As hinted at in the Trello card Greg posted, it could be much simpler if
the citation tag just took a DOI. It appears that the DOI to bibtex
conversion can be done by Crossref:
http://tex.stackexchange.com/questions/6848/automatically-dereference-doi-to-bib

-Will



On Tue, May 27, 2014 at 10:16 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:

> Peter, this may be the Trello card you were thinking of.
>
> https://trello.com/c/kY7RCnd0/95-tool-shed-citation-for-tools-dois
>
> Greg Von Kuster
>
>
> On May 27, 2014, at 1:09 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>
> > 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 <ja...@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.e...@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
> >>> e...@tamu.edu
> >>> rasche.e...@yandex.ru
> >>> -----BEGIN PGP SIGNATURE-----
> >>> Version: GnuPG v2.0.17 (GNU/Linux)
> >>>
> >>> iQIcBAEBAgAGBQJThMEUAAoJEMqDXdrsMcpVe9AP/1BjPbP5JdK6KDybOeV2ElvC
> >>> jvmUGetAjdQzkKO1Ikeuxb46yp0j4abAGGG92AccxlBYALsT3jsPv5dYjm505vcU
> >>> IwlfTBE7gc5y19x3zx1CuAd7PB11tryODz2LwXNKI75f39bNdX6Qe5aA74Vn/k8a
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> >>> qkk4U6gBcmcFolCeItlLPa/C4uiyOK2wVWHyTnEeKjdpD6dwLuemRmwtZrModbQu
> >>> PPPFkKzQhUnh5Wgq8TIP4kSc2t1/jSpdV8MHqM0piqOFnR52fExPrwLn82WEFcp8
> >>> tXfHHTaZj+6gL+IGswdAgqvxk1V+6QTjH57igWmYtcENpIDbhZVBh+HOD8SS2qdv
> >>> ohwFg/Vn8VrCeTGGehNSBvkam0HXjXXq7mZ8W4xrOS8vxv8HPAFZHze2sPlUG/Ob
> >>> WeOdiLgD2HCH95SXYDDBNFG6HwFkLETA3DjpfvgHqPdaLmEfIZW+ks1WF9RG+Pmo
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> >>> 7Vu5UFeL8gcigRmQv5NA
> >>> =ceAo
> >>> -----END PGP SIGNATURE-----
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