Linking Text Mining with Ontology and Systems Biology

乔治城大学获得了一笔赠款，用于开展一系列生物创意挑战评估和生物模拟研讨会，以解决目前在生物领域使用文本挖掘工具方面的障碍。具体而言，将组织三个讲习班，使生物研究界和文本挖掘工具的开发者汇聚一堂，进行用户需求分析、基于用户的评价和工具整合的标准开发。讲习班的具体目的是：(1)确定要求和评价标准，以最大限度地提高广大生物用户对文本挖掘工具的利用；(2)提供基于系统和基于用户的评价，采用衡量精确度和查全率的指标(基于系统)，以及文本挖掘对生物发现和知识发现的影响，如吞吐量和质量(以用户为基础)；(3)通过、制定和建议社区标准，以改进文本挖掘工具在数据交换和工具集成方面的互操作性。其结果将是通过将重点放在数据库管理和知识发现的生物学用例上，弥合将文献与知识联系起来的差距。讲习班的成果将包括：(1)文本挖掘工具，包括由BioCreative进行基准和评价的交互式和/或综合文本挖掘系统；(2)用于BioCreative评价的文献语料库；以及(3)这些讲习班在载有结果、评价和评论文章的高影响力期刊特刊上发表的科学出版物，包括对文本挖掘社区标准的建议。乔治敦大学将与Mitre公司合作开展这一系列研讨会。研讨会将把文本挖掘和生物社区联系起来，以制定共同的标准和用户要求，其影响超越了本项目中特定的文本挖掘应用。该项目将为参与该项目或参加研讨会的学生和研究人员提供跨学科的研究经验。该项目将为生物学的广泛领域提供研究和教育基础设施，使文本挖掘系统成为生物发现和知识发现的有利基础设施。有关生物创造研讨会活动的更多信息，请访问http://biocreative.sourceforge.net/。

Georgetown University is awarded a grant to conduct a series of BioCreative Challenge Evaluations and Biocuration Workshops to address the current barriers in using text mining tools in the biology domain. Specifically, three workshops will be organized to bring together the biological research community and developers of text mining tools for user requirement analysis, user-based evaluations and standard development for tool integration. The specific aims of the workshops are to: (i) define requirements and evaluation criteria that will maximize utilization of text mining tools by the broad biological user community; (ii) provide both system- and user-based evaluations, with metrics that measure precision and recall (system-based), as well as the effect of text mining on biocuration and knowledge discovery such as throughput and quality (user-based); and (iii) adopt, develop and recommend community standards to improve interoperability of text mining tools for data exchange and tool integration. The outcome will be to bridge the gap in linking literature to knowledge by focusing on biological use cases for database curation and knowledge discovery. The deliverables from the workshops will consist of: (i) text mining tools, including interactive and/or integrated text mining systems, that are benchmarked and evaluated by BioCreative, (ii) literature corpora used in the BioCreative evaluations, and (iii) scientific publications from these workshops in special issues of high impact journals containing results, evaluations and critical articles, including recommendations for community standards for text mining. Georgetown will collaborate with the Mitre Corporation in carrying out this workshop series.The workshops will connect the text mining and biological communities to develop common standards and user requirements, with broad impact beyond the specific text mining applications in this project. The project will provide interdisciplinary research experience for students and researchers involved in the project or participate in the workshops. The project will provide a research and educational infrastructure for broad areas of biology, allowing text mining systems to become an enabling infrastructure for biocuration and knowledge discovery. Further information on the Biocreative workshop activities may be found at http://biocreative.sourceforge.net/