Final Program
Second BioCreAtIvE Challenge Workshop:
Critical Assessment of Information Extraction in Molecular Biology
Venue: Auditorium Centro Nacional de Investigaciones Oncológicas (CNIO) Madrid, April, 23-25, 2007
Main Organizer
Prof. Alfonso Valencia, Centro Nacional de Investigaciones Oncológicas (CNIO) Co-organizers
Lynette Hirschman, Biomedical Informatics for the Information Technology Center (MITRE Corporation)
Martin Krallinger, Centro Nacional de Investigaciones Oncológicas (CNIO)
Monday – April 23 9:00- 10:00 Registration
Welcome Address
10:00-10:30 Welcome and Introduction to Second BioCreative Challenge Alfonso Valencia
Session 1: Detection and Evaluation of Gene Mentions (GM) Chair 1: Hagit Shatkay
10:30-11:15 BioCreative II: Gene mention task W. John Wilbur
11:15-11:30 Coffee break / Registration
11:30-11:45 [GM1] Identifying Gene Mentions by Case-based Classification Mariana Lara Neves
11:45-12:00 [GM2] A Novel Feature Representation: Integrate GM Results into Interaction Abstract Identification
Richard Tsai
12:00-12:15 [GM3] Combined Conditional Random Fields and n-Gram Language Models for Gene Mention Recognition
Craig A. Struble
12:15-12:30 [GM4] Tackling the BioCreative2 Gene Mention task with Conditional Random Fields and Syntactic Parsing
Andreas Vlachos
12:30-12:45 [GM5] Named Entity Recognition with Combinations of Conditional Random Fields
Roman Klinger
12:45-13:00 [GM6] Gene Mention Recognition Using Lexicon Match Based Two-Layer Support Vector Machines
Yifei Chen 13:00-14:00 Lunch break Chair 2: John Wilbur
14:00-14:15 [GM7] Using Semi-Supervised Techniques to Detect Gene Mentions Sophia Katrenko
14:15-14:30 [GM8] BioCreative II Gene Mention Tagging System at IBM Watson Rie Kubota Ando
14:30-14:45 [GM9] Rich Feature Set, Unification of Bidirectional Parsing and Dictionary Filtering for High F-Score Gene Mention Tagging Cheng-Ju Kuo
14:45-15:00 [GM10] High-Recall Gene Mention Recognition by Unification of Multiple Backward Parsing Models
Chun-Nan Hsu
15:00-15:15 [GM11] Attribute Analysis in Biomedical Text Classification Francisco Carrero
15:15-15:30 [GM12] Three tricks can lead to a 24% relative reduction in error Kuzman Ganchev
15.30 -15:45 Coffee break / Registration
15:45-16:15 Invited speaker: Corpus Annotation and Its Use in BioNLP JunichiTsujii
16:15-17:00 Panel discussion: Current state and future demands in Bio-NER (Chaired by John Wilbur)
17:00-18:00 Poster session I
Tuesday - April 24 8:45- 9:30 Registration
Session II: Introduction and Evaluation of Gene Normalization (GN) task Chair 3: Luis Rocha
9:30-10:15 Overview of BioCreative II Gene Normalization Lynette Hirschman
10:15-10:30 [GN1] Text Detective: Gene/protein annotation tool by Alma Bioinformatics
Christian Blaschke
10:30-10:45 [GN2] Peregrine: Lightweight gene name normalization by dictionary lookup
Martijn Schuemie
10:45-11:00 [GN3] Gene Normalization Using Machine Learning and Flexible Dictionary Lookup
Hongfang Liu, Manabu Torii
11:00-11:15 [GN4] Me and my friends: gene mention normalization within background knowledge
Jörg Hakenberg
11:1-11:30 Coffee break / Registration Chair 4: Lynette Hirschman
11:30-11:45 [GN5] Context-Aware Mapping of Gene Names using Trigrams ThaiBinh Luong
11:45-12:00 [GN6] ProMiner: Recognition of Human Gene and Protein Names using regularly updated Dictionaries
Juliane Fluck
12:00-12:15 [GN7] Human Gene Normalization by an Integrated Approach including Abbreviation Resolution and Disambiguation
Katrin Fundel
12:15-12:30 [GN8] A Hybrid Gene Normalization approach with capability of disambiguation
Heng-hui Liu
12:30-12:45 [GN9] Exploring Match Scores to Boost Precision of Gene Normalization
Bo-Hou Yang
12:45-13:00 [GN10] Rule-based Gene Normalization with a Statistical and Heuristic Confidence Measure
William Lau 13:00 -14:00 Lunch break
14:00-14:30 Panel discussion: Importance of Gene Normalization for 'down-stream' text mining
