An Illustrated Guide to Managing Knowledge on Paper

01Leave space at the top and start writing

Put an A4 sheet in portrait orientation and leave some space at the top. Start with the text. Choose the ID for the upper left later, once you see where this note fits among your existing notes.

I use a blue ballpoint pen for the note text and the sheet’s own ID, and a red one for references. That makes IDs in indexes, citations, and continuation links easy to spot. When I list several IDs in an index, I write the commas between them in red, too. I also use red for the dot marking an entry to a Topic Index. I use non-erasable ballpoint pens in both colors.

Put the date at the upper right. When writing it by hand, use 2026 10 02, with spaces between the year, month, and day. The COLOP Mini Dater S 120 with a numeric month (CLP120B2) stamps the date in year–month–day order. Sample imprint from the Japanese distributor

02Keep the sheets you thought on

The figure shows one way a sheet can look when you think on paper. This one is about a village in a game. A sheet with loose ideas, unfinished sentences, sketches, and connecting lines can go straight into the system.

Here, I wondered whether to add more people and wrote down what the villagers were already doing. Looking at both sides gave me another idea: maybe what was missing was what happens between errands. I drew a line to connect the thoughts. Later, I filed this sheet as 6a under my existing “Village design” note, 6, with the question still open.

As the sheets pile up, add the words you are likely to remember when looking for them. The Global Index searches across the collection, while a Topic Index gives you entries within a topic. Together they form the Double Index.

03Assign an ID based on how the ideas relate

Give a new note its own branch under an existing note when it broadens, deepens, or relates to what you wrote there. Similarity is enough to make a branch. If several placements make sense, choose the one that makes the connection easiest to see when you reread the notes.

Suppose I write on an A4 sheet, “The same beans taste different depending on how I brew them. The beans’ condition and the equipment may matter.” I give the sheet the ID 1.

Later I write, “With a pour-over and a French press, the grounds spend different amounts of time in contact with the water.” I file that note at 1a because it develops what I wrote about brewing in 1. Then I write, “Would the taste change if I poured more water at a time in a pour-over?” That follows up on 1a, so I file it under 1a at 1a1. A note on how to run the comparison while changing only the amount in each pour can go one level deeper, at 1a1a.

Next I write about how long to steep the grounds in a French press. That develops a different part of the brewing note 1a, so I give it 1a2, alongside the pour-over note 1a1. If I write, “Using the same brewing method, I found the darker roast more bitter,” I’m following up on what I wrote about the beans in 1. That note goes at 1b, alongside 1a. Later, I reread what I wrote about brewing and beans and start pulling my observations together on one sheet. I file that sheet at 1c, another branch of 1.

Suppose I write, “With the same brewing method, the more heavily roasted hojicha tasted more bitter.” I noticed a similar connection between roasting and bitterness in my coffee note 1b. I can give the tea note the ID 1b2 and file it under 1b because of that similarity.

I use 1c1 onward for more pages of the summary and for later versions. See the example in step 11.

File 1c1a right behind 1c1, before 1c2. Notes 2 and 3 each start a separate series.

Why branching on every continuation makes IDs grow

If every follow-up goes under the note you just wrote, the IDs keep getting longer. Even when the subject has broadened, the sequence makes each note look like a closer examination of the one immediately before it.

To suggest what to read next, add a continuation link such as :1b in the note itself. You can choose the reading order separately from the branches you assign.

04Mark sources and continuations

Write (1) or (2) at the end of a passage you may want to cite. For example, the Paper PKM note 7a could say “Where you put a paper note can help you find it.  (1)”.

To refer to that passage on the same sheet, write (1):Like this. To point to it from another note, write 7a(1). In the Search comparison note 7d, you could write 7a(1):Compare this with digital search.

To cite a whole note, write ID: (for example, 7a:). To point to the continuation, write :ID (for example, :7a1). Put the colon right next to the ID. Write the full citation or continuation mark in red, including parentheses, numbers, and colons. Write the note’s own ID in blue at the upper left.

05Find a keyword in the Global Index

Fold an A8 sheet in half with the crease parallel to the long edge. With the slip facing you in its reading orientation, punch a hole on the left and put it on a metal binder ring or similar fastener.

Write one keyword per slip, with its associated IDs. The slips for “Personal knowledge management” and “PKM” can both list 7. To find the note from step 03 by looking up “Coffee,” write “Coffee 1” on a slip. Sort the slips by the reading of the keyword, in Japanese kana order or alphabetically for English keywords.

A spreadsheet makes it easier to reorder the paper slips. Enter the keywords, readings, and IDs, then sort by reading or alphabetically. Use that order to rearrange the slips on the ring.

06Find a note within a topic

When you have several notes about PKM, take a separate portrait A4 sheet and write 7-PKM at the upper left. Write keyword–ID pairs in two columns, one on each side. Leave out column headings and grid lines.

1. Global IndexPKM 7
2. Topic Index7-PKM
3. Note7a Paper PKM

For example, look up “PKM” in the Global Index and open the A4 sheet marked 7-PKM. Find “Paper PKM 7a” there, then read note 7a. To find the village brainstorm, start from “Village design 6” in the Global Index. Open 6-Village design and look up “Village life 6a”.

