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I migrated away from Mendeley the day I found out Elsevier bought them. So ever since then, I've been paying yearly for storage with for Zotero. Overall, I've been very pleased with Zotero thus far. I've never had an issue getting data in or out of Zotero.

Now Endnote on the other hand... if I could just get collaborators to switch away from Endnote...

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I got a lesson the hard-way. Mendeley crashed and refused to start up again. There was a known bug that they had not fixed for months. Almost a year of annotations gone. Even though I could find the PDF on disk I could not get to my annotations. they store it in a sqlitedb. I needed to reverse engineer the sqlitedb to get anything out. Total nightmare.

Still searching for a better solution for annotations + referencing. I use zotero and the highlights app at the moment.

I use a standard PDF reader and then the ZotFile plugin. ZotFile processes highlighted text and comments made in PDF compliant ways and turns then into notes in Zotero.

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