{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,19]],"date-time":"2026-01-19T02:36:23Z","timestamp":1768790183979,"version":"3.49.0"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2019,4,12]],"date-time":"2019-04-12T00:00:00Z","timestamp":1555027200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000050","name":"National Heart Lung Blood Institute","doi-asserted-by":"crossref","award":["HL122703"],"award-info":[{"award-number":["HL122703"]}],"id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"crossref"}]},{"name":"National Institute of Health"},{"DOI":"10.13039\/100019109","name":"Environmental Molecular Sciences Laboratory","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100019109","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100011661","name":"Pacific Northwest National Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011661","name":"PNNL","doi-asserted-by":"publisher","award":["DE-AC05-76RLO 1830"],"award-info":[{"award-number":["DE-AC05-76RLO 1830"]}],"id":[{"id":"10.13039\/100011661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Here we introduce Lipid Mini-On, an open-source tool that performs lipid enrichment analyses and visualizations of lipidomics data. Lipid Mini-On uses a text-mining process to bin individual lipid names into multiple lipid ontology groups based on the classification (e.g. LipidMaps) and other characteristics, such as chain length. Lipid Mini-On provides users with the capability to conduct enrichment analysis of the lipid ontology terms using a Shiny app with options of five statistical approaches. Lipid classes can be added to customize the user\u2019s database and remain updated as new lipid classes are discovered. Visualization of results is available for all classification options (e.g. lipid subclass and individual fatty acid chains). Results are also visualized through an editable network of relationships between the individual lipids and their associated lipid ontology terms. The utility of the tool is demonstrated using biological (e.g. human lung endothelial cells) and environmental (e.g. peat soil) samples.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Rodin (R package: https:\/\/github.com\/PNNL-Comp-Mass-Spec\/Rodin), Lipid Mini-On Shiny app (https:\/\/github.com\/PNNL-Comp-Mass-Spec\/LipidMiniOn) and Lipid Mini-On online tool (https:\/\/omicstools.pnnl.gov\/shiny\/lipid-mini-on\/).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz250","type":"journal-article","created":{"date-parts":[[2019,4,7]],"date-time":"2019-04-07T11:08:15Z","timestamp":1554635295000},"page":"4507-4508","source":"Crossref","is-referenced-by-count":46,"title":["Lipid Mini-On: mining and ontology tool for enrichment analysis of lipidomic data"],"prefix":"10.1093","volume":"35","author":[{"given":"Geremy","family":"Clair","sequence":"first","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah","family":"Reehl","sequence":"additional","affiliation":[{"name":"Computing and Analytics Division, Pacific Northwest National Laboratory , Richland, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kelly G","family":"Stratton","sequence":"additional","affiliation":[{"name":"Computing and Analytics Division, Pacific Northwest National Laboratory , Richland, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew E","family":"Monroe","sequence":"additional","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Malak M","family":"Tfaily","sequence":"additional","affiliation":[{"name":"Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, WA, USA"},{"name":"Soil, Water, and Environmental Science Department , Tuscon, AZ, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charles","family":"Ansong","sequence":"additional","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jennifer E","family":"Kyle","sequence":"additional","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,4,12]]},"reference":[{"key":"2023062803480448400_btz250-B1","author":"Chang","year":"2018"},{"key":"2023062803480448400_btz250-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkn923","article-title":"Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists","volume":"37","author":"Huang da","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023062803480448400_btz250-B3","doi-asserted-by":"crossref","first-page":"13455","DOI":"10.1038\/s41598-018-31640-x","article-title":"Cell type-resolved human lung lipidome reveals cellular cooperation in lung function","volume":"8","author":"Kyle","year":"2018","journal-title":"Sci. Rep"},{"key":"2023062803480448400_btz250-B4","doi-asserted-by":"crossref","first-page":"1744","DOI":"10.1093\/bioinformatics\/btx046","article-title":"LIQUID: an-open source software for identifying lipids in LC-MS\/MS-based lipidomics data","volume":"33","author":"Kyle","year":"2017","journal-title":"Bioinformatics"},{"key":"2023062803480448400_btz250-B5","doi-asserted-by":"crossref","first-page":"D527","DOI":"10.1093\/nar\/gkl838","article-title":"LMSD: lIPID MAPS structure database","volume":"35","author":"Sud","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023062803480448400_btz250-B6","author":"Team","year":"2013"},{"key":"2023062803480448400_btz250-B7","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"key":"2023062803480448400_btz250-B8","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1093\/bioinformatics\/btu684","article-title":"DOSE: an R\/Bioconductor package for disease ontology semantic and enrichment analysis","volume":"31","author":"Yu","year":"2015","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz250\/28369190\/btz250.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/21\/4507\/50721625\/bioinformatics_35_21_4507.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/21\/4507\/50721625\/bioinformatics_35_21_4507.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,28]],"date-time":"2023-06-28T03:48:44Z","timestamp":1687924124000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/21\/4507\/5448863"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,4,12]]},"references-count":8,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2019,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz250","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,11,1]]},"published":{"date-parts":[[2019,4,12]]}}}