BibTeX, biblatex and biber ⇒ Advanced citing - What package combination are you using?

[twotoneblue]

Dear everyone,

I am a recent LaTeX-user, and I am loving the flexibility and esthetically pleasing result it gives when writing scientific documents. At the moment, I find myself in the quite steep learning curve of the LaTeX-language. To learn faster I am using both LyX and Kile, looking at the source generated by LyX to generate the document elements that I am interested in. I should also state that I enjoy Linux(Ubuntu 9.04) as my OS of choice, where I use JabRef to manage my BibTeX-file containing the references of hundreds of articles and books.

Being a worker in organic chemistry, publications are important documentations of our labour and thus the style of these even more so. Let me use an image to introduce my question:

citationss.jpeg (133.04 KiB) Viewed 14900 times

The markings on the image mean to draw attention to a couple of dynamic uses of citations in chemical literature:

1. 1 - the grouping of references into a sublist of a single bibliographic element (one of the multiple citation bibliographical styles), and the use of specified elements(here letters in the citation of "9bc,11b,39") of a sublist i.e. when re-citing selected publications of relevance to a given argument, having already cited the group as a whole in an earlier more general argument

1. 2 - the use of notes in the bibliography to give additional information i.e. to mention an experimental detail, or to point out that one of the references is a review

1. 3 - the direct citation of a complete reference in the middle of the text, in this example within the bibliographical note(here the note+reference in citation "38")

1 can be achieved, in part, using the mciteplus bundle. I can't, however, control the citation style to the detail of citing specific sublist components.

2 would correspond to a \bibnote in the notes2bib bundle, which actually works quite well, except for not always updating if the \bibnote is changed(in LyX this can be solved by dissolving and reconstructing the TeX code entry(CTRL-L)

3 is possible using the \bibentry package from the natbib bundle, but I can't seem to make it work using the \usepackage{bibentry} \nobibliography* combination in the preamble, as I also need to show the bibliography at the end of the document.

As you've already noticed in the topic, I am interested to hear what working combinations you are using, as there are several possible packages that can be used to achieve detailed control of citations (natbib, jurabib, biblatex, mciteplus, chemstyle, notes2bib to mention a few)

It would be of great value to me, and hopefully to many others, to see an example of a working LaTeX or LyX document that is up to the mentioned challenges, especially the citing of (non-consecutive) sublist elements!

Your replies are much appreciated.

[phi]

A very challeging problem! I'd probably go for biblatex because I think this package provides a quite flexible yet consistent interface. However, currently I don't know where to start. If you don't get an answer here, try to post on comp.text.tex.

[twotoneblue]

Hi there,
Thanks for your answer. The specific citation style is indeed a challenge.
Probably I just need some help to edit and implement a citestyle-file or the like
I will post on comp.text.tex if we can't figure it out here

[josephwright]

Dear everyone,
1 can be achieved, in part, using the mciteplus bundle. I can't, however, control the citation style to the detail of citing specific sublist components.

You should be able to cite a specific entry with \mciteSubRef (see the manual p. 8). Speaking personally, I prefer it when people separate out items they will cite separately:

We followed the literature (1,2), and then took a particular procedure (2) and ...

(1) a) ... b) ... c) ...
(2) One reference only.

2 would correspond to a \bibnote in the notes2bib bundle, which actually works quite well, except for not always updating if the \bibnote is changed(in LyX this can be solved by dissolving and reconstructing the TeX code entry(CTRL-L)

Not quite sure why that is happening. notes2bib always writes a new BibTeX database on each LaTeX run, so as long as you run BibTeX between each LaTeX run all should be well. Perhaps Lyx does not do this? I use LaTeX "raw", so I don't know.

3 is possible using the \bibentry package from the natbib bundle, but I can't seem to make it work using the \usepackage{bibentry} \nobibliography* combination in the preamble, as I also need to show the bibliography at the end of the document.

Not sure I follow: could we have an example, please.

As I've written or been involved with several of the packages you mention, I've got a good feel for what is needed for chemists. biblatex covers almost everything, and if it had a slightly different method to handle sub-lists it would be ideal. As I'm a LaTeX developer, I might see what can be done about that.

