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papers annotations

Highlights workflow

Colours for each different type of annotation References to follow up Metadata

Summarise .md and exporting to DEVONthink.


The two main apps used are Bookends and DEVONthink. The key difference between the material and level of organisation that goes into these two apps is as follows:

  • DEVONthink: project / paper specific organisation.
  • Bookends: general organisation, relevant to any writing task.

Even if a subject area keyword is consistent across both Bookends and DEVONthink, DEVONthink will contain only a subset of those in Bookends - i.e. only those references I wish to cite in a particular paper or project.


Metadata features

  1. label colours - status (To read, reading, RFP in DEVONthink, processed - notes only, processed - annotated bibliography)
  2. keywords - subject area, discipline, field, key themes and content
  3. folders and smart folders - groups of papers with the same keywords or status

Location of attachments

Attachments folder in Dropbox With a subfolder called /Attachments/annotated_bib This is for papers who are being, who have been annotated using the highlights app.


There are two ways that pdf’s and highlights / notes can get into DTP:

Different levels and types of materials going into DTP:

  • whole pdf. These are indexed automatically by DEVONthink from Bookends/Attachments/ (.pdf).
  • A raw summary file containing all those quotes and notes (.md)
  • An edited and summarised file as an entry in my annotated bibliography / electronic notebook. But only for important papers (.Rmd)
  • individual quotes from a pdf, as well as my personal notes (multiple .md contained within a folder)
  1. The pdf is indexed from Bookends’ attachments folder
  2. Once I’ve completed annotating and note-taking in the file, I export a split copy of the file. All the quotes go into their own files, which are grouped together under a single folder, and these appear in the global inbox.

Create subject area groups and file whole papers

Whole papers will tend to be examples or evidence of a particular category or code within a literature review. These can be organised into groups or folders. The groups or folders within Bookends, will contain all papers falling under a particular keyword, but those in DEVONthink will only be relevant to the specific project or paper being undertaken.

Organise individual notes into groups

These groups correspond to particular parargraphs, keypoints I wish to make, because they contain very specific pieces of evidence. They might also pertain to a particular code or category within a literature review topic.

Individual quotes and notes from highlights app will be shifted from the global inbox into specific folders. Not all highlights will be organised.

Creating an organised web: linking together in DEVONthink

Would be cool if the keywords in Bookends would also appear in DEVONthink…


Omni-outliner for creating paper outlines

This will contain the outline structure for a given paper. Each of the different folders and individual notes in DEVONthink will be organised into a logical and hierarchical structure into a single omni-outliner project.

Individual notes can be dragged across into omni-outliner.

Write up using text-editor of choice

Cite with Bookends

Double-tap ctrl to search for the citation, Cmd+Y to copy the citation. Getting pandoc citations in Bookends