How best to archive MarginNote-annotated files?

Dear @Support-Team – Have you been able to make any progress on this front?

Many thanks.

As you know, @Lanco_Support-Team , @marginnote , @Support-Team , this is a super important feature for many MarginNote users. In fact, I’d venture to say it’s among the most important features we need – especially because it affects our entire workflow.

I understand that you’re very busy and it’s probably a lot of work to accomplish something like this. Of course, we’d love to help you out with this as much as possible. I don’t know if it’s helpful for you guys, but maybe it’s worth checking out how the Highlights app accomplishes this. Just a thought – hope that’s helpful…

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I concur.


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@Lanco_Support-Team - was that helpful?

Do you have a rough sense when you might have a solution for this issue involving how to archive MarginNote-annotated files?


Hi @jprint ,

Our developer Min has confirmed your request about export this afternoon(GMT +8). I will gather all the details of your demands to Min and the build is coming soon. Congratulations and thanks so much for your proposition with continuous concern ! I’ m also very happy to achieve it.
Welcome if you have any further discussion about it. I will deliver a tech-solution to you check later tonight.

Yours sincerely ,
Support Team

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That’s great, @Lanco_Support-Team … We’re thrilled to hear it!

Do you guys have a sense of when it’ll be ready? I’ve had to hold off on working on MarginNote until this features is set, so I’m hoping it’s something that Min and your colleagues can turn around in the near future!

BTW, I think you mean “requests” not “demands” – I’m certainly not being that harsh!

Thanks again for your help, and I hope to see this archive feature in the very near future!

Glad you are online, could you please check if the solution that a fully worked OPML export with detailed URL-Scheme and tags which could link back to MN Documents pages is useful for the request of this thread since Pandoc support OPML and support transforming it into tons of format. @jprint @JournoProf

Now you can attach any supplement elements to this OPML solution report like you want URL-scheme etc. You could make a list of it. I guess it works just like an enhanced OmniOutliner export. When you click a URL-scheme, it jumps back to MN original book.

About the timeline,

If you agree with the solution,OPML support will come very quickly. (about within 1-month dev+test)
Furthermore, we plan to develop an extension platform to MN with fully functional export python SDK. Any user could build their favorite export workflow by coding a plugin. This platform is contained in MN Version 4.0 which will be released in Aug. 2020.

Now I‘m very confused, is JournoProf agree with URL -scheme jump back mechanism. I put a video from our user here, he uses Maestro to generate URL-Scheme from MN and put into Markdown or Voodoopad note, as well as Devonthink.
If MN supports OPML, you will directly have a Markdown file by Pandoc. All these kinds of workflow based on Url Link. This means you have to keep the files stored in the local MN space.

If you guys want to delete MN and just keep the note data with the complete book file, you have to save the PDF and exported-notebook separately. I don’t have the idea about how to make them connected unless just export an annotated—PDF which displays the mindmap on a PDF page.

I’ve just checked Highlights app. Is it what you want?

I think if you got an open source format as OPML or Markdown is, it will be easily to write a script to transform the MN PDF Url into Devonthink PDF url.

Thank you for your reply, @Lanco_Support-Team I think you might be conflating two things that me and others have been discussing in two different posts, namely: (1) how MarginNote users need some way to archive our PDF files after we’re done annotating them – i.e., offline, and not connected to the iCloud / MarginNote file & notebook management structure while still be able to use MarginNote-created URLs, and (2) the HASHTAG WORKFLOW via KEYBOARD MAESTRO that @jprint laid out.

@jprint’s HASHTAG WORKFLOW uses KEYBOARD MAESTRO. But what I’ve requested, and what other users have been begging for, is the ability to archive our annotated PDF files offline (again, while still be able to use MarginNote-created URLs so that clicking them refers right back to that section of annotated text) has nothing to do with KEYBOARD MAESTRO at all.

I’m afraid I don’t have the technical prowess, or familiarity with python SDK, to weigh in on this. I’ll do my best to respond if you can give me a clear explanation about the ultimate effect of this approach.

