Adding to Tim’s comment, I would not expect a tremendous amount of spurious comments about a single PDB out of 100,000 unless there was a problem. Especially if the Pubmed Commons model was applied, and only depositors could comment. I would assume this would be very beneficial, given that we are conscientious professionals. Could actually be a great forum for authors to go a little deeper into specific approaches or problems that they had with a structure. Not all interesting details make it to the pub.
Best regards, Z *********************************************** Zachary A. Wood, Ph.D. Associate Professor Department of Biochemistry & Molecular Biology University of Georgia Life Sciences Building, Rm A426B 120 Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab: 706-583-0303 FAX: 706-542-1738 *********************************************** On May 15, 2014, at 9:39 AM, Tim Gruene <[email protected]> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear all, > > isn't the ccp4bb a very good example that spam may not be such an > issue for a discussion platform on structures in the PDB? There is a > great variety of opinions, some to agree with, some to disagree, but > all of them interesting and contributing, and I hardly remember a > message I would classify as spam. And it all works without restraints. > > Best, > Tim > > > On 05/15/2014 03:21 PM, Zachary Wood wrote: >> I agree with Martyn, >> >> Pubmed Commons could be a great model. I believe you have to be a >> published author to obtain an account. It might cut down on some of >> the spam/noise if the PDB adopted such a model for depositors. >> >> Best regards, >> >> Z >> >> >> *********************************************** Zachary A. Wood, >> Ph.D. Associate Professor Department of Biochemistry & Molecular >> Biology University of Georgia Life Sciences Building, Rm A426B 120 >> Green Street Athens, GA 30602-7229 Office: 706-583-0304 Lab: >> 706-583-0303 FAX: 706-542-1738 >> *********************************************** >> >> >> >> >> >> >> >> On May 15, 2014, at 7:29 AM, MARTYN SYMMONS >> <[email protected]> wrote: >> >>> I agree some forum for community annotation and commenting would >>> be a good thing for users of structural data. There was an >>> attempt to do that with the pdbwiki project which was a community >>> resource for the bioinformatics community. Unfortunately pdbwiki >>> has now folded (see http://pdbwiki.org/) They are now directing >>> people to Proteopedia. However Proteopedia has a more educative >>> focus I think - rather than capturing technical questions and >>> input. >>> >>> Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), >>> which is a forum for discussing the literature, is currently >>> under testing. Perhaps this is the sort of thing that could work >>> for structural data? >>> >>> cheers Martyn >>> >>> From: Ethan A Merritt <[email protected]> To: >>> [email protected] Sent: Wednesday, 14 May 2014, 19:22 >>> Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone >>> >>> On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote: >>>> As long as it's just a Technical Comments section - an obvious >>>> concern would be the signal/noise in the comments themselves. >>>> I'm sure PDB would not relish having to moderate that lot. >>>> >>>> Alternatively PDB can overtly link to papers that discuss >>>> technical issues that reference the particular structure - >>>> wrong or fraudulent structures are often associated with >>>> refereed publications that point that out, and structures with >>>> significant errors often show up in that way too. I once did a >>>> journal club on Muller (2013) Acta Cryst F69:1071-1076 and wish >>>> that could be associated with the relevant PDB file(s). >>> >>> Perhaps some combination of those two ideas? >>> >>> The PDB could associate with each deposited structure a >>> crowd-sourced list of published articles citing it. They >>> already make an effort to attach the primary citation, but so far >>> as I know there is currently no effort to track subsequent >>> citations. >>> >>> While spam comments in a free-format forum are probably >>> inevitable, spam submission of citing papers seems less likely to >>> be a problem. >>> >>> - Ethan >>> >>>>> On Wed, May 14, 2014 at 12:32 PM, Zachary Wood >>>>> <[email protected] <mailto:[email protected]>> wrote: >>>>> >>>>> Hello All, >>>>> >>>>> Instead of placing the additional burden of policing on the >>>>> good people at the PDB, perhaps the entry page for each >>>>> structure could contain a comments section. Then the >>>>> community could point out serious concerns for the less >>>>> informed users. At least that will give users some warning in >>>>> the case of particularly worrisome structures. The authors of >>>>> course could still reply to defend their structure, and it >>>>> may encourage some people to even correct their errors. >>>>> >>> -- Ethan A Merritt Biomolecular Structure Center, K-428 Health >>> Sciences Bldg MS 357742, University of Washington, Seattle >>> 98195-7742 >>> >>> >> >> > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Icedove - http://www.enigmail.net/ > > iD8DBQFTdMOTUxlJ7aRr7hoRAinqAJ9tAzMX6DSeFO7hiyEEqFhCPV7IxQCgg0Ay > Ya6HwJD/ugPU1dwGHNAJfkQ= > =JABI > -----END PGP SIGNATURE----- >
