在GO中关系的自我预测有助于其质量审计
Cheng Chen1, Lingyun Luo1, Chunlei Zheng2
1School of Computer Science, University of South China, Hengyang, Hunan, 421001, China.
Journal of biomedical informatics
|July 12, 2023
概括
本研究介绍了一种机器学习框架,用于将基因本体学 (GO) 进行自我审计. 该模型有效地识别了GO的潜在错误.
科学领域:
- 生物医学信息学 生物医学信息学
- 生物信息学是一种生物信息学.
- 本体学 工程学 工程学
背景情况:
- 基因本体学 (GO) 在生物医学研究中至关重要,需要强有力的质量审计.
- 目前的GO审计方法依赖于有局限性的规则,模式或假设.
研究的目的:
- 开发和评估基于机器学习的框架,用于对基因本体学进行自我审计.
- 通过预测IS-A关系来识别政府内部的潜在错误.
主要方法:
- 将GO分类结构转换为带有关系标签 (IS-A或ndrs) 的概念对数据集.
- 在基于子字符串的拓图中集成概念名称,定义和节点嵌入.
- 在模型培训和测试中采用了10倍交叉验证方法.
主要成果:
- 该模型预测了4,640个现有的IS-A对作为非直接关系 (ndrs),其中340个在以后的GO发布中得到验证 (p < 1.60e-46).
- 从2,840个预测的ndrs中确定了924个潜在的缺失IS-A关系,其中30个由来自200个随机样本的专家验证.
结论:
- 一种新的机器学习方法可以有效地审计生物医学本体学,如基因本体学.
- 这种预测框架有助于发现政府内部潜在的错误和缺失的关系.
相关概念视频
Evolutionary Relationships through Genome Comparisons
5.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.8K
Genome Annotation and Assembly
18.9K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.9K
Gene Families
8.9K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
8.9K
Protein Folding Quality Check in the RER
3.8K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
3.8K
Pedigree Analysis
84.5K
Overview
84.5K
Synthetic Biology
4.9K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Golden rice
Golden rice is a genetically modified...
4.9K


