How I Use ObsidianMD and Zotero For Academic Research

[@yvonnemosley]

Excellent tutorial. I am new to Obsidian and this is exactly what I needed to maximize my workflow. Thank you!

[@drbones8946]

I found this video interesting but I think that connecting articles or papers in Obsidian is actually pointless from a research point of view. When doing research we need to extract the information from the papers and then use Obsidian to create notes on concepts and ideas, creating links between these ideas found in the papers. Therefore, the notes in Obsidian should be on ideas and concepts and not focused on papers and articles. This way Obsidian can be used as a way to link the ideas and concepts you learn instead of linking your papers (based on its contents) which ResearchRabbit already does with AI within seconds and for free.

[@fabsanh]

Thank you very much. I improved my workflow by looking yours. Especially in terms of the Zotero-Obsidian integration via BibLaTeX/Citations plugins. Sending cheers from Chile! 🇨🇱

[@elodiegradlife6904]

5:41 obsidian style settings 11:30 link papers together See description for more resources

[@TheJoshtheboss]

03:41 renaming the citation key does not change/update for me for some reason. Also what if an author has 2 papers in the same year?..

[@TheJoshtheboss]

Okay, needed to click Beter Bibtext and refresh key. Also letters are automatically added if more works in a year.

[@gkcadadr]

Thank you for the tutorial! I was curious about Obsidian and this helps a lot because a lot of the other stuff is filled with weird faff about hoity toity big brain productivity nonsense, whereas you present it in a sensible approachable manner useful to someone who wants to see if they can use this software or not for doing normal human work lol. Interestingly, it looks like we developed a very similar reading/litreview note structure and template, and at about the same time too. Back then I was using Emacs and Org Mode, now I am trying to use Markdown files without depending on any one app.

[@mrguizos]

Lots of useful tips here. Thank you so much for sharing them in this great video!

[@noneliadf]

Such a great video. I come from Holly's study sessions and I love your channel. Thank you for the video and all the links. I'm starting with Obdisian, so I appreciate all this information. 😊🤗😘

[@peerreviewed]

So glad it could be helpful for you! And lovely to see a familiar username from Holly's sessions 🥰

[@BrendanDoody]

Hey great video. Not sure if someone already mentioned this in the comments (or if you have since discovered this), but there is also a 'local graph view' which only opens the graph with links for a specific note.

[@FonteyneMargot]

Yay, great to see another PhD student using Obsidian and Zotero! It was interesting to see your approach, as you link references directly to each other instead of through topics (if I have notes on two papers on a certain topic, I create a link for that topic in both notes). Two questions: 1) I think having emoji as tags in Zotero looks really great, but isn't typing emoji all the time a bit cumbersome? Or is there a secret trick that makes typing them really easy? 2) Is there a reason why you copy-paste all your quotes and write down page references manually? Why not use the extract annotations feature in Zotero? And lastly, have you looked at the graph analysis plugin for Obsidian? I think the co-citations feature would be really interesting for you!

[@peerreviewed]

Ah, yay, same! I love seeing how other PhD students and academics use it! To address your comment about topics, I also do this! I didn't go through it in the video, but I have 'maps of content' for the big areas of my research and I will link articles to the ones that are relevant. I'm also starting to experiment with more zettlekasten style notes and linking those together as well as to articles. As for your questions: 1) it definitely is a little bit of a faff to type the emojis out, but I've got them all in a 'key' note in Obsidian and usually just copy them from there. I prefer them over words because it sets them apart from my topic tags. 2) I keep trying to justify this to myself, but the reality is that I have so far been too lazy to figure out how to set up the MD notes part of the workflow I literally linked in the description 🙈 However, that workflow doesn't use the citations plugin so I would have to figure out how it all comes together. 3) I have not! I will definitely check it out now though! I love going down a plug-in rabbit hole

[@peerreviewed]

Okay I'm looking into the co-citations and my mind is blown! This is exactly what I hoped existed but didn't know how to go looking for

[@FonteyneMargot]

@@peerreviewed Aaaaah, okay, you're also doing MOCs. I discovered today that the Windows + ; shortcut works quite nicely for adding emoji! I've played around with the citation plugin, but finally switched to the bibnotes plugin, which loads both user notes and extracted annotations from Zotero without first having to convert those into MD notes. Quite happy with my setup now, but it did take a while to figure everything out, haha. The only annoying thing is that bibnotes doesn't have an "insert literature note link" feature, so I still use the citation plugin for that.

[@neil6407]

@@peerreviewed A year late, but you could add a text replacement of probably some key characters, for instance “~~” which links to one emoji. Makes the workflow smoother, if that helps.

[@rays6580]

13:00 what happens if you have authoryear format and same author and same year has two papers? how do the link work?

