Conference on Semantics in Healthcare and Life Sciences (CSHALS)

Tutorial (hands on)

Updated February 21, 2011

CSHALS will be preceded by a full-day Tutorial focused on the current Semantic Web standard RDF tools to show participants how this technology meets drug development needs.

Note: You must be registered for the CSHALS 2011 conference to register for the full-day tutorial on Wednesday, February 23.


Go directly to: [ Hands-on Tutorial Synopsis] [ Tutorial Agenda ] [ Reading List ]

Multi-stakeholder Perspectives on Translational Medicine Tutorial
Presented by W3C

The W3C's Health Care and Life Sciences Interest Group (HCLS IG) has been working since 2005 with multiple communities and Semantic Web technologies towards goals such as immediate availability of scientific publications; improved synthesis between scientific findings; better patient recruitment for drug trials; and early redirection of non-promising clinical trials.

Today, there is a new convergence of communities in health care and life sciences. Pharmaceutical companies, clinical care providers and individual patients have intersecting interests in Translational Medicine. Pharmaceutical companies have a new interest in more detailed patient records rather than aggregate data because of the shift towards tailored therapeutics.

Consumers advocating for personally controlled health care records are a new audience interested in health care data. Clinicians, pharmaceutical companies and individuals will benefit from health care data which is easy to integrate with genomics, bio informatics chem informatics and environmental data.

In this tutorial session, we will show you how W3C's HCLS IG is integrating data across these domains. We will demonstrate the use of commodity Semantic Web tools to ask valuable questions of a corpus of health care data, and show how this corpus draws on such systems as the Indivo EHR system, the I2B2 clinical information exchange protocols, and databases backing conventional clinical data stores.

Attendees will learn to use and customize these open source tools to meet their clinical or research needs.


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

Presented by RPI



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The tutorial team from RPI have provided instructions for your use prior to attending the Tutorial on Wednesday, Feb 23 at the Royal Sonesta Hotel.


Please take a moment to visit and review the instructions posted at:
http://sparql.tw.rpi.edu/?page_id=57


If you have questions or problems please email presenters Dominic, Tim, or Jim identified below.

RPI Tutorial Coordinator: Joanne Luciano,  This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Presenters:
Tim Lebo,  This e-mail address is being protected from spambots. You need JavaScript enabled to view it
Dominic DiFranzo,  This e-mail address is being protected from spambots. You need JavaScript enabled to view it
Jim McCusker,  This e-mail address is being protected from spambots. You need JavaScript enabled to view it
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CSHALS has always been about the practical application of semantic technology to life sciences and pharmaceutical R&D. In keeping with that spirit, this hands-on tutorial will give participants practical experience using Semantic Web tools and technologies to develop mashups using data from the Linked Open Data cloud together with semantic data they create themselves from raw data. Participants will load data into a triple store, query it using SPARQL, use inference to expand the experimental knowledge, and build dynamic visualizations from their results. The tutorial will be loosely based on the book Programming the Semantic Web*, by Toby Segaran (one of our keynote speakers), Colin Evans, & Jamie Taylor, and will be led by Rensselaer Polytechnic Institute’s Tetherless World Constellation. Bring your laptops! It’s going to be fun.

(* All CSHALS participants will receive an eBook copy of Programming the Semantic Web, courtesy of O’Reilly Media.)


Tutorial Agenda

1. Part I – Semantic Data (11:00 a.m. - 12:15 p.m.)
Brief introduction to the basics of the Semantic Web, its principles, and its technologies. Here we will discuss what the Semantic Web is, why we need it, what technologies make up the Semantic Web, and how we can use them to link and query data.

1.1. Why do we need a Semantic Web?
1.2. Intro to basic Semantic Web technology
1.3. Just Enough RDF - Converting data to RDF
- a few technologies that can be used to convert data to RDF
1.4. Data Linking
1.5. SPARQL

2. Part II - Mashup Workflows (1:00 p.m. - 3:00 p.m.)
In this section we will discuss the workflow of building a mashup using semantic data. We will discuss the iterative process of discovering, exploring, linking our data, and publishing on the web. The aim is to learn the semantics and syntax of the data, and how to bring them together.

2.1. Data identification – what data sets to utilize
2.2. Data understanding – the semantics and syntax of your data
2.3. Data linking – how to link together your data

3. Part III - Data visualization - (3:15 p.m. - 5:00 p.m.)
Once we’ve gone through the data and discovered what’s inside it and how to link it to other datasets, we can begin to query the data and visualize the results. This allows us to see new patterns and correlations that weren’t visible before. We can also use our visualization to communicate these patterns and ideas to others. We will also cover some popular visualization APIs that can be used for visualization.

3.1. Uses
3.1.1. Data discovery - exploring your data through visualization. See new patterns that emerge from visually exploring your data
3.1.2. Data communication - communicate the story that is within your data, and see more effective ways to visually present your data for better communication
3.2. Visualization APIs
3.2.1. Google visualization APL
3.2.2. MIT Simile Exhibit


Reading List and References (as of November 3, 2010)

  • "What is RDF and what is it good for?"
    by Joshua Tauberer
    www.rdfabout.com/intro/
  • Quick Intro to RDF
    Joshua Tauberer
    www.rdfabout.com/quickintro.xpd
  • RDF Primer
    Turtle version
    www.w3.org/2007/02/turtle/primer/
  • Semantic Web for the Working Ontologist: Effective Modeling in RDFS and OWL
    by Dean Allemang and James Hendler
  • Natalya F. Noy and Deborah L. McGuinness. Ontology Development 101: A Guide to Creating Your First Ontology. Stanford Knowledge Systems Laboratory Technical Report KSL-01-05 and Stanford Medical Informatics Technical Report SMI-2001-0880, March 2001.
  • Semantic Web Programming
    by John Hebeler et al, Wiley, 2009
  • Foundations of Semantic Web Technologies
    by Hitzler et al., Chapman & Hall/CRC, 2009

 

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