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README.md

IRIDIA BibTeX Repository

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This is a collection of BibTeX files organized in a way that tries to avoid redundancy, minimise mistakes and facilitate customization.

Most customizations (such as shorter journal or conference names) do not require changing the existing .bib files. You should not need to edit the entries directly unless you find mistakes. You only need to fork (or link) the git repository in your papers and sync with the main copy to send/receive updates.

PDF file listing all references: testbib.pdf

PDF with abbreviated references: testshortbib.pdf

HTML page listing all references: IRIDIA BibTeX Repository Webpage

NOTE: Before modifying a .bib file, please read and follow the instructions at the top of the file.

Table of Contents

Rationale

The main motivation for having a single repository is to incrementally fine-tune and perfect the references by sharing bibtex entries that have been curated over time by as many people as possible and that are used without further alteration. Significantly, while errors tend to persist if they were present when the entry was added, they are almost never introduced at a later phase since entries are almost never adjusted and any customization happens via overriding @String definitions. Thus, the quality of the references monotonically increases with time.

By contrast, manually copying and customizing a subset of entries often fails to backport any improvements, tends to introduce errors when entries are incorrectly modified for the sake of consistency and leads to repeated work and mistakes.

The motivation for the current separation between authors, journals, abbrev, biblio and crossref files is to avoid spurious divergences of common strings. In particular, keeping author names consistent is problematic given non-ascii characters, the not-so-obvious grouping rules for names with more than two words and differences between full names and abbreviated names. With the current system, there is a single definition of an author's name in authors.bib and any mistake will result in a warning for an undefined string when compiling with bibtex. Moreover, the @Strings labels tend to be shorter than what they expand to and they make searching / grepping much easier. In addition, the use of crossref.bib makes easier to keep consistency in the data for related publications (conference proceedings, book series, different editions).

Finally, the separation makes trivial to apply various "tricks", such as switching to abbreviated conference and journal names by overriding the desired @String definitions rather than editing the .bib files. Typical abbreviations are provided by abbrevshort.bib.

Some software tools (Mendeley, Zotero, etc) aim to achieve similar goals, however, they tend to introduce spurious fields, many of them fail to achieve consistency, they do not export correct bibtex entries in corner cases, and not everyone wishes to use the same software. The current system is software agnostic and can be used with any editor (although Emacs is certainly recommended).

In addition, this repository has further benefits: automatic generation of HTML and PDF output, which makes easier to search for entries, copy them to non-LaTeX documents and inspect them for errors; automatic testing with various BibTeX/BibLaTeX styles (.bst files) and checks for common errors in encoding entries; and the use of git branches allows users to have personal copies for specific papers, while making very easy to sync with the main branch.

Format of keys

When any bib entry is added, the key should be constructed following these rules:

  1. Only use alphanumeric characters plus :, -. Never use accents or non-ASCII characters.

  2. Use the first three letters of the first surname of each author (up to four authors, first letter capitalized), the full year of publication (if this is not known, make a good guess because this should not be changed afterwards and it is confusing that the year in the key does not match the year of publication), and the acronym of the conference, journal, or publisher. Examples:

      @Article{NouGhiBirDor2005ki,
         author = 	 {S. Nouyan and R. Ghizzioli and
                         M. Birattari and M.  Dorigo},
         journal = 	 KI,
         year = 	 2005,
  1. If there is a conflict, use another distinct single word, either from the title of the paper, or the title of the proceedings. Exceptions are:

    • Proceedings: keys should be the acronym of the proceedings followed by the year. Examples: ANTS2008, GECCO2010, etc.

    • Technical Reports: use the identificative key that technical reports often have, for example, IRIDIA-2009-015. Be careful to not use "/", "\" or "," in keys.

    • Theses (PhD, etc): after the year, add the type of thesis. Example: Birattari2004PhD.

Using the IRIDIA BibTeX Repository

The IRIDIA BibTex repository is essentially a collection of bib files, so all you need to do is to include these files in your paper.

