Hi Nat,
I agree that journals should be doing the heavy lifting here, for the
reasons that you note. I also want to be clear that I believe the PDB is a
crowning achievement of transparency and open access in the sciences,
which is one reason that I am so concerned about this issue. I am in no
way trying to impugn the hard and superb work that they have done over
many decades. I still contend, however, that having models whose
integrity is highly suspect lurking in the PDB with no indications of
problems beyond a dodgy validation report is a non-optimal outcome. As
for the meaning of integrity, I'm using this word in place of others that
might be considered more legally actionable. A franker conversation would
likely more clearly draw the line that we're wrestling with here.
Best regards,
Mark
Mark A. Wilson
Associate Professor
Department of Biochemistry/Redox Biology Center
University of Nebraska
N118 Beadle Center
1901 Vine Street
Lincoln, NE 68588
(402) 472-3626
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On 5/14/14 12:41 PM, "Nat Echols" <[log in to unmask]> wrote:
>On Wed, May 14, 2014 at 10:26 AM, Mark Wilson <[log in to unmask]> wrote:
>
>Getting to Eric's point about an impasse, if the PDB will not claim the
>authority to safeguard the integrity of their holdings (as per their
>quoted statement in Bernhard's message below), then who can?
>
>
>
>I think this may in part boil down to a semantic dispute over the meaning
>of "integrity". I interpreted it to mean "integrity (and public
>availability) of the data as deposited by the authors", which by itself
>is quite a lot of work. Safeguarding
> the integrity of the peer-review process is supposed to be the job of
>the journals, some of which - unlike the PDB - are making a tidy profit
>from our efforts. Since they justify this profit based on the value they
>supposedly add as gatekeepers, I don't think
> it's unreasonable for us to expect them to do their job, rather than
>leave it to the PDB annotators, who surely have enough to deal with.
>
>
>I do share some of the concern about 2hr0, but I am curious where the
>line should be drawn. This is an extraordinary case where the
>researcher's institution requested retraction, but I think everyone who's
>been in this field for a while has
> a list of dodgy structures that they think should be retracted - not
>always with justification.
>
>
>-Nat
>
>
>
>
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