DEMO_3_Obsidian_for_research_presentation - RDM-BY

## What Obsidian is - A tool that helps you think by organizing and connecting information in whatever way you need. - In community jargon, a knowledge management platform/personal knowledge graph tool - [Free to download and use](https://obsidian.md/pricing) - Purchasing a license is encouraged to support the project, 40% educational discount - [Cross-platform](https://obsidian.md/download) - Win, Mac, Linux, iOS, Android, web clippers - Extremely versatile and customizable for many applications - Base program expandable with several thousand official + community plugins - Flexibility encourages uptake (see presentation on ELNs by Inge Mannaerts: researchers want highly customised solutions) - Beginner-friendly - Choose your level of complexity, enormous amount of user-created demos and resources, e.g. on YouTube --- ## What Obsidian is not - Not open source - But open data, no lock-in, data only local by default (see later) - Not a full-fledged data collection/analysis/visualization platform - Advanced functionality depends on community plugins that are usually maintained by individuals - Not designed for collaboration, though it can be used for such - Sync conflict management is very basic, may or may not be sufficient for you - Advanced functionality again depends on community plugins - Not based in the US - For Obsidian Sync/Publish, whereby data are synced from hard drive to servers: European data center in Germany ([Security](https://help.obsidian.md/sync/security)) - Sync servers chosen based on IP address (see OSF presentation by Marleen Marynissen: researchers often don't change/consider default settings, so offering the right option "by default" is helpful) --- ## Basic concepts ### Basic concepts: Vaults - Obsidian creates a layer of extra functionality over a standard file folder + subfolders on your hard drive, J-drive, Sharepoint, Onedrive, external hard drive, ... - Your Obsidian folder(s) behave 100% like a simple folder containing files; anything you can do with a file containing folders, you can do with your Obsidian content - A "vault" is the unit of your folder + the Obsidian functionality, plugins, etc., you added - New "notes" you create are saved as individual markdown (.md) files --- A vault on your file explorer: ![[DEMO_Project_data/DEMO_Screenshots/Pasted image 20250605155806.png]] --- Opening a vault in Obsidian: ![[DEMO_Project_data/DEMO_Screenshots/Pasted image 20250605155835.png]] --- A vault with markdown files: ![[DEMO_Project_data/DEMO_Screenshots/Pasted image 20250605155927.png]] --- ### Basic concepts: Markdown - See Erik Verraedt's LaTeX presentation: Markdown is a bit like mini LaTeX - Obsidian uses [markdown](https://help.obsidian.md/syntax) to add *formatting/structure* and *functionality* to notes - Formatting/structure: italic, bold, headings, lists, tables, ... - Functionality: wikilinks, tags, metadata (properties), ... - Plain text lightweight markup language, widely used, files can be opened with any simple text editor - Using markdown in Obsidian: Right-click for formatting options or install [Editing Toolbar plugin](https://github.com/PKM-er/obsidian-editing-toolbar) for easily accessible buttons --- ![[Pasted image 20250617105446.png]] --- ### Basic concepts: File formats - When you open a folder in Obsidian as a vault, only the markdown files in that folder are shown by default - To show non-markdown files in the Obsidian file tree, enable "Detect all file extensions" in Settings -> Files and Links - Various plugins to view, edit, or convert other file formats inside Obsidian itself - [Docxer plugin](https://github.com/Developer-Mike/obsidian-docxer) for .docx files (view and convert to markdown for editing) - [JSON/CSV importer plugin](https://github.com/farling42/obsidian-import-json) - Official [Obsidian Importer](https://github.com/obsidianmd/obsidian-importer) plugin to import from other note-taking applications and formats (Apple Notes, Bear, Evernote, Google Keep, OneNote, Notion, Roam, HTML files, markdown files) - ... (Check out plugins containing ["import"](https://obsidian.md/plugins?search=import) or "[convert"](https://obsidian.md/plugins?search=convert)) --- ### Basic concepts: Templates and properties - Create complex templates to apply to any note - Apply properties to notes (and also templates) to create structured metadata - Templates can also be used to gather data via the browser plugin --- Example of a template: ![[DEMO_Project_data/DEMO_Screenshots/Pasted image 20250605160915.png]] --- The filled template: ![[DEMO_Project_data/DEMO_Screenshots/Pasted image 20250605161027.png]] --- The template in the Obsidian browser plugin: ![[DEMO_Project_data/DEMO_Screenshots/Pasted