Choose where to put an entry

When a note discusses a subject itself, give that subject an entry in the Global Index. When it discusses that subject within a particular context, list it in the Topic Index for that context.

For example, a note about GUI principles or usability in general belongs under “GUI” in the Global Index. A note about how to design the GUI of your PKM app belongs under “GUI” in the PKM Topic Index. When a term appears in a note, consider what the note is actually discussing before choosing where to index it.

If thinking about a particular app leads you to write something about GUIs in general, you can also list that note under “GUI” in the Global Index. A sheet covering several subjects can have entries appropriate to each. If there is no suitable Topic Index yet, first give the contextual subject its own Global Index entry and make a Topic Index when needed.

If you use both “Passage references” and “In-text references,” both can lead to notes about that subject itself in the Global Index. Within a Topic Index, usually choose one wording. Tidy up headings as they fall out of use.

Use note IDs in indexes. Use markers such as (1) when referring to a specific passage from the body of a note.

Use a Topic Index to reach a more specific Topic Index

As notes on Digital PKM accumulate, you can make 7b-Digital PKM using its entry ID, 7b. If the notes on title search grow into a subject of their own, use the same pattern to make 7b1-Title search.

Repeat the pattern at any depth where it helps. Each broader index gives you an entry point, and each narrower index holds the detailed entries for its subject.

07Add a dot when both conditions apply

Add a dot only when one keyword lists two or more IDs and you have made a Topic Index for that keyword. Put a red dot directly above the ID you used for the Topic Index. The rule applies to both Global Index slips and entries in a Topic Index. Keep the IDs already written. The dot identifies the ID whose Topic Index gathers the notes on that subject, so you can add the index without rewriting the original list.

Say the Global Index slip reads “Zettelkasten 7c, 7c1.” Once you make 7c1-Zettelkasten, add one red dot directly above 7c1. Keep the heading and the original list, 7c, 7c1, as written. To read the overview, go to note 7c. To see the notes gathered under this subject, follow the dot to 7c1-Zettelkasten.

A keyword with only one ID gets no dot, even if it has an index. A keyword with several IDs gets no dot while its index is still unmade.

Make a dedicated Topic Index and add to it

Two or three notes under one heading can be a good time to make a dedicated Topic Index if you want to see several aspects of the subject together. The count is a guideline. Keep using the same entry as long as it is easy to find what you need.

Choose an entry ID that makes the subject easy to follow. Consider a note with many connections to related notes, a note that gives an organized overview, or an early ID that is easy to reach when flipping through the folder. Each ID can have one Topic Index.

Say “Passage references” in 7-PKM lists 7c3, 7c6, 7c8, and 7c6 gives the overview. Make 7c6-Passage references and put a red dot directly above 7c6 in the original entry. List all three existing notes in the dedicated index as well.

Add the fourth note, 7c9, to the dedicated index first. You can already get there through 7-PKM. If you also want to find it while working on reports, list the same 7c9 in the reports Topic Index. If a note develops thoughts about passage referencing itself, you can also list it under “Passage references” in the Global Index.

Keep one Topic Index for the same subject

Give each ID one Topic Index. Several indexes at the same ID would leave you unsure which one to open. For example, “PKM” and “Personal knowledge management” both point to 7 and lead to 7-PKM. To index Zettelkasten as its own subject, make 7c1-Zettelkasten at the ID for that subject, 7c1.

Keep one index for each subject at the same scope. If 7c1-Zettelkasten already exists and you make another index at 7c with the same scope, entries can end up split between the two. It becomes harder to tell where to find the full list. Before making an index, check other names for the subject in the Global Index and look through related Topic Indexes. Add entries to the existing index if it already covers the subject, and use ★ links to reach it from related subjects.

Index GUI itself and GUI within PKM in their own contexts

Suppose note 8 discusses GUI design principles, note 7b5 discusses the layout of a PKM app, and note 7b6 discusses how to operate that app. These IDs are examples.

Write GUI 8 in the Global Index and GUI 7b5,7b6 in the PKM Topic Index, 7-PKM. To find the app-specific notes, start at “PKM” in the Global Index and open 7-PKM.

Why use this approach?

Collecting every occurrence of “GUI” in the Global Index mixes discussions about PKM, other apps, and programming. Each new context can force you to reconsider the scope of the GUI hub or gather its entries again.

Collecting notes about GUI itself under the global “GUI” entry makes its scope easier to understand. Discussions about GUI within particular contexts remain accessible through their respective topics. Adding a new context is less likely to require rebuilding the hub.

Make a Topic Index within the shared context

The notes in the PKM index’s “GUI” entry discuss the same app, so they are straightforward to gather. As they accumulate, make 7b5-PKM GUI with entries such as Layout 7b5 and Operating steps 7b6. Keep GUI 7b5,7b6 in 7-PKM and put a red dot directly above 7b5. Add further references about that app’s GUI to the dedicated index.

As notes about GUI itself accumulate, make 8-GUI to gather entries such as Design principles 8 and Thoughts on usability 8a. Develop each index according to its own subject and context.

