BioLit: Open Source Tools for Integrating Biological Literature and Databases

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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.