MzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.

ABSTRACT:

Summary

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

SUBMITTER: Larralde M 

PROVIDER: S-EPMC5870861 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature