Bookmarked Web Annotation Data Model by World Wide Web Consortium (W3C)

I wasn’t aware of it, but there’s a W3C model for annotations (in JSON). It was mentioned in the book Annotation I’ve been reading in the past weeks. Not sure if this is something I have a use for, but it may be an interesting way to transform and share book notes on this site. It was suggested that Hypothes.is uses this model. There’s also a Hypothes.is API which suggests it might be possible to pull annotations from there, although I don’t suppose you could push them there as a way of publishing annotations.

The Web Annotation Data Model specification describes a structured model and format to enable annotations to be shared and reused across different hardware and software platforms. … The specification provides a specific JSON format for ease of creation and consumption of annotations based on the conceptual model …, and the vocabulary of terms that represents it. This specification was derived from the Open Annotation Community Group’s outcomes. … This document was published by the Web Annotation Working Group as a Recommendation

W3C

I’m taking the liberty to put three questions before Chris Aldrich about his Hypothes.is experiences, after reading Annotation by Remi Kalir and Antero Garcia. Kalir and Garcia make much of the social affordances that annotation can provide. Where annotation is not an individual activity, jotting down marginalia in solitude, but a dialogue between multiple annotators in the now, or incrementally adding to annotators from the past. Like my blogposts are an ongoing conversation with the world as well. Hypothes.is is one of the mentioned tools that make such social annotating possible. I am much more used to individually annotating (except for shared work documents), where my notes are my own and for my own learning. Yet, I follow Chris Aldrich’s use of Hypothes.is with interest, his RSS feed of annotations is highly interesting, so there’s a clear sign that there can be benefit in social annotation. In order to better understand Chris’s experience I have three questions:

1. How do you beat the silo?

Annotations are anchored to the annotated text. Yet in my own note making flow, I lift them away from the source text to my networked set of notions and notes in which emergent structures produce my personal learning. I do maintain a link to the right spot in the source text. Tools like Hypothes.is are designed as silos to ensure that its social features work. How do you get your annotations into the rest of your workflow for notes and learning? How do you prevent that your social annotation tool is yet another separate place where one keeps stuff, cutting off the connections to the rest of one’s work and learning that would make it valuable?

2. What influence does annotating with an audience have on how you annotate?

My annotations and notes generally are fragile things, tentative formulations, or shortened formulations that have meaning because of what they point to (in my network of notes and thoughts), not so much because of their wording. Likewise my notes and notions read differently than my blog posts. Because my blog posts have an audience, my notes/notions are half of the internal dialogue with myself. Were I to annotate in the knowledge that it would be public, I would write very differently, it would be more a performance, less probing forwards in my thoughts. I remember that publicly shared bookmarks with notes in Delicious already had that effect for me. Do you annotate differently in public view, self censoring or self editing?

3. Who are you annotating with?

Learning usually needs a certain degree of protection, a safe space. Groups can provide that, but public space often less so. In Hypothes.is who are you annotating with? Everybody? Specific groups of learners? Just yourself and one or two others? All of that, depending on the text you’re annotating? How granular is your control over the sharing with groups, so that you can choose your level of learning safety?

Not just Chris is invited to comment on these questions obviously. You’re all invited.


Opticks, with marginalia, image by Open Library, license CC BY

I’ve read something, so then what?

How and when do I turn what I read into notes, for learning, for retention, for use elsewhere? Having at least some system for this I found is crucial to have somewhere to go with the ideas, associations and thoughts that reading non-fiction creates. I know this because how the absence of a system to take note of my reading feels. For an extended time at some point I did not read any non-fiction simply because I had nowhere to go with the material I learned about, no application, no outlet, and the ideas plus the urge to do something with them kept swirling around in my head creating noisy chaos and frustration.

Having some system is key therefore. What I describe below is my current incarnation of a system, it shifts over time, tools come and go, and therefore it is a snapshot. At the same time my general information strategies and personal knowledge management haven’t fundamentally changed in 20 years. The source of any continuity or consistency is me, not my tools. That said, none of what follows is very strict, it is meant to be forgiving. The source of inconsistency is also me, not my tooling. Not much of it is blind routine. Yet it is way more than doing nothing. My notes create a ratcheting effect, not allowing movement backwards, which is very valuable to me.

Inputs to outputs and the role of friction

Previously I described the flows of various reading inputs to my main tool in working with notes, Obsidian (my entire Obsidian set-up I described in Oct 2000), and the few outputs that flow from them. The image below gives an overview (click for larger version).

The specific steps and tools mentioned in the image are of less importance here. Key is the locus and role of friction in the depicted flows. There is friction in getting material, both source texts and my annotations for them, into my note making tool. This friction I seek to reduce, making it easier to get material to the place where I can work with it. Similarly I’ve reduced friction in getting outputs into the world (my blog, client websites, book lists for instance). Where I don’t seek to reduce friction is in working with notes (expect perhaps for functionality like search), because there friction is the actual work, where the thinking, rewriting, rearranging etc is happening. There is no way around friction there, because it is how I add value to my notes, how I learn and remember things.

