HMDB 5.0: the Human Metabolome Database for 2022

David S Wishart; AnChi Guo; Eponine Oler; Fei Wang; Afia Anjum; Harrison Peters; Raynard Dizon; Zinat Sayeeda; Siyang Tian; Brian L Lee; Mark Berjanskii; Robert Mah; Mai Yamamoto; Juan Jovel; Claudia Torres-Calzada; Mickel Hiebert-Giesbrecht; Vicki W Lui; Dorna Varshavi; Dorsa Varshavi; Dana Allen; David Arndt; Nitya Khetarpal; Aadhavya Sivakumaran; Karxena Harford; Selena Sanford; Kristen Yee; Xuan Cao; Zachary Budinski; Jaanus Liigand; Lun Zhang; Jiamin Zheng; Rupasri Mandal; Naama Karu; Maija Dambrova; Helgi B Schiöth; Russell Greiner; Vasuk Gautam

doi:10.1093/nar/gkab1062

HMDB 5.0: the Human Metabolome Database for 2022

David S Wishart (Corresponding Author), AnChi Guo, Eponine Oler, Fei Wang, Afia Anjum, Harrison Peters, Raynard Dizon, Zinat Sayeeda, Siyang Tian, Brian L Lee, Mark Berjanskii, Robert Mah, Mai Yamamoto, Juan Jovel, Claudia Torres-Calzada, Mickel Hiebert-Giesbrecht, Vicki W Lui, Dorna Varshavi, Dorsa Varshavi, Dana AllenDavid Arndt, Nitya Khetarpal, Aadhavya Sivakumaran, Karxena Harford, Selena Sanford, Kristen Yee, Xuan Cao, Zachary Budinski, Jaanus Liigand, Lun Zhang, Jiamin Zheng, Rupasri Mandal, Naama Karu, Maija Dambrova, Helgi B Schiöth, Russell Greiner, Vasuk Gautam

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Abstract

The Human Metabolome Database or HMDB (https://hmdb.ca) has been providing comprehensive reference information about human metabolites and their associated biological, physiological and chemical properties since 2007. Over the past 15 years, the HMDB has grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in internet and computing technology. This year's update, HMDB 5.0, brings a number of important improvements and upgrades to the database. These should make the HMDB more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of metabolite entries (from 114 100 to 217 920 compounds); (ii) enhancements to the quality and depth of metabolite descriptions; (iii) the addition of new structure, spectral and pathway visualization tools; (iv) the inclusion of many new and much more accurately predicted spectral data sets, including predicted NMR spectra, more accurately predicted MS spectra, predicted retention indices and predicted collision cross section data and (v) enhancements to the HMDB's search functions to facilitate better compound identification. Many other minor improvements and updates to the content, the interface, and general performance of the HMDB website have also been made. Overall, we believe these upgrades and updates should greatly enhance the HMDB's ease of use and its potential applications not only in human metabolomics but also in exposomics, lipidomics, nutritional science, biochemistry and clinical chemistry.

Original language	English
Pages (from-to)	D622-D631
Journal	Nucleic Acids Research
Volume	50
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkab1062
Publication status	Published - 7 Jan 2021
Externally published	Yes

Field of Science*

1.4 Chemical sciences
1.6 Biological sciences
3.1 Basic medicine

Publication Type*

1.1. Scientific article indexed in Web of Science and/or Scopus database

Access to Document

10.1093/nar/gkab1062Licence: CC BY

HMDB 5.0Final published version, 1.16 MBLicence: CC BY

Cite this

Wishart, D. S., Guo, A., Oler, E., Wang, F., Anjum, A., Peters, H., Dizon, R., Sayeeda, Z., Tian, S., Lee, B. L., Berjanskii, M., Mah, R., Yamamoto, M., Jovel, J., Torres-Calzada, C., Hiebert-Giesbrecht, M., Lui, V. W., Varshavi, D., Varshavi, D., ... Gautam, V. (2021). HMDB 5.0: the Human Metabolome Database for 2022. Nucleic Acids Research, 50(D1), D622-D631. https://doi.org/10.1093/nar/gkab1062

@article{095ccda6e7494a5d8247addb698e62ae,

title = "HMDB 5.0: the Human Metabolome Database for 2022",

abstract = "The Human Metabolome Database or HMDB (https://hmdb.ca) has been providing comprehensive reference information about human metabolites and their associated biological, physiological and chemical properties since 2007. Over the past 15 years, the HMDB has grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in internet and computing technology. This year's update, HMDB 5.0, brings a number of important improvements and upgrades to the database. These should make the HMDB more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of metabolite entries (from 114 100 to 217 920 compounds); (ii) enhancements to the quality and depth of metabolite descriptions; (iii) the addition of new structure, spectral and pathway visualization tools; (iv) the inclusion of many new and much more accurately predicted spectral data sets, including predicted NMR spectra, more accurately predicted MS spectra, predicted retention indices and predicted collision cross section data and (v) enhancements to the HMDB's search functions to facilitate better compound identification. Many other minor improvements and updates to the content, the interface, and general performance of the HMDB website have also been made. Overall, we believe these upgrades and updates should greatly enhance the HMDB's ease of use and its potential applications not only in human metabolomics but also in exposomics, lipidomics, nutritional science, biochemistry and clinical chemistry.",

