Thank you for your efforts to try to resolve the ongoing dispute with regards to Dr. Stein’s decision to “split/fork” the BioMart code base and eventually eliminate BioMart altogether in order to re-create a new ICGC data management solution. I am disappointed that you have remained unreceptive to the proposed amendments to the review process of Dr Stein/OICR’s decision included in my open letter dated December 11th, 2012. I am also disappointed that despite numerous requests Dr. Stein/OICR have been unable to provide scientific rationale for this decision. Finally, I find it quite disconcerting that contrary to public re-assurances made by Dr. Stein in his email dated January 23rd 2012, OICR continues referring to BioMart under a different name to attract funding.
I am concerned that by not addressing these issues we are allowing the situation to deteriorate further. I would like to respectfully remind you that in 2007 a disagreement between Dr. Stein and Editor-in-Chief of the Genome Knowledgebase (later renamed to Reactome) deteriorated so much that eventually became the subject of legal proceedings (Joshi-Tope v. Cold Spring Harbor Laboratory et al, U.S. District Court Eastern District of New York, case number 2:07-cv-03346. All information regarding this case is in a public domain and accessible to anyone who registers with the Public Access to Court Electronic Records (PACER) service (http://www.pacer.gov/)).
I have no doubt that Dr. Stein/OICR are as keen as I am to achieve a more positive resolution this time. To facilitate this process, I have decided to request help on our behalf from OICR’s major funder, the Ontario Ministry for Research and Innovation. I intend to:
Such clarification would be helpful since as I've mentioned in a number of previous email exchanges, this decision is problematic for the ICGC and the rest of the scientific community as it leads to incompatibilities and thus impedes collaborations and creates problems for users. I had an opportunity to experience these problems first hand whilst embarking on a new project on behalf of a major translational institute. I am yet to comprehend why, given all these problems it was so critical for Dr. Stein/OICR to dismantle perfectly working ICGC data management system that I put in place. Considering OICR has spent millions of dollars on BioMart’s development, which has proved to be a highly innovative, successful and publicised data management solution, it seems absurd to reinvent the wheel, thereby wasting time and public funding to simply remove the BioMart brand from the ICGC.
I am convinced that the Ministry will agree with me that it will be in the best interest of the scientific community if OICR revokes Dr. Stein’s decision and restores single BioMart code base. This would rectify the multiple problems Dr. Stein/OICR’s decision creates, make data available to a much wider scientific audience, deliver all the solutions that are required in a fraction of time but most importantly would save the funding agencies the millions of dollars that would be required to unnecessarily develop a new ICGC data management system. I would like to add that the BioMart community is prepared to provide their top expertise to guide OICR through the process of restoring the single BioMart code base to ensure a smooth transition.
I look forward to discussing with you what communication to make to the Ministry, failing which; I will provide my own communication.
Arek Kasprzyk, MD, MSc, PhDBioMart Project Lead
On 15 April 2013 14:35, Arek Kasprzyk <[hidden email]> wrote:
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