8 ms·

Zotero Better Notes – Knowledge management inside Zotero

263 points by mickelsen 3y ago

applied_heat 3y ago
I used to use and recommend qiqqa for full text search, highlighting, and annotating pdfs and managing bibliographies but it seems like zotero has stayed the course and qiqqa wound down. Glad to see a solution still available!
smitty1e 3y ago
I love Zotero. It's the only tool I use that is an .xpi. What are some learning resources for this programming system?
maxmalkav 3y ago
Zotero was key to finish my long delayed thesis, reducing the toil of managing a lot of references on a topic that I disliked more and more by the minute. Unfortunately back in the day they did not have yet the embedded PDF reader and highlighting features, but still was super helpful (I decided to stay away from Mendeley for license and affiliation reasons) I still keep Zotero around for some projects that require more serious bibliography management. Glad to see advances in the note management direction, even if it is a add-on. While serviceable, the default note options always felt a bit rough to me.
- hfo 3y ago
  > Zotero was key to finish my long delayed thesis, reducing the toil of managing a lot of references on a topic that I disliked more and more by the minute. Exactly the same for me, I'm forever grateful.
- xeromal 3y ago
  Same. Hearing Zotero brought back memories of undergrad for me. lol
mrmincent 3y ago
I’ve just started using zotero again after 10 or so years, being back at uni for some further learning. I’m so impressed that zotero has remained useful and these plugins look super handy, will be giving them a red-hot go. Thanks for sharing!
janwillemb 3y ago
Nice! This seems to actually solve a problem in my workflow with Zotero: manage the _personal_ metadata around the references. How did I find the reference? What parts are relevant? Etc. Definately going to give it a try.
- mickelsen 3y ago
  Yeah, I just stumbled upon this project and wanted to share, I'm currently using Obsidian for my personal wiki, but I use Zotero a lot as a paper repo and reader, the organization and metadata tools are great, and extending it to a more powerful note-taking tool seems like a no-brainer. Now it just needs an EPUB reader to replace Calibre, then it'd just be the perfect all-in-one personal library. For now I'm using this plugin that exports and keeps in sync the calibre library to Zotero: https://www.mobileread.com/forums/showthread.php?p=3339191 https://www.mobileread.com/forums/showthread.php?p=3339191 Very grateful that this open source project stays alive, I've seen attempts over the years from startups and other projects to tackle on spaces like pkm, research, paperless office, to then be abandoned yet Zotero keeps getting updates. There's also Tropy, from the same organization that develops Zotero, for organizing digital assets: https://tropy.org/ https://tropy.org/ Getting a bit off-topic, but this thing could use some sort of Moodboard designer to visually sort the assets in a canvas, kind of what you can do with Miro, Notion, Mural or locally with Obsidian Canvas/Excalidraw. On that note, there's also this project that takes on that space, previously featured on HN but has made significant progress lately: https://github.com/toeverything/AFFiNE https://github.com/toeverything/AFFiNE
  - imsaw 3y ago
    I also think an epub reader in zotero would make it a complete library manager. I used Calibre just for reading epubs, so I want to ask how and why do you need to sync its metadata with zotero?
    - mickelsen 3y ago
      I just like having the entire collection of files in one place, some of them are textbooks or reference books that don't sit well in either app entirely, and while I also keep novels there in a separate subcollection, most of my ebooks are non-fiction, where topics are the same or related to the rest of material I already keep in Zotero. Some are non-academic PDFs, blueprints, guides, whitepapers or manuals that I refer to for a given project, and while this is not the main purpose of Zotero, as it is a research-oriented tool, it still proves more useful than other tools, tidier than classical folders+files, and less of a hassle than coming up with my own system using something like Obsidian's dataview plugin. Calibre I prefer it to fix the metadata of my ebooks, but the local reading story isn't ideal for me. I've tried serving the collection over self-hosted web apps, to keep the page progress like calibre-web, but it wasn't ideal for me or conducive to what I look for: https://github.com/janeczku/calibre-web https://github.com/janeczku/calibre-web
