Dear list, I use org-mode to write scientific papers, exporting mostly to LaTex/pdf (and sometimes to Word via ODT when I have to collaborate with less enlightened colleagues). I keep my references in a .bib file, and so far I have been using bibtex in a more or less standard way, using reftex to insert citations in the documents. I am planning in revamping the way I deal with citations, and I was wondering if I can get your opinions in what is the "state of the art" in using citations in org-mode, in particular - Should I use biblatex instead of bibtex? - Are there any contributed packages that I should consider? - What would be the best way to get citations into html or odt? Any comments or tips will be welcomed! All the best, Julian -- Julian Mariano Burgos, PhD Hafrannsóknastofnun/Marine Research Institute Skúlagata 4, 121 Reykjavík, Iceland Sími/Telephone : +354-5752037 Bréfsími/Telefax: +354-5752001 Netfang/Email: julian@hafro.is
Is there a sub-group dedicated to this? It is on my TODO list to catch up on the state of the art, too. Grant Rettke | AAAS, ACM, ASA, FSF, IEEE, SIAM, Sigma Xi grettke@acm.org | http://www.wisdomandwonder.com/ “Wisdom begins in wonder.” --Socrates ((λ (x) (x x)) (λ (x) (x x))) “Life has become immeasurably better since I have been forced to stop taking it seriously.” --Thompson On Fri, Apr 25, 2014 at 7:11 AM, Julian M. Burgos <julian@hafro.is> wrote: > Dear list, > > I use org-mode to write scientific papers, exporting mostly to LaTex/pdf > (and sometimes to Word via ODT when I have to collaborate with less > enlightened colleagues). I keep my references in a .bib file, and so > far I have been using bibtex in a more or less standard way, using > reftex to insert citations in the documents. > > I am planning in revamping the way I deal with citations, and I was > wondering if I can get your opinions in what is the "state of the art" > in using citations in org-mode, in particular > > - Should I use biblatex instead of bibtex? > - Are there any contributed packages that I should consider? > - What would be the best way to get citations into html or odt? > > Any comments or tips will be welcomed! > All the best, > > Julian > > -- > Julian Mariano Burgos, PhD > Hafrannsóknastofnun/Marine Research Institute > Skúlagata 4, 121 Reykjavík, Iceland > Sími/Telephone : +354-5752037 > Bréfsími/Telefax: +354-5752001 > Netfang/Email: julian@hafro.is >
Hi all, > - Should I use biblatex instead of bibtex? You should. It is very powerful and straightforward. The manual is great. As for citations, I find that the most flexible way is to define my own link types, that allows control on both org formatting and export Let's say for example that you want to cite an entry of your .bib file, which key is Chiles:2012:Geostatistics. Something like : see Chilès 2012, p.145 Note (i) the "see" (ii) the "p.145", they are both part of the citation. In this case, biblatex provides the following command \cite[see][p.145]{Chiles:2012:Geostatistics} For readability purposes, the citation should appear as is in the org file, the "\cite{Chiles:2012:Geostatistics}" command should only appear when exporting to LaTeX. Furthermore, this should be a link to the entry in the .bib file, so the complete org link would look like [[ref:Chiles:2012:Geostatistics][(see for example Chilès 2012, p.145)]] Where ref is a custom link type to the said bib file. To do that, I have defined the following link-type in my init.el : (org-add-link-type "ref" (lambda (key) (org-open-file cby-references-file t nil key)) (lambda (path desc format) (cond ((eq format 'html) (format "(<cite>%s</cite>)" path)) ((eq format 'latex) (let* ((postnote (cby-org-link-get-postnote desc)) (prenote (cby-org-link-get-prenote desc))) (cond ((and prenote postnote) (format "\\cite[%s][%s]{%s}" prenote postnote path)) (postnote (format "\\cite[%s]{%s}" postnote path)) (prenote (format "\\cite[%s][]{%s}" prenote path)) (t (format "\\cite{%s}" path)))))))) Some remarks : 1. `cby-references-file` is my master .bib file. 2. The html export is rather rudimentary, it simply takes the org link description (%s) and puts it between <cite> markups. 3. To get the prenote (the "see") and postnote (the "p.145"), I use very shaky functions (`cby-org-link-get-postnote`) that strip the link description. I haven't come up with a proper solution yet so here is one for reference : (defun cby-org-link-get-postnote (desc) "Extract postnote from org-mode link description. Postnote starts at last ',' and ends at last ')'." (let ((postnote (cadr (split-string desc "[,)]")))) (if postnote (copy-sequence ;; clean string (replace-regexp-in-string "[ \t\n]" "" postnote))))) 4. To use the wide range of commands provided by biblatex, I also have a "pref" link type that exports to "\parencite{}" and a "tref" type that exports to "\texcite{}" This is all work in progress, but custom link types make both your org source file readable and export flexible. > I use org-mode to write scientific papers, exporting mostly to LaTex/pdf > (and sometimes to Word via ODT when I have to collaborate with less > enlightened colleagues) I also tried to do that, but do you have a way to get odt files back to org ? I saw a package for that somewhere. Bye, Clément
Hi all, > - Should I use biblatex instead of bibtex? You should. It is very powerful and straightforward. The manual is great. As for citations, I find that the most flexible way is to define my own link types, that allows control on both org formatting and export Let's say for example that you want to cite an entry of your .bib file, which key is Chiles:2012:Geostatistics. Something like : see Chilès 2012, p.145 Note (i) the "see" (ii) the "p.145", they are both part of the citation. In this case, biblatex provides the following command \cite[see][p.145]{Chiles:2012:Geostatistics} For readability purposes, the citation should appear as is in the org file, the "\cite{Chiles:2012:Geostatistics}" command should only appear when exporting to LaTeX. Furthermore, this should be a link to the entry in the .bib file, so the complete org link would look like [[ref:Chiles:2012:Geostatistics][(see for example Chilès 2012, p.145)]] Where ref is a custom link type to the said bib file. To do that, I have defined the following link-type in my init.el: (org-add-link-type "ref" (lambda (key) (org-open-file cby-references-file t nil key)) (lambda (path desc format) (cond ((eq format 'html) (format "(<cite>%s</cite>)" path)) ((eq format 'latex) (let* ((postnote (cby-org-link-get-postnote desc)) (prenote (cby-org-link-get-prenote desc))) (cond ((and prenote postnote) (format "\\cite[%s][%s]{%s}" prenote postnote path)) (postnote (format "\\cite[%s]{%s}" postnote path)) (prenote (format "\\cite[%s][]{%s}" prenote path)) (t (format "\\cite{%s}" path)))))))) Some remarks : 1. `cby-references-file` is my master .bib file. 2. The html export is rather rudimentary, it simply takes the org link description (%s) and puts it between <cite> markups. 3. To get the prenote (the "see") and postnote (the "p.145"), I use very shaky functions (`cby-org-link-get-postnote`) that strip the link description. I haven't come up with a proper solution yet so here is one for reference : (defun cby-org-link-get-postnote (desc) "Extract postnote from org-mode link description. Postnote starts at last ',' and ends at last ')'." (let ((postnote (cadr (split-string desc "[,)]")))) (if postnote (copy-sequence ;; clean string (replace-regexp-in-string "[ \t\n]" "" postnote))))) 4. To use the wide range of commands provided by biblatex, I also have a "pref" link type that exports to "\parencite{}" and a "tref" type that exports to "\texcite{}" This is all work in progress, but custom link types make both your org source file readable and export flexible. > I use org-mode to write scientific papers, exporting mostly to LaTex/pdf > (and sometimes to Word via ODT when I have to collaborate with less > enlightened colleagues) I also tried to do that, but do you have a way to get odt files back to org ? I saw a package for that somewhere. Bye, Clément
[-- Attachment #1: Type: text/plain, Size: 790 bytes --] Hi Julian et al., I am not sure if this helps, but I am in the process of writing a new package for inserting citations into org buffers using RefTeX. This solution would make citation insertion very convenient, but it would not be quite as easy to read as Clément's solution, and it would only work for latex export. (It might work with html export if you used bibtex to html, but I do not have enough experience with bibtex to html to know.) On the other hand, it will work with multicite commands, whereas Clement's does not look like it will. I was also thinking of adding out of the box biblatex support for org-bibtex (see my previous post). Let me know if you might be interested in either of these, as I will try to work on them this week. All best, Leonard [-- Attachment #2: Type: text/html, Size: 932 bytes --]
