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Volume 9 Supplement 2
Edited by Lynette Hirschman, Martin Krallinger, John Wilbur and Alfonso Valencia
The BioCreative II - Critical Assessment for Information Extraction in Biology Challenge.
Madrid, Spain
23-25 April 2007
Review
Efficient access to information contained in online scientific literature collections is essential for life science research, playing a crucial role from the initial stage of experiment planning to the final i...
Genome Biology 2008 9(Suppl 2):S8
Published on: 1 September 2008
Research
Genome sciences have experienced an increasing demand for efficient text-processing tools that can extract biologically relevant information from the growing amount of published literature. In response, a rang...
Genome Biology 2008 9(Suppl 2):S1
Published on: 1 September 2008
Research
Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A ...
Genome Biology 2008 9(Suppl 2):S2
Published on: 1 September 2008
Research
The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature. It is a cha...
Genome Biology 2008 9(Suppl 2):S3
Published on: 1 September 2008
Research
The biomedical literature is the primary information source for manual protein-protein interaction annotations. Text-mining systems have been implemented to extract binary protein interactions from articles, b...
Genome Biology 2008 9(Suppl 2):S4
Published on: 1 September 2008
Research
In the absence of consolidated pipelines to archive biological data electronically, information dispersed in the literature must be captured by manual annotation. Unfortunately, manual annotation is time consu...
Genome Biology 2008 9(Suppl 2):S5
Published on: 1 September 2008
Software
We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://bcms.bioinfo.cnio.es/). This pr...
Genome Biology 2008 9(Suppl 2):S6
Published on: 1 September 2008
Research
This article collects opinions from leading scientists about how text mining can provide better access to the biological literature, how the scientific community can help with this process, what the next steps...
Genome Biology 2008 9(Suppl 2):S7
Published on: 1 September 2008
Research
Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasin...
Genome Biology 2008 9(Suppl 2):S9
Published on: 1 September 2008
Research
The tasks in BioCreative II were designed to approximate some of the laborious work involved in curating biomedical research papers. The approach to these tasks taken by the University of Edinburgh team was to...
Genome Biology 2008 9(Suppl 2):S10
Published on: 1 September 2008
Research
We participated in three of the protein-protein interaction subtasks of the Second BioCreative Challenge: classification of abstracts relevant for protein-protein interaction (interaction article subtask [IAS]...
Genome Biology 2008 9(Suppl 2):S11
Published on: 1 September 2008
Research
Deciphering physical protein-protein interactions is fundamental to elucidating both the functions of proteins and biological processes. The development of high-throughput experimental technologies such as the...
Genome Biology 2008 9(Suppl 2):S12
Published on: 1 September 2008
Research
Research scientists and companies working in the domains of biomedicine and genomics are increasingly faced with the problem of efficiently locating, within the vast body of published scientific findings, the ...
Genome Biology 2008 9(Suppl 2):S13
Published on: 1 September 2008
Research
The goal of text mining is to make the information conveyed in scientific publications accessible to structured search and automatic analysis. Two important subtasks of text mining are entity mention normaliza...
Genome Biology 2008 9(Suppl 2):S14
Published on: 1 September 2008
