-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Will,
Nice! I follow the tex.SE and missed that one. That's incredibly useful. I believe the final implementation will include both options (doi/citation) Jim, Great, agreed. I want to represent non-published/non-DOI materials, so this is better than restricting to DOI-only materials. PROV + dublin core would be good for a reference implementation and we can build outwards from there if we need special entries. My background of LaTeX pushed me in BibTeX, but these are definitely better options in terms of generalising the implementation. Cheers, Eric On 05/27/2014 12:21 PM, Will Holtz wrote: > 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 > <mailto: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 > <mailto: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 <mailto: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 <mailto:rasche.e...@yandex.ru>> wrote: > 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 > >>> ___________________________________________________________ > >>> Please keep all replies on the list by using "reply all" > >>> in your mail client. To manage your subscriptions to this > >>> and other Galaxy lists, please use the interface at: > >>> http://lists.bx.psu.edu/ > >>> > >>> To search Galaxy mailing lists use the unified search at: > >>> http://galaxyproject.org/search/mailinglists/ > >> ___________________________________________________________ > >> Please keep all replies on the list by using "reply all" > >> in your mail client. To manage your subscriptions to this > >> and other Galaxy lists, please use the interface at: > >> http://lists.bx.psu.edu/ > >> > >> To search Galaxy mailing lists use the unified search at: > >> http://galaxyproject.org/search/mailinglists/ > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > - -- Эрик Раше -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) iQIcBAEBAgAGBQJThMtxAAoJEMqDXdrsMcpV25cQAJcYgwcusxEyZIRqKS/v/KH3 2YKRIajITJ6TqDQuUkL+QC/4/adc5TNxE11M4eJZSdjVolUgMGyOxPz4+44hWS+z gbgn767RW2b4+RQCKb5HD1WHheKusrZ4ZYoPCV+m52fLjTYhH/WXBP3WvYH4V2DS MV3MYgigVJ1YNrs7M/raPP6p21Rf07m3cgDhSKn4dlNKHAoMLewzSzcKUNWbpF+k jMdfjRfTPvKN3+Xr9HSyTGAzaEXJO7G7aPPtd0mgD5qcvlav7Tu72/RbycAT1J1g 5WioExlqHLSpx2/nm6z3cXfqcKMwTBVLU2QzFrbTisuWD9SJ1HPCLcvwbhi9yIwx ne1y745DhByyVWgfxjWWKoLX6l8WBQ/Db/ueqn5J3IfERnibQKBLzw9sy4XHTYvv jYpJ7V797aPodq4oCXARlAIgnUVqDjkeimeiZRm+jC6glMWmrgYsaaHYdv4L+JDS L3gB4SGmtxVypwfTRMy9II9JhEYhCIUQGVC4FtriFSUS5dXvTHgfO7+kle9jN2xz oE16hl9AkUkQrViOHS/61RSsA8GsTaUs8yx0HnZsD5GSAhctPS3lte35SYb1NZlJ WtyOO/eJAP0A6+Ink5TzSousexDCHXlwj+IrDJKVifdyCqoes4nuVRWeL83xxNaN 8c+Oxf83TD8eHNjKhP2Z =J15M -----END PGP SIGNATURE----- ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
