MetaboLights: a resource evolving in response to the needs of its scientific community

被引：550

作者：

Haug, Kenneth ^{[1
]}

Cochrane, Keeva ^{[1
]}

Nainala, Venkata Chandrasekhar ^{[1
]}

Williams, Mark ^{[1
]}

Chang, Jiakang ^{[1
]}

Jayaseelan, Kalai Vanii ^{[1
]}

O'Donovan, Claire ^{[1
]}

机构：

[1] EBI, EMBL, Wellcome Genome Campus, Cambridge CB10 1SD, England

来源：

NUCLEIC ACIDS RESEARCH | 2020年 / 48卷 / D1期

基金：

欧盟地平线“2020”; 英国生物技术与生命科学研究理事会; 英国惠康基金; 英国医学研究理事会;

关键词：

D O I：

10.1093/nar/gkz1019

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

MetaboLights is a database for metabolomics studies, their raw experimental data and associated metadata. The database is cross-species and cross-technique and it covers metabolite structures and their reference spectra as well as their biological roles and locations. MetaboLights is the recommended metabolomics repository for a number of leading journals and ELIXIR, the European infrastructure for life science information. In this article, we describe the significant updates that we have made over the last two years to the resource to respond to the increasing amount and diversity of data being submitted by the metabolomics community. We refreshed the website and most importantly, our submission process was completely overhauled to enable us to deliver a far more user-friendly submission process and to facilitate the growing demand for reproducibility and integration with other 'omics. Metabolomics resources and data are available under the EMBL-EBI's Terms of Use via the web at https: //www.ebi.ac.uk/metabolights and under Apache 2.0 at Github (https://github.com/EBI-Metabolights/).

引用

页码：D440 / D444

页数：5

共 11 条

[1]

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses [J].

Cooper, Laurel ;

Walls, Ramona L. ;

Elser, Justin ;

Gandolfo, Maria A. ;

Stevenson, Dennis W. ;

Smith, Barry ;

Preece, Justin ;

Athreya, Balaji ;

Mungall, Christopher J. ;

Rensing, Stefan ;

Hiss, Manuel ;

Lang, Daniel ;

Reski, Ralf ;

Berardini, Tanya Z. ;

Li, Donghui ;

Huala, Eva ;

Schaeffer, Mary ;

Menda, Naama ;

Arnaud, Elizabeth ;

Shrestha, Rosemary ;

Yamazaki, Yukiko ;

Jaiswal, Pankaj .

PLANT AND CELL PHYSIOLOGY, 2013, 54 (02) :E1-+

[2]

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy [J].

Feunang, Yannick Djoumbou ;

Eisner, Roman ;

Knox, Craig ;

Chepelev, Leonid ;

Hastings, Janna ;

Owen, Gareth ;

Fahy, Eoin ;

Steinbeck, Christoph ;

Subramanian, Shankar ;

Bolton, Evan ;

Greiner, Russell ;

Wishart, David S. .

JOURNAL OF CHEMINFORMATICS, 2016, 8 :1-20

[3]

The Units Ontology: a tool for integrating units of measurement in science [J].

Gkoutos, Georgios V. ;

Schofield, Paul N. ;

Hoehndorf, Robert .

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2012, :bas033

[4]

The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources [J].

Gremse, Marion ;

Chang, Antje ;

Schomburg, Ida ;

Grote, Andreas ;

Scheer, Maurice ;

Ebeling, Christian ;

Schomburg, Dietmar .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D507-D513

[5]

ChEBI in 2016: Improved services and an expanding collection of metabolites [J].

Hastings, Janna ;

Owen, Gareth ;

Dekker, Adriano ;

Ennis, Marcus ;

Kale, Namrata ;

Muthukrishnan, Venkatesh ;

Turner, Steve ;

Swainston, Neil ;

Mendes, Pedro ;

Steinbeck, Christoph .

NUCLEIC ACIDS RESEARCH, 2016, 44 (D1) :D1214-D1219

[6]

MetaboLights-an open-access general-purpose repository for metabolomics studies and associated meta-data [J].

Haug, Kenneth ;

Salek, Reza M. ;

Conesa, Pablo ;

Hastings, Janna ;

de Matos, Paula ;

Rijnbeek, Mark ;

Mahendraker, Tejasvi ;

Williams, Mark ;

Neumann, Steffen ;

Rocca-Serra, Philippe ;

Maguire, Eamonn ;

Gonzalez-Beltran, Alejandra ;

Sansone, Susanna-Assunta ;

Griffin, Julian L. ;

Steinbeck, Christoph .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D781-D786

[7]

PubChem 2019 update: improved access to chemical data [J].

Kim, Sunghwan ;

Chen, Jie ;

Cheng, Tiejun ;

Gindulyte, Asta ;

He, Jia ;

He, Siqian ;

Li, Qingliang ;

Shoemaker, Benjamin A. ;

Thiessen, Paul A. ;

Yu, Bo ;

Zaslavsky, Leonid ;

Zhang, Jian ;

Bolton, Evan E. .

NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) :D1102-D1109

[8]

Chemical Name to Structure: OPSIN, an Open Source Solution [J].

Lowe, Daniel M. ;

Corbett, Peter T. ;

Murray-Rust, Peter ;

Glen, Robert C. .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2011, 51 (03) :739-753

[9]

Modeling sample variables with an Experimental Factor Ontology [J].

Malone, James ;

Holloway, Ele ;

Adamusiak, Tomasz ;

Kapushesky, Misha ;

Zheng, Jie ;

Kolesnikov, Nikolay ;

Zhukova, Anna ;

Brazma, Alvis ;

Parkinson, Helen .

BIOINFORMATICS, 2010, 26 (08) :1112-1118

[10]

Toward interoperable bioscience data [J].

Sansone, Susanna-Assunta ;

Rocca-Serra, Philippe ;

Field, Dawn ;

Maguire, Eamonn ;

Taylor, Chris ;

Hofmann, Oliver ;

Fang, Hong ;

Neumann, Steffen ;

Tong, Weida ;

Amaral-Zettler, Linda ;

Begley, Kimberly ;

Booth, Tim ;

Bougueleret, Lydie ;

Burns, Gully ;

Chapman, Brad ;

Clark, Tim ;

Coleman, Lee-Ann ;

Copeland, Jay ;

Das, Sudeshna ;

de Daruvar, Antoine ;

de Matos, Paula ;

Dix, Ian ;

Edmunds, Scott ;

Evelo, Chris T. ;

Forster, Mark J. ;

Gaudet, Pascale ;

Gilbert, Jack ;

Goble, Carole ;

Griffin, Julian L. ;

Jacob, Daniel ;

Kleinjans, Jos ;

Harland, Lee ;

Haug, Kenneth ;

Hermjakob, Henning ;

Sui, Shannan J. Ho ;

Laederach, Alain ;

Liang, Shaoguang ;

Marshall, Stephen ;

McGrath, Annette ;

Merrill, Emily ;

Reilly, Dorothy ;

Roux, Magali ;

Shamu, Caroline E. ;

Shang, Catherine A. ;

Steinbeck, Christoph ;

Trefethen, Anne ;

Williams-Jones, Bryn ;

Wolstencroft, Katherine ;

Xenarios, Ioannis ;

Hide, Winston .

NATURE GENETICS, 2012, 44 (02) :121-126

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