HMDB: The human metabolome database
David S. Wishart,Dan Tzur,Craig Knox,Roman Eisner,An Chi Guo,Nelson Young,Dean Cheng,Kevin Jewell,David Arndt,Summit Sawhney,Chris Fung,Lisa Nikolai,Michael J. Lewis,Marie-Aude Coutouly,Ian D. Forsythe,Peter Tang,Savita Shrivastava,Kevin Jeroncic,Paul Stothard,Godwin Amegbey,David Block,David Hau,James Wagner,Jessica Miniaci,Melisa Clements,Mulu Gebremedhin,Natalie Guo,Ying Wen Zhang,Gavin E. Duggan,Glen D. MacInnis,Alim M. Weljie,Reza Dowlatabadi,Fiona Bamforth,Derrick L. J. Clive,Russell Greiner,Liang Li,Thomas J. Marrie,Brian D. Sykes,Hans J. Vogel,Lori M.M. Querengesser +39 more
TLDR
The Human Metabolome Database is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community.Abstract:
The Human Metabolome Database (HMDB) is currently the most complete and comprehensive curated collection of human metabolite and human metabolism data in the world. It contains records for more than 2180 endogenous metabolites with information gathered from thousands of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the HMDB also contains an extensive collection of experimental metabolite concentration data compiled from hundreds of mass spectra (MS) and Nuclear Magnetic resonance (NMR) metabolomic analyses performed on urine, blood and cerebrospinal fluid samples. This is further supplemented with thousands of NMR and MS spectra collected on purified, reference metabolites. Each metabolite entry in the HMDB contains an average of 90 separate data fields including a comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, SNP and mutation data as well as extensive links to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided. The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. The HMDB is available at: www.hmdb.caread more
Citations
More filters
Journal ArticleDOI
The human microbiome project.
Peter J. Turnbaugh,Ruth E. Ley,Micah Hamady,Claire M. Fraser-Liggett,Rob Knight,Jeffrey I. Gordon +5 more
TL;DR: A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease.
Journal ArticleDOI
Enrichr: Interactive and collaborative HTML5 gene list enrichment analysis tool
Edward Y. Chen,Christopher M. Tan,Yan Kou,Qiaonan Duan,Zichen Wang,Gabriela Vaz Meirelles,Neil R. Clark,Avi Ma'ayan +7 more
TL;DR: Enrichr is an easy to use intuitive enrichment analysis web-based tool providing various types of visualization summaries of collective functions of gene lists, and can be embedded into any tool that performs gene list analysis.
Journal ArticleDOI
HMDB 3.0—The Human Metabolome Database in 2013
David S. Wishart,Timothy Jewison,An Chi Guo,Michael Wilson,Craig Knox,Yifeng Liu,Yannick Djoumbou,Rupasri Mandal,Farid Aziat,Edison Dong,Souhaila Bouatra,Igor Sinelnikov,David Arndt,Jianguo Xia,Philip Liu,Faizath S. Yallou,Trent C. Bjorndahl,Rolando Perez-Pineiro,Roman Eisner,Felicity Allen,Vanessa Neveu,Russell Greiner,Augustin Scalbert +22 more
TL;DR: New database visualization tools and new data content have been added or enhanced to the HMDB, which includes better spectral viewing tools, more powerful chemical substructure searches, an improved chemical taxonomy and better, more interactive pathway maps.
Journal ArticleDOI
HMDB 4.0: the human metabolome database for 2018.
David S. Wishart,Yannick Djoumbou Feunang,Ana Marcu,An Chi Guo,Kevin Y. H. Liang,Rosa Vázquez-Fresno,Tanvir Sajed,Daniel Johnson,Carin Li,Naama Karu,Zinat Sayeeda,Elvis J. Lo,Nazanin Assempour,Mark V. Berjanskii,Sandeep Singhal,David Arndt,Yongjie Liang,Hasan Badran,Jason R. Grant,Arnau Serra-Cayuela,Yifeng Liu,Rupa Mandal,Vanessa Neveu,Allison Pon,Craig Knox,Michael Wilson,Claudine Manach,Augustin Scalbert +27 more
TL;DR: This year's update to the HMDB, HMDB 4.0, represents the most significant upgrade to the database in its history and should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science.
Journal ArticleDOI
DrugBank: a knowledgebase for drugs, drug actions and drug targets
David S. Wishart,Craig Knox,An Chi Guo,Dean Cheng,Savita Shrivastava,Dan Tzur,Bijaya Gautam,Murtaza Hassanali +7 more
TL;DR: The latest version of DrugBank (release 2.0) has been expanded significantly over the previous release and contains 60% more FDA-approved small molecule and biotech drugs including 10% more ‘experimental’ drugs.
References
More filters
Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI
SMILES, a chemical language and information system. 1. introduction to methodology and encoding rules
TL;DR: This chapter discusses the construction of Benzenoid and Coronoid Hydrocarbons through the stages of enumeration, classification, and topological properties in a number of computers used for this purpose.
Journal ArticleDOI
The KEGG resource for deciphering the genome
TL;DR: A knowledge-based approach for network prediction is developed, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes.
Journal ArticleDOI
The Universal Protein Resource (UniProt)
Amos Marc Bairoch,Rolf Apweiler,Cathy H. Wu,Winona C. Barker,Brigitte Boeckmann,Serenella Ferro,Elisabeth Gasteiger,Hongzhan Huang,Rodrigo Lopez,Michele Magrane,Maria Jesus Martin,Darren A. Natale,Claire O'Donovan,Nicole Redaschi,Lai-Su L. Yeh +14 more
TL;DR: During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; the UniProt keyword list got augmented by additional keywords; the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications.
Related Papers (5)
HMDB 3.0—The Human Metabolome Database in 2013
David S. Wishart,Timothy Jewison,An Chi Guo,Michael Wilson,Craig Knox,Yifeng Liu,Yannick Djoumbou,Rupasri Mandal,Farid Aziat,Edison Dong,Souhaila Bouatra,Igor Sinelnikov,David Arndt,Jianguo Xia,Philip Liu,Faizath S. Yallou,Trent C. Bjorndahl,Rolando Perez-Pineiro,Roman Eisner,Felicity Allen,Vanessa Neveu,Russell Greiner,Augustin Scalbert +22 more
'metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological nmr spectroscopic data
Proposed minimum reporting standards for chemical analysis
Lloyd W. Sumner,Alexander Amberg,Dave Barrett,Michael H. Beale,Richard D. Beger,Clare A. Daykin,Teresa W.-M. Fan,Oliver Fiehn,Royston Goodacre,Julian L. Griffin,Thomas Hankemeier,Nigel Hardy,James M. Harnly,Richard M. Higashi,Joachim Kopka,Andrew N. Lane,John C. Lindon,Philip J. Marriott,Andrew W. Nicholls,Michael D. Reily,John J. Thaden,Mark R. Viant +21 more