Tutorials


Looking up references with ease

Highlights comes with some special power tools for academics. The PDF underline tool for reference lookups is a super fast and easy way to get to the source of a reference without touching the keyboard.

How do I enable it?

Go to Preferences –> PDF –> Underlining power tools and select a color for your reference lookups:

This color should be a color you do not use for other types of annotations as it will no longer be extracted along aside your regular annotations.

How do I use it?

To look up a reference, select the text in the PDF and underline it using the color you set in the preferences:

If the references are ordered by number you can include the numbering:

Underlined references show up at the bottom in the notes panel:

Highlights will do an online search for the reference and if successful link it to the source:

If you enabled integration with Papers or Bookends the link will send you to your reference manager otherwise it will open in your default browser.

If the reference number is included in the underlined text, Highlights will look for this number in your notes. Here is an instance of it in a highlighted section:

..and replaces it with a footnote-link to the reference at the bottom:




Integrating Highlights with Papers

Highlights can be integrated with the popular referene management apps Papers and Bookends (tutorial here) on the Mac.

How do I enable it?

To enable the integration in Highlights go to Preferences –> Customize –> Reference Manager and select “Papers”:

For the best experience you should set Papers to open PDFs in Highlights by default. To do this, select Highlights in the list of applications in the “Open PDF files:”-preference of Papers in Preferences –> Papers:

How does it work?

When enabled, clicking links to references (DOI-links) in the notes pane of Highlights will redirect you to Papers. This includes the link in the header after fetching metadata:

and any references looked up using the underline power tool:

If Papers has the PDF for the specific reference in its library it will open it:

If Highlights is set as the default reader, it will bounce back to Highlights and open it there directly.

If Papers does not have the PDF, it will open the link in the built-in browser so you can download it:

This allows for seemless reading and checking of references in Highlights without using the keyboard or downloading the same article twice.

The integration works for both Papers.app version 2 and version 3 as it is based on URL-schemes. If you have multiple versions of Papers installed, Highlights will talk to the currently open version of Papers first. If no instance of Papers is running, Highlights will open the most recent version of Papers installed on you Mac.




Integrating Highlights with Bookends

Highlights can be integrated with the popular referene management apps Bookends and Papers (tutorial here) on the Mac.

How do I enable it?

To enable the integration in Highlights go to Preferences –> Customize –> Reference Manager and select “Bookends” from the list:

For the best experience you should set Bookends to open PDFs in Highlights. As Bookends does not have a default reader preference, you will have to do this at the system level. Keep in mind that this will make Highlights as the default application for opening all PDFs on your Mac.

To do this, right-click any PDF file in the Finder and go to “Get Info”. In the window that opens go to “Open with” and select Highlights from the list of applications:

Select “Change All…”:

Select “Continue” in the dialog:

How does it work?

When enabled, clicking links to references (DOI-links) in the notes pane of Highlights will redirect you to Bookends. This includes the link in the header after fetching metadata:

and any references looked up using the underline power tool:

If Bookends has the PDF for the specific reference in its library it will open it:

If Highlights is set as the default reader, it will bounce back to Highlights and open it there directly.

If Bookends does not have the PDF, it will open the link in the built-in browser so you can download it:

This allows for seemless reading and checking of references in Highlights without using the keyboard or downloading the same article twice.





Highlights in the Mac App Store

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