BioLit: Open Source Tools for Integrating Biological Literature and Databases

加州大学圣地亚哥分校获得了一笔赠款，用于开发整合生物学文献和数据库的工具。科学出版行业的变化模糊了生物数据库和生物文献之间的区别，是时候利用这种迄今为止未被认识到的相似性了。将开发工具，以便在传统上保存在生物期刊中的知识和数据与传统上保存在生物数据库中的相关信息之间提供无缝集成。开源软件工具统称为BioLit，它将促进这种集成，并为广泛的社区提供潜力，以实现对科学努力成果的高效理解的新水平。最初，BioLit将包括写作工具，以方便生物学家使用现有的本体，手稿提交后的工具，以提取相关事实从手稿存储为元数据，期刊内容的数据库和工具，可视化和进一步分析的数据和知识呈现在这个数据库的在线发表的论文。BioLit的开发和测试将在一个独特的环境中进行，该环境包括公共科学图书馆（PLoS）期刊的完整语料库，以及蛋白质数据库（PDB），这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个初始阶段取得的成果有多有用。根据与加州大学的一项特殊协议，这项工作的工具将是开源的，并通过sourceforge.net发布，因此任何愿意使用它们的出版商或数据库提供商都可以使用。提议的活动所产生的更广泛的影响，首先来自于本文所定义的工具和原则在任何科学领域的应用。其次，也是最重要的一点，该提案为科学消费者带来了一种新的、强大的学习媒介。通过同行评议和高质量的编辑，保留了高质量科学期刊的所有知识价值，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一个数据点到文献中关于该项数据得出结论的横向信息。通过本文提出的工具对综合方法进行积极评价，可能对科学传播和消费的手段产生深远的影响。

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.