Biblatex: submitting to a journal

Question

Suppose that I moved from BibTeX to biblatex. With BibTeX I just copied the content of .bbl file into final version of my paper before submitting it to a journal. What should I do at same stage having .bbl file produced by biblatex? It is of quite different format.

Answer 1

it is also possible, but not so easy as with bibtex. When you finished your document write into the preamble after the already existing biblatex definition:

\documentclass{...}
...
\usepackage[style=numeric-verb]{biblatex}% change it for your needs 
\bibliography{examples}
%-------------- start insert modified commands ------------------
\makeatletter
\def\blx@bblfile@biber{%
  \blx@secinit
  \begingroup
  \blx@bblstart
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%% copy here the contents of the created bbl file
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  \blx@bblend
  \endgroup
  \csnumgdef{blx@labelnumber@\the\c@refsection}{0}}
\makeatother
%-------------- end insert modified commands ------------------
...
\begin{document}
...
\printbibliography
\end{document}

the only difference is that \printbibliography now takes the contents of the bib not from the external file but from the inserted bbl contents.

If you run bibtex instead of biber (btw: biber is the better choice) then you have to use it in this way:

\usepackage[...,backend=bibtex]{biblatex}
....
\def\blx@bblfile@bibtex{% instead of ...\blx@bblfile@@biber
  \blx@secinit
  \begingroup
  \blx@bblstart
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    %
    %% copy here the contents of the created bbl file
    %
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  \blx@bblend
  \endgroup
  \csnumgdef{blx@labelnumber@\the\c@refsection}{0}%
  \iftoggle{blx@reencode}{\blx@reencode}{}}

Pay attention that you do not insert the last line of the bblfile which is the command \endinput. This one should be deleted or commented with a preceding %.

Answer 2

For journal submission, I'm afraid my answer would be 'do not use biblatex'. The bibliography is generated at the LaTeX end by biblatex, and so it is not possible to 'paste in the formatted result'. Most journals want you to either do this or use their own BibTeX style, so biblatex is a bad choice. (This is a shame, but unless/until the journals update their workflows that is how it is.)

---

One point to note in particular is that you cannot be sure of the package or engine availability on journal systems. For example, the American Chemical Society do not have the e-TeX extensions available on their servers (at the time of writing). These were finalised in 1999, so the time lag is significant. biblatex requires e-TeX, so it would be impossible to use if for a submission to the ACS.

---

A second area to bear in mind is journal work flows. Depending on the journal, your LaTeX source may be converted into some other format for publishing. To do that, the publisher may use additional data written to the .bbl file (for example the data repeated in an XML 'comment') or some form of .bbl parser to convert the bibliography. That will not work with biblatex unless they have set up their workflow to deal with it.

Answer 3

This is a well-known problem, but a little workaround has recently been created: CTAN, GitLab

Usage

In preamble, after the biblatex package is loaded via \usepackage[...]{biblatex}:

\usepackage{biblatex2bibitem}

At the very end of document:

\printbibitembibliography

The desired bibitems will be written directly to the PDF file.

When it's time to switch to bibitems (e.g. before sending the paper to the journal), just copy them to your .tex file, remove biblatex commands and load cite package.

See also

• https://github.com/plk/biblatex/issues/783

• https://github.com/plk/biblatex/issues/292

• https://github.com/odomanov/biblatex-gost/issues/20 (in Russian)

Answer 4

I have spent some time on submitting through Springer's "Editorial manager", this may work for other submissions too. Although the latex system of the journal must not be too old.

Basically there are three problems that I have run into.

1. Match .bbl file with biblatex version. Just now "Editorial manager" uses texlive-2015, but my .bbl file is produced with texlive-2016 so "Editorial manager" biblatex version does not match my biber version. Solution: submit the biblatex style files.

2. Have "Editorial manager" accept the file extensions of the biblatex style files. "Editorial manager" forces most of the biblatex style files to be Supplementary material, and as such it is not available at compilation time. Solution: use the filecontents package to generate the biblatex style files from a .sty file.

