The thing Iβm most stuck on is changing the output format from the default. From the documentation it looks really technical and Iβm a little scared of it.
Thank you for doing this!
Will this be recorded?
Please record it if itβs possible. There already is an Obsidian talk channel in Youtube.
+1
(I wonβt be able to attend it sadly - I am helping a friend out on that day)
Iβm aware of the channel! I still havenβt decided if I want to record the session or not, but in case I donβt, and you canβt make it to the meeting, do not despair! Catβs wonderful write-up already covers a lot of what Iβll be showing and some more advanced topics (e.g. dataview): Zotero -> zotfile -> mdnotes -> obsidian -> dataview Workflow. Briβs talk in the Obsidian Office Hours channel could also be of interest to you: Merging library & information science and PKM - How Bri Watson uses Obsidian - YouTube
I have a lot of technical (non-academic) PDFs stored locally on my laptop that I want to annotate and move into zotero. Does the workflow differ from PDFs downloaded from the web. When I initially setup Zotero and dragged in a local PDF, I got an error when I tried to extract the annotations with mdnotes. It said that I needed a parent item so I used the create parent item and entered the authors name manually. Once I did that, it was happy and did the md conversion. Can you discuss what else would be considered best practice in respect to manually populating the metadata. Additionally, recommended folder structure in Zotero libary. Thanks!
Zotero can extract the metadata of PDFs that have the information properly input and create a parent-item from that. To enable this, go to zoteroβs preferences, and in the βGeneralβ tab, enable βAutomatically retrieve metadata for PDFsβ.
For folder structure, you can use zotfileβs wildcards to get it to automatically move your files into particular folders using the wildcards listed here, meaning you can organise your library however you best recall files, whether by collection, year, authorβs name, item type, etc. Itβs advisable to find what works best for you, rather than go with what others recommewd here. For instance, I recall subjects best, so I have zotero collections organised by subjects, and zotfile automatically moves PDFs into the relevant folders labelled according to the collection (wild card %c). Many people prefer organising by authorβs name instead, as thatβs how they recall files best - by who wrote it - and therefore can find the article if the PDFs are organised by authorβs name.
Edit: I believe I now know, it is the Obsidian Community Talks channel on YouTube. Will be there! Thanks for setting these up!
Hi @miguelmarcos, the talk will be held in Zoom! The announcement (and reminders) for the talks usually happens on Discord (click on the arrow thingy):
The specific message with the announcement is here: Discord
Hope to see you there tomorrow!
Oh, OK. Thanks for the heads up.
Here are the answers to the remaining Q&As from todayβs session
Q&A
This is a great question:
Imagine we are writing a paper and we use citekeys in the [citekey] format for pandoc to render it properly as a citation. but we also have md pages in our vaults which can be found at [[citekey]]
How would I link the md page without having to write these twice when referencing the source in the paper md draft: βextract from paper - [citekey] [[citekey]]β
Iβm a bit opinionated on this, my notes use [[citekey]] , and is what I use in obsidianβ¦ I donβt use [@citekey] very often because I do my writing in LaTeX, but when I do use them itβs as part of the final product (that Iβm exporting to PDF). So far I do it when I bring my paper back from LaTeX β markdown to store in obsidian
When annotations are converted to markdown, is it ok to rename the md file before moving it to Obsidian?
Renaming the file when you create it should be alright! If you rename it afterwards, you might need to update the links added in Zotero by mdnotes
Sometimes when I use Citation plugin Word, usually adds the first & last mame of the author, e.g APA. I just want to automatically display only the last name.
You might need to use a different citation style that uses the authors last names
Do you know any way to get highlights from Calibre/Epubs?
I donβt, there might be a plugin for it that Iβm not aware of: plugins [Zotero Documentation]
What is the timeline of this Zotero support/change? Coming soon?
If itβs referring to mdnotes, coming as soon as I have some time! Hard to estimate a timeline
Iβm trying to use custom placeholders, which I set in the config editor. They are not being rendered when choosing 'Create full export note". Do you know why?
Probably you are adding the placeholders to the wrong template, the placeholders should be in the Mdnotes Default Template.md
file (youβre using single file exports)
what OS are you using? Your screen looks rad!
