ArticleBioinformatics (Oxford, England)2017
mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- High-Resolution Mass Spectrometry for Human Exposomics: Expanding Chemical Space Coverage.Environmental science & technology · 2024Review
- Article
- Cloud-based archived metabolomics data: A resource for in-source fragmentation/annotation, meta-analysis and systems biology.Analytical science advances · 2020Article
- Balancing sufficiency and impact in reporting standards for mass spectrometry imaging experiments.GigaScience · 2018Article
- Compliance with minimum information guidelines in public metabolomics repositories.Scientific data · 2017Article
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Authors and funding
9 authors.
Funding
Abstract
summarySubmission 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. AVAILABILITY AND IMPLEMENTATION: 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/. CONTACT: reza.salek@ebi.ac.uk or isatools@googlegroups.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.