Create a note that linked to a specific paragraph in a pdf

Background
I am a academic user of obsidian and absolutely I like this software. I use zotero to manage academic papers and use zotfile plugin of zotero to redirect all the pdf attachments in zotero to a folder inside obsidian vault, so that I could view this pdf in obsidian.
feature request
I have used many knowledge software like marginnote and liquidtext, and they have the ability to link a excerpt and annotation to it’s original potion in a pdf. I kindly hope that obsidian could include this feature:

  1. make pdf text selectable in obsidian.
  2. add highlight tool and frame tool to pdf. Once you highlight a paragraph or frame a graph , a new note will be created that linked to this paragraph of this pdf. when you read lots of papers, a nested links of note will be created and it could be easily traced back to it’s original pdf source.
    This could facilitate research work around the world.

update:
Dear all, Logseq 0.3.2 supports the exact function I have proposed,you can check it out on Release Desktop APP 0.3.2 (Beta Testing) · logseq/logseq · GitHub

Obsidian is very flexible when jumping to a specific paragraph of a pdf fil:
methods like:

  1. Zotero with these two plugins: Zotfile and Mdnote
    When you choose to use this method, you can read pdf and annotate it with pdf reader like “pdf xchange editor” and then extract the annotation by Zotfile plugin and export it to Obsidian by Mdnote plugin.
  2. using internal wikilink format [[myfile.pdf#page=5]]
  3. using other software like Polar, liquid text,marginnote,Bookxnote,etc. to organize literature notes and summarized them into Obsidian afterwards, hopefully, some of these software previde global external links to allow you to link back to the original sources.
    These workflows interrupt the pdf reading experience to a different extent.
    Logseq 0.3.2 may provide a more direct solution to practice linking back to a specific paragraph in a pdf file, and it provides a development route for obsidian to improve its own pdf editor which is quite the same in logseq but lack the function to highlight texts and automatically generate a copy of the highlights with the link like[[myfile.pdf#page=x]]
    https://logseq.github.io/assets/2021-08-06_21.46.20_1628257857150_0.gif
38 Likes

Similar request, but only about specific pages: Link to the exact page of and external pdf file

In that thread they discuss some workflows with Zotero, for linking to highlights. (I’ve never tested Zotero. I just saw the thread exists.)

I suspect this is a long-range feature request. Other PDF handlers can do this, but outside of Skim I’ve never seen something that can do effective management of paragraphs, and even Skim doesn’t do a great job of it. I also suspect that developing the capacity to provide content links within PDFs would require quite a lot of effort, given that it isn’t common in many other apps, either.

As @rigmarole hints, you may be better off looking for a complimentary app to use with Obsidian for these links. If you’re on macOS, DEVONthink provides unique URLs for every file you store in it, and you can link to specific pages with them if a file is a PDF.

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I use MarginNote. It works great to annotate and to organize using mindmap/outline. But Obsidian offers us a more general way to link notes. If features of 2 apps can be integrated, it will be a very powerful tool but the development workload should be huge.

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What you are looking for has been implemented by Citavi. Citavi is, at the same time, a very good reference management software and a very bad knowledge management software. It does allow you to link each highlight/note to the specific text of the PDF, but it does not allow you to link highlights/notes together – which is for academic thinking and writing a fundamental step. Moreover, it only works in Windows and at best in Microsoft Word.

I’m also eager to see something like you mentioned developed in Obsidian. I completely agree with you that that would really boost research work all over the world.

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RemNote implemented this requested feature in their recent updates.
It works pretty well, I’m very amazed.
The problem is just that it is not markdown and it’s not plaintext that you can use in other markdown editors.

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An app called Highlights (Mac) does this as well, and it saves annotations as markdown with the appropriate links.

To link to an exact Para or text, A hacky solution would be harvesting the in-file search, just creating a link to the exact search term and order, this has to be implemented internally in the software, it can’t be achieved using a plugin, I guess so.

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That would indeed be amazing, if Obsidian would adapt LiquidText features.

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Can we display only one page of a pdf?
I am reading from a book that has <900 pages, I only need page 42 for a specific topic to take notes underneath. ‘#page=42’ is starting from 42, yeah, but goes all the way 900. I want only that page or maybe 42 to 43, not all. I could not find a way to do it. Does anybody know?

Not exactly sure what your exact question is - #page=42 only means that when opening your pdf it will jump to that page; it will not fragment your document in the sense of “show only pages 42 and following”…

What you want, perhaps, is to embed specific pages into your note? Maybe you should have a look at this new plugin - I haven’t tried it myself and according to the discussions there still seem to be some installation problems in this early development stage; but that might be what you are looking for!