evolve2k 3y ago
I’m using Zotero + Obsidian for my academic work and PhD. If anyone is trying to work out a Zotero to Obsidian to Word/Libre Office workflow, give it a look. I’ve created a GitHub repo README with instructions on linking everything together. Hopefully someone finds this useful, happy for more contributions also (hence why used a repo to do this) https://github.com/evolve2k/obsidian-pandoc-academic-word-doc-guide https://github.com/evolve2k/obsidian-pandoc-academic-word-do...
- maxmalkav 3y ago
  It looks like a powerful combo. Back in the day I went the LaTeX path, nowadays I’ll be tempted to follow your approach. I have tried Obsidian a couple of times, but it never stuck with me. For some reason I cannot go back to “regular editors” after years of vim (and now neovim), it is not only the modal editing (IIRC Obsidian has a decent vi mode), I guess it is more about having all your editing in the same tool (and the terminal). Nowadays I stick to neovim plus Telekasten plugin, not as polished as Obsidian, but with enough features.
- flor1s 3y ago
  +1 for Obsidian, though until now I haven't felt the need to write actual papers in. Zotero + latexmk + vim + Skim/SumatraPDF mostly scratches that itch for me.
- BOOSTERHIDROGEN 3y ago
  any examples of generated pdf ?
  - evolve2k 3y ago
    Oh good suggestion. I can’t get to it straight away but happy to add one. Feel free to add an issue in the repo, then I can report in once it’s added.
  - evolve2k 3y ago
    In practice the markdown to pdf conversion is performed by pandoc. Pandoc has functionality to recognise academic formatting styles (like APA, Harvard etc) Pandoc also has functionality to turn a table of contents on based off of the semantic headers. My guide is pulling together issues that arise across Zotero <> Obsidian <> Pandoc <> Word I’ve found most forums are concerned with one or two of these steps depending which forums you’re visiting.
impissedoff1 3y ago
Seems pretty similar to Joplin, but Joplin has tons of sync options and an Android version
Galicarnax 3y ago
Zotero is awful. It's heavyweight - in fact, a whole separate browser only to manage my bibligraphy (ever tried to use it with ~10k items?). Provides no CLI interface (to automate workflows with scripts). It's data model is weird - e.g., item types include such thing as "instant message", but more academia-relevant types (e.g., "dataset") are absent ("preprint" was incorporated only recently); ISSNs are treated as properties of articles rather than journals. And it boasts it has included its own PDF viewer, whereas I see it as down-side rather than improvement (more bloatware included - why not just follow the division of labor and delegate this functionality to external viewers... ahhh, yes, there is no annotating standard among PDF viewers...). But all other alternatives for bibliography management I know of are even worse.
- bronzecarnage 3y ago
  I had written a script to manage my pdf literature using crossref and arxiv to fetch metadata and store them in pdf tags, and just renaming the pdf in place. No hidden complexity, no gui. I hacked it into a python package a couple of months ago in an ADHD hyperfocus induced frenzy. Sounds like you might like it. Still a long way to go, but it's out there and FOSS. Contributions are welcome. https://github.com/jayghoshter/prem https://github.com/jayghoshter/prem
- ar-jan 3y ago
  > ever tried to use it with ~10k items? Yes, around 13k currently. Startup is slow, but I keep it open so that doesn't matter much. With Zotero 6, speed isn't great for general usage, but workable. Zotero 7 (beta) however feels very fast. I've switched to it already -- most plugins haven't been upgraded yet, but (at least currently) you can switch between v6 and 7 since there's no database updates involved.
kaffeeringe 3y ago
I just recently discovered Zotero and it makes my life so much easier. It finally makes sense to read PDFs and work with their content, when I know where to store the notes and find them, when I need them.
Helmut10001 3y ago