I’ve looked at this video several times, but I’m afraid I don’t quite follow what you’re doing – or seeking to do. I fear part of my confusion is a result of the Chinese characters. I certainly understand that we’re both doing our best to bridge the language gap, so I really do appreciate your effort. But I’m just not quite following what you’re doing in the process, as expressed in the video. Again, if you’re able to clarify it a bit more, I’ll do my best to give you helpful feedback.

Just let me know how you’d like to proceed whenever possible, and thank you again for your hard work and assistance.

Hi @JournoProf

Sorry, my last post may confuse.
I make it clear for you.

If we make the DEVONthink script of Highlights also works for Marginnote. The URL will be replaced with the same PDF page in Devonthink. Then you will be able to delete all the related data in MN. And read or index your notes in OPML or Markdown, using the URL in notes to jump back to the original book, do all these things in Devonthink. Let Devonthink take care of your archive MN annotated files.

If we don’ t support that Devonthink script. Just support OPML export. You will be able to use Tinderbox, OmniOutliner, Mindmap software to read your notes, but the difference is when using the URL in notes it will jump back to the certain page of Marginnote PDF. And you can not delete any related data in local MN space.

I want to know which way is acceptable for you or both of them are acceptable.

Could that section of annotated text is still in marginnote-PDF-viewer? Or you want that section of annotated text could also works in other PDF viewer like Devonthink-PDF-viewer?


Hi @jprint

the OPML export must contain
1,“space+hashtag+space” syntax which could be recognized by other apps
2,each note has a unique ID like established time

any supplement?

Hi @Lanco_Support-Team, Let me jump in here and try to answer your questions.

I think we’re all seeking some way to archive files – both the original PDF’s that we annotate as well as the export files – so that they’re off the iCloud and MarginNote folders, so that we can store them locally and (most crucially) we’re able to click on MarginNote URL’s and have the connect to the annotated text of the original PDF, even when it’s offline and archived.

I wrote up some very specific suggestions in this post on Requests for PDF exports, namely, I suggested that MarginNote…

create the ability to click on the right margin for the PDF annotations outline (which signifies page number) so it takes users to the annotated text within the PDF document. In MarginNote X, that icon seems to click – but then doesn’t do anything.

Also, it would be great if this function – i.e., clicking on the annotations and/or the right margin for the PDF annotations outline – could work within any app (e.g., DEVONthinkPro, Tinderbox, etc.) instead of having to open up the file within MarginNote. That just creates confusion, and jumbled mess if MarginNote opens (and imports) a file – just so one can see the reference to a particular annotation.

It also creates a cradle-to-grave problem: it forces users to wholly rely on MN when clicking on MN-created PDFs and therefore it means that all documents and links opened in MN can overwhelm its library. Make sense?

Hi @Lanco_Support-Team, Thanks for sending this. I think you might be mixing some things up, so let me clarify.

  1. The “space+hashtag+space” syntax is desirable for inter-application functions, such as making the hashtags exportable to apps like Tinderbox (which many users rely on). But, as you’ve mentioned above, developers – especially the Tinderbox developers – really want other export formats, especially CSV and tab-delim formats. So, that’s far more desirable that “space+hashtag+space” syntax, which is basically a clunky work around solution that so many of us use.

  2. As I explained in my post re: Any way to create an UID in annotated files?, we’re hoping that MarginNote can “create an UID in MarginNote-annotated files – and, by extension, the notes they create” so that " MarginNote-annotated files & notes could generate create an UID – one UID for one file – that would apply to all of the MN-created annotated notes linked to that file. Seems like this UID could be auto-generated much the same that MN creates URLs per note." Make sense?

  3. Yes, a URL – but, crucially, as I said above, MarginNote-created URL’s that enable users to connect to the annotated text of the original PDF, even when it’s offline and archived. Make sense?

Happy to answer any other questions you have. I’ll leave it to @JournoProf to chime in…


1,We already could make CSV,
the Anki format, apkg export, could be transformed via Anki CSV extension. The apkg also keeps hashtags from MN. In this way, our user could use Quizlet and other card software.

2, Marginnote already has the unique URL to every note. And you can type your time ID like what zettelkasten do. MN datebase also recorded the time of notes creating. If you want,we cloud generate OPML with Time ID. But I don’ t know which app supports recognizing this ID unless search manually

3, Url-scheme works offline, you just have to use a certain PDF reader that supports URL-scheme like PDF expert, notability, etc.

