Linking, Literature, Information, and Knowledge for Biologie: Workshop of the BioLINK Special Interest Group, ISBM/ECCB 2009, Stockholm, June 28-29, 2009, Revised Selected Papers

by Christian Blaschke (Editor), Hagit Shatkay (Editor)

Overview

This volume of Lecture Notes in Bioinformatics contains selected papers from the workshop of the BioLINK Special Interest Group (SIG) on Linking Literature, Information and Knowledge for Biology. The workshop was held June 28- 29, 2009 at the ISMB/ECCB 2009 conference in Skholm.

Product Details

ISBN-13:	9783642131301
Publisher:	Springer Berlin Heidelberg
Publication date:	07/21/2010
Series:	Lecture Notes in Computer Science , #6004
Edition description:	2010
Pages:	81
Product dimensions:	6.10(w) x 9.20(h) x 0.30(d)

Table of Contents

BioLINK 2009

Overview of the Ninth Annual Meeting of the BioLINK SIG at ISMB: Linking Literature, Information and Knowledge for Biology Christian Blaschke Lynette Hirschman Hagit Shatkay Alfonso Valencia 1

Principles of Bioimage Informatics: Focus on Machine Learning of Cell Patterns Luis Pedro Coelho Estelle Glory-Afshar Joshua Kangas Shannon Quinn Aabid Shariff Robert F. Murphy 8

Summary of the BioLINK Special Interest Group Session on the Future of Scientific Publishing Scott Markel 19

Sturctured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature Luís Pedro Coelho Amr Ahmed Andrew Arnold Joshua Kangas Abdul-Saboor Sheikh Eric P. Xing Willam W. Cohen Robert F. Murphy 23

Toward Computer-Assisted Text Curation: Classification Is Easy (Choosing Training Data Can Be Hard...) Robert Denroche Ramana Madupu Shibu Yooseph Granger Sutton Hagit Shatkay 33

Mining Protein-Protein Interactions from GeneRIFs with OpenDMAP Andrew D. Fox William A. Baumgartner Jr. Helen L. Johnson Lawrence E. Hunter Donna K. Slonim 43

Combining Semantic Relations and DNA Microarray Data for Novel Hypotheses Generation Dimitar Hristovski Andrej Kastrin Borut Peterlin Thomas C. Rindflesch 53

Learning from Positive and Unlabeled Documents for Retrieval of Bacterial Protein-Protein Interaction Literature Hongfang Liu Manabu Torii Guixian Xu Zhangzhi Hu Johannes Goll 62

Extracting and Normalizing Gene/Protein Mentions with the Flexible and Trainable Moara Java Library Mariana L. Neves José Maria Carazo Alberto Pascual-Montano 71

Author Index 81