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

Big Data

Volumn 1, Issue 4, 2013, Pages 196-201

  Kolker, Eugene ^a,b,c   Özdemir, Vural ^c,d,e   Martens, Lennart ^c,f,g   Hancock, William ^c,h   Anderson, Gordon ^c,i   Anderson, Nathaniel ^a,c   Aynacioglu, Sukru ^c,d   Baranova, Ancha ^c,j   Campagna, Shawn R ^c,k   Chen, Rui ^c,l   Choiniere, John ^a,c   Dearth, Stephen P ^c,k   Feng, Wu Chun ^c,m,n   Ferguson, Lynnette ^c,o   Fox, Geoffrey ^c,p   Frishman, Dmitrij ^c,q   Grossman, Robert ^c,r,s   Heath, Allison ^c,r,s   Higdon, Roger ^a,b,c   Hutz, Mara H ^c,t   Janko, Imre ^a,c   Jiang, Lihua ^c,l   Joshi, Sanjay ^c,u   Kel, Alexander ^c,v   Kemnitz, Joseph W ^c,w,x   Kohane, Isaac S ^c,y   Kolker, Natali ^a,b,c   Lancet, Doron ^c,z   Lee, Elaine ^a,c   Li, Weizhong ^c,aa   Lisitsa, Andrey ^c,ab,ac   Llerena, Adrian ^c,ad   MacNealy Koch, Courtney ^a,c   Marshall, Jean Claude ^c,ae   Masuzzo, Paola ^c,f,g   May, Amanda ^c,k   Mias, George ^c,l   Monroe, Matthew ^c,i   Montague, Elizabeth ^a,b,c   Mooney, Sean ^c,af   Nesvizhskii, Alexey ^c,ag,ah   Noronha, Santosh ^c,ai   Omenn, Gilbert ^c,ag,ah   Rajasimha, Harsha ^c,aj   Ramamoorthy, Preveen ^c,ak   Sheehan, Jerry ^c,al   Smarr, Larry ^c,al   Smith, Charles V ^a,c   Smith, Todd ^c,am   Snyder, Michael ^c,l,an   Rapole, Srikanth ^c,ao   Srivastava, Sanjeeva ^c,ai   Stanberry, Larissa ^a,b,c   Stewart, Elizabeth ^a,c   Toppo, Stefano ^c,ap   Uetz, Peter ^c,aq   Verheggen, Kenneth ^c,f,g   Voy, Brynn H ^c,k   Warnich, Louise ^c,ar   Wilhelm, Steven W ^c,k   Yandl, Gregory ^a,c   more..

^a SEATTLE CHILDREN S RESEARCH INSTITUTE   (United States)

^b Predictive Analytics   (United States)

^c Data Enabled Life Sciences Alliance International DELSA Global   (United States)

^d GAZIANTEP UNIVERSITY   (Turkey)

^e Universite Bulvar   (Turkey)

^f DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^g GHENT UNIVERSITY   (Belgium)

^h NORTHEASTERN UNIVERSITY   (United States)

ⁱ PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^j GEORGE MASON UNIVERSITY   (United States)

^k UNIVERSITY OF TENNESSEE   (United States)

^l STANFORD UNIVERSITY   (United States)

^m State University   (United States)

ⁿ VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

^o UNIVERSITY OF AUCKLAND   (New Zealand)

^p INDIANA UNIVERSITY   (United States)

^q TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^r UNIVERSITY OF CHICAGO   (United States)

^s UNIVERSITY OF CHICAGO   (United States)

^t FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^u GNSS Technology for Rail Transportation   (United States)

^v GeneXplain GmbH   (Germany)

^w UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

^x UNIVERSITY OF WISCONSIN   (United States)

^y HARVARD MEDICAL SCHOOL   (United States)

^z WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^aa UNIVERSITY OF CALIFORNIA   (United States)

^ab RHUPO Russian Human Proteome Organization   (Russian Federation)

^ac INSTITUTE OF BIOMEDICAL CHEMISTRY   (Russian Federation)

^ad UNIVERSITY OF EXTREMADURA   (Spain)

^ae Center for Translational Research United States of America   (United States)

^af BUCK INSTITUTE FOR RESEARCH ON AGING   (United States)

^ag UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^ah UNIVERSITY OF MICHIGAN   (United States)

^ai INDIAN INSTITUTE OF TECHNOLOGY BOMBAY   (India)

^aj Jeeva Informatics Solutions LLC   (United States)

^ak DEPARTMENT OF MEDICINE   (United States)

^al UNIVERSITY OF CALIFORNIA   (United States)

^am Digital World Biology   (United States)

^an STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^ao NATIONAL CENTRE FOR CELL SCIENCE   (India)

^ap UNIVERSITY OF PADOVA   (Italy)

^aq VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^ar STELLENBOSCH UNIVERSITY   (South Africa)

more..

