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 >> FBeFL/EvkZwI8Z6CvuTGtZrEHvDXVvTFoxMX875f59g2vNy7W8Fh5wQCQ8qgiogi >> 0SWGIGZ6OJdqX60h2hOjJ06NhzBcTsjQea+AwTo5wAkyGPFJy4DV78jKOvsd5PMG >> qkk4U6gBcmcFolCeItlLPa/C4uiyOK2wVWHyTnEeKjdpD6dwLuemRmwtZrModbQu >> PPPFkKzQhUnh5Wgq8TIP4kSc2t1/jSpdV8MHqM0piqOFnR52fExPrwLn82WEFcp8 >> tXfHHTaZj+6gL+IGswdAgqvxk1V+6QTjH57igWmYtcENpIDbhZVBh+HOD8SS2qdv >> ohwFg/Vn8VrCeTGGehNSBvkam0HXjXXq7mZ8W4xrOS8vxv8HPAFZHze2sPlUG/Ob >> WeOdiLgD2HCH95SXYDDBNFG6HwFkLETA3DjpfvgHqPdaLmEfIZW+ks1WF9RG+Pmo >> jhbWH8OmtTk5A/Zh63uRowMaDe7QSCruPIfIwlrgqLozOj8htMyJPBIW9oZGGkqC >> 7Vu5UFeL8gcigRmQv5NA >> =ceAo >> -----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/ > ___________________________________________________________ > 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/
