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
