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Copyright (C) 2025 Free Software Foundation, Inc.

     Permission is granted to copy, distribute and/or modify this
     document under the terms of the GNU Free Documentation License,
     Version 1.3 or any later version published by the Free Software
     Foundation; with no Invariant Sections, with the Front-Cover Texts
     being “A GNU Manual,” and with the Back-Cover Texts as in (a)
     below.  A copy of the license is included in the section entitled
     “GNU Free Documentation License.”

     (a) The FSF’s Back-Cover Text is: “You have the freedom to copy and
     modify this GNU manual.”

INFO-DIR-SECTION Emacs misc features
START-INFO-DIR-ENTRY
* Org Gnosis : (org-gnosis). Roam-like Knowledge Management System.
END-INFO-DIR-ENTRY


File: doc5DvGju.info,  Node: Top,  Next: Installation & Configuration,  Up: (dir)

Org Gnosis User Manual
**********************

Copyright (C) 2025 Free Software Foundation, Inc.

     Permission is granted to copy, distribute and/or modify this
     document under the terms of the GNU Free Documentation License,
     Version 1.3 or any later version published by the Free Software
     Foundation; with no Invariant Sections, with the Front-Cover Texts
     being “A GNU Manual,” and with the Back-Cover Texts as in (a)
     below.  A copy of the license is included in the section entitled
     “GNU Free Documentation License.”

     (a) The FSF’s Back-Cover Text is: “You have the freedom to copy and
     modify this GNU manual.”

   This manual, authored by Thanos Apollo, offers installation
instructions, customization options, and recommendations for effectively
using ‘org-gnosis’.

   The documentation furnished herein corresponds to stable version
0.0.4, released on 2025-02-13.

   • Name: Org Gnosis | Organization Of Gnosis (knowledge/information)
   • Homepage: <https://thanosapollo.org/projects/org-gnosis/>

   Org Gnosis (GNU-sis) is an org-mode parsing tool that organizes notes
as atomic nodes in an SQLite database.  Each heading with an ID is
treated as an atomic note (node), storing its metadata, such as title
and links, in a relational database to facilitate efficient linking and
navigation.

   This tool also offers special functionality for journal entries,
stored in a separate directory with support for customizable templates.
This can serve as an additional space for temporary notes.

* Menu:

* Installation & Configuration::
* Taking Notes With Org Gnosis::
* Contributing::

— The Detailed Node Listing —

Taking Notes With Org Gnosis

* Organizing your notes::
* Importing Notes::

Contributing

* Sources::
* Patches Require Copyright Assignment To The FSF::



File: doc5DvGju.info,  Node: Installation & Configuration,  Next: Taking Notes With Org Gnosis,  Prev: Top,  Up: Top

1 Installation & Configuration
******************************

   • The ‘org-gnosis’ package is available from the GNU ELPA archive,
     which is enabled by default.

        • Prior to querying an archive, make sure to update the index,
          with ‘M-x package-refresh-contents’.

   • Then all you need to do is type ‘M-x package-install’ and specify
     the ‘org-gnosis’ package.

   Example installation & configuration using ‘use-package’
     (use-package org-gnosis
       :ensure t
       :init
       ;; Example for separated journaling & notes keymap
       (define-prefix-command 'my/notes-map)
       (define-prefix-command 'my/journal-map)
       :config
       ;; Common settings you might want to tweak to your liking
       (setf org-gnosis-dir "~/Notes"
           ;; Whe non-nil, create notes as gpg encrypted files
           org-gnosis-create-as-gpg nil
           ;; TODO files, commonly used for templates.
           org-gnosis-todo-files org-agenda-files
           ;; Used in #'org-gnosis-todos for template generation
           org-gnosis-bullet-point-char "+"
           ;; Default completing-read function
           org-gnosis-completing-read-func #'org-completing-read
           ;; Recommended if you use a vertical completion system (e.g vertico)
           org-gnosis-show-tags t)

       (defun example/org-gnosis-book-template ()
         (let ((date (format-time-string "%Y-%m-%d"))
             (book-title (completing-read
                        "Example book: "
                        '("Free Software, Free Society" "How to Take Smart Notes"))))
           (format "#+DATE: %s \n#+BOOK_TITLE: %s\n\n* Main Idea\n* Key Points\n* Own Thoughts"
                 date book-title)))

       (add-to-list 'org-gnosis-node-templates
                  '("Book Example" example/org-gnosis-book-template))
       :bind (("C-c n" . thanos/notes-map)
            ("C-c n j" . thanos/journal-map)
            :map thanos/notes-map
            ("f" . org-gnosis-find)
            ("i" . org-gnosis-insert)
            ("t" . org-gnosis-find-by-tag)
            :map thanos/journal-map
            ("j" . org-gnosis-journal)
            ("f" . org-gnosis-journal-find)
            ("i" . org-gnosis-journal-insert)
            :map org-mode-map
            ("C-c C-." . org-gnosis-insert-tag)
            ("C-c i" . org-id-get-create)))


File: doc5DvGju.info,  Node: Taking Notes With Org Gnosis,  Next: Contributing,  Prev: Installation & Configuration,  Up: Top

2 Taking Notes With Org Gnosis
******************************

For Org Gnosis there are 2 types of notes,

   • Your “permanent” notes, which you can visit & and create using ‘M-x
     org-gnosis-find’

   • Your journal notes, which you can visit & create using ‘M-x
     org-gnosis-journal-find’, which optionally can serve as “fleeting”
     notes.

