IanM
I'd like to be able to read ebooks, PDFs, etc.., and have my annotations link to or become thoughts. I'm not really committed to any reading platform, but some I have used are kindle, google drive (using comments), and I've been dabbling with systems like Polar, Calibre, etc... Has anyone done this or something similar? 
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srv181
Hello IanM,

There a number of ways to do this, the simplest being to create a child thought with your notes under the relevant object (thought) in theBrain - you can then open the thought for the notes in a separate window and work on both thoughts in parallel. The drawbacks are that you don't really "annotate" the file (I use only .pdf files for such texts).

I have a similar need and, working with Windows PC and Android tablets have come up with a system that works for me as follows:

  1. On my Windows machine, I use Calibre to manage around 10.000 Books and Articles. I have set the Calibre Library to be stored on OneDrive. All texts that I want to work with are stored as pdf files.
  2. When I want to really work on a text, I copy its pdf file from the Calibre library directory (Author/Title) to a separate directory under OneDrive called "_Work in Progress".
  3. In TheBrain, I create a thought for the text. book or article. Initially, as long as I am working on the text, I use a link to the pdf file in the "_Work in Progress" directory.  This way, I can always see the current, annotated version of the file in my Brain.
  4. To annotate the pdf file, I access the thought in my Brain and open the attached file - this opens the file in a pdf viewer/editor. There I can do all the highlighting or notes, etc. Because it is accessed by a link in my Brain, all changes are immediately visible there.
  5. Once I am done working with a pdf, I export the annotations and notes to a separate pdf file in the "_Work in Progress" directory. I then add both the edited pdf and the shorter annotations pdf from the  "_Work in Progress" directory to the actual Calibre directory for the text. Now I have both the original and the annotated versions there. 
  6. I change the link in my Brain from the "_Work in Progress" directory to the file in the Calibre directory.
  7. The new file containing only the annotations can be added as another attachment to my thought for the text. However, I usually add it as a child thought to the main text thought, because then I can use a different thought type to quickly find all of my annotations.

Sorry this has turned out to be such a long answer, but I hope it helps. If you are interested in how this system works with android tablets let me know.

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srv181
PS: The business with OneDrive is only necessary because I work on files on my tablets as well. If you don't do that, you could always work directly with the pdf file in the Calibre library.
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IanM
Thanks for posting, and for the detail.

I think even with all your effort (which may very well work for you) the essential thing I'm looking for is missing: I want to annotate something I'm reading, then seamlessly connect that annotation to other thoughts in my brain. If I've understood, your workflow allows you to keep the document in context within your brain, but any annotations you make within your document remain in the document reader context/domain, and you would have to duplicate them as separate thoughts in your brain if you wanted to connect those annotations to other thoughts. 

The more I think about this, the more I think the next wave of adaption will be driven by the platforms/products that reduce and eliminate the "chore" of making connections of all kinds.

Side note: How do you like Calibre for managing articles in addition to ebooks? Do you import articles posted online (in html), and if so what's your workflow? 

Have you seen hypothes.is (social annotations; works on epub though maybe only using a web-based reader; I'm still tinkering to confirm)? 
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srv181
You are correct that the annotations I make are kept in the original document. However, I use PDF-Exchange Editor which lets me export any (or all) annotations to a new pdf file. I add this file to the brain, sometimes containing all of the annotations, sometimes only one or two relevant for a link and add links to related thoughts. That way I can link even a single highlighted paragraph to other thoughts.

Being a pack-rat by nature, my normal tendency is just to save everything - I have used Evernote and OneNote to quickly snap up information, and wound up with databases of thousands of entries, with little organization and ultimately of limited use. TheBrain is so much better for really working with information within a context (of related thoughts) than either of the other products.

Articles from the web that are not in ebook or pdf formats don't go into Calibre. Firstly, because the steps are tedious - Calibre does not do well with html, it gets imported as a .zip file and conversion to a pdf or epub makes most information almost unreadable. More  importantly, calibre cannot link items. So I use TheBrain for that type of information, the brainbox makes it so simple.

Regarding hypothes.is , I had a quick look, but I don't have a need for collaboration and I often do work offline, which seemingly would not work. Also, it seems that getting annotations out of the cloud is not quite as simple as I would need it to be.

Do you work mostly with longer texts such as ebooks, or is your need more for collecting and annotating short information from the web?
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metta
@IanM ~

I may be a "bear of little brain", so could you help me understand what I'm missing in your request?

When I want to annotate an ebook or PDF, I put the following items into the brain:
> ebook: attach a link to the ebook URL or file to one unique thought
> PDF: attach the PDF URL and a copy of the PDF document to one unique thought

Then I take my notes in the unique thought to which the ebook or PDF has been attached -- and then brain links can be added as needed.

