相关实验视频

Updated: Jun 8, 2025

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

Published on: October 13, 2023

生物KGrapher:从生物医学文献中对自动化知识图构建的初步评估

Henning Schäfer^1,2, Ahmad Idrissi-Yaghir^2,3, Kamyar Arzideh⁴

¹Institute for Transfusion Medicine, University Hospital Essen, Hufelandstraße 55, Essen, 45147, Germany.

Computational and structural biotechnology journal

|November 6, 2024

概括

生物KGrapher自动从出版物中构建生物医学知识图 (KG),改进疾病和药物信息提取. 该工具通过结构化复杂的生物医学数据来帮助研究人员进行增强的分析和应用.

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
知识表示知识表示

背景情况:

越来越多的生物医学文献需要有效的知识提取和结构化的方法.
生物医学知识图 (KG) 的手工构建是资源密集型的,推动了对自动化解决方案的需求.
生物KGrapher通过从大规模出版数据中实现自动KG构造来解决这个问题.

研究的目的:

介绍BioKGrapher,这是一个用于构建生物医学知识图的自动化工具.
专注于提取和结构化与特定疾病相关的生物医学概念.
为了促进从PubMed ID中构建KG,用于研究应用.

主要方法:

使用命名实体识别和链接 (NER+NEL) 来从PubMed中提取和规范化生物医学概念,将其映射到统一的医学语言系统 (UMLS).
使用Kullback-Leibler分歧和局部频率平衡进行概念权重和重新排名.
将概念集成到使用标准术语 (SNOMED CT,NCIt) 的等级KG中,并将其应用于使用变压器模型的多标签文档分类.

主要成果:

生成的概念与临床实践指南 (瘤学德国指南计划) 保持一致,达到高达0.6的F1-Score.
使用BioKGrapher癌症特异性KG的适配器注入模型,与非特异性KG相比,多标签分类微型F1-分数提高了高达0.89%.
一个药物疾病提取案例研究成功确定了Nivolumab和Rituximab的指示.

结论:

生物KGrapher提供了一个自动化和可扩展的解决方案,用于构建生物医学知识图.
该工具与临床指南保持一致,并提高了下游任务 (如文档分类) 的性能.
潜在的应用包括文献推,临床决策支持和药物重新用途.

关键词:

临床指南临床指南实体链接实体链接知识图表知识图表命名实体认可命名实体认可软件软件软件软件软件

更多相关视频

A Web Tool for Generating High Quality Machine-readable Biological Pathways

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Augmenting Large Language Models via Vector Embeddings to Improve Domain-Specific Responsiveness

Augmenting Large Language Models via Vector Embeddings to Improve Domain-Specific Responsiveness

Published on: December 6, 2024

相关概念视频

Genome Annotation and Assembly

Genome Annotation and Assembly

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.

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...