   As mentioned before, opening & searching your notes should be done
using ‘M-x org-gnosis-find’ as this will enable ‘org-gnosis-mode’.

   If ‘org-gnosis-mode’ is not enabled, files will not be parsed and
saved in the database when you run ‘save-buffer’.

   Org Gnosis does not automatically sync the database.  To delete a
file, use ‘org-gnosis-delete-file’ or run ‘org-gnosis-db-sync’ after
manual deletion.

* Menu:

* Organizing your notes::
* Importing Notes::


File: doc5DvGju.info,  Node: Organizing your notes,  Next: Importing Notes,  Up: Taking Notes With Org Gnosis

2.1 Organizing your notes
=========================

‘org-gnosis’ provides a zettelkasten-inspired approach to note-taking,
treating knowledge (gnosis) as valuable and not merely something to be
boxed into a single category, to be disposed after a certain period of
time or task accomplishment.

   Using directories to organize your notes is not recommended, a
preferred method is to create *MOC* files (Maps Of Contents) for
specific categories/projects that you are working on.

   An MOC file can be the syllabus of a class or a project road map.
For example, you might create an MOC like this for a class on
‘Biopolymers’:

   • First create a node using ‘M-x org-gnosis-find’ followed by
     ‘Biopolymers’, which will be created if it does not already exist.
   • Use ‘M-x org-gnosis-insert-tags’ to insert ‘moc’ tag.
   • Start inserting your syllabus points with ‘M-x org-gnosis-insert’
     as nodes, which will be automatically created & saved in separated
     files.

   Example:
     :PROPERTIES:
     :ID:       15edada1-9815-4fb3-9b8f-7da08107bdb2
     :END:
     #+title: Biopolymers Syllabus
     #+filetags: :moc:

     * Proteins
     - Protein Structure Levels
     - Protein Domains
     - Protein MOTIF
     - Difference between a motif and a domain in a protein
     - Protein Families

     * Nucleic acids
     - DNA
     - RNA
     - Recognition and self-assembly of macromolecules
     - Cytoskeleton

   Note: Items with ‘-’ would be links.  The headings in the above
example could be links to an MOC as well.

   This way your notes are atomic & can be reused in future
classes/projects.

   • For example you’d reuse your notes on nucleic acids in a genetics
     class MOC for your next semester.


File: doc5DvGju.info,  Node: Importing Notes,  Prev: Organizing your notes,  Up: Taking Notes With Org Gnosis

2.2 Importing Notes
===================

If you are a previous user of packages that use ‘org-mode’ and org ids,
your current note collection should be able to work with ‘org-gnosis’
without you having to change anything.

   To sync your note collection use ‘M-x org-gnosis-db-sync’


File: doc5DvGju.info,  Node: Contributing,  Prev: Taking Notes With Org Gnosis,  Up: Top

3 Contributing
**************

* Menu:

* Sources::
* Patches Require Copyright Assignment To The FSF::


File: doc5DvGju.info,  Node: Sources,  Next: Patches Require Copyright Assignment To The FSF,  Up: Contributing

3.1 Sources
===========

   • Main repository: <https://git.thanosapollo.org/org-gnosis/>
   • Mirrors:
        • <https://codeberg.org/thanosapollo/emacs-org-gnosis>


File: doc5DvGju.info,  Node: Patches Require Copyright Assignment To The FSF,  Prev: Sources,  Up: Contributing

3.2 Patches Require Copyright Assignment To The FSF
===================================================

Code contributions are most welcome.  For any major edit (more than 15
lines, or so, in aggregate per person), you need to make a copyright
assignment to the Free Software Foundation.  This is necessary as the
FSF must at all times be in a position to enforce the GNU General Public
License.

   Here’s the process:

  1. Review and adapt the request form below.
  2. Email the specified address with your request.
  3. Await a legal agreement from the FSF.
  4. Sign and return the document, which can be done via email.

   The entire process usually takes about a week and needs to be
completed only once, allowing you to contribute to GNU Emacs.

     Please email the following information to assign@gnu.org, and we
     will send you the assignment form for your past and future changes.

     Please use your full legal name (in ASCII characters) as the subject
     line of the message.

     REQUEST: SEND FORM FOR PAST AND FUTURE CHANGES

     [Additional people we should notify about the progress of the assignment.]

     Thanos Apollo <public@thanosapollo.org>

     [What is the name of the program or package you're contributing to?]

     Emacs

     [Did you copy any files or text written by someone else in these changes?
     Even if that material is free software, we need to know about it.]


     [Do you have an employer who might have a basis to claim to own
     your changes?  Do you attend a school which might make such a claim?]


     [For the copyright registration, what country are you a citizen of?]


     [What year were you born?]


     [Please write your email address here.]


     [Please write your postal address here.]


     [Which files have you changed so far, and which new files have you written
     so far?]




Tag Table:
Node: Top849
Node: Installation & Configuration2784
Node: Taking Notes With Org Gnosis5302
Node: Organizing your notes6298
Node: Importing Notes8183
Node: Contributing8593
Node: Sources8790
Node: Patches Require Copyright Assignment To The FSF9079

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