Toward more transparent and reproducible omics studies through a common metadata checklist and data publications.
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.
1 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.
Eugene
E
Kolker
Vural
V
Özdemir
Lennart
L
Martens
William
W
Hancock
Gordon
G
Anderson
Nathaniel
N
Anderson
Sukru
S
Aynacioglu
Ancha
A
Baranova
Shawn R
SR
Campagna
Rui
R
Chen
John
J
Choiniere
Stephen P
SP
Dearth
Wu-Chun
WC
Feng
Lynnette
L
Ferguson
Geoffrey
G
Fox
Dmitrij
D
Frishman
Robert
R
Grossman
Allison
A
Heath
Roger
R
Higdon
Mara H
MH
Hutz
Imre
I
Janko
Lihua
L
Jiang
Sanjay
S
Joshi
Alexander
A
Kel
Joseph W
JW
Kemnitz
Isaac S
IS
Kohane
Natali
N
Kolker
Doron
D
Lancet
Elaine
E
Lee
Weizhong
W
Li
Andrey
A
Lisitsa
Adrian
A
Llerena
Courtney
C
Macnealy-Koch
Jean-Claude
JC
Marshall
Paola
P
Masuzzo
Amanda
A
May
George
G
Mias
Matthew
M
Monroe
Elizabeth
E
Montague
Sean
S
Mooney
Alexey
A
Nesvizhskii
Santosh
S
Noronha
Gilbert
G
Omenn
Harsha
H
Rajasimha
Preveen
P
Ramamoorthy
Jerry
J
Sheehan
Larry
L
Smarr
Charles V
CV
Smith
Todd
T
Smith
Michael
M
Snyder
Srikanth
S
Rapole
Sanjeeva
S
Srivastava
Larissa
L
Stanberry
Elizabeth
E
Stewart
Stefano
S
Toppo
Peter
P
Uetz
Kenneth
K
Verheggen
Brynn H
BH
Voy
Louise
L
Warnich
Steven W
SW
Wilhelm
Gregory
G
Yandl
D057225:Data Mining; D006801:Humans; D033181:Information Dissemination / Q000941:ethics*; D056186:Metagenomics / Q000191:economics / Q000706:statistics & numerical data* / Q000639:trends; D011643:Publishing; D015203:Reproducibility of Results; D012107:Research Design / Q000592:standards*