[Proteopedia] NMR format, bot tasks

Dan Bolser dan.bolser at gmail.com
Sun Feb 8 09:44:46 EST 2009

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.


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,

> Eran
>> Regards,
>> ralf
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> Eran Hodis
> eran.hodis at weizmann.ac.il
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