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+[[!meta title="An enhanced bibliography in org-mode for scientific research and self-directed learning"]]
+[[!meta copyright="Copyright © 2025 Blaine Mooers"]]
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+<!-- Initially generated with emacsconf-publish-talk-page and then left alone for manual editing -->
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+# An enhanced bibliography in org-mode for scientific research and self-directed learning
+Blaine Mooers (he, him) - blaine-mooers@ouhsc.edu, <mailto:blaine-mooers@ouhsc.edu>
+
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+
+This 20-minute talk introduces a modernized approach to creating annotated bibliographies using Org-mode.
+This new approach overcomes the limitations of traditional BibTeX-based methods.
+Unlike classical annotated bibliographies, this system supports rich content including text-wrapped figures, tables, code listings, equations, and appendices.
+These features transform static reference collections into visual knowledge repositories.
+
+The presentation will demonstrate how this system leverages Org-mode's unique capabilities, particularly literate programming, to enable real-time data transformation and visualization from cited papers.
+I introduce a modular architecture to overcome BibTeX's whitespace limitations in the annotation field, which stores notes for assembling annotated bibliographies in the classical approach.
+
+Key features of the new approach include:
+
+-   A modular design that supports the reuse of annotation files between bibliographies and with literature notes in org-roam and denote
+-   Support for including figures, tables, equations, code listings, and literature programming blocks
+-   Citation key injection into subsection headings
+-   Automated PDF downloading, relabeling, and storing
+-   Property drawers for keywords, links to annotation note files to ease making further edits, and links to PDF documents
+-   Specialized sorting function for bibliography organization (by author, year, or keywords)
+-   Inclusion of a table of contents with hyperlinks
+-   Specialized glossaries for acronyms, software packages, equations, and mathematical notation
+
+I will address how this approach complements, rather than replaces, modern personal knowledge management systems like org-roam and denote.
+This approach strengthens project-focused knowledge organization.
+I will discuss the practical benefits, including improved visual memory reinforcement through embedded figures and reduced context switching during in-depth academic work.
+
+I will share the implementation details of the Emacs Lisp functions that power this system (available as a package).
+The presentation will include demonstrations of how these functions streamline everyday tasks such as adding new entries, navigating between bibliography and source material, and preparing project-specific BibTeX files.
+These functions reduce the friction in the academic reading and writing workflow.
+
+For those interested in adopting this approach, I will discuss adaptations for various workflows and address practical considerations, such as copyright implications when sharing illustrated bibliographies.
+The talk will conclude with thoughts on how this system supports different reading styles (reference, survey, and deep reading) as identified by Stephen Heard in his 2022 book "A Scientist's Guide to Writing".
+This approach is particularly valuable for researchers, graduate students, and knowledge workers who need to maintain project-specific literature collections.
+The approach recognizes the reality that most scientists do not need access to their entire knowledge corpus when working on a specific paper.
+Instead, they need a visually reinforced understanding of a targeted subset of the literature.
+
+The format is a 20-minute talk presented as a narrated slideshow. The outline follows:
+
+-   The role of the annotated bibliography in my three-pronged approach to scientific writing project management, which I introduced last year in my talk about writing logs.
+-   My innovative use of a modular approach, along with numerous enhancements, promotes deep work.
+-   Why make an annotated bibliography in the Age of Zettelkastens and Generative AI?
+-   Why not assemble a notebook instead?
+-   The classic annotated bibliography and its deficits (i.e., why I developed the enhanced bibliography).
+-   The advantages of Org-mode for making this annotated bibliography.
+-   Defining the scope of the enhanced bibliography: research program level versus writing project-specific.
+-   Tour of the master org file that controls the assembly of the final PDF.
+-   Project file tree and version control with helper functions.
+-   The annotation file and accommodation of three levels of detail for reference, survey, and deep reading.
+-   Demonstrations of creating an entry by wrapping a citar, org-ref, and org-cite citekeys.
+-   Show how to use literature programming to carry out further analyses using data from a specific paper.
+-   Show integration with Zettelkasten by including annotation org files in literature notes.
+-   Feeding annotation files into generative AI for help with querying, brainstorming, planning, and synthesis.
+-   How does working on an annotated bibliography fit into my weekly writing schedule?
+-   Tour of the GitHub repository for this project.
+-   Copyright of figures and limits on sharing the enhanced bibliography in public.
+-   Summary
+-   Acknowledgements
+
+About the speaker:
+
+Blaine Mooers is an associate professor of biochemistry at the University of Oklahoma Health Sciences, where he specializes in macromolecular crystallography. His research focuses on RNA structures and protein-drug complexes important in cancer.
+As an avid Emacs user for five years and LaTeX and Python user for 15 years, Dr. Mooers has developed tools to optimize scientific writing workflows.
+In this talk, he shares his system for managing academic literature using Org-mode, which he developed as a solution to his frustration with traditional annotated bibliographies.
+This new approach enhances scientific creativity and productivity by combining visual memory reinforcement with project-focused knowledge organization.
+This approach addresses the challenging reality of scientific research, where focus is often more valuable than breadth.
+
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