GDReCo:细粒度基因疾病关系提取集团
Hui Yu1, Jing Wu2, Suyan Bian3
1Medical Innovation Research Department of PLA General Hospital, Beijing, 100853, China; Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, China.
Computer methods and programs in biomedicine
|April 17, 2025
概括
创建了一个新的基因疾病关系提取群体 (GDReCo),用于训练自然语言处理模型,以改善生物医学研究中的基因疾病关系提取.
科学领域:
- 生物医学信息学 生物医学信息学
- 计算生物学 计算生物学
- 自然语言处理自然语言处理.
背景情况:
- 了解基因与疾病的关系对于医学研究和药物发现至关重要.
- 现有的自然语言处理 (NLP) 模型缺乏高质量,细粒度的训练数据来提取知识.
研究的目的:
- 解决缺少在基因疾病关联研究中NLP模型的正式描述系统和培训集的问题.
- 开发一个新的本体学框架和一个全面的数据集,用于基因疾病关系的提取.
主要方法:
- 开发一种新的本体学框架,用于基因疾病的关联.
- 创建了基因疾病关系提取库 (GDReCo),一个包含超过24,000个实例的数据集.
- 2,300多个实例的手动注释和超过22,000个实例的基于模型的预测.
主要成果:
- 在GDReCo上训练的基于BERT的NLP模型在事件和关系提取方面获得了高F1分.
- 开发的数据库在基因-疾病关系提取 (GDRE) 任务中表现出有效性.
- 通过关系提取中的高性能指标验证库的实用性.
结论:
- GDReCo是推动生物医学研究和知识提取的宝贵资源.
- 这项研究强调了NLP模型在分析基因与疾病关系方面的潜力.
- 确定了像ChatGPT这样的现有模型在细粒度关系提取中的局限性.
相关概念视频
Genome-wide Association Studies-GWAS
12.1K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
12.1K
Genomics
35.3K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
35.3K
Gene Families
8.7K
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...
8.7K
Genetic Screens
4.8K
Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
4.8K
Human Genetics
470
Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
The complex relationship between genetics and psychology is observable through common biological components such...
The complex relationship between genetics and psychology is observable through common biological components such...
470
Exon Recombination
3.5K
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon...
Exon shuffling follows “splice frame rules.” Each exon...
3.5K


