Conference on Semantics in Healthcare and Life Sciences

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Conference on Semantics in Healthcare and Life Sciences (CSHALS)

Full Agenda*

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) . . . . . . . . . . . . . . . . . . . . . . . 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) EDWARD H. SHORTLIFFE, MD, PhD, MACP, FACMI 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 Linguamatics
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 CSIRO ICT Centre 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 Presenters: Charles Mead Octo Consulting Group Washington, United States Eric Prud'hommeaux W3C 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) LYNETTE HIRSCHMAN, PhD 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 Presenter: 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) STEFAN DECKER, PhD National University of Ireland, Galway Digital Enterprise Research Institute (DERI) Ireland
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 Presenter: 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
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Conference on Semantics in Healthcare and Life Sciences

Conference Sponsors

Updated Feb 19, 2013

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Conference on Semantics in Healthcare and Life Sciences

Tutorial (hands on)

Updated March 06, 2013

Indicates that presentation slides or other resources are available.

*Please note tutorial is included in registration fee. Please confirm during registration you will attend:

SADI Tutorial System Requirements:

The following MUST be installed PRIOR to the tutorial - SADI

Participants will receive a fully configured virtual machine image loaded with open source software for practical SADI exercises (writing SADI services and running SPARQL queries).

Participants must have 10GB of free space on their hard drive to uncompress the VM image.

Install VMWare player > To test the installation of VMWare player use this small image (http://www.trendsignals.net/vm/ubuntu1004t/).

SADI Workshop participants who use Apple Computers:

There is no version of VMware Player for OS X. Instead, there is a VMWare Fusion software for Mac.

The 30-day trial can be downloaded here:

https://my.vmware.com/web/vmware/evalcenter?p=vmware-fusion5

The price of the full version is $49.99.

The tutorial presenters have tested the Ubuntu VM image on a Mac machine (Mac OS 10.8.2) with licensed VMWare Fusion (Full Version). All the programs were working fine. The only thing is the memory of Virtual machine must be set to 1GB or more in the VM Settings.

We strongly recommend to download and test your VMWare Player/Fusion with small image (http://www.trendsignals.net/vm/ubuntu1004t/).

Links within this page: SADI | Semantics 101

Semantic Automated Discovery and Integration (SADI) Web Services Tutorial
Wednesday, February 27
1:00 p.m. - 5:00 p.m.

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)

The SADI tutorial will begin with an overview of the project, including the history and "philosophy" behind it, and how it fits into the broader Semantic Web and Linked Data ecosystem. We will then talk about what a SADI service "is", and the specific design patterns advocated by SADI. After seeing a few examples of pipelining services together using the SADI SPARQL client ("SHARE") attendees will then be invited to compose their own ad hoc pipelines, based on a simple template we will provide. The hands-on component will then continue, with workshop participants being shown how to extend the template through building services of their own. In particular, participants will write, and deploy, two additional services that can be fed by data from existing services. Finally, participants will add these new services into the SPARQL queries they wrote earlier.

Tutorial Attendee Profile:

The first half of the tutorial will be accessible to newcomers learning the principles underlying the SADI framework. For the hands on part of the tutorial attendees are expected to be comfortable working in the in Linux environment (editor, terminal), and have working knowledge of Java, RDF/OWL, SPARQL (highly desired) Web Services (HTTP, Tomcat), and the Protege Ontology Editor. Knowledge of Description Logics is optional.

Biographies of SADI Instructors

Dr. Mark Wilkinson
Polytechnic University of Madrid, and University of British Columbia
www.hli.ubc.ca/research/PIs/Wilkinson.html

Dr Mark Wilkinson is an Isaac Peral Distinguished Researcher at the Center for Plant Biotechnology and Genomics, Polytechnic University of Madrid, and Adjunct Professor of Medical Genetics in the Faculty of Medicine, University of British Columbia. His research over the past decade has focused on the problem of enabling bio/medical researchers to execute their own data manipulation and analysis. Much of this work has involved the application of "semantics" to both scientific data and the analytical services that operate on them. He was founder of the BioMoby Semantic Web Service interoperability framework which, at its peak, included more than 1600 bioinformatics data-sources and tools. More recently he created SADI - a set of design practices that enhance interoperability between semantic Web services - and SHARE, a novel query resolver that combines a workflow engine with a logical reasoner to dynamically generate, and execute, a data retrieval and analysis workflow in response to questions posed by the user. His work on supporting multi-lingual end-user query construction in SHARE won first prize for "Best Demonstration of Semantic Technology" at the Semantic Web Applications and Tools for Life Sciences 2010 meeting in Berlin. He is 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. Mark has a Ph.D. in Botany from the University of British Columbia.