author = "Wishart, {David S} and AnChi Guo and Eponine Oler and Fei Wang and Afia Anjum and Harrison Peters and Raynard Dizon and Zinat Sayeeda and Siyang Tian and Lee, {Brian L} and Mark Berjanskii and Robert Mah and Mai Yamamoto and Juan Jovel and Claudia Torres-Calzada and Mickel Hiebert-Giesbrecht and Lui, {Vicki W} and Dorna Varshavi and Dorsa Varshavi and Dana Allen and David Arndt and Nitya Khetarpal and Aadhavya Sivakumaran and Karxena Harford and Selena Sanford and Kristen Yee and Xuan Cao and Zachary Budinski and Jaanus Liigand and Lun Zhang and Jiamin Zheng and Rupasri Mandal and Naama Karu and Maija Dambrova and Schi{\"o}th, {Helgi B} and Russell Greiner and Vasuk Gautam",

note = "{\textcopyright} The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.",

year = "2021",

month = jan,

day = "7",

doi = "10.1093/nar/gkab1062",

language = "English",

volume = "50",

pages = "D622--D631",

journal = "Nucleic Acids Research",

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number = "D1",

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Wishart, DS, Guo, A, Oler, E, Wang, F, Anjum, A, Peters, H, Dizon, R, Sayeeda, Z, Tian, S, Lee, BL, Berjanskii, M, Mah, R, Yamamoto, M, Jovel, J, Torres-Calzada, C, Hiebert-Giesbrecht, M, Lui, VW, Varshavi, D, Varshavi, D, Allen, D, Arndt, D, Khetarpal, N, Sivakumaran, A, Harford, K, Sanford, S, Yee, K, Cao, X, Budinski, Z, Liigand, J, Zhang, L, Zheng, J, Mandal, R, Karu, N, Dambrova, M, Schiöth, HB, Greiner, R & Gautam, V 2021, 'HMDB 5.0: the Human Metabolome Database for 2022', Nucleic Acids Research, vol. 50, no. D1, pp. D622-D631. https://doi.org/10.1093/nar/gkab1062

TY - JOUR

T1 - HMDB 5.0

T2 - the Human Metabolome Database for 2022

AU - Wishart, David S

AU - Guo, AnChi

AU - Oler, Eponine

AU - Wang, Fei

AU - Anjum, Afia

AU - Peters, Harrison

AU - Dizon, Raynard

AU - Sayeeda, Zinat

AU - Tian, Siyang

AU - Lee, Brian L

AU - Berjanskii, Mark

AU - Mah, Robert

AU - Yamamoto, Mai

AU - Jovel, Juan

AU - Torres-Calzada, Claudia

AU - Hiebert-Giesbrecht, Mickel

AU - Lui, Vicki W

AU - Varshavi, Dorna

AU - Varshavi, Dorsa

AU - Allen, Dana

AU - Arndt, David

AU - Khetarpal, Nitya

AU - Sivakumaran, Aadhavya

AU - Harford, Karxena

AU - Sanford, Selena

AU - Yee, Kristen

AU - Cao, Xuan

AU - Budinski, Zachary

AU - Liigand, Jaanus

AU - Zhang, Lun

AU - Zheng, Jiamin

AU - Mandal, Rupasri

AU - Karu, Naama

AU - Dambrova, Maija

AU - Schiöth, Helgi B

AU - Greiner, Russell

AU - Gautam, Vasuk

PY - 2021/1/7

Y1 - 2021/1/7

N2 - The Human Metabolome Database or HMDB (https://hmdb.ca) has been providing comprehensive reference information about human metabolites and their associated biological, physiological and chemical properties since 2007. Over the past 15 years, the HMDB has grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in internet and computing technology. This year's update, HMDB 5.0, brings a number of important improvements and upgrades to the database. These should make the HMDB more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of metabolite entries (from 114 100 to 217 920 compounds); (ii) enhancements to the quality and depth of metabolite descriptions; (iii) the addition of new structure, spectral and pathway visualization tools; (iv) the inclusion of many new and much more accurately predicted spectral data sets, including predicted NMR spectra, more accurately predicted MS spectra, predicted retention indices and predicted collision cross section data and (v) enhancements to the HMDB's search functions to facilitate better compound identification. Many other minor improvements and updates to the content, the interface, and general performance of the HMDB website have also been made. Overall, we believe these upgrades and updates should greatly enhance the HMDB's ease of use and its potential applications not only in human metabolomics but also in exposomics, lipidomics, nutritional science, biochemistry and clinical chemistry.

AB - The Human Metabolome Database or HMDB (https://hmdb.ca) has been providing comprehensive reference information about human metabolites and their associated biological, physiological and chemical properties since 2007. Over the past 15 years, the HMDB has grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in internet and computing technology. This year's update, HMDB 5.0, brings a number of important improvements and upgrades to the database. These should make the HMDB more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of metabolite entries (from 114 100 to 217 920 compounds); (ii) enhancements to the quality and depth of metabolite descriptions; (iii) the addition of new structure, spectral and pathway visualization tools; (iv) the inclusion of many new and much more accurately predicted spectral data sets, including predicted NMR spectra, more accurately predicted MS spectra, predicted retention indices and predicted collision cross section data and (v) enhancements to the HMDB's search functions to facilitate better compound identification. Many other minor improvements and updates to the content, the interface, and general performance of the HMDB website have also been made. Overall, we believe these upgrades and updates should greatly enhance the HMDB's ease of use and its potential applications not only in human metabolomics but also in exposomics, lipidomics, nutritional science, biochemistry and clinical chemistry.

UR - http://www.scopus.com/inward/record.url?scp=85123229089&partnerID=8YFLogxK

U2 - 10.1093/nar/gkab1062

DO - 10.1093/nar/gkab1062

M3 - Article

C2 - 34986597

SN - 0305-1048

VL - 50

SP - D622-D631

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -

HMDB 5.0: the Human Metabolome Database for 2022

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