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-   -   output format content & tag mayhem (http://seqanswers.com/forums/showthread.php?t=4886)

alperyilmaz 04-28-2010 01:07 PM

output format content & tag mayhem
 
(Eric already got this question and wanted me to post it here as well)

1. Currently, when people click on a output format, they see an empty page (at least the ones i checked). I think it will be nice to create a form for output format and allow people to paste 5-10 lines of sample and then explain each column in format.

2. Tagging of operating system, programming language, method and domain is great but I think it needs standardization (check out MacOSX variants).
I was trying to clean it up by updating each entry one by one. it's very slow, if there's an alternative interface (commandline, perl,..) to do this faster, I can do the cleanup..

dan 05-02-2010 02:31 PM

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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