Targeted metabolomics and biochemical studies complement the ongoing investigations led by the Human Proteome Organization (HUPO) Biology/Disease-Driven Human Proteome Project (B/D-HPP). However, it is challenging to identify and prioritize metabolite and chemical targets. Literature-mining-based approaches have been proposed for target proteomics studies, but text mining methods for metabolite and chemical prioritization are hindered by a large number of synonyms and nonstandardized names of each entity. In this study, we developed a cloud-based literature mining and summarization platform that maps metabolites and chemicals in the literature to unique identifiers and summarizes the copublication trends of metabolites/chemicals and B/D-HPP topics using Protein Universal Reference Publication-Originated Search Engine (PURPOSE) scores. We successfully prioritized metabolites and chemicals associated with the B/D-HPP targeted fields and validated the results by checking against expert-curated associations and enrichment analyses. Compared with existing algorithms, our system achieved better precision and recall in retrieving chemicals related to B/D-HPP focused areas. Our cloud-based platform enables queries on all biological terms in multiple species, which will contribute to B/D-HPP and targeted metabolomics/chemical studies.

中文翻译：

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用于生物/疾病驱动的人类蛋白质组计划的基于云的代谢物和化学优先级排序系统

靶向代谢组学和生化研究补充了由人类蛋白质组组织（HUPO）生物学/疾病驱动的人类蛋白质组项目（B / D-HPP）领导的正在进行的研究。然而，鉴定代谢产物和化学靶标并确定其优先顺序具有挑战性。已经针对目标蛋白质组学研究提出了基于文献挖掘的方法，但是每个实体的大量同义词和非标准化名称阻碍了代谢物和化学优先级排序的文本挖掘方法。在这项研究中，我们开发了一个基于云的文献挖掘和汇总平台，该平台将文献中的代谢物和化学物质映射到唯一的标识符，并使用蛋白质通用参考出版物-原始搜索总结了代谢物/化学物质和B / D-HPP主题的共出版趋势。引擎（目的）分数。我们成功地确定了与B / D-HPP靶向领域相关的代谢物和化学物质的优先级，并通过对照专家策划的关联和富集分析来验证结果。与现有算法相比，我们的系统在检索与B / D-HPP重点领域有关的化学药品方面具有更高的精度和召回率。我们基于云的平台可以查询多个物种中的所有生物学术语，这将有助于B / D-HPP和目标代谢组学/化学研究。