Even you have deleted files stored in MN, the exported PDF still has an MN-page-number on every page. You will be able to jump page manually.

4, Tinderbox supports opening OPML directly, Devonthink supports opening Markdown which could be easily generated by OPML via Pandoc. That’s why I ask you if OPML satisfy your workflow.

OPML is also one of delim formats. Is this right ?

5, cradle-to-grave problem:
MN is the only app I known supports URL linking to certain sentence of a page. Others app I only know Devonthink has a URL to page (based on page number not sentence). So create a Script to replace the MN-URL in exported files with corresponding Devonthink-URL is feasible.(Like what Highlights app done)

Attachment to point 5:
If you know any other way to manage original PDF files in IpadOS,Please notify me. It seems MN is the only grave to PDF library so far. Even Script URL replacement can’t help.

(As MacOS has Devonthink to replace MN for URL-back destination)

Hello again, @Lanco_Support-Team … Thank you again for your replies. I feel like we’re making good progress in understanding each other, and hope that it can help you and the MarginNote team. I’ll answer your replies in turn, just as I’ve done before.

1. I’m glad to hear that you can make CSV exports, but I didn’t quite follow how you’re saying it could be done. If I follow you, you’re saying that MarginNote users should first export files in an Anki format, and then render them further via an Anki CSV extension to get a CSV export. Is that correct?

2. I understand that Marginnote already creates a unique URL to every note, and that’s one of its best features! But in my last reply to you I was describing something else that MN users are seeking: to “create an UID in MarginNote-annotated files – and, by extension, the notes they create” so that " MarginNote-annotated files & notes could generate create an UID – one UID for one file – that would apply to all of the MN-created annotated notes linked to that file.

Let me back up and explain… One of the Tinderbox developers actually suggested that MarginNote create an UID in MarginNote-annotated files – and, by extension, the notes they create” – so that users could locate all of the notes (i.e., MarginNote-created annotations) that pertain to particular files / documents. And part of the reason why Tinderbox developers suggested this approach was so to help users trace particular files / documents and correct or amend the annotations, and then re-export them from MarginNote, and import them, anew, into Tinderbox. This seems like an especially necessary approach given the way that MarginNote bundles files / documents in its notebooks. Does this make sense? I’m happy to clarify this further if you’d like – just let me know.

BTW, I haven’t yet experimented with the zettelkasten approach, but I’m happy to do so if it helps achieve what I and other MarginNote users are seeking in this respect.

3. Ok, you said: “Url-scheme works offline, you just have to use a certain PDF reader that supports URL-scheme like PDF expert, notability, etc.” First of all, this is the first I’ve head that MarginNote has created a URLs that can work offline. Wow. How didn’t we know this!? Forgive me for saying this, but it shows how much more MarginNote needs to explain its features and functions to users. Don’t get me wrong: I’m glad that such features exist! But @marginnote really needs to better communicate these things with its users.

Second, while I’m thrilled to hear that MarginNote-created URLs can work offline, it seems strange to expect users to purchase another app to use it! I’d suggest that MarginNote build on this feature so that we can still enjoy the benefits of our MarginNote experience, and use MN-created URLs in other apps. Does that make sense?

For my part, I archive all of my material in DEVONthink Pro, given the way it’s able to organize and collate files, run robust searches, and utilize IA for search terms. So, I’d love to be able to store my MarginNote-annotated PDF files in DEVONthink Pro (once I’m done with them) – i.e., so that they’re offline / off the iCloud and out of MarginNote, and then click on the MarginNote-created URLs so that it can refer back to the annotated part of the text. This seems to be what many other users want as well! But I think we’d all prefer to be able to do this in various apps. Again, I’m happy to expand on this further if that’s helpful.