The rest of this posting focuses mostly on what happens in the middle section, where the work is, between the inputs and outputs: what do I do there with annotations from what I read?

Web articles via browser

I use a markdown clipper in my browser to save web articles directly as markdown in a folder NewClippings that is part of my notes vault in Obsidian. Usually these come from my feedreading (over 400 individual blogs) or clicking links in those blogs. Saving is not a postponement and promise to self to ‘read later’ which never happens. It is the result of a curation decision, an intentional step, after skimming the web article. I skim looking for suprisal, and I jot down specific reasons for saving it with the web article. This way my future self will know why I was interested in the article originally. Those reasons may be a novel insight in the article, associations I make with other notes I have etc.

Two examples:

Reason: good overview of AI algo’s not doing what we think they’re doing. Types of mistakes made in training models. Rich source of examples. Compare to note [[Relevance of ethics for machine learning 20201219142147]].

Reason: Steps by Chinese gov against BATX’s ANT group. I see this in light of geopolitical positioning w.r.t. digital and data (compare to [[Data is a geopolitical factor 20180419080356]] and to [[Euproposition]]). Also see notes in [[Logic Magazine 7 China]]. Read for notes, not notions. Is there a usable contrast with the EU’s proposition?

I currently have some 825 clippings, of which about 150 are my own old blogposts recycling my earlier writings that way. I do not intend to always process them into other more permanent notes, I don’t treat it as an inbox. It is a repository in its own right, that I can search for additional material. I do pick out clipped webpages for processing, if that is logical from what I’m doing at some point in time.
Whenever I do process an article, it means deleting everything that I don’t think is interesting from my point of view, and summarising and paraphrasing the points I do find interesting. At the top, where the original reason for saving an article is, I keep track of the status of that process. The reworked article remains in the same folder as the other saved articles during this process. If I lift specific notes or notions from the article that can stand on their own, those will link to the original web article by url as source, and end up in one of three notes folders (one for conceptual notes, one for actionable ideas, one for more factual notes and examples) where they are woven into the wider collection by linking. Where that lifting is done I delete the original article from the clippings folder.

Scientific Articles and PDFs via Zotero

I use Zotero to keep a library of scientific articles and other PDFs (e.g. European Commission legal documentation). My motivation for saving them is stored as remark with the material in Zotero. When I save something I usually mention it in my Day logs in my notes, so that I can stumble across it again for processing.
I read those PDFs and highlight and comment in the PDF itself.
Until last week’s Zotero update I could easily grab those highlights and notes using a plugin and save them in markdown into my Obsidian notes vault. The update broke the plugin, so that flow is temporarily out of order. Any highlights and annotations in such a markdown file have a link to the corresponding location in the PDF in Zotero, meaning I can directly jump to the source.

Then, like with web articles I summarise, paraphrase and connect to other notes in steps. Notes/notions that stand on their own, contain the links to Zotero sources. I write, link and fill those stand alone notes from within the annotations first. Once I’ve taken out all I want from an article I delete the annotations note, because all created individual notes link to their source in Zotero. Currently some 10% of learning related notes link to a source in Zotero, after two years of using Zotero.

Books via Kindle

I don’t nearly read the amount of non-fiction I’d like. So none of this is ‘routine’ but it is what has emerged so far as workflow.

When I start reading a non-fiction book, I create a note that serves as the place for thinking and processing what I read. I prefill that note with a template that contains some datafields for my book lists and provide a structure of questions to explore the book before reading. What do I think it is about, what seems the author’s purpose with this book, why am I interested in reading it, what kind of surprisal am I after? What do the different chapters discuss, which ones seem most interesting to me and why? This all before I start reading parts of the book.

While I’m reading I follow two ways of making notes:

  • I make notes alongside reading the book, and put them in the note I created for the book. These are descriptions and summaries of key ideas, but also associations and links to other things, questions that arise while reading. Basically my half of being in dialogue with the book. This is what I’ve done exlusively until recently.
  • Recently I started using the Kindle sync plugin for Obsidian, which grabs all my Kindle highlights and annotations and puts them in a markdown note in my Obsidian vault, including links to the right paragraph in the book. I link that note with annotations to the note I made about the book. I never was a big highlighter / annotator in my e-books because of the difficulty of doing anything with it, but thanks to this plugin removing the barriers I started annotating and highlighting much more intensively.

In the book note that I created before reading I then work through the things I highlighted and annotated. Thinking about connections, contrasts etc, and linking to existing notes accordingly. It is also where I start paraphrasing and writing snippets that can become notes in their own right. The book note is the jumping off point for it. When I’m done with a book, the book note will have the links to the notes it brought forth, and the material that I didn’t in the end use for new notes. I keep the book note, and I keep the note with the highlights and annotations (it would resync from Kindle anyway), so I can always trace a note back to the book note and the location in the book itself.

Handwritten notes

I write some reading notes by hand on my BOOX Nova 2 e-ink device, as well as hand written marginalia, but I don’t have an easy flow bringing those to my notes in Obsidian yet. They are stored as PDFs on my e-ink device, and I need to bring them manually into Zotero, from which there then is a working flow to my notes.
This friction on the input side hinders regular use.

