Tinderbox Forum

Composites or footnotes to keep annotations and quoted text together?

I would like to keep my reading annotations together with the literal text they quote. This is a fairly common use case, so I wonder what is the preferred way to go: composites or footnotes.

As far as I can tell, both composites and footnotes are treated as separate notes in Outline view. This is kind of unfortunate because moving the related notes together will involve considerable attention.

Composites’ have the important advantadge of showing the text of several notes together in Outline and Map views. Surprisingly, their behaviour seems a bit inconsistent: they don’t show at all in the Attribute browser view, so using composites heavily may render unusable this otherwise useful view. In search results, composites’ text doesn’t appear toghether at first; only when clicking on the note itself; if using them heavily, this would mean clicking on each search result.

Double linked footnotes within the text can be accessed in all views, but they seem to be more practical just for one-to-one note relation.

This is an essential part of my use of TB, so I better get it right from start. Any advise from seasoned users?

A composite is a visual clue about the relationship between notes – so they work best in maps, and would be difficult to represent in outlines (attribute browser is a cousin of outline views.) Because you normally composite notes on the map, and the arrangement of notes on a map is frequently different than in an outline, the notes that are visually contiguous in a composite on the map will not be in an outline. There is an independent spatial relationship of notes on maps and outlines. This is a good thing, because you would not want changes made to a map view to rejigger the outline’s sequence.

Anyway – my approach to the topic of the thread is to concentrate on one view or the other – map or outline. In a map, I would use links and the arrangement of the notes to indicate topic/annotation relationships. Or, I would not use a map and I would use the hierarchy that outlines excel at: a container for the topic and children of the container for the annotations. Or, again on an outline, a topic note and footnotes.

Overall I prefer maps for this sort of thing, unless I need to export the work, and then in that case I’ll use an outline.

I don’t think there is “the” answer to this. And others will surely join in with their own approaches.

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I have toyed with an approach which uses unique ID numbers to tie notes together. It is an idea that is explained very fully on the Zettlekasten site:


In a sense, it is not unlike the method of temporary citations that you use with a bibliographic database like Bookends. If you insert the unique ID in the text somewhere, you can do a search and find all the notes that include that number. I suppose in a Tinderbox environment, you could have an adornment on a map that would pull all the texts together and display them. I’m not being very clear, but reading a few articles on the Zettelkasten site will show how that method works. Basically, if you have something like “Source: 201711041128” in the text of your note, you can never lose the connection with the original. Even if you export all the notes to plain text. The system has its merits, though not everyone will find it congenial.

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I am copying your suggestion on using a unique identifier. I think using TB’s $ID might not be a good idea, because it’s not persistent in aliases. It can be generated in Terminal with uuidgen. But I don’t know if Tinderbox could generate it automatically for a field. I am tempted to place it in a user field, so that it can be inherited automatically by children notes with:


A system I used (suggested on the Zettelkasten site) was to have a number consisting of the year, month, day, hour and minute combined into a single number. If you want, you can add seconds to this. You can use the creation date of the item as the ID – it’s not all that common to create two items at exactly the same second (if you are doing it manually).

Yes – if your user attribute is myUUID then try


In an agent or Attribute Browser you could query for all notes where $myUUID==""; and then apply the above as the action. Once the action runs, the query will find nothing, so the myUUID will not get overwritten.

If you want to export the notes, as @MartinBoycott-Brown mentioned WRT his version of the identifier, with the UUID in the note text, then your export template can handle appending the UUID to the end of the text.

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For IDs that are unique within a document, consider sequential attributes as well. They’re not globally unique, but easier and shorter than uuids.

Composites and attribute browser: Attribute browser lists the component notes of composites but pays no attention to the composite as a whole. One could, I think, use composite predicates in the scope rules for an attribute browser view, perhaps with excellent effect.

For any graduate students watching, there’s a perfectly good research paper to be written for ACM Hypertext on composites and attribute browser…

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Thanks for letting me know about sequential numbers, @eastgate

Actually, I am already used to UUID for annotations. Before adopting MarginNote, I was using a nice script for DEVONthink that makes good use of them, Annotation Pane:

I wonder if it is possible to use DT’s own UUIDs.

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@jmm – that’s a VERY interesting thread that I somehow completely missed. Many thanks for linking it. It may change my methodology.

