https://www.zotero.org/blog/zotero-6/
IN the past couple of months, Zotero has seen an incredible transformation. It is really catching up with Bookends.

There are even some feature which appear superior to Bookends.

- BetterBibtex in Zotero is much more advanced system for sycing for bib. BE has also introduced syncing to Bib files. But, Zotero's addon is much more advanced.
- ISBN metadata detection doesn't exist in BE; zotero has it
- The translators in Zotero are amazing: they are over 500 of them to extract metadata from websites--BE is no where close to that.

- Zotero is also introducing a new mechanism to update an existing reference from the Internet; if the source has updated. If the source url, for example, has a new information about the reference, Zotero is going to go that url and update the reference data. This is amazing new feature.

The new Zotero 6 looks great. Any suggestions for importing Bookends data into Z6? I just spent some time trying this with no luck. Didn't realize BE had such limited export options.

There are lots of good improvements in Zotero 6, but I don't really like their decision to store highlights and other annotations in a database rather than directly in the PDF. That complicates working with other tools so much.

I appreciate seeing the improvements in Zotero for managing Web-based content and the improvements in Bookends for managing PDF-based content. Each has made great strides in cutting out friction and adding powerful features even just over the last year. One may live at home primarily in one or the other tool and be very happy indeed. The dismay is, as already noted, when one wants to translate annotations made on PDFs between Zotero and Bookends. Sadly it seems, the two tools cannot work as seamlessly as one would hope on this one possibly critical aspect to managing research information.

Thank you for the information about version 6. I have not taken a look at it yet and have a (perhaps stupid) question. Can the pdf with annotations be viewed as a document withing Zotero? If so, can it be printed? Then would printing to a pdf partially help? I know it is not the same thing but perhaps some might be OK with it for now.

Jon

Thank you for the heads up. It appears that you can move annotations from Zotero into the PDF, but it's a manual step as far as I can tell. See https://www.zotero.org/support/kb/annotations_in_database

Chris Thompson wrote:

There are lots of good improvements in Zotero 6, but I don't really like
their decision to store highlights and other annotations in a database
rather than directly in the PDF. That complicates working with other
tools so much.

“Store Annotations in File…”

yes, that is the way to embed Zotero annotations into the pdf.
It works like Skim. They want to primarily embed them in the database because they want to have the freedom for advanced note taking and annotations.
Bookends always embeds the annotation in the pdf.