title: mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.
abstract: CONCLUSIONS
  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 & 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.
  
  
  METHODS
  mzML2ISA & 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/.
  
  
  BACKGROUND
  reza.salek@ebi.ac.uk or isatools@googlegroups.com.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: École Normale Supérieure de Cachan, 94230 Cachan, France.
authors.forename: Martin
authors.initials: M
authors.lastname: Larralde
authors.affiliation: School of Biosciences.
authors.forename: Thomas N
authors.initials: TN
authors.lastname: Lawson
authors.affiliation: School of Biosciences.|Phenome Centre Birmingham, University of Birmingham, Birmingham B15 2TT, UK.
authors.forename: Ralf J M
authors.initials: RJM
authors.lastname: Weber
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK.
authors.forename: Pablo
authors.initials: P
authors.lastname: Moreno
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Haug
authors.affiliation: University of Oxford e-Research Centre, Oxford OX1 3QG, UK.
authors.forename: Philippe
authors.initials: P
authors.lastname: Rocca-Serra
authors.affiliation: School of Biosciences.|Phenome Centre Birmingham, University of Birmingham, Birmingham B15 2TT, UK.
authors.forename: Mark R
authors.initials: MR
authors.lastname: Viant
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK.|Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Lessingstr. 8, D-07743 Jena, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Steinbeck
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK.
authors.forename: Reza M
authors.initials: RM
authors.lastname: Salek
mesh_terms: D057225:Data Mining / Q000379:methods; D016247:Information Storage and Retrieval; D055432:Metabolomics / Q000379:methods*; D000071253:Metadata; D012984:Software