The bib files define some commands, for example \MaxMinAntSystem. You can override any command by just defining it with \newcommand or \providecommand before the bibliography line. This trick also works for other commands defined by BibTeX styles (.bst). For example, disabling doi information can be normally achieved with \providecommand{\doi}[1]{}.

However, one of the purposes of this repository is to keep the list of references as independent as possible from the working paper(s), whenever possible. Hence, we suggest two main ways of setting up your local copy of the IRIDIA BibTex repository. The instructions below work for Linux/Mac, but can of course be adapted for Windows too.

Method A: Symbolic links

This method is suggested when working on your paper offline, whether you are using a versioning system for your paper or not. In case you use a versioning system to work on your paper with other collaborators, make sure everyone in the team uses the IRIDIA BibTex repository and follows the same instructions.

  1. Clone the repository

    cd /path/to/work/
    git clone https://github.com/iridia-ulb/references.git
    
  2. In the folder of the working paper, create a link to the local copy of the repository.

    cd /path/to/paper/
    ln -s /path/to/work/references references
    

    If you use a versioning system to work on the paper with other coauthors, do not add the link to the paper repository; instead, ask your collaborators to do the same in their working copy.

  3. In the main tex file of your paper, include the BibTex files with

     \bibliography{references/abbrev,references/journals,references/authors,references/biblio,references/crossref}
  4. See the sections "Updating", "Contributing", and "Before Submitting a paper".

Method B: fake submodule

This method is suggested in case you work on your paper (alone or with your collaborators) on web-based systems such as Overleaf.

  1. Within your existing local repository, create a fake submodule. The trailing "slash (/) is important!
    git clone https://github.com/iridia-ulb/references.git references
    git add references/
  1. Now git commands at the top directory operate in your own git repository, but git commands within the directory references operate in the iridia-ulb repository. The references directory will be available to all users of the repository, however, only the users who perform the above command can perform operations in the iridia-ulb repository.

  2. In the main tex file of your paper, include the BibTex files with

     \bibliography{references/abbrev,references/journals,references/authors,references/biblio,references/crossref}
  3. See the sections "Updating", "Contributing", and "Before Submitting a paper".

Method C: Branches and Worktrees

This method is suggested if you have write access to the iridia-ulb repository and you want to update the master repository frequently. The script setup_worktree.sh will do all these steps for you.

  1. Get a copy of the master repository in some folder, e.g., /path/to/references-master:
    git clone https://github.com/iridia-ulb/references.git /path/to/references-master
  1. Now, assuming that your paper resides in /path/to/mypaper, create a branch and a worktree for your paper:
    cd /path/to/references-master
    git worktree add -b mypaper /path/to/mypaper/references
  1. If you wish to import changes from the master branch, you do:
    cd /path/to/mypaper/references
    git rebase -i master
  1. If you wish to push changes to iridia-ulb master, you do:
    cd /path/to/references-master
    git merge --ff-only mypaper
    git push
  1. You can also easily find out which worktrees need to be merged into master:
    git branch --no-merged master

Other methods

You might prefer alternative ways of setting up the local copy of this repository. However, be aware that this might come with additional burden (for you) of managing the consistency and compatibility with the main central repository. We especially discourage methods that "break" the tracking of the changes, such as copying or linking single files.

Should you go this way (e.g. because you or your collaborators are already used to a certain workflow) please be aware that it will be your responsibility to keep your local copy updated, in particular when you submit your changes (see Section "Contributing").

Updating your working copy

You may update your working copy with the changes in the repository with the following command:

git pull

This will change your local files and you may need to resolve conflicts between your changes and the changes in the repository. To resolve a conflict, edit the file, look for markers such as:

>>>>
my change
---------
the repository change
<<<<<

Remove the incorrect text and the markers, save, commit and push the changes

    git add FILE
    git commit -m "FILE: conflict resolved"
    git push

Git may create a merge commit when you pull/push if you have local commits. It is better to configure git to replay your commits on top of the changes in the server:

git config branch.master.rebase true

If you are making many dirty commits locally before syncing with the server, it is better to create a branch/fork and merge it with master once you are ready.