Hi Leonard, > I am in the process of writing a new package for inserting > citations into org buffers using RefTeX. I'd be interested to know what you have in mind. I use something of the sort, by customising `reftex-cite-format`, e.g: (setq reftex-cite-format '((?\C-m . "\\cite[]{%l}") (?b . "[[ref:%l][%A (%y)]]"))) This makes inserting custom links ("ref") easier with the usual `reftex-citation` bound to C-c [. > On the other hand, it will work with multicite commands, > whereas Clement's does not look like it will. It does not, and that's a big limitation. That being said, I don't know how to go about mixing multiple citations and links to the bib file. This is definitely something I care about, being able to quickly jump from the text to the bibliographic entry, PDF file, or whatever source I am using to write is one of the main reasons I use org instead of plain LaTeX. Bye, Clément
Hi Clément and Others,
On 2014-04-27 at 10:14, Clément B. wrote:
> (setq reftex-cite-format
> '((?\C-m . "\\cite[]{%l}")
> (?b . "[[ref:%l][%A (%y)]]")))
I've been using reftex in Org -> LaTeX for a while and have my Org text
sprinkled with \cite{foo:yyyy}. I just saw the customized
reftex-cite-format from Clément (above). It looks much nicer in the
text, but raises two questions:
1) Can the link just use lastname? It looks like %A is the only way to
access author names, and does full names, so perhaps not without writing
some custom function? And more importantly,
2) When I export this to LaTeX, it is not treated as a proper LaTeX
citation. The text is just the "%A (%y)" part. Is there some way to
export so that the ref:%l turns into a \cite{%l}?
Thanks,
-k.
Hi Ken,
> When I export this to LaTeX, it is not treated as a proper
> LaTeX citation. The text is just the "%A (%y)" part. Is there
> some way to export so that the ref:%l turns into a \cite{%l}?
The "ref" is a custom link type, you can define those in org with
`org-add-link-type`, and they allow control over the export
behaviour. See the previous posts in this thread for an example.
Bye,
Clément
On 2014-04-27 at 10:53, Clément B. wrote:
> Hi Ken,
>
>> When I export this to LaTeX, it is not treated as a proper LaTeX
>> citation. The text is just the "%A (%y)" part. Is there some way to
>> export so that the ref:%l turns into a \cite{%l}?
>
> The "ref" is a custom link type, you can define those in org with
> `org-add-link-type`, and they allow control over the export
> behaviour. See the previous posts in this thread for an example.
Ah! Got it. This is really nice. Thank you.
I find the best way to support ODT is simply add something like this:
((eq format 'odt)
(format "(%s)" desc))
This doesn't create a bibliography section, but that section is awkward
to export to anyway. It requires the 3rd party Org hack that isn't
officially supported, java, jabref, is awfully slow (~2
seconds/reference), etc. I now put the references inline as above, and
then manually add the references by exporting to PDF and copying/paste
that reference section.
Not great, but less of a hack than ODT-supported references, and working
with ODT/Word is a hack anyway.
Still looking into "lastname (Year)" format...
-k.
Clément B. <clement@inventati.org> writes: > Hi Leonard, > >> I am in the process of writing a new package for inserting >> citations into org buffers using RefTeX. > > I'd be interested to know what you have in mind. I use something > of the sort, by customising `reftex-cite-format`, e.g: > > (setq reftex-cite-format > '((?\C-m . "\\cite[]{%l}") > (?b . "[[ref:%l][%A (%y)]]"))) > > This makes inserting custom links ("ref") easier with the usual > `reftex-citation` bound to C-c [. > > >> On the other hand, it will work with multicite commands, >> whereas Clement's does not look like it will. > > It does not, and that's a big limitation. That being said, I don't > know how to go about mixing multiple citations and links to the > bib file. This is definitely something I care about, being able > to quickly jump from the text to the bibliographic entry, PDF > file, or whatever source I am using to write is one of the main > reasons I use org instead of plain LaTeX. One approach for muliticites is to drop a placeholder and then replace it with an export filter. I've been using these two for a while and they seem to work fine. ** Filters for multicites *** Filter for parencites Add the placeholder with alt-p #+name: tsd-parencites #+BEGIN_SRC emacs-lisp (defun tsd-latex-filter-parencites (text backend info) "Replace parencites placeholders in Beamer/LaTeX export." (when (memq backend '(beamer latex)) (replace-regexp-in-string "π" "\\parencites" text nil t))) (add-to-list 'org-export-filter-plain-text-functions 'tsd-latex-filter-parencites) #+END_SRC *** Filter for textcites Add the placeholder with alt-t #+name: tsd-textcites #+BEGIN_SRC emacs-lisp (defun tsd-latex-filter-textcites (text backend info) "Replace textcites placeholders in Beamer/LaTeX export." (when (memq backend '(beamer latex)) (replace-regexp-in-string "†" "\\textcites" text nil t))) (add-to-list 'org-export-filter-plain-text-functions 'tsd-latex-filter-textcites) #+END_SRC It looks like this in the text: A recent replication experiment that used stone tools in the manufacture of an outrigger canoe identified six functional types of stone adze that correspond generally with the six types established by Duff π[[multicite:turner00:_funct_desig_distr_new_zealan_adzes][;;turner diss]] [[multicite:turner05:_funct_and_techn_explan_for][;;turner nzja]]. My link syntax is a bit different, but the same basic idea: (org-add-link-type "multicite" 'ebib-open-org-link (lambda (path desc format) (cond ((eq format 'latex) (if (not desc) (format "{%s}" path) (format "[%s][%s]{%s}" (cadr (split-string desc ";")) (car (split-string desc ";")) path)))))) hth, Tom -- Thomas S. Dye http://www.tsdye.com
> I find the best way to support ODT is simply add something like this: > > ((eq format 'odt) > (format "(%s)" desc)) > > This doesn't create a bibliography section, but that section is awkward > to export to anyway. It requires the 3rd party Org hack that isn't > officially supported, java, jabref, is awfully slow (~2 > seconds/reference), etc. I now put the references inline as above, and > then manually add the references by exporting to PDF and copying/paste > that reference section. > > Not great, but less of a hack than ODT-supported references, and working > with ODT/Word is a hack anyway. I came to a similar conclusion for html export, it is very hard to match bibtex/biblatex to produce a proper bibliography, so one might as well use it. At one point, the thought of writing a custom citation style that would output html code crossed my mind (I think biblatex would allow that), but I just don't use html export enough. Although if this is possible, it could work with xml for odt as well. > Still looking into "lastname (Year)" format... I hadn't noticed that before, but now that you mention it, I think this is related to the way you format your bib file. For example "%A (%y)" with: 1. name = {Darwin, Charles} year = {1859} will yield "Darwin (1859)" 2. name = {Charles Darwin} year = {1859} will yield "Charles Darwin (1859) Not very consistent. This might be something to take to the AUCTeX guys.
On 2014-04-27 at 12:05, Clément B. wrote: >> Still looking into "lastname (Year)" format... > > I hadn't noticed that before, but now that you mention it, I > think this is related to the way you format your bib file. > > For example "%A (%y)" with: > > 1. name = {Darwin, Charles} > year = {1859} > > will yield "Darwin (1859)" > > > 2. name = {Charles Darwin} > year = {1859} > > will yield "Charles Darwin (1859) > > Not very consistent. This might be something to take to the AUCTeX >guys. I've asked about this here: https://tex.stackexchange.com/questions/173804/best-practices-for-bibtex-author-field Maybe bibtool or some other tool can reformat my BibTeX file to "Last, First". -k.
On 2014-04-27 at 12:01, Thomas S. Dye wrote:
> Clément B. <clement@inventati.org> writes:
>
>> This makes inserting custom links ("ref") easier with the usual
>> `reftex-citation` bound to C-c [.
>>
>>> On the other hand, it will work with multicite commands,
>>> whereas Clement's does not look like it will.
>>
>> It does not, and that's a big limitation.
It appears to work for multicite for me. Or at least well enough. If I
select multiple entries, I get this:
[[ref:Author1:YYYY,Author2:YYYY,Author3:YYYY][()]]
I can then easily insert the text I want into the (). It exports
properly to LaTeX as \cite{Author1:YYYY,Author2:YYYY,Author3:YYYY}.
Maybe most people multi-cite more than me, but I think it is only a bit
of extra work to add what I want in the () and then it exports properly
to LaTeX and, using the references-via-LaTeX, to ODT/HTML too!
-k.
> It appears to work for multicite for me. Or at least well enough. If I
> select multiple entries, I get this:
>
> [[ref:Author1:YYYY,Author2:YYYY,Author3:YYYY][()]]
>
> I can then easily insert the text I want into the (). It exports
> properly to LaTeX as \cite{Author1:YYYY,Author2:YYYY,Author3:YYYY}.
