Textbook PDF annotation and workflow

I read medical journal articles mainly in BrowZine->Zotero. The rest of my reference texts are large (300-400) mb several thousand page pdf.

Am trying to combine workflows, and started using DEVONthink as everything bucket and obsidian for text (indexed to DEVONthink, but lots of links a la “sparky is.”

Struggling with how to work with the large textbook PDFs as I do all reading on iPad. Zotero isn’t great for this. DTTG takes a while to sync (even a single highlight seems it uploads whole file). Keeping files outside of DEVONthink adds complexity if I am indexing and moving files so was trying to keep everything but obsidian folder inside. Considering just importing textbook after read, but lose out on the search inside text and ability to link directly to a page in the pdf from text editor (currently obsidian but may go back to Apple notes).

Anyone have any luck with a workflow for large pdf and DEVONthink on iPad?

I suspect PDF file syncs will always mean reuploading and redownloading the whole file. No sync engine is going to understand exactly what bits of the file changed.

Perhaps break up the textbooks into chapters? That has worked well for me in the past.

Zotero is much quicker since only syncing “notes” not pdf. Also it’s fine for small articles but prefer more robust pdf experience.

Smaller files may work. I may jus live with syncing on local network via WebDAV rather than when away from house. Makes it more bearable.

Do you in fact want your annotations inside each large PDF?

I arrange my annotations in RTF files by topic, not by book or journal article, along with item-links back to the page within the source PDF.

Thus if I am taking notes on potential treatment options for a given disease, my “annotations” link to all sorts of references sources on the topic.

Is your work different in that you only focus on one source at a time?

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GoodNotes works great for this kind of reading/annotating, but I’m not sure that it is consistent (maybe, synergistic would be a better term) with your other practices. If you’re going to annotate outside of Zotero, you probably need a tool the makes standard PDF annotations so you can extract them into your zotero database. Admittedly, I have been having a hard time settling on a workflow for this process, myself.

These are primary sources. Most of what I do is obviously current articles, and the Zotero link to obsidian for linking works well. Trying to consolidate into DEVONthink and like the idea of the linkable pdf to page option. With a 3,000 page textbook not sure it’s a great option.

I think hook would be the right app for this……but doesn’t work on iOS/iPadOS and devonthink gives this option.

GoodNotes is the app I have been using to annotate (works amazingly well with these huge pdf), but the pulling everything into Zotero or DEVONthink to consolidate workflows has been hard to get a good system.

I thought this as well, but as follow up when I place large pdf in iCloud and edit with pdf expert the changes sync near instantly even via cell. It does not appear to update full pdf. And I thought maybe the highlights are not truely embedded (such as Zotero), but when I move the same pdf to my synology NAS and open in its previewer they do show up (as well as in pdf viewer, preview, etc).

Active large pdf with this workflow allow pdf expert annotations and sync and may move final pdf DT when done.