When an index sheet fills up, add a continuation sheet. If a hub needs to move, gather its references in the new index and leave a reference to it at the old hub. If you rewrite a Global Index slip with only the new entry ID, that row takes no dot.

08Add index pages and links to related topics

When 7-PKM fills up, write 7-PKM 2 at the upper left of the next A4 sheet and keep adding entries. The final 2 is the sheet number. The entry ID is still 7.

Draw a one-stroke star at the start of an entry that points to another, related Topic Index. In 7c1-Zettelkasten, for example, write ★PKM 7 or ★KJ method 3a1.

You can list the same note in different indexes. If 7d compares finding things on paper and digitally, you can list it in both 7-PKM and 7b-Digital PKM.

09File the sheets in A4 clear folders

Put the notes and A4 Topic Index sheets into A4 clear folders. Start another folder when one fills up.

Use a permanent marker to number the front of each folder 1, 2, and so on. The number tells you where the folder goes in the sequence. Note IDs identify the sheets inside.

Start at the front face of the clear folder. Stack the notes in order from front to back, for example 1, 1a, 1a1, 1a1a, 1a2, and so on. Put lower-numbered series first and keep their branches together.

For a topic with lots of notes, or a note with a numeric ID such as 1 or 2, put a sticky tab with the ID near the top so you can find it while flipping through.

Keep a Topic Index and the note with the same ID together in one clear folder. For example, put 1-Coffee in front, with note 1 immediately behind it. You can find both even when the entry lists only one ID and has no dot.

10Keep the diary in a separate clear folder

Write the date at the upper left using the same format as the notes, for example 2026 10 02. A stamp that prints in this order works here, too. Write about anything you want. A brief note about what you wrote or concluded that day can help when you look back. If the details are in another note, write “See” followed by the note ID in red.

Use one page per day as a default, even for a short entry. If you need another sheet, put the date and page number at the upper left, as in 2026 10 02 2. Give the diary its own A4 clear folder.

11Write a summary and track its versions

Suppose I reread my coffee notes and write, “In the batches I tried, changing the brewing method changed the taste even with the same beans. With the same method, the darker roast tasted more bitter to me.” I give the first sheet of the summary the ID 1c.

If the first version takes several sheets, I use 1c, 1c1, 1c2, and 1c3 in order. To point to the next sheet, I can write :1c1, :1c2, and :1c3 in red at the ends of the respective sheets. A separate note expanding on something in 1c1 goes at 1c1a.

If I revisit the summary after my thinking has changed, I start version 2 at the next available ID, 1c4 in this example. I make a Topic Index using the first ID, 1c-Coffee summary, so I can find the opening sheet of either version.

Build an overview from smaller summaries

A Topic Index can have an entry called “Summary.” In the Goals index it covers all your goals. In the Finances index it covers your financial goals. Write both summaries as ordinary notes.

Start with smaller subjects, such as financial goals, goals related to mysticism, or recent goals. In the overall summary, write a short account of what matters now in each area and link to the smaller summaries for details. When you update the overview, you can reuse those summaries without copying every detail again.

In the Finances Topic Index at 2a, the summary has one entry, Summary 2a1. Put the versions, Summary 1 2a1 and Summary 2 2a1b, in the Topic Index at 2a1. Their note titles can be Summary-2026 10 01 and Summary-2026 10 02. Do the same for the overall summary. Put Summary 2d in the Goals index and list the versions in the Topic Index at 2d.

Digitally, open “Finances” from the Goals Topic Index. In that note’s BranchGroup/Group, open “Summary.” The Summary note has its own BranchGroup/Group, where you find the dated summaries. On paper, follow the same route using the IDs written in the indexes.

12Link subject-by-subject progress to a daily overview

A “Progress” entry tells you how far you had got by that date. For example, a philosophy progress note could say “Compared two arguments,” and a history note could say “Divided the timeline into three periods.”

In the overall study progress note, add a short review of the day and the IDs for the philosophy and history progress notes. As the updates accumulate, give Progress its own Topic Index so you can find the dated notes, just as with summaries.

When progress notes accumulate, add a “Progress” entry in each subject’s Topic Index and list dated notes in the index it leads to. Use the same pattern for overall progress. For example, 4-Study can lead to “Philosophy 4a,” “History 4b,” and “Progress 4c.” The subject indexes lead to “Progress 4a1” and “Progress 4b1.” The overall index, 4c-Progress, lists the daily overview at 4c1.

13Collect short items in Fragment Notes

Add trivia and one-line discoveries to a single A4 sheet. In the Global Index, write “Fragment Notes” followed by the ID you gave the first sheet. If the first sheet has ID 5, write Fragment Notes 5.

In this example, when the sheet fills up, use 5a, then 5b. You can keep unrelated short items on one sheet. To refer to a particular entry later, add a marker such as (1) at that spot and refer to it as 5(1).

14Review the whole workflow

Write, decide on an ID, add an entry to an index, and file the sheet. When you want to read it again, find it through an index or a sticky tab. As a topic grows, summarize smaller parts of it and link to those summaries wherever you need them.