From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: Citation processing via Zotero + zotxt Date: Thu, 03 Dec 2015 20:49:49 -0500 Message-ID: References: <87wpt1yj5k.fsf@berkeley.edu> <87d1uqyiva.fsf@berkeley.edu> <8737vkidgl.fsf@fastmail.fm> <87mvtrqdv4.fsf@gmx.us> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:52452) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a4fVU-0004pl-52 for emacs-orgmode@gnu.org; Thu, 03 Dec 2015 20:49:57 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1a4fVQ-0007nO-SI for emacs-orgmode@gnu.org; Thu, 03 Dec 2015 20:49:56 -0500 Received: from mail-qg0-x22c.google.com ([2607:f8b0:400d:c04::22c]:33156) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a4fVQ-0007nI-N3 for emacs-orgmode@gnu.org; Thu, 03 Dec 2015 20:49:52 -0500 Received: by qgea14 with SMTP id a14so77012810qge.0 for ; Thu, 03 Dec 2015 17:49:52 -0800 (PST) In-reply-to: <87mvtrqdv4.fsf@gmx.us> List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: Rasmus Cc: emacs-orgmode@gnu.org >> What do you think? > > My guess is that it is orders of magnitudes harder with author (year) and > footnotes and whatnot. footnotes... The only place I can see this is in org/odt export. In org I can see it ok with the approach I described. For odt, I guess it would be about the same, if you know the markup code to insert for a footnote. Other formats are continuous pages, so the footnotes would end up at the end of the document. > But bibtex.el helps in some regards (indeed in an > ancestor to this thread we discussed whether bibtex.el + reftex.el could > be used). Then comes the formatting and sorting of the bibliography, also > when using different languages (Marcin talks about this) or types of > publications (bibtex.el lists 27 when you switch the dialect to > biblatex)... CSL does not currently support multiple languages according to http://citationstyles.org/styles/, although a fork of zotero is supposed to support it. CSL also does not support composite citations, e.g. that are common in chemistry journals. It doesn't support journal abbreviations. If a reference type is not listed in the CSL, it also will not be supported by CSL I suppose. I also suppose the CSL must be backend specific to output formats appropriate to org, html, LaTeX, markdown, etc... for any particular style. The point is there is no single solution now, or ever that will easily handle all reference databases, all reference types, to any output, in arbitrary format/style. We should not try to support all of these things. We could support a small number of things that could be improved or increased in the future. > As a small example comes out of your example which has mistakes such as > "17()". this is from missing information in the bibtex file, and the single format string in reftex. This kind of error is easy to fix. More difficult changes are to the authors (e.g. initials, et al after 3 authors, etc...), journal abbreviations, and for different types of references. For a blogpost I consider that acceptable. For a publication/proposal not so much. For that, I would use LaTeX export which wouldn't have that issue. A key point here is I don't think you can have it both ways. A bibtex file with LaTeX markup of equations cannot be used to make an html/org/markdown/etc.. bibliography that looks right without handling the LateX markup in it and converting it some way to the right format. A bibtex file that uses strings to switch between full journal names and abbreviated journal names will be challenging for any system other than bibtex. This is not special to bibtex, it is general to any reference database I think. CSL does not save us from this. No doubt there are many corner cases that could be problematic. I don't have the feeling there would be more than using CSL though. Good luck getting the CSL to make the in text citations clickable hyperlinks with tooltips of the citation in html. I would rather learn to use elisp for this than CSL for that sole purpose. > The fact that the documentation of biblatex-chicago (a biblatex *style*) > is 149 pages might also serve as a warning. The CSL for this is only 651 lines (https://github.com/citation-style-language/styles/blob/master/chicago-author-date.csl). Its either very concise, or not complete ;) There are plenty of warning signs ;) If you want perfect biblatex-chicago, I think the answer is use biblatex. The issue as I see it is one of balancing something that mostly works, and is improveable and something that currently doesn't exist for org-mode for something other than latex. > Note, I use a similar system myself when exporting citations outside of > latex (lookup stuff from bibtex and cross-fingers), but fitted to > author-year. It’s certainly doable when you know your fixed needs, but it > is harder to convince yourself it’s a good general solution. > > It would be nice if you could prove me wrong. I cannot. I don't think you are wrong. The only time-tested, publication quality solutions for citations in my opinion right now are bib(la)tex, MS Word/reference manager, and "by hand". Even these get "edited" in their final print versions by journals. I think we can provide some fixed solutions for non-LaTeX exports that will be pretty good. At least until a proven external cite-processor solution exists. As a finishing thought: Just imagine if this CSL snippet (https://github.com/citation-style-language/styles/blob/master/acs-nano.csl): was really this much more readable sexp form :) (citation (:collapse "citation-number") (sort () (key (:variable "citation-number"))) (layout (:delimiter "," :vertical-align "sup") (text (:variable "citation-number")))) It might start making more sense to think of a lisp based citation processor. It might even address some limitations of bib(la)tex. Now, about those cross-references and labels... > > Rasmus -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http://kitchingroup.cheme.cmu.edu