Conference on Semantics in Healthcare and Life Sciences (CSHALS)

Keynote Speaker - Dr. Chris Welty

Chris Welty IBM Research Scientist T.J. Watson Research Center New York, USA Presentation Title: Inside the Mind of Watson Abstract: Watson is a computer system capable of answering rich natural language questions and estimating its confidence in those answers at a level rivaling the best humans at the task. On Feb 14-16, in an historic event, Watson triumphed over the best Jeopardy! players of all time.  In this talk I will discuss how Watson works at a high level with examples from the show. Biography: Chris Welty is a Research Scientist at the IBM T.J. Watson Research Center in New York. Previously, he taught Computer Science at Vassar College, taught at and received his Ph.D. from Rensselaer Polytechnic Institute, and accumulated over 14 years of teaching experience before moving to industrial research. Chris' principal area of research is Knowledge Representation, specifically ontologies and the semantic web, and he spends most of his time applying this technology to Natural Language Question Answering as a member of the DeepQA/Watson team and, in the past, Software Engineering. Dr. Welty was a co-chair of the W3C Rules Interchange Format Working Group (RIF), serves on the steering committee of the Formal Ontology in Information Systems Conferences, is past president of KR.ORG, on the editorial boards of AI Magazine, The Journal of Applied Ontology, and The Journal of Web Semantics, and was an editor in the W3C Web Ontology Working Group. While on sabbatical in 2000, he co-developed the OntoClean methodology with Nicola Guarino. Chris Welty's work on ontologies and ontology methodology has appeared in CACM, and numerous other publications.

Conference on Semantics in Healthcare and Life Sciences (CSHALS)

Keynote Speaker - Dr. Rinke Hoekstra

Rinke Hoekstra, PhD Knowledge Representation & Reasoning Group VU University Amsterdam Leibniz Center for Law, University of Amsterdam  Netherlands Presentation Title: The Knowledge Reengineering Bottleneck >>Presentation (.pdf) Abstract: Knowledge engineering upholds a longstanding tradition that emphasizes methodological issues associated with the acquisition and representation of knowledge in some (formal) language. This focus on methodology implies an ex ante approach: "think before you act". The rapid increase of linked data poses new challenges for knowledge engineering, and the Semantic Web project as a whole. Although the dream of unhindered knowledge reuse is a technical reality, it has come at the cost of control. Semantic web content can no longer be assumed to have been produced in a controlled task-independent environment. When reused, Semantic Web content needs to be remoulded, refiltered and recurated for a new task. Traditional ex ante methodologies do not provide any guidelines for this ex post knowledge reengineering; forcing developers to resort to ad hoc measures and manual labour: the knowledge reengineering bottleneck. Biography: Rinke Hoekstra is a researcher at the Knowledge Representation & Reasoning group of the VU University Amsterdam and at the Leibniz Center for Law of the University of Amsterdam, where he received his Ph.D. on the topic of ontology representation and design patterns. Rinke's main area of research is knowledge representation and engineering, specifically ontologies, the semantic web and linked data. He spends most of his time applying this technology to law and government information, and recently forayed into the domains of science and the humanities. Rinke was a member of the OWL Working Group that developed OWL 2, and the eGov Interest Group of the W3C, and is editorial board member of the Semantic Web journal. He was program chair of OWLED 2009, and served on several program committees for conferences on AI and Law, and Semantic Web. Rinke is the main author of the LKIF Core ontology of basic legal concepts, and one of the initial developers of the MetaLex XML format for legal sources.

