Thursday, 23 October 2014

Which journals release more public proteomics data!!!

I'm a big fan of data and the -omics family. Also, I like the idea of make more & more our data public available for others, not only for reuse, but also to guarantee the reproducibility and quality assessment of the results (Making proteomics data accessible and reusable: Current state of proteomics databases and repositories). I'm wondering which of these journals (list - http://scholar.google.co.uk/) encourages their submitters and authors to make their data publicly available:



Journal
h5-index
h5-median
Molecular & Cellular Proteomics
74
101
Journal of Proteome Research
70
91
Proteomics
60
76
Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics
52
78
Journal of Proteomics
49
60
Proteomics - Clinical Applications
35
43
Proteome Science
23
32

After a simple statistic, based on PRIDE data:


Number of PRIDE projects by Journal


The final list:


Mol Cell Proteomics
88
J Proteome Res
71
Proteomics
51
PLoS One
25
J Proteomics
13
Nat Commun
12
BMC Microbiol
6
Proc Natl Acad Sci U S A
6
Anal Chem
5
Cell Rep
5
Nature
4
Antioxid Redox Signal
3
Electrophoresis
3
Front Microbiol
3
Biol Reprod
2
BMC Biol
2
BMC Genomics
2
Cell Commun Signal
2
Clin Proteomics
2
Elife
2
EMBO J
2
Fungal Genet Biol
2
Genome Biol
2
J Am Soc Nephrol
2
J Immunol
2
Mol Syst Biol
2
Nucleic Acids Res
2
PLoS Genet
2
Sci Signal
2
BMC Syst Biol
2
Electrophoresis
2
Science
2
Mol Cell Biol
2
Proteome Sci
2

Plos One the open access peer-reviewed scientific journal published by the Public Library of Science (PLOS) is one of the big contributors to PRIDE and ProteomeXchange. This fact can be related with the type of authors submitting papers to Plos One. Plos One philosophy is be as more open and possible and most of the authors know how to make visible their manuscript data. Molecular Cell Proteomics , Journal of Proteome Research and Proteomics have encouraged the authors to make public their data for years. In contrast other journals more close to the proteomics topic are far from the top like Analytical Chemistry, Electrophoresis or Proteome Science.

More interesting than that, more than 700 projects in PRIDE do not have a publication behind. It means that the community enjoy the idea of make public their data to be reuse, analyse and inspect by others. Data sharing in proteomics is now a mature field [1], authors know from other fields like software development and the open-source movement [2] that they can advance and progress more if they share.  Hopefully in the near future we will see in every proteomics journal a box asking if you made your data public and requesting the url.

[1] Perez-Riverol Y. et al. Making proteomics data accessible and reusable: Current state of proteomics databases and repositories. Proteomics. 2014 Aug 26. doi: 10.1002/pmic.201400302. [Epub ahead of print]

[2] Perez-Riverol Y et al. Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective. Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):63-76. doi: 10.1016/j.bbapap.2013.02.032. Epub 2013 Mar 1.