Obsidian Vault for Systematic Literature Reviews in Computer Science

This repository hosts an Obsidian vault tailored for conducting a Systematic Literature Review (SLR). An SLR is a meticulous and transparent approach to synthesizing and evaluating existing literature related to a specific research question. Obsidian is a robust note-taking application that offers features such as linking, tagging, and graphing of notes. By utilizing GitHub, the vault can be synchronized, backed up, and shared with other researchers. GitHub is a web-based platform that hosts code repositories and offers version control, collaboration, and documentation capabilities. This vault template is intended for computer science researchers seeking to perform an SLR using Obsidian and GitHub.

What You Need to Do Before Joining this class 🚀

1. Fork and Star the Obsidian-slr Repository

Please fork and star the repository named "obsidian-slr". You can find it here. We will use this repository a lot during the workshop.

2. Download Obsidian Vault for Systematic Literature Reviews

To use the Obsidian Vault for Systematic Literature Reviews, please follow these steps:

1. Click on this link to download the file named mySLR_mso.zip.
2. Extract the file to a folder of your choice.
3. Install Obsidian software from this website if you don't have it already.
4. Open Obsidian and select Open another vault.
5. Choose the folder where you extracted the file in step 2.
6. You can now access the Obsidian Vault for Systematic Literature Reviews and start your training.

3. Install Zotero Plugin

a. Zotfile

ZotFile is a third-party plugin for Zotero that helps you manage your attachments, such as PDFs. It can automatically rename, move, and sync your files with your mobile device or cloud storage. It can also extract annotations from PDFs and save them as Zotero notes. Here are the steps to install and use ZotFile:

1. On the ZotFile site, click Download and the xpi file will be downloaded.
2. In the Zotero application, go to Tools > Add-Ons.
3. Click on the gear icon and choose "Install Add-on from file"

4. Locate your downloaded xpi file and click Open
5. Restart Zotero and go to Tools -> ZotFile Preferences to configure the plugin settings according to your needs.
6. To use ZotFile, you can right-click on any Zotero item or attachment and select Manage Attachments from the menu. You will see various options to rename, move, send, or get files from your tablet or cloud service. You can also extract annotations from PDFs by selecting Extract Annotations.

For more details and examples, you can watch this video tutorial or visit the ZotFile website or the GitHub repository for more information and support.

b. Better BibTeX

Better BibTeX is a plugin for Zotero that enhances its functionality for LaTeX users. It allows you to generate customized citation keys, export your library in BibTeX or BibLaTeX format, and sync your attachments with your tablet or cloud service. Here are the steps to install and use Better BibTeX:

1. Download the ‘Better BibTeX for Zotero’ plugin from here. Hover your cursor to zotero-better-bibtex-6.7.36.xpi, then right-click and select ‘Save link as’ to download the addon.

3. Open Zotero and go to Tools -> Add-ons -> Tools for all Add-ons (the small, drop-down wheel in the top right corner) -> Install Add-on From File and select the downloaded file.
4. Restart Zotero and go to Tools -> Better BibTeX Preferences to configure the plugin settings according to your needs.
5. To use Better BibTeX, you can right-click on any Zotero item or attachment and select Manage Attachments from the menu. You will see various options to rename, move, send, or get files from your tablet or cloud service. You can also extract annotations from PDFs by selecting Extract Annotations.
6. To export your library in BibTeX or BibLaTeX format, you can right-click on a collection or the whole library and select Export Collection. Then, choose Better BibTeX or Better BibLaTeX as the format and save the file.
7. To generate customized citation keys, you can use the Citation key formula option in the Better BibTeX Preferences. You can use various placeholders and modifiers to create your own pattern. For example, [auth:lower]_[year] will generate keys like shahizan_2024.

For more details and examples, read this guide.

4. Obsidian Plugins

Obsidian is a powerful note-taking app that allows you to create and link your notes in various ways. To enhance your note-taking experience, you can use plugins that add extra features and functionalities to Obsidian. The plugins used in this vault are as follows:

No.	Plugins	Description
1	Admonition	A plugin that allows you to create block-styled admonitions (notes, warnings, tips, etc.) in your notes.
2	Autocomplete	A plugin that provides autocomplete suggestions for words, tags, links, and commands in your notes.
3	Better Word Count	A plugin that shows the word count, character count, and reading time of your notes in the status bar.
4	Calendar	A plugin that adds a calendar view to your notes, where you can see and create notes based on dates.
5	cMenu	A plugin that adds a customizable context menu to your notes, where you can access various commands and actions.
6	Dataview	A plugin that allows you to query, filter, sort, and display data from your notes using a simple query language.
7	Excalidraw	A plugin that integrates Excalidraw, a tool for creating hand-drawn diagrams, into your notes.
8	Iconize	A plugin that lets you add icons to your folders and notes in the file explorer.
9	Pandoc Reference	A plugin that generates a reference list from your citations using Pandoc.
10	Kanban	A plugin that allows you to create and manage kanban boards in your notes.
11	Zotero Integration	A plugin that integrates Zotero, a tool for managing bibliographic data, into your notes.
12	Meta bind	A plugin that allows you to create input and view fields inside your notes. Those input and view fields can then be bound to frontmatter properties, which keeps them in sync those frontmatter properties. Allowing you to edit and view your frontmatter properties inside your notes.
13	Templater	Templater is a template plugin for Obsidian.md. It defines a templating language that lets you insert variables and functions results into your notes. It will also let you execute JavaScript code manipulating those variables and functions.

These plugins can help you make your notes more organized, informative, and creative. You can install them from the Obsidian community plugins page or from their GitHub repositories.

To check for updates for your plugins, please follow these steps:

1. Go to Settings → Community plugins → Current plugins.
2. Click on the Check for updates button. You will update all plugins.

5. Install GitHub Desktop

GitHub Desktop is a free and open source application that lets you interact with GitHub repositories using a graphical user interface. You can use it to clone, create, commit, push, pull, and merge your code, as well as manage branches, issues, pull requests, and more.

To install GitHub Desktop, you need to have a supported operating system, which currently include macOS 10.13 or later and Windows 10 64-bit or later. Here are the steps for each platform:

• macOS:

  1. Visit the download page for GitHub Desktop.
  2. Click Download for macOS.
  3. In your computer's Downloads folder, double-click the GitHub Desktop.zip file.
  4. Unpack the application and put it wherever you want.
  5. Launch GitHub Desktop and sign in with your GitHub account.

• Windows:

  1. Visit the download page for GitHub Desktop.
  2. Click Download for Windows.
  3. In your computer's Downloads folder, double-click the GitHubDesktopSetup.exe file.
  4. Allow the installation to download and install.
  5. Launch GitHub Desktop and sign in with your GitHub account.

Contribution 🛠️

Please create an Issue for any improvements, suggestions or errors in the content.

You can also contact me using Linkedin for any other queries or feedback.