Foundation Medicine



IO Informatics

Conference on Semantics in Healthcare and Life Sciences (CSHALS)

Full Agenda*

(*Updated March 07, 2013. Schedule subject to change. )

Indicates that presentation slides or other resources are available.

go directly to :[Thursday - February 28] [Friday - March 01]

Wednesday – February 27, 2013
11:00 am - 6:30 pm Registration
1:00 pm - 2:45 pm SADI (Tutorial)

Mark Wilkinson Presentation slides (web site)
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Artjom Klein:
- Introduction (pdf)
- Writing Service Demo - Part 1 (pdf)
- Writing Service Demo - Part 2 (pdf)
- Semantic Benchmarking Infrastructure for Text Mining (pdf)
2:45 pm - 3:00 pm Break
3:00 pm - 5:00 pm SADI (Tutorial) (continues)
3:00 pm - 5:00 pm Semantics 101 (Tutorial)
4:00 pm - 5:00 pm Poster (Author) Set-up
5:00 pm - 6:30 pm Poster Reception

Thursday – February 28, 2013
7:30 am - 10:00 am Registration
8:15 am - 8:45 am Breakfast (continental)
9:00 am - 9:15 am Welcome & Conference Overview:
- Fran Lewitter, ISCB Board Member
- Diane Kovats, ISCB Executive Director
- Conference Chairs, Jonas Almeida & Ted Slater
9:15 am - 10:00 am Keynote 1
The Amplification of Informatics Challenges in the Era of Genomic Medicine

Presentation (pdf)

Clinical Professor and Senior Advisor to the
Executive Vice Provost
Health Solutions, Arizona State University
Adjunct Professor of Biomedical Informatics
Columbia University
Scholar in Residence, New York Academy of Medicine
New York, United States
10:05 am - 10:55 am Clinical Healthcare Building the App Store for Health and Discovery
Presenter: Kenneth Mandl
Harvard Medical School/Boston Children's Hospital
Boston, United States

Presentation (pdf)
Semantically Enabling Genetic Medicine to Facilitate Patients and Guidelines Matching and Enhanced Clinical Decision Support
Presenter: Matthias Samwald
Medical University of Vienna
Vienna, Austria
10:55 am - 11:20 am Break
11:20 am - 11:40 am Tech Talk 1 Linguamatics, Linking Data with Agile Text Mining
Presenter: David Milward
Chief Technology Officer
11:45 am -12:05 pm Tech Talk 2 Semantic Indexing of Unstructured Documents Using Taxonomies and Ontologies
Presenter: Jans Aasman
Franz Inc.
Oakland, CA, US
12:05 pm - 1:15 pm Lunch
1:15 pm - 2:00 pm Keynote 2
From Biomedical Information Integration to Knowledge Discovery Through the Semantic Web

Presentation (pdf)

Olivier Bodenreider, M.D., Ph.D.
Chief, Cognitive Science Branch
National Library of Medicine
National Institutes of Health
Bethesda, MD, United States
2:05 pm - 3:20 pm Clinical Healthcare Enabling Australia Wide Use of SNOMED CT
Presenter: David Hansen

Brisbane, Australia

Presentation (pdf)
The Disease and Clinical Measurements Knowledgebase: A Case Study of Data-driven Ontology Class Evaluation and Enrichment
Presenter: Nophar Geifman
Ben Gurion University, Dept. of Microbiology
Immunology and Genetics
Faculty of Health Sciences
The National Institute for Biotechnology in the Negev
Be'er Sheva, Israel

Presentation (pdf)
Building a Knowledge Base for Cancer Genomics
Presenters: Eric Neumann, Alex Parker,
Rachel Erlich
Foundation Medicine
3:20 pm - 3:45 pm Break
3:45 pm - 4:35 pm Clinical Healthcare A Clinical Information Management Platform Using Semantic Technologies
Presenter: Christian Seebode
ORTEC Medical
Berlin, Germany

Presentation (pdf)
CDISC2RDF - Make Clinical Data Standards Linkable, Computable and Queryable
Charles Mead
Octo Consulting Group
Washington, United States

Eric Prud'hommeaux
Cambridge, United States

Presentation (pdf)
4:35 pm - 4:45 pm Daily Closing Remarks Jonas Almeida & Ted Slater, Conference Chairs

Friday – March 01, 2013
7:30 am - 10:00 am Registration
8:00 am - 8:30 am Breakfast (continental)
8:30 am - 8:45 am Review - Previous Day
Jonas Almeida & Ted Slater, Conference Chairs
8:45 am - 9:30 am Keynote 3
Unlocking the Patient Record for Translational Medicine

Presentation (pdf)

The MITRE Corporation
Bedford, MA
9:35 am - 10:50 am Text Mining & Annotation Domeo Web Annotation Tool: Linking Science and Semantics Through Annotation
Paolo Ciccarese
Mass General Hospital and Harvard Medical School
Boston, United States
Semantic Benchmarking Infrastructure for Text Mining: Leverage of Corpora, Ontologies and SPARQL to Evaluate Mutation Text Mining Systems
Presenter: Artjom Klein
University of New Brunswick
Saint John, Canada
Connecting Vocabularies in Linked Data
Presenter: Nadia Anwar
General Bioinformatics
Reading, United Kingdoms

Presentation (pdf)
10:50 am - 11:15 am Break
11:15 am - 12:30 pm Drug Discovery,
Linked Data
Bio2RDF Release 2: Improved coverage, Interoperability and Provenance of Life Science Linked Data
Presenter: Michel Dumontier
Carleton University
Ottawa, Canada
The ISA Infrastructure for the Biosciences: from Data Curation at Source to the Linked Data Cloud
Alejandra Gonzalez-Beltran

University of Oxford
Oxford, United Kingdom

Presentation (pdf)
Producing, Publishing and Consuming Linked Data Three Lessons from the Bio2RDF Project
Presenter: François Belleau
Centre de recherche du CHUQ
Laval University
Québec, Canada
12:30 pm - 1:30 pm Lunch
1:30 pm - 2:15 pm Keynote 4
From Linked Data to Networked Knowledge or Science is a Social Construct

Presentation (pdf)

National University of Ireland, Galway
Digital Enterprise Research Institute (DERI)
2:20 pm - 2:40 pm Tech Talk 3 Enabling Drug Discovery Applications Through a Linked Data Platform
Presenter: Alasdair J G Gray

University of Manchester, UK
2:45 pm – 3:05 pm Tech Talk 4
Practical Usage of Linked Data and Semantic Annotations by the Enterprise
Vassil Momtchev, Ontotext, Bulgaria
3:10 pm – 3:35 pm Linked Data Yes, We Can!
Lessons from Using Linked Open Data (LOD) and Public Ontologies to Contextualize and Enrich Experimental Data

Presenter: Erich A. Gombocz
IO Informatics, Inc., Berkeley, CA, USA

Presentation (pdf)
3:40 pm – 4:00 pm Future Actions and Conference Closing Remarks
Jonas Almeida & Ted Slater, Conference Chairs
4:00 pm Conference Adjourns