3. "Editorial manager" does not accept the .bbl file anyway. I have noticed that any comments added at the beginning of the file makes biblatex think biber did not produce the file, and refuse to use it. Perhaps Editorial manager adds something, I do not know. Solution: use the filecontents package to generate the .bbl file.

To this end, I wrote a Python program to generate the needed .sty file, the below program assumes your .bbl file is named Manuscript.bbl:

#! /usr/bin/env python
from os import path

# Author: Jan-AAke Larsson <jan-ake.larsson@liu.se>

f=open("biblatex-files.sty","w")
f.write("""% File containing the needed environment for biblatex
% 
% Included here to bypass Editorial Manager heavy-handed file classification
% 
% The .bbl file needs to be included too, probably Editorial Manager adds
% a LaTeX comment header that makes biblatex think biber did not produce it 

% Enable overwriting files
\\RequirePackage{filecontents}


""")

for i in ["Manuscript.bbl",
    "/usr/share/texlive/texmf-dist/tex/latex/biblatex/biblatex.sty",
    "/usr/share/texlive/texmf-dist/tex/latex/biblatex/blx-dm.def",
    "/usr/share/texlive/texmf-dist/tex/latex/biblatex/blx-compat.def",
    "/usr/share/texlive/texmf-dist/tex/latex/biblatex/biblatex.def",
    "/usr/share/texlive/texmf-dist/tex/latex/biblatex/bbx/numeric.bbx",
    "/usr/share/texlive/texmf-dist/tex/latex/biblatex/bbx/standard.bbx",
    "/usr/share/texlive/texmf-dist/tex/latex/biblatex/cbx/numeric.cbx",
    "/usr/share/texlive/texmf-dist/tex/latex/biblatex/biblatex.cfg",
    "/usr/share/texlive/texmf-dist/tex/latex/biblatex/lbx/english.lbx"]:
    f.write("\\begin{filecontents*}{"+path.basename(i)+"}\n")
    g=open(i)
    for j in g.readlines():
        f.write(j)
    g.close()
    f.write("\\end{filecontents*}\n\n\n")
f.close()

This generates biblatex-files.sty that you can include in your submission instead of the .bbl file. The biblatex style files I found by doing grep latex/biblatex Manuscript.log, you may need to include other files if you use a different biblatex style than me. Of course, you need put the following in your preamble.

\usepackage{biblatex-files.sty}

In my submission there are now only two manuscript files: Manuscript.tex and biblatex-files.sty, and a collection of figures.

A final hint: a recurring problem in all this is that "Editorial manager" only returns the log file if LaTeX fails completely, otherwise an incomplete manuscript PDF. So there is no way to know what went wrong if there are warnings only and an incomplete PDF. If you run into problems and need to know the cause, I recommend putting the following in the preamble, this will include the LaTeX log at the end of your PDF. Do not OK this PDF in the submission system, though. :)

\usepackage{fancyvrb}
\AtEndDocument{\VerbatimInput{Manuscript.log}}

Answer 5

I fought with this myself for quite a bit, so I thought others might benefit:

IF the journal/repository actually runs biber (e.g. via latexmk) when compiling the document, then there is another simple option available (which is probably also the intended one):

1. Compile the original document as usual, using also biber. This gives you a file "article.bcf".

2. Create a .bib file containing only the cited references:

     biber --output-format=bibtex article.bcf 
   

   The outputfile should be named "article_biber.bib".

3. Enter "article_biber.bib" as a bibresource instead of your full library in "article.tex".
4. Send "article_biber.bib" along with the other files to the journal.

Note that biber version 2.9 is known to have a bug with the above output option. This is fixed in biber version 2.10. The binaries can be found here.

Biblatex has been around for quite a while now and has become somewhat established, so I think it is reasonable to ask of the journals/repositories to be able to handle it.