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. 2016 Sep;17(14):1533-45.
doi: 10.2217/pgs-2016-0015. Epub 2016 Aug 22.

Minimum information required for a DMET experiment reporting

Judit Kumuthini  1 , Mamana Mbiyavanga  1 , Emile R Chimusa  1   2 , Jyotishman Pathak  3 , Panu Somervuo  4 , Ron Hn Van Schaik  5 , Vita Dolzan  6 , Clint Mizzi  7   8 , Kusha Kalideen  9 , Raj S Ramesar  9 , Milan Macek  10 , George P Patrinos  7   11 , Alessio Squassina  12
Affiliations

Minimum information required for a DMET experiment reporting

Judit Kumuthini et al. Pharmacogenomics. 2016 Sep.

Abstract

Aim: To provide pharmacogenomics reporting guidelines, the information and tools required for reporting to public omic databases.

Material & methods: For effective DMET data interpretation, sharing, interoperability, reproducibility and reporting, we propose the Minimum Information required for a DMET Experiment (MIDE) reporting.

Results: MIDE provides reporting guidelines and describes the information required for reporting, data storage and data sharing in the form of XML.

Conclusion: The MIDE guidelines will benefit the scientific community with pharmacogenomics experiments, including reporting pharmacogenomics data from other technology platforms, with the tools that will ease and automate the generation of such reports using the standardized MIDE XML schema, facilitating the sharing, dissemination, reanalysis of datasets through accessible and transparent pharmacogenomics data reporting.

Keywords: DMET; bioinformatics; minimum information requirement guidelines; personalized genomics; personalized medicine; pharmacogenomics; standardization.

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Conflict of interest statement

Financial & competing interests disclosure

The CPGR is supported through institutional funding from TIA (Technology Innovation Agency) and the DST (Department of Science and Technology). This work is partially funded by NIH Common Fund Award/NHGRI Grant Number U41HG006941 through H3AbioNet project. M Macek was supported by NF-CZ11-PDP-3-003-2014, 00064203 and COST LD14073. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Figures

<b>Figure 1.</b>
Figure 1.. DMET analysis workflow.
Data analysis of a DMET experiment is divided into primary (preparation of raw microarray data), secondary (through DMET Console) and tertiary (interpretation of the results) steps.
<b>Figure 2.</b>
Figure 2.. Graphical representation of minimum information required for a DMET experiment XML 1.0 format.
This figure shows the minimum required for DMET experiment described by elements which are grouped by source, study aim, sample_collection_and_process, sample_information, data_processing and experiment. Some elements have been collapsed (+) for ease of visualization. The full MIDE XML 1.0 schema is accessible from the MIBBI project page [38]. MIDE: Minimum information required for DMET experiment
<b>Figure 3.</b>
Figure 3.. Graphical representation of the experiment element of minimum information required for a DMET experiment XML 1.0.
The experiment is formed by a number of attributes, which hold information on the description of the experiment, the type of experiment, protocols used, data files and tertiary data analysis.
See this image and copyright information in PMC

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