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Old 05-02-2010, 02:31 PM   #2
dan
wiki wiki
 
Location: Cambridge, England

Join Date: Jul 2008
Posts: 266
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Yup, it helps to get wiki questions in one place here, if only to start getting a community together :-)


To answer point 1)

I set it up so that output and input format *should* take you to a form to describe the format (for example, try looking at the sam or fasta formats, where the form was used to create the page). I'm not sure why you are being taken to an empty page, so I'll have a look. I think it's a great idea to have forms to describe formats. If we get the ball rolling on this, SEQwiki could quickly be the biggest file format resource for bioinformatics on the web!

To answer point 2)

About cleaning up the tags... I know what you mean! My long term plan is to integrate the wiki with the EMBRACE software ontology (or similar), to provide a strict, community developed controlled vocabulary for describing bioinformatics software. I've been talking with Jon Ison and some people from 'BioCatalogue' about that. Unfortunately I haven't got round to that yet :-/

The next best thing is to decide how the tags should be used, and document that better on the form.

I noticed the 'MacOSX' heterogeneity too... wherever you think it appropriate, we can make the free text entries into drop down boxes (based on existing values) to provide a much stricter entry system (users would have to go through several steps to add a new value to the set of existing values). I've shied away from enforcing values on the user, but in some cases its probably appropriate.

Finally, yup, there is a Perl interface via the MW API!

* http://www.mediawiki.org/wiki/API
* http://www.mediawiki.org/wiki/API:Client_code


This is the one I've been using (not a particular vote of confidence, but I'm familiar enough with it / have example scripts written using it):

* http://search.cpan.org/~exobuzz/MediaWiki-API/


I'll post some examples of bots I've written using this framework on the wiki itself. If you write a bot, don't forget to set the bot bit on your edits! It hides them from the default 'recent changes' lists.

All the best,
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Homepage: Dan Bolser
MetaBase the database of biological databases.
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