Linking, Literature, Information, and Knowledge for Biologie

This volumeofLecture Notes in Bioinformatics (LNBI) containsselectedpapers from the workshop of the BioLINK Special Interest Group (SIG) on Linking Literature,InformationandKnowledgeforBiology. TheworkshopwasheldJune 28 29, 2009 at the ISMB/ECCB 2009 conference in Stockholm . The BioLINK SIG meeting has been regularly held in association with the ISMB conferences since 2001, focusing on the development and application of resources and tools for biomedical text mining. The SIG is interdisciplinary in nature, and brings together researchers applying natural language processing, textmining,informationextractionandretrievalinthebiomedicaldomain,with scientistsfrombioinformaticsandbiology. ThisyeartheSIGincludedtwospecial sessions, one on the analysis of images and ?gures, which play a critial role in scienti?c papers, and the other on the future of scienti?c publication. Overview papers concerned with both these topics are included in this volume. Themeetingfeaturedinvitedtalks,presentationsofpeer-reviewedcontributed papers, reports from recent evaluations and workshops, as well as a poster s- sion. The SIG solicited papers that discuss current biological image- and te- related needs, the challenges of meeting them, and the tools that may help address them. Speci?c topics include: biological image analysis and its relati- ship to biomedical text mining, application of text-mining tools to biomedical research, automated indexing of the biomedical literature, generation of str- tured digital abstracts, new evaluation measures to measure utility and usab- ity of text mining tools integrated into the biologist s work?ow, as well as new tools and applications, and future directions in biomedical text mining.

BioLINK 2009.- Overview of the Ninth Annual Meeting of the BioLINK SIG at ISMB: Linking Literature, Information and Knowledge for Biology.- Principles of Bioimage Informatics: Focus on Machine Learning of Cell Patterns.- Summary of the BioLINK Special Interest Group Session on the Future of Scientific Publishing.- Structured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature.- Toward Computer-Assisted Text Curation: Classification Is Easy (Choosing Training Data Can Be Hard...).- Mining Protein-Protein Interactions from GeneRIFs with OpenDMAP.- Combining Semantic Relations and DNA Microarray Data for Novel Hypotheses Generation.- Learning from Positive and Unlabeled Documents for Retrieval of Bacterial Protein-Protein Interaction Literature.- Extracting and Normalizing Gene/Protein Mentions with the Flexible and Trainable Moara Java Library.