Despite that there are gigabytes of writings on this topic, ranging from the recipes for managing a bunch of markdown files on GitHub to the manuals for setting up a local MediaWiki server, I will describe the solution that works for me.
Any note-taking tool with the following four features is suitable for establishing a pretty usable knowledge base:
- Hierarchical data organization
- Hyperlinking and cross-referencing
- Tagging
- Search
For a worthy knowledge base, it may be vital to implement a note-taking system, such as Zettelkasten invented by Niklas Luhmann. As described in the book How to Take Smart Notes, Luhmann did his primary work by elaborately wringing notes on the reading material. He created a sophisticated system of links and indexes to keep the notes together. Through links, his indexes branched into multiple contexts. This helped him to understand the researched topic in many ways.
A concept- or mind-mapping application would also be a good addition. This means that our software should have the ability to easily attach and open large quantities of documents, such as PDF files or files produced by concept mapping tools.
Most of my demands are fulfilled by the two following software packages:
Scrapyard, is an advanced bookmark manager that is able to clip fragments of pages, it has cloud bookmarking, and also could be used for note-taking. Much like the good old ScrapBook. I use Scrapyard to store and organize bookmarks to online resources and keep a local archive of web pages and PDF documents.
org-wiki is an Emacs module based on org-mode markup. It provides a bunch of commands for wiki-related manipulations. For example, there are commands to download and insert attachment files, or commands to quickly insert links. In Windows, an instance of org-wiki may be automatically installed and configured as a part of RHO Emacs distribution. I use org-wiki to store any files that I need less often and to keep free-form notes, for which Emacs is indispensable.
Although Emacs requires some technical background, the huge benefit is that everything costs exactly zero shekels per month, and you own all your data. If you enjoy the software, though, the authors will undoubtedly be happy to receive a small donation.
Let’s consider the features of the applications above in more detail.
1. Hierarchical organization
Elaborate and carefully maintained hierarchical organization allows to effortlessly find any necessary content. It takes some effort to keep a good taxonomy on your area of interest, but this provides an immense advantage.
Scrapyard utilizes shelves at its top level of the hierarchy. Bookmarks and page fragments could be grouped into trees of folders.
org-wiki uses files at the top level of its organizational structure. There are topic files and index files. Index files contain links to the topic files. The topic files are divided into collapsible headings and subheadings of various levels. Emacs SpeedBar allows to quickly access any file, if necessary. A bunch of org-wiki files could also be added to the Scrapyard files shelf, where they are rendered into HTML and are available as editable notes.
There are also non-hierarchical approaches to note-taking. The org-roam Emacs package, which is also available in RHO Emacs, is a popular example.
2. Hyperlinking and cross-referencing
Scrapyard allows referring any bookmark or page archive from the text of its notes through
a link with ext+scrapyard:// protocol. Such links require a UUID of the
referred item (the addon help provides more details on linking).
org-mode provides a wide variety of hyperlinking possibilities to files and headings in them. Usually, you need a unique ID in the property drawer of a heading to be able to refer to it from a link.
3. Tagging
Tags allow to put documents into a context thad does not explicitly present in its content. Scrapyard allows to specify tags inside bookmark properties and provides a tag filtering mode in the sidebar.
org-mode allows adding tags at the end of a headline, separated by colons, and searching by them.
4. Text Search
Both Scrapyard and Emacs provide text search. It is a built-in feature in Scrapyard. In Emacs, it may be necessary to use grep in all its possible flavors.
Hyperlinking from org-wiki to Scrapyard and vice versa
It is possible to create links from org-wiki to archives and documents in Scrapyard and vice versa.
Referencing from org-wiki to Scrapyard
At first, it is necessary to register ext+scrapyard protocol in Windows registry
using a .reg file with the following content:
REGEDIT4
[HKEY_CLASSES_ROOT\ext+scrapyard]
@="URL:Scrapyard Protocol"
"URL Protocol"=""
[HKEY_CLASSES_ROOT\ext+scrapyard\shell]
[HKEY_CLASSES_ROOT\ext+scrapyard\shell\open]
[HKEY_CLASSES_ROOT\ext+scrapyard\shell\open\command]
@="\"C:\\Program Files\\Mozilla Firefox\\firefox.exe\" \"%1\""
RHO Emacs adds this registry entry on installation.
Then add the following code to your .emacs configuration file:
(defcustom scrapyard-url-protocol "scrapyard"
"Scrapyard protocol"
:group 'scrapyard
:type 'string)
(defun scrapyard-follow (uuid)
"Open Scrapyard URL"
(browse-url (concat "ext+scrapyard://" uuid)))
(org-link-set-parameters scrapyard-url-protocol :follow #'scrapyard-follow)
Now you may use the following links in your org markup:
[[scrapyard:B79C8A274D0B4378835976C2B2554ACD][link text]]
The link includes a Scrapyard UUID of the referred item, which is available from the item properties.
Referencing from Scrapyard to org-wiki
Since we assume that org-protocol is already configured in your system by RHO Emacs,
just add the following code to your .emacs configuration file:
(defun org-protocol-open-reference (args)
(org-open-link-from-string (plist-get args :link)))
(add-to-list 'org-protocol-protocol-alist
'("open-reference"
:protocol "open-reference"
:function org-protocol-open-reference
:kill-client t))
Add a unique CUSTOM_ID property to the headline being referred, for example,
with the value my_headline.
Now you can use the following links from Scrapyard notes:
[[org-protocol://open-reference?link=file:path/to/file.org::#my_headline][link text]]