Thank you! Iβm using Ubuntu with i3 https://i3wm.org/
I have Zotero loaded and up, but it looks nothing like what you are working in. What is the tool she is showing us? Vault? Word processor? ???
This is due to my system setup, Iβve added this theme and that changes the Zotero appearance: https://github.com/EliverLara/Nordic (I use a nord color scheme almost everywhere)
how do i get memos to obsidian?
If those are the little yellow notes, then using the Export to markdown
menu should do it
My main question is βhow do I change how the formatting looks when it gets extracted and plopped into Obsidianβ for what itβs worth.
I hope the tag example helped, but if it didnβt let me know, and I can set up a couple of gists with more examples for customizing the formatting
Alright! Videos and handouts are up, and Iβve just added them to the bottom of the main post:
I have Zotero loaded and up, but it looks nothing like what you are working in. What is the tool she is showing us? Vault? Word processor? ???
Apparently there are technical reasons well beyond my understanding that limit the Zotero developersβ ability to create a Dark Mode option. Other folkx (also with technical capabilities well beyond mine) created a CSS file to simulate a dark mode. For Windows it is available here; for Mac here. NOTE: The location for Mac is a little tricky: Create a Chrome folder inside /Users/username/Library/Application Support/Zotero/Profiles/bunchofletters.default (mine is named βlio0a6gq.defaultβ) and copy the userChrome.css to that folder.
Thanks for the video! I was surprised that the obsidian citations plugin wasnβt even mentioned. I assume that this is because @argentum isnβt using it? In any case, Iβm trying to wrap my head around how mdnotes and citations relate to each other.
There is obviously some overlap in the functionality: both can create notes with metadata for articles/books in zotero. One pushes them from zotero to obsidian, the other pulls them out of zotero to obsidian. Both allow me to customize the templates based on which those notes are created, so I assume, I can create more or less identical notes in both. But I like the way how citations allows me to create a reference to a book/article for which I donβt even have a literature note yet (it creates a link to a non-existing note). I also like the way how I can create a literature note in obsidian and pull over the metadata from zotero.
So what Iβm wondering is: does it make sense to use both the citations plugin and the mdnotes add-on? If so, what is a good way of setting this up?
At the moment, Iβm thinking to create the meta-data notes with the citations plugin and push my annotations notes from zotero and transclude them in the meta-data note. But I still need to figure out how I need to name my notes-files so that this can be automated via a template. Iβm also not sure what mdnotes features Iβm missing if I go down that pathβ¦
Thanks in advance for any clarifications.
@tophee we do cover it (albeit very very briefly) in the 2nd part when I talk about Better Bibtex. The talk itself was more about how to set up Zotero and its plugins (but it is roughly what I covered for the citations plugin too).
There is some overlap between Mdnotes and the citations plugins, it depends on the information you might want to include in your templates which one might be more suitable.
The citations plugin has access to what is exported in your bib/csl file. Mdnotes has access to any Zotero field and meta information (e.g. collection names, dates, etc.) or the ability to add/format your extracted annotations and fields, e.g. what Cat demoed here and/or adding block IDs to your extracted annotations.
You can still use both, depending on your preferences. Personally, I find the citations plugin great for navigating my literature notes in Obsidian! But as you said, you can use it to create templates too and export annotations with mdnotes or just the citations plugin too!
You are right, of course. It is right here:
That seems like a humble way of saying that Mdnotes is better because it has access to everything in the zotero database But I do agree that using the citations plugin still has its place for quickly referring to books and articles that are in zotero (and which you may not even have read yet).
So I think for it to work well with mdnotes, I should make sure that it produces notes whose file names are identical with the metadata notes created by mdnotes, right? - It obviously depends on what exactly you want to achieve, but I agree with your approach of keeping your own notes (in obsidian) separate from the literature metadata and annotations so as to be able to update those without losing your notes (in obsidian). So letβs stick with that approach for now.
As I think about it, I actually see two ways of integrating citations and mdnotes.
