Dear Jaime and Joel, Perhaps an easier solution would be to get the PDB to put an obvious link on each entry directing the user to the Proteopedia site for discussion and additional details. I would personally prefer a comments/discussion section on the PDB page, but as long as one is easily accessible I would be happy. By the way, you guys are doing a great job, and I will now go officially register on your site so that I can be user 2,601 ;-)
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 10:00 AM, Joel Sussman <[email protected]> wrote: > 15-May-2014 > Dear Martyn > Proteopedia's (http://proteopedia.org) goal goes well beyond just > education - it is aimed at Structural Biology and non Structural Biology > Community and it would be pleased to be a forum for discussion of structures > that are questionable. There are now over 2,600 registered users, who are > contributing to Proteopedia, in over 50 different countries. > Proteopedia has a special area for discussions related to each structure. > To access it, you go to the structure's page, e.g. > http://proteopedia.org/w/2x24 and click on the 'discussion' tab on the page's > upper border. Everyone can read the comments there, and it will open a fully > editable page for every registered user to add their comments on the > structure and their full name will be listed below their comments. > If you would like to contribute to this, we’d be pleased to welcome your > input. > Best regards, > Jaime Prilusky & Joel Sussman > > > On 15May, 2014, at 7:29, 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 >> >> >
