses Drupal?
Who uses Drupal?
Who uses Drupal?
Who uses Drupal?
Who uses Drupal?            http://buytaert.net/tag/drupal-sites
Drupal   ●   Open & modular       architecture   ●   Extensible by modules   ●   Standards-based   ●   Low resource hostin...
Building a Drupal site        http://www.flickr.com/photos/toomuchdew/3792159077/
Building a Drupal site●   Create the content types    you need    Blog, article, wiki, forum, polls,    image, video, podc...
Building a Drupal site●   Enable the features you    want    Comments, tags, voting/rating,    location, translations, rev...
Building a Drupal site
Building a Drupal siteThousands of freecontributed modules●   Google Analytics●   Wysiwyg●   Captcha●   Calendar●   XML si...
The Drupal Community          http://www.flickr.com/photos/x-foto/4923221504/
Use Case #1:Stem Cell Commons http://stemcellcommons.org
Repository•   New repository for stem cell data as part of Stem    Cell Commons•   Harvard Stem Cell Institute (HSCI): Blo...
Content types
Integrated with Analysis tools
What about RDF?
Drupal 7 default RDF Schema
SCC RDF Schema
Backend architecture
Modules used●   Contributed module for more features    ●   RDF Extensions           ●   Serialization formats: RDF/XML, T...
SPARQL Endpoint●   SPARQL Endpoint available at /sparql
SPARQL Endpoint●   Need to query Drupal data across different    classes from R●   Need a standard query language●   SQL?●...
Backend architecture (revisited)
SPARQL queryPREFIX obo: <http://purl.obolibrary.org/obo/>PREFIX mged: <http://mged.sourceforge.net/ontologies/MGEDontology...
Wrap up use case #1●   Drupal is a good fit for building web frontends●   Editing User Interfaces out of the box●   Queryi...
Use Case #2: Data LayersDomeo + Drupal
Domeo●   Annotation Tool developed by MIND    Informatics, Massachusetts General Hospital●   Annotate HTML documents●   Sh...
Domeo
Domeo
Domeo
Domeo
JSON-LD●   JSON for Linked Data●   Client side as well as server side friendly●   Browser Scripting:       –   Native java...
List of publications in Drupal
Can we layer personal annotations on top?
What do we have?●   RDFa markup for each publication
RDFa API●   Extract structured data from RDFa documents●   Green Turtle: RDFa 1.1 library in Javascriptdocument.getElement...
RDFa API
Domeo + Drupal●   Data mash up from independent sources
Domeo + Drupal
Wrap up use case #2●   Another use case for exposing data as RDFa●   RDFa and JSON-LD fit well together    ●   HTML → RDFa...
Thanks!●   Stéphane Corlosquet    ●   scorlosquet@gmail.com    ●   @scorlosquet    ●   http://openspring.net/●   MIND Info...
Drupal as a Semantic Web platform - ISWC 2012
Drupal as a Semantic Web platform - ISWC 2012
Drupal as a Semantic Web platform - ISWC 2012
Drupal as a Semantic Web platform - ISWC 2012
Drupal as a Semantic Web platform - ISWC 2012
Drupal as a Semantic Web platform - ISWC 2012
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.

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Drupal as a Semantic Web platform - ISWC 2012

  1. 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. 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. 3. Who uses Drupal?
  4. 4. Who uses Drupal?
  5. 5. Who uses Drupal?
  6. 6. Who uses Drupal?
  7. 7. Who uses Drupal?
  8. 8. Who uses Drupal?
  9. 9. Who uses Drupal?
  10. 10. Who uses Drupal?
  11. 11. Who uses Drupal?
  12. 12. Who uses Drupal? http://buytaert.net/tag/drupal-sites
  13. 13. Drupal ● Open & modular architecture ● Extensible by modules ● Standards-based ● Low resource hosting ● Scalable http://drupal.org/getting-started/before/overview
  14. 14. Building a Drupal site http://www.flickr.com/photos/toomuchdew/3792159077/
  15. 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. 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. 17. Building a Drupal site
  18. 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. 19. The Drupal Community http://www.flickr.com/photos/x-foto/4923221504/
  20. 20. Use Case #1:Stem Cell Commons http://stemcellcommons.org
  21. 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. 22. Content types
  23. 23. Integrated with Analysis tools
  24. 24. What about RDF?
  25. 25. Drupal 7 default RDF Schema
  26. 26. SCC RDF Schema
  27. 27. Backend architecture
  28. 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. 29. SPARQL Endpoint● SPARQL Endpoint available at /sparql
  30. 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. 31. Backend architecture (revisited)
  32. 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. 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. 34. Use Case #2: Data LayersDomeo + Drupal
  35. 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. 36. Domeo
  37. 37. Domeo
  38. 38. Domeo
  39. 39. Domeo
  40. 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. 41. List of publications in Drupal
  42. 42. Can we layer personal annotations on top?
  43. 43. What do we have?● RDFa markup for each publication
  44. 44. RDFa API● Extract structured data from RDFa documents● Green Turtle: RDFa 1.1 library in Javascriptdocument.getElementsByType(http://schema.org/ScholarlyArticle);
  45. 45. RDFa API
  46. 46. Domeo + Drupal● Data mash up from independent sources
  47. 47. Domeo + Drupal
  48. 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. 49. Thanks!● Stéphane Corlosquet ● scorlosquet@gmail.com ● @scorlosquet ● http://openspring.net/● MIND Informatics ● http://www.mindinformatics.org/
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