Open Access Highly Accessed Open Badges Database

GCOD - GeneChip Oncology Database

Fenglong Liu, Joseph A White*, Corina Antonescu, Daniel Gusenleitner and John Quackenbush

BMC Bioinformatics 2011, 12:46  doi:10.1186/1471-2105-12-46

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Misleading representation of existing databases

Philip Zimmermann   (2013-03-08 16:57)  NEBION email

The resource presented in this paper is interesting and beneficial for the cancer research community. I would like to thank this team for making it available. It's a pity, however, that the authors have not accurately represented existing databases - ArrayExpress, Oncomine and Genevestigator. For example, the claim that Oncomine and Genevestigator "focus on analyses of subsets of the data and neither fully addresses the problem of integration across studies" is wrong. In fact, Genevestigator data is normalized using a global scheme that allows integration across studies, and its tools are specialized on global type analyzes rather than looking at individual experiments in detail. As far as I know Oncomine also has made a major effort to integrate data across studies.
Another false statement is that "Genevestigator only includes data from GEO and not those from ArrayExpress". The truth is, Genevestigator included ArrayExpress data already in 2004, long before including those from GEO.
I fully understand that to be able to publish one's own work, it is important to show where we offer an improvement over existing solutions. But the comparison must be done accurately and avoid any type of misrepresentation, especially since this type of publication is perceived as peer-reviewed and thereby authoritative.

Competing interests

In part, since we develop a solution that they compare with in the introduction, but our platform is not restricted to oncology and also covers many other disease areas.


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