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Toward more transparent and reproducible omics studies through a common metadata checklist and data publications

Eugene Kolker, Vural Özdemir, Lennart Martens (UGent) , William Hancock, Gordon Anderson, Nathaniel Anderson, Sukru Aynacioglu, Ancha Baranova, Shawn R Campagna, Rui Chen, et al.
(2014) OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY. 18(1). p.10-14
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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.
Keywords
MINIMUM INFORMATION

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MLA
Kolker, Eugene, et al. “Toward More Transparent and Reproducible Omics Studies through a Common Metadata Checklist and Data Publications.” OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, vol. 18, no. 1, 2014, pp. 10–14, doi:10.1089/omi.2013.0149.
APA
Kolker, E., Özdemir, V., Martens, L., Hancock, W., Anderson, G., Anderson, N., … Yandl, G. (2014). Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. https://doi.org/10.1089/omi.2013.0149
Chicago author-date
Kolker, Eugene, Vural Özdemir, Lennart Martens, William Hancock, Gordon Anderson, Nathaniel Anderson, Sukru Aynacioglu, et al. 2014. “Toward More Transparent and Reproducible Omics Studies through a Common Metadata Checklist and Data Publications.” OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY. https://doi.org/10.1089/omi.2013.0149.
Chicago author-date (all authors)
Kolker, Eugene, Vural Özdemir, Lennart Martens, William Hancock, Gordon Anderson, Nathaniel Anderson, Sukru Aynacioglu, Ancha Baranova, Shawn R Campagna, Rui Chen, John Choiniere, Stephen P Dearth, Wu-Chun Feng, Lynnette Ferguson, Geoffrey Fox, Dmitrij Frishman, Robert Grossman, Allison Heath, Roger Higdon, Mara H Hutz, Imre Janko, Lihua Jiang, Sanjay Joshi, Alexander Kel, Joseph W Kemnitz, Isaac S Kohane, Natali Kolker, Doron Lancet, Elaine Lee, Weizhong Li, Andrey Lisitsa, Adrian Llerena, Courtney Macnealy-Koch, Jean-Claude Marshall, Paola Masuzzo, Amanda May, George Mias, Matthew Monroe, Elizabeth Montague, Sean Mooney, Alexey Nesvizhskii, Santosh Noronha, Gilbert Omenn, Harsha Rajasimha, Preveen Ramamoorthy, Jerry Sheehan, Larry Smarr, Charles V Smith, Todd Smith, Michael Snyder, Srikanth Rapole, Sanjeeva Srivastava, Larissa Stanberry, Elizabeth Stewart, Stefano Toppo, Peter Uetz, Kenneth Verheggen, Brynn H Voy, Louise Warnich, Steven W Wilhelm, and Gregory Yandl. 2014. “Toward More Transparent and Reproducible Omics Studies through a Common Metadata Checklist and Data Publications.” OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY. doi:10.1089/omi.2013.0149.
Vancouver
1.
Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, et al. Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. Vol. 18, OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY. 2014. p. 10–4.
IEEE
[1]
E. Kolker et al., “Toward more transparent and reproducible omics studies through a common metadata checklist and data publications,” OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, vol. 18, no. 1. pp. 10–14, 2014.
@misc{4259669,
  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.}},
  author       = {{Kolker, Eugene and Özdemir, Vural and Martens, Lennart and Hancock, William and Anderson, Gordon and Anderson, Nathaniel and Aynacioglu, Sukru and Baranova, Ancha and Campagna, Shawn R and Chen, Rui and Choiniere, John and Dearth, Stephen P and Feng, Wu-Chun and Ferguson, Lynnette and Fox, Geoffrey and Frishman, Dmitrij and Grossman, Robert and Heath, Allison and Higdon, Roger and Hutz, Mara H and Janko, Imre and Jiang, Lihua and Joshi, Sanjay and Kel, Alexander and Kemnitz, Joseph W and Kohane, Isaac S and Kolker, Natali and Lancet, Doron and Lee, Elaine and Li, Weizhong and Lisitsa, Andrey and Llerena, Adrian and Macnealy-Koch, Courtney and Marshall, Jean-Claude and Masuzzo, Paola and May, Amanda and Mias, George and Monroe, Matthew and Montague, Elizabeth and Mooney, Sean and Nesvizhskii, Alexey and Noronha, Santosh and Omenn, Gilbert and Rajasimha, Harsha and Ramamoorthy, Preveen and Sheehan, Jerry and Smarr, Larry and Smith, Charles V and Smith, Todd and Snyder, Michael and Rapole, Srikanth and Srivastava, Sanjeeva and Stanberry, Larissa and Stewart, Elizabeth and Toppo, Stefano and Uetz, Peter and Verheggen, Kenneth and Voy, Brynn H and Warnich, Louise and Wilhelm, Steven W and Yandl, Gregory}},
  issn         = {{1536-2310}},
  keywords     = {{MINIMUM INFORMATION}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{10--14}},
  series       = {{OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY}},
  title        = {{Toward more transparent and reproducible omics studies through a common metadata checklist and data publications}},
  url          = {{http://doi.org/10.1089/omi.2013.0149}},
  volume       = {{18}},
  year         = {{2014}},
}
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