{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T22:57:46Z","timestamp":1773442666422,"version":"3.50.1"},"reference-count":2,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2017,9,14]],"date-time":"2017-09-14T00:00:00Z","timestamp":1505347200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["105614\/Z\/14\/Z"],"award-info":[{"award-number":["105614\/Z\/14\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"BBSRC","doi-asserted-by":"publisher","award":["BB\/L018616\/1"],"award-info":[{"award-number":["BB\/L018616\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>We recently published MS2LDA, a method for the decomposition of sets of molecular fragment data derived from large metabolomics experiments. To make the method more widely available to the community, here we present ms2lda.org, a web application that allows users to upload their data, run MS2LDA analyses and explore the results through interactive visualizations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Ms2lda.org takes tandem mass spectrometry data in many standard formats and allows the user to infer the sets of fragment and neutral loss features that co-occur together (Mass2Motifs). As an alternative workflow, the user can also decompose a data set onto predefined Mass2Motifs. This is accomplished through the web interface or programmatically from our web service.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The website can be found at http:\/\/ms2lda.org, while the source code is available at https:\/\/github.com\/sdrogers\/ms2ldaviz under the MIT license.<\/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\/btx582","type":"journal-article","created":{"date-parts":[[2017,9,13]],"date-time":"2017-09-13T19:13:03Z","timestamp":1505329983000},"page":"317-318","source":"Crossref","is-referenced-by-count":107,"title":["Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3068-4664","authenticated-orcid":false,"given":"Joe","family":"Wandy","sequence":"first","affiliation":[{"name":"Glasgow Polyomics University of Glasgow, Glasgow, UK"}]},{"given":"Yunfeng","family":"Zhu","sequence":"additional","affiliation":[{"name":"Wellcome Centre for Molecular Parasitology, Glasgow, UK"}]},{"given":"Justin J J","family":"van der Hooft","sequence":"additional","affiliation":[{"name":"Glasgow Polyomics University of Glasgow, Glasgow, UK"}]},{"given":"R\u00f3n\u00e1n","family":"Daly","sequence":"additional","affiliation":[{"name":"Glasgow Polyomics University of Glasgow, Glasgow, UK"}]},{"given":"Michael P","family":"Barrett","sequence":"additional","affiliation":[{"name":"Glasgow Polyomics University of Glasgow, Glasgow, UK"},{"name":"Wellcome Centre for Molecular Parasitology, Glasgow, UK"}]},{"given":"Simon","family":"Rogers","sequence":"additional","affiliation":[{"name":"School of Computing Science, University of Glasgow, UK"}]}],"member":"286","published-online":{"date-parts":[[2017,9,14]]},"reference":[{"key":"2023012712241589000_btx582-B1","doi-asserted-by":"crossref","first-page":"225.","DOI":"10.1186\/1471-2105-6-225","article-title":"Pathway level analysis of gene expression using singular value decomposition","volume":"6","author":"Tomfohr","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023012712241589000_btx582-B2","doi-asserted-by":"crossref","first-page":"13738","DOI":"10.1073\/pnas.1608041113","article-title":"Topic modeling for untargeted substructure exploration in metabolomics","volume":"113","author":"van der Hooft","year":"2016","journal-title":"Proc Natl Acad Sci USA"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/2\/317\/48913407\/bioinformatics_34_2_317.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/2\/317\/48913407\/bioinformatics_34_2_317.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:08:54Z","timestamp":1674824934000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/2\/317\/4158166"}},"subtitle":[],"editor":[{"given":"Oliver","family":"Stegle","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,9,14]]},"references-count":2,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2018,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx582","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,1,15]]},"published":{"date-parts":[[2017,9,14]]}}}