I'm currently studying and need to consult various pdfs on any given topic. Bookmarking PDF doesn't work since previous bookmarks take up space and the list of bookmarks gets confusing. Is there a good app to store various locations in various PDFs in one place/by topic and then open the PDFs jumped to the relevant part when you go explore a topic and your written notes on it? So basically like a link to specific parts of various pdfs, maybe even offline html or doc paragraphs. Does such a thing exist? I know logseq and siyuan let you upload a pdf and when you put a reference to the highlight inside the pdf, it jumps to that part. But for some reason I still found it hard to organize the snippets per topic. Please let me know if there are other more advanced solutions to this. This is for windows or web.

There is also RemNote, which functions similarly to LogSeq in this regard.

You could also check out Zotero, Mendeley, and Citavi, and see if any of them meet your needs. But I have yet to find a satisfactory tool for this. (In my case, interoperability is also a concern, since not all PDF tools store highlights in the same way.)

Heh, if you were working on Mac/iPad, I’d recommend MarginNote (marginnote.com), but I’m not aware of an equivalent on Windows.

Actually, I’d forgotten about LiquidText, which is also available for Windows. It uses a slightly different model from MarginNote, but does much the same thing: https://www.liquidtext.net

Another possibility to look into is Heptabase. See this video (I've cued up the appropriate time slot in the video), which demonstrates how to extract text from a PDF and get a link back to the original:

https://youtu.be/HgvR2QkfwG0?si=fm9KiTe101ur24-t&t=760

Steve

A few more notes:

I was looking for these criteria (in addition to the criteria stated above):
1) notes created automatically from highlights
2) highlight-notes accessible in an integrated view rather than only in connection with a given PDF
3) preferably, highlights saved permanently to PDF.

RemNote and Logseq seem to excel at criteria 1 and 2, although they don't meet criteria 3. I find RemNote to work a bit more intuitively than Logseq for this purpose.

However, there is also a lot to be said for using Readwise for all of one's PDF highlighting, and Readwise has integrations with Logseq, RemNote, Obsidian, etc. In this regard, I found the integration with Logseq to work well, whereas I didn't get it to work with RemNote. So Readwise plus Logseq is a compelling option. RemNote would potentially be even better if the sync would work (and it has the advantage that changes to highlights are supposed to sync as well).

(In Logseq, one would potentially want to create a special query to find all highlights. This is probably a bit easier to do in RemNote.)

Also worth mentioning is this Obsidian plugin:

https://github.com/RyotaUshio/obsidian-pdf-plus

It's highly configurable and includes an options to create notes from highlights and to save the highlights permanently to the PDF.

Again, do check out LiquidText, which allows you to pull together notes from multiple PDFs in a single document (PDF) consisting of notes and excerpts.

LiquidText is very nice on devices with input devices like Pencil or the like. On keyboard-only devices it's a PITA. It's also become pricey -- $175/year for a subscription. The subscription isn't necessary, if you just want to use the app on one device only.

MadaboutDana wrote:

Actually, I’d forgotten about LiquidText, which is also available
for Windows. It uses a slightly different model from MarginNote, but
does much the same thing: https://www.liquidtext.net

I was looking for something like this for my research many years ago, when I didn't find anything for my needs, I asked one company to create pdf link collector for me, based exactly on my specifications.
In specified directory (or recursively), it goes over all pdf files and collects all pages where there is at least one comment (highlight/text/rectangle/etc), it puts all those pages into one master pdf, adds bookmark and on top of each page also puts a link to exact location of that comment.
So you have in one file collection of all your pdf file notes/comments etc and links to open those pdf files on exact location with one click.

The program is called "A-PDF Comment Collect Tool" created by this company:

http://www.a-pdf.com/comment-collector/index.htm

It's being sold for much less than it cost me to develop it ;-)
Still my main research tool for pdf files (along with UltraRecall, as can be guessed from my username).

Lucine wrote:

I'm currently studying and need to consult various pdfs on any given
topic. Bookmarking PDF doesn't work since previous bookmarks take up
space and the list of bookmarks gets confusing. Is there a good app to
store various locations in various PDFs in one place/by topic and then
open the PDFs jumped to the relevant part when you go explore a topic
and your written notes on it? So basically like a link to specific parts
of various pdfs, maybe even offline html or doc paragraphs. Does such a
thing exist? I know logseq and siyuan let you upload a pdf and when you
put a reference to the highlight inside the pdf, it jumps to that part.
But for some reason I still found it hard to organize the snippets per
topic. Please let me know if there are other more advanced solutions to
this. This is for windows or web.