Dear Zachary I once suggested this sort of discussion forum to a PDB PI as a possible service that could be a ' validation fight-club ' - which suggestion was not well received ;) But as you say it is down to setting the correct professional tone.
One thing that would allow a visual discussion would be the possibility to share molecular representations - similar to the way Proteopedia uses Jmol scripting to drive the graphics from the webpages. In this way commentators could share viewpoint and representations to make their points. This would make it most useful to the wider biological community. all the best Martyn ________________________________ From: Zachary Wood <[email protected]> To: [email protected] Sent: Thursday, 15 May 2014, 14:47 Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone 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----- > >
