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:
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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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux)
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