Re: Can "PDB" license be considered free ?
On Tue, 08 Mar 2016, Bas Wijnen wrote:
> On Mon, Mar 07, 2016 at 04:38:55PM -0600, Don Armstrong wrote:
> > On Mon, 07 Mar 2016, Peter Rice wrote:
> > > The conclusion was that scientific data (SwissProt, PDB, etc.) are
> > > scientific facts and it is not reasonable to require permission to
> > > change them.
> >
> > This isn't true; there are loads of reasons to change sequences and
> > structural models of proteins. Protein sequences are just based on
> > references which have inaccuracies and do not represent ancestral
> > sequences or the true variation present in real populations; in my lab
> > we modify UniProt sequences and redistribute those modifications in
> > publications all of the time.
>
> Note that this text only says that if you modify things, you're
> required to change the name.
The text also says
Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are
free of all copyright restrictions and made fully and freely
available for both non-commercial and commercial use.
So I suspect that this is yet-another case of confusion about what
copyright means and licensing allows you to do.
But that said, the DFSG allows us to redistribute software which
requires renaming.
However, the restriction on modifying "HEADER, CAVEAT, REVDAT, SPRSDE,
DBREF, SEQADV, and MODRES" isn't DFSG compatible, as those are records
in the PDB file which one would actually want to modify if someone was
redistributing a PDB which had been renamed to avoid confusion.
I suspect this is an oversight, and someone could communicate with the
PDB group to get this resolved during their next meeting.
Does anyone on the -med group have contacts with any of the PDB groups?
--
Don Armstrong http://www.donarmstrong.com
[T]he question of whether Machines Can Think, [...] is about as
relevant as the question of whether Submarines Can Swim.
-- Edsger W. Dijkstra "The threats to computing science"
Reply to: