# Using Zotero and Obsidian for Literature Reviews

> [!NOTE]
> - Presenter: Christopher Burr
> - Date and Time: 12th February 2025, 13:00 (UK Time)
> - Notes: [HackMD Link](https://hackmd.io/vv6kD8txR_iKbz1u06Bp5Q)
> - Recording: [OneDrive Link](https://thealanturininstitute-my.sharepoint.com/:v:/g/personal/cburr_turing_ac_uk/ETZhNXIrjs9Fg3NGK6GjOzcB-6PMTFnevS8bNrwDnOBz3w?e=ykBNuX)

## 📚 Shared Resources

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- Obsidian Zotero Template: https://gist.github.com/chrisdburr/69e93570bc8e904fefd1d6464c084bd2

## :link: Software Links

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- [Zotero](https://www.zotero.org/): a reference manager for articles and papers
- [Obsidian](https://obsidian.md/): an extensible Markdown editor with an excellent ecosystem of community plugins

### Obsidian Plugins

- Zotero Integration
- Dataview
- Table to CSV Exporter

## :pushpin: Session Plan

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- Import PDF into Zotero
- *Sidenote*: using [Research Rabbit](https://researchrabbitapp.com/) to augment literature searches
- Annotate using a pre-defined codebook
- Import annotations into Obsidian using template
- *Sidenote*: installing and using Obsidian plugins
- Analysing the Markdown using Dataview
- Exporting to CSV for richer data analysis

## ❓ Group Notes or Questions

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Thematic analysis in Zotero.

ATI has a subscription to Zotero.

Starting, e.g., with a search on Google Scholar - as you go through pages, Zotero has a plug-in that allows downloading the citation (including pdf) straight from the webpage into Zotero.

Zotero has a pdf reader that allows highlights and making comments on portions of text in the article.

Long list of papers from Pubmed, IEEE, and scopus

For collaborative work on literature review, it is particularly useful to design a code for literature review, with a detailed list of issues that are expected to come up in the selected papers - codes can be assigned in Zotero to each paper as comments to specific portions of text.
E.g.: [ethical issue::patient autonomy].

Using the "annotations" tool allows to include information on the page the comment refers to. Using the options "comment" rather than "tag" allows for easier integration with Obsidian.

Obsidian comes with an extensive ecosystem, plenty of plug-ins (mostly open-source) developed by the community to expand its potential.

Obsidian Plugins:
1. Zotero Integration: allows to import into Obsidian information from Zotero, including comments, pages the comments they refer to,...
2. Dataview
3. Table to CSV

Research Rabbit

Code book

## :paperclip: Other stuff

Re: AI research tools, did you try undermind.ai ?

- [name=Chris] No, but thanks for the recommendation.

## :speech_balloon: Session Feedback

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- Very helpful - good to see people using tools in practice.
- Turing should be doing more of this kind of thing!
- We need to make sure it's a safe space - we don't want polished presentations. This was good because it was real and interactive.
- What ther tools are people interested in?
I use similar workflow but I have learned many new things today to improve my Obsidian notes, thank you so much for sharing! (can we have the link to recording?)

Extremely useful to see the workflow in practice - I have never looked Obsidian before, but this has given me a good idea of its potential applications and what to look for. And the recording will be very appreciated in case I missed some notes :slightly_smiling_face:

It is a good overview to the people who doesn't use the tool previously, a very constructed sequencing of information you presented. massive thank you for this! I suppose if there are follow up seesion, it will be good to know more of the senarios of using those tools to understand the potential. For example what is the good set up if working solo, what good if to work collaboratively with others, etc.

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### DW:
Very nice and clear description of a workflow, thanks! It would be great to do more. FWIW I'd be interested in doing:
- more on obsidian and its file management and organisational structure; linking between files etc.
- plugins for things like visualisation, outlining, mindmaps and so forth for note-taking and brainstorming; ideally which are open-format and can link out and export to MD;
- further integrations with other ways of sharing and communicating findings, e.g., pandoc/latex for writing but also more visual or structured formats such as Quarto/Jupyter Books or slideshows for presentations and teaching as well.