Over the years I’ve filled many note books by hand, not just with reading notes, but also annotations of talks, conversations and any other things I jotted down. Recent notes from the past day(s) I usually go through as needed and transcribe into my digital notes. I add them to my Day Log notes, which then can be a jumping off point to create additional individual notes.
Older notebooks, I have in the past scanned a lot of the key material, and have more recently scanned a few note books entirely. In my digital notes I have created an index file for each scanned notebook, where next to a link to each scanned page there’s a brief description of the content, and perhaps a link to relevant other material. That makes it possible to stumble across those notes in search.

Invitation to share

This post describes how I currently make notes from things that I read or wrote. It is a transcription and adaptation of a presentation I gave on April 3rd to the Micro.blog Readers Republic (video), an informal group of book readers around the world meeting every month for conversation. The question of note taking and learning came up as ‘So you’ve read a book, and then what?’ and a few of us volunteered to show what we do. I’m always interested in how other people organise their work, and I think that requires I also share how I work.

Essentially, this description of how I digest my reading is an invitation to you to write up your modes of working too.

Bookmarked (Re)Introducing Readlists by Jim Nielsen

This is another good example to put on my list of ‘discontinued services that deserve to be re-created’, although not necessarily as a central tool and more like a personal tool that can network. Delicious, Dopplr are others that come to mind. Also relevant because, in terms of reading, pulling together a collection of web articles on the same topic and then reading and annotating them in one go, this might be more effective in terms of learning. Might give this a try with some already saved articles on one topic or other. (found via Frank Meeuwsen)

I found myself every few weeks thinking, “gosh, I wish that service was still up. I really need to make a readlist out these handful of articles.” … I finally asked myself: “well then why don’t you recreate it?”

Jim Nielsen

Part of the conversations in the Micro.blog Republic of Readers group, are about what we do with what we read. I was invited to share a bit about how I (try to) process what I’m reading into something I can re-use over time in last weekend’s meeting. I couldn’t make it, but will do so in the next meet-up early April. As a first step I made a sketch of what my current flow and set-up looks like.

That’s not to say this is frictionless, and I’m not making claims as to its effectiveness. It’s what it is, warts and all. Also, any way you approach it, processing what I read, finding the bits that provide informational surprise, tying it to things I’ve written earlier, connecting it to the things currently relevant to me and hence to outputs, is intensive work. It is the work, and while I can strive to reduce friction on the interfaces between steps in my workflow, that work will always remain. Only through the work does reading gain meaning at all, because it is how you think things through.


Reading processing flow sketch. Click to enlarge. Image by Ton Zijlstra, license CC BY NC SA

Most of the removable friction in the reading-to-used-notes process is towards the left in the image. I use multiple devices, and getting notes in and out of them requires some jumping through hoops. It all ends up in Obsidian as my current note making tool of choice.

Only there the actual work starts: adding associations to highlights, lifting out bits and pieces from source texts and rephrasing them, creating the jumping off points for newly resulting notions. This is never a smooth process, and I usually struggle to allocate time for myself to think and write.

Output is a recombination of those notions into something that can be shared again, and if I have my notes in order it is a step that is less daunting than writing something from scratch. In the past months I have created several tools to make publishing something from my notes as frictionless as possible again.

I’ve been making notes basically always, even in primary school I filled many notepads (‘kladblok’) of grey recycled paper I bought myself. It still means I can cycle back to e.g. conversations I had in 2014 with the notes often being more or less verbatim. Two years ago in April, a few weeks into the first pandemic lockdown, I revamped my personal note taking system and added something I hadn’t done structurally before: a day log. In it I list the things that I worked on during the day, or thought about, or came across etc. Below is a basic example from July 2020 when I just started using Obsidian for my day log notes.


Example day log, with links jumping off to more detailed notes

The day logs have quickly become much more than a simple list of things I’ve done in a day. It also forms a jumping off point for any notes that belong to an entry in a day log. It is a habit fully part of my routines.

As a result I am now structurally not only taking notes during conversations as I’ve been doing for decades, but also much better documenting things as I’m doing them. Basically I find myself much better logging my actions, and thus the status of my activities. When I return to something I don’t need time to reconstruct what it was I was doing or thinking, or to figure out what I can do next.

It means that when I was e.g. figuring out how to build my own Micropub client I could do so incrementally, and even spending ten minutes could be fruitful. Before those ten minutes would be lost to switching costs. It also means I find it easier to let something rest for a while, because I know it will be easy to pick up again.

Two years on I feel keeping day logs, by structurally leading to notes jumping off of them, causes a very specific effect for me: My notes now stop me from having to go backwards whenever I pick up something again at a level unlike ever before. Ideas stay intact and usable, concepts don’t need to be reworded each time, experiments can be incremental, projects can stand still for a while but can restart immediately when I return to them. That’s valuable return on the time spent making those notes.


Ratchet, image by Paul van de Velde, license CC BY