ChEBI in 2016: Improved services and an expanding collection of metabolites

被引：656

作者：

Hastings, Janna ^{[1
]}

Owen, Gareth ^{[1
]}

Dekker, Adriano ^{[1
]}

Ennis, Marcus ^{[1
]}

Kale, Namrata ^{[1
]}

Muthukrishnan, Venkatesh ^{[1
]}

Turner, Steve ^{[1
]}

Swainston, Neil ^{[2
]}

Mendes, Pedro ^{[2
]}

Steinbeck, Christoph ^{[1
]}

机构：

[1] EMBL EBI, Cheminformat & Metab, Hinxton, Cambs, England

[2] Univ Manchester, Manchester Ctr Integrat Syst Biol, Manchester M13 9PL, Lancs, England

来源：

NUCLEIC ACIDS RESEARCH | 2016年 / 44卷 / D1期

基金：

英国生物技术与生命科学研究理事会;

关键词：

CHEMICAL ENTITIES; ONTOLOGY; DATABASE; REPOSITORY;

D O I：

10.1093/nar/gkv1031

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

ChEBI is a database and ontology containing information about chemical entities of biological interest. It currently includes over 46 000 entries, each of which is classified within the ontology and assigned multiple annotations including (where relevant) a chemical structure, database cross-references, synonyms and literature citations. All content is freely available and can be accessed online at http://www.ebi.ac.uk/chebi. In this update paper, we describe recent improvements and additions to the ChEBI offering. We have substantially extended our collection of endogenous metabolites for several organisms including human, mouse, Escherichia coli and yeast. Our front-end has also been reworked and updated, improving the user experience, removing our dependency on Java applets in favour of embedded JavaScript components and moving from a monthly release update to a 'live' website. Programmatic access has been improved by the introduction of a library, libChEBI, in Java, Python and Matlab. Furthermore, we have added two new tools, namely an analysis tool, BiNChE, and a query tool for the ontology, OntoQuery.

引用

页码：D1214 / D1219

页数：6

共 22 条

[1] KNApSAcK Family Databases: Integrated Metabolite-Plant Species Databases for Multifaceted Plant Research [J].

Afendi, Farit Mochamad ;

Okada, Taketo ;

Yamazaki, Mami ;

Hirai-Morita, Aki ;

Nakamura, Yukiko ;

Nakamura, Kensuke ;

Ikeda, Shun ;

Takahashi, Hiroki ;

Altaf-Ul-Amin, Md. ;

Darusman, Latifah K. ;

Saito, Kazuki ;

Kanaya, Shigehiko .

PLANT AND CELL PHYSIOLOGY, 2012, 53 (02) :e1

[2] UniProt: a hub for protein information [J].

Bateman, Alex ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Apweiler, Rolf ;

Alpi, Emanuele ;

Antunes, Ricardo ;

Arganiska, Joanna ;

Bely, Benoit ;

Bingley, Mark ;

Bonilla, Carlos ;

Britto, Ramona ;

Bursteinas, Borisas ;

Chavali, Gayatri ;

Cibrian-Uhalte, Elena ;

Da Silva, Alan ;

De Giorgi, Maurizio ;

Dogan, Tunca ;

Fazzini, Francesco ;

Gane, Paul ;

Cas-tro, Leyla Garcia ;

Garmiri, Penelope ;

Hatton-Ellis, Emma ;

Hieta, Reija ;

Huntley, Rachael ;

Legge, Duncan ;

Liu, Wudong ;

Luo, Jie ;

MacDougall, Alistair ;

Mutowo, Prudence ;

Nightin-gale, Andrew ;

Orchard, Sandra ;

Pichler, Klemens ;

Poggioli, Diego ;

Pundir, Sangya ;

Pureza, Luis ;

Qi, Guoying ;

Rosanoff, Steven ;

Saidi, Rabie ;

Sawford, Tony ;

Shypitsyna, Aleksandra ;

Turner, Edward ;

Volynkin, Vladimir ;

Wardell, Tony ;

Watkins, Xavier ;

Zellner, Hermann ;

Cowley, Andrew ;

Figueira, Luis ;

Li, Weizhong ;

McWilliam, Hamish .

NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D204-D212

[3] Chemical Entities of Biological Interest: an update [J].

de Matos, Paula ;

Alcantara, Rafael ;

Dekker, Adriano ;

Ennis, Marcus ;

Hastings, Janna ;

Haug, Kenneth ;

Spiteri, Inmaculada ;

Turner, Steve ;

Steinbeck, Christoph .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D249-D254

[4] ChEBI:: a database and ontology for chemical entities of biological interest [J].

Degtyarenko, Kirill ;

de Matos, Paula ;

Ennis, Marcus ;

Hastings, Janna ;

Zbinden, Martin ;

McNaught, Alan ;

Alcantara, Rafael ;

Darsow, Michael ;

Guedj, Mickael ;

Ashburner, Michael .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D344-D350

[5] The University of Minnesota Biocatalysis/Biodegradation Database: Post-genomic data mining [J].

Ellis, LBM ;

Hou, BK ;

Kang, WJ ;

Wackett, LP .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :262-265

[6] Exploiting disjointness axioms to improve semantic similarity measures [J].

Ferreira, Joao D. ;

Hastings, Janna ;

Couto, Francisco M. .

BIOINFORMATICS, 2013, 29 (21) :2781-2787

[7] PubChemRDF: towards the semantic annotation of PubChem compound and substance databases [J].

Fu, Gang ;

Batchelor, Colin ;

Dumontier, Michel ;

Hastings, Janna ;

Willighagen, Egon ;

Bolton, Evan .

JOURNAL OF CHEMINFORMATICS, 2015, 7

[8] The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013 [J].

Hastings, Janna ;

de Matos, Paula ;

Dekker, Adriano ;

Ennis, Marcus ;

Harsha, Bhavana ;

Kale, Namrata ;

Muthukrishnan, Venkatesh ;

Owen, Gareth ;

Turner, Steve ;

Williams, Mark ;

Steinbeck, Christoph .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D456-D463

[9] 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

[10] A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology [J].

Herrgard, Markus J. ;

Swainston, Neil ;

Dobson, Paul ;

Dunn, Warwick B. ;

Arga, K. Yalcin ;

Arvas, Mikko ;

Bluethgen, Nils ;

Borger, Simon ;

Costenoble, Roeland ;

Heinemann, Matthias ;

Hucka, Michael ;

Le Novere, Nicolas ;

Li, Peter ;

Liebermeister, Wolfram ;

Mo, Monica L. ;

Oliveira, Ana Paula ;

Petranovic, Dina ;

Pettifer, Stephen ;

Simeonidis, Evangelos ;

Smallbone, Kieran ;

Spasic, Irena ;

Weichart, Dieter ;

Brent, Roger ;

Broomhead, David S. ;

Westerhoff, Hans V. ;

Kirdar, Betuel ;

Penttila, Merja ;

Klipp, Edda ;

Palsson, Bernhard O. ;

Sauer, Uwe ;

Oliver, Stephen G. ;

Mendes, Pedro ;

Nielsen, Jens ;

Kell, Douglas B. .

NATURE BIOTECHNOLOGY, 2008, 26 (10) :1155-1160

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