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I have dozens of papers in Mendeley. Most are filled with post-it notes, what Mendeley calls "private annotations". Unfortunately, these are not searchable.

Mendeley users have been asking this feature for years. It still hasn't been implemented.

There is a workaround: exporting the article as PDF. The private annotations are added in pages appended to the PDF. But it is tedious: it requires to manually export each and every paper one by one...

I know Zotero's annotations are searchable. So I exported my Mendeley Library to Zotero. But the private annotations don't follow. Furthermore, Zotero only has a 300 Mb capacity, whereas Mendeley offers 2 Gb. So back to square one.

Would anyone have found a way (maybe a programmatic way) to search Mendeley's private annotations?

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    Just use Zotero Standalone with your PDFs database synchronized to the cloud of you choice (e.g. Google Drive, MEGA, DropBox...). For better file management, use ZotFile. Basic idea is to separate meta-data from PDFs. Meta-data are synced to Zotero account, and PDFs are synced to your cloud. – ikashnitsky Jul 25 '16 at 14:00
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You CAN search your notes from the library/folders page (searches all notes for all documents) by selecting "Notes" on the drop-down menu in the search box. I don't know why you can't search notes from within a specific file.

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    As far as I can tell this only searches within General Notes, not Private Annotations – BauerPower Dec 19 '17 at 14:54
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There is a tool for exporting the annotations from the whole Mendeley database: Menextract2pdf.

From their github page:

Menextract2pdf extracts highlights and notes from the Mendeley database and adds them directly to all relevant PDF files, which can then be read by most PDF readers.

Why? PDF highlights and notes in Mendeley are stored in the Mendeley database and can not be read by other programs. While it is possible to extract and save the annotations to the PDF file, this is a tedious manual process requiring to open every PDF and selecting export to PDF for that file. Menextract2pdf provides a bulk export functionality.

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