Zotero is great, but only if enhanced with plugins and a few settings. I don't use Zotero Better Notes so far, but here's my list: - [Opinionated decision] disable sync - [Opinionated decision] set “Base directory” (Preferences > Advanced > Files and Folders) to local literature folder - every time you download literature PDFs, create a new subfolder with the motivation for search, - prepend folder names by date-string (yyyy-mm-dd_look_for_albert_einstein_lit) - 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-DRAG to drop files into Zotero as Links, see [#77](https://github.com/zotero/zotero/issues/77) - use CTRL-Shift-C to copy bibliography to clipboard - Dark Theme [1]: - Go to `%AppData%\Zotero\Zotero\Profiles\` (`XXXXXXXX.default`) - Create `chrome` folder - Place the `userChrome.css` - Start Zotero - Add-Ons: - zotero-pdfkit [2] - allows to modify/select a “default” PDF attachment to be opened - ZoteroDuplicatesMerger [3] - easier merging of duplicates - zotero-folder-import [4] - bulk import PDFs from a folder - zotero-tag [5] - allows to add stars to items (Num Key `1`, `2`, `3` etc.) - example see [6] [1]: https://github.com/Rosmaninho/Zotero-Dark-Theme [2]: https://github.com/sharpevo/zotero-pdfkit/ [3]: https://github.com/frangoud/ZoteroDuplicatesMerger [4]: https://github.com/retorquere/zotero-folder-import [5]: https://github.com/windingwind/zotero-tag [6]: https://ad.vgiscience.org/links/imgs/zotero_stars.webp
- Eddy_Viscosity2 3y ago
  Thanks for sharing these. I already use a number of these on your list. Though I don't use copy-by-link for files. For me one of the key purposes of zotero is that its the place where I keep these files so I don't have to keep them elsewhere where they aren't as easily searchable. I'm excited to try the duplicates merger tool, I've been forever putting off this because the normal way is such a slog. The Tag one also looks good. To add to the list, my key add-ons are: - better bibtex, this one is essential for me as a latex user - zotfile. This one is cool because if you add annotations to a pdf, like highlighting or comments while you read it, then zotfile will pull those out into notes in the zotero entry. This makes it really easy to see both that I've read this document, and what parts I thought were important. [1] https://retorque.re/zotero-better-bibtex/ https://retorque.re/zotero-better-bibtex/) [2] http://zotfile.com/ http://zotfile.com/
noisy_boy 3y ago
Obsidian has replaced all (work, home, mobile) note taking solutions everywhere for me. The last want from my side is removing the friction related to editing markdown tables (e.g. multi-line content in cells) - Obsidian has some plugins that makes things better but it is miles behind what, say, confluence wiki offers for tables.
- deelly 3y ago
  Is it ok for you to pay 8$ monthly for sync between devices? Or did you use another way of sync or don't use it at all?
  - ssss11 3y ago
    That’s my only gripe with obsidian.. I’d like sync between my devices that avoids central servers.
    - hoppyhoppy2 3y ago
      SyncThing can accomplish that.
      - ssss11 3y ago
        Thank you - I’ll check it out
    - vs4vijay 3y ago
      You can use SyncThing
      - ssss11 3y ago
        Thank you I’ll check it out
    - evolve2k 3y ago
      Charging for the sync is their primary revenue model. Zotero is doing the same. I don’t bemoan this approach that basically gives everything local away for free.
trallnag 3y ago
I've only ever used Citavi during my BSc and MSc.
zmmmmm 3y ago
Does it give you a way to link a fragment of text in a PDF to notes about it somewhere else and navigate between the two? This is the biggest pain point that I basically solved manually in my PhD with a kind of made up system with hash tags embedded in PDF notes. It's such a painful process maintaining a collection of citations around a particular topic, and being able to map what papers support what pieces of knowledge along with context around that. Still seems relatively unsolved problem to me.
- adr1an 3y ago
  That's what it does, see its readme
RhodesianHunter 3y ago
This seems like the best place to ask, does anyone have any recommendations for a very simple notes tool that can be easily shared amongst a family or team? Preferably mobile friendly, Even if just in browser.
- stavros 3y ago
  I like Joplin, and the sharing is done via Dropbox or a number of other backends. Have a Dropbox shared folder that everyone has access to, and you can edit notes. Joplin is a great note taker in general, as well, and the mobile app is great.
  - whatyesaid 3y ago
    Joplin isn't that easy to setup for family. It also doesn't work like that for Dropbox, it links to a specific app folder on your own account. I'm also not sure about distributed editing it would result in a lot of conflict notes that you manually must fix. Just use Notion or Google Drive folder with docs if you don't have too many notes.
