Extracting bibtex file from an org-buffer

Posted February 19, 2014 at 06:45 PM | categories: bibtex, org-mode | tags:

Updated February 19, 2014 at 07:27 PM

Table of Contents

We use citation links a lot in our org-files, like this: 

cite:thompson-2014-co2-react
. Sometimes there are multiple citations like this 
cite:mehta-2014-ident-poten,hallenbeck-2013-effec-o2
. It would be convenient at times to extract a bibtex file from these citations. That way we could easily share files. This is possible in RefTeX from a LaTeX file. Org makes it easy to export to LaTeX, so this seems like it should be easy. It would be easy, if I always put the bibliography link in the file. I usually do not, so let us check if that is the case, and if it is not add the bibliography to the end before we export. Then, with the LaTeX file in hand, we open it, and call the RefTeX functions to get the bibliography. Finally, we will create a link to the actual created file, and add it as a source block that can be tangled at the end of the file.

Here is a function that does the extraction and some house cleaning. We actually take the contents of the buffer and save it in a temporary file, so that we do not accidentally clobber a tex or bibtex file here. 

(defun kg-extract-bibtex ()
  "create bibtex file of entries cited in this buffer"

  (let* ((tempname (make-temp-file "extract-bib"))
         (contents (buffer-string))
         (cb (current-buffer))
         basename texfile bibfile results)

    (find-file tempname)
    (insert contents)
    (setq basename (file-name-sans-extension
                    (file-name-nondirectory buffer-file-name))
          texfile (concat basename ".tex")
          bibfile (concat basename ".bib"))

  (save-excursion
    (goto-char (point-min))
    (unless (re-search-forward "^bibliography:" (point-max) 'end)
      (insert (format "\nbibliography:%s" (mapconcat 'identity reftex-default-bibliography ",")))))

    (org-latex-export-to-latex)
    (find-file texfile)
    (reftex-parse-all)
    (reftex-create-bibtex-file bibfile)
    (setq results (buffer-string))
    (kill-buffer bibfile)
    (kill-buffer texfile)
    (delete-file texfile)
    (delete-file tempname)

    (switch-to-buffer cb)
    (save-excursion
      (goto-char (point-max))
      (insert (format "

** Bibtex entries

#+BEGIN_EXAMPLE: 
%s
#+END_EXAMPLE" results)))))

(kg-extract-bibtex)

There it is! The src block does not render in HTML very well, since it appears to be simple text. It looks fine in the org file though.

It might be a good idea to replace the bibliography line with the new file, but I will leave that as an exercise for later.

1 Bibtex entries

#+BEGINEXAMPLE: @article{hallenbeck-2013-effec-o2, author = "Hallenbeck, Alexander P. and Kitchin, John R.", title = "Effects of \ce{O_2} and \ce{SO_2} on the Capture Capacity of a Primary-Amine Based Polymeric \ce{CO_2} Sorbent", year = 2013, doi = "10.1021/ie400582a", eprint = "http://pubs.acs.org/doi/pdf/10.1021/ie400582a ", journal = "Industrial \& Engineering Chemistry Research", pages = "10788-10794", url = "http://pubs.acs.org/doi/abs/10.1021/ie400582a ", }

@article{mehta-2014-ident-poten, author = {Mehta, Prateek and Salvador, Paul A. and Kitchin, John R.}, title = {Identifying Potential BO2 Oxide Polymorphs for Epitaxial Growth Candidates}, journal = {ACS Applied Materials \& Interfaces}, volume = 0, number = 0, pages = {null}, year = 2014, doi = {10.1021/am4059149}, URL = {http://pubs.acs.org/doi/abs/10.1021/am4059149 }, eprint = {http://pubs.acs.org/doi/pdf/10.1021/am4059149 } }

@Article{thompson-2014-co2-react, author = {Thompson, Robert L. and Albenze, Erik and Shi, Wei and Hopkinson, David and Damodaran, Krishnan and Lee, Anita and Kitchin, John and Luebke, David Richard and Nulwala, Hunaid}, title = {\ce{CO_2} Reactive Ionic Liquids: Effects of functional groups on the anion and its influence on the physical properties}, journal = {RSC Adv.}, year = 2014, pages = "-", publisher = {The Royal Society of Chemistry}, doi = {10.1039/C3RA47097K}, url = {https://doi.org/10.1039/C3RA47097K }, abstract = "Next generation of gas separation materials are needed to alleviate issues faced in energy and environmental area. Ionic liquids (ILs) are promising class of material for CO2 separations. In this work{,} CO2 reactive triazolides ILs were synthesized and characterized with the aim of developing deeper understanding on how structural changes affect the overall properties for CO2 separation. Important insights were gained illustrating the effects of substituents on the anion. It was found that substituents play a crucial role in dictating the overall physical properties of reactive ionic liquids. Depending upon the electronic and steric nature of the substituent{,} CO2 capacities between 0.07-0.4 mol CO2/mol IL were observed. Detailed spectroscopic{,} CO2 absorption{,} rheological{,} and simulation studies were carried out to understand the nature and influence of these substituents. The effect of water content was also evaluated{,} and it was found that water had an unexpected impact on the properties of these materials{,} resulting in an increased viscosity{,} but little change in the CO2 reactivity." } #+ENDEXAMPLE

Copyright (C) 2014 by John Kitchin. See the License for information about copying.

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