{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,8]],"date-time":"2026-02-08T00:14:59Z","timestamp":1770509699706,"version":"3.49.0"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2017,4,11]],"date-time":"2017-04-11T00:00:00Z","timestamp":1491868800000},"content-version":"vor","delay-in-days":4,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["202952\/Z\/16\/Z"],"award-info":[{"award-number":["202952\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Submission to the MetaboLights repository for metabolomics data currently places the burden of reporting instrument and acquisition parameters in ISA-Tab format on users, who have to do it manually, a process that is time consuming and prone to user input error. Since the large majority of these parameters are embedded in instrument raw data files, an opportunity exists to capture this metadata more accurately. Here we report a set of Python packages that can automatically generate ISA-Tab metadata file stubs from raw XML metabolomics data files. The parsing packages are separated into mzML2ISA (encompassing mzML and imzML formats) and nmrML2ISA (nmrML format only). Overall, the use of mzML2ISA &amp; nmrML2ISA reduces the time needed to capture metadata substantially (capturing 90% of metadata on assay and sample levels), is much less prone to user input errors, improves compliance with minimum information reporting guidelines and facilitates more finely grained data exploration and querying of datasets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>mzML2ISA &amp; nmrML2ISA are available under version 3 of the GNU General Public Licence at https:\/\/github.com\/ISA-tools. Documentation is available from http:\/\/2isa.readthedocs.io\/en\/latest\/.<\/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\/btx169","type":"journal-article","created":{"date-parts":[[2017,4,5]],"date-time":"2017-04-05T19:57:27Z","timestamp":1491422247000},"page":"2598-2600","source":"Crossref","is-referenced-by-count":12,"title":["mzML2ISA &amp; nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data"],"prefix":"10.1093","volume":"33","author":[{"given":"Martin","family":"Larralde","sequence":"first","affiliation":[{"name":"\u00c9cole Normale Sup\u00e9rieure de Cachan, Cachan, France"}]},{"given":"Thomas N","family":"Lawson","sequence":"additional","affiliation":[{"name":"School of Biosciences, University of Birmingham, Birmingham, UK"}]},{"given":"Ralf J M","family":"Weber","sequence":"additional","affiliation":[{"name":"School of Biosciences, University of Birmingham, Birmingham, UK"},{"name":"Phenome Centre Birmingham, University of Birmingham, Birmingham, UK"}]},{"given":"Pablo","family":"Moreno","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK"}]},{"given":"Kenneth","family":"Haug","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK"}]},{"given":"Philippe","family":"Rocca-Serra","sequence":"additional","affiliation":[{"name":"University of Oxford e-Research Centre, Oxford, UK"}]},{"given":"Mark R","family":"Viant","sequence":"additional","affiliation":[{"name":"School of Biosciences, University of Birmingham, Birmingham, UK"},{"name":"Phenome Centre Birmingham, University of Birmingham, Birmingham, UK"}]},{"given":"Christoph","family":"Steinbeck","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK"},{"name":"Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Lessingstr. 8, Jena, Germany"}]},{"given":"Reza M","family":"Salek","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK"}]}],"member":"286","published-online":{"date-parts":[[2017,4,7]]},"reference":[{"key":"2023020206264685300_btx169-B1","doi-asserted-by":"crossref","first-page":"W3","DOI":"10.1093\/nar\/gkw343","article-title":"The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update","volume":"44","author":"Afgan","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020206264685300_btx169-B2","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1007\/s11306-007-0070-6","article-title":"The metabolomics standards initiative (MSI)","volume":"3","author":"Fiehn","year":"2007","journal-title":"Metabolomics"},{"key":"2023020206264685300_btx169-B3","doi-asserted-by":"crossref","first-page":"S11.","DOI":"10.1186\/1471-2105-15-S1-S11","article-title":"The risa R\/Bioconductor package: integrative data analysis from experimental metadata and back again","volume":"15","author":"Gonz\u00e1lez-Beltr\u00e1n","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023020206264685300_btx169-B4","doi-asserted-by":"crossref","first-page":"2363","DOI":"10.1002\/pmic.200400884","article-title":"Advances in the development of common interchange standards for proteomic data","volume":"4","author":"Orchard","year":"2004","journal-title":"Proteomics"},{"key":"2023020206264685300_btx169-B5","doi-asserted-by":"crossref","first-page":"14.13.1","DOI":"10.1002\/0471250953.bi1413s53","article-title":"MetaboLights: An Open-Access database repository for metabolomics data","volume":"53","author":"Kale","year":"2016","journal-title":"Curr. 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Biotechnol"},{"key":"2023020206264685300_btx169-B10","doi-asserted-by":"crossref","first-page":"2354","DOI":"10.1093\/bioinformatics\/btq415","article-title":"ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level","volume":"26","author":"Rocca-Serra","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020206264685300_btx169-B11","doi-asserted-by":"crossref","first-page":"1587","DOI":"10.1007\/s11306-015-0810-y","article-title":"COordination of standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access","volume":"11","author":"Salek","year":"2015","journal-title":"Metabolomics"},{"key":"2023020206264685300_btx169-B12","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1038\/nbt0807-846b","article-title":"The metabolomics standards initiative","volume":"25","author":"Sansone","year":"2007","journal-title":"Nat. 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