- cfiggers 3y ago
  Assuming you're well aware of something like a shared Google Doc and you need something a little more fully featured... For "easily shared" it's hard to beat Notion. They have a really good mobile experience and the ability to control permissions and sharing at a detailed level. The only drawback with that recommendation is you also asked for "very simple," which Notion is definitely not. But, you don't have to use all the features available--you can use the complicated tool in a simple way if you like.
- x2dhump 3y ago
  for Apple ecosystem, the Notes application works well for "simple" shared notes
ykonstant 3y ago
I just updated Zotero from the AUR and, during the build process, the pdf.js dependency reported 25 vulnerabilities, of which 5 being critical. Given that we sometimes pull pdf from questionable sources/websites, should that not be a priority to fix? Or is there a standard mitigation process that I am not aware of?
ss48 3y ago
How well will this work when accessing Zotero notes via the Mobile App. Will the notes still be viewable from iOS Zotero App, even with more limited functionality?
nestock 3y ago
Installation does not work, unfortunately
ukuina 3y ago
For those considering a commerical solution, DEVONthink handles personal knowledge as well as PDF and other files, split into separate "databases" that can sync across local WiFi to other devices running DEVONthink. I recently discovered it can handle Markdown files and link across entries. Search is powerful and fast. There are very few sync issues. Downsides: MacOS/iOS/iPadOS only, and not free or open-source (but it's a one-time purchase). Not affiliated, just a happy user.
- tengwar2 3y ago
  The strong point for me is that DEVONthink uses RTF (and RTFD) as the native format. RTF is, along with Markdown, a document format that I expect to be widely supported for the next 40 years, but has the advantage of being WYSIWYG and supporting more advanced formatting. RFTD supports embedded images - it is less widely supported, but there are third party editors. The "databases" are MacOS packages, and they document how to get the files out if DEVONthink becomes unavailable. Hence for me it gives a good balance of functionality and longevity.
superposeur 3y ago
I like to annotate pdfs by hand, so import from Zotero into Notability on my ipad. Does anyone know of a good way to automatically reintegrate hand annotated pdfs back into Zotero? Ideally a given Zotero reference entry would have two pdfs, original and annotated, as well as a .note file. (The various plug in options seem only to manage text annotations.)
- jmhammond 3y ago
  I realize that below I'm not answering your direct question (and instead just talking about the text-based annotations), but I wanted to document it because I went from handwritten to highlighting and typing (clumsily on the ipad) I used to do this myself (though with GoodNotes), but I'm switched the Zotero in-built PDF viewer. The annotations you make in the in-built PDF reader are separate from the PDF file itself to: 1. Easier syncing - the annotations are light, rather than syncing the entire PDF > "We'll always try to support external workflows as efficiently as possible, but it will never match the seamless experience we're able to provide when everything is done within the app." [1] 2. The internal (text-based) annotations show up as notes, which has a neat effect that when I started using BetterNote this morning, it already has every one of my annotations ready to be used. I was surprised and a little delighted (there's a tiny button on the tab bar with a magnifying glass[2], it show all your notes/annotations from EVERY file and lets you link them to your workspace note). 3. You can export your annotations onto the PDF if you want to store them on the PDF itself. The bad: handwritten annotations don't show up in the notes list (in the Zotero 7 beta build I'm running, at least)[3]. [1]: https://www.zotero.org/support/kb/annotations_in_database https://www.zotero.org/support/kb/annotations_in_database [2]: https://app.screencast.com/gv9JBZNpJyoSF https://app.screencast.com/gv9JBZNpJyoSF [3]: https://app.screencast.com/0YQjZSV54R1Ha https://app.screencast.com/0YQjZSV54R1Ha
  - superposeur 3y ago
    Thanks for this information — I’ll give the built in Zotero annotation took a closer look.

