Abbreviated journal names in bibtex

Posted October 11, 2014 at 05:31 PM | categories: bibtex | tags:

Some journals require abbreviated journal names in the bibliography, and some require full names. Unfortunately, it is not possible to have both in your bibtex file. Or is it…

It is possible to define a @string that is replaced in your bibtex file. If we have the definition of the @string in a separate file, we can specify its definition there, e.g. as an abbreviation, or as the full name. To make this useful, we need a simple way to add new journals, and to generate the definitions.

First, you can find accepted journal name abbreviations here: http://cassi.cas.org/search.jsp .

We are going to define a variable to hold the string definition, journal full name and an abbreviation. You can find our production version of what follows here: https://github.com/jkitchin/jmax/blob/master/jmax-bibtex.el 

(defvar jmax-bibtex-abbreviations
  '(("ACAT" "ACS Catalysis" "ACS Catal.")
    ("AM" "Acta Materialia" "Acta Mater.")
    ("AMM" "Acta Metallurgica et Materialia" "Acta Metall. Mater.")
    ("AMiner" "American Mineralogist" "Am. Mineral.")
    ("AngC" "Angewandte Chemie-International Edition" "Angew. Chem. Int. Edit.")
    ("APLM" "APL Materials" "APL Mat.")
    ("ACBE" "Applied Catalysis B: Environmental" "Appl. Catal. B-Environ.")
    ("APL" "Applied Physics Letters" "Appl. Phys. Lett.")
    ("ASS" "Applied Surface Science" "Appl. Surf. Sci.")
    ("CL" "Catalysis Letters" "Catal. Lett.")
    ("CT" "Catalysis Today" "Catal. Today")
    ("CPL" "Chemical Physics Letters" "Chem. Phys. Lett")
    ("CR" "Chemical Reviews" "Chem. Rev.")
    ("CSR" "Chemical Society Reviews" "Chem. Soc. Rev.")
    ("CSR" "Chemical Society Reviews" "Chem. Soc. Rev.")
    ("CM" "Chemistry of Materials" "Chem. Mater.")
    ("CSA" "Colloids and Surfaces, A: Physicochemical and Engineering Aspects" "Colloids Surf., A")
    ("CPMS" "Computational Materials Science" "Comp. Mater. Sci.")
    ("CPC" "Computer Physics Communications" "Comput. Phys. Commun.")
    ("CGD" "Crystal Growth \\& Design" "Cryst. Growth Des.")
    ("CEC" "CrystEngComm" "CrystEngComm")
    ("ECST" "ECS Transactions" "ECS Trans.")
    ("EES" "Energy \\& Environmental Science" "Energy Environ. Sci.")
    ("HPR" "High Pressure Research" "High Pressure Res.")
    ("IC" "Inorganic Chemistry" "Inorg. Chem.")
    ("IECR" "Industrial \\& Engineering Chemistry Research" "Ind. Eng. Chem. Res.")
    ("JJAP" "Japanese Journal of Applied Physics" "Jpn. J. Appl. Phys.")
    ("JMatR" "Journal of  Materials Research" "J. Mater. Res.")
    ("JALC" "Journal of Alloys and Compounds" "J. Alloy Compd.")
    ("JAC" "Journal of Applied Crystallography" "J. Appl. Crystallogr.")
    ("JAP" "Journal of Applied Physics" "J. Appl. Phys.")
    ("JC" "Journal of Catalysis" "J. Catal.")
    ("JCP" "Journal of Chemical Physics" "J. Chem. Phys.")
    ("JCG" "Journal of Crystal Growth" "J. Crys. Growth")
    ("JMC" "Journal of Materials Chemistry" "J. Mater. Chem.")
    ("JMC" "Journal of Materials Chemistry" "J. Mater. Chem.")
    ("JMSL" "Journal of Materials Science Letters" "J. Mater. Sci. Lett.")
    ("JMS" "Journal of Membrane Science" "J. Memb. Sci.")
    ("JPE" "Journal of Phase Equilibria" "J. Phase Equilib.")
    ("JPCS" "Journal of Physics and Chemistry of Solids" "J. Phys. Chem. Solids")
    ("JPCM" "Journal of Physics: Condensed Matter" "J. Phys.: Condens. Matter")
    ("JSSC" "Journal of Solid State Chemistry" "J. Solid State Chem.")
    ("JACerS" "Journal of the American Ceramic Society" "J. Am. Ceram. Soc.")
    ("JACS" "Journal of the American Chemical Society" "J. Am. Chem. Soc.")
    ("JES" "Journal of The Electrochemical Society" "J. Electrochem. Soc.")
    ("JES" "Journal of The Electrochemical Society" "J. Electrochem. Soc.")
    ("JMS" "Journal of Membrane Science" "J. Memb. Sci.")
    ("JVST" "Journal of Vacuum Science \\& Technology A" "J. Vac. Sci. Technol. A")
    ("ML" "Materials Letters" "Mater. Lett.")
    ("MSE-BS" "Materials Science and Engineering B" "Mat. Sci. Eng. B-Solid")
    ("MOLSIM" "Molecular Simulation" "Mol. Sim.")
    ("Nature" "Nature" "Nature")
    ("NM" "Nature Materials" "Nat. Mater.")
    ("PML" "Philosophical Magazine Letters" "Phil. Mag. Lett.")
    ("PMA" "Philosophical Magazine A" "Phil. Mag. A")
    ("PA" "Physica A: Statistical Mechanics and its Applications" "Physica A")
    ("PB" "Physica B-Condensed Matter" "Physica B")
    ("PCCP" "Physical Chemistry Chemical Physics" "Phys. Chem. Chem. Phys.")
    ("PSSB" "physica status solidi (b)" "Phys. Status Solidi B")
    ("PRA" "Physical Review A" "Phys. Rev. A")
    ("PRB" "Physical Review B" "Phys. Rev. B")
    ("PRL" "Physical Review Letters" "Phys. Rev. Lett.")
    ("PCM" "Physics and Chemistry of Minerals" "Phys. Chem. Miner.")
    ("PSurfSci" "Progress in Surface Science" "Prog. Surf. Sci.")
    ("Science" "Science" "Science")
    ("SABC" "Sensors and Actuators B: Chemical" "Sensor. Actuat. B-Chem.")
    ("SS" "Surface Science" "Surf. Sci.")
    ("EPJB" "The European Physical Journal B" "Eur. Phys. J. B")
    ("JPC" "The Journal of Physical Chemistry" "J. Phys. Chem.")
    ("JPCB" "The Journal of Physical Chemistry  B" "J. Phys. Chem. B")
    ("JPCC" "The Journal of Physical Chemistry C" "J. Phys. Chem. C")
    ("JCP" "The Journal of Chemical Physics" "J. Chem. Phys.")
    ("TSF" "Thin Solid Films" "Thin Solid Films")
    ("TC" "Topics in Catalysis" "Top. Catal.")
    ("WR" "Water Research" "Water Res."))
  "List of (string journal-full-name journal-abbreviation)")

