Sunday, 28th March

13:30 - 15:00:

 Lunch

15:00 - 16:45:

Welcome and Introduction (30 min.)

Task 1A results (25 min. + 10 min. discussion) [ppt talk with notes]   [pdf without notes]

Task 1A talks (15 min. + 5 min. discussion)

user1 [talk]
user11 [talk]

16:45 - 17:15:

 Coffee break

17:15 - 18:55:

John Wilbur: Problems in annotation of text and creation of a "gold standard".  (30 min.) [talk]

Task 1A talks (15 min. + 5 min. discussion)

user13 [talk]
user26 [talk]

Mark Craven: Applied text mining: gene regulation. How to Integrate the results with data from other sources. (30 min.)[talk]
 

Monday, 29th March

9:30 - 11:10:

Task 1B results (40 min. + 10 min. discussion) [Data preparation]   [Gene list extraction]

Task 1A + 1B talks (20 min. + 5 min. discussion)

user5 [talk]
user6 [talk]

11:10 - 11:40:

 Coffee break

11:40 - 13:30:

user8 [talk]

Task 1B talks (15 min. + 5 min. discussion)

user16 [talk]
user24 [talk]

Discussion: tasks 1A + 1B (45 min.)

13:30 - 15:00:

 Lunch

15:00 - 17:00:

Sophia Ananiadou: Challenges of term extraction in biomedical texts. (30 min.) [talk]

Andrey Rzhetsky: Implementation of large scalable text mining systems and use of "noisy" data collected from different sources. (30 min.) [talk]

Task 2 results I (30 min.) [talk]
Task 2 results II (30 min.) [talk]

17:00 - 17:20:

 Coffee break

17:20 - 19:10:

Rolf Apweiler: The role of text analysis in database curation. Needs, applications, future. (30 min.) [talk]

Task 2 talks (15 min. + 5 min. discussion)

user5 [talk]
user4 [talk]
user7 [talk]
user9 [talk]
 

Tuesday, 30th March

9:30 - 11:50:

Task 2 talks (15 min. + 5 min. discussion)

user14 [talk]
user15 [talk]
user17 [talk]
user20 [talk]

Discussion task 2 (60 min.)
11:50 - 12:10:

 Coffee break

12:10 - 13:40:

Les Grivel: The ORIEL/E-BioSci projects. The role of text analysis for information access in the life sciences. (30 min.) [talk]

Eric Gaussier: IR in the biomedical domain. How to find the relevant documents. With an example of a prototype system for Swiss-Prot annotators. (30 min.) [talk in Openoffice]   [talk in ppt]

Discussion: impact on publishing, chair Matthew Cockerill (30 min.) [talk]

13:40 - 15:00:

 Lunch

15:00 - 16:00:

Explanation of publishing process for BMC Bioinformatics papers.

Afternoon: social activities

Wednesday, 31th March

9:30 - 11:30:

William Hersh: The TREC Genomics Track. (30 min.) [talk]

Round table discussion: next year/future, chairs Rolf Apweiler, Judith Blake and Alfonso Valencia (90 min.)

11:30 - 12:00:

 Coffee break

12:00 - 13:30:

More time for discussions (90 min.)

13:30 - 15:00:

 Lunch and departure