Day 1 - June 4

8:00 am            Check-in and continental breakfast

Morning session 

9:00 – 9:15     
Welcome 
Overview of the workshop structure, tutorials, collaborative tools, assignments and games 
[Jonas Almeida]

9:15 am            
Introduction to Semantic Web [Eric Neumann]

10:30 am
S3DB game [Jonas Almeida / Lena Deus]

10:45 - break - 

11:45 pm          
Hands on part 1 – SPARQL-Uniprot Tutorial [Eric Neumann]

Uniprot example, Eric's material.

12:00 pm          
Lunch

Afternoon session

12:45 pm          
Hands On part 2 – Exhibit Tutorial [Eric Neumann]

1:40 pm            
Informatics Mining using SW standards [Eric Neumann]

3:40 pm            
S3DB game – status report [Jonas Almeida / Lena Deus]

3:50 pm            
Wrap-up Day 1 / Overview Day 2

 

Day 2 - June 5

8:00 am            Check-in and continental breakfast

Morning session 

9:00 am            
Q/A on SPARQL and SW standards deriving from tutorial and hands-on exercises in the previous day. 
A Target Gene ontology example illustrating how OWL (DL) classification can be used to determine whether a Gene (instance) is a possible candidate for drug therapeutic targeting. [Eric Neumann]

9:30 am            
Brief History of Biomolecular Data Formats; Data analysis application web-based deployment scenarios – web 1.0, 2.0 and 3.0. What did the S3DB game teach us about a) distinguishing domain from instantiation, b) formulate SPARQL queries, c) embed user permissions to manage chain of custody for the data elements. [Jonas Almeida]

11:00 am          
Semantic Web in the Life Sciences [David States]

12:30 pm          
Lunch

Afternoon session 

1:30 pm            
Ontology modeling. Hands on applications to text mining. [Parsa Mirhaji]

3:30 am            
Conclusions and Open Discussion 

The dictum "I hear and I forget, I see and I believe, I do and I understand" drives the organization of this workshop on the Semantic Web. This two day event articulate 4 half-day modules where key technologies are described. This is presented in the context of their formulation and, most important, the participants are guided in the the use of those tools on their own personal computers, applying them to both reference datasets and their own data.

1. Schedule - The workshop will run between 9 am and 4 pm June 4-5 at Rice University's Duncan Hall. Breakfast and check-in registration start at 8 am in the main foyer called Martel Hall. The facilities will open at 8 am. 

2. Parking is available in visitor’s lots: (1) the Founder’s Court Lot between entrances 2 and 3 or (2) the North Lot annex between entrances 18 and 20 (Rice map). The campus and Duncan Hall are also within walking distance of the MetroRail stop at Herman Park/Rice U. Shuttles are available from the Texas Medical Center to Rice University (shuttle map and schedule). More information about location:

http://ricetv.rice.edu/rooms/roomsearch.php?building=DUN&room=1064

http://www.cs.rice.edu/~keith/DuncanHall/

http://www.cs.rice.edu/~keith/DuncanHall/martel.html

3. The workshop will be very interactive with the material being constantly edited and updated in response to your questions and participation. Accordingly, we will need an authentication system to let you use workshop resources. We will be using Google Authentication, which you can activate by either creating a Google account (if you don't have one already), or by associating a Google password with your email at https://www.google.com/accounts/.

4. During the workshop itself we'll be using a wiki and a text feed. The starting point for this interactivity is the text feed at http://friendfeed.com/gcc. Please get acquainted with it.

5. Now we know you were planning on bringing laptops all along. Please do, a wireless network will be in place for you.

History / context

Participants in the recent GCC futures meeting on personalized medicine“Rate-limiting Factors in Delivering the Promise” recognized semantic web (SW) technology as a potentially critical enabler of personalized medicine. For close to a decade now, the emergence of semantic web technologies has been object of careful design and regulation by the World Wide Web consortium (W3C), the same entity that regulates the current version of the web. The biggest challenge and highest benefit are found in applications to the Life Sciences where heterogeneity and need for automated discovery are defining characteristics. At the previous GCC futures meeting, several participants called for a hands-on workshop to teach new technologies and underlying scientific challenges. A few groups in the Texas Medical Center are active participants in the development of SW technology so this was also seen as an opportunity to capitalize on local expertise, promote collaboration and to expose that community to the latest work ongoing at SW research centers such as W3C and MIT. Finally, this ensemble creates unique opportunities to recruit new students into a field that is already recognized as critical role for systematic approaches to biomedical research. Accordingly, the workshop is structured as a succession of introductory modules, hands-on experimentation, and group discussion of challenges and merits.