Conference on Semantics in Healthcare and Life Sciences (CSHALS)

Keynote Speaker - Dr. Isaac (Zak) Kohane

Isaac (Zak) Kohane, MD, PhD Director, Children’s Hospital Informatics Program Henderson Professor of Pediatrics and Health Sciences and Technology Harvard Medical School (HMS) Co-Director, HMS Center for Biomedical Informatics Director of the HMS Countway Library of Medicine Cambridge, MA, USA Presentation Title: SMArt Semantics for Clinical Healthcare Delivery >>Presentation (.pdf) Biography: Isaac (Zak) Kohane is the director of the Children’s Hospital Informatics Program and is the Henderson Professor of Pediatrics and Health Sciences and Technology at Harvard Medical School (HMS). He is also the co-Director of the HMS Center for Biomedical Informatics and Director of the HMS Countway Library of Medicine. Dr. Kohane leads multiple collaborations at Harvard Medical School and its hospital affiliates in the use of genomics and computer science to study diseases (particularly cancer and autism) through the perspective of biological development. He also has developed several computer systems to allow multiple hospital systems to be used as “living laboratories” to study the genetic basis of disease while preserving patient privacy. Among these, the i2b2 (Informatics for Integrating Biology and the Bedside) National Computing Center has been deployed at over 52 academic health centers internationally. Dr. Kohane has published over 200 papers in the medical literature and authored a widely used book on Microarrays for an Integrative Genomics. He has been elected to multiple honor societies including the American Society for Clinical Investigation, the American College of Medical Informatics, and the Institute of Medicine. He leads a doctoral program in genomics and bioinformatics at the Division of Health Sciences and Technology at Harvard and MIT. He is also a practicing pediatric endocrinologist and father of three energetic children.

Conference on Semantics in Healthcare and Life Sciences (CSHALS)

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Semantic Healthcare and Life Sciences Tutorial: Mashing HC and LS Data

Presented by RPI:

Conference on Semantics in Healthcare and Life Sciences (CSHALS)

News

Feb 21: The CSHALS 2012 Program Book is available here (.pdf)

Feb 07:

Special Offer: CSHALS 2012 Tutorial Registration

Wednesday, February 22
8:30 a.m. - 5:00 p.m.

Registration is now open for the February 22nd CSHALS Tutorial without the requirement of attending the main conference on February 23-24. If you decide after attending the Tutorial to also register for the main conference, 50% of your $250 Tutorial fee will be applied toward your on-site conference registration fee. This special Tutorial-only registration offer must be completed by Monday, February 20 (5:00 pm Eastern).  Full details available at www.iscb.org/cshals2012-registration

Oct 31: CSHALS 2012 -- Register Now and Save!  Click here.

Sept 15: Stay connected to CSHALS news and events by visiting:
http://lanyrd.com/2012/cshals/

August 29: CSHALS 2012 Call for Oral & Poster Presentations is Open.  Click here.

Announcing CSHALS Webinar: Computational Acceleration of Biomedical Discovery

Date: Tuesday, September 20, 2011
Time: 1:00 PM to 2:00 PM (ET)
Register: Visit http://cshals-webinar-1.eventbrite.com/
Location: Actual location of the webinar will be emailed to registrants closer to the event

Details: Please join us for this free webinar reprising and updating Dr. Lawrence Hunter's keynote address from the 2011 Conference for Semantics in Healthcare and Life Sciences (CSHALS). All you need to attend is a computer, an Internet connection, and a free hour on Tuesday, September 20th at 1pm EDT.

Once registered for the event, you will be emailed a link to join the webinar live.

Abstract: The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. However, effective design and implementation of computational tools that genuinely facilitate the generation of novel and significant scientific insights remains poorly understood. In this talk, I will describe a set of efforts that combines natural language processing for information extraction, graphical network models for semantic data integration, and some novel user interface approaches into a system that has recently played a pivotal role in making a significant biomedical discovery.

Biography: Dr. Lawrence Hunter is the Director of the Computational Bioscience Program and of the Center for Computational Pharmacology at the University of Colorado School of Medicine, and a Professor in the departments of Pharmacology and Computer Science (Boulder). He received his Ph.D. in computer science from Yale University in 1989, and then spent more than 10 years at the National Institutes of Health, ending as the Chief of the Molecular Statistics and Bioinformatics Section at the National Cancer Institute. He inaugurated two of the most important academic bioinformatics conferences, ISMB and PSB, and was the founding President of the International Society for Computational Biology. Dr. Hunter's research interests span a wide range of areas, from cognitive science to rational drug design. His primary focus recently has been the integration of natural language processing, knowledge representation and machine learning techniques and their application to interpreting data generated by high throughput molecular biology.

