About Us

[ Dr. Mark Wilkinson, Principal Investigator]

University of British Columbia

Dr. Mark Wilkinson is an Assistant Professor of Medical Genetics at the University of British Columbia Faculty of Medicine, and Principal Investigator in Bioinformatics at the Institute for Heart and Lung Health, St. Paul's Hospital, Vancouver. His research is centered around creating, evaluating, and optimizing data and knowledge representation frameworks that allow bench biologists and clinicians to find the data or tool that they need, when they need it (sometimes even before they realize they need it!), without any formal bioinformatics training. Dr. Wilkinson is a Co-Lead PI of the national Bioinformatics Innovation Center of Genome Canada, and is founder and leader of the international BioMoby consortium.

Dr. Wilkinson invented the Semantic Automated Discovery and Integration (SADI) Framework that allows data and analytical resources to be automatically discovered, integrated, and utilized by software applications. In 2009, CANARIE approved the C-BRASS project to pursue its goal of implementing SADI over a broad range of national and international bioinformatics resources. Our success will help ensure that the hundreds of millions of dollars invested by private and public funding agencies into bioinformatics data generation is maximized through harmonizing the interfaces of these disparate, yet inter-related resources. Just as importantly, C-BRASS aims to train the data and service providers themselves in Semantic Web and Semantic Web Service technologies, such that the resulting knowledge infrastructure and expertise is both distributed and self-sustaining. By fulfilling this mandate, we will also enhance the number of Canadian Highly Qualified Personnel trained in these cutting-edge technologies, adding to Canada's international visibility and competitive advantage in the knowledge-based economy.

Areas of expertise: bioinformatics, genetics, molecular biology, botany, semantic web, knowledge representation, ontology, personalized medicine

 

Research Team:

[ Luke Mc Carthy, B.Sc.] - Lead Developer, SADI Framework

Luke McCarthy is the lead developer on SADI. He has spent the last nine years developing bioinformatics software tools in an attempt to put himself out of a job, but sees no end in sight.

[ Ben Vandervalk, M.Sc. Candidate ] - Programmer

An M. Sc. candidate, Ben's current interest is the application of Semantic Web standards and technologies to problem of data integration in bioinformatics. Under C-BRASS, Ben will be developing SADI services for key biology resources such as the Generic Model Organism Database (GMOD).

[ Mélanie Courtot, Ph.D. Candidate ] - C-BRASS Project Manager

Melanie joined the team in November 2010 as our project manager. She is interested in knowledge representation and data integration, and currently pursue PhD studies on Semantic Web technologies.

 

 

[ Dr. Michel Dumontier, Principal Investigator ]

Carleton University

Dr. Michel Dumontier is an Associate Professor of Bioinformatics at Carleton University in the Department of Biology, the Institute of Biochemistry and School of Computer Science. His research aims to improve our ability to represent and reason about biomedical knowledge, from experimental data to general textbook knowledge, towards building predictive systems for personalized medicine. Dr. Dumontier currently serves as the lead for the Translational Medicine task force of the World Wide Web Consortium's Semantic Web in Health Care and Life Sciences Interest Group (W3C HCLSIG) and is an expert in developing and applying semantic web technologies in the biomedical and life sciences. With over 40 research publications in workshops, conferences, and journals, his innovative research is developing exciting opportunities towards pharmacogenomic based knowledge discovery.

As Co-Principal Investigator in the CANARIE funded C-BRASS project, Dr. Dumontier's role is to guide the development of ontologies (primary the Semanticscience Integrated Ontology) that accurately express C-BRASS service offering and to facilitate their interoperability. Dr. Dumontier is also the lead PI for the Bio2RDF project which aims to provide interlinked life science data to support biological knowledge discovery.

Areas of expertise: medicine, molecular and cell biology, biochemistry, organic chemistry, computational biology, computer science and engineering.

 

Research Team:

[ Natalia Villanueva Rosales, Ph.D. Candidate] - Ontologist

Natalia's current research is focused on the semi-automated creation of Semantic Web knowledge bases for (but not limited to) biological research. Her experience includes the creation, population and query of several OWL ontologies. She specialized in Knowledge Engineering during her Masters studies at the University of Edinburgh and has participated/leaded several projects in the areas of automated reasoning, data mining, data integration and exchange. She joined the C-BRASS team as ontologist, with the initial goal of incorporating relevant bioinformatics web services into the SADI framework.

[ Leonid Chepelev, Ph.D. Candidate] - Web Service Developer

His interests lie at the intersection of Semantic Web technologies, cheminformatics, computational chemistry, metabolomics, and bioinformatics. Leonid's ultimate goal is to distribute computational metabolism, and in particular, metabolic fate and toxicity predictions, as a set of self-organizing SADI web services.

[ Jose Miguel Cruz-Toledo, Ph.D. Candidate] - Programmer, System Administrator

His research is focused on nucleic acid structure prediction and nucleic acid small molecule interaction. His work at Carleton University revolves around this research with a special interest in using Semantic Web technologies to develop related software including SADI Semantic Web Services.

[ Steve Etlinger, P. Eng.] - User Experience Developer

President of Wirespeak Inc., a specialized web and database consulting firm in Ottawa's ByWard Market, he applied his expertise in web and scalable database architectures. His work with SADI is centred around user experience development, and in particular, graphical SPARQL query browsers and interfaces.

[ Nichealla Keath, Undergraduate Student] -Technician, developing the Dataset Registry

She is an undergraduate student of Computational Biochemistry, interested in developing her skills and knowledge of the Semantic Web and its applications. She has spent her time developing the dataset registry however she is eager to be a part of developing SADI Semantic Web services in the near future.

