{"id":15062874,"url":"https://github.com/mooerslab/annotated-bibliography-org","last_synced_at":"2026-02-28T04:13:43.880Z","repository":{"id":253567145,"uuid":"843886334","full_name":"MooersLab/annotated-bibliography-org","owner":"MooersLab","description":"Template for making annotated bibliography in org-mode","archived":false,"fork":false,"pushed_at":"2024-10-24T12:23:23.000Z","size":231,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-22T04:33:29.481Z","etag":null,"topics":["emacs","knowledge-management","manuscript-preparation","note-taking","org-mode"],"latest_commit_sha":null,"homepage":"","language":"Emacs 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Lisp","funding_links":[],"categories":[],"sub_categories":[],"readme":"![Version](https://img.shields.io/static/v1?label=annotated-bibliography-org\u0026message=0.3\u0026color=brightcolor)\n[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)\n\n\n# Template for Classic Annotated Bibliography in Org-mode with BibTeX\n\n## What is this?\nAn annotated bibliography summarizes notes about papers being read during a research project.\nIt is one of several methods for applying the knowledge gained from reading.\n\n## Why org-mode\nOrg-mode is an enhanced markup language that supports the writing of scientific manuscripts.\nOrg-mode descended from Outline-mode. \nIt supports managing documents with a hierarchical structure.\nAfter folding the sections, subtrees of the document are easily shuffled using the Meta-UP or Meta-Down keys.\nThis feature eases the reorganization of the annotated bibliography.\nIt was developed for use with the Emacs text editor.\n\n## Annote field in BibTeX entry\nThe summary is stored in the `annote` field in the BibTeX entry in the BibTeX file, like in the example below:\n\n![Screenshot 2024-08-17 at 1 36 04 PM](https://github.com/user-attachments/assets/447df2ef-bf02-49bc-a86f-ad3ee843e233)\n\n\nThis file was opened in Emacs.\nEmacs provided the line numbers and syntax highlighting (font locking in Emacs parlance).\n\n## PDF of Annotated Bibliography\nWhen exported to a PDF, the org file reads the BibTeX file with formatting set by the *apacannx.bst* file. \nThe top of the output PDF looks like the following:\n\n\n![Screenshot 2024-08-17 at 1 30 54 PM](https://github.com/user-attachments/assets/eb5d5ee9-b110-4c37-b8ea-0a013a7529f4)\n\nI have also attached an Emacs configuration file (*init.el*) for working with manuscripts and annotated bibliographies in org-mode on macOS.\nThis 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.\nThis configuration depends on a handful of external packages.\nThe *init.el* file takes 2-3 seconds to load. \nYou will have to edit some file paths.\n\nI swapped the option and command keys because I use the command key as the Meta key.\nI did not include org-agenda or org-roam.\n\n\n## Bash Function to generate subfolder with required files\n\nEdit the file paths as needed.\nTakes a project ID as the only argument.\nRun from the top level of the writing project directory.\n\n```bash\nfunction abiborg {\necho \"Create annotated bibliopgraphy subfolder and populate with required files with project number in title.\"\nif [ $# -lt 1 ]; then\n  echo 1\u003e\u00262 \"$0: not enough arguments\"\n  echo \"Usage1: abiborg projectIndexNumber\"\n  return 2\nelif [ $# -gt 1 ]; then\n  echo 1\u003e\u00262 \"$0: too many projectIndexNumber\"\n  echo \"Usage1: abiborg projectIndexNumber\"\n  return 2\nfi\nprojectID=\"$1\"\nmkdir abib$1\ncp ~/6112MooersLabGitHubLabRepos/annotated-bibliography-org/compile.sh ./abib$1/.\ncp ~/6112MooersLabGitHubLabRepos/annotated-bibliography-org/apacannx.bst ./abib$1/.\ncp ~/6112MooersLabGitHubLabRepos/annotated-bibliography-org/ab0519.bib ./abib$1/ab$1.bib\ncp ~/6112MooersLabGitHubLabRepos/annotated-bibliography-org/ab0519.org ./abib$1/ab$1.org\n}\n\n\nfunction orgabib {\necho \"Create annotated bibliography subfolder and populate with required files with project number in title.\"\nif [ $# -lt 1 ]; then\n  echo 1\u003e\u00262 \"$0: not enough arguments\"\n  echo \"Usage1: orgabib projectDirectory\"\n  return 2\nelif [ $# -gt 1 ]; then\n  echo 1\u003e\u00262 \"$0: too many projectIndexNumber\"\n  echo \"Usage1: orgabib projectIndexNumber\"\n  return 2\nfi\nprojectID=\"$1\"\nmkdir abib$1\ncp ~/6112MooersLabGitHubLabRepos/annotated-bibliography-org/compile.sh ./abib$1/.\ncp ~/6112MooersLabGitHubLabRepos/annotated-bibliography-org/apacannx.bst ./abib$1/.\ncp ~/6112MooersLabGitHubLabRepos/annotated-bibliography-org/ab0519.bib ./abib$1/ab$1.bib\ncp ~/6112MooersLabGitHubLabRepos/annotated-bibliography-org/ab0519.org ./abib$1/ab$1.org\n}\n\n```\n\n\n## Installation\n\n1. git clone this project to your software directory\n2. Copy one of the bash function and paste into your `.bashrc` or `.zshrc` file.\n3. source .bashrc\n4. cd project directory\n3. orgabib \u003cprojectID\u003e to create subfolder \n\n## Related projects\n\nHaving to add notes to the note field is extremely limiting.\nThe LaTeX software will strip out any white spaces between paragraphs.\nYou have to go to extreme measures to enclose the paragraphs in some LaTeX code.\nYou can insert equations, and you can include figures with difficulty.\n\nTo ease the writing of annotations that contain\n\n- multiple paragraphs\n- big blocks of equations\n- figures\n- tables\n- code listings\n- interactive code blocks for literate programming\n\nI am developing a modular and illustrated approach to the annotated bibliography.\nIn this approach, annotations are stored in Org-mode files that are imported into the final document upon compilation to PDF.\nThese files can utilize either pure Org-mode syntax or LaTeX to add graphical features.\nThe graphical features are very effective at stimulating the recall of a paper's content much faster than a wall of text.\n\nThis modular approach is independent of the annote field.\nThe annote field no longer needs to be utilized for storing the notes in global.bib file.\nThis modular approach enables the reuse of note files across multiple annotated bibliographies for various writing projects.\n\nI plan to make a variant that uses tex files for use in pure LaTeX.\nThis approach also supports the management of annotated bibliographies using Rmarkdown.\n\n## Sources of funding\n\n- NIH: R01 CA242845\n- NIH: R01 AI088011\n- NIH: P30 CA225520 (PI: R. Mannel)\n- NIH: P20 GM103640 and P30 GM145423 (PI: A. West)\n\n## Update history\n\n| Version          |  Changes                                                                                                            | Date                      |\n|:-----------------|:--------------------------------------------------------------------------------------------------------------------|:--------------------------| \n|  0.1             |   Initial commit. Added badges, funding, and updated the table.                                                     | 2024 August 17            |\n| 0.2              |   Updated compile.sh to take ProjectNumber as argument. Add bash function to ease install.                          | 2024  October 1           |\n| 0.3              |   Added to header code to add short author list, running title, date printed, and Page of N pages.                  | 2024  October 24          |\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmooerslab%2Fannotated-bibliography-org","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmooerslab%2Fannotated-bibliography-org","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmooerslab%2Fannotated-bibliography-org/lists"}