title: 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.
authors.affiliation: 1 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.|2 Predictive Analytics , Seattle Children's, Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.
authors.forename: Eugene
authors.initials: E
authors.lastname: Kolker
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|4 Office of the President, Gaziantep University , International Affairs and Global Development Strategy.|5 Faculty of Communications, Universite Bulvarı , Kilis Yolu, Turkey.
authors.forename: Vural
authors.initials: V
authors.lastname: Özdemir
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|6 Department of Medical Protein Research, Vlaams Instituut voor Biotechnologie , Ghent, Belgium.|7 Department of Biochemistry, Ghent University, Ghent , Belgium.
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|8 Department of Chemistry, Barnett Institute, Northeastern University , Boston, Massachusetts.
authors.forename: William
authors.initials: W
authors.lastname: Hancock
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|9 Fundamental & Computational Sciences Directorate, Pacific Northwest National Laboratory , Richland, Washington.
authors.forename: Gordon
authors.initials: G
authors.lastname: Anderson
authors.affiliation: 1 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.
authors.forename: Nathaniel
authors.initials: N
authors.lastname: Anderson
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|10 Department of Pharmacology, Gaziantep University , Gaziantep, Turkey.
authors.forename: Sukru
authors.initials: S
authors.lastname: Aynacioglu
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|11 School of Systems Biology, George Mason University , Manassas, Virginia.
authors.forename: Ancha
authors.initials: A
authors.lastname: Baranova
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|12 Department of Chemistry, University of Tennessee Knoxville , Knoxville, Tennessee.
authors.forename: Shawn R
authors.initials: SR
authors.lastname: Campagna
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|13 Department of Genetics, Stanford University , Stanford, California.
authors.forename: Rui
authors.initials: R
authors.lastname: Chen
authors.affiliation: 1 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.
authors.forename: John
authors.initials: J
authors.lastname: Choiniere
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|12 Department of Chemistry, University of Tennessee Knoxville , Knoxville, Tennessee.
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Dearth
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|14 Department of Computer Science, Virginia Tech, Blacksburg Virginia.|15 Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg Virginia.|16 SyNeRGy Laboratory, Virginia Tech, Blacksburg, Virginia.
authors.forename: Wu-Chun
authors.initials: WC
authors.lastname: Feng
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|17 Department of Nutrition, Auckland Cancer Society Research Centre, University of Auckland , Auckland, New Zealand.
authors.forename: Lynnette
authors.initials: L
authors.lastname: Ferguson
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|18 School of Informatics and Computing, Indiana University , Bloomington, Indiana.
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Fox
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|19 Technische Universitat Munchen , Wissenshaftzentrum Weihenstephan, Freising, Germany.
authors.forename: Dmitrij
authors.initials: D
authors.lastname: Frishman
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|20 Institute for Genomics and Systems Biology, University of Chicago , Chicago Illinois.|21 Department of Medicine, University of Chicago , Chicago, Illinois.
authors.forename: Robert
authors.initials: R
authors.lastname: Grossman
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|20 Institute for Genomics and Systems Biology, University of Chicago , Chicago Illinois.|22 Knapp Center for Biomedical Discovery, University of Chicago , Chicago, Illinois.
authors.forename: Allison
authors.initials: A
authors.lastname: Heath
authors.affiliation: 1 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.|2 Predictive Analytics , Seattle Children's, Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.
authors.forename: Roger
authors.initials: R
authors.lastname: Higdon
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|23 Departamento de Genetica, Instituto de Biociencias, Federal University of Rio Grande do Sul , Porto Alegre, Brazil.
authors.forename: Mara H
authors.initials: MH
authors.lastname: Hutz
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|24 High-Throughput Analysis Core, Seattle Children's Research Institute , Seattle, Washington.
authors.forename: Imre
authors.initials: I
authors.lastname: Janko
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|13 Department of Genetics, Stanford University , Stanford, California.
authors.forename: Lihua
authors.initials: L
authors.lastname: Jiang
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|25 Life Sciences , EMC, Hopkinton, Massachusetts.
authors.forename: Sanjay
authors.initials: S
authors.lastname: Joshi
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|26 GeneXplain GmbH , Wolfenbüttel, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Kel
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|27 Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin.|28 Wisconsin National Primate Research Center, University of Wisconsin-Madison , Madison, Wisconsin.
authors.forename: Joseph W
authors.initials: JW
authors.lastname: Kemnitz
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|29 Pediatrics and Health Sciences Technology, Children's Hospital and Harvard Medical School , Boston, Massachusetts.|30 HMS Center for Biomedical Informatics, Countway Library of Medicine , Boston, Massachusetts.
authors.forename: Isaac S
authors.initials: IS
authors.lastname: Kohane
authors.affiliation: 2 Predictive Analytics , Seattle Children's, Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|24 High-Throughput Analysis Core, Seattle Children's Research Institute , Seattle, Washington.
authors.forename: Natali
authors.initials: N
authors.lastname: Kolker
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|31 Department of Molecular Genetics, Crown Human Genome Center , Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Doron
authors.initials: D
authors.lastname: Lancet
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|24 High-Throughput Analysis Core, Seattle Children's Research Institute , Seattle, Washington.
authors.forename: Elaine
authors.initials: E
authors.lastname: Lee
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|32 Center for Research in Biological Systems, University of California , San Diego, La Jolla, California.
authors.forename: Weizhong
authors.initials: W
authors.lastname: Li
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|33 Russian Human Proteome Organization (RHUPO) , Moscow, Russia.|34 Institute of Biomedical Chemistry , Moscow, Russia.
authors.forename: Andrey
authors.initials: A
authors.lastname: Lisitsa
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|35 Clinical Research Center, Extremadura University Hospital and Medical School , Badajoz, Spain.
authors.forename: Adrian
authors.initials: A
authors.lastname: Llerena
authors.affiliation: 1 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.
authors.forename: Courtney
authors.initials: C
authors.lastname: MacNealy-Koch
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|36 Center for Translational Research, Catholic Health Initiatives , Towson, Maryland.
