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Author: MooersLab

barebones-modulated-annotated-bibliography-orgmode/README.md

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+![Version](https://img.shields.io/static/v1?label=barebones-modulated-annotated-bibliography-orgmode&message=0.0&color=brightcolor)
+[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
+
+
+# A bare-bones modular annotated bibliography for org-mode
+
+This repo is for a template for a bare-bones modular annotated bibliography that uses a small Latex preamble.
+The idea is to reduce LaTeX package conflicts between what is in the preamble and what is pre-configured in org-mode.
+
+The annotated bibliography resides in a subfolder in a writing project.
+The subfolder has the address ./ab----, where ---- is a four digit project number.
+The project number is stored in a database.
+The number is used to label folders and files, categorize projects, and navigate between projects.
+'ab' stands for annotated bibliography.
+
+The annotated bibliography notes are stored in individual files in the communal folder in the home directory.
+This enables the reuse of an annotated bibliography entry in more than one annotated bibliography.
+The communal folder has the name ~/abibNotes.
+Image files that are called by these notes are stored in ~/abibNotes/images.
+
+The note files start out as empty files with the cite key serving as the base of the file name and 'org' serving as a file extension.
+This file extension is all that is needed for Emacs to recognize this file as a orgmode file.
+The note file can contain subheadings written in org-mode.
+It is simpler to use the `#+LATEX: \paragraph` environment to avoid jumping between org-mode and \LaTeX.
+
+The note file can contain org-mode tables that are formatted following the book tabs package, which supports the use of three kinds of rules: toprule, midrule, and bottomrule.
+The note file can also contain images and code listings that have syntax highlighting.
+
+This template is agnostic with regard to which Emacs bibliographic entry manager that you are using.
+However, it does depend on the use of a global.bib file.
+
+This function ml/wrap-citar-citekey-and-create-abibnote-org assumes that you are utilizing the citar Emacs package for managing the bibliography.
+The function is found in MooersLab/mooerslab-functions-el.
+You first insert a citekey.
+Then you place the cursor inside of the citekey.
+You execute the above function in the mini buffer and the cite key will be replaced with the bibliographic information injected into a \subsubsection{} heading.
+At the same time, a new buffer will open with the new note file so that you can go about editing it.
+This file will have been created in the abibNotes folder in your home directory.
+The corresponding did tech entry is supposed to be appended to the file ab----.bib so that you can have a local copy of BibTeX entries to ease sharing the annotated bibliography.
+
+
+## Update history
+
+|Version | Changes | Date |
+|:-----------|:------------------------------------------------------------------------------------------------------------------------------------------|:--------------------|
+| Version 0.1 | Added badges, funding, and update table. Initial commit. | 5/14/2025 |
+
+## Sources of funding
+
+- NIH: R01 CA242845
+- NIH: R01 AI088011
+- NIH: P30 CA225520 (PI: R. Mannel)
+- NIH: P20 GM103640 and P30 GM145423 (PI: A. West)