(Chaired by Lynette Hirschman)
Session III: Extraction of Biological Annotations: Protein-Protein Interaction task Chair 5: Alfonso Valencia
14:30-15:00 Invited speaker: Annotating molecular interactions in the MINT database Gianni Cesareni
15:00-15:30 Invited speaker: Enhancing access to the bibliome for genomics with evaluation tasks derived from user information needs:
The TREC Genomics Track Aaron M. Cohen
15:30-16:00 Invited speaker: The application of ontologies in the biological realm Suzanna Lewis
16:00-16:15 Coffee break / Registration Chair 6: Christian Blaschke
16:15-16:35 The Interaction-Article Sub-Task (IAS) evaluation Martin Krallinger
16:35-16:50 [PPI1] The BioCreAtIve 2 GN and PPI-IAS Tasks: Approaches and Analysis
Aaron Cohen
16:50-17:05 [PPI2] Semi-supervised Learning of Relevant Articles Mark Stevenson
17:05-17:20 [PPI3] ProtIR Prototype: Finding Relevant Abstracts for Protein-Protein Interaction in the BioCreAtIvE2 Challenge
Yan Hua Chen
17:20-17:35 [PPI4] A Term Investigation and Majority Voting for Protein Interaction Article Sub-task 1 (IAS)
Lan Man
17:35-17:50 [PPI5] Identifying Protein-Protein Interaction Sentences Using Boosting and Kernel Methods
Sun Kim
17:50-18:20 Invited speaker: IntAct - Serving the text-mining community with high quality molecular interaction data
Samuel Kerrien
Wednesday- April 25 8:45- 9:00 Registration
Chair 7: Carlos Rodriguez
9:00-9:40 The Interaction-Pair and Interaction Method Sub-Task evaluation Martin Krallinger
9:40-9:55 [PPI6] OntoGene in Biocreative II Fabio Rinaldi
9:55-10:10 [PPI7] GeneTeam Site Report for BioCreative II: Customizing a Simple Toolkit for Text Mining in Molecular Biology
Patrick Ruch
10:10-10:25 [PPI8] AKANE System: Protein-Protein Interaction Extraction in the BioCreAtIvE2 Challenge
Rune Saetre
10:25-10:40 Coffee break / Registration
10:40-10:55 [PPI9] Consensus pattern alignment to find protein-protein interactions in text
Jörg Hakenberg
10:55-11:10 [PPI10] Using predication for identifying Protein-Protein interactions in Biomedical publications
Alejandro Figueroa, Günter Neumann
11:10-11:25 [PPI11] Integrating knowledge extracted from biomedical literature:
normalization and evidence statements for interactions Graciela Gonzalez
11:25-11:40 [PPI12] Mining physical protein-protein interaction by exploiting abundant features
Minlie Huang
11:40-11:55 [PPI13] Uncovering Protein-Protein Interactions in the Bibliome Luis Rocha
11:55-12:25 Invited speaker: to be confirmed Matthew Day
12:25-12:30 Group Picture
12:30-13:25 Lunch break 13:25-14:00 Poster session II Chair 8: Patrick Ruch
14:00-14:30 The Interaction-Sentence Sub-Task evaluation Martin Krallinger
14:30-14:45 [PPI14] An integrated approach to concept recognition in biomedical text Larry Hunter
14:45-15:00 [PPI15] Adapting a Relation Extraction Pipeline for the BioCreAtIvE II Tasks
Barry Haddow 15:00-15:30 Coffee break
15:30-15:45 [PPI17] Extracting Interacting Protein Pairs and Evidence Sentences by using Dependency Parsing and Machine Learning Techniques
Arzucan Ozgur
15:45-16:00 [PPI18] Protein Interaction Sentence Identification by Using Hierarchical Template-Based Approach
Heng-hui Liu
16:00-16:30 Invited speaker: OregAnno database and RegCreative Casey Bergman
16:30-17:30 Panel discussion: Text mining and biological annotations Closing session
17:30-18:30 The future of text mining and information extraction challenge evaluations in the biomedical domain
Lynette Hirschman, Alfonso Valencia, John Wilbur
Notes: Lunch will be served at the CNIO’s cafeteria
The panel discussion session will be moderated and will address specific questions, prepared before the sessions, related to the topic of the day
Legend: GM: Gene Mention task, GN: Gene Normalization Task, IAS: Interaction Article Sub-task, IPS:
Interaction Pairs Sub-task, IMS: Interaction Method Sub-task, ISS Interaction Sentence Sub-task.