Yeah! That’s exactly what I was looking for!
I know it goes to page 42, but you see the rest of the pages, too. Not only one 42. I will check the plugin!

Thanks,
HA

I’m hoping keypoints will be released soon with an Obsidian plugin, but who knows how long it will take.
But yes maybe Obsidian could so something similar.

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Does anyone know if there has been any progress on the development of this request by @Ocarinalover ? Is it on Obsidians development roadmap?

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I don’t know anything official, but I wouldn’t bet on this anytime soon. I imagine this kind of feature would require building a PDF handling engine from the ground up. (That’s based on the knowledge that only a select few PDF editors can do this kind of linking at present, and they are all exclusively PDF apps…)

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@DarrenMcDonald Hook can do something similar. See for example here, especially the section entitled “Hook and reference management software (PDFs)”. I wonder, if anyone can/want showcase her or his workflow with Hook and Obsidian.

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Interesting that Roam Research and Remnote has already has this feature. Roam Research as an extension and Remnote has it built into the app.

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Both of these apps have a different fundamental data structure than Obsidian.

In Roam’s case, I assume you mean the extension mentioned here: https://mobile.twitter.com/cococ_rr/status/1366654227506991105

If so, it uses Roam blocks to emulate highlight locations.

As for RemNote, it’s purpose-built with this feature in mind.

It might be possible in Obsidian someday, but it makes more sense for a good PDF editor to provide this functionality and for Obsidian to leverage that app than for Obsidian to build it from the ground up. (After all, shouldn’t we be able to link to and use these annotations outside the context of the note-writing app?)

zotero has a plugin called zotfile,it can extract highlights and annotations from pdf files edited by acrobat pro 11. and there is another zotero plugin named mdnotes, which could export all the zotfile-extracted notes and metadata of a item in zotero to obsidian in md format. and you can jump back to pdf paragraph when both obsidian and zotero are opened.

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Actually, there is a quite simple way to make references to exact positions within pdf files. I used to do it manually once (unfortunately, I can’t script to make the process automatic). But I’m not a programmer and don’t know how difficult is to implement it and how useful it would be for other users.

The things needed are:

  1. a simple pdf-annotating tool embedded within Obsidian,
  2. a search engine that can search and preview pdf files and show “hits”, and
  3. little programming.

The functionality should work like this:

  1. You highlight a passage, take notes, annotate, and do all your work within a PDF file using the embedded pdf-annotating tool. I believe, this is already a requested feature.

  2. If you wish to make a reference, you will select an option “Create an anchor (reference)” and insert the cursor in a place in the PDF file where you want to create it.

  3. The program will create an anchor at the exact place by inserting a little text in the PDF file with a generated unique string of characters (perhaps using the exact time stamp). The string will be copied to the clipboard.

  4. Now, you should just paste that string in an Obsidian file with a special syntax – let’s call it a “pdf block link”. The string doesn’t need to contain the name of the pdf file, since it’s always unique.

  5. Later, by clicking on the pdf block link, the system launches the indexed search for that string in PDF files, finds the hit and previews the pdf file in the exact position.

So, it works in a way similar to block references in Obsidian.

Visually, the anchor string should be invisible or barely visible in the PDF file (for example, small, transparent style letters can be used). Or the string in the pdf file could appear as a little anchor icon (so that you can see, where you have your anchors; you can move them around to adjust their position; and you can copy their id-string to create a pdf block link to it in an Obsidian file, when necessary; and so on). Sure, there are plenty of possibilities here.

The good thing is that these links won’t be broken by renaming or moving pdf files within your vault – the search engine will automatically reindex all the files that has been modified or moved and find the unique string in a new location without any problems.

You don’t even need OCR-processed files – because you can write (i.e., create anchors) even on top of images. So, this method can work also with images - you can for example refer to the exact point in the image.

The method can be adjusted for other file types that can be edited, searched, and previewed by the search engine with hits higlighted.

I used to do this manually using PDF X-Change Editor (for annotating PDFs and manually creating “anchors”) and DtSearch Desktop (for searching the “anchors” in the PDF files). After manually creating an anchor in a PDF file, I just copied the string into my note-taking app. And when I wanted to find the exact location in the source PDF file, I just ran the desktop search for that string. But any pdf annotation tool (that can write on top of PDF) and any search engine (that can search PDFs and highlight “hits”) will do.

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