Contributing to the IRIDIA BibTeX Repository

If you are a member of the iridia-ulb GitHub organization, or if you have been given access to the references repository, you can push your commits directly to the repository. Otherwise, you can submit your contribution with a pull request.

Before committing any change, follow first "Updating your working copy", then use

git diff

and

git status

to check that your local changes are really what you want to commit. Please do not commit changes that do not follow the rules described above and within each bib file. Changes that are not incremental to the latest online version will be rejected.

Add the files with the changes you want to submit to the repository using

git add LIST OF FILES

and commit the changes with any of the following commands:

git commit -m "log_message"
git commit -F LOG_MESSAGE_FILE
git commit

(see git help commit for more ways to specify the log message).

The third method will open an editor (set the environment variable $EDITOR to customize it) where you can write your commit message. The first line of the commit is equivalent to the "log_message" specified using the -m option, and it is essentially a title.

In case of a commit with many edits, it is recommended to use either the -F or the editor option, with the possibility of having a longer and more clear message body.

The commit message (log message) should be of the following form:

* file (entry): What changed.

Example:

    * biblio.bib (AngWoo2009:ejor): New entry.
    (Asc2001t:cor): Update year.
    * crossref.bib (GECCO2000): Fix editor names.

Finally, push the commits to the repository with

git push

IMPORTANT: If you use non-ASCII characters BE SURE that your editor uses UTF8 encoding. Otherwise, DO NOT USE non-ASCII characters.

IMPORTANT: If you have modified a tex or bib file (as it is often the case), the push will trigger a compilation using the Travis continuous integration system (which should take at most a couple of minutes). If the compilation fails, you will receive an email; in this case, fix the error and retry. If the build is successful, the resulting file test/testbib.pdf will be automatically pushed to the repository. This automatic step is effectively a new commit, so make sure you do another

git pull

to sync your local repo before modifying again the files.

Before submitting a paper

If you prefer to not submit several *.bib files, just use the program aux2bib to generate a BibTeX file with only the entries that you are using.

If you find a mistake on the generated file or want to add new entries, you should modify your working copy, and then run aux2bib again to regenerate the file.

Some bibtex styles generate separated entries for cross references. See the corresponding answer in the FAQ below.

If you want to modify a bibtex style to use short names (only the initial for the name), edit the *.bst file, search for something such as:

    {ff~}{vv~}{ll}{, jj}" format.name$

and replace it with:

    {f.~}{vv~}{ll}{, jj}" format.name$

List of most often used git commands

This is a very basic list of the most useful commands, to get the most out of Git, please read the book: https://git-scm.com/book/en/

An explanation of the commands can also be found with

    git help

in general, or

    git help COMMAND

to get the various option of the specific command COMMAND.

  • Checkout a copy of the files to some directory:

      git clone https://github.com/iridia-ulb/references references
    
  • Update your local copy with the changes in the repository

      git pull
    

    (avoid empty merge commits with git config branch.master.rebase true or git pull --rebase)

  • See your local changes (both staged and not staged yet)

      git diff HEAD
    
  • See the current status of your local copy, such as which files have been modified since the last commit, or which files are untracked

      git status
    
  • Select the files that you want to include (stage) in the commit. There might be files with changes not yet ready for commit, so include only what you consider to be in a consistent state

      git add LIST OF FILES
    
  • Commit changes to your local repository:

      git commit -m "log_message"
      git commit -F COMMIT_FILE
      git commit
    

    (see git help commit for more ways to specify the log message). The third method will open an editor (set the environment variable $EDITOR to customize it) where you can write your commit message. The first line of the commit is equivalent to the "log_message" specified using the -m option, and it is essentially a title.

  • Send changes to the github repository:

      git push
    

BibTeX Advice

There is advice at the top of each .bib file about the contents within that file. The following is general advice on how to format bib entries.

  • Do not use non-ASCII characters unless you use UTF-8. It may be better to just use LaTeX syntax instead, that is, instead of "í" use {\'i}. In Emacs, one can use '(occur "[^[:ascii:]]"))' to find all non-ASCII characters.

  • Do not use \i to create accented letters. biblatex does not like it and it will complain. Using {\'i} should produce the correct results.