263 points by mickelsen 3y ago

I used to use and recommend qiqqa for full text search, highlighting, and annotating pdfs and managing bibliographies but it seems like zotero has stayed the course and qiqqa wound down. Glad to see a solution still available!

smitty1e 3y ago

I love Zotero. It's the only tool I use that is an .xpi. What are some learning resources for this programming system?

maxmalkav 3y ago

Zotero was key to finish my long delayed thesis, reducing the toil of managing a lot of references on a topic that I disliked more and more by the minute. Unfortunately back in the day they did not have yet the embedded PDF reader and highlighting features, but still was super helpful (I decided to stay away from Mendeley for license and affiliation reasons) I still keep Zotero around for some projects that require more serious bibliography management. Glad to see advances in the note management direction, even if it is a add-on. While serviceable, the default note options always felt a bit rough to me.

hfo 3y ago
> Zotero was key to finish my long delayed thesis, reducing the toil of managing a lot of references on a topic that I disliked more and more by the minute. Exactly the same for me, I'm forever grateful.
xeromal 3y ago
Same. Hearing Zotero brought back memories of undergrad for me. lol

mrmincent 3y ago

I’ve just started using zotero again after 10 or so years, being back at uni for some further learning. I’m so impressed that zotero has remained useful and these plugins look super handy, will be giving them a red-hot go. Thanks for sharing!

janwillemb 3y ago

Nice! This seems to actually solve a problem in my workflow with Zotero: manage the _personal_ metadata around the references. How did I find the reference? What parts are relevant? Etc. Definately going to give it a try.

mickelsen 3y ago
Yeah, I just stumbled upon this project and wanted to share, I'm currently using Obsidian for my personal wiki, but I use Zotero a lot as a paper repo and reader, the organization and metadata tools are great, and extending it to a more powerful note-taking tool seems like a no-brainer. Now it just needs an EPUB reader to replace Calibre, then it'd just be the perfect all-in-one personal library. For now I'm using this plugin that exports and keeps in sync the calibre library to Zotero: https://www.mobileread.com/forums/showthread.php?p=3339191 https://www.mobileread.com/forums/showthread.php?p=3339191 Very grateful that this open source project stays alive, I've seen attempts over the years from startups and other projects to tackle on spaces like pkm, research, paperless office, to then be abandoned yet Zotero keeps getting updates. There's also Tropy, from the same organization that develops Zotero, for organizing digital assets: https://tropy.org/ https://tropy.org/ Getting a bit off-topic, but this thing could use some sort of Moodboard designer to visually sort the assets in a canvas, kind of what you can do with Miro, Notion, Mural or locally with Obsidian Canvas/Excalidraw. On that note, there's also this project that takes on that space, previously featured on HN but has made significant progress lately: https://github.com/toeverything/AFFiNE https://github.com/toeverything/AFFiNE
- imsaw 3y ago
  I also think an epub reader in zotero would make it a complete library manager. I used Calibre just for reading epubs, so I want to ask how and why do you need to sync its metadata with zotero?
  - mickelsen 3y ago
    I just like having the entire collection of files in one place, some of them are textbooks or reference books that don't sit well in either app entirely, and while I also keep novels there in a separate subcollection, most of my ebooks are non-fiction, where topics are the same or related to the rest of material I already keep in Zotero. Some are non-academic PDFs, blueprints, guides, whitepapers or manuals that I refer to for a given project, and while this is not the main purpose of Zotero, as it is a research-oriented tool, it still proves more useful than other tools, tidier than classical folders+files, and less of a hassle than coming up with my own system using something like Obsidian's dataview plugin. Calibre I prefer it to fix the metadata of my ebooks, but the local reading story isn't ideal for me. I've tried serving the collection over self-hosted web apps, to keep the page progress like calibre-web, but it wasn't ideal for me or conducive to what I look for: https://github.com/janeczku/calibre-web https://github.com/janeczku/calibre-web

evolve2k 3y ago

I’m using Zotero + Obsidian for my academic work and PhD. If anyone is trying to work out a Zotero to Obsidian to Word/Libre Office workflow, give it a look. I’ve created a GitHub repo README with instructions on linking everything together. Hopefully someone finds this useful, happy for more contributions also (hence why used a repo to do this) https://github.com/evolve2k/obsidian-pandoc-academic-word-doc-guide https://github.com/evolve2k/obsidian-pandoc-academic-word-do...

