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Comment by felipefar | Hacker News Reader

I've been working on having my notes better integrated with the content I read. I try to gather references to where an idea is developed/contradicted in the literature, or just collect good ideas.

Cahier (https://getcahier.com), the software I'm developing, supports creating cards with references to passages in the PDFs read.

It's exciting to see the developments that are being made in this area in the past few years.

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Cahier looks like exactly what I’ve been hoping for for a long time. People have been taking “knowledge management” seriously for a few years now and we have a number of great tools like Obsidian, Zotero, Anki, and their brethren. But there’s still no real good solution to properly highlight and annotate documents, then link those outside their originating document into the broader context of one’s notes. Instead you end up with multiple silos—a Zotero full of papers, an Obsidian full of notes etc. This strikes me as a definite step in the right direction—thinking about knowledge management as an integrated process, with a workflow right through from reading, to taking notes, to organising those notes, to actively employing them to generate new insights and effectively write.

(I guess my only concern is around potentially reinventing the wheel when it comes to some of these areas. E.g. do you plan to integrate every feature from Zotero, like the web-integrated grabber? That sounds like a prodigious amount of work, but without it it’s hard to fully supplant Zotero as a reference management solution. I’m curious as to your roadmap for this and what you see as the ultimate feature set and user workflow.)

Hypothesis https://web.hypothes.is/ is pretty good at keeping notes on PDF.

Normally it anchors the annotations for any url but i believe that for PDF is also doing some extra checksum magic to uniquely identify the PDF and apply the annotations.

Furthermore you can have collaboration features such as group annotations. Useful for classes or science labs...

I have been thinking about this program for a long time now, and one area I haven’t seen covered are references that work even across different versions of the same document (e.g. the book got a new version, but still has the same chapter more or less unchanged, or you highlighted something based on the epub, and switched to the PDF). Hypothesis’s implementation works quite well, as they were sort of forced to handle it due to web pages always changing (they store some of the surrounding context).

Have you tried Heptabase? (https://heptabase.com/)

No, will check it out, thanks!

This is exactly why I created Cahier. I want to make it excel at the capture and processing steps of the research workflow. We're close to having the foundational features of the software in place and will release the beta soon.

But we want to expand the supported attachment file formats (possibly with video and audio as well), with full annotation and referencing support, more formatting options in the note editor, .bib import/export, synchronization, linux and mobile apps.

I don't plan on having feature parity with Zotero. I think we can provide more value by focusing on the features that explore the interaction between the annotations and notes and on supporting more media types.

This looks really good, thanks for sharing. Like other commenters, I use Zotero and will probably stick to that for the near future. The main feature for me in Zotero is sync'ing across devices. I usually read and annotate papers on iPad, and love that my highlights and notes are synced for when I write and need to reference them on either my MacBook or Windows desktop.

Your note-taking solution seems far superior though. Sometimes I wish we could smash together different software into just the right thing for us.

I'm eager to add synchronization and mobile support for Cahier. It could take some time because the amount of work is not trivial, but I know I'm able to deliver.

What other features are essential for you? Do you work on academia or in the industry?

Thanks for this. Your current features plus mobile synchronization will be awesome. I'm a researcher in industry. My current workflow is primarily in zotero. But definitely needed a better tool to synthesize notes from multiple papers in a high-level notebook. So this will be ideal.

I use an eink device (kindle scribe) for reading papers as well. Right now, the syncing between this device and the rest of the knowledge base is manual. It'll be perfect to have this also integrated into the workflow smoothly somehow.

On the other hand, the lack of synchronization might be a selling point for others, who militantly support "local only".

Solid highlighting is important to me. Zotero does it fairly well, but doesn't support freehand highlighting on files that lack OCR.

I've recently gone back to school after a decade in tech.

Could you expand on what you see as exciting developments? I’ll have to check out the op post link as well as yours and others in the thread.

It’s been a few years since I seriously looked at options for my personal use, but I remember being quite disappointed in the options I found. Zotero and org-noter seemed two of the best (though in completely different ways) pieces of software I could find regarding reading or organizing pdfs. I trialed OneNote for a year and liked it in the moment, but zero support for navigation or discovery or review of information make it untenable for building a knowledge base or doing literature review.

I imagine that software which makes reading and connecting document information (in any form: pdf, html, video or other) could be so much better than what I use daily.

1) The post-roam research note-taking apps (Obsidian, logseq) have shown the usefulness of creating notes with links, back-links and databases.

2) Document editor apps (Notion, Craft) have popularized the concept of documents as a set of text and non-text blocks. They're useful and provide rich building blocks for documents.

3) Some design engineers are exploring multi-modal text editors. Text, audio and video in the same document, integrated with CRDTs for collaboration.

One would think that digital text editing had already reached state of the art, but the work above shows that there's plenty to discover yet. I'd love to hear your take on what you think could be much better.

I wanted to check out the website and saw that your SSL certificate expired today, just a heads up to get a new one :)

That was unfortunate. Thanks for the heads-up, it's fixed now!

That looks very interesting. An essential feature for me is data, including my notes and annotations, that will remain usable in the long run - many decades into the future.

Otherwise, my work of today is lost. What happens if you stop making Cahier someday or if I need to move to another system?

I agree with you. We're expanding our support for import/export as time goes by, there will be no lock-in. We already have markdown support and plan on adding markdown import/.bib export and import/pdf export. Plenty of formats to choose from. Your notes can already be exported and opened on Obsidian today.

If there's enough interest, I'm also open to documenting the file format we use.

This looks really, really cool! Is there a plan to make this available in Linux I wonder?

Thanks! Yes, we plan on adding a Linux version. The framework we use is cross-platform, but there is a thin layer that has to be ported.

Congrats, looks great!

For reference management I'm finally sticking with Zotero after maybe 15 years of trying it. With version 7 beta it's finally becoming really good for my use-cases.

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