- One is the one that came to mind first (above): use the same file name for the metadata-note in both citations and mdnotes. You can refer to that file even when it doesnβt exist yet or you can let citations create a preliminary version which will be overwritten once you export annotations via mdnotes.
βββββββββββ βββββββββ
βcitationsβ βmdnotesβ
ββββββ¬βββββ βββ¬ββββββ
β β
writes (over)writes
β β
βββΌβββββββββββββββΌββββββββββββββββββ
β main note-file (incl. metadata) β
βββ¬βββββββββββββββββββββββββββββββββ
β
links to
β
β ββββ-ββββββββββββββ
ββββΊannotations file1β
β ββββ-ββββββββββββββ
β
β βββββββ-βββββββββββ
ββββΊannotations file2β
ββββββββ-ββββββββββ
- The second one is perhaps better, but adds some complexity. Instead of letting both plugins write the same main-note-file, which then links to the annotation files, we could add another level in the note hierarchy: citations would then create the main-note file which links to the mdnotes metadata file as well as all the annotation files. Only mdnotes overwrites these. And thanks to your ingenious idea to create the block reference id by hashing the annotation, all links and transclusions will still work after mdnotes updates the annotations (as long as annotations are not changes but only added).
βββββββββββ ββββββ βββββββββββ
βcitationsβ βuserβ β mdnotes β
ββββββ¬βββββ βββ¬βββ βββ¬ββββββ¬ββ
β β β β
creates edits writes writes
β β β β
βββΌβββββββββββΌββββββ β β
β main note-file β β β
βββ¬βββββββββββββββββ β β
β β β
links to/transcludes β β
β β β
β ββββββββββββββΌββββ β
ββββββββΊ metadata file β β
β ββββββββββββββββββ β
β β
β ββββββββββββββββββββΌββ
ββββββββΊ annotation files β
ββββββββββββββββββββββ
In fact, with that (second) approach you donβt even have to split the metadata and annotation files and just write them into a single file, depending on preference.
What I like about approach 2 is that it has a dedicated space for my own post-reading reflections in the main note-file. Integrating the annotations i make in the pdf during reading with more elaborate reflections in obsidian after (and sometimes already during) reading has been a major headache for me. It looks like this could be a solution.
Does this make any sense? (I havenβt tried it in practice yetβ¦)
BTW: the diagrams show the files for a single article/book in zotero.
Not necessarily better, just different! If you donβt need access to those things, the citations plugin might be better, since itβs easier to set up if youβre not very technical, and you can trigger everything from within Obsidian without needing to configure (the sometimes extremely confusing and unfriendly) Zotero settings.
It does, I think! Thatβs roughly what I wouldβve suggested: You can create your βmainβ note with the citations plugin and export your annotations using the Export to markdown
menu in the little yellow Zotero notes. If you use multiple files like I do, in mdnotes, you can automatically transclude/link the annotations into your main note. I think people have managed to set up templates with the citations plugin to do this as well, but Iβm not familiar with how! However, if you are using a single note with everything (metadata, annotations, etc), the citations plugin is also able to include everything in your note (I donβt know how to do that however).
In the end, as with all these things, itβs mostly a matter of preferences and of willingness/ability to invest some effort in the configuration.
I am old and really trying to understand this chat. I read books (PDFs and epubs). I have zotero and Obsidian. I want to read, highlight, add my own notes and the move them to Obsidian. I would like to include the citation and a link to the page where it came from. Is there a post or website or blog or book that could give me a step by step on how to do this? Things never used to be this hard but my brain keeps forgetting. (thus need for obsidian). Maybe I should be using Calibre instead. Maybe I should put books inside Obsidian but I am afraid it would get too large.
Maybe you donβt know it yet: There is a very good tutorial by Danny Hatcher on Youtube: Zotero Obsidian Integration - YouTube, or on Zotero Obsidian Integration - Danny Hatcher. I donβt have experience with Zotero/Obsidian, but the video seems to be very easy to understand.
Another post by Alexandra Phelan: An Academic Workflow: Zotero & Obsidian | by Alexandra Phelan | Medium. A little more technical, but it shows different aspects, e.g. how to collect the literature notes in your vault via Dataview.
Hope this helps. A.