BTW – I deduce from what you say that you are no longer using the script in DT. Is MarginNote better for what you do?

I haven’t used MarginNote thoroughly enough to give you a clear answer. To find the part of the pdf that a note belongs to is equally easy with the DT script and MN. From the pdf it is easier to find the note in DT that was created in MarginNote and later exported; but it is not impossible with the DT script.

I use MarginNote only to underline pdfs and export these fragments to DT. It is very good at that because one can choose what fragments to consolidate or export as individual notes. Also because they have a permanent URL (not dependant on the path: marginnoteapp://note/) that imports into DT’s URL field, so it is easy to click it and view its source in the pdf. This is what I use it for, so for this use the DT script can be used as well. It is possible to write free notes in MN whilst reading but I don’t find it nice for writing. I don’t use it for its maps either.

I am convinced about using TB and DT, but still have to work out how to integrate well these apps. TB is the most important one because my workflow has been lacking the possibility to view and organize my own notes in a structured manner. Only later will MN come into the picture to integrate sources into the workflow.

I have a similar problem. When I wrote a history book I used DEVONthink to organise source material, and I did it in a very crude manner by simply putting everything related to Chapter 1 into a folder named Chapter 1, and so on. It worked very well, but of course the problem arises that there may be thematic links that cross more than one folder, and the same item may be useful in more than one place. You can address that by using replicants, but it has never quite felt completely integrated to me. I find the Zettelkasten method interesting, but I like visual representations of material, so that has its limitations.

I have also discovered that I have a habit of jotting things down, then forgetting them, so I write something very similar on another occasion. I end up with scattered thoughts that are not linked together in any way, so they remain scattered and do not amount to anything much. I have recently begun to make more use of iThoughts, which gives me a visual presentation of material, which I like, but it is not the best for long pieces of text. For all these reasons, I have begun to think that I ought to make more use of Tinderbox, but I am not sure how. I think I’ve had a licensed copy for well over ten years, but I’ve never really used it much. Now might be the time.

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Consider, also, TheBrain 9. This supports extensive linking between notes (“thoughts”), each note has its own URL, PDFs or numerous other file types can be embedded, an iOS companion app, etc.

Thanks for the suggestion.

Hmmm – it is VERY expensive, and it doesn’t seem to offer much that isn’t available in iThoughts (which I am very happy with). I think I will probably pass on that one! But thanks anyway.

Ah, no, TheBrain and iThoughts are as apples-and-oranges as one can be, but yes, expensive. And Tinderbox will serve your requirement perfectly anyway.

Really? I didn’t get that impression from watching their (admittedly brief) introductory video. However, at this point it no doubt makes more sense to play around with Tinderbox and see if I can come up with a working method that suits me.

Thanks again.

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I don’t know iThoughts at all, but I know TheBrain very well, and have spent a lot of time thinking about and exploring it.

It has distinct advantages, including visual appeal, and I know that Jerry Michalski (a friend) has essentially archived all of his years’ worth of knowledge, thoughts, and references in “Jerry’s Brain.” For my purposes, though, I find that Tinderbox has held up better in being more (a) flexible and (b) scalable. People’s tastes differ, but this is a big part of why I have concentrated my work, references, filing, organizing, etc in TB.

(And I use Scrivener for writing, and the Scrivener-ally Scapple for quick-and-easy concept-sketching.)

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I’ve used Scrivener since version 1-point-something and I’m an admirer of the program. I have a licence for Scapple, but I’ve never used it because iThoughts is about as fast and has an iOS version. Moreover, iThoughts mind-maps can be placed in DEVONthink, which makes them searchable inside that program (from where they can also be viewed and opened on a Mac). iThoughts is one of my most-used programs, and I find it utterly indispensable. It took me a while to realise that Tinderbox is not really a mind-mapping program, which is probably the main reason why I have struggled to use it. It is for something different, but I don’t yet know what.

I am interested in your experience with TheBrain discussed here. I think I would benefit from having my sources visually organized and better-structured than they are in DEVONthink. No doubt DT is a good app but I cannot avoid thinking that to come across again what I have forgotten I threw at it is left to chance.

I wonder if you use theBrain instead of DT, if your experience has been good when referencing sources in The Brain from annotations in Tinderbox, how good it is at searching thougths, if you find it an accomplished and reasonably future-proof app…