Self-service Semantic Data Federation for Clinical Intelligence, Genomics and BioCuration

Chris Baker
University of New Brunswick

11:15am-12:15pm, 3 August 2015
EM 1.70


State-of-the-art approaches to data integration; data warehousing and workflow scripting are limited in scope, brittle and poorly reusable, and depend on highly trained technical staff for their efficient use. Data federation based on SADI semantic web services is a significant and cost effective alternative technology offering interoperable access to life science data.

IPSNP's HYDRA is a SPARQL engine for querying SADI Web Services. HYDRA enables non-technical users to run multiple "self-service" and "ad hoc" queries over networks of web services. Combined with graphical query composition end users can now formulate queries in the terminology of their application domain, without knowing how the underlying data is structured or specific mechanisms of access to the data and thereby perform complex knowledge discovery tasks.

This talk will illustrate a range of complex queries made possible with SADI and HYDRA for online or enterprise scale data integration with examples from the domains of Clinical Surveillance, Genomics and Bioinformatics.


Chris Baker is co-founder and CEO of IPSNP Computing Inc. established in 2011 to commercialize a unique query engine which provides fully integrated access to analytical software and online databases for the bio-pharmaceutical sector. Chris is also full professor and research chair at the University of New Brunswick focused on knowledge management, data and service integration, semantic technologies, text mining, and web services. In addition to an academic career Chris held numerous positions in industry and government research labs. Up until 2008 he was the head of the Semantic Technology Group at the Data Mining Department, I2R, (A-STAR) Singapore and served as Chief Scientific Officer for Knorex Pte Ltd (Singapore). Prior to this he was a group leader of In-Silico Discovery at Ecopia BioSciences (now BELLUS Health) and Bioinformatics Manager at Concordia University in Montreal. He received postdoctoral training in micro and molecular biology at the University of Toronto and at Iogen Corporation in Ottawa and has a PhD in Microbiology from Cardiff University. Chris has served as invited expert at the World Wide Web Consortium (W3C) for three years.

Host: Albert Burger