Maybe a prominent link in the summary page of e.g. PDBe 2a01 would help. So far, you need to go there and expand Links -> pdb_redo -> links -> Proteopedia to get to the corresponding warning.
http://www.ebi.ac.uk/pdbe-srv/view/entry/2a01/summary_details.html# http://www.cmbi.ru.nl/pdb_redo/a0/2a01/index.html http://proteopedia.org/wiki/index.php/2a01 'More information about this (or any) entry may be available in Proteopedia' Best, BR Ceterum censeo structurae Murthius delendati erunt. (Marcus Tullius Raaijmakers) From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Joel Sussman Sent: Donnerstag, 15. Mai 2014 16:01 To: [email protected] Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone 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