4. Yes, Tinderbox does support opening OPML directly, but Tinderbox does not work well with MarginNote-created notes. Believe me – I’ve tried! I’ve tried to do this via MN exports to iThoughts X, and then another export to OMPL–>Tinderbox, and I’ve tried MN exports in RTF formats -->Tinderbox, and I’ve tried MN exports in OmniOutliner, and then another export to OMPL–>Tinderbox. All of them have been seriously problematic for various reasons, and that’s mostly because MarginNote’s exports continue to be glitchy for the reasons why I’ve mentioned in several posts, such as: Problems with OmniOutliner export and Problem with DEVONthink exports, and others that I’ve mentioned here.

5. Yes, you’re right about MN being the only app that I know of that supports URL linking to certain sentence of a page – and that’s part of why I’ve been using it, and advocate of your app! The only other app that does this is Highlights. Like you, I thought that there might be ways to borrow some of the ways that Highlights and DEVONthink uses their URLs for linking to certain sentence of a page – or, better yet, some ways that MarginNote can work in tandem with those apps (esp. DEVONthink) for their URL functionality. That would be ideal. And any kind of conflict between those apps and their functionality would be a disaster, so lets hope we can avoid that!

Thanks so much. Let me know if I can answer any other question. Happy to help as best I can…

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Dear @Lanco_Support-Team , I’m sorry for my late reply to your post. Honestly, I did not notice that you posted a reply to me, however it seems that @jprint and other users have articulated our desires better than I could have explained it myself. I feel like he summed it up perfectly, and I would follow his lead.

I think I speak for many other users by saying that we’re looking for both kind of archive file options that you (and others) have mention on this thread; that would be ideal.

Furthermore, I’d make the following points as you complete this feature:

  • Is @marginnote expecting that users ought to keep their documents and notebooks on the iCloud in perpetuity so that they can make use of the URLs and other features? Or should we have to use yet another pricey third-party software that would enable us to do so? I challenge @marginnote and @Support-Team to consider these questions in formulating an approach to archiving MarginNote-annotated files;

  • One point that @jprint did NOT raise is the prohibitively large size of MarginNote-annotated PDFs. I believe other users have raised this concern in the forum, but it bears repeating – especially as you’re formulating an approach to archiving MarginNote-annotated files. After all, the files come into MarginNote as PDFs, and my colleagues and I are hoping that MarginNote-annotated files can be exported as reasonable sized PDFs and still enable users to use MarginNote features, e.g., the MarginNote-created URLs;

  • Forgive me for repeating this, but I think I speak for many users when I say that part of our concern about MarginNote files is that the export formats are still quite problematic. I understand you and your co-workers are working hard to improve and repair many MarginNote features, but this remains one of the most frustrating and pernicious problems that we face. Quite simply, many of us cannot yet use the export files given the various formatting problems that they create;

Thank you.

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Hi @JournoProf ,

Firstly, its an misunderstood that for using URLS and other features needs to keep their documents and notebooks on the iCloud. I found Josh also have this question as he mentioned :

If you have a strong desire to make everything stable and also could using URLs for notebooks shifting, just close all the icloud options.

thanks for your reply! We will study your guys needs.

Best regards,
Support Team

Sorry, @Lanco_Support-Team I’m a bit confused by your last reply.

I’ve selected the “Automatically upload a document when start taking notes” option (under the “Sync documents to iCloud” header). I believe that’s the default setting anyway, right?

But you’re now saying if we want to “make everything stable”…“just close the iCloud options.” Is that right?

Does that mean you’re saying one can increase stability – and offline MarginNote-created URLs – by unchecking the “Automatically upload a document when start taking notes” option?

Please explain what you mean when you can. Thanks!


Ok, that’s cool. But based on how MarginNote is set up right now, it sure seems like we’d either have to rely on keeping files on the iCloud or use specific 3rd party apps in order to use the URLs. Is that correct?


To clarify,

We shut down icould drive permission for Marginnote.

And we don’t have any cloud files of MN3. Keeping the network shut down, the offline MarginNote also create URLs. Offline MarginNote-created URLs also work well across OmniOutliner, PDF expert, Ithoughts, Notability, and Marginnote even if the Mac or Ipad computer is offline.

It’s an Apple system inner shift mechanism which called URL-Scheme. Tinderbox is
also working on this mechanism. The unique UUID for every notes or interface is designed for this purpose.

Support Team