1. The BioText Project: Recent Work Marti Hearst SIMS, UC Berkeley http://biotext.berkeley.edu Supported by NSF DBI-0317510 and a gift from Genentech

2. Project Team Project Leaders: PI: Marti Hearst Co-PI: Adam Arkin Computational Linguistics Preslav Nakov Emilia Stoica Sarah Poon IR/Databases/Software Ariel Schwartz Itai Brickner Brian Wolf Bioscience Janice Hamer Alumni Dr. Barbara Rosario Dr. TingTing Zhang Gaurav Bhalotia

3. BioText Project Goals Provide flexible, intelligent access to information for use in biosciences applications. Focus on Textual Information from Journal Articles Tightly integrated with other resources Ontologies Record-based databases

4. BioText Architecture Sophisticated Text Analysis Annotations in Database Improved Search Interface

5. Today’s Talks 1. Intro (Marti) 2. Design and Implementation of the Layered Query Language (Ariel & Brian) 3. Adding Fulltext to LQL (Itai) 4. Determining Gene Function from Text (Emilia) 5. Using the Web as an Implicit Training Corpus (Presley) 6. Identifing Protein-Protein Interactions (Marti, covering Barbara’s work) 7. Citances (Marti) 8. Discussion: what should our user interface do?

6. Recent Papers Predicting Gene Functions from Text Using a Cross- Species Approach, Emilia Stoica and Marti Hearst, to appear in PSB 2006. Multi-way Relation Classification: Application to Protein- Protein Interaction, Barbara Rosario and Marti Hearst, in HLT/EMNLP 2005. Using the Web as an Implicit Training Set: Application to Structural Ambiguity Resolution, Preslav Nakov and Marti Hearst, in HLT/EMNLP 2005.

7. Recent Papers Scaling Up BioNLP: Application of a Text Annotation Architecture to Noun Compound Bracketing, Preslav Nakov, Ariel Schwartz, Brian Wolf, and Marti Hearst, in ACL/ISMB SIGLINK 2005. Search Engine Statistics Beyond the n-gram: Application to Noun Compound Bracketing, Preslav Nakov and Marti Hearst, in CoNNL 2005. Citances: Citation Sentences for Semantic Analysis of Bioscience Text, Preslav Nakov, Ariel Schwartz, and Marti Hearst, in the SIGIR'04 workshop on Search and Discovery in Bioinformatics.