[Proteopedia] NMR format, bot tasks
eran.hodis at weizmann.ac.il
Sun Feb 8 12:59:48 EST 2009
Thanks for the suggestions Dan. In particular, DPL looks quite
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:
>>> first, to introduce myself, I'm an IT guy, privately interested
>>> in molecular biology. After writing some time for the german
>>> 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
>> doing this (of course automatically)? Let's say you're on the page
>> 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
> 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.
> All the best,
>>> Proteopedialist-for-users mailing list
>>> Proteopedialist-for-users at bioinformatics.org
>> Eran Hodis
>> eran.hodis at weizmann.ac.il
>> Proteopedialist-for-users mailing list
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eran.hodis at weizmann.ac.il
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