bibtex-abbreviations

This data structure will serve a few purposes.

  1. We will generate the bib files that define the @string definitions
  2. We will use it to modify bibtex files to use those strings.

First, here are some simple functions to generate the @string definitions. 

(defun jmax-bibtex-generate-longtitles ()
  (interactive)
  (with-temp-file "longtitles.bib"
    (dolist (row bibtex-abbreviations)
      (insert (format "@string{%s=\"%s\"}\n"
                      (nth 0 row)
                      (nth 1 row))))))

(defun jmax-bibtex-generate-shorttitles ()
  (interactive)
  (with-temp-file "shorttitles.bib"
    (dolist (row bibtex-abbreviations)
      (insert (format "@string{%s=\"%s\"}\n"
                      (nth 0 row)
                      (nth 2 row))))))

jmax-bibtex-generate-shorttitles

(jmax-bibtex-generate-longtitles)
(jmax-bibtex-generate-shorttitles)

Here are the results of running that code: shorttitles.bib and longtitles.bib . This is the first step. We have the @strings defined. Now, we need to convert the names in a bibtex entry to use our string. We want to replace full names and abbreviated names with the @string. 

(defun jmax-stringify-journal-name (&optional key start end)
  "replace journal name with a string. The strings are defined in `bibtex-abbreviations'."
  (interactive)
  (bibtex-beginning-of-entry)
  (when
      (string= "article"
               (downcase
                (cdr (assoc "=type=" (bibtex-parse-entry)))))
    (let* ((full-names (mapcar
                        (lambda (row)
                          (cons  (nth 1 row) (nth 0 row)))
                        bibtex-abbreviations))
           (abbrev-names (mapcar
                          (lambda (row)
                            (cons  (nth 2 row) (nth 0 row)))
                          bibtex-abbreviations))
           (journal (s-trim (bibtex-autokey-get-field "journal")))
           (bstring (or
                     (cdr (assoc journal full-names))
                     (cdr (assoc journal abbrev-names)))))
      (when bstring
        (bibtex-set-field "journal" bstring t)
        (bibtex-fill-entry)))))

jmax-stringify-journal-name

Now, with a single command, we can convert this: 

@article{lizzit-2001-surfac-ru,
  author =       {S. Lizzit and A. Baraldi and A. Groso and K. Reuter
                  and M. Ganduglia-Pirovano and C. Stampfl and
                  M. Scheffler and M. Stichler and C. Keller and
                  W. Wurth and D. Menzel},
  title =        {Surface Core-level Shifts of Clean and
                  Oxygen-covered {R}u(0001)},
  journal =      {Physical Review B,
  volume =       63,
  number =       20,
  pages =        {nil},
  year =         2001,
  doi =          {10.1103/physrevb.63.205419},
  url =          {https://doi.org/10.1103/PhysRevB.63.205419},
  month =        5,
}

into this: 

@article{lizzit-2001-surfac-ru,
  author =       {S. Lizzit and A. Baraldi and A. Groso and K. Reuter
                  and M. Ganduglia-Pirovano and C. Stampfl and
                  M. Scheffler and M. Stichler and C. Keller and
                  W. Wurth and D. Menzel},
  title =        {Surface Core-level Shifts of Clean and
                  Oxygen-covered {R}u(0001)},
  journal =      PRB,
  volume =       63,
  number =       20,
  pages =        {nil},
  year =         2001,
  doi =          {10.1103/physrevb.63.205419},
  url =          {https://doi.org/10.1103/PhysRevB.63.205419},
  month =        5,
}

If you have a lot of entries you want to modify, you can use bibtex-map-entries like this. Basically, put the elisp form in a comment, and then execute the elisp form 

%% (bibtex-map-entries 'jmax-stringify-journal-name)  <- put cursor here. C-x C-e

This saves some effort. Over time, I will keep adding entries to the abbreviation table. As long as a standard journal name or abbreviation is in your bibtex file, this approach should work pretty well. After you replace the journal names with @string entries, you have to generate the string file, either shorttitles.bib or longtitles.bib, and in your LaTeX file, change your bibliography line to: 

\bibliography{shorttitles,references}

The order is important. The @string definitions are in shorttitles.bib, and your bibtex entries in references.bib.

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

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