[Proteopedia] NMR format, bot tasks

Eran Hodis eran.hodis at weizmann.ac.il
Tue Feb 10 05:40:25 EST 2009

Hi Ralf,

We're concerned about DPL exerting too much load on the server. Please talk to Jaime about this.


-----Original Message-----
>From Ralf Stephan <ralf at ark.in-berlin.de>
Sent Tue 2/10/2009 10:30 AM
To Forum for the Proteopedia User Community <proteopedialist-for-users at bioinformatics.org>
Subject Re: [Proteopedia] NMR format, bot tasks

[Reposted. Sorry if you see this twice]

Dan wrote 
> >> 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

Thanks for that link. Indeed, it should be possible to implement
something approximating my ideas using DPL.

1) What appears possible: having a link on each structure page
   'List topics where this structure is used in a scene'.
   Pages are selected according to the title matching a regexp AND
   the content matching a regexp (titleregexp, includematch)
2) What appears possible: a link somewhere that lists all structure
   pages in a specific category (like Single protein) or all structure
   pages in general (pages starting with digit) where the last
   change was not done by OCA (notlastmodifiedby).

As this is more or less what I intended, and writing and running a bot
is so much more hassle, I'm all for installing DPL on the server.


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