How best to archive MarginNote-annotated files?

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?

1 Like

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…

1 Like

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.

1 Like

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

Sorry, @Lanco_Support-Team … I’m even more confused now!

You said:

Maybe it’s because I’m using an older OS (10.11.6), but it sure seems like my MarginNote MacOS (and iOS) app(s) are still listed in the iCloud system menu options – and therefore seem to be utilizing the iCloud system.

Can you please clarify what’s happening for all of your users, as this seems like a rather important development!

It also seems like it would have a direct impact on archiving, syncing, and many other MarginNote-related functions.

Please clarify.


1 Like

Does this suggest that MarginNote is not using the iCloud in some capacity?

I’d appreciate an explanation as well.

Thank you.

1 Like

Can @marginnote / @Support-Team please answer my last question, as it seems especially germane to most users.

Thank you.


Hi @Lanco_Support-Team or @Sushi_Support-Team or @Relight_Support-Team – I know you’ve got your hands full sorting out the sync problems, but I’m just wondering if there’ve been any new developments with archiving. Specifically, I’m wondering if you’ve figured out new solutions to the questions that @JournoProf raised some time ago:


1 Like

Hello, jprint & JournoProf,

First, I’m sorry to be so late reply to you. Actually, I have noticed your post a few days before. After reading all these posts, now I think I can give you a relatively adequate answer. Firstly, I want to point out the biggest misunderstanding between you and Lanco.

In fact, what lanco said doesn’t mean


He just want to show you URL Scheme and iCloud is irrelevant.

Then let me answer your questions in detail.
1. what is URL Scheme?
It makes @jprint and @JournoProf puzzeled. According to Apple Developer Documents: Custom URL schemes provide a way to reference resources inside your app. Users tapping a custom URL in an email, for example, launch your app in a specified context. Other apps can also trigger your app to launch with specific context data; for example, a photo library app might display a specified image.
And here is the link:Apple Developer Documentation

Further more, I’d like to give you a comparison which may promote your understanding. On windows systems, you may named a file which is on your desktop as “xxx”. If you want to find this file, you just key the file location " C:\Users\Desktop\xxx" in the URL bar and press enter. Then you will open the Specified file“xxx”. Besides, you needn’t to connect to the network. In other words, you are able to jump to that file without network connection.

Similarly, URL Scheme is also a link to content within your app.

Then why @Lanco_Support-Team mentioned iCloud? He just want to correct wrong views.:upside_down_face:

2. the first question

After an explanation of URL Scheme, I think @JournoProf already knows the answer to the question. As URL Scheme has no relations with iCloud & network, you can make use of the URLs in other softwares which support URL-scheme, like PDF expert, notability, etc. And I see that

I guess you want to export your PDFs to your colleagues, hoping the URL-scheme can work at their devices successfully. Please note that URL-Scheme is just a link to content within your app, so if you want these URL-Schemes still work , you have to export(backup then share with airdrop) the certain files, such as mindmap notebooks, to your coworkers’ MarginNote 3 in advance.

In general, you needn’t to use another pricey third-party software or iCloud. What you should do is just exporting the corresponding files(i.e. files which URL-Scheme points to) to other devices. If you still have some trouble in understanding me, I will use some screenshots or GIFs to explain how to make use of URL-Schemes in different devices.

3.the second problem

You are right, the export of large size of MarginNote-annotated PDFs is indeed a tricky issue. We will discuss how to export them faster. Thanks for your suggestion. I guess may be there would be a better solution after version 3.7.

4. the third question

I don’t quite understand. Are you still emphasizing the second question? Please forgive my rudeness.

Really really thanks for all of your replys. If you @jprint &@JournoProf and any other devoted users still have some questions about URL-Scheme, please tell us.

Best Regards!

Hi @Sushi_Support-Team, Thanks for your detailed answers! They’re very helpful. Let me answer them, below…

Thanks for all of this. I think I have a good, general understand of URL schemes and hyperlinks, and I get that they’re not all created equal. Let me give you some examples of the kind of problems users might be facing, and the what kinds of solutions / applications we might be envisaging for MN3-created URL schemes / hyperlinks.

