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eFIP:一种从文献中挖掘磷酸化功能影响的工具。

eFIP: a tool for mining functional impact of phosphorylation from literature.

作者信息

Arighi Cecilia N, Siu Amy Y, Tudor Catalina O, Nchoutmboube Jules A, Wu Cathy H, Shanker Vijay K

机构信息

Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA.

出版信息

Methods Mol Biol. 2011;694:63-75. doi: 10.1007/978-1-60761-977-2_5.


DOI:10.1007/978-1-60761-977-2_5
PMID:21082428
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4563866/
Abstract

Technologies and experimental strategies have improved dramatically in the field of genomics and proteomics facilitating analysis of cellular and biochemical processes, as well as of proteins networks. Based on numerous such analyses, there has been a significant increase of publications in life sciences and biomedicine. In this respect, knowledge bases are struggling to cope with the literature volume and they may not be able to capture in detail certain aspects of proteins and genes. One important aspect of proteins is their phosphorylated states and their implication in protein function and protein interacting networks. For this reason, we developed eFIP, a web-based tool, which aids scientists to find quickly abstracts mentioning phosphorylation of a given protein (including site and kinase), coupled with mentions of interactions and functional aspects of the protein. eFIP combines information provided by applications such as eGRAB, RLIMS-P, eGIFT and AIIAGMT, to rank abstracts mentioning phosphorylation, and to display the results in a highlighted and tabular format for a quick inspection. In this chapter, we present a case study of results returned by eFIP for the protein BAD, which is a key regulator of apoptosis that is posttranslationally modified by phosphorylation.

摘要

在基因组学和蛋白质组学领域,技术和实验策略有了显著改进,这有助于分析细胞和生化过程以及蛋白质网络。基于众多此类分析,生命科学和生物医学领域的出版物数量大幅增加。在这方面,知识库难以应对如此庞大的文献量,可能无法详细捕捉蛋白质和基因的某些方面。蛋白质的一个重要方面是其磷酸化状态及其在蛋白质功能和蛋白质相互作用网络中的作用。因此,我们开发了eFIP,这是一个基于网络的工具,可帮助科学家快速找到提及特定蛋白质磷酸化(包括位点和激酶)的摘要,以及提及该蛋白质相互作用和功能方面的内容。eFIP整合了eGRAB、RLIMS-P、eGIFT和AIIAGMT等应用程序提供的信息,对提及磷酸化的摘要进行排名,并以突出显示的表格形式展示结果,以便快速查看。在本章中,我们展示了eFIP针对蛋白质BAD返回结果的案例研究,BAD是细胞凋亡的关键调节因子,可通过磷酸化进行翻译后修饰。

相似文献

[1]
eFIP: a tool for mining functional impact of phosphorylation from literature.

Methods Mol Biol. 2011

[2]
The eFIP system for text mining of protein interaction networks of phosphorylated proteins.

Database (Oxford). 2012-12-5

[3]
Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature.

Methods Mol Biol. 2017

[4]
RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information.

Database (Oxford). 2014-8-13

[5]
Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system.

Database (Oxford). 2015-3-31

[6]
eGIFT: mining gene information from the literature.

BMC Bioinformatics. 2010-8-9

[7]
An online literature mining tool for protein phosphorylation.

Bioinformatics. 2006-7-1

[8]
iPTMnet: an integrated resource for protein post-translational modification network discovery.

Nucleic Acids Res. 2018-1-4

[9]
RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information.

IEEE/ACM Trans Comput Biol Bioinform. 2015

[10]
MinePhos: a literature mining system for protein phoshphorylation information extraction.

IEEE/ACM Trans Comput Biol Bioinform. 2011-4-27

引用本文的文献

[1]
Identification of Novel Kinases of Tau Using Fluorescence Complementation Mass Spectrometry (FCMS).

Mol Cell Proteomics. 2022-12

[2]
Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources.

Clin Proteomics. 2020-7-11

[3]
Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over.

Front Genet. 2016-3-31

[4]
RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information.

Database (Oxford). 2014-8-13

[5]
topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins.

Nucleic Acids Res. 2013-12-2

[6]
Application of text-mining for updating protein post-translational modification annotation in UniProtKB.

BMC Bioinformatics. 2013-3-22

[7]
The eFIP system for text mining of protein interaction networks of phosphorylated proteins.

Database (Oxford). 2012-12-5

本文引用的文献

[1]
Incorporating rich background knowledge for gene named entity classification and recognition.

BMC Bioinformatics. 2009-7-17

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BMC Bioinformatics. 2007-9-1

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Front Biosci. 2007-9-1

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