Drupal as aSemantic Web platform

Stéphane Corlosquet, Sudeshna Das, Emily Merrill, Paolo Ciccarese, and Tim ClarkMassachusetts General HospitalISWC 2012, Boston, USA – Nov 14th, 2012

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/

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 hosting● Scalable

http://drupal.org/getting-started/before/overview

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, podcast, e-commerce... (be creative)

http://www.flickr.com/photos/georgivar/4795856532/

Building a Drupal site

● Enable the features you want

Comments, tags, voting/rating, location, translations, revisions, search...

http://www.flickr.com/photos/skip/42288941/

Building a Drupal site

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/

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): 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

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, Turtle, N-Triples

● SPARQL● Expose Drupal RDF data in a SPARQL Endpoint

● Features and packaging● Build distributions / deployment workflow

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?● Query Drupal data with SPARQL

Backend architecture (revisited)

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_titleORDER BY ASC(dc:date)

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

Use Case #2:

Data Layers

Domeo + Drupal

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/

Domeo

Domeo

Domeo

Domeo

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

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 Javascript

document.getElementsByType('http://schema.org/ScholarlyArticle');

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● JSON → JSON-LD

● CORS support not yet available everywhere● Grails didn't have it● Use JSONP instead

Thanks!

● Stéphane Corlosquet ● scorlosquet@gmail.com● @scorlosquet● http://openspring.net/

● MIND Informatics● http://www.mindinformatics.org/