The PRIDE database at 20 years: 2025 update.

IF 16.6 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Nucleic Acids Research Pub Date : 2024-11-04 DOI:10.1093/nar/gkae1011

Yasset Perez-Riverol, Chakradhar Bandla, Deepti J Kundu, Selvakumar Kamatchinathan, Jingwen Bai, Suresh Hewapathirana, Nithu Sara John, Ananth Prakash, Mathias Walzer, Shengbo Wang, Juan Antonio Vizcaíno

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引用次数: 0

Abstract

The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's leading mass spectrometry (MS)-based proteomics data repository and one of the founding members of the ProteomeXchange consortium. This manuscript summarizes the developments in PRIDE resources and related tools for the last three years. The number of submitted datasets to PRIDE Archive (the archival component of PRIDE) has reached on average around 534 datasets per month. This has been possible thanks to continuous improvements in infrastructure such as a new file transfer protocol for very large datasets (Globus), a new data resubmission pipeline and an automatic dataset validation process. Additionally, we will highlight novel activities such as the availability of the PRIDE chatbot (based on the use of open-source Large Language Models), and our work to improve support for MS crosslinking datasets. Furthermore, we will describe how we have increased our efforts to reuse, reanalyze and disseminate high-quality proteomics data into added-value resources such as UniProt, Ensembl and Expression Atlas.

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PRIDE 数据库 20 年：2025 年更新。

PRoteomics IDEntifications (PRIDE) 数据库 (https://www.ebi.ac.uk/pride/) 是世界领先的基于质谱的蛋白质组学数据资源库，也是 ProteomeXchange 联盟的创始成员之一。本手稿总结了过去三年 PRIDE 资源和相关工具的发展情况。向 PRIDE Archive（PRIDE 的档案部分）提交的数据集数量已达到平均每月约 534 个。这要归功于基础设施的不断改进，如针对超大型数据集的新文件传输协议（Globus）、新的数据重新提交管道和数据集自动验证流程。此外，我们还将重点介绍 PRIDE 聊天机器人（基于开源大型语言模型的使用）的可用性，以及我们为改进 MS 交叉链接数据集的支持而开展的工作等新活动。此外，我们还将介绍我们是如何加大力度将高质量蛋白质组学数据重新利用、重新分析并传播到 UniProt、Ensembl 和 Expression Atlas 等增值资源中的。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.