  • 'doi' field is just the DOI, without the http://dx.doi.org/

Frequently Asked Questions

Q: Why are there so many rules?

A: An incomplete list of reasons:

  • Rules are there to prevent mistakes that may not be obvious in your document but that will be when using a different citation style (author-year, numerical, alphanumerical, ...) and/or bibliography style.

  • We owe to authors whom we cite that we reference their work as faithfully as possible. Rules are there to ensure consistency and correctness.

  • References in published work are often parsed by machines to determine citation counts. If the reference is incorrect or not detailed enough, the citation may not be counted correctly by such systems.

  • Experience has shown that there are some common tricks and tips that are rather obscure but prevent certain errors. Many of the rules are inspired by the document: BibTeX Tips and FAQ.

Q: Why not take the entries directly from Google Scholar, DBLP, Elsevier,...?

A: BibTeX entries generated by Google Scholar and Citeseer are of extremely poor quality and should NEVER be trusted. Entries generated by DBLP are much better but they often use the full title of proceedings, which includes the date and location of the conference in the title, as the @booktitle, which is impractical. Also, fields that only matter to DBLP, such as @bibsource, are useless and should be removed. BibTeX entries provided by publishers such as ACM, Elsevier or Springer are often wrong and contradict their own suggested way of citing a work. It is often better to look at how they suggest to cite it and write a BibTeX entry that recreates it.

Q: Some entries don't have DOI. This is inconsistent. Or I don't like the DOIs in the references list

A: Ideally, we would have the DOI of everything, since it helps to find the actual paper and verify its details. Let the bibtex style control whether to show it or not. In practice, it is very easy to hide all DOIs, either by redefining the command that prints the doi or commenting out a few lines in the bibtex style. Thus, one should ALWAYS add a DOI if possible.

Q: Some entries are Proceedings published by LNCS but the entry does not mention the word "Proceedings" or "Conference"

A: Those are the official names of the books (except for mistakes that should be fixed). This is how Springer recommends to cite them and how DBLP cites them. There is no reason to call the book by a different title from its actual title.

Q: Do we need to mention that the Proceedings are published by LNCS? Why not use @Proceedings for those?

A: There is an important difference in terms of publication importance. LNCS are books (@Book) published by Springer and they contain peer-reviewed article-length papers/chapters. That is different from conference proceedings (@Proceedings) published by the conference organisation themselves that may not be available in book form, may not be peer-reviewed and may contain only abstracts. Citations from/to LNCS are counted by JCR. For some funding agencies, LNCS count almost as much as journal publications.

Q: A journal insists on using "Springer-Verlag" instead of "Springer", how to change everything?

A: You could generate the *.bbl file once and edit it, but if you need to recompile the bibliography, you'll have to edit it again.

A better way is to create a dummy.bib file with:

    @string{springer = "Springer-Verlag"}
    @string{springer-lncs = "Springer-Verlag, Heidelberg, Germany"}

... and so on, and then include it after abbrev.bib:

    \bibliography{abbrev,authors,journals,dummy,biblio,crossref}

Q: I want to save space and abbreviate journal names and titles of books. Should I just edit the journal.bib and abbrev.bib files?

A: You could do that, but you cannot commit the changes. So it would be cumbersome for you to maintain your own copy.

You could generate the *.bbl file once and edit it, but if you need to recompile the bibliography, you'll have to edit it again.

The best way is to add the shorter variants to abbrevshort.bib, and then include it after both abbrev.bib and journals.bib:

    \bibliography{abbrev,authors,journals,abbrevshort,biblio,crossref}

Moreover, if you want to abbreviate titles of books but not journal names, then use:

    \bibliography{abbrev,authors,abbrevshort,journals,biblio,crossref}

Q: I want to save space and reduce the number of editors (say et al. for any editor after the first one), or remove all DOIs, URLs, publisher address or other such fields. Can I edit the .bib files?

A: You could do that, but you cannot commit the changes since the additional information could be useful for others. It would be cumbersome for you to maintain your own copy, so an automatic way to make these changes would be better.

