A Community Knowledgebase to Evaluate Host-Microbial Salivary Proteomics

摘要 口腔、牙齿和颅面生物学研究界的一个重要目标是了解宿主和 微生物之间的相互作用在每个生态位内发挥作用，并广泛传播数据。由于唾液的复杂性， 基于生物流体的蛋白质组学评价提供了与组合物相关的新资源和知识， 功能人类唾液蛋白质组维基（HSP Wiki）的开发旨在允许口腔研究 社区扩大可用信息。然而，要实现真实的进步并捕获分子 唾液的复杂性，新的资源必须到位。该提案概述的调查是 准备最终提供关于口腔中宿主-微生物相互作用的新信息， 从唾液蛋白质组获得的信息。该项目的长期目标是建立资源 并开发新的工具，使唾液研究的科学发现和诊断的连续性 应用.为此，第一目标将转移并为研究界提供一个功能性的 和精心策划的数据库，是可靠的和创新的评估蛋白质组学研究。作为社区资源， 存储、注释和研究唾液蛋白质组数据，HSP Wiki平台的目标是提供 访问一系列信息和分析工具。第二个目标将实现一个新的计算 唾液蛋白质组数据集的基础设施，包括可视化分析，更快的处理， 衡量成功的标准。第三个目标将利用人类口腔微生物组数据库（HOMD）提供网络- 为研究界提供可获得的分类、基因组和蛋白质组信息和分析工具。 因为它目前正在扩大到包括感染口腔细菌的病毒（HIV）的信息 和古细菌，我们的目标是整合HOMD的蛋白质组数据到HSP Wiki数据库。在这里，我们的目标是 进行了一系列的研究，以确定如何增加唾液蛋白质组鉴定覆盖率， 将蛋白质组参考文库从人类蛋白质扩展到来自口腔细菌、古细菌、 和。HSP和HOMD整合的预期结果将为研究界提供一个 大大增强了在线资源，用于检查唾液蛋白质组的组成及其对 人类健康和疾病。该项目的广泛传播和HSP Wiki的更多使用将促进 发现，提高严谨性，并最终将增加向精准医学转化的机会， 唾液来源的生物标志物的诊断应用。

ABSTRACT An important goal of the oral, dental and craniofacial biology research community is to understand how host and microbes interactions work within each niche and disseminate the data widely. Because of saliva’s complexity, biofluid-based proteomic evaluations provide new resources and knowledge related to the composition and function. The Human Salivary Proteome Wiki (HSP Wiki) was developed with the aim to allow the oral research community to expand the available information. Yet, to achieve real advance and capture the molecular complexity of saliva, novel resources must be put into place. The investigations outlined on this proposal are poised to ultimately provide novel information on host-microbial interactions in the oral cavity by harnessing information gained from the salivary proteome. The Long-Term Goal of this project is to establish the resources and develop new tools to allow continuity in salivary research for both scientific discovery and diagnostic applications. For that purpose, the First Aim will transfer and provide the research community with a functional and curated database that is reliable and innovative to evaluate proteomic studies. As a community resource for depositing, annotating, and studying salivary proteomic data, the HSP Wiki platform has a goal to provide access to of an array of information and analytic tools. The Second Aim will implement a novel computational infrastructure for salivary proteomic datasets that includes visual analytics, faster processing, and efficient measures of success. The Third Aim will utilize the Human Oral Microbiome Database (HOMD) to provide web- accessible taxonomic, genomic and proteomic information and analysis tools for the research community. Because it is currently being expanded to include information on the viruses (phages) that infect the oral bacteria and archaea, we aim to integrate proteome data from HOMD into the HSP Wiki database. Here, we aim to perform a series of studies to determine how the salivary proteome identification coverage is increased by expanding the proteome reference library from just human proteins to those derived from oral bacteria, archaea and phages. The expected outcome of HSP and HOMD integration will provide the research community with a greatly enhanced online resource for examining the composition of the salivary proteome and its impact on human health and disease. Broad dissemination of this project and increased use of the HSP Wiki will catalyze discovery, enhance rigor, and will eventually increase chances of translation towards precision medicine and diagnostic applications of saliva-derived biomarkers.