Critical Assessment of Information Extraction in Biology

生物数据库为文本挖掘的统计和机器学习方法提供了丰富的数据来源；它们还为系统性能评估提供专家策划的“黄金标准”数据。该策略的重点是解决生物学家工作中的重要问题，如克服生物学文献的检索瓶颈，提供更好的生物本体和文本之间的映射，以及让生物学家更好地访问文献和检索数据库中的文本信息。本建议的重点是发展机制，以促进文本挖掘的进展，以解决具有生物学意义的问题。短期重点是继续组织生物创新：生物学信息提取的关键评估。长期重点是改进文本挖掘工具，以支持专家管理员以经济有效的方式获取生物数据库的信息，并通过使用共享语义（本体）改善对生物信息的访问，特别关注交互式工具和提取复杂关系，如宿主-病原体或生态系统相互作用。这里提出的具体任务是：1)运行BioCreAtIvE II的基因规范化任务（2006-2007年），分析和传播BioCreAtIvE II的数据和结果；2)为BioCreAtIvE路线图的创建提供输入；3)定义新的评估任务，以满足更广泛的生物策展人的需求；这将包括与RegCreative Jamboree一起对互动策展工具进行评估；以及表示和捕获复杂生物关系的方法，例如宿主-病原体相互作用和生态系统相互作用，与标准联盟一起。

The biological databases provide a rich source of data to serve as training data for statistical and machine learning approaches to text mining; they also provide expert-curated, "gold standard" data for evaluation of system performance. The strategy is to focus on problems of importance to working biologists, such as overcoming the curation bottleneck for biological literature, providing better mappings between biological ontologies and text, and giving biologists better access to textual information in both in the literature and in curated databases. This proposal focuses on development of mechanisms to promote progress in text mining to problems of biological significance. The short term focus is to continue work in organizing BioCreAtIvE: Critical Assessment for Information Extraction in Biology. The long term focus is to improve text mining tools to support expert curators in their cost-effective acquisition of information for biological databases, as well as to improve access to biological information via the use of shared semantics (ontologies), with particular focus on interactive tools and extraction of complex relations, such as host-pathogen or ecosystem interactions. The specific tasks proposed here are 1) running the Gene Normalization task for BioCreAtIvE II (to take place in 2006-2007) and analyzing and disseminating the data and results of the BioCreAtIvE II; 2) providing input into the creation of a Roadmap for BioCreAtIvE; 3) defining new evaluation tasks to meet needs of a wider range of biological curators; this will include an evaluation of interactive curation tools, done in conjunction with the RegCreative Jamboree; and methods for the representation and capture of complex biological relations, such as host-pathogen interaction and ecosystem interactions, in conjunction with standards consortia.