As one of the responsible people for the pdbwiki project I feel I should
comment on this one. We went out of business simply for lack of
resources, it was difficult to keep things up-to-date and specially it
was very difficult to combat spam. So in the end we decided to shut down
the project.
In any case we always thought of the project more as a proof-of-concept
than anything else. We wanted to show that a community-driven feedback
and annotation system is needed for the PDB. I personally think that if
such a system were to be set up by the PDB, it would be a great service
for anyone (including the PDB themselves since some of that feedback
could eventually go back to the main database).
In my opinion the system should stay as open as possible, allowing
anyone to comment. The community can self-moderate it and do continuous
reviewing. This kind of system is already used in many places and works
extremely well. See for instance stackoverflow.com for computing-related
questions, or even biostars.org for bioinformatics-related ones.
Upvoting/downvoting together with user-scoring mechanisms produce
stunningly good results.
Just my 2 cents
Jose
On 15/05/14 13:29, MARTYN SYMMONS 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 <merr...@u.washington.edu>
*To:* CCP4BB@JISCMAIL.AC.UK
*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 <z...@bmb.uga.edu
<mailto:z...@bmb.uga.edu>
> > <mailto:z...@bmb.uga.edu <mailto:z...@bmb.uga.edu>>> 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
