PLUTo: Phyloinformatic Literature Unlocking Tools. Software for making published phyloinformatic data discoverable, open, and reusable

系统发育数据，以及由此推断出的树，是进化生物学研究的宝贵资源。获取这些数据往往既昂贵又耗时，而对这些数据的分析结果——通常是树木——代表了全球生物信息学家和系统学家对努力和专业知识的巨大投入。树及其潜在的特征数据经常在生物学的其他领域被重新利用；特别是在试图测试基因组进化模式或宏观进化趋势的进化研究中。尽管它们价值巨大，但PDRA最近的研究估计，2010年发表的系统发育树中，只有不到4%是机器可读的。我们的提案站在了内容挖掘技术的前沿。我们将创建开源的“数据解放”软件工具，使我们能够从目前埋藏在文献中的更大比例的系统信息数据中解脱出来。这些将包括系统发育树、分支长度和支持值（从PDF文件的SVG内容中提取）、数据质量的分析方法和指标（来自图例和文本主体）以及底层的分子和形态特征数据。我们还将为每个源论文导出完整的书目和地理数据。我们将测试、改进和完善这些工具，将它们应用于21世纪的PLoS、BMC、Elsevier、Wiley和b施普林格在线内容。一旦数据被提取出来，我们将确保其巨大的跨学科（进化生物学，生态学，动物行为学，古生物学和保护）和遗产潜力通过明确开放的方式在网上提供实现。我们自己也将使用这些数据来解决有关研究工作、系统信息数据质量和系统研究进展的几个相关问题。虽然对管理基础研究数据和结果有了新的兴趣和重视（例如TreeBASE、Dryad、BMC与LabArchives的合作以及FigShare等项目），但这些项目依赖于作者提交，而期刊很少强制要求作者提交。发展缓慢，覆盖范围也很糟糕。NCBI/GenBank对核苷酸序列（不是比对、树或其他结果，当然也不是形态学）的数据归档成功是生物科学中的例外，而不是规则。因此，在可预见的未来，迫切需要从已发表的文献中回顾性地收集数据。这个项目在规模和野心上都非常新颖。如果成功地重新提取了过去十年的大部分系统发育数据，该软件将很容易被其他人调整和修改，以适应其他科学领域的数据重新提取需求。这将更好地利用迄今为止投入在获取和分析数据上的数十亿英镑的研究资金，但当项目完成时，这些数据却被锁定并随后在PDF出版物中被混淆。该项目也是一个广泛的跨学科项目，汇集了一位宏观进化系统发育学家（Wills）、一位化学信息学家（Murray-Rust）和一位年轻的、崭露头角的研究员（Mounce）。该项目潜在的更广泛利益是巨大而多样的；据估计，仅在欧洲，内容挖掘技术每年就能创造高达2000亿英镑的附加值。我们不能声称直接产生这些好处，但我们将创造开放的工具和产生开放的数据，这将极大地促进其他商业、工业和学术企业。

Phylogenetic data, and the trees inferred from them, represent a hugely valuable resource for evolutionary biological research. The data are often expensive and time-consuming to acquire, and the results from analyses of these data - typically trees - represent a vast investment of effort and expertise across the global community of bioinformaticians and systematists. Trees, and their underlying character data, are often repurposed in other areas of biology; notably in evolutionary studies that seek to test patterns of genomic evolution or macroevolutionary trends. Despite their enormous value, recent research by the PDRA estimates that less than 4% of the phylogenetic trees published in 2010 are available in machine-readable form.Our proposal stands at the leading edge of content mining technology. We will create Open Source 'data liberation' software tools that will allow us to unlock the greater proportion of phyloinformatic data from where they are currently buried in the literature. These will include phylogenetic trees, branch lengths and support values (extracted from the SVG content of PDF files), analytical methods and indices of data quality (from figure legends and the main body of the text) and the underlying molecular and morphological character data. We will also derive full bibliographic and geographical data for each source paper. We will test, refine and perfect these tools by applying them to PLoS, BMC, Elsevier, Wiley and Springer online content from the 21st Century. Once the data are extracted, we will ensure that their immense interdisciplinary (evolutionary biology, ecology, ethology, palaeobiology and conservation) and legacy potential is realised by making them available online in an explicitly open manner. We will also use the data ourselves in order to address several related questions concerning research effort, phyloinfomatic data quality and the progress of systematic research.While there is renewed interest and emphasis on curating underlying research data and results (exemplified by projects such as TreeBASE, Dryad, BMC's partnership with LabArchives, and FigShare) these ventures rely upon author submission, which is rarely mandated by journals. Uptake has been slow and coverage is woeful. The data archiving success of NCBI/GenBank for nucleotide sequences (N.B., not alignments, trees or other results, and certainly not morphology) is the exception rather than the rule in the Biological Sciences. For the foreseeable future, therefore, there is a pressing need to retrospectively gather data from the published literature.This project is extremely novel in its scale and ambition. If successful in re-extracting the majority of phylogenetic data from the last decade, the software will easily be adapted and modified by others to suit the data re-extraction needs of other areas of science. This will better harness the billions of pounds of research money hitherto invested into obtaining and analyzing data, only for it to have been locked down and subsequently obfuscated in PDF publications when projects are completed. The project is also widely trans-disciplinary, bringing together a macroevolutionary phylogeneticist (Wills), a chemoinformaticist (Murray-Rust), and a young, up-coming Researcher (Mounce). The potential wider benefits of this project are vast and diverse; content mining techniques are estimated to be capable of generating up to £200 billion annually in added value for Europe alone. We cannot claim to generate those benefits directly, but we will create open tools and generate open data that will greatly facilitate other commercial, industrial and academic ventures.