Hard-links, where the same document can be placed into multiple files.
Ease of syncing between devices
The “save to Zotero” extension in Chrome
Text and area annotations on the sidebar, which you can edit, comment, tag, and click to jump to the annotated section.
The ability to create new, editable notes by extracting annotations from one or more documents with the “create note from annotations” feature.
The major limitation here is that there’s no way to selectively search and extract annotations based on tags.
Also, the difference between a “tag,” “annotation,” “note” and “document” feels messy. Other Zotero users have complained that there’s no built-in way to delete tags (you can edit them manually in the sqlite3 database, but that’s beyond most users). Airtable does a better job with tags, giving auto-suggestions and a place to edit or delete existing tags. The ability to define “tag sets” that apply across documents that you can toggle between, combine, etc would be much better.
I wish Zotero had the ability to alter the main view of documents, or offered some sort of hover preview of the document. Title/creator/year usually doesn’t capture well why I care about that document or why I added it to a particular file. Zotero thinks of itself as a tool to track citations. I want it to be a tool to create custom views of my document collection. As it is, I get overwhelmed and confused by folders that contain a lot of documents.
Obsidian’s ability to create links between documents and its canvas feature are nice, but I rarely use them in practice. I think this is for a couple reasons:
Obsidian doesn’t allow me to add the same document to multiple files, so I have to put a lot of thought into choosing which file it will live in. Then if I want to find it later, I have to hunt for it. This makes me very conservative about creating new notes, which is exactly the opposite of what a link-friendly note system ought to do.
Often, I don’t want to click through to another document to see a note. I want information all in one place. But Obsidian doesn’t let me embed notes, only link to them.
Also, I straight up don’t care at all about the graph view, I think it’s a nonsense way to view your notebase.
What I get the most value from in Obsidian are:
Its markdown interface with seamless support for LaTeX and monospaced code blocks
Ease of syncing between devices
The traditional file structure (when Google Drive shifted to an AI-sorted “home” menu as its landing page, I hated it)
The “outline” view, which transforms different header levels into a clickable table of contents.
To some extent, the ability to collapse and expand bullet points—I’d like more of this.
I wish that Obsidian had code cells, like Jupyter or Collab notebooks. There’s a community extension but it is not seamless, and I haven’t managed to get it to work yet. The ability to construct images and diagrams within the application would be very nice—perhaps support for embedded Mermaid charts?
Personally, I see the role of LLMs in this setting as primarily a search tool. “Find all the documents containing figures with single base pair resolution DNA methylation information” is a question I’d love to be able to pose to my notebase. I don’t want the LLM to construct the note for me. The point of the notebase is to have the human gain an understanding of the notebase, and having the LLM construct notes isn’t very helpful for that.
Based on these observations, it seems to me that text and areas of documents are the “raw material” of a notebase. The priority should be on tools that make it easier to define, select, morph the visibility of, and remix units of raw material into new documents. I think that Git has shown it’s not particularly important to minimize redundancy in this type of setting—just create new copies of the material and let users build on them.
On a more abstract level, this is about minimizing the need to commit early to a particular ontology and making it much easier to rapidly define and edit lightweight ontologies. The note taking software should enable you to rapidly construct new views of the raw material in your “note lake.” It should enable some sort of “lineage tracing” that lets you reconstruct where, originally, the material in a particular document came from—if you create views of views of views, you should be able to click back through until you reach bottom.
Obsidian doesn’t allow me to add the same document to multiple files, so I have to put a lot of thought into choosing which file it will live in. Then if I want to find it later, I have to hunt for it. This makes me very conservative about creating new notes, which is exactly the opposite of what a link-friendly note system ought to do.
I haven’t had this problem, and usually use the image-wiki syntax for this, that is ![[file-name.pdf.png.html]]
I’ve been using Zotero and Obsidian for a while.
Zotero has a few nice features:
Hard-links, where the same document can be placed into multiple files.
Ease of syncing between devices
The “save to Zotero” extension in Chrome
Text and area annotations on the sidebar, which you can edit, comment, tag, and click to jump to the annotated section.
The ability to create new, editable notes by extracting annotations from one or more documents with the “create note from annotations” feature.
The major limitation here is that there’s no way to selectively search and extract annotations based on tags.
Also, the difference between a “tag,” “annotation,” “note” and “document” feels messy. Other Zotero users have complained that there’s no built-in way to delete tags (you can edit them manually in the sqlite3 database, but that’s beyond most users). Airtable does a better job with tags, giving auto-suggestions and a place to edit or delete existing tags. The ability to define “tag sets” that apply across documents that you can toggle between, combine, etc would be much better.
I wish Zotero had the ability to alter the main view of documents, or offered some sort of hover preview of the document. Title/creator/year usually doesn’t capture well why I care about that document or why I added it to a particular file. Zotero thinks of itself as a tool to track citations. I want it to be a tool to create custom views of my document collection. As it is, I get overwhelmed and confused by folders that contain a lot of documents.
Obsidian’s ability to create links between documents and its canvas feature are nice, but I rarely use them in practice. I think this is for a couple reasons:
Obsidian doesn’t allow me to add the same document to multiple files, so I have to put a lot of thought into choosing which file it will live in. Then if I want to find it later, I have to hunt for it. This makes me very conservative about creating new notes, which is exactly the opposite of what a link-friendly note system ought to do.
Often, I don’t want to click through to another document to see a note. I want information all in one place. But Obsidian doesn’t let me embed notes, only link to them.
Also, I straight up don’t care at all about the graph view, I think it’s a nonsense way to view your notebase.
What I get the most value from in Obsidian are:
Its markdown interface with seamless support for LaTeX and monospaced code blocks
Ease of syncing between devices
The traditional file structure (when Google Drive shifted to an AI-sorted “home” menu as its landing page, I hated it)
The “outline” view, which transforms different header levels into a clickable table of contents.
To some extent, the ability to collapse and expand bullet points—I’d like more of this.
I wish that Obsidian had code cells, like Jupyter or Collab notebooks. There’s a community extension but it is not seamless, and I haven’t managed to get it to work yet. The ability to construct images and diagrams within the application would be very nice—perhaps support for embedded Mermaid charts?
Personally, I see the role of LLMs in this setting as primarily a search tool. “Find all the documents containing figures with single base pair resolution DNA methylation information” is a question I’d love to be able to pose to my notebase. I don’t want the LLM to construct the note for me. The point of the notebase is to have the human gain an understanding of the notebase, and having the LLM construct notes isn’t very helpful for that.
Based on these observations, it seems to me that text and areas of documents are the “raw material” of a notebase. The priority should be on tools that make it easier to define, select, morph the visibility of, and remix units of raw material into new documents. I think that Git has shown it’s not particularly important to minimize redundancy in this type of setting—just create new copies of the material and let users build on them.
On a more abstract level, this is about minimizing the need to commit early to a particular ontology and making it much easier to rapidly define and edit lightweight ontologies. The note taking software should enable you to rapidly construct new views of the raw material in your “note lake.” It should enable some sort of “lineage tracing” that lets you reconstruct where, originally, the material in a particular document came from—if you create views of views of views, you should be able to click back through until you reach bottom.
I haven’t had this problem, and usually use the image-wiki syntax for this, that is
![[file-name.pdf.png.html]]