Does this not accomplish what you are needing? if so, what have I missed?

As for the "chore" of making connections in TheBrain, these connections are (to me) the real genius of TB since each of the connections can be customized based on my own unique needs, either current and/or future. I'm also not sure that any AI system could ever discern what those specific needs might be.

In light of this, any additional clarification you can provide will be appreciated since I'm always interested in learning how others are using TheBrain.
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IanM
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That way I can link even a single highlighted paragraph to other thoughts.

This is getting at what I ultimately want to add to my reading followup and research. I'm just looking for a workflow that is as simple as highlight > link.

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Do you work mostly with longer texts such as ebooks, or is your need more for collecting and annotating short information from the web?

It's about 50/50. Lots of ebooks, lots of PDF articles (mostly published in academic journals), and lots of articles of varying lengths and types published natively in HTML. I'd like to have one platform where all my reading occurs, but it seems like there are solutions for ebooks, and those for scholarly reading/information management, and each is a compromise to add the other type of content to. 
 


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IanM
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When I want to annotate an ebook or PDF, I put the following items into the brain:
> ebook: attach a link to the ebook URL or file to one unique thought
> PDF: attach the PDF URL and a copy of the PDF document to one unique thought


What I'm looking for is going to the next step, and wanting to have the least effort path to creating thoughts out of annotations within the ebooks and PDFs. 

Say I've just read an article, and I've made twelve highlights and four notes. If I want a unique thought in my brain for each annotation, then I need to go through and create a thought that is a copy of the annotation within my source document. This violates the digital principle of "link to instead of duplicating," because after I'm done I'll have duplicate thoughts in my brain for each fo the annotations in my source document. 

That's what I mean by reducing the chore of the thing. I make the highlight because it connects to something else in my real or digital brain. I want to highlight, connect, and move on (or highlight, keep reading, then come back and connect in my followup study). 

What I can do now using the brain is: highlight (in my source document), make a copy of the highlighted text or idea as a thought in my brain, link my new thought to the document thought in my brain, then move on. 

I've noticed that in google drive, slack, atlassian products (jira and trello), and I'm sure many others every object is being assigned a unique URL. Every slack message, every google document (that's long been the case), every comment and comment response within a google document, every trello card, etc.. What this means is that you can almost always respect the link don't copy approach, which reduces the chore of managing information and focuses your time on the meaning of the information and what you are doing with it. 
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metta
Thanks so much for clarifying, IanM.

Appreciate the detail about what you are hoping to accomplish, and I'll be interested to see how your strategy develops over time.

Please do keep us posted.
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fblittle
I don't know if this is applicable to you but I have for 3 or 4 years been Collecting quotations for religious material and the Bible. I have a Brain Called "Bible and Quotes". The Home Thought is Bible and Quotes, Then it is split intochild thoughts Bible and Quotes . All the books that I use are listed in the Quotes branch under a child thought called Library. You could use the Bible Branch for Book Texts and store all the Books (PDF, docx, files etc..) there. When Reading these books in any form (Kindle, PDF on my desktop or in theBrain), I then copy the paragraph that I want all or part highlighted and make a thought in the Quotes branch under child thought Library where there is a child thought for each Book that I have is listed by an individual Book thought.

The quotation is put as a child thought under that Book. The book name (abbreviation in my case) is put with the page and paragraph at the end of the quote Book Code. (Example:
SOJ 213.3, that means "The Story of Jesus page 213 paragraph 3". Note, Paragraph #1 is always the first full paragraph on the page, headings not included) I can find this quote in the main text even if there is no link to the book in theBrain using this Book code.

I then have a child thought of Topics (I also have subtopics under the topics thought) that is a child thought off the Home (Bible and Quotes) thought called Topics all Quotations are then linked to these Topics thoughts so that I can organize (link) all the Quote thoughts to Topics and Books (one or multiple links). I can look up a quotation from the original book or by a topic that it is linked to. If I still can't find the Quotation then I can use the Search/BrainBox function to find it. I have 2,275 Quotes in this Brain and find it very useful for recall. Since there are many quotes and many books (300 to 400) I don't use it for all book annotations that I make, I only use it for the best and most powerful annotations that I would like to use or find later. I also do not store the Book Text in theBrain. Just a link to the text or web address for the text and the Book Code.

The Basic idea is to have two branches one for Books, and for Topics. The Quotes (with the Book Code) are a child thought under the Book it is from and then they are linked to the Topics (or Subtopics which are treed from the Topics) branch.

If this is not useful for you then I hope it will be for someone else.
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