More fundamentally, we need to stop disseminating scholarly work as PDFs, a format primarily designed for print. Plain HTML would be an improvement. Even better than HTML would be an extended variant with scholarly-specific semantic markup and universal, animated, explorable figures. Embedded notebooks would be cool, too, but disseminating data would still be a major challenge. (And I don't just mean storage/transfer; a lot of researchers are reluctant to share source data to the world.)
On the paper organization side, I would also like to find out a better way of doing it. What helps me a lot, from a more methodological perspective, is to categorize books according to time period, school of thoughts, or perspective.
Also, is the data store encrypted at rest even when the app is actively being used?
folders:
- for every literature search, create a folder with date and name
- e.g. 2024-03-21_Quantum_Entanglement
- use CTRL-SHIFT-DRAG to drop files into Zotero as Links, see [#77](https://github.com/zotero/zotero/issues/77)
- You _can_ organize in Zotero, but you don't have to. Files can be linked
to multiple Zotero folders (simply copy library entries in Zotero)
- sync literature folder and zotero database with nextcloud to somewhere, for backup
zotero:
- disable sync
- set “Base directory” (Preferences > Advanced > Files and Folders) to local literature folder
- set PDF View to “System default” (Preferences > General > “Open PDFs using..”)
- Enable recursive quick search in folders: go to Preferences > Advanced > Config Editor, search for `recursiveCollections`, double click (set to True)
- use CTRL-Shift-C to copy bibliography to clipboard
- Dark Theme:
- https://github.com/Rosmaninho/Zotero-Dark-Theme
- Go to `%AppData%\Zotero\Zotero\Profiles\` (`XXXXXXXX.default`)
- Create `chrome` folder
- Place the `userChrome.css`
- Start Zotero
- Add-Ons:
- zotero-pdfkit
- https://github.com/sharpevo/zotero-pdfkit/
- allows to modify/select a “default” PDF attachment to be opened
- ZoteroDuplicatesMerger
- https://github.com/frangoud/ZoteroDuplicatesMerger
- easier merging of duplicates
- zotero-folder-import
- https://github.com/retorquere/zotero-folder-import
- bulk import PDFs from a folder
- zotero-tag
- https://github.com/windingwind/zotero-tag
- allows to add stars to items (Num Key `1`, `2`, `3` etc.)
- PDF Tools:
- qpdf
- removing passwords, unlocking PDFs, conversion
- install in WSL with `apt-get install qpdf`
- remove password with `qpdf --decrypt --password="" input.pdf output.pdf`
- `SumatraPDF`
- _Really_ fast Viewing of PDFs and adding annotations (highlight, comment etc.)
- Highlight Text: `A`, Save to file: `CTRL+SHIFT+S`
- it is much faster than Adobe Acrobat
- [pdfplumber](https://github.com/jsvine/pdfplumber)
- Awesome python package to extract tables from PDFs into data pipelines. Use with Jupyter Lab.
- [PDF X-Change viewer](https://www.tracker-software.com/product/pdf-xchange-editor), `choco install pdfxchangeviewer`
- for manual OCR of pages/PDFsI have a google docs for each research project and thus I can share them with my collaborators. Each person has their own section within the doc so we can also easily share information with each other!
The Elsevier account integration is disgusting though, and I hate the idea of using all Elsevier product.
I did try all the devices you listed above, even had my department pay serious money, and ended up barely using them for all those reasons. I am a mathematician, I am clumsy and I want to focus on my problem-solving; I want to think, and babysitting devices and tools is not what I want to spend my brainspace on.
Edit: Also, Chrome now defaults to this extension for rendering any PDFs you load.
I don't even want to imagine having to migrate all annotations and citations to something else when they inevitably pull the plug on it some years down the road.
It feels a bit dated sometimes, but I'm yet to find anything that comes close.
DrawboardPDF if you want something more full featured and like to annotate, highlight, bookmark and whatnot, particularly if there's any chance you'll also use a stylus
But most importantly.. ALT+'left arrow' allows you to go back before you clicked on the citation! It doesn't work all the time, but usually it does after some left arrows ;)
Also, in Android: you can click on the 'scrolling sign' on the right of the pdf and specify the page, or see the link to 'jump back' to before you clicked on a link!
I hope that will help
STDU Viewer might also be worth looking into. Default shortcut for jumping back is ctrl+z.
I figure in addition to the feedback they received from me (and presumably others) at the time they saw a drop in usage and restored the functional version. But they'll try again.
I'm pretty optimistic that by the time google scholar really goes to shit they'll be good enough to pick up the slack.
Let you import and read PDF directly, annotate, comment and share with people.
* Summarisation
* Succinctly placing the research in context of the broader field
* Highlighting limitations or flaws in research methods, etc.
* An outline view to summarise each paragraph/section and then drill down into the ones you actually want to read in more detail
* Rephrasing into plain English. A lot of academics enjoy sounding clever and usling long words so it'd be nice to be able to switch off "ego mode" and just read stuff in plain English instead of having to wade through their word-soup.
With more effort maybe Google could create a PDF reader that is actually innovative.
"Sounding smarter through obscurity"
I like the experience of reading in Muse.app on the iPad. It's a nested whiteboarding thing, but also can act as a PDF reader. (It'll let you pull out chunks of the PDF and put it on your canvas with a link back into your document, if that fits your flow.) I often read on my phone, so this is not an option for me.
Apple Notes and Muse slow down with a lot of ink. For taking a page full of notes I'm using Notability.
I've heard good things about GoodReader, but haven't played with it in years.
https://apps.apple.com/us/app/pdf-expert-editor-reader/id743...
MacOS and iPad: DevonThink paid app with sync via P2P, WebDAV or cloud services.
Optional local mirror/sync of web pages and PDFs, with full text search.
It seems to work in MacOS and iOS; an iCloud account is probably required.
What are you trying to do? Why is webgl the key here?
Unless you need to scroll left and right on your phone instead of absorbing
Maybe this just needs a script? I just paid $100 for EndNote 21 yesterday and don’t think these needs justify that cost.
This makes me nervous. I'm often looking at PDFs that are embedded in a page (either grad school software for commenting on PDFs, or publishers' sites). Is it going to play nicely with those? Is this only for navigating directly to a PDF?
So it's a closed ecosystem for now ... pass.