>
> Maybe most people multi-cite more than me, but I think it is only a bit
> of extra work to add what I want in the () and then it exports properly
> to LaTeX and, using the references-via-LaTeX, to ODT/HTML too!
>
> -k.
The problem is that you can't link to a bibtex entry,
[[ref:Author1:YYYY,Author2:YYYY]] is not picked up by org search
function of `org-open-file`. And even if it was, it couldn't link
to several entries at once. So to preserve the ability to jump
quickly to a reference, I quite like the export filter approach,
which I was unaware of (thank you Thomas! ).
Clément
[-- Attachment #1: Type: text/plain, Size: 3987 bytes --] It seems there are a lot of variants of citation handling out there! I will add to the list my own variants here: https://github.com/jkitchin/jmax/blob/master/jorg-bib.el. My citation needs are simple, I basically only use \cite{key1,key2} in LaTeX. And I only use bibtex, because I have not gotten around to anything else, bibtex works fine if your needs are simple (like mine). There is certainly duplication of some things, but the following are features in mine that I am not aware of anywhere else. 1. Integration with reftex. You type C-c ] and select keys from reftex and insert a cite link. If you type it again on a citation, the new entries are appended to the end. This current conversation inspired me to implement this! 2. Clickable cite links. If you have a citation link like cite:key1,key2,key3 you can click on key1 and open the bibliography file to key1, and you can click on key2 and have it open at key 2. This link would export in latex as \cite{key1,key2,key3}. Other cite formats, e.g. citep, citep*, etc... are defined too, but are relatively untested. You can also use completion to enter a bibtex key. 3. citation tooltips. If clicking is too disruptive, you can run a command and get a tooltip of the citation under point. If clicking is too tiring, you can turn on an idle timer that shows a tooltip if the cursor is on a citation. 4. clickable label links. clicking checks the buffer for another label by the same name. 5. Clickable ref links. Clicking on the ref:label takes you to the label, and provides C-c & to get back to that point. You can also use completion to get a list of labels in the buffer to make a ref to. 6. A bibliographystyle and bibliography link. The bibliography link opens the bibtex file that was clicked on. 7. Code to make a clickable list of figures and tables. 8. Code to extract the bibtex entries cited in an org-file to a text block at the end of the org-file 9. variables to point to a notes file and pdf directory, and functions to jump to your notes and the pdf file from a bibtex entry. 10. a function to build a complete pdf bibliography from your bibtex file. This is handy for checking the entries are spelled correctly, etc... 11. A little function and python script to upload a bibtex entry to citeulike. I have not tried to do much with anything but LaTeX, so these links are not likely to be that good for html or odt I suspect. Anyway, there are some very interesting ideas in this code, and I am using it on a pretty regular basis. Maybe some of you would also find them interesting/helpful. I look forward to see this continue developing! John ----------------------------------- John Kitchin Associate Professor Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 http://kitchingroup.cheme.cmu.edu On Sun, Apr 27, 2014 at 12:57 PM, Clément B. <clement@inventati.org> wrote: > > > It appears to work for multicite for me. Or at least well enough. If I > > select multiple entries, I get this: > > > > [[ref:Author1:YYYY,Author2:YYYY,Author3:YYYY][()]] > > > > I can then easily insert the text I want into the (). It exports > > properly to LaTeX as \cite{Author1:YYYY,Author2:YYYY,Author3:YYYY}. > > > > Maybe most people multi-cite more than me, but I think it is only a bit > > of extra work to add what I want in the () and then it exports properly > > to LaTeX and, using the references-via-LaTeX, to ODT/HTML too! > > > > -k. > > The problem is that you can't link to a bibtex entry, > [[ref:Author1:YYYY,Author2:YYYY]] is not picked up by org search > function of `org-open-file`. And even if it was, it couldn't link > to several entries at once. So to preserve the ability to jump > quickly to a reference, I quite like the export filter approach, > which I was unaware of (thank you Thomas! ). > > > Clément > > [-- Attachment #2: Type: text/html, Size: 4815 bytes --]
