Logically Research Assistant (Obsidian)

Chat with Logically’s research assistant inside Obsidian (right sidebar), with optional context from your vault notes.

What you get

• Right sidebar chat view with persistent history
• Search modes:
  • Files (Document Retrieval): use selected vault notes as reference context
  • Google: enrich answers with web results
  • Scholar (Semantic Scholar): research paper discovery
• Model selection (Standard / Advanced / Reasoning), with upgrade prompts for locked tiers
• Reference files (up to 5) via file picker or drag & drop
• Citations + sources:
  • Citation tokens in responses render as clickable superscripts
  • A Sources table is shown for assistant messages when sources exist
• Message actions:
  • Insert into active note (assistant messages)
  • Regenerate (assistant messages)
  • Delete from here down (user messages)
• Quick controls: Settings panel and Clear chat
• Custom instruction (saved, applied to every message)

Requirements

• Obsidian
• A Logically account (logically.app)
• Internet access (messages are sent to Logically’s API)

Install

Option A – Community Plugins

1. Open Settings → Community plugins
2. Select Browse and search for Logically Research Assistant
3. Install, then enable the plugin

Option B – Private distribution

If it is not listed in the Community Plugins browser, you will need a direct install bundle from Logically. Please reach out to Logically support for access.

Set up

1. Open Settings → Logically Research Assistant
2. Sign in with your Logically email + password (or paste a token under Advanced → Login with token)
3. (Optional) Choose a Default model
4. (Optional) Use Verify connection to test your login/API

Use

1. Open the assistant:
   • Click the Logically ribbon icon, or
   • Use command palette: Logically: Open Research Assistant / Logically: Toggle Research Assistant
2. Pick a mode (Files / Google / Scholar)
3. Pick a model (Standard / Advanced / Reasoning)
4. Ask your question

Files mode: add reference context

You can include up to 5 Markdown notes as reference context for the next message.

• Click Files to open the file picker (search your vault and select notes)
• Or drag a note from Obsidian’s file explorer into the assistant panel (you’ll see a drop overlay)

Notes:

• Dropping files that are already selected won’t error; the plugin will add the new ones and tell you which were already added.
• When the limit is reached, additional dropped/selected files are skipped.

Citations & sources

• When the backend returns citations, the plugin renders citation markers as clickable superscripts.
• Assistant messages with sources show a Sources table where you can:
  • Open external links (Google / Scholar)
  • Open vault notes used as reference files

Insert an answer into your note

Use Insert into active note on an assistant message.

• Citation markers are converted into Obsidian footnotes ([^1], [^2], …)
• Footnote definitions are appended at the bottom
• A Sources section is added with links to reference files and/or external URLs

Settings panel (in the assistant header)

• Shows the signed-in email
• Lets you logout
• Lets you edit and save a Custom Instruction (applied to every message)

Privacy & data

• When you send a message, the plugin sends your prompt and relevant chat history to Logically’s API.
• If you add reference files, the contents of those selected notes are included with the request.

Avoid adding sensitive/private content you don’t want processed remotely.

Troubleshooting

• Login fails: confirm your credentials work on https://logically.app and try Verify connection in settings.
• Network / connection errors: check your internet connection and try Verify connection.
• Dragging notes doesn’t add them: only Markdown notes can be added; try dragging a .md note from the Obsidian file explorer.
• File picker is empty: ensure your vault contains Markdown files and Obsidian has finished indexing.

Links

• https://logically.app
• https://obsidian.md