A Cloud-Based Metabolite and Chemical Prioritization System for the Biology/Disease-Driven Human Proteome Project

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.

靶向代谢组学与生化研究可作为由人类蛋白质组组织（Human Proteome Organization, HUPO）主导的生物学/疾病驱动人类蛋白质组计划（Biology/Disease-Driven Human Proteome Project, B/D-HPP）现有研究的重要补充。然而，代谢物与化学靶点的鉴定及优先级排序颇具挑战。此前已有研究提出基于文献挖掘的方法用于靶向蛋白质组学研究，但针对代谢物与化学靶点排序的文本挖掘方法，因各实体存在大量同义词与非标准化命名而发展受限。本研究开发了一款云端文献挖掘与综述平台，可将文献中的代谢物与化学物质映射至唯一标识符，并通过蛋白质通用参考文献起源搜索引擎（Protein Universal Reference Publication-Originated Search Engine, PURPOSE）评分，总结代谢物/化学物质与B/D-HPP主题的共发表趋势。本研究成功对B/D-HPP靶向领域相关的代谢物与化学物质完成优先级排序，并通过与专家审定的关联关系及富集分析比对验证了研究结果。相较于现有算法，本系统在检索B/D-HPP重点领域相关化学物质时，取得了更优的精确率与召回率。本云端平台支持多物种全生物术语检索，可为B/D-HPP及靶向代谢组学/化学研究提供助力。