Exploring autophagy with Gene Ontology

Autophagy is a fundamental cellular process that is well conserved among eukaryotes. It is one of the strategies that cells use to catabolize substances in a controlled way. Autophagy is used for recycling cellular components, responding to cellular stresses and ridding cells of foreign material. Perturbations in autophagy have been implicated in a number of pathological conditions such as neurodegeneration, cardiac disease and cancer. The growing knowledge about autophagic mechanisms needs to be collected in a computable and shareable format to allow its use in data representation and interpretation. The Gene Ontology (GO) is a freely available resource that describes how and where gene products function in biological systems. It consists of 3 interrelated structured vocabularies that outline what gene products do at the biochemical level, where they act in a cell and the overall biological objectives to which their actions contribute. It also consists of ‘annotations’ that associate gene products with the terms. Here we describe how we represent autophagy in GO, how we create and define terms relevant to autophagy researchers and how we interrelate those terms to generate a coherent view of the process, therefore allowing an interoperable description of its biological aspects. We also describe how annotation of gene products with GO terms improves data analysis and interpretation, hence bringing a significant benefit to this field of study.

细胞自噬（Autophagy）是真核生物中高度保守的基础细胞过程，是细胞以受控方式分解代谢物质的策略之一。细胞自噬可用于回收细胞组分、应对细胞应激以及清除细胞内外来物质。细胞自噬失调与多种病理状态相关，例如神经退行性疾病、心脏疾病以及癌症。目前关于细胞自噬机制的日益增长的研究知识，需要以可计算、可共享的格式进行汇总，以便用于数据表示与解读。基因本体（Gene Ontology，GO）是一个免费公开的资源，用于描述基因产物在生物系统中的功能发挥方式与作用位置。其包含三个相互关联的结构化词汇表，分别阐明基因产物在生物化学层面的功能、在细胞内的作用位点，以及其行为所服务的整体生物学目标。此外，基因本体还包含注释条目，用于将基因产物与上述词汇表中的术语相关联。本文阐述了我们如何在GO中表征细胞自噬、如何创建并定义与细胞自噬研究者相关的术语，以及如何将这些术语相互关联以形成该过程的连贯认知，从而实现其生物学特性的可互操作描述。本文同时阐述了使用GO术语对基因产物进行注释，如何优化数据分析与解读过程，进而为该研究领域带来显著价值。

搜集汇总

背景与挑战

背景概述

该数据集通过基因本体论（GO）研究自噬过程，提供了自噬相关术语的定义和关联，以支持数据分析和解释。数据集涵盖了自噬在多种疾病中的作用，并得到了多个研究机构的资金支持。