From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: Citation processing via Zotero + zotxt Date: Sat, 05 Dec 2015 17:23:45 -0500 Message-ID: References: <87wpt1yj5k.fsf@berkeley.edu> <87d1uqyiva.fsf@berkeley.edu> <8737vkidgl.fsf@fastmail.fm> <87mvtrqdv4.fsf@gmx.us> <87610ch9wr.fsf@fastmail.fm> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:57144) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a5LFA-0007DO-V7 for emacs-orgmode@gnu.org; Sat, 05 Dec 2015 17:23:54 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1a5LF7-0006zc-Lx for emacs-orgmode@gnu.org; Sat, 05 Dec 2015 17:23:52 -0500 Received: from mail-qg0-x230.google.com ([2607:f8b0:400d:c04::230]:34815) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a5LF7-0006zV-D9 for emacs-orgmode@gnu.org; Sat, 05 Dec 2015 17:23:49 -0500 Received: by qgeb1 with SMTP id b1so118439752qge.1 for ; Sat, 05 Dec 2015 14:23:48 -0800 (PST) In-reply-to: <87610ch9wr.fsf@fastmail.fm> 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: Matt Lundin Cc: emacs-orgmode@gnu.org, Rasmus Matt Lundin writes: > Hi John, > > John Kitchin writes: > >> If a reference type is not listed in the CSL, it also will not be >> supported by CSL I suppose. > > How is this different than biblatex or bibtex? A user could just modify > the style or put in a request with a maintainer. Its not different. Just to point out CSL has limitations too. >> I also suppose the CSL must be backend specific to output formats >> appropriate to org, html, LaTeX, markdown, etc... for any particular >> style. > > AFAIU, CSL styles are backend agnostic (otherwise they wouldn't be of > much use). It is the processor (citeproc-js, pandoc, etc.) that takes > the instructions (e.g., font-style="italic" in a CSL file) and adds the > appropriate markup for a defined backend. So once you add a new output > format to a processor, it works with all styles. I believe that. I still don't totally see where font-style="italic" gets converted to /text/ or text or \it{text} etc... I trust it happens, I just don't see it. Where does one do something fancier like: text It sounds trivial, but imagine a day when we all have an orcid, and our names are linked to our orcid pages in bibliographies, e.g. my name would be J. R. Kitchin or some other format. See this highly linked bibliography: http://kitchingroup.cheme.cmu.edu/dept-publications-2014.html Where almost every part of each entry is linked to something (true to some stuff that is behind a paywall, but lets not get distracted by that). Is that something a CSL/citation processor could do? These aren't reasons not to do CSL, and they aren't mission critical to citations. They just make them richer and more useful. And to be fair, the information these pieces are linked to came from a bibliographic record from Scopus, not a bibtex file I maintain, which only has a doi in it to access that information. Clearly I still don't see how a cite-processor actually works. I gather that 1. you extract citation data from a document. 2. send citation data, style and bibliography data to the citation processor 3. It returns replacement text, and the bibliography string 4. you substitute the replacements in the text and insert the bibliography string somewhere. If the CSL doesn't have the backend information, and the citation processor doesn't know about org/html/etc... then somewhere between step 3 and 4 you add the formatting right? Does the processor get another piece of information to tell it how to format the output? For example, if your CSL says a citation should be superscripted, how does the citation processor know to output 4 vs. $^4$? or ^{4}. >> 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. > > I would suggest that tapping into a CSL tool like zotero of citeproc-js > is in fact *a small thing* we can do right now that would have a big > payoff for lots of users, even if it does not support 100% of use > cases. I have no objection to it. Getting high quality references into Word documents from org-mode is one barrier to convincing more people org-mode is a competitive writing tool for publications in my mind. Clearly we need an external program for this. I looked at pandoc before