[ Marc-Alexandre Nolin, Ph.D. Candidate] - Database Developer

His interest are in Linked Data and methods to create new links in it. His main project is Bio2RDF. Marc-Alexandre is working from Laval University in Quebec updating and maintaining the Bio2RDF Sparql Endpoints and servers. Also expend the numbers of converted databases.

 

[ Dr. Christopher Baker, Principal Investigator]

University of New Brunswick

Dr. Christopher Baker is currently an Associate Professor at the University of New Brunswick, Canada and Industrial Research Chair for Innovatia Inc. Up until 2008 he was the Head of the Semantic Technology Group at the Data Mining Department, I2R, (A-STAR) where his team developed KnowleSuite, which is now being licensed from I2R by Knorex Pte Ltd, in Singapore. Dr. Baker has considerable experience in Biomedical Informatics and Semantic Technologies and was co-editor of the book Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences published by Springer in 2007. In 2005, his team won the Semantic Web Challenge (2nd prize) at the International Semantic Web Conference. He now serves on the Editorial Board of the Journal of Biomedical Semantics and is an invited expert for the W3C's Semantic Web in Health Care and Life Sciences Interest Group (HCLSIG).

Dr. Baker is a Co-PI on C-BRASS project and is team lead of the Eastern Canada group developing SADI services for text mining and developing application use cases in genomics, proteomics, lipidomics and data warehousing in healthcare.

Areas of expertise: semantic web technologies, ontology, text mining and bioinformatics.

 

Research Team:

[ Dr. Alexandre Riazanov ] - Reasoning and Knowledge Engineering Specialist

Dr. Riazanov has world renowned expertise in the implementation of automated reasoning. Currently he is working in semantic technologies, specifically in relation to relational database query and semantic web services. His work at UNB Saint John is dedicated to the publication of biomedical data and analytical resources with SADI Semantic Web services. He holds a PhD from the University of Manchester, UK. He was formerly R&D Engineer at North Side Inc.

[M. Sc. Artjom KleinI]- Research Scientist Computational Linguistics -

Artjom Klein is a computational linguist with a Masters degree from the University of Heidelberg, Germany. He is knowledgeable in Semantic Web techniques. Recent projects involved the provision of natural language query interfaces to semantic knowledge bases. Current work includes the deployment of text mining services in SADI Framework.

[ Matthew M. Hindle, Ph.D. Candidate] - Bioinformatics Scientist

Matthew Hindle is a bioinformatician with many years of industrial and academic experience. Currently working on developing SADI Semantic Web Services for fish toxicology data, his research interests also include developing a functional annotation pipelines for sequence data that leverages multi-evidence reasoning over an integrated knowledgebases. He has core expertise in the impact of drought stress on genes and metabolic pathways using wheat time-series transcriptome data .

[ Dr. Silvane Paixao ] - C-BRASS Trainer Coordinator & Instructor Design

Silvane Paixao joined the CBRASS team in November 2010 after graduating from UNB Fredericton with a PhD in Land Information Management. In previous roles as Research Assistant and as Project Manager at UNB, Canadian International Development Agency (CIDA) and other Brazilian Institutions, Dr. Paixao gained experience on teaching and developed core expertise in the design, implementation and delivery of training courses.

The NEP-59 CBRASS: Canadian Bioinformatics as Semantic Services project is funded by CANARIE

 

C-BRASS

The The C-BRASS Project - Canadian Bioinformatics Resources as Semantic Services initiative is mandated to provide semantic service descriptions to bioinformatics resources available across Canada and to leverage the SADI  Framework http://sadiframework.org/.

C-BRASS will provide a toolkit for resource providers serving bioinformatics data and analyses on the web to wrap existing web services with semantic descriptors. This will provide bioinformatics researchers with advances tools for discovering services, integrating data and orchestration of workflows.

As these new technologies become standardized the importance of face-to-face communication and training for users cannot be underestimated. A common understanding of how these standards evolve will allow us to build an efficient national network to maximize return-on-investment in research, and improve and hasten Discovery.

C-BRASS will allow machines to make many of the complex decisions about where and how to retrieve and analyze data, leaving the researcher free to focus on what the results mean and how this new knowledge can be used to improve the health of Canadians.

This Open Source, CANARIE-funded initiative is led by a team of Canadian Semantic Web researchers from the University of British Columbia, Carleton University, and University of New Brunswick.

 

SADI

SADI – Semantic Automated Discovery and Integration <http://sadiframework.org> – is a set of standards-compliant Semantic Web Service design patterns that combines simple, stateless, GET/POST-based Web Services with standards from the W3C Semantic Web initiative.

It simply defines an open set of best-practices and conventions, within the spectrum of existing standards, that describe how Web Services and the Semantic Web can seamlessly work together. These conventions, when followed by providers of informatics services, provide a high degree of semantic discoverability, interoperability, and integrative behaviours that are surprisingly powerful and in many cases have not been observed before.

SADI enables the data sources and analytical websites that you use every day to provide their resources to you in a much more intuitive way. This means that the software you use to interact with these resources will also become “smarter” when it is SADI-enabled, because SADI is specifically designed to “think” the way you “think”.

The open-source SADI project provides a place where participants can submit software and/or ontological tools that adhere to these conventions, and can be used by others. This helps to “spread the word” and make it easier for new resources to become semantically interoperable.

More details

 

SADI Registry

Check out more than 200 existing bioinformatics resources wrapped as SADI Services.

More details

 

 

 

 

 

Links:

Semantic Web languages:

 

Principal Investigators Labs:

Vancouver,BC

Ottawa, ON

Saint John, NB