Hi John, This is great ! Way more advanced than anything I have said. > 2. Clickable cite links. If you have a citation link like > cite:key1,key2,key3 you can click on key1 and open the bibliography file to > key1, and you can click on key2 and have it open at key 2. This link would > export in latex as \cite{key1,key2,key3}. Other cite formats, e.g. citep, > citep*, etc... are defined too, but are relatively untested. You can also > use completion to enter a bibtex key. This was my main concern, glad to see you can treat the different parts of the links as separate citations, and access their respective bibtex entry. The completion is very handy too. > 9. variables to point to a notes file and pdf directory, and functions to > jump to your notes and the pdf file from a bibtex entry. I use something similar, but only for the pdf file. I think the open-in-browser function is implemented in the latest bibtex-mode (`bibtex-url` bound to C-c C-l). Bye, Clément
Hi Clément and all, Clément B. <clement@autistici.org> writes: > As for citations, I find that the most flexible way is to define > my own link types, that allows control on both org formatting and > export... Replacing my inline \cite commands with custom link types is something I've been meaning to do for a while. Thanks for the implementation ideas! I have a setup that for some people may complement the one Clément describes. Rather than dealing with .bib files and RefTeX, I represent my bibliography in Org, and use org-bibtex to (re-)generate a .bib file as needed. Here's how it works, in brief; I described it more fully at: http://article.gmane.org/gmane.emacs.orgmode/79016/ 1) I store each reading as a TODO headline using a capture template. I use the post-capture hook to call org-bibtex-create-in-current-entry as appropriate. This allows me to keep notes, links, deadlines etc. associated with each reading in Org, as well as the bibliographic data. 2) I have a function that uses org-map-entries to walk over the headlines for my readings and export them to a .bib file. This regenerates my .bib file on an as-needed basis; the real bibliographic database is stored in Org. (I call this function from a Makefile, but it could just as easily be used from within the Org export process.) The next step, which I haven't yet implemented but which would connect this setup to one like Clément described, would be to add behavior to the custom link types so that *following* the link would jump to the associated TODO entry for the reading, rather than the entry in the .bib file. This should be straightforward, since org-bibtex uses the CUSTOM_ID property to store the cite key. And jumping to my own notes about a reference (which might further link to the original text), rather than to a .bib file, is usually what I want. -- Best, Richard
Hi Leonard,
Yes, I will be definitively interested on this! Thanks!
Julian
Leonard Randall writes:
> Hi Julian et al.,
> I am not sure if this helps, but I am in the process of writing a new
> package for inserting citations into org buffers using RefTeX. This
> solution would make citation insertion very convenient, but it would not be
> quite as easy to read as Clément's solution, and it would only work for
> latex export. (It might work with html export if you used bibtex to html,
> but I do not have enough experience with bibtex to html to know.) On the
> other hand, it will work with multicite commands, whereas Clement's does
> not look like it will.
>
> I was also thinking of adding out of the box biblatex support for
> org-bibtex (see my previous post).
>
> Let me know if you might be interested in either of these, as I will try to
> work on them this week.
>
> All best,
>
> Leonard
--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax: +354-5752001
Netfang/Email: julian@hafro.is
Thanks Clément and everybody else for their comments/ideas. I will go
through these carefully.
John Kitchin writes:
> It seems there are a lot of variants of citation handling out there! I will
> add to the list my own variants here:
> https://github.com/jkitchin/jmax/blob/master/jorg-bib.el. My citation needs
> are simple, I basically only use \cite{key1,key2} in LaTeX. And I only use
> bibtex, because I have not gotten around to anything else, bibtex works
> fine if your needs are simple (like mine).
>
> There is certainly duplication of some things, but the following are
> features in mine that I am not aware of anywhere else.
>
>
> 1. Integration with reftex. You type C-c ] and select keys from reftex and
> insert a cite link. If you type it again on a citation, the new entries are
> appended to the end. This current conversation inspired me to implement
> this!
>
> 2. Clickable cite links. If you have a citation link like
> cite:key1,key2,key3 you can click on key1 and open the bibliography file to
> key1, and you can click on key2 and have it open at key 2. This link would
> export in latex as \cite{key1,key2,key3}. Other cite formats, e.g. citep,
> citep*, etc... are defined too, but are relatively untested. You can also
> use completion to enter a bibtex key.
>
> 3. citation tooltips. If clicking is too disruptive, you can run a command
> and get a tooltip of the citation under point. If clicking is too tiring,
> you can turn on an idle timer that shows a tooltip if the cursor is on a
> citation.
