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An Academic Knowledge Management System

by Dr Chris Lovejoy.

The purpose of an academic knowledge management (AKM) system is to enable you to:

  1. Aggregate and organise academic papers of interest
  2. Extract and synthesise their key findings and insights
  3. Combine these insights for a birds-eye view of a research field's cutting edge
  4. Exporting references and citations when conducting a research project

This folder contains a template academic knowledge management system. It is best utilised by using the free Obsidian software.

For a more detailed description of this system, its motivations and configuration, see this article.

(NOTE: This README is best read in Obsidian, to enable all links to be visualised correctly and followed.)

How does this system work?

The pipeline works as follows:

1. Find an interesting paper

  • Save it into a citation manager (e.g. Zotero - using the chrome extension "Zotero Connector")
  • Configure that citation manage to automatically download the PDF and save it into the folder '3_PDFs' (using the Zotfile plugin)

(I use a folder structure to organise my papers in Zotero, with folders for projects and for areas of interest - [[Zotero_folders.png|see this screenshot]].)

2. Read a paper

  • Create a note within folder '1_papers' with the title of the paper (see [[Blockchain-Based Access Control Scheme for Secure Shared Personal Health Records over Decentralised Storage|this example]])
  • Add the [[paper_template]] template (using the 'Templater' Obsidian plug-in)
  • Read the paper in PDF format while adding highlights
  • Export those highlights into markdown format (using the Zotero Mdnotes plugin)
  • Put those highlights into the note that was created (in the 'Highlights' section)
  • Write a summary and high-level thoughts in own words

3. Process the paper insights

  • When reading many papers on a particular topic, create a note for that topic within the folder '2_topics' (see example [[Decentralised data storage|here]])
  • Add the [[topic_template]] template (using the 'Templater' Obsidian plug-in)
  • Create links for all relevant papers that you read from within that note
  • Review the summary and high-level thoughts for all linked papers and write a topic summary

Over time, these summaries can be improved and serve as a key self-reference on topics of interest.

4. Export the citations

  • Generate a unique citation key for each paper (using the Better BibTex plugin for Zotero) and include these in each papers markdown note
  • When writing the research paper, add citations using \cite{citation_key}. These will automatically be recognised in LaTeX.
  • Export the bib file from Zotero and add to LaTeX.

NOTE: The Obsidian Citation Plugin provides an alternative to elements of this flow - I'd recommend checking it out too.

Examples

Some example papers are shown here:

  • [[Blockchain-Based Access Control Scheme for Secure Shared Personal Health Records over Decentralised Storage]]
  • [[GluNet - A Deep Learning Framework for Accurate Glucose Forecasting]]

An example topic-level note is shown here:

  • [[Decentralised data storage]]

This demo vault was Runner up in the Obsidian October 2022 competition. See all competition submissions here.