Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications.

Abstract

Biological processes are fundamentally driven by complex interactions between biomolecules. Integrated high-throughput omics studies enable multifaceted views of cells, organisms, or their communities. With the advent of new post-genomics technologies, omics studies are becoming increasingly prevalent; yet the full impact of these studies can only be realized through data harmonization, sharing, meta-analysis, and integrated research. These essential steps require consistent generation, capture, and distribution of metadata. To ensure transparency, facilitate data harmonization, and maximize reproducibility and usability of life sciences studies, we propose a simple common omics metadata checklist. The proposed checklist is built on the rich ontologies and standards already in use by the life sciences community. The checklist will serve as a common denominator to guide experimental design, capture important parameters, and be used as a standard format for stand-alone data publications. The omics metadata checklist and data publications will create efficient linkages between omics data and knowledge-based life sciences innovation and, importantly, allow for appropriate attribution to data generators and infrastructure science builders in the post-genomics era. We ask that the life sciences community test the proposed omics metadata checklist and data publications and provide feedback for their use and improvement.

DOI: 10.1089/omi.2013.0149

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@article{Kolker2013TowardMT, title={Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications.}, author={Eugene Kolker and Vural {\"{O}zdemir and Lennart Martens and William Hancock and Gordon Anderson and Nathaniel Anderson and Sukru Aynacioglu and Ancha Baranova and Shawn R Campagna and Rui Chen and John Choiniere and Stephen P Dearth and Wu-Chun Feng and Lynnette Ferguson and Geoffrey Fox and Dmitrij Frishman and Robert Grossman and Allison Heath and Roger Higdon and Mara H Hutz and Imre Janko and Lihua Jiang and Sanjay Joshi and Alexander Kel and Joseph W Kemnitz and Isaac S Kohane and Natali Kolker and Doron Lancet and Elaine Lee and Weizhong Li and Andrey Lisitsa and Adrian Llerena and Courtney MacNealy-Koch and Jean-Claude Marshall and Paola Masuzzo and Amanda May and George Mias and Matthew Monroe and Elizabeth Montague and Sean Mooney and Alexey Nesvizhskii and Santosh Noronha and Gilbert Omenn and Harsha Rajasimha and Preveen Ramamoorthy and Jerry Sheehan and Larry Smarr and Charles V Smith and Todd Smith and Michael Snyder and Srikanth Rapole and Sanjeeva Srivastava and Larissa Stanberry and Elizabeth Stewart and Stefano Toppo and Peter Uetz and Kenneth Verheggen and Brynn H Voy and Louise Warnich and Steven W Wilhelm and Gregory Yandl}, journal={Omics : a journal of integrative biology}, year={2013}, volume={18 1}, pages={10-4} }