系统生物学中标准与数据管理实践的演变

The evolution of standards and data management practices in systems biology.

作者信息

Stanford Natalie J, Wolstencroft Katherine, Golebiewski Martin, Kania Renate, Juty Nick, Tomlinson Christopher, Owen Stuart, Butcher Sarah, Hermjakob Henning, Le Novère Nicolas, Mueller Wolfgang, Snoep Jacky, Goble Carole

机构信息

Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK School of Computer Science, University of Manchester, Manchester, UK

Leiden Institute of Advanced Computer Science, Leiden Institute of Advanced Computer Science, Leiden University, Leiden, The Netherlands.

出版信息

Mol Syst Biol. 2015 Dec 23;11(12):851. doi: 10.15252/msb.20156053.

DOI:10.15252/msb.20156053

PMID:26700851

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4704484/

Abstract

A recent community survey conducted by Infrastructure for Systems Biology Europe (ISBE) informs requirements for developing an efficient infrastructure for systems biology standards, data and model management.[Image: see text]

摘要

欧洲系统生物学基础设施（ISBE）最近开展的一项社区调查为开发一个高效的系统生物学标准、数据和模型管理基础设施提供了需求信息。[图片：见正文]

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/33a8/4704484/f603fb3d2c57/MSB-11-851-g001.jpg

相似文献

The evolution of standards and data management practices in systems biology.

Mol Syst Biol. 2015 Dec 23;11(12):851. doi: 10.15252/msb.20156053.

Top-down standards will not serve systems biology.

Nature. 2006 Mar 2;440(7080):24. doi: 10.1038/440024a.

Standards, tools, and databases for the analysis of yeast 'omics data.

Methods Mol Biol. 2011;759:345-65. doi: 10.1007/978-1-61779-173-4_20.

Standards for systems biology.

Nat Rev Genet. 2006 Aug;7(8):593-605. doi: 10.1038/nrg1922.

Standards, databases, and modeling tools in systems biology.

Methods Mol Biol. 2011;696:413-27. doi: 10.1007/978-1-60761-987-1_26.

MathSBML: a package for manipulating SBML-based biological models.

Bioinformatics. 2004 Nov 1;20(16):2829-31. doi: 10.1093/bioinformatics/bth271. Epub 2004 Apr 15.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.

J Integr Bioinform. 2018 Mar 29;15(1):20180013. doi: 10.1515/jib-2018-0013.

Resources, standards and tools for systems biology.

Brief Funct Genomic Proteomic. 2007 Sep;6(3):240-51. doi: 10.1093/bfgp/elm027. Epub 2007 Oct 17.

Defining systems biology: a brief overview of the term and field.

Methods Mol Biol. 2013;1021:1-11. doi: 10.1007/978-1-62703-450-0_1.

Guidelines for Reproducibly Building and Simulating Systems Biology Models.

IEEE Trans Biomed Eng. 2016 Oct;63(10):2015-20. doi: 10.1109/TBME.2016.2591960. Epub 2016 Jul 18.

引用本文的文献

An Early Stage Researcher's Primer on Systems Medicine Terminology.

Netw Syst Med. 2021 Feb 25;4(1):2-50. doi: 10.1089/nsm.2020.0003. eCollection 2021 Feb.

From whole-mount to single-cell spatial assessment of gene expression in 3D.

Commun Biol. 2020 Oct 23;3(1):602. doi: 10.1038/s42003-020-01341-1.

SBML Level 3: an extensible format for the exchange and reuse of biological models.

Mol Syst Biol. 2020 Aug;16(8):e9110. doi: 10.15252/msb.20199110.

Community standards to facilitate development and address challenges in metabolic modeling.

Mol Syst Biol. 2020 Aug;16(8):e9235. doi: 10.15252/msb.20199235.

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).

Bioinformatics. 2021 Apr 5;36(24):5712-5718. doi: 10.1093/bioinformatics/btaa622.

BioModels Parameters: a treasure trove of parameter values from published systems biology models.

Bioinformatics. 2020 Nov 1;36(17):4649-4654. doi: 10.1093/bioinformatics/btaa560.

Computational models of melanoma.

Theor Biol Med Model. 2020 May 14;17(1):8. doi: 10.1186/s12976-020-00126-7.

BioModels-15 years of sharing computational models in life science.

Nucleic Acids Res. 2020 Jan 8;48(D1):D407-D415. doi: 10.1093/nar/gkz1055.

A blueprint for human whole-cell modeling.

Curr Opin Syst Biol. 2018 Feb;7:8-15. doi: 10.1016/j.coisb.2017.10.005. Epub 2017 Nov 9.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.

J Integr Bioinform. 2018 Mar 29;15(1):20180013. doi: 10.1515/jib-2018-0013.

本文引用的文献

SEEK: a systems biology data and model management platform.

BMC Syst Biol. 2015 Jul 11;9:33. doi: 10.1186/s12918-015-0174-y.

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative.

Front Bioeng Biotechnol. 2015 Feb 24;3:19. doi: 10.3389/fbioe.2015.00019. eCollection 2015.

BioModels: ten-year anniversary.

Nucleic Acids Res. 2015 Jan;43(Database issue):D542-8. doi: 10.1093/nar/gku1181. Epub 2014 Nov 20.

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.

Nucleic Acids Res. 2013 Jan;41(Database issue):D456-63. doi: 10.1093/nar/gks1146. Epub 2012 Nov 24.

Controlled vocabularies and semantics in systems biology.

Mol Syst Biol. 2011 Oct 25;7:543. doi: 10.1038/msb.2011.77.

Minimum Information About a Simulation Experiment (MIASE).

PLoS Comput Biol. 2011 Apr;7(4):e1001122. doi: 10.1371/journal.pcbi.1001122. Epub 2011 Apr 28.

Systems biology standards--the community speaks.

Nat Biotechnol. 2007 Apr;25(4):390-1. doi: 10.1038/nbt0407-390.

Minimum information requested in the annotation of biochemical models (MIRIAM).

Nat Biotechnol. 2005 Dec;23(12):1509-15. doi: 10.1038/nbt1156.

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Nat Genet. 2001 Dec;29(4):365-71. doi: 10.1038/ng1201-365.

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Nat Genet. 2000 May;25(1):25-9. doi: 10.1038/75556.

文献AI研究员

20分钟写一篇综述，助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型，支持多种主流文档格式。

立即体验

系统生物学中标准与数据管理实践的演变

The evolution of standards and data management practices in systems biology.

作者信息

机构信息

出版信息

相似文献

引用本文的文献

本文引用的文献

文献AI研究员

用中文搜PubMed

文档翻译

Suppr 超能文献

系统生物学中标准与数据管理实践的演变

The evolution of standards and data management practices in systems biology.

作者信息

机构信息

出版信息

相似文献

引用本文的文献

本文引用的文献