The best way is to edit the BibTeX style file (.bst) to not emit these fields. Unfortunately, editing .bst files is sometimes not trivial, but often one can find examples in Internet. If you edit a popular bst file to make it shorter, commit the new version to optbib so others can use it. Currently, there is an abbreviated version of Springer's LNCS bst file.

Q: I made a mistake in the commit message. Can this be fixed?

A: Yes, using: git commit --amend. More information here.

Q: There is a separate entry for each cross-reference, and individual references cite it. I think it is ugly, how to prevent this?

A: Unhelpfully, bibtex generates by default separated entries for cross references. To avoid this, use bibtex -min-crossrefs=9000. Or use the bibtex wrapper included in the repository. If you use Overleaf, you can add a file .latexmkrc with the following line:

$bibtex = "bibtex -min-crossrefs=999 %O %S";

Q: Why I should not use {{Title}} in title? If not, should I use title case or sentence case?

A: Because it prevents the bibtex style to change the case of the title to the style used by the journal, it breaks consistency: Some titles will be in a case style different from others. In fact, most journals use sentence case for journal papers. Sentence case is like "This is a title". However, some journals use title case: "This Is a Title". Since a bibtex style can convert from title case to sentence case, but not the other way around, it is always better to use title case in bib files without adding braces around the whole title. That is, instead of:

title = {{This is a title that Manuel likes}}

use

title = "This Is a Title that {Manuel} Likes"

Q: I want to keep an eye on someone else altering my references by mistake.

A: You can click on the "Watch" and "Star" buttons on top of the GitHub page. You can also fork the repository and only merge changes into your fork that you have reviewed.

Q: I want to highlight the name of some authors.

A: There are at least two ways to accomplish this.

  • Method 1: Edit the .bst file

You need to edit the .bst file. For example, for plain.bst, you would add:

FUNCTION {cv.author}
{ "L{\'o}pez-Ib{\'a}{\~n}ez, M." } 

FUNCTION {highlight}
{ duplicate$ empty$
      { pop$ "" }
      { "\textcolor{red}{" swap$ * "}" * }
   if$
}

FUNCTION {highlight.if.cv.author}
{ duplicate$ purify$ cv.author purify$ =
    { highlight }
    'skip$
  if$
}
FUNCTION {format.author.names}
{ 's :=
  #1 'nameptr :=
  s num.names$ 'numnames :=
  numnames 'namesleft :=
    { namesleft #0 > }
    { s nameptr "{vv~}{ll}{, jj}{, f{.}.}" format.name$ highlight.if.cv.author
      't :=
      nameptr #1 >
	{ namesleft #1 >
	    { ", " * t * }
	    { numnames #2 >
		{ "," * }
		'skip$
	      if$
	      t "others" =
		{ " et~al." * }
		{ " and " * t * }
	      if$
	    }
	  if$
	}
	't
      if$
      nameptr #1 + 'nameptr :=
      namesleft #1 - 'namesleft :=
    }
  while$
}
  • Method 2: Rewrite names with an extra .bib file.

For this method to work, the names have to be encoded in authors.bib. Then, we can create a file highlight.bib:

@String{Lopez-Ibanez = " \textcolor{red}{Manuel} \textcolor{red}{L{\'o}pez-Ib{\'a}{\~n}ez} "}

And include it just after authors.bib:

\bibliography{references/abbrev,references/journals,references/authors,highlight.bib,references/biblio,references/crossref}

Q: Should I only use entries from the repository? What should I do if I'm in a hurry or unsure about the correctness of an entry?

A: Since the goal is to share high-quality entries rather than a comprehensive repository, it is better to not add entries if one is unsure about correctness and short of time to double-check and fix them. In that case, it is better to keep those entries in a separate personal .bib file until one has time to fix them and submitted to the main repository.

Copyright

To the extent that the contents of bib files may be subject to copyright, the contents of the IRIDIA BibTeX Repository are placed under the public domain by associating it to the Creative Commons CC0 1.0 Universal license (http://creativecommons.org/publicdomain/zero/1.0/).

As a personal note, we will appreciate if modifications are submitted back to us for consideration.

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