Conference on Semantics in Healthcare and Life Sciences (CSHALS)

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.This e-mail address is being protected from spambots. You need JavaScript enabled to view it
Telephone: 1+780-414-1663

Conference on Semantics in Healthcare and Life Sciences (CSHALS)

Promotion

(updated February 21, 2012)

Description	File type/link
CSHALS 2012 Program Book	.pdf
CSHALS 2012 Promotional Flyer	.pdf

Conference on Semantics in Healthcare and Life Sciences (CSHALS)

Tutorial (hands on)

Updated February 24, 2012

Indicates that presentation slides or other resources are available.

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Special Offer: CSHALS 2012 Tutorial Registration

Wednesday, February 22
8:30 a.m. - 5:00 p.m.

Registration is now open for the February 22nd CSHALS Tutorial without the requirement of attending the main conference on February 23-24. If you decide after attending the Tutorial to also register for the main conference, 50% of your $250 Tutorial fee will be applied toward your on-site conference registration fee. This special Tutorial-only registration offer must be completed by Monday, February 20 (5:00 pm Eastern).  Full details available at www.iscb.org/cshals2012-registration

Wednesday, Feb 22, 2012
8:30 am. - 5:00 p.m.

Location:
Charles Suite - 2nd Floor
Royal Sonesta Hotel

Semantic Healthcare and Life Sciences Tutorial: Mashing HC and LS Data
Hands-on Tutorial Synopsis

Presented by RPI


CSHALS Tutorial Coordinator: Lee Feigenbaum, Cambridge Semantics
RPI Tutorial Coordinator: Joanne Luciano,  This email address is being protected from spambots. You need JavaScript enabled to view it.

Presenters:

• Dominic DiFranzo, This email address is being protected from spambots. You need JavaScript enabled to view it.
  Presentation (.pdf)

• Jim McCusker, This email address is being protected from spambots. You need JavaScript enabled to view it.
  
• Joshua Shinavier. This email address is being protected from spambots. You need JavaScript enabled to view it.
  Presentation resource: http://services.fortytwo.net/linked-data
  Linked Data diagram (click here for PDF)
  

Notice to Tutorial Participants:

In the tutorial, you will download and use an existing virtual machine (VM) that has been setup with an RDF store and other tools you will need. Before the tutorial, please install the Virtual Box software on your laptop. Virtual Box can be installed on Windows, Mac, or Linux laptops. To install Virtual Box, please follow the instructions at:

• www.virtualbox.org/manual/ch02.html

The tutorial will feature three parts:

• In part 1, you will be introduced to Semantic Web technologies, including RDF, RDFS, OWL, and SPARQL. You'll also learn how to issue basic SPARQL queries from JavaScript.
• In part 2, you will learn about Linked Data--Semantic Web data on the Web. This section will cover crawling and querying Linked Data, and then will take a look at health-related linked data such as DrugBank, DailyMed, SIDER, Diseasome, DBpedia, poss. LinkedCT, and PubMed. You'll also look at mashing up linked data with personal health records and talk about some use cases and demo applications.
  
  • http://services.fortytwo.net/linked-data
  • Linked Data diagram (click here for PDF)
    
• In part 3, you will build on what you've learned to accomplish these tasks:
  • Convert a MAGE-TAB file from ArrayExpress to linked data and publish it using LODspeakr
  • Add a summary graph to the experiment page to display the distribution of biospecimens by characteristic
  • Load the data into GenePattern and extract differentially expressed genes
  • Convert the gene list to RDF data cube and load into the triple store
  • Create a heatmap from the gene list

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