maxmalkav 3y ago
It looks like a powerful combo. Back in the day I went the LaTeX path, nowadays I’ll be tempted to follow your approach. I have tried Obsidian a couple of times, but it never stuck with me. For some reason I cannot go back to “regular editors” after years of vim (and now neovim), it is not only the modal editing (IIRC Obsidian has a decent vi mode), I guess it is more about having all your editing in the same tool (and the terminal). Nowadays I stick to neovim plus Telekasten plugin, not as polished as Obsidian, but with enough features.
flor1s 3y ago
+1 for Obsidian, though until now I haven't felt the need to write actual papers in. Zotero + latexmk + vim + Skim/SumatraPDF mostly scratches that itch for me.
BOOSTERHIDROGEN 3y ago
any examples of generated pdf ?
- evolve2k 3y ago
  Oh good suggestion. I can’t get to it straight away but happy to add one. Feel free to add an issue in the repo, then I can report in once it’s added.
- evolve2k 3y ago
  In practice the markdown to pdf conversion is performed by pandoc. Pandoc has functionality to recognise academic formatting styles (like APA, Harvard etc) Pandoc also has functionality to turn a table of contents on based off of the semantic headers. My guide is pulling together issues that arise across Zotero <> Obsidian <> Pandoc <> Word I’ve found most forums are concerned with one or two of these steps depending which forums you’re visiting.

impissedoff1 3y ago

Seems pretty similar to Joplin, but Joplin has tons of sync options and an Android version

Galicarnax 3y ago

Zotero is awful. It's heavyweight - in fact, a whole separate browser only to manage my bibligraphy (ever tried to use it with ~10k items?). Provides no CLI interface (to automate workflows with scripts). It's data model is weird - e.g., item types include such thing as "instant message", but more academia-relevant types (e.g., "dataset") are absent ("preprint" was incorporated only recently); ISSNs are treated as properties of articles rather than journals. And it boasts it has included its own PDF viewer, whereas I see it as down-side rather than improvement (more bloatware included - why not just follow the division of labor and delegate this functionality to external viewers... ahhh, yes, there is no annotating standard among PDF viewers...). But all other alternatives for bibliography management I know of are even worse.

bronzecarnage 3y ago
I had written a script to manage my pdf literature using crossref and arxiv to fetch metadata and store them in pdf tags, and just renaming the pdf in place. No hidden complexity, no gui. I hacked it into a python package a couple of months ago in an ADHD hyperfocus induced frenzy. Sounds like you might like it. Still a long way to go, but it's out there and FOSS. Contributions are welcome. https://github.com/jayghoshter/prem https://github.com/jayghoshter/prem
ar-jan 3y ago
> ever tried to use it with ~10k items? Yes, around 13k currently. Startup is slow, but I keep it open so that doesn't matter much. With Zotero 6, speed isn't great for general usage, but workable. Zotero 7 (beta) however feels very fast. I've switched to it already -- most plugins haven't been upgraded yet, but (at least currently) you can switch between v6 and 7 since there's no database updates involved.

kaffeeringe 3y ago

I just recently discovered Zotero and it makes my life so much easier. It finally makes sense to read PDFs and work with their content, when I know where to store the notes and find them, when I need them.

