Addressing Sparsity in Metabolomics Data Analysis

样品中的小分子库的综合分析被称为代谢组学， 用于解决生物医学研究中的各种科学问题。最新技术进展 基于质谱的代谢组学允许更全面和灵敏的测量 代谢物。尽管技术进步，充分利用代谢组学的瓶颈 数据通常是分析工具的可用性和可用性。家长奖（U 01 CA 235488）的目标是 为研究界开发新的统计方法和软件，以提高 代谢组学数据，这将有助于最大限度地发挥代谢组学的潜力， 疾病病因学、诊断和药物开发。专为代谢组学设计的软件工具 数据，像那些在父母U 01奖和附带RFA（NIH RFA-RM-17-012）中提出的，正在被 发展速度越来越快。其中许多工具都是开源的，可以免费获得，但它们非常 在编程语言、数据格式和代谢组学管道的阶段方面不同。几 NIH共同基金代谢组学计划中认识到的挑战之一是“满足日益增长的 对用于数据分析和解释的用户友好的、开放源码的生物信息学工具的需求”， “协调社区范围内的识别和采用最佳实践的严谨性，可重复性和数据 再利用”为了缓解这些挑战并进一步实现联盟的目标，我们建立了MSCAT数据库 （https：mscat.metabolomicsworkbench.org）的代谢组学软件工具，可以可持续地， 持续更新（U 01 CA 235488 - 02 S1）。该数据库提供了可用工具的概况 并且可以帮助研究人员根据他们的特定需求选择数据分析工作流程。这 一项补充提案旨在通过进一步挖掘文献以表征工具来扩展该数据库项目 通过在代谢组学研究中的使用以及通过分析收集的数据， 软件工具，以提取有助于工具采用、可用性和实用性的因素。在目标1中，我们将开发一个 文本挖掘过程，其中挖掘代谢组学研究的全文和共同引用，以确定 在过去的研究中使用了工具的组合来验证我们的数据库所建议的工具集。在Aim中 2、我们评估代谢组学软件环境的工具冗余（基于功能）， 软件特性与工具采用和互操作性。

Comprehensive profiling of the small molecule repertoire in a sample is referred to as metabolomics and it is being used to address a variety of scientific questions in biomedical studies. Recent technological advances in mass spectrometry-based metabolomics have allowed for more comprehensive and sensitive measurements of metabolites. Despite the technological advances, the bottleneck for taking full advantage of metabolomics data is often the availability and usability of analysis tools. The goal of the parent award (U01CA235488) is to develop novel statistical methods and software for the research community to improve the utilization of metabolomics data, which will help maximize the potential of metabolomics to provide new discoveries in disease etiology, diagnosis, and drug development. Software tools specifically designed for metabolomics data, like those proposed in the parent U01 award and attendant RFA (NIH RFA-RM-17-012), are being developed at an increasing rate. Many of these tools are open-source and freely available, but they are very diverse with respect to programming language, data formats, and stage in the metabolomics pipeline. Several of the challenges recognized in the NIH Common Fund Metabolomics Program are to “meet increasing demand for user-friendly, open-source, bioinformatics tools for data analysis and interpretation” and “coordinate community-wide identification and adoption of best practices for rigor, reproducibility and data reuse.” To mitigate these challenges and further the consortium’s goals, we have built the MSCAT database (https://mscat.metabolomicsworkbench.org) of metabolomics software tools that can be sustainably and continually updated (U01CA235488-02S1). The database provides a survey of the landscape of available tools and can assist researchers in the selection of data analysis workflows according to their specific needs. This supplement proposal aims to extend this database project by further mining the literature to characterize tool interoperability as outlined by their use in metabolomics studies and by analyzing the collected data about software tools to extract factors contributing to tool adoption, usability, and utility. In Aim 1, we will develop a text-mining process where the full text and co-citations of metabolomics studies are mined to identify which combinations of tools were used in past studies to validate the set of tools suggested by our database. In Aim 2, we assess the metabolomics software landscape for tool redundancy (based on functionality) and correlate software characteristics with tool adoption and interoperability.