[twotoneblue]

Thanks a lot for the answers, JW. I quite agree with your statement about rational citing. It is important to build the text in this perspective from the beginning.

The sublistitem-specific citing can earn its right to life when you need to point out a special publication within a group of previously cited publications.
A poor example(I will have to do it without superscripts):

...this reaction has been employed in the synthesis of several natural products [1]... || ...in the synthesis of Lomaiviticin B [1c] the standard work-up procedure [1a] proved itself inadequate....

References and Notes
[1] a) b) c) d) %% belonging to one theme
[2] a) b) c) d) %% belonging to some other theme
[3] A note for the enthusiast

I am of the opinion that when the bibliography is large, having the references in thematic groups(in the poor example: natural product synthesis utilizing a given reaction), makes the bibliography more informative and more easily searched.

Anyway, I am rambling, let's get to the follow-up questions:
1)
I can make the \mciteSubRef{cite key} work, but only with one item of the sublist i.e. it will complain about \mciteSubRef{cite key, cite key} or \mciteSubRef{cite key,*cite key}

Also, the formatting of the default output is i.e. "9.b" , and I would like it to be "9b" in superscript like in the example pictures.
- Can I edit this somewhere?

3)
I am sorry I expressed myself unclearly. An example for my /bibentry-question would be; say you want to write an entry in the bibliography i.e. using \bibnote, in the middle of which you want to state a full reference/citation(which is the correct word?), pulling it from the bibfile instead of having to type it in by hand.
I will borrow the example from the journal clippings above:

You write:

Code: Select all

\bibnote{ Such an orientation...with R-diazoester: \bibentry{Salvatella2001} }

To get the following in the bibliography:

(38) Such orientation of ester carbonyl group was also noted in theoretical studies
of copper-catalyzed cyclopropanation reaction with R-diazoester: Fraile,
J. M.; García, J. I.; Martínez-Merino, V.; Mayoral, J. A.; Salvatella, L. J.
Am. Chem. Soc. 2001, 123, 7616-7625.

The thing is, I can't make this work putting the following in the preamble: \usepackage{bibentry}
\nobibliography*
and when I want to print a reference/citation, I would issue
\bibentry{cite key}

But I get no error in LyX(probably because of the batch-mode), and nothing is printed in the spot I issued the code. If I saw an example file, I feel pretty sure I could figure out what I am doing wrong.

4)
A new question:
I am currently using the achemso-bibliography style (by Joseph Wright) modified as described in the mciteplus documentation to suit the mciteplus-package. How can I get the Angewandte-style(initials before lastname) in my bibliography?
- Can I edit my achemso-mciteplus.bst in any particular spot to effect this change?


In the meantime - let us sign the campaign for a new and better sublist handling in biblatex!

[josephwright]

4)
A new question:
I am currently using the achemso-bibliography style (by Joseph Wright) modified as described in the mciteplus documentation to suit the mciteplus-package. How can I get the Angewandte-style(initials before lastname) in my bibliography?
- Can I edit my achemso-mciteplus.bst in any particular spot to effect this change?

With the latest version of achemso (v3.3a) you should be able to use the BibTeX style file with mciteplus with no editing at all (it is designed to work with mciteplus and "degrade gracefully" if it is not in use). The Angew. Chem. style I've produced in the rsc bundle works in the same wayy. So all you need to do is change

\bibliographystyle{achemso}

to

\bibliographystyle{angew}

and all should be fine. Just make sure you have the latest versions from CTAN.

[twotoneblue]

Dear everyone,

JW, thanks for making the Angewandte bibstyle compatible with mciteplus (which you also coauthored) and making these packages available to us all. It is of great significance to chemists all around the world.

