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

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

doi:10.1093/nar/gkad896

Journal article 284 views 33 downloads

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

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

Nucleic Acids Research

Swansea University Author: William Griffiths

PDF | Version of Record

© 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).
Download (724.27KB)

Check full text

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...

Full description

Published in:	Nucleic Acids Research
ISSN:	0305-1048 1362-4962
Published:	Oxford University Press (OUP) 2023
Online Access:	Check full text
URI:	https://cronfa.swan.ac.uk/Record/cronfa64901
Tags:	Add Tag No Tags, Be the first to tag this record!

first_indexed	2023-11-02T16:41:13Z
last_indexed	2023-11-02T16:41:13Z
id	cronfa64901
recordtype	SURis
fullrecord	<?xml version="1.0" encoding="utf-8"?><rfc1807 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema"><bib-version>v2</bib-version><id>64901</id><entry>2023-11-02</entry><title>LIPID MAPS: update to databases and tools for the lipidomics community</title><swanseaauthors><author><sid>3316b1d1b524be1831790933eed1c26e</sid><ORCID>0000-0002-4129-6616</ORCID><firstname>William</firstname><surname>Griffiths</surname><name>William Griffiths</name><active>true</active><ethesisStudent>false</ethesisStudent></author></swanseaauthors><date>2023-11-02</date><deptcode>BMS</deptcode><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 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.</abstract><type>Journal Article</type><journal>Nucleic Acids Research</journal><volume/><journalNumber/><paginationStart/><paginationEnd/><publisher>Oxford University Press (OUP)</publisher><placeOfPublication/><isbnPrint/><isbnElectronic/><issnPrint>0305-1048</issnPrint><issnElectronic>1362-4962</issnElectronic><keywords>LIPID MAPS, databases, metadata, lipid structural data, lipid biochemical data</keywords><publishedDay>19</publishedDay><publishedMonth>10</publishedMonth><publishedYear>2023</publishedYear><publishedDate>2023-10-19</publishedDate><doi>10.1093/nar/gkad896</doi><url>http://dx.doi.org/10.1093/nar/gkad896</url><notes/><college>COLLEGE NANME</college><department>Biomedical Sciences</department><CollegeCode>COLLEGE CODE</CollegeCode><DepartmentCode>BMS</DepartmentCode><institution>Swansea University</institution><apcterm>Another institution paid the OA fee</apcterm><funders>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.</funders><projectreference/><lastEdited>2023-12-04T13:35:28.6279327</lastEdited><Created>2023-11-02T09:06:44.3322518</Created><path><level id="1">Faculty of Medicine, Health and Life Sciences</level><level id="2">Swansea University Medical School - Biomedical Science</level></path><authors><author><firstname>Matthew J</firstname><surname>Conroy</surname><orcid>0000-0001-7297-9623</orcid><order>1</order></author><author><firstname>Robert M</firstname><surname>Andrews</surname><orcid>0000-0002-3491-2361</orcid><order>2</order></author><author><firstname>Simon</firstname><surname>Andrews</surname><orcid>0000-0002-5006-3507</orcid><order>3</order></author><author><firstname>Lauren</firstname><surname>Cockayne</surname><order>4</order></author><author><firstname>Edward A</firstname><surname>Dennis</surname><orcid>0000-0003-3738-3140</orcid><order>5</order></author><author><firstname>Eoin</firstname><surname>Fahy</surname><orcid>0000-0003-3196-522x</orcid><order>6</order></author><author><firstname>Caroline</firstname><surname>Gaud</surname><orcid>0000-0002-0453-9260</orcid><order>7</order></author><author><firstname>William</firstname><surname>Griffiths</surname><orcid>0000-0002-4129-6616</orcid><order>8</order></author><author><firstname>Geoff</firstname><surname>Jukes</surname><order>9</order></author><author><firstname>Maksim</firstname><surname>Kolchin</surname><orcid>0000-0002-3851-9874</orcid><order>10</order></author><author><firstname>Karla</firstname><surname>Mendivelso</surname><order>11</order></author><author><firstname>Andrea F</firstname><surname>Lopez-Clavijo</surname><orcid>0000-0002-6249-7767</orcid><order>12</order></author><author><firstname>Caroline</firstname><surname>Ready</surname><order>13</order></author><author><firstname>Shankar</firstname><surname>Subramaniam</surname><order>14</order></author><author><firstname>Valerie B</firstname><surname>O’Donnell</surname><orcid>0000-0003-4089-8460</orcid><order>15</order></author></authors><documents><document><filename>64901__29183__c870450b4c674065a56e11113dfa7fe7.pdf</filename><originalFilename>64901.VOR.pdf</originalFilename><uploaded>2023-12-04T13:18:16.6821831</uploaded><type>Output</type><contentLength>741654</contentLength><contentType>application/pdf</contentType><version>Version of Record</version><cronfaStatus>true</cronfaStatus><documentNotes>© 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).</documentNotes><copyrightCorrect>true</copyrightCorrect><language>eng</language><licence>https://creativecommons.org/licenses/by/4.0/</licence></document></documents><OutputDurs/></rfc1807>
spelling	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 BMS 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 Oxford University Press (OUP) 0305-1048 1362-4962 LIPID MAPS, databases, metadata, lipid structural data, lipid biochemical data 19 10 2023 2023-10-19 10.1093/nar/gkad896 http://dx.doi.org/10.1093/nar/gkad896 COLLEGE NANME Biomedical Sciences COLLEGE CODE BMS 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. 2023-12-04T13:35:28.6279327 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
publishDate	2023
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	2023-10-19T13:35:29Z
_version_	1784358559850430464
score	11.028886

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

Similar Items