BioCreative-2012 Virtual Issue

C H Wu,A Valencia,C Mattingly,K B Cohen,L Hirschman,M Krallinger,W John Wilbur,Z Lu,T C Wiegers,C N Arighi

doi:10.1093/database/bas049

Abstract

BioCreative: Critical Assessment of Information Extraction in Biology is an international community-wide effort for evaluating text mining and information extraction systems applied to the biological domain (http://www.biocreative.org/). The Challenge Evaluations and the accompanying BioCreative Workshops bring together the text mining and biology communities to drive the development of text mining systems that can be integrated into the biocuration workflow and the knowledge discovery process. To address the current barriers in using text mining in biology, BioCreative has further been conducting user requirement analysis, user-based evaluations and fostering standard development for text mining tool re-use and integration. This DATABASE virtual issue captures the major results from the BioCreative-2012 Workshop on Interactive Text Mining in the Biocuration Workflow and is the fifth special issue devoted to BioCreative.

Highlights

The initial BioCreative challenges provided a valuable analysis of tool performance on component tasks of the biocuration workflow and promoted the implementation of text mining applications and web services
To address the utility and usability of text mining tools beyond formal offline evaluation metrics, BioCreative III introduced an Interactive Task as a demonstration task focusing on gene-based document retrieval
BioCreative-2012 took the step in this process, bringing together the biocuration and text mining communities to develop and evaluate interactive text mining tools and systems and improve utility and usability in the biocuration workflow

Summary

Introduction

The initial BioCreative challenges provided a valuable analysis of tool performance on component tasks of the biocuration workflow and promoted the implementation of text mining applications and web services. To address the utility and usability of text mining tools beyond formal offline evaluation metrics, BioCreative III introduced an Interactive Task as a demonstration task focusing on gene-based document retrieval.

Results

Conclusion