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LIPID MAPS: update to databases and tools for the lipidomics community

Matthew J Conroy Orcid Logo, Robert M Andrews Orcid Logo, Simon Andrews Orcid Logo, Lauren Cockayne, Edward A Dennis Orcid Logo, Eoin Fahy Orcid Logo, Caroline Gaud Orcid Logo, William Griffiths Orcid Logo, Geoff Jukes, Maksim Kolchin Orcid Logo, Karla Mendivelso, Andrea F Lopez-Clavijo Orcid Logo, Caroline Ready, Shankar Subramaniam, Valerie B O’Donnell Orcid Logo

Nucleic Acids Research, Volume: 52, Issue: D1, Pages: D1677 - D1682

Swansea University Author: William Griffiths Orcid Logo

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DOI (Published version): 10.1093/nar/gkad896

Abstract

LIPID MAPS (LIPID Metabolites and Pathways Strategy), www.lipidmaps.org , provides a systematic and standardized approach to organizing lipid structural and biochemical data. Founded 20 years ago, the LIPID MAPS nomenclature and classification has become the accepted community standard. LIPID MAPS p...

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Published in: Nucleic Acids Research
ISSN: 0305-1048 1362-4962
Published: Oxford University Press (OUP) 2024
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URI: https://cronfa.swan.ac.uk/Record/cronfa64901
first_indexed 2023-11-02T16:41:13Z
last_indexed 2024-11-25T14:14:57Z
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spelling 2024-09-30T13:52:46.2125413 v2 64901 2023-11-02 LIPID MAPS: update to databases and tools for the lipidomics community 3316b1d1b524be1831790933eed1c26e 0000-0002-4129-6616 William Griffiths William Griffiths true false 2023-11-02 MEDS LIPID MAPS (LIPID Metabolites and Pathways Strategy), www.lipidmaps.org , provides a systematic and standardized approach to organizing lipid structural and biochemical data. Founded 20 years ago, the LIPID MAPS nomenclature and classification has become the accepted community standard. LIPID MAPS provides data bases for cataloging and identifying lipids at varying levels of characterization in addition to numerous software tools and educational resources, and became an ELIXIR-UK data resource in 2020. This paper describes the expansion of existing databases in LIPID MAPS, including richer metadata with literature provenance, taxonomic data and improved interoperability to facilitate FAIR compliance. A joint project funded by ELIXIR-UK, in collaboration with WikiPathways, curates and hosts pathway data, and annotates lipids in the context of their biochemical pathways. Updated features of the search infrastructure are described along with implementation of programmatic access via API and SPARQL. New lipid-specific databases have been developed and provision of lipidomics tools to the community has been updated. Training and engagement have been expanded with webinars, podcasts and an online training school. Journal Article Nucleic Acids Research 52 D1 D1677 D1682 Oxford University Press (OUP) 0305-1048 1362-4962 5 1 2024 2024-01-05 10.1093/nar/gkad896 http://dx.doi.org/10.1093/nar/gkad896 COLLEGE NANME Medical School COLLEGE CODE MEDS Swansea University Another institution paid the OA fee Wellcome Trust [203014/Z/16/Z]; National Institutes of Health [U2CDK119886]; EAD is supported by National Institutes of Health NIGMS MIRA [R35 GM139641]. We gratefully acknowledge unrestricted sponsorship to LIPID MAPS from Cayman Chemical, Merck and Avanti Polar Lipids. Funding for open access charge: Cardiff University via the OUP Full Collection Read and Publish Agreement 2021-2023. 2024-09-30T13:52:46.2125413 2023-11-02T09:06:44.3322518 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Biomedical Science Matthew J Conroy 0000-0001-7297-9623 1 Robert M Andrews 0000-0002-3491-2361 2 Simon Andrews 0000-0002-5006-3507 3 Lauren Cockayne 4 Edward A Dennis 0000-0003-3738-3140 5 Eoin Fahy 0000-0003-3196-522x 6 Caroline Gaud 0000-0002-0453-9260 7 William Griffiths 0000-0002-4129-6616 8 Geoff Jukes 9 Maksim Kolchin 0000-0002-3851-9874 10 Karla Mendivelso 11 Andrea F Lopez-Clavijo 0000-0002-6249-7767 12 Caroline Ready 13 Shankar Subramaniam 14 Valerie B O’Donnell 0000-0003-4089-8460 15 64901__29183__c870450b4c674065a56e11113dfa7fe7.pdf 64901.VOR.pdf 2023-12-04T13:18:16.6821831 Output 741654 application/pdf Version of Record true © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. Distributed under the terms of a Creative Commons Attribution 4.0 International License (CC BY 4.0). true eng https://creativecommons.org/licenses/by/4.0/
title LIPID MAPS: update to databases and tools for the lipidomics community
spellingShingle LIPID MAPS: update to databases and tools for the lipidomics community
William Griffiths
title_short LIPID MAPS: update to databases and tools for the lipidomics community
title_full LIPID MAPS: update to databases and tools for the lipidomics community
title_fullStr LIPID MAPS: update to databases and tools for the lipidomics community
title_full_unstemmed LIPID MAPS: update to databases and tools for the lipidomics community
title_sort LIPID MAPS: update to databases and tools for the lipidomics community
author_id_str_mv 3316b1d1b524be1831790933eed1c26e
author_id_fullname_str_mv 3316b1d1b524be1831790933eed1c26e_***_William Griffiths
author William Griffiths
author2 Matthew J Conroy
Robert M Andrews
Simon Andrews
Lauren Cockayne
Edward A Dennis
Eoin Fahy
Caroline Gaud
William Griffiths
Geoff Jukes
Maksim Kolchin
Karla Mendivelso
Andrea F Lopez-Clavijo
Caroline Ready
Shankar Subramaniam
Valerie B O’Donnell
format Journal article
container_title Nucleic Acids Research
container_volume 52
container_issue D1
container_start_page D1677
publishDate 2024
institution Swansea University
issn 0305-1048
1362-4962
doi_str_mv 10.1093/nar/gkad896
publisher Oxford University Press (OUP)
college_str Faculty of Medicine, Health and Life Sciences
hierarchytype
hierarchy_top_id facultyofmedicinehealthandlifesciences
hierarchy_top_title Faculty of Medicine, Health and Life Sciences
hierarchy_parent_id facultyofmedicinehealthandlifesciences
hierarchy_parent_title Faculty of Medicine, Health and Life Sciences
department_str Swansea University Medical School - Biomedical Science{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Biomedical Science
url http://dx.doi.org/10.1093/nar/gkad896
document_store_str 1
active_str 0
description LIPID MAPS (LIPID Metabolites and Pathways Strategy), www.lipidmaps.org , provides a systematic and standardized approach to organizing lipid structural and biochemical data. Founded 20 years ago, the LIPID MAPS nomenclature and classification has become the accepted community standard. LIPID MAPS provides data bases for cataloging and identifying lipids at varying levels of characterization in addition to numerous software tools and educational resources, and became an ELIXIR-UK data resource in 2020. This paper describes the expansion of existing databases in LIPID MAPS, including richer metadata with literature provenance, taxonomic data and improved interoperability to facilitate FAIR compliance. A joint project funded by ELIXIR-UK, in collaboration with WikiPathways, curates and hosts pathway data, and annotates lipids in the context of their biochemical pathways. Updated features of the search infrastructure are described along with implementation of programmatic access via API and SPARQL. New lipid-specific databases have been developed and provision of lipidomics tools to the community has been updated. Training and engagement have been expanded with webinars, podcasts and an online training school.
published_date 2024-01-05T05:16:19Z
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