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Marshall
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|6 Department of Medical Protein Research, Vlaams Instituut voor Biotechnologie , Ghent, Belgium.|7 Department of Biochemistry, Ghent University, Ghent , Belgium.
authors.forename: Paola
authors.initials: P
authors.lastname: Masuzzo
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|12 Department of Chemistry, University of Tennessee Knoxville , Knoxville, Tennessee.
authors.forename: Amanda
authors.initials: A
authors.lastname: May
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|13 Department of Genetics, Stanford University , Stanford, California.
authors.forename: George
authors.initials: G
authors.lastname: Mias
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|37 Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington.
authors.forename: Matthew
authors.initials: M
authors.lastname: Monroe
authors.affiliation: 1 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.|2 Predictive Analytics , Seattle Children's, Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Montague
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|38 The Buck Institute for Research on Aging , Novato, California.
authors.forename: Sean
authors.initials: S
authors.lastname: Mooney
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|39 Department of Pathology, University of Michigan , Ann Arbor, Michigan.|40 Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan.
authors.forename: Alexey
authors.initials: A
authors.lastname: Nesvizhskii
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|41 Department of Chemical Engineering, Indian Institute of Technology Bombay , Powai, Mumbai, India.
authors.forename: Santosh
authors.initials: S
authors.lastname: Noronha
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|42 Center for Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan.|43 Departments of Molecular Medicine & Genetics and Human Genetics, University of Michigan , Ann Arbor Michigan.|44 Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan.|45 School of Public Health, University of Michigan , Ann Arbor, Michigan.
authors.forename: Gilbert
authors.initials: G
authors.lastname: Omenn
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|46 J eeva Informatics Solutions LLC , Derwood, Maryland.
authors.forename: Harsha
authors.initials: H
authors.lastname: Rajasimha
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|47 Molecular Diagnostics Department, National Jewish Health , Denver Colorado.
authors.forename: Preveen
authors.initials: P
authors.lastname: Ramamoorthy
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|48 California Institute for Telecommunications and Information Technology, University of California-San Diego , La Jolla, California.
authors.forename: Jerry
authors.initials: J
authors.lastname: Sheehan
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|48 California Institute for Telecommunications and Information Technology, University of California-San Diego , La Jolla, California.
authors.forename: Larry
authors.initials: L
authors.lastname: Smarr
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|49 Center for Developmental Therapeutics, Seattle Children's Research Institute , Seattle, Washington.
authors.forename: Charles V
authors.initials: CV
authors.lastname: Smith
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|50 Digital World Biology , Seattle, Washington.
authors.forename: Todd
authors.initials: T
authors.lastname: Smith
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|13 Department of Genetics, Stanford University , Stanford, California.|51 Stanford Center for Genomics and Personalized Medicine, Stanford University , Stanford, California.
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|52 Proteomics Laboratory, National Centre for Cell Science, University of Pune , Pune, India.
authors.forename: Srikanth
authors.initials: S
authors.lastname: Rapole
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|53 Proteomics Laboratory, Indian Institute of Technology Bombay , Mumbai, India.
authors.forename: Sanjeeva
authors.initials: S
authors.lastname: Srivastava
authors.affiliation: 1 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.|2 Predictive Analytics , Seattle Children's, Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.
authors.forename: Larissa
authors.initials: L
authors.lastname: Stanberry
authors.affiliation: 1 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Stewart
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|54 Department of Molecular Medicine, University of Padova , Padova, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Toppo
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|55 Center for the Study of Biological Complexity (CSBC), Virginia Commonwealth University , Richmond, Virginia.
authors.forename: Peter
authors.initials: P
authors.lastname: Uetz
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|6 Department of Medical Protein Research, Vlaams Instituut voor Biotechnologie , Ghent, Belgium.|7 Department of Biochemistry, Ghent University, Ghent , Belgium.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Verheggen
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|56 Department of Animal Science, University of Tennessee Institute of Agriculture , Knoxville, Tennessee.
authors.forename: Brynn H
authors.initials: BH
authors.lastname: Voy
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|57 Department of Genetics, Faculty of AgriSciences, University of Stellenbosch , Stellenbosch, South Africa.
authors.forename: Louise
authors.initials: L
authors.lastname: Warnich
authors.affiliation: 3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.|58 Department of Microbiology, University of Tennessee-Knoxville , Knoxville, Tennessee.
authors.forename: Steven W
authors.initials: SW
authors.lastname: Wilhelm
authors.affiliation: 1 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.|3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.
authors.forename: Gregory
authors.initials: G
authors.lastname: Yandl