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BPBible allows for two types of user notes: Topical notes and passage notes. To make notes on a range of verses, select text from that range of verses before making the note.
To create passage notes, select the verses that you wish to make a note on, choose "Bible > Add Comment to Verses", and then enter the text of the note. The note will then be displayed with a dagger sign at the end of each of the affected verses. Hovering over this will show the content of the note in a tooltip. Clicking on it will allow you to edit the note or change the passage it applies to.
Topical notes allow you to associate your notes on a passage with a particular topic, and then view your notes on all of the passages you have associated with a particular topic. "Bible > Tag Verses" allows you to add a comment to the currently selected verses, and associate this comment with a topic. If the topic does not already exist, it will automatically be created.
The topic will then be displayed as a tag with the name of the topic at the end of every verse included in the topic (though these tags can be hidden). Clicking on this tag will then show all of the passages with comments associated with the topic and allow the comments and passages to be edited.
Manage Topics ("Bible > Manage Topics") allows you to view all of your topics and the passages and comments that you have associated with each topic. It also allows you to add, edit, copy and delete passage comments and topics, and change the colours of topic tags to allow them to be distinguished from each other.