image 20250605161158.png]] --- ### Basic concepts: Graphs - [Graphs help](https://help.obsidian.md/plugins/graph) - Obsidian can represent notes as a networked graph - Graph can be customized to show note links based on wikilinks, tags, properties, etc --- ![[DEMO_Project_data/DEMO_Screenshots/Pasted image 20250529191221.png]] --- ### Basic concepts: Canvases - [Canvases help](https://help.obsidian.md/plugins/canvas) - ![[DEMO_Project_data/DEMO_Screenshots/demo-help-vault.png]] --- ### Basic concepts: Plugins - Extend basic functionality with "Core" plugins by Obsidian + "Community" plugins - Install, activate, and personalize plugins in Settings - Most plugins are open source and free - [Search Community plugins online](https://obsidian.md/plugins) --- ![[DEMO_Project_data/DEMO_Screenshots/Pasted image 20250529191613.png]] --- ![[DEMO_Project_data/DEMO_Screenshots/Pasted image 20250529191722.png]] --- ### Basic concepts: Interface - Standard: - Left sidebar: [File tree](https://help.obsidian.md/plugins/file-explorer), [search](https://help.obsidian.md/plugins/search), [bookmarks](https://help.obsidian.md/plugins/bookmarks) - Fun search plugin (e.g. search content from images): [Omnisearch](https://github.com/scambier/obsidian-omnisearch) - [Various file tree alternative plugins](https://obsidian.md/plugins?search=file%20tree) - Middle: Notes - Right sidebar: links between notes, tags, properties, other plugin functionality - Get creative: - Notes can be rearranged almost without limits - Save particular configurations as [Workspaces](https://help.obsidian.md/plugins/workspaces) --- Basic interface: ![[DEMO_Project_data/DEMO_Screenshots/Pasted image 20250605162125.png]] --- Customized interface: ![[DEMO_Project_data/DEMO_Screenshots/Pasted image 20250605162426.png]] --- ### Basic concepts: Hotkeys and Command Palette - Set Hotkeys in Settings to launch any core Obsidian or plugin-related factions - Command palette (ctrl/cmd+P OR click icon in far left sidebar) is also a quick and easy way to find available actions and execute them --- ## Use cases #### Obsidian for project and task management - Templates: - Basic functionality available as core plugin - Intense templates: [Templater plugin](https://github.com/SilentVoid13/Templater) and other community plugins - "(Templater) 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." - [Workspaces](https://help.obsidian.md/plugins/workspaces) - Wide range of calendar plugins --- - Plugins for project and task management: - [Tasks plugin](https://github.com/obsidian-tasks-group/obsidian-tasks): gather tasks from around your vault - [Daily notes plugin](https://help.obsidian.md/plugins/daily-notes): generate a new daily note from a template when you open Obsidian - [Projects plugin](https://github.com/marcusolsson/obsidian-projects): manage notes in an Airtable/Baserow/MS Lists-like interface, development recently discontinued - [Kanban plugin](%3Chttps://github.com/mgmeyers/obsidian-kanban%3E): makes a nice kanban :) - [Day planner plugin](https://github.com/ivan-lednev/obsidian-day-planner): show calendars (eg from outlook), time-block, show timelines --- <https://github.com/mgmeyers/obsidian-kanban>: ![[Screen Shot 2021-09-16 at 12.58.22 PM.png]] --- <https://github.com/ivan-lednev/obsidian-day-planner> (screenshot via [@chaemin](https://velog.io/@chaemin/obsidian-Day-Planner-plugin-%ED%85%8C%EB%A7%88-%EB%B3%80%EA%B2%BD)): ![[image.png]] --- #### Obsidian for research data management - Integrate RDM-related documents with the research data - Make RDM documents part of a researcher's daily workflow - DMPs, README files, etc., can be shown right next to the data, everything editable in one interface - Write better, more consistent documentation - templates - activity logging - intertextual links - Easy to create data sharing pipeline - e.g. Obsidian vault on Sharepoint folder -> RDR integration dashboard -> RDR --- - Plugins for data management: - [QuickAdd](https://github.com/chhoumann/quickadd): add updates to a file that isn't open (demonstration now ;) - ![[Pasted image 20250617141608.png]] - [Obsidian daily activity](https://github.com/trydalch/obsidian-daily-activity): log changes made to files and folders - [Chronology plugin](https://github.com/Canna71/obsidian-chronology): Creates interactive calendar view of notes --- #### Obsidian for gathering and annotating data - Plugins for gathering data: - [Web clipper](https://obsidian.md/clipper) - Clip highlights - Extract structured data from webpages using templates - [Obsidian PDF++ plugin](https://github.com/RyotaUshio/obsidian-pdf-plus) for PDF annotation - Various Zotero integration plugins (see Leah Budke's presentation for note-taking and annotation capabilities of