Artjom Klein
Research Scientist, University of New Brunswick, Canada
www.linkedin.com/in/artjomklein

Artjom Klein is a computational linguist with a Masters degree from the University of Heidelberg, Germany. He is has many years of hands on experience in Semantic Web techniques. Recent projects involved the provision of natural language query interfaces to semantic knowledge bases and deployment of text mining services in SADI Framework. Artjom was a core developer on the C-BRASS project (Canadian Bioinformatics Resources as Semantic Services) deploying more than 200 SADI services in Dr Chris Baker's lab at UNB, Saint John.

Semantics 101 Tutorial

Wednesday, February 27
3:00 p.m. - 5:00 p.m.

This two-hour tutorial will present a practical introduction to Semantic Web technologies. We will motivate the introductions with use cases and examples, and we will also attempt to dispel some of the myths and some of the hype around the Semantic Web. The tutorial will cover the following topics:

• What is the Semantic Web? What are Semantic Web technologies? What's the difference?

• How does the Semantic Web relate to other technologies such as semantic search or text analytics/NLP?

• How are some life sciences organizations using Semantic Web technologies today?

The tutorial will also introduce the following Semantic Web technologies:

• RDF -- the foundational data model of the Semantic Web
• SPARQL -- the query language of the Semantic Web
• RDFS & OWL -- schema and ontology language for describing data and reasoning on the Semantic Web
• Linked Data -- best practices for publishing data in an easily consumable manner
• RDFa -- for embedding data in Web pages and XML documents

The tutorial is aimed both at people who are brand new to the Semantic Web and also those who have some experience but are looking for a broader understanding of the state of the Semantic Web in 2013 and how the various pieces of the Semantic Web fit together.   The tutorial draws on highly regarded educational material from Semantic University.

Biography of Semantic 101 Instructor

Lee Feigenbaum (@LeeFeigenbaum) is a co-founder of Cambridge Semantics, where he serves as VP of Marketing and Technology. Lee brings over a decade of experience with Semantic Web technologies to this role, helping to direct the development of the Anzo product suite to solve customers' ever-changing and diverse data challenges. Prior to co-founding Cambridge Semantics, Lee spent over five years as an engineer with IBM's Advanced Internet Technology Group. There, Lee helped architect and develop successive iterations of a semantic application architecture, culminating in the open-source release of the IBM Semantic Layered Research Platform.

Lee is an active member of the W3C Semantic Web standards community, and currently serves as the Co-Chair of the W3C's SPARQL Working Group. Lee authored a 2007 Scientific American article on the Semantic Web, and writes regularly about Semantic Web technologies at his blog, TechnicaLee Speaking. Lee is also a co-creator and editor-in-chief of Semantic University.

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Conference on Semantics in Healthcare and Life Sciences

Keynote Speaker - Dr. Olivier Bodenreider

OLIVIER BODENREIDER, M.D., Ph.D. Chief, Cognitive Science Branch National Library of Medicine National Institutes of Health Bethesda, MD, United States Presentation Title: From Biomedical Information Integration to Knowledge Discovery Through the Semantic Web Presentation (pdf) Abstract:  Over the past decade, knowledge resources have become increasingly available not only for humans to read and make sense of, but also electronically, which make these data amenable to automated processing. Structured knowledge sources have been developed and integrated in systems such as Entrez, developed by the National Center for Biotechnology Information (NCBI). Vast amounts of biomedical text have also been processed in order to extract entities and relations. In the clinical domain, data warehouses created from electronic health record systems have been created in virtually every institution involved in translational research. Finally, the biomedical domain is rich of many ontologies, which provide the vocabulary for normalizing entities and relationships in these knowledge sources, as well as the domain knowledge to interpret the content of these resources. Semantic Web technologies have emerged as the infrastructure of choice for integrating biomedical information. This talk will focus on the experimental Biomedical Knowledge Repository being developed at the National Library of Medicine. This repository leverages Semantic Web technologies to integrate the Unified Medical Language System (UMLS), 60 M relations extracted from PubMed/MEDLINE abstracts by the SemRep natural language processing (NLP) system, as well as features from Entrez Gene. We will show how definitional knowledge from biomedical ontologies can complement assertional knowledge extracted from the literature in support of hypothesis generation and knowledge discovery. Biography:  Olivier Bodenreider is a Senior Scientist and Chief of the Cognitive Science Branch of the Lister Hill National Center for Biomedical Communications at the US National Library of Medicine. His research focuses on terminology and ontology in the biomedical domain, both from a theoretical perspective (quality assurance, interoperability) and in their application to natural language processing, knowledge discovery and information integration  Dr. Bodenreider is a Fellow of the American College of Medical Informatics. He received a MD degree from the University of Strasbourg, France in 1990 and a PhD in Medical Informatics from the University of Nancy, France in 1993. Before joining the National Library of Medicine in 1996, he was assistant professor for Biostatistics and Medical Informatics at the University of Nancy Medical School. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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Conference on Semantics in Healthcare and Life Sciences

