LipidFun：脂质功能数据库。

LipidFun: a database of lipid functions.

作者信息

Lin Wen-Jen, Liu Chia-Hsin, Huang Ming-Siang, Shen Pei-Chun, Liu Hsiu-Cheng, Tsai Meng-Hsin, Lai Yo-Liang, Wang Yu-De, Hung Mien-Chie, Chang Nai-Wen, Cheng Wei-Chung

机构信息

School of Medicine, China Medical University, Taichung 404333, Taiwan.

Graduate Institute of Biomedical Science, China Medical University, Taichung 404333, Taiwan.

出版信息

Bioinformatics. 2025 Mar 29;41(4). doi: 10.1093/bioinformatics/btaf110.

DOI:10.1093/bioinformatics/btaf110

PMID:40080702

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11974499/

Abstract

MOTIVATION

Lipids play crucial roles in various biological functions and diseases. However, a gap exists in databases providing information of lipids functions based on curated information. Consequently, LipidFun is purposed as the first lipid function database with sentence-level evidence detailing lipid-related phenotypes and biological functions.

RESULTS

Potential lipid functions were extracted from the biomedical literature using natural language processing techniques, with accuracy and reliability ensured through manual curation by four domain experts. LipidFun constructs classification systems for lipids, biological functions, and phenotypes for named entity recognition. Sentence-level evidence is extracted to highlight connections to lipid-associated biological processes and diseases. Integrating these classification systems and a large amount of sentence-level evidence allows LipidFun to provide an overview of lipid-phenotype and lipid-biological function associations through concise visualizations. Overall, LipidFun unravels the relationships between lipids and biological mechanisms, underscoring their overarching influence on physiological processes.

AVAILABILITY AND IMPLEMENTATION

LipidFun is available at https://lipidfun.bioinfomics.org/.

摘要

动机

脂质在各种生物学功能和疾病中发挥着关键作用。然而，基于精心策划的信息提供脂质功能信息的数据库存在空白。因此，LipidFun旨在成为首个具有句子级证据的脂质功能数据库，详细阐述脂质相关的表型和生物学功能。

结果

利用自然语言处理技术从生物医学文献中提取潜在的脂质功能，并由四位领域专家进行人工策划以确保准确性和可靠性。LipidFun构建了用于脂质、生物学功能和表型的分类系统，以进行命名实体识别。提取句子级证据以突出与脂质相关的生物学过程和疾病的联系。整合这些分类系统和大量句子级证据，LipidFun能够通过简洁的可视化展示脂质-表型和脂质-生物学功能关联的概况。总体而言，LipidFun揭示了脂质与生物学机制之间的关系，强调了它们对生理过程的总体影响。