One way that I produce a PDF with links is by first creating a Word document, setting up links to external sites and “anchored” or bookmaker passages (i.e., links that refer to internal sections of the same document), and then “Save As…” or export the document as a PDF (selecting the “Best for electronic distribution and accessibility” – as opposed to “Best for printing”). When complete, I can use the links in this PDF to open external site and “anchored” / bookmaker passages in an app that opens the PDF – for MacOS and Windows.

But when I send a colleague a MN3-produced PDF, they cannot use the links that it has create in the same way since they either refer to using MN3 or some other third party app. That’s a case study in the frustrations that many users experience with with MN3-produced PDFs. Ideally, I’d like to be able open MN3-produced PDFs in virtually any app that can read PDFs, and use links in the way that I’ve laid out in my example, above, with the Word-created PDF. Is that possible?

Onto the next passage…

Ok, thanks, though I’m still not clear on how he was clearing up my confusion. In the past, it seems that when users clicked on MN3-produced PDFs it would re-open the documents / notebooks in MarginNote. I understand that MN3 has made changes so that no longer happens, but…if users want to click on links in MN3-produced PDFs so that they’re offline / not connected to the iCloud, we still need to do so through specific 3rd party apps like PDF Expect, no?

Is that correct? If not, please clarify this for us. Thanks!

I feel like we’re going in circles around the same question / issue.

Let me underscore my point this way: I work with many different clients and colleagues, and many of them don’t have MarginNote or the other documents you mentioned, and it’s unfair for me to expect that they purchase these apps in order to open my MN3-produced PDFs. Therefore, we’re seeking a solution that will make the MN3-produced PDFs more universally accessible so that we can use them with other non-MN3 apps, and so non-MN3 users can use the links as well!

BTW, as you know, it seems many MN3 users often use DEVONthinkPro (and Tinderbox), so it might be worth at least developing MN3 so that users can open MN3-produced PDFs in DEVONthinkPro. Please consider this seriously, as it would be a huge help to many MN3 users… Thanks!

Yes, please. That would be very helpful.

Onto your next answers, and my follow up replies to them…

(BTW, it looks like I referred to myself instead of referencing @JournoProf’s point. Apologies for the misattribution.)

Ok, great. We certainly appreciate that you’re aware of this, and aiming to change the PDF size. Frankly, the size is a real problem – I just cannot use MN3-prodcued PDFs because their size is too big, and therefore prohibitive to store. So, I’m really hoping you guys can tackle this problem soon…since I desperately want to store and archive my MN3-prodcued PDFs! Right now, it’s causing a major logjam.


Nope. I wan’t emphasizes the same question. Instead, I was referring to the other export problems, namely: all of the formatting problem resulting from MN3 exports to OmniOutliner, RTF / RTFD formats, etc. @JournoProf and I, along with many other users, have identified many, specific formatting problems with these MN3 exports. I’m happy to share those links with you again.

Let me be clear about two points… (1) PDFs are, for many of us, the go-to export format given its (generally) universal accessibility, and that’s what we’re hoping the links created in MN3-prodcued PDFs can work better / with greater universal accessibility, and (2) While we greatly appreciate how MN3 creates exports for many file formats, these exports essentially become unusable if there are so many formatting problems.

Again, we’re grateful for what MN3 does and is trying to do. And we’re thankful that you and other members of the @marginnote team have been receptive to our concerns and criticism. Please understand that we’ve been pressing on these concerns because many of us genuinely believe that MN3 is a terrific app with great potential, but it isn’t quite there yet. But if you’re able to fix some of these basic, core issues it’ll be the kind of amazing app we’re all hoping it can be!

Hope I’ve answered your questions in ways that are helpful. Please let me know if there’s anything else I – or any other users – can provide that will be useful to you and your colleagues.


1 Like


Really thanks for your reply. But please forgive me, I don’t quite understand what your word “link” exactly means. In other word, is it a link to external sites or a link to MarginNote 3’s cards or mindmap notebooks.

Best regards!