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84991585446     PISSN: 21676461     EISSN: 2167647X     Source Type: Journal    
DOI: 10.1089/big.2013.0039     Document Type: Review

References (40)

1. Smarr L. Quantifying your body: A how-To guide from a systems biology perspective. Biotechnology Journal 2012; 7: 980-991.
2. Bowden M. The Measured Man. The Atlantic; June 13, 2012. www.theatlantic.com/magazine/print/2012/0.7/themeasured-man/309018/.(Last accessed on October 17, 2013
3. Chen R, Mias G, Li-Pook-Than J, et al. Personal omics profiling reveals dynamic molecular, and medical phenotypes. Cell 2012; 148: 1293-1307.
4. Mias G, Snyder M. Personal genomes, quantitative dynamic omics, and personalized medicine. Quantitative Biology 2013; 1: 71-90.
5. Tennenbaum JD, Sansone S-A, Haendel M. A sea of standards for omics data: sink or swim? J Am Med Inform Assoc 2013. http://jamia.bmj.com/content/early/.2013/09/27/amiajnl-2013-002066.full.html (Last accessed on October 17, 2013
6. Field D, Sansone SA, Collis A, et al. Omics data sharing. Science 2009; 326: 234-236.
7. Editorial. On the table. Nature Genetics 2011; 43: 1.
8. Taylor C, Field D, Sansone S, et al. Promoting coherent minimum reporting guidelines for biological, and biomedical investigations: the MIBBI project. Nat Biotechnol 2008; 8: 889-896.
9. Kettner C, Field D, Sansone SA, et al. Meeting report from the second Minimum Information for Biological, and Biomedical Investigations (MIBBI) workshop. Stand Genomic Sci 2010; 3: 259-266.
10. Taylor CF, Paton NW, Lilley KS, et al. The minimum information about a proteomics experiment (MIAPE). Nat. Biotechnol 2007; 25: 887-893.
11. Alvis B, Hingamp P, Quackenbush J, et al. Minimum information about a microarray experiment (MIAME)-Towards standards for microarray data. Nat. Genet 2001; 29: 365-371.
12. Yilmaz P, Kottmann R, Field D, et al. Minimum information about a marker gene sequence (MIMARKS), and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology 2011; 29: 415-420.
13. Barrett T, Clark K, Gevorgyan R, et al. BioProject, and BioSample databases at NCBI: facilitating capture, and organization of metadata. Nucleic Acids Res 2012; 40: D57-D63.
14. Editorial. Announcement: Reducing our irreproducibility. Nature 2013; 496: 398.
15. Reporting Checklist for Life Sciences Articles. Nature Publishing Group, May 2013. www.nature.com/authors/.policies/checklist.pdf (Last accessed on August 1, 2013
16. Kolker E, Altinas I, Bourne P, et al. In praise of open research measures. Nature 2013; 498: 170.
17. Data-Enabled Life Sciences Alliance. 2013. www.delsaglobal.org
18. Kolker E, Stewart E. Opinion: Data to Knowledge to Action: Introducing DELSA Global, a community initiative to connect experts, share data, and democratize science. The Scientist, April 18, 2012. www.the-scientist.com/.?articles.view/articleNo/31985/title/Opinion-Data-To-Knowledge-To-Action/.(Last accessed October 23, 2013
19. Kolker E, Stewart E, and Ozdemir V. Opportunities, and challenges for the life sciences community. OMICS 2012; 16: 138-147.
20. Kolker E, Stewart E, and Ozdemir V. DELSA Global for big data , and the bioeconomy: Catalyzing collective innovation. Industrial Biotechnology 2012; 8: 176-178.
21. Stewart E, Smith T, De Souza A, et al. DELSA Workshop IV: Launching the Quantified Human Initiative. Big Data 2013; 1: 187-190.
22. Data-Enabled Life Sciences Alliance.Multi-omics metadata checklist. 2013. www.delsaglobal.org/news/publications/.item/84-checklist (Last accessed on October 23, 2013
23. NanoPub. 2013. nanopub.org
24. MicroPub. 2013. micropub.org
25. ISA tools. 2013. isa-Tools.org
26. Scientific Data. 2013. www.nature.com/scientificdata (Last accessed on October 13, 2013
27. Snyder M, Mias G, Stanberry L, et al. Metadata checklist for the integrated personal omics study: Proteomics, and metabolomics experiments. Published in parallel: Big Data 2013; 1 In Press, and OMICS 2014; 18 In Press
28. OMICS Journal of Integrative Biology. 2013. www.liebertpub.com/OMI
29. Journal of Proteome Research. 2013. pubs.acs.org/journal/.jprobs (Last accessed on October 23, 2013
30. eLife. 2013. elife.elifesciences.org (Last accessed on October 23, 2013
31. PubMed commons. 2013. www.ncbi.nlm.nih.gov/pubmed commons (Last accessed on October 23, 2013
32. Swartz A. Post-publication peer review mainstreamed. The Scientist. www.the-scientist.com/?articles.view/articleNo/.37969/title/Post-Publication-Peer-Review-Mainstreamed/.(Last accessed October 23, 2013
33. Rustici G, Kolesnikov N, Brandiz, M, et al. ArrayExpress update-Trends in database growth, and links to data analysis tools. Nucleic Acids Res 2013; 41: D987-990.
34. Barrett T, Wilhite SE, Ledoux P, et al. NCBI GEO: archive for functional genomics datasets-update. Nucleic Acids Res. 2013; 41: D991-995.
35. Vizcaíno JA, Côté RG, Csordas A, et al. The Proteomics Identifications (PRIDE) database, and associated tools: status in 2013. Nucleic Acids Res. 2013; 41: D1063-1069.
36. Proteome Exchange. 2013. proteomexchange.org (Last accessed on October 23, 2013
37. Open Science Data Cloud. 2013. www.opensciencedata cloud.org (Last accessed on October 23, 2013
38. Dryad. 2013. datadryad.org (Last accessed on October 23, 2013
39. Higdon R, Stewart E, Stanberry L, et al. MOPED enables discoveries through consistently processed proteomics data. J Proteome Research 2013; Publication Date (web): November 18, 2013.
40. Kolker E, Higdon R, Haynes W, et al. MOPED: Model Organism Protein Expression Database. Nucleic Acids Research 2012; 40: D1093-D1099.