[MOBY-l] How will MOBY provide for proprietary information suppliers?

[Richard J. Feldmann]

Dear BioMOBY Correspondents,

I attended the MOBY and Ontology session at the Plant and Animal 
Genome (PAG) meeting in San Diego in January.  It was a very 
impressive session.  Subsequently I wrote an e-mail to Mark Wilkinson 
about how I could (1) work toward inserting my (hopefully soon to be) 
patented discovery of connectrons into the gene ontology, (2) get 
some graphics working with GMOD and (3) using BioMOBY to be the 
information broker.  In my view, connectrons will be "the greatest 
thing since sliced bread" and can be a good way to make MOBY popular 
and useful.

A connectron is a 4-sequence construct that regulates gene 
expression.  Two sequences are in the 3'UTR of some genes.  When 
promoted and expressed, the RNA tropes around in the cell/nucleus to 
find two cognate ds DNA sequences.  The RNA forms two linked 
triple-stranded generalized Hoogsteen helices.  The loop between the 
two DNA sequences can be up to 100kb.  The loop stabilizes into 30nm 
chromatin structure and the included genes are then not capable of 
being expressed because they are tied up in the chromatin structure. 
We have preliminary experiments In the NCI in progress to prove 
physically that this hypothesis is true.  In advance of physical, I 
have computationally processed over 100 genomes from NCBI to 
determine their connectron structure.  There are connectrons in good 
numbers in all prokaryotic, Archeal and eukaryotic genomes that I 
have investigated.

I would like to offer information to the world on all the connectron 
structure of all genomes.  BioMOBY seems like an ideal mechanism. 
Mark Wilkinson, however, says that BioMOBY has not yet made 
provisions for proprietary information.

My goal is that every scientist in the world should be able to have 
and use connectron information supplied by Global Determinants, Inc. 
- the sole license vendor of our Intellectual Property (IP) - for 
research purposes for free.  However, when products using the 
connectron technology are developed, Global will insist that a 
license be obtained by the product manufacturer.  I view this as a 
reasonable strategy.

I would like to discuss with you'all the idea of how I could supply 
proprietary information using BioMOBY.  From my point of view, all 
that would be necessary is that the user would have to do the 
equivalent of "breaking the software package seal".  This could be 
accomplished by having the potential information recipient print a 
form, sign it, and fax it to Global.  Global would then send BioMOBY 
a signal releasing the data to that person.  Anyone who had signed 
the form could then access the connectron structure of all genomes.

I hope that we can come to a "balanced" view of this issue.


Richard J. Feldmann.
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  Richard J. Feldmann                                 (v) 301-926-0921
  Global Determinants, Inc.                         (f) 301-926-7954
  17800 Mill Creek Dr.                                (c) 301-526-8524
  Derwood, Maryland 20855-1019       rjfeldma at erols.com 
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