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.
HTML Injection Attacks: Impact and Mitigation Strategies
Drupal as a Semantic Web platform - ISWC 2012
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
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/
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/
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
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
36. SPARQL Endpoint
● Need to query Drupal data across different
classes from R
● Need a standard query language
● SQL?
● Query Drupal data with SPARQL
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
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/
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
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');
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
