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Error-Free Data Visualization and Processing through imzML and mzML Validation

Title data

Race, Alan M. ; Römpp, Andreas:
Error-Free Data Visualization and Processing through imzML and mzML Validation.
In: Analytical Chemistry. Vol. 90 (2018) Issue 22 . - pp. 13378-13384.
ISSN 1520-6882
DOI: https://doi.org/10.1021/acs.analchem.8b03059

Abstract in another language

Open data formats are key to facilitating data processing, sharing, and integration. The imzML format (http://imzml.org/) has drastically improved these aspects of mass spectrometry imaging data. Efficient processing of data depends on data sets which are consistent and adhere to the specifications; however, this is not always the case. Here we present a validation tool for data stored in both imzML and the HUPO-PSI mass spectrometery counterpart, mzML, to identify any deviations from the published (i)mzML standard which could cause issues for the user when visualizing or processing data. The tool is released in two forms, a graphical user interface (GUI) for ease of use, and a command line version to fit into existing workflows and pipelines. When certain known issues are encountered, such as the presence of negative values for the location of the binary data, the validator resolves the issue automatically upon saving. The GUI version of the validator also allows editing of the metadata included within the (i)mzML files in order to resolve inconsistencies. We also present a means of performing conditional validation on the metadata within (i)mzML files, where user-defined rules are validated against depending on whether specific metadata are present (or not). For example, if the MALDI term is present, then additional rules related to MALDI (such as the requirement of inclusion of laser parameters) can be validated against this. This enables a flexible and more thorough automated validation of (i)mzML data. Such a system is necessary for validating data against more comprehensive sets of metadata such as minimum reporting guidelines or metadata requirements prior to submission and acceptance of data to data repositories. We demonstrate how this tool can be used to validate against the proposed minimum reporting guidelines in MSI as well as institute specific metadata criteria. The validator tool is endorsed for validation of imzML (http://imzml.org/) and mzML (http://www.psidev.info/mzml) and is made available through the respective Web sites. The validator is also released as open source under Mozilla Public License 2.0 at https://gitlab.com/imzML/imzMLValidator.

Further data

Item Type: Article in a journal
Refereed: Yes
Additional notes: ISI:000451246100035
Institutions of the University: Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Biology > Lehrstuhl Bioanalytik und Lebensmittelanalytik > Lehrstuhl Bioanalytik und Lebensmittelanalytik - Univ.-Prof. Dr. Andreas Römpp
Graduate Schools > Bayreuth Graduate School of Mathematical and Natural Sciences (BayNAT) > Molecular Biosciences
Result of work at the UBT: Yes
DDC Subjects: 500 Science > 500 Natural sciences
500 Science > 540 Chemistry
500 Science > 570 Life sciences, biology
Date Deposited: 31 Jul 2019 10:08
Last Modified: 31 Jul 2019 10:08
URI: https://eref.uni-bayreuth.de/id/eprint/51670