[@peerreviewed]

It doesn’t 😂 If it’s a reference from Zotero it will get an added a, b, c etc at end end of the year as I get more papers from that author in that year, but as for the citations I’ve manually put in from other papers it’s a guessing game. However, so far if I’ve run into this I just go back to the original paper that cited it and check which ones it was and add the letters manually to distinguish

[@phdee-m4s]

thank you SO MUCH - LOVE this!! have been using this for several months now with great success and have recommended it to others as well. wondering about the significance of the @ in the citekey - I am leaving it out (removed it in the options) because I have other notes coming into obsidian titled by author last name and i want them all to sort together. so far so good. curious if anyone else ran into this?

[@jcboom]

I have the same question.

[@elliotthe1216]

Thanks a lot. I was looking for a way to integrate my bibliography in zotero with my notes in obsidian. I wanted to make notes that reference my bibliography by the way "auhtoryear" but I didnt have found how. Sorry, enlgish is not my mother language, probably there is some mistakes in the previous paragraph.

[@HollyJaneYT]

I’m here. With popcorn.

[@peerreviewed]

Hope it was helpful, Holly!

[@naren1705]

Thank you! Found the video very useful! When I used 'Shift + option + Y' and a new document is created. With few references the top part of the created new document is in red font. Would you know why this might be so?

[@toddpeterson5812]

Great video. I am retired and want to think like a PhD :). How do you go to the next step and take all your notes to wire an article?

[@BetterOffRead]

Such a great video! Thank you :)

[@k1tajfar714]

Too cute! Don't be scared of the code. It'll be ok.

[@daviddrouin7223]

Great tool, thanks for sharing. Is there a way to pull the PDF from zotero and physically store it in the appropriate folder in obsidian vault ?

[@DanteHaroun]

I second this

[@SliceofLife1]

A couple of quesitons. I don't see low contrast background option. Seocnd, how do you have color and a darker yellow color for text panel? what is it hex code? how can I change the color of markdown links? Thanks

[@tylerdurden4396]

I think I have watched every Zotero Obsidian workflow video now and this is the first one that has actually worked. I can now end the two week sh*tshow of trying to figure out a suitable workflow. Thank you! I do have a question though. You mentioned at one point that you use a paperclip tag to negate clutter on the graph. How do I do this please?

[@peerreviewed]

I’m so glad it’s working for you! I just tag everything I want to show up on the graph with the paperclip and then filter the graph to only show notes with the paperclip tag

[@tylerdurden4396]

@@peerreviewed so simple. I should probably click around rather than just watch videos! Thank you for your reply, much appreciated.

[@solperezmartinez1896]

Great video! Thank you! I am having problems with my Obsidian notes not updating after changing information in my Zotero library even though I have the .bib and .json file to keep update. Any workarounds please?

[@ryanwwest]

Great video! I was wondering what you do if you have conflicting Citation Keys? I'm working on my PhD as well and have a few references from the same group of people on the same year which resolve to exactly the same key. Sometimes I see the convention of appending 'a', 'b', 'c', etc to keys to disambiguate this in papers, but this would probably be hard to do given that you create the keys in Obsidian on-the-fly and might forget that there was a duplicate. Do you have a workaround? On a separate note, does the pdf annotation syncing between your iPad and laptop work well? Does Zotero have some way to recognize such annotations? I wonder if it plays well with pdf/epub annotations from multiple source applications.

[@lauragallagher7488]

I came to the comments to ask the same thing!

[@lauragallagher7488]

Have you found a solution since?

[@ryanwwest]

@@lauragallagher7488 No, but I'd like to... I've mainly just been using the full paper title as the note title to link to, then for the Zotero select URIs, using the zotero parent item ID which never changes to link the note back to zotero. It's not ideal, as the item ID has no meaning but is currently the most likely to persist over time (citekeys change if you change the author name, published year, or method in which citekeys are generated in the first place - which would cause a ripple effect unlinking mentions of the outdated citekeys through Obsidian).

[@ryanwwest]

My other wish list item is annoation support for ePUBs and HTML in Zotero. Then virtually all of my documents, books, and articles could be managed through Zotero.

[@peerreviewed]

Oops, sorry I completely forgot to reply to this! To be honest, I just use the 'a', 'b' etc and once I start running into it, I'll just double check references

[@benjaminsaubolle-camacho9558]

I really appreciate the time you took to cover your workflow. Quick question: Do you currently compose your own writing or manuscripts in Obsidian? Or is your vault a repository for article notes & connections, and you complete your manuscript/draft/publishable writing elsewhere?

[@peerreviewed]

Glad you enjoyed it! So far I am still doing most of my own writing in Google Docs, but I am looking for ways to improve that part of my workflow, because I'm not really loving it citations wise. I really appreciate using an online tool though and being able to access it on the go.