Helmut10001 3y ago

Zotero is great, but only if enhanced with plugins and a few settings. I don't use Zotero Better Notes so far, but here's my list: - [Opinionated decision] disable sync - [Opinionated decision] set “Base directory” (Preferences > Advanced > Files and Folders) to local literature folder - every time you download literature PDFs, create a new subfolder with the motivation for search, - prepend folder names by date-string (yyyy-mm-dd_look_for_albert_einstein_lit) - 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-DRAG to drop files into Zotero as Links, see [#77](https://github.com/zotero/zotero/issues/77) - use CTRL-Shift-C to copy bibliography to clipboard - Dark Theme [1]: - Go to `%AppData%\Zotero\Zotero\Profiles\` (`XXXXXXXX.default`) - Create `chrome` folder - Place the `userChrome.css` - Start Zotero - Add-Ons: - zotero-pdfkit [2] - allows to modify/select a “default” PDF attachment to be opened - ZoteroDuplicatesMerger [3] - easier merging of duplicates - zotero-folder-import [4] - bulk import PDFs from a folder - zotero-tag [5] - allows to add stars to items (Num Key `1`, `2`, `3` etc.) - example see [6] [1]: https://github.com/Rosmaninho/Zotero-Dark-Theme [2]: https://github.com/sharpevo/zotero-pdfkit/ [3]: https://github.com/frangoud/ZoteroDuplicatesMerger [4]: https://github.com/retorquere/zotero-folder-import [5]: https://github.com/windingwind/zotero-tag [6]: https://ad.vgiscience.org/links/imgs/zotero_stars.webp

Eddy_Viscosity2 3y ago
Thanks for sharing these. I already use a number of these on your list. Though I don't use copy-by-link for files. For me one of the key purposes of zotero is that its the place where I keep these files so I don't have to keep them elsewhere where they aren't as easily searchable. I'm excited to try the duplicates merger tool, I've been forever putting off this because the normal way is such a slog. The Tag one also looks good. To add to the list, my key add-ons are: - better bibtex, this one is essential for me as a latex user - zotfile. This one is cool because if you add annotations to a pdf, like highlighting or comments while you read it, then zotfile will pull those out into notes in the zotero entry. This makes it really easy to see both that I've read this document, and what parts I thought were important. [1] https://retorque.re/zotero-better-bibtex/ https://retorque.re/zotero-better-bibtex/) [2] http://zotfile.com/ http://zotfile.com/

noisy_boy 3y ago

Obsidian has replaced all (work, home, mobile) note taking solutions everywhere for me. The last want from my side is removing the friction related to editing markdown tables (e.g. multi-line content in cells) - Obsidian has some plugins that makes things better but it is miles behind what, say, confluence wiki offers for tables.

deelly 3y ago
Is it ok for you to pay 8$ monthly for sync between devices? Or did you use another way of sync or don't use it at all?
- ssss11 3y ago
  That’s my only gripe with obsidian.. I’d like sync between my devices that avoids central servers.
  - hoppyhoppy2 3y ago
    SyncThing can accomplish that.
    - ssss11 3y ago
      Thank you - I’ll check it out
  - vs4vijay 3y ago
    You can use SyncThing
    - ssss11 3y ago
      Thank you I’ll check it out
  - evolve2k 3y ago
    Charging for the sync is their primary revenue model. Zotero is doing the same. I don’t bemoan this approach that basically gives everything local away for free.

trallnag 3y ago

I've only ever used Citavi during my BSc and MSc.

zmmmmm 3y ago

Does it give you a way to link a fragment of text in a PDF to notes about it somewhere else and navigate between the two? This is the biggest pain point that I basically solved manually in my PhD with a kind of made up system with hash tags embedded in PDF notes. It's such a painful process maintaining a collection of citations around a particular topic, and being able to map what papers support what pieces of knowledge along with context around that. Still seems relatively unsolved problem to me.

adr1an 3y ago
That's what it does, see its readme

RhodesianHunter 3y ago

This seems like the best place to ask, does anyone have any recommendations for a very simple notes tool that can be easily shared amongst a family or team? Preferably mobile friendly, Even if just in browser.