Zotero) - [Obsidian Zotero Integration](https://github.com/mgmeyers/obsidian-zotero-integration) - [Zotlit](https://zotlit.aidenlx.top/) - How researchers actually combine Zotero and Obsidian depends entirely on their preferred workflows - Various plugins for querying APIs - Integration plugins for a range of other tools: [Readwise](https://github.com/readwiseio/obsidian-readwise), [Kobo](https://github.com/OGKevin/obsidian-kobo-highlights-import), AI tools, git, ... - Search for your preferred tool among the community plugins and give us feedback about if/how it integrates with Obsidian! - Globus bv? - ... --- ![[303649533-0c1c8ad7-1194-408f-bb47-5a847f960025.png]] Source: https://github.com/RyotaUshio/obsidian-pdf-plus --- #### Obsidian for exploring, analyzing, and visualizing data - Plugins for exploring, analyzing, and visualizing data: - [Graph view:](https://help.obsidian.md/plugins/graph) display and filter vault content in a networked graph (tip: try the timelapse video) - [Dataview plugin](https://github.com/blacksmithgu/obsidian-dataview): annotate content with metadata (in frontmatter or inline), then query and display that metadata in a range of ways - [Obsidian Tracker plugin:](https://github.com/pyrochlore/obsidian-tracker) track mentions in vault content with a range of different graphs (makes use of Dataview) - [Obsidian-Charts plugin](https://github.com/phibr0/obsidian-charts): more data visualization - [Obsidian-Chartsview plugin:](https://github.com/caronchen/obsidian-chartsview-plugin) yet more data visualization based on [Ant Design Charts](https://ant-design-charts.antgroup.com/) - [Juggl:](https://github.com/HEmile/juggl) Interactive graph view - ... --- ![[screenshot_v1.9.png]] Source: https://github.com/pyrochlore/obsidian-tracker --- ![[Pasted image 20230224202045.png]] Source: <https://charts.phib.ro/Meta/Charts/Charts+Documentation> --- #### Obsidian for writing --- - Obsidian can function as... - A research wiki/knowledge base - A knowledge management platform to feed writing projects in other apps - An actual writing platform - Integrate bibliography management with various Zotero integration plugins - [Obsidian Zotero Integration](https://github.com/mgmeyers/obsidian-zotero-integration) - [Zotlit](https://zotlit.aidenlx.top/ - [Excalidraw plugin](https://github.com/zsviczian/obsidian-excalidraw-plugin) to use [Excalidraw sketching and whiteboarding tool](https://plus.excalidraw.com/) to visualize notes, write by hand, save as markdown --- #### Obsidian for presenting - Plugins for presenting: - Slides core plugin - [Advanced Slides](https://github.com/MSzturc/obsidian-advanced-slides) adds live preview, note embeds, HTML export, ... - [Obsidian Advanced Canvas](https://github.com/Developer-Mike/obsidian-advanced-canvas) - [Obsidian Teleprompter](https://github.com/lumetrium/obsidian-teleprompter) adds a teleprompter to go with your presentation in the browser --- #### Obsidian for publishing and exporting data - Plugins for publishing an Obsidian vault as a website: - [Obsidian Publish](https://obsidian.md/publish) (paid) - [Collaborating on Publish site](https://help.obsidian.md/publish/collaborate) is well supported - [Obsidian Enveloppe plugin](https://github.com/Enveloppe/obsidian-enveloppe) (free, publishes site via Github) - [Quartz](https://quartz.jzhao.xyz/) static site generator - Plugins for exporting text and data out of Obsidian in various formats: - [Pandoc](https://pandoc.org/index.html) universal document converter-based plugins (e.g.[Enhancing Export](https://github.com/mokeyish/obsidian-enhancing-export)) - [Metadata Extractor plugin](https://github.com/kometenstaub/metadata-extractor): export Obsidian data to JSON - Table to CSV exporter - [Bulk exporter plugin](https://github.com/symunona/obsidian-bulk-exporter) to filter on metadata before exporting - Various other export plugins - ... --- #### Obsidian for studying - Plugins for studying: - Note-taking according to various methods using templates - Flashcards - Various Anki integration plugins - [Spaced Repetition plugin](https://github.com/st3v3nmw/obsidian-spaced-repetition) --- #### Coming soon: New core plugin Bases adds MS Lists/Notion/Airtable/Baserow-like functionality - [Bases](https://help.obsidian.md/bases) is currently in early beta - ![[2025-05-21-bases-noshadow.png]] --- ![[Pasted image 20250617140213.png]] --- #### Important: Make Obsidian look pretty - [Iconic](https://github.com/gfxholo/iconic) and [Iconize](https://github.com/FlorianWoelki/obsidian-iconize) plugins - ![[banner.webp]] --- - Themes: - Install new themes from Settings -> Appearance - Then install Style Settings plugin to customize themes further - This theme: AnuPpucin - ![[Pasted image 20250617111830.png]] ---