Payton Alexis, Roell Kyle R, Rebuli Meghan E, Valdar William, Jaspers Ilona, Rager Julia E
Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
Center for Environmental Medicine, Asthma and Lung Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
Front Toxicol. 2023 May 26;5:1171175. doi: 10.3389/ftox.2023.1171175. eCollection 2023.
Toxicology research has rapidly evolved, leveraging increasingly advanced technologies in high-throughput approaches to yield important information on toxicological mechanisms and health outcomes. Data produced through toxicology studies are consequently becoming larger, often producing high-dimensional data. These types of data hold promise for imparting new knowledge, yet inherently have complexities causing them to be a rate-limiting element for researchers, particularly those that are housed in "wet lab" settings (i.e., researchers that use liquids to analyze various chemicals and biomarkers as opposed to more computationally focused, "dry lab" researchers). These types of challenges represent topics of ongoing conversation amongst our team and researchers in the field. The aim of this perspective is to i) summarize hurdles in analyzing high-dimensional data in toxicology that require improved training and translation for wet lab researchers, ii) highlight example methods that have aided in translating data analysis techniques to wet lab researchers; and iii) describe challenges that remain to be effectively addressed, to date, in toxicology research. Specific aspects include methodologies that could be introduced to wet lab researchers, including data pre-processing, machine learning, and data reduction. Current challenges discussed include model interpretability, study biases, and data analysis training. Example efforts implemented to translate these data analysis techniques are also mentioned, including online data analysis resources and hands-on workshops. Questions are also posed to continue conversation in the toxicology community. Contents of this perspective represent timely issues broadly occurring in the fields of bioinformatics and toxicology that require ongoing dialogue between wet and dry lab researchers.
毒理学研究发展迅速,利用高通量方法中日益先进的技术来获取有关毒理学机制和健康结果的重要信息。毒理学研究产生的数据因此变得越来越多,常常产生高维数据。这类数据有望传授新知识,但本质上具有复杂性,使其成为研究人员的一个限制因素,特别是对于那些在“湿实验室”环境中的研究人员(即使用液体分析各种化学物质和生物标志物的研究人员,与更侧重于计算的“干实验室”研究人员相对)。这类挑战是我们团队与该领域研究人员正在讨论的话题。本观点的目的是:i)总结毒理学中分析高维数据时需要为湿实验室研究人员改进培训和转化的障碍;ii)强调有助于将数据分析技术转化给湿实验室研究人员的示例方法;iii)描述毒理学研究中迄今为止仍有待有效解决的挑战。具体方面包括可以引入湿实验室研究人员的方法,包括数据预处理、机器学习和数据简化。讨论的当前挑战包括模型可解释性、研究偏差和数据分析培训。还提到了为转化这些数据分析技术而实施的示例努力,包括在线数据分析资源和实践工作坊。还提出了一些问题,以继续毒理学界的讨论。本观点的内容代表了生物信息学和毒理学领域广泛出现的及时问题,需要湿实验室和干实验室研究人员之间持续对话。