Keynote Speaker - Dr. Stefan Decker

STEFAN DECKER, PhD National University of Ireland, Galway Digital Enterprise Research Institute (DERI) Ireland Presentation Title: From Linked Data to Networked Knowledge or Science is a Social Construct Presentation (pdf) Biography: Prof Stefan Decker is a full professor at the National University of Ireland and the director of the Digital Enterprise Research Institute (DERI) in Galway. Prof Decker obtained in 1995 a masters in Computer Science at the University of Kaiserslautern (awarded with distinction). From 1995 to 1999 he worked towards a Ph.D. degree in Computer Science at the University of Karlsruhe (awarded 2002 with distinction). From 1999-2002 he worked as a Postdoc and Research Associate at the Computer Science Department of Stanford University and established one of the first Semantic Web research groups. From July 2002 to July 2005, he worked as a Computer Scientist and Research Assistant Professor at the Information Sciences Institute of the University of Southern California, USA. In October 2003 Prof Decker moved to Ireland to help to set up a new Research Institute concerned with the Semantic Web. Since July 2006 Prof Decker is full professor and director of the Digital Enterprise Research Institute.  His current research interests include the Semantic Web, metadata, ontologies and semi-structured data, web services, and applications for Digital Libraries, Knowledge Management, Information Integration and Peer-to-Peer technology. He published around 80 papers as books and journal, book, conference, and workshop contributions. He co-organized around 35 scientific workshops and conferences and has edited several special issues of scientific journals. He was editor-in-chief of Elsevier's Journal of Web Semantics, editoral committee member of the Electronic Transactions on Artificial Intelligence (ETAI) (the Semantic Web), the Journal on Internet Research and the Journal on Web Intelligence and Agent Systems (WIAS) and is recognized as one of the most widely cited Semantic Web scientists. His dissertation work was quoted as one of the inspirations for the DARPA DAML program, which span the Semantic Web effort. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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Conference on Semantics in Healthcare and Life Sciences

News

2013:

• Jan 30:  Poster presentations now available on-line.   Visit the Poster Presentations page >>click here<< and check back as full detailed posters are added to the site.
  
  
• Jan 17:  ISCB is pleased to note the Joint SWAT4LS and CSHALS Thematic Series published by the Journal of Biomedical Sementics is available at: http://www.jbiomedsem.com/series/SWAT4LSCSHALS
  
  This thematic series focuses on the application of web based technologies for knowledge representation and data integration in life sciences, that seek to facilitate biomedical research and healthcare practice. The series originates in research presented at two conferences, SWAT4LS (Semantic Web Application and Tools for Life Sciences) which is held annually in Europe, and CSHALS (Conference on Semantics in Healthcare and Life Sciences), which is held annually in the United States. These two venues foster critical discussions on the limits, challenges, and opportunities in the adoption of semantic web technologies in healthcare and life sciences.
  
  The emergence of the Web as the primary communication medium; the ever increasing amount of biomedical information and the convergence of disciplines in the biomedical spectrum are all phenomena that point at the Web as a promising technology platform to increase the efficiency of biomedical research and healthcare delivery. At the same time, they make evident the need for semantic approaches in order to integrate information that arises from different processes and disciplines in a meaningful way. At this convergence of Web and semantic solutions we are witnessing a front of innovation where various approaches, including Semantic Web and Linked Data solutions, are proposed.
  
  The objective of this thematic series, and of the events that underpin it, is to explore this front of innovation, both in the critical assessment of current technologies and in novel proposals.
  
  The series is open for any submission that fits into these objectives.
  
  
• Jan 11: Agenda and Conference Presentation details now available.  Click HERE. 
  
  

• Jan 07: FINAL CALL for Poster Presentations - Deadline Jan 11.
  Full Details are available here.
  
  

2012:

• Nov 09: Introducing the CSHALS 2013 Keynote Speakers  Click HERE. 

Conference on Semantics in Healthcare and Life Sciences

Contacts

Please direct inquiries about CSHALS to:

Steven Leard
ISCB Conferences Director
This email address is being protected from spambots. You need JavaScript enabled to view it.
Telephone: 1+780-414-1663