>
> 4. clickable label links. clicking checks the buffer for another label by
> the same name.
>
> 5. Clickable ref links. Clicking on the ref:label takes you to the label,
> and provides C-c & to get back to that point. You can also use completion
> to get a list of labels in the buffer to make a ref to.
>
> 6. A bibliographystyle and bibliography link. The bibliography link opens
> the bibtex file that was clicked on.
>
> 7. Code to make a clickable list of figures and tables.
>
> 8. Code to extract the bibtex entries cited in an org-file to a text block
> at the end of the org-file
>
> 9. variables to point to a notes file and pdf directory, and functions to
> jump to your notes and the pdf file from a bibtex entry.
>
> 10. a function to build a complete pdf bibliography from your bibtex file.
> This is handy for checking the entries are spelled correctly, etc...
>
> 11. A little function and python script to upload a bibtex entry to
> citeulike.
>
> I have not tried to do much with anything but LaTeX, so these links are not
> likely to be that good for html or odt I suspect.
>
> Anyway, there are some very interesting ideas in this code, and I am using
> it on a pretty regular basis. Maybe some of you would also find them
> interesting/helpful. I look forward to see this continue developing!
>
> John
>
> -----------------------------------
> John Kitchin
> Associate Professor
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> http://kitchingroup.cheme.cmu.edu
>
>
>
> On Sun, Apr 27, 2014 at 12:57 PM, Clément B. <clement@inventati.org> wrote:
>
>>
>> > It appears to work for multicite for me. Or at least well enough. If I
>> > select multiple entries, I get this:
>> >
>> > [[ref:Author1:YYYY,Author2:YYYY,Author3:YYYY][()]]
>> >
>> > I can then easily insert the text I want into the (). It exports
>> > properly to LaTeX as \cite{Author1:YYYY,Author2:YYYY,Author3:YYYY}.
>> >
>> > Maybe most people multi-cite more than me, but I think it is only a bit
>> > of extra work to add what I want in the () and then it exports properly
>> > to LaTeX and, using the references-via-LaTeX, to ODT/HTML too!
>> >
>> > -k.
>>
>> The problem is that you can't link to a bibtex entry,
>> [[ref:Author1:YYYY,Author2:YYYY]] is not picked up by org search
>> function of `org-open-file`. And even if it was, it couldn't link
>> to several entries at once. So to preserve the ability to jump
>> quickly to a reference, I quite like the export filter approach,
>> which I was unaware of (thank you Thomas! ).
>>
>>
>> Clément
>>
>>
--
Julian Mariano Burgos, PhD
Hafrannsóknastofnun/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax: +354-5752001
Netfang/Email: julian@hafro.is
On 26-Apr-2014, at 6:56 pm, Clément B. <clement@inventati.org> wrote:
> Hi all,
>
>> - Should I use biblatex instead of bibtex?
>
> You should. It is very powerful and straightforward. The manual
> is great.
>
Is the choice so clearcut?
A lot of bibliographic databases provide bibtex-compatible citation information. How do you deal with that, when you shift to biblatex?
Of course, this is not an org-mode specific limitation at all. But still relevant, I think, when we are discussing what should be the recommended way of dealing with citations in org-mode.
Vikas
> Hi all,
>
>> - Should I use biblatex instead of bibtex?
>
> You should. It is very powerful and straightforward. The manual
> is great.
>
ox-bibtex provides a usable implementation of including bibtex citations in html export. Can this be done if using biblatex?
Vikas
Hi Vikas,
Vikas Rawal Lists <vikaslists@agrarianresearch.org> writes:
> On 26-Apr-2014, at 6:56 pm, Clément B. <clement@inventati.org> wrote:
>
>> Hi all,
>>
>>> - Should I use biblatex instead of bibtex?
>>
>> You should. It is very powerful and straightforward. The manual
>> is great.
>
> Is the choice so clearcut?
>
> A lot of bibliographic databases provide bibtex-compatible citation
> information. How do you deal with that, when you shift to biblatex?
As I recently learned (thanks to this list!), biblatex supports .bib
files. So switching to biblatex is not an issue from this perspective:
you can continue to drop bibtex-compatible citation information into
your .bib file and use it with biblatex.
If ox-bibtex reads .bib files, that should continue to work, too.
Best,
Richard