[@benjaminsaubolle-camacho9558]

@@peerreviewed If you alter the workflow, please keep us updated! Currently, I am making the switch from MS Word to Obsidian (I sync my vault in iCloud) for all academic writing. There are even tools to automate the citation process in plain text and markdown...but it takes some elbow grease. If you're ever interested, I can send some links your way! Anyway, thanks again for the video!

[@elliotthe1216]

Friendly reminder for windows users: Use the reverse slash ( \ ), not the slash ( / ) to reference the path of your bibliography database. I was getting frustrated until I have figured out why obsidian wasn't been able to find my database.

[@rachie11]

Really great video, thank you so much! Quick question - How do you display the **notes** and **readings** sections on the bottom left corner? Thanks :)

[@alissa6380]

seconded, is that a note that's opened in a split view somehow?

[@peerreviewed]

It’s as Alissa aid, it’s opened in split view! It’s just the way I have my workspace set up and there are loads of tutotials on nifty things you can do with workspace setups in Obsidian

[@paulanunes95]

This is so genius, thank you! I’m contemplating doing it, but I’m so lazy with technology 😂

[@lzairong128]

Thank you very much for sharing your experience with zotero and obsidian, it's very helpful for me! May I ask you how did you add the little keys on zotero? As shown from 1:28 in the video. 😉

[@jonazmoreno3718]

You just add tags to your articles. You can use emojis as tags by doing whatever shortcut you have on your computer to evoke emojis. There's a plugin for Zotero that's called Zotero tags and is very neat because it auto creates tags as you add new documents, open the document, and close the document. Is really nice!

[@lzairong128]

Oh, thank you very much for your tips! What I have tried is using emojis in the Zotero with shortcut of the windows system. I'll try out what you just suggested! ;)@@jonazmoreno3718

[@jandresmusic]

Could you share your template, please?

[@amberscheepers9566]

the path for me doesnt work, i have tried every path i could think about but the annotations or the docs from zotero do not get uploaded to obsidian

[@yvonnemosley]

I had the same problem. I had to remove the quotation marks from the path that I copied from Windows.

[@DanteHaroun]

Lovely accent, reminds me of my high school English teacher... She was so cute. I miss her (RIP she unalived herself).

[@andrewwilkie463]

Hi, Thanks for the video. It's been(ing) really useful and the attached links. Returning to formal study/writing after a long time. Learning Obsidian. Learning Zotero. Weaning myself off MS OneNote and various ways of working with it that I'm use to. Can you list all of your HEX codes for the various formatting options? Not sure I've got them correct or all that I've seen on your pages. How did you create your little next Notes/Reading lists, the pane on the bottom left of Obsidian or make it visible?

[@peerreviewed]

Glad you enjoyed it! The hex codes for my theme modifications are all listed in the description. As for the little note, it is just a note like any other, but what is so great about Obsidian is that when you've got a note open, you can drag it around your workspace and drop it where it would be most useful. So I dropped mine just underneath my sidebar. I've also seen people do several important reference notes along the bottom of their workspace which looks neat!

[@busimo]

Do you not use the notes feature within Zotero? Will that also import to Obsidian?

[@rachelhorst547]

This is SO fantastic. Thanks-you!!! Do you know how I can view item type and citation key in a column as you have it in zotero? That seems really helpful but I can't figure out how to change the columns? Thanks a million!

[@peerreviewed]

If you right click on the columns in Zotero you should be able to tick which fields you wants visible

[@baroftheoppressed]

hello and thank you for your tutorial :) quick question - how do you set up your obsidian workspace so that you have a **reading** list on the bottom left hand corner?

[@peerreviewed]

the reading list is a separate note that i’ve just dragged down into the corner. just like you can open several notes side by side for example, you can also drag them down into that spot in the side bar 😊

[@baroftheoppressed]

@@peerreviewed Perfect and thank you for letting me know :)

[@tom22333]

Thanks! Can citations pull notes from zotero automatically (if they have been exported to a new file in zotero already)

[@peerreviewed]

I know next to nothing about automation, sorry! I create a note in Zotero from my annotations and then just copy that manually into Obsidian

[@scootergandoogle1278]

Just what I'm looking for. I have never seen Obsidian in light mode😂

[@dot.dot.dot.]

which addons do you use in zotero?

[@peerreviewed]

I just use Zotfile and BetterBibTex

[@BlackPantherElite]

Great video thanks so much! Totally off topic - hope it is not mean/too personal, but since I have learned about it recently, I am wondering if you notice your own "vocal fry" when you talk? Its not intense, but noticeable. I have always wondered if people having these voice or speaking patterns/characteristics notice it themselves, and how they started with it. Have a great week!

[@Rebecca-qg8pb]

The fact that it can't print bothers me a little.