http://kitchingroup.cheme.cmu.edu/blog/2015/01/29/Export-org-mode-to-docx-with-citations-via-pandoc/ and it was ok, but had some issues getting to Word with citations. Would zotero or citeproc-js be any better? >> 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. > > Is this assessment based on your particular disciplinary experience? Certainly ;) Those have met 100% of my needs, and about 10% of my desires in scientific publishing for the past 15 years. org-ref now meets 99.9% of my desires ;) Also, by time-tested, I mean I have published papers by those methods specifically, so I know they work (including using org-mode to make bibtex/latex files). I have not published any papers using org mode with export to Word, so I don't know if it is possible to do it. The final details of formatting may prove too difficult in some cases for direct export. > I > ask because many of us in the humanities have not enjoyed the benefits > of automated, text-based citation processing until quite recently, so > *both* biblatex and CSL seem awesome. So even Word/Endnote\|Papers\|Zotero has not been a citation/bibliography solution? >The citation style in my field > (the Chicago Manual of Style) is more quirky and complex than any > scientific citation style. Thus, it is likely more feasible to implement > basic bibtex functionality in lisp than it is to re-implement > biblatex-chicago.[fn:1] CSL offers the advantage of allowing export to > backends that can easily be converted to Word (the format that > humanities publishers require). Somewhat ironically, CSL won't support some standard citation formats in chemistry journals! Luckily, those are supported in bibtex. >> It might start making more sense to think of a lisp based citation >> processor. It might even address some limitations of bib(la)tex. > > That would be very cool, especially if we could import/convert CSL files > (I don't want to rewrite all 1200+ lines of the > chicago-fullnote-bibliography CSL style). :) It is easy to read in the xml files, and they read into a lisp data structure. That isn't helpful on its own, of course, without a lisp citation processor to send them too ;) > > Matt > > Footnotes: > > [fn:1] I cloned the CSL repository and did a quick sort by word count. > Not surprisingly, the longest files were all in the humanities: > > 1296 2700 44202 chicago-fullnote-bibliography-fr.csl > 1273 2590 40935 chicago-fullnote-bibliography.csl > 1264 2576 40674 chicago-fullnote-bibliography-no-ibid.csl > 1241 2531 39515 chicago-library-list.csl > 1241 2530 39535 chicago-annotated-bibliography.csl > 1240 2524 39445 chicago-note-bibliography.csl > 1235 2506 40168 zeitschrift-fur-religionswissenschaft-note.csl > 1227 2508 39077 chicago-note-biblio-no-ibid.csl > 1132 2620 41990 mcgill-fr.csl > 1060 2149 34008 moorlands-college.csl > 998 2175 34470 lluelles.csl > 927 2066 31551 lluelles-no-ibid.csl > 911 1862 29828 proinflow.csl > 906 1961 28990 irish-historical-studies.csl > 878 1828 29238 universite-laval-faculte-de-theologie-et-de-sciences-religieuses.csl > 862 1830 29437 chicago-author-date-fr.csl > 856 1782 28244 oxford-studies-in-ancient-philosophy.csl > 809 1941 27717 university-college-dublin-school-of-history-and-archives.csl > 809 1796 26790 turabian-fullnote-bibliography.csl > 806 1857 27140 wheaton-college-phd-in-biblical-and-theological-studies.csl > 796 1791 26472 modern-language-association-6th-edition-note.csl > 793 1671 26453 sheffield-hallam-university-history.csl > 792 1910 30773 pour-reussir-note.csl > 788 1792 26377 svensk-exegetisk-arsbok.csl > 781 1782 26316 early-christianity.csl > 779 1772 26038 society-of-biblical-literature-fullnote-bibliography.csl > 775 1808 26461 new-testament-studies.csl > 768 2350 29928 clio-medica.csl > 714 1533 22993 iso690-author-date-cs.csl > 708 1578 25548 chicago-author-date-basque.csl > 708 1520 22731 iso690-author-date-sk.csl > 707 1605 24582 melbourne-school-of-theology.csl > 701 1533 22280 moore-theological-college.csl > 696 1756 25783 associacao-brasileira-de-normas-tecnicas-ufjf.csl > 694 1474 22229 podzemna-voda.csl > 692 2315 29639 foerster-geisteswissenschaft.csl > 692 1591 24881 oscola.csl -- 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