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使用pubchem.bio R包为任何物种创建分类学信息的代谢组库

Corey D Broeckling¹

¹Colorado State University, Analytical Resources Core - Bioanalysis and Omics Center, Fort Collins, CO, 80523, USA. cbroeckl@colostate.edu.

|December 24, 2025

概括

pubchem.bio R包通过提供精选的PubChem子集来构建自定义代谢物库来简化代谢学. 它有助于各种物种的关键代谢物注释过程.

科学领域:

代谢学代谢学代谢学
生物信息学是一种生物信息学.
化学信息学化学信息学

背景情况:

由于小分子的巨大结构多样性,代谢学注释具有挑战性.
PubChem是一个大型的化学结构数据库,包含大量的生物元数据.
许多PubChem结构与典型的代谢学实验无关.

研究的目的:

介绍R包,pubchem.bio,旨在解决代谢学方面的挑战.
允许用户下载PubChem.的一个以代谢学为重点的子集.
促进为特定物种创建定制的代谢物结构库.

主要方法:

pubchem.bio R包允许下载PubChem.chem的以代谢为中心的子集.
它可以构建结构化的代谢组图书馆和定制的特定物种图书馆.
使用最低共同祖先化学分类学方法,将PubChem CID与NCBI分类学联系起来.

主要成果:

用户可以为任何物种或物种组创建量身定制的代谢物库.
该包方便定义一个核心的生物代谢组.
它允许超出报告物种的分类学范围的推断.

结论:

该pubchem.bio包简化了在代谢学研究中的代谢物注释.
它将生物元数据集成到注释工作流中.
该包增强了PubChem数据对代谢学的可发现性和实用性.

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