LBM 2007 program

Thursday, 6 Dec 2007

9:00 – 9:15

Welcome address

9:15 –10:15


Keynote 1 (Chaired by Jong C. Park)

Terminological systems in biomedicine: From terminology integration to information integration

Olivier Bodenreider

10:15 – 10:45 Tea Break

10:45 – 12:15

 Session 1A: Terminology and Named Entity, chaired by Nigel Collier

10:45 – 11:15

Normalizing biomedical terms by minimizing ambiguity and variability
Yoshimasa Tsuruoka, John McNaught, Sophia Ananiadou

11:15 – 11:45

Assessment of diseases named entity recognition on a corpus of annotated sentences
Antonio Jimeno, Ernesto Jimenez-Ruiz, Vivian Lee, Sylvain Gaudan, Rafael Berlanga-Llavori, Dietrich Rebholz-Schuhmann


Analysis and enhancement of conditional random fields gene mention taggers in BioCreative II Challenge Evaluation

Yu-Ming Chang, Cheng-Ju Kuo, Han-Shen Huang, Yu-Shi Lin, Chun-Nan Hsu

12:00-1:00 Lunch Break



Keynote 2 (Chaired by Su Jian)

Delivering text mining services for the biosciences

Sophia Ananiadou


Session 1B: Text Classification (I), chaired by Hongfang Liu


Exploiting and integrating rich features for biological literature classification
Hongning Wang, Minlie Huang, Shilin Ding, Xiaoyan Zhu


The integration of multiple feature representations for protein-protein interaction classification task

Man Lan and Chew Lim Tan


Protein-protein interaction abstract identification with contextual bag of words

Richard Tzong-Han Tsai, Hsieh-Chuan Hung, Hong-Jie Dai and Yi-Wen Lin


3:00-3:30 Tea Break


Session 1C: Text Mining, chaired by Dietrich Rebholz-Schuhmann


New challenges for text mining: Mapping between text and manually curated pathways

Kanae Oda, Jin-Dong Kim, Tomoko Ohta, Yuka Tateisi, Jun'ichi Tsujii


A comparative analysis of five protein-protein interaction corpora

Sampo Pyysalo, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter ,Tapio Salakoski


Syntactic features for protein-protein interaction extraction

Rune Saetre, Kenji Sagae and Jun'ichi Tsujii


Recognition of multisentence n-ary subcellular localization mentions in biomedical abstracts

Gabor Melli, Martin Ester, Anoop Sarkar

19:00-10:00 Conference Banquet @ Made In China Museum, Haw Par Villa

Bus leaves from Biopolis to Haw Par Villa at 5:20 pm. Delegates are invited to tour the museum before banquet

Friday, 7 Dec 2007



Keynote 3 (Chaired by Christopher Baker)

Aligning biomedical ontologies

Patrick Lambrix

10:00-10:30 Tea Break


Session 2A: Ontologies and Logic, chaired by Mark Schreiber


Monitoring the evolutionary aspect of the Gene Ontology to enhance predictability and usability

Jong C. Park, Tak-eun Kim, Jinah Park


Structuring an event ontology for disease outbreak detection

Ai Kawazoe, Hutchatai Chanlekha, Mika Shigematsu, Nigel Collier


Combining Gene Ontology and argumentative features for automatic geneRIF extraction

Julien Gobeill, Patrick Ruch


Decentralised clinical guidelines modelling with lightweight coordination calculus

Bo Hu, Srinandan Dasmahapatra, David Robertson, Paul Lewis

12:15-1:30 Lunch Break


Session 2B: Text Classification (II), chaired by Minlie Huang


Automatic construction of rule-based ICD-9-CM coding systems

Richard Farkas, Gyorgy Szarvas


Identification of transcription factor contexts in literature using machine learning approaches

Hui Yang, Goran Nenadic


Classifier ensemble for biomedical document retrieval

Manabu Torii, Hongfang Liu

2:45-3:30 Tea Break


Panel Discussion

Biomedical language and biomedical knowledge: Emerging synergies

Panel: Jun-ichi Tsujii (chair), Olivier Bodenreider, Sophia Ananiadou, Patrick Lambrix


Closing address

* Papers for LBM BMC special issue  and long oral presentations are in black.  Short oral presentations are in blue.