Hi Peter,

Thanks, I didn't realise it had been discussed!

I don't know what would be a good markup system for citations.
However, the current situation is that people are putting their
citations into the <help> tag with no special markup, and it seems to
work reasonably well. Maybe a simple field is all that's needed?


On 18 June 2012 19:50, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Mon, Jun 18, 2012 at 10:29 AM, Clare Sloggett <s...@unimelb.edu.au> wrote:
>> Hi all,
>> I'd like to suggest, or request, a feature - I think that posting to
>> galaxy-dev is the right place to start?
>> After I've done an analysis, it would be useful to be given a list of
>> references for all the tools I used in that history, which I could use
>> to cite the appropriate papers.
>> At the moment, it seems that most tool developers add a "please cite
>> the following paper" note to the <help> tag in the wrapper so that it
>> displays on the tool screen before you run it. I'd like to suggest:
>> * adding a <cite> tag to the tool wrappers xml,
>> * adding a feature to the history UI which will list all the
>> references to cite for the a history.
>> I think this would encourage people to cite the tools they use
>> properly and hence encourage developers to put their tools into the
>> toolshed! With the standard tools moving into the toolshed it will be
>> really important for tool wrappers to be maintained.
>> Any thoughts?
>> Clare
> Hi Clare,
> We talked about this at the end of last year, and yes, it would
> be a good idea:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html
> Are you familiar enough with the area of semantic web/linked
> data to know what would be the best XML based markup to
> use for embedding the citations?
> Peter


Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357          M: 0414 854 759

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