My Academic Reading Workflow

Sep 8, 2020

Tools

Skim

• notes are saved in a separate .skim file, cannot be extracted in Zotero
• resolution not as sharp as acrobat
• only one highlight color
• no type machine function
• small and fast, good for note taking

Adobe Acrobat

• highlights color coding:

  • light green: key word
    • !
  • light yellow: key statement
    • !
  • light pink: method, operationalisation, key results
    • !

Preview

• fast and simple, have all the necessary annotation functions, and can be extracted to Zotero
• rich hotkey support

Zotero

• create child note while reading
• create notes for: quotation, summary, comment
• add or modify tags according to Article tags

MindNode

• Use MindNode to create a map for the classic literatures/authors

Emacs + Zotero

• requires Emacs package: pdf-tools, org-noter, zotxt
• requires Zotero plugin: zotxt, zotxt-emacs
• also see /posts/my-reference-literature-management-workflow/

Workflow in Emacs

• in Zotero, open the attachment for annotation (set default pdf viewer to emacs)
• start org-noter, save a new note file, or an existing note file will shown
• M-i insert note at precise location (create a new heading in corresponding org notes file)
• document view → notes view: the note heading will automatically expand when scrolling through document buffer. navigate
• notes view → document view: M-p, M-., M-n sync previous/current/next note, meaning the document buffer will scroll to the location associated with the previous/current/next note
• org-noter-create-skeleton imports the PDF outline or annotations as notes

Template