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 [email protected]
On 5/14/14 12:41 PM, "Nat Echols" <[email protected]> wrote: >On Wed, May 14, 2014 at 10:26 AM, Mark Wilson <[email protected]> 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 > > > >
