Hi Eric,

I was sure there was a Trello card for this, but I can't find it right now...

I've pushed this idea on the mailing list before, and in person at
the Galaxy Community Conference too. See also these threads:

http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html

http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010178.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?

i.e. We should not reinvent the wheel here ;)

Peter

On Tue, May 27, 2014 at 5:54 PM, James Taylor <james@jamestaylor.org> wrote:
> Eric, I'm very much in favor of this feature, and particularly the
> idea of generating a list of citations from a history or workflow. I
> imagine the only thing to quibble about will be the syntax. There are
> already some efforts to represent bibtex in xml (e.g.
> https://github.com/Zearin/BibTeXML), however they have always struck
> me as overly verbose.
>
> -- jt
>
>
> On Tue, May 27, 2014 at 12:45 PM, Eric Rasche <rasche.eric@yandex.ru> wrote:
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> I'd want to open up discussion on a feature I'd like to see. I'll try
>> and implement it if I can find time this summer. I didn't see a trello
>> card for anything like this yet, but please feel free to direct me there
>> if I missed it.
>>
>>
>> I'd like to see citations as a part of every tool.
>>
>> This would happen in the form of a <citation> block in the XML, which
>> would contain sub-elements with text. These sub-elements could be based
>> off of BibTeX, since they have existing specs for citing things:
>> https://en.wikipedia.org/wiki/BibTeX
>>
>> These citations would then be accessible in the HTML generated tool
>> pages, or via a View/Download button somewhere on the tool page. By
>> storing as an XML tree, we could render these citations as BibTeX
>> entries for the LaTeX users, and I believe there are ways to convert
>> BibTeX to EndNote XML and so on.
>>
>> This could be extended for use in workflows so that when you run
>> workflows, somehow a list of citations for all tools used could be
>> generated.
>>
>> Anyone have thoughts or opinions on this?
>>
>>
>>
>>
>> Using the example bibtex entry from the wikipedia page:
>>
>> @Book{abramowitz+stegun,
>>  author    = "Milton {Abramowitz} and Irene A. {Stegun}",
>>  title     = "Handbook of Mathematical Functions with
>>               Formulas, Graphs, and Mathematical Tables",
>>  publisher = "Dover",
>>  year      =  1964,
>>  address   = "New York",
>>  edition   = "ninth Dover printing, tenth GPO printing"
>> }
>>
>> I imagine it'd look like the following in a real-life tool:
>>
>> <tool>
>>   ...
>>   <citation type="book">
>>     <author>Milton Abramowitz and Irene A. Stegun"</author>
>>     <title>Handbook of Mathematical Functions with Formulas, Graphs, and
>> Mathematical Tables</title>
>>     <publisher>Dover</publisher>
>>     <year>1964</year>
>>     <address>New York</address>
>>     <edition>ninth Dover printing, tenth GPO printing</edition>
>>   </citation>
>> </tool>
>>
>>
>> Cheers,
>> Eric
>> - --
>> Eric Rasche
>> Programmer II
>> Center for Phage Technology
>> Texas A&M University
>> College Station, TX 77843
>> 404-692-2048
>> esr@tamu.edu
>> rasche.eric@yandex.ru
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