stavros 3y ago
I like Joplin, and the sharing is done via Dropbox or a number of other backends. Have a Dropbox shared folder that everyone has access to, and you can edit notes. Joplin is a great note taker in general, as well, and the mobile app is great.
- whatyesaid 3y ago
  Joplin isn't that easy to setup for family. It also doesn't work like that for Dropbox, it links to a specific app folder on your own account. I'm also not sure about distributed editing it would result in a lot of conflict notes that you manually must fix. Just use Notion or Google Drive folder with docs if you don't have too many notes.
cfiggers 3y ago
Assuming you're well aware of something like a shared Google Doc and you need something a little more fully featured... For "easily shared" it's hard to beat Notion. They have a really good mobile experience and the ability to control permissions and sharing at a detailed level. The only drawback with that recommendation is you also asked for "very simple," which Notion is definitely not. But, you don't have to use all the features available--you can use the complicated tool in a simple way if you like.
x2dhump 3y ago
for Apple ecosystem, the Notes application works well for "simple" shared notes

ykonstant 3y ago

I just updated Zotero from the AUR and, during the build process, the pdf.js dependency reported 25 vulnerabilities, of which 5 being critical. Given that we sometimes pull pdf from questionable sources/websites, should that not be a priority to fix? Or is there a standard mitigation process that I am not aware of?

ss48 3y ago

How well will this work when accessing Zotero notes via the Mobile App. Will the notes still be viewable from iOS Zotero App, even with more limited functionality?

nestock 3y ago

Installation does not work, unfortunately

ukuina 3y ago

For those considering a commerical solution, DEVONthink handles personal knowledge as well as PDF and other files, split into separate "databases" that can sync across local WiFi to other devices running DEVONthink. I recently discovered it can handle Markdown files and link across entries. Search is powerful and fast. There are very few sync issues. Downsides: MacOS/iOS/iPadOS only, and not free or open-source (but it's a one-time purchase). Not affiliated, just a happy user.

tengwar2 3y ago
The strong point for me is that DEVONthink uses RTF (and RTFD) as the native format. RTF is, along with Markdown, a document format that I expect to be widely supported for the next 40 years, but has the advantage of being WYSIWYG and supporting more advanced formatting. RFTD supports embedded images - it is less widely supported, but there are third party editors. The "databases" are MacOS packages, and they document how to get the files out if DEVONthink becomes unavailable. Hence for me it gives a good balance of functionality and longevity.

superposeur 3y ago

I like to annotate pdfs by hand, so import from Zotero into Notability on my ipad. Does anyone know of a good way to automatically reintegrate hand annotated pdfs back into Zotero? Ideally a given Zotero reference entry would have two pdfs, original and annotated, as well as a .note file. (The various plug in options seem only to manage text annotations.)

jmhammond 3y ago
I realize that below I'm not answering your direct question (and instead just talking about the text-based annotations), but I wanted to document it because I went from handwritten to highlighting and typing (clumsily on the ipad) I used to do this myself (though with GoodNotes), but I'm switched the Zotero in-built PDF viewer. The annotations you make in the in-built PDF reader are separate from the PDF file itself to: 1. Easier syncing - the annotations are light, rather than syncing the entire PDF > "We'll always try to support external workflows as efficiently as possible, but it will never match the seamless experience we're able to provide when everything is done within the app." [1] 2. The internal (text-based) annotations show up as notes, which has a neat effect that when I started using BetterNote this morning, it already has every one of my annotations ready to be used. I was surprised and a little delighted (there's a tiny button on the tab bar with a magnifying glass[2], it show all your notes/annotations from EVERY file and lets you link them to your workspace note). 3. You can export your annotations onto the PDF if you want to store them on the PDF itself. The bad: handwritten annotations don't show up in the notes list (in the Zotero 7 beta build I'm running, at least)[3]. [1]: https://www.zotero.org/support/kb/annotations_in_database https://www.zotero.org/support/kb/annotations_in_database [2]: https://app.screencast.com/gv9JBZNpJyoSF https://app.screencast.com/gv9JBZNpJyoSF [3]: https://app.screencast.com/0YQjZSV54R1Ha https://app.screencast.com/0YQjZSV54R1Ha
- superposeur 3y ago
  Thanks for this information — I’ll give the built in Zotero annotation took a closer look.