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

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

* Menu:

* Organizing your notes::
* Importing Notes::


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

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

‘org-gnosis’ offers a zettelkasten-like workflow for note taking where
knowledge/information (gnosis) is considered precious and should not
viewed as something disposable to be put inside a box category.

   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 for example the syllabus of a class you are
taking, let’s say for example on biopolymers, you’d create an MOC
similarly to this:

   • First create a file my running ‘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’,
     their files will be automatically created & saved.

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

     * [[id:<node-id>][Proteins]]
     + [[id:<node-id>][Protein Structure Levels]]
     + [[id:<node-id>][Protein Domains]]
     + [[id:<node-id>][Protein MOTIF]]
     + [[id:<node-id>][Difference between a motif and a domain in a protein]]
     + [[id:<node-id>][Protein Families]]

     * [[id:<node-id>][Nucleic acids]]
     + [[id:<node-id>][DNA]]
     + [[id:<node-id>][RNA]]
     + [[id:<node-id>][Recognition and self-assembly of macromolecules]]
     + [[id:<node-id>][Cytoskeleton]]


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

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


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

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

* Menu:

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


File: docftAexV.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: docftAexV.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

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

     GNU 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.]

     Copied a few snippets from the same files I edited.  Their author,
     Protesilaos Stavrou, has already assigned copyright to the Free Software
     Foundation.

     [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 notes5550
Node: Importing Notes7443
Node: Contributing7847
Node: Sources8044
Node: Patches Require Copyright Assignment To The FSF8333

End Tag Table


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