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.

1. Drupal as a
Semantic Web platform
Stéphane Corlosquet, Sudeshna Das, Emily Merrill, Paolo Ciccarese,
and Tim Clark
Massachusetts General Hospital
ISWC 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 site
Thousands of free
contributed 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

26. Content types

29. Integrated with Analysis tools

30. What about RDF?

31. Drupal 7 default RDF Schema

32. SCC RDF Schema

33. Backend architecture

34. 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

35. SPARQL Endpoint
● SPARQL Endpoint available at /sparql

36. SPARQL Endpoint
● Need to query Drupal data across different
classes from R
● Need a standard query language
● SQL?
● Query Drupal data with SPARQL

37. Backend architecture (revisited)

39. SPARQL query
PREFIX 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_title
ORDER BY ASC(dc:date)

40. 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

41. Use Case #2:
Data Layers
Domeo + Drupal

42. 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/

43. Domeo

44. Domeo

45. Domeo

46. Domeo

47. 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

48. List of publications in Drupal

49. Can we layer personal annotations on top?

50. What do we have?
● RDFa markup for each publication

51. RDFa API
● Extract structured data from RDFa documents
● Green Turtle: RDFa 1.1 library in Javascript
document.getElementsByType('http://schema.org/ScholarlyArticle');

52. RDFa API

53. Domeo + Drupal
● Data mash up from independent sources

54. Domeo + Drupal

55. 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 didn't have it
● Use JSONP instead

56. Thanks!
● Stéphane Corlosquet
● scorlosquet@gmail.com
● @scorlosquet
● http://openspring.net/
● MIND Informatics
● http://www.mindinformatics.org/