[Bioperl-l] TFBS databases, Bio::Matrix::PSM suitable?

Sendu Bala bix at sendu.me.uk
Tue Aug 22 11:47:46 EDT 2006


Chris Fields wrote:
> ...
> My opinion: if the data is publicly available and we can use a subset for
> testing, I have no problem with what Sendu proposes.  If there are
> copyright/patent/legal issue, we must figure out what the restrictions are
> on their use (i.e. do the restrictions cover the data, the format, any use
> of the format (including manipulation, the use of TRANSFAC as a name, etc).

I've sent an email to their support address (though this may take a long 
time to get a reply to, going on past experience).

This is the full legal spiel they have:
http://www.gene-regulation.com/pub/databases/transfac/doc/misc.html

There's nothing about restrictions on using the data format, they 
haven't tried to shut down the TFBS:: modules, and it would be illegal 
for them to do so according to fair use in many countries, their home 
country of Germany especially. In short, the module itself would not be 
a problem. The only cause for concern is the test data, which is not 
possible without express permission. I've asked for permission so now we 
just wait.


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