Critical Assessment of Information Extraction in Biology

生物学信息提取的批判性评估

• 批准号: 0640153
• 负责人: Lynette Hirschman
• 金额: --
• 依托单位: Mitre Corporation Virginia
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-10-01 至 2008-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0640153&HistoricalAwards=false
• 关键词: Critical; Assessment; Information; Extraction; Biology

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.

生物数据库提供了丰富的数据来源，作为文本挖掘的统计和机器学习方法的训练数据；它们还为评估系统性能提供了专家管理的“黄金标准”数据。该战略是将重点放在对工作的生物学家来说重要的问题上，例如克服生物文献的管理瓶颈，在生物本体论和文本之间提供更好的映射，以及让生物学家更好地获取文献和精选数据库中的文本信息。这项建议的重点是发展机制，以促进在对具有生物学意义的问题进行文本挖掘方面取得进展。短期的重点是继续组织BioCreAtIVE：生物学信息提取的关键评估。长期的重点是改进文本挖掘工具，以支持专家馆长以成本效益的方式为生物数据库获取信息，并通过使用共享语义(本体)改善对生物信息的获取，特别侧重于交互工具和复杂关系的提取，如宿主-病原体或生态系统的相互作用。这里建议的具体任务是：1)执行BioCreAtIVE II的基因标准化任务(将于2006-2007年进行)，分析和传播BioCreAtIVE II的数据和结果；2)为BioCreAtIVE路线图的创建提供投入；3)确定新的评估任务，以满足更广泛的生物管理者的需求；这将包括与Regative Jamboree一起对互动式管理工具进行评估；以及与标准联盟一起表示和捕获复杂生物关系的方法，例如宿主与病原体的相互作用和生态系统的相互作用。