Scientific Workflows with Zotero

[quote="nhanjkl, post:11, topic:8205]

I’m new to Zotero so I don’t know much about it. Is it that you feel the development is slow or is this relative to another reference manager? Do you have an alternative in mind?

[/quote]
Zotero is a great program and I don’t see anything coming even remotely close, but still I have the feeling that Zotero is starting to lag behind. I am sure many problems are due to technical debt from being tied to the browser platform, this also makes it difficult to interface with 3rd party software. If you compare Zotero to Calibre, the latter has a much more vibrant developer company that has created a huge amount of plugins.
Over the years, I have run into many limitations of Zotero, such as

  • no easy way to transfer items between libraries while maintaining all information
  • no way to support complex workflows
  • search is very slow
  • too much emphasis on cloud sync, which has privacy issues
  • citation picker is very slow
  • no supported local API
  • tag system is primitive compared to how it should be.
  • no way to automatically populate collections based on tags (search folders have to hierarchy)
  • no automatic renaming of tags.
  • Zotero notes are great, but they lack Logseq’s features for assembling the information into other documents. Can’t tag individual blocks in Zotero’s Notes, tags are per note.
  • The new note support is great, but it still doesn’t support TeX, and currently there is no good way to export notes. Writing a note is a substantial investment (many hours per article), and I don’t like my notes to end up in a format that I can’t export properly. I don’t want to rely on a plugin either that might stop working in a few years when they move to Electron.

All of these issues could be addressed with a couple lines of Python, but the lack of a local API makes this difficult and one has to rely on the unofficial debug-bridge or write a Zotero plugin.
The Zotero development is also not very open, they have a mailing list, but no public roadmap.
I don’t want to be too critical of Zotero, like I said, it is a unique program, but I am still worried about putting too much of my intellectual work into the Zotero ecosystem.

[quote="nhanjkl, post:11, topic:8205]
Could you give a few links of example of workflow using .bib file? I don’t know anything and would like to learn about this.
[/quote]

There is a plugin for Better Bibtex that automatically writes a bib file and keeps it sync’ed. It still misses some information that would be useful (such as Zotero ID’s for zotero://select links, but probably the author would be willing to add those).
Logseq could then parse this file. This has some major advantages, it still works if Zotero is down and it doesn’t rely on the cloud, so no latency or privacy issues.
I wrote some more comments here.

[quote="nhanjkl, post:11, topic:8205]

Zotero also plans to switch to Electron

They’ve talked about it for 5 years and the latest is “won’t be […] anytime soon” ha ha.
[/quote]

That’s a good example for the lack of openness. Three years ago it was supposed to happen within half a year and now it has been postponed forever without much of an explanation. I don’t care about the GUI, but if the switch eventually happens it might break add-ons. I am also not very inclined to write add-ons for this reason.

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