I have decided to try to get this working with Kile, so I am trying out a test file, based on the rsc-demo.tex example file:

Code: Select all

\documentclass[a4paper]{article}

\usepackage[T1]{fontenc} % Modern font encoding
\usepackage{float}       % For creating charts, graphs and schemes
\usepackage{helvet}      % Helvetica font for sans serif
\usepackage{mathptmx}    % Times font ("Word-like")
\usepackage{rsc}         % Loads natbib, etc.
\usepackage{setspace}    % For double-spacing
\AtBeginDocument{\doublespacing}

\newfloat{chart}{htbp}{loc}
\newfloat{graph}{htbp}{loh}
\newfloat{scheme}{htbp}{los}

\usepackage[version=3]{mhchem} % Formula subscripts using \ce{}

%% My preamble additions
\usepackage{notes2bib}
\usepackage{mciteplus}
%% End my preamble additions

\begin{document}


\section{Introduction}

An argument \bibnote{Well, it is not really an argument} 
about \ce{Rh2L4} with support in the literature \cite{Amat1996,*Amat1997},
 followed by another one \cite{Amat2001,*Amat1997a,*Coelho2008}.

\bibliographystyle{angew}
\bibliography{refs}

\end{document}

I run the LaTeX-BibTex-LaTeX-LaTeX sequence, however, it does not make the sublists from mciteplus appear.
Also, the number [1] in the bibliography is empty (in the test.bbl the first bibitem states \bibitem{rsc-control} )

All files are uploaded under the name test.* in the archive test.tar.gz
I have certainly made a mistake somewhere - it would be great if you would have a look and point out to me what it is I have left out.

[josephwright]

Dear everyone,
I run the LaTeX-BibTex-LaTeX-LaTeX sequence, however, it does not make the sublists from mciteplus appear.
Also, the number [1] in the bibliography is empty (in the test.bbl the first bibitem states \bibitem{rsc-control} )

There is nothing wrong with your test files: I get a proper compilation if I run your files on my system. The clue to the issue is in your .blg (BibTeX log) file:

Warning--entry type for "rsc-control" isn't style-file defined
--line 4 of file rsc-test.bib
Database file #2: niib-test.bib
Database file #3: refs.bib
`title' is a missing field, not a string, for entry rsc-control
while executing---line 1032 of file angew.bst
Warning--all relevant fields are empty in rsc-control
`title' is a missing field, not a string, for entry Bibnote1
while executing---line 1032 of file angew.bst

BibTeX doesn't list the version numbers, so I am slightly guessing, but this looks to me like you have an older version of agnew.bst on your system. The mciteplus compatibility is a newer feature, so you probably should grab the entire rsc bundle from CTAN and do a local installation.

[twotoneblue]

Your intuition is excellent, JW!
I did indeed have previous(2007) rsc, achemso and natbib bundles on my system. Replacing with the new ones and doing a texhash was all it needed! I think I see the interest of a local install when using specialized packages.

Now the only thing that remains, is the formatting of the \mciteSubRef{cite key} - that is it outputs "9.b" in the same font and I would prefer "9b" in superscript. (the superscript can be fixed by using $^{\mciteSubRef{cite key}}$ )
Can I edit this somewhere to make it default?

Also, is it possible to refer to several bibliography sublist-items and stack them into one citation - as in "9bc" or even a list "9a-c"? EDIT: I just read in the documentation that it will only accept 1 cite key


best regards
Aasmund

PS. To correct my own mistake above about the capabilities of the bibentry package: It can output a full reference based on the cite key as given in the .bib file, however it will also include an item(number) in the bibliography. So, in my case that would mean an entry with notes+reference and then another entry repeating the reference - which doesn't make much sense.

[josephwright]

Now the only thing that remains, is the formatting of the \mciteSubRef{cite key} - that is it outputs "9.b" in the same font and I would prefer "9b" in superscript. (the superscript can be fixed by using $^{\mciteSubRef{cite key}}$ )
Can I edit this somewhere to make it default?

Look at the \mcitesubrefform function:

Code: Select all

\renewcommand*\mcitesubrefform{%
  \textsuperscript{\arabic{mcitebibitemcount}\alph{mcitesubitemcount}}%
}

seems to work for me.

Also, is it possible to refer to several bibliography sublist-items and stack them into one citation - as in "9bc" or even a list "9a-c"? EDIT: I just read in the documentation that it will only accept 1 cite key

Yes, as you say there are limitations (if we can get Philipp to modify biblatex then life would be easier).