[Proteopedia] NMR format, bot tasks

Eran Hodis eran.hodis at weizmann.ac.il
Sun Feb 8 12:59:48 EST 2009


Thanks for the suggestions Dan.  In particular, DPL looks quite  
interesting.

Eran
On Feb 8, 2009, at 4:44 PM, Dan Bolser wrote:

> 2009/2/8 Eran Hodis <eran.hodis at weizmann.ac.il>:
>> Hi Ralf,
>>
>>
>> On Feb 8, 2009, at 12:10 PM, Ralf Stephan wrote:
>>
>>> Hello,
>>> first, to introduce myself, I'm an IT guy, privately interested
>>> in molecular biology. After writing some time for the german  
>>> language
>>> Wikipedia, the lack of 3D visualisation for my protein pages drove
>>> me to Proteopedia. At the moment, I'm playing.
>>>
>>> Does someone of you know where code can be had that collects
>>> several structures into one, presumably using the NMR format?
>>> I know it's easy to do but why reinvent the wheel...
>>>
>>> The question, however, that's bothering me is that IMHO there should
>>> be a link from any structure page to that topic pages where the
>>> structure is used. It could be text like 'See also the topics:' at
>>> the top or a row in the info box 'Topic pages:' or a paragraph in
>>> the section 'About this structure' reading e.g. 'This structure is
>>> also used in the pages ...'
>>>
>>> Since it can't be relied on that authors do such backlinks, and this
>>> can be automatized, it should be automatized at some time.
>>
>> That's a really great idea if it can be done well. How would you  
>> suggest
>> doing this (of course automatically)?  Let's say you're on the page  
>> for
>> 1ea5, do you want to list, on the page for 1ea5, all other pages  
>> that link
>> to 1ea5?  Or all other pages that link to 1ea5 but are not PDB- 
>> entry pages?
>> I'm just worried that such an automatically generated list might,  
>> in some
>> instances, be long and irrelevant.  Of course as you've said, the  
>> person who
>> created the Topic page should link from the topic page to the PDB  
>> entry page
>> and vice versa, but they will sometimes neglect to do this.
>>
>>>
>>>
>>> On another note, I would like to see a list of all structure pages
>>> that have been enhanced by other authors than OCA. This should be
>>> automatized, too.
>>
>> Eric, at one point you were interested in such a list -- what did  
>> you do?
>
> We do something similar over on PDBWiki using an extension known as  
> DPL.
>
> http://www.mediawiki.org/wiki/Extension:DynamicPageList
>
>
> This allows us to write a query that generates a list of structure
> pages that have been edited by users other than 'our bot'. We then
> tailor the output format of the resulting list (again using DPL
> syntax) to generate a click-able list of PDB IDs or a gallery of PDB
> images (see the Main Page at http://PDBWiki.Org for some examples).
>
> Please feel free to use PDBWiki to learn about and to experiment  
> with DPL.
>
>
> Just thinking about it now, DPL should also be able to create the list
> of structure 'back links' that is discussed above. i.e. instead of
> calculating this list 'off line' and updating every structure page
> with the result, inserting an appropriate DPL query into the structure
> template would generate this list automatically.
>
>
>>> Which leads me to the question, is there a way of running a bot like
>>> in Wikipedia? I have a one time experience with writing a bot and
>>> would be willing to write something that does the abovementioned
>>> tasks in Proteopedia.
>>
>> Good to know! Let's brainstorm this idea a bit further before  
>> talking about
>> implementation. As Jaime said, there are currently no user-owned  
>> bots on
>> Proteopedia, so, at least for now, we would run your bot for you.
>
> It may not be policy, but I'd just like to point out that any user
> account can be accessed by a bot. Having a specific bot account makes
> the bot edits a bit cleaner, but its not a technical requirement.
> Recently I've been using the Perl MediaWiki::API 'framework' to script
> queries and edits on the MetaBase wiki, http://MetaDatabase.org. If
> your running a recent version of MediaWiki, the API is a very
> convenient way to perform such automatic tasks.
>
> http://search.cpan.org/dist/MediaWiki-API/lib/MediaWiki/API.pm
>
>
> All the best,
> Dan.
>
>> Eran
>>>
>>>
>>>
>>> Regards,
>>> ralf
>>>
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>>
>> Eran Hodis
>> eran.hodis at weizmann.ac.il
>>
>>
>>
>>
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>>
>
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Eran Hodis
eran.hodis at weizmann.ac.il






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