BioLit: Open Source Tools for Integrating Biological Literature and Databases

BioLit：用于集成生物文献和数据库的开源工具

• 批准号: 0544575
• 负责人: Philip Bourne
• 金额: $ 95.35万
• 依托单位: University of California-San Diego
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-04-01 至 2009-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0544575&HistoricalAwards=false
• 关键词: BioLit; Open; Source; Tools; Integrating

The University of California at San Diego is awarded a grant to develop tools for integrating biological literature and databases. Changes in the scientific publishing industry blur the distinction between biological databases and the biological literature and it is the time to capitalize on this hitherto unappreciated similarity. Tools will be developed to provide seamless integration between the knowledge and data traditionally held within biological journals with the related information, which is traditionally held within biological databases. The open source software tools are collectively called BioLit and will facilitate this integration and provide a broad community with the potential to achieve a new level of efficient comprehension of the products of the scientific endeavor. Initially, BioLit will comprise authoring tools to facilitate biologists in employing existing ontologies, post manuscript submission tools to extract relevant facts from the manuscript which are stored as metadata, a database of journal content and tools for the visualization and further analysis of data and knowledge presented in this database of on-line published papers. BioLit development and testing will be performed in a unique environment consisting of the complete corpus of Public Library of Science (PLoS) journals integrated with the Protein Data Bank (PDB), one of the oldest and most used databases in all biology. In the third year of the project an evaluation of the tools will be performed as will a survey of how useful the community regards what has been achieved in this initial phase. Under a special agreement with the University of California tools from this effort will be open source and distributed through sourceforge.net and hence available to any publisher or database provider who cares to employ them. The broader impacts resulting from the proposed activity comes from, first, the application of the tools and principles defined herein to any field of science. Second, and most important, the proposal brings the promise to the scientific consumer of a new and powerful medium from which to learn. A medium that retains all of the intellectual merits of high quality scientific journals, achieved through peer review and high quality editing, yet adds direct access to the data upon which conclusions are reached. Conversely, access through biological databases provided transversal from a data point to the conclusions reached in the literature about that item of data. A positive evaluation of the integrative approach enabled by the tools proposed here could have a far-reaching impact on the means by which science is disseminated and consumed.

位于圣地亚哥的加州大学获得了一笔赠款，用于开发整合生物文献和数据库的工具。科学出版业的变化模糊了生物学数据库和生物学文献之间的区别，现在是利用这种迄今未被重视的相似性的时候了。将开发各种工具，使传统上保存在生物学期刊中的知识和数据与传统上保存在生物学数据库中的相关信息实现无缝整合。这些开源软件工具统称为BioLit，将促进这种整合，并提供一个广泛的社区，有可能实现对科学奋进的新水平的有效理解。最初，BioLit将包括创作工具，以方便生物学家采用现有的本体论，后手稿提交工具，从存储为元数据的手稿中提取相关事实，期刊内容数据库和工具，用于可视化和进一步分析在线发表论文数据库中的数据和知识。BioLit的开发和测试将在一个独特的环境中进行，该环境由公共科学图书馆（PLoS）期刊的完整语料库与蛋白质数据库（PDB）集成组成，PDB是所有生物学中最古老和最常用的数据库之一。在项目的第三年，将对这些工具进行评估，并调查社区认为在这一初始阶段取得的成果有多大用处。根据与加州大学的一项特别协议，这项工作的工具将是开源的，并通过sourceforge.net分发，因此可供任何愿意使用它们的出版商或数据库提供商使用。拟议活动产生的更广泛影响首先来自于将本文定义的工具和原则应用于任何科学领域。第二，也是最重要的一点，该提案为科学消费者带来了一种新的、强大的媒介，他们可以从中学习。一种媒介，保留了高质量科学期刊的所有知识优势，通过同行评审和高质量编辑实现，但增加了对得出结论的数据的直接访问。相反，通过生物数据库的访问提供了从数据点到文献中关于该数据项得出的结论的横向。对本文提出的工具所促成的综合方法进行积极评价，可能会对传播和消费科学的手段产生深远影响。