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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
> <[log in to unmask]> 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 <[log in to unmask]> To:
>> [log in to unmask] 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
>>>> <[log in to unmask] <mailto:[log in to unmask]>> 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
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