An annotated bibliography summarizes notes about papers being read during a research project. It is one of several methods for working with the knowledge gleaned from reading.
Org-mode is an enhanced markup language that supports the writing of scientific manuscripts. Org-mode descended from Outline-mode. It supports managing documents with a hierarchical structure. After folding the sections, subtrees of the document are easy to shuffle using the Meta-UP or Meta-Down keys. This feature eases the reorganizing of a doc. It was developed for use with the Emacs text editor.
The summary is stored in the annote field in the BibTeX entry in the BibTeX file, like in the example below:
This file was opened in Emacs. Emacs provided the line numbers and syntax highlighting (font locking in Emacs parlance).
When exported to a PDF, the org file reads the BibTeX file with formatting set by the apacannx.bst file. The top of the output PDF looks like the following:
I have also attached an Emacs configuration file (init.el) for working with manuscripts and annotated bibliographies in org-mode on macOS. This configuration includes the Vertico-Orderless-Corfu-Cape-Consult-Embark auto-completion stack, org-ref for managing bibliographies, and pdf-tools for viewing PDFs inside Emacs. This configuration depends on a handful of external packages. The init.el file takes 2-3 seconds to load. You will have to edit some file paths.
I swapped the option and command keys because I use the command key for the Meta key. I did not include org-agenda or org-roam.
Edit the file paths as needed. Takes a project ID as the only argument. Run from the top level of the writing project directory.
function abiborg {
echo "Create annotated bibliopgraphy subfolder and populate with required files with project number in title."
if [ $# -lt 1 ]; then
echo 1>&2 "$0: not enough arguments"
echo "Usage1: abiborg projectIndexNumber"
return 2
elif [ $# -gt 1 ]; then
echo 1>&2 "$0: too many projectIndexNumber"
echo "Usage1: abiborg projectIndexNumber"
return 2
fi
projectID="$1"
mkdir abib$1
cp ~/6112MooersLabGitHubLabRepos/annotated-bibliography-org/compile.sh ./abib$1/.
cp ~/6112MooersLabGitHubLabRepos/annotated-bibliography-org/apacannx.bst ./abib$1/.
cp ~/6112MooersLabGitHubLabRepos/annotated-bibliography-org/ab0519.bib ./abib$1/ab$1.bib
cp ~/6112MooersLabGitHubLabRepos/annotated-bibliography-org/ab0519.org ./abib$1/ab$1.org
}
function orgabib {
echo "Create annotated bibliopgraphy subfolder and populate with required files with project number in title."
if [ $# -lt 1 ]; then
echo 1>&2 "$0: not enough arguments"
echo "Usage1: orgabib projectDirectory"
return 2
elif [ $# -gt 1 ]; then
echo 1>&2 "$0: too many projectIndexNumber"
echo "Usage1: orgabib projectIndexNumber"
return 2
fi
projectID="$1"
mkdir abib$1
cp ~/6112MooersLabGitHubLabRepos/annotated-bibliography-org/compile.sh ./abib$1/.
cp ~/6112MooersLabGitHubLabRepos/annotated-bibliography-org/apacannx.bst ./abib$1/.
cp ~/6112MooersLabGitHubLabRepos/annotated-bibliography-org/ab0519.bib ./abib$1/ab$1.bib
cp ~/6112MooersLabGitHubLabRepos/annotated-bibliography-org/ab0519.org ./abib$1/ab$1.org
}
- git clone this project to your software directory
- Copy one of the bash function and paste into your .bashr or .zshrc file.
- source .bashrc
- cd project directory
- orgabib to create subfolder
- NIH: R01 CA242845
- NIH: R01 AI088011
- NIH: P30 CA225520 (PI: R. Mannel)
- NIH: P20 GM103640 and P30 GM145423 (PI: A. West)
| Version | Changes | Date |
|---|---|---|
| 0.1 | Initial commit. Added badges, funding, and update table. | 2024 August 17 |
| 0.2 | Updated compile.sh to take ProjectNumber as argument. Add bash function to ease install. | 2024 October 1 |
| 0.3 | Added to header code to add short author list, running title, date printed, and Page of N pages. | 2024 October 24 |