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This guide has basic information on using the Paperpile Google Chrome app to manage your PDFs and other bibliographic references, and to create bibliographies in Google Documents.
To annotate (highlight text, add notes) to a PDF, you will want to activate Paperpile's beta Google Chrome extension in your Settings. To do this, first go to your Paperpile settings:
Then, go to "Browser Integration" and select "Viewer with annotations (beta)" choice in the drop-down:
Once you have activated the beta PDF viewer in Google Chrome, select a section of text in any PDF in your Paperpile collection. You will see your options to Highlight that text. Click the box dropdown to add a "text box" to any place on your PDF page. You can then add comments to that PDF that are then saved in the PDF.