# Logically AI Research Assistant (Obsidian) - Beta

> **We're in beta!** Thank you for trying out the Logically AI Research Assistant in Obsidian. We'd love your feedback on features, bugs, and ideas for improvement. Please reach out to us at [support@logically.app](mailto:support@logically.app) to share your thoughts, or visit [logically.app](http://logically.app) see how you can use Logically to help you research, cite, and write with AI.

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Use Logically’s AI Research Assistant directly inside Obsidian and conduct citation-backed research on the files in your vault.

[![YouTube Video Il--shPteIM](https://img.youtube.com/vi/Il--shPteIM/maxresdefault.jpg)](https://www.youtube.com/watch?v=Il--shPteIM)

## Features

- **Access to Logically AI Research Assistant** next to your writing canvas.
- All search modes, including **Semantic Scholar Mode**, **Google Mode**, and **Document Retrieval Mode**, where you **can connect files from your vault**.
- The latest AI models from **OpenAI, Anthropic, and Gemini.**
- Access to standard AI models if you're subscribed to the Free plan, and access to standard, advanced, and reasoning AI models if you're subscribed to the Unlimited plan.
- **Inline citations and data sources with every answer.** Data sources will appear inside a table when shown.
- The ability to **add your chat output to your active Obsidian document** in one click.
- **Custom instructions** for your chat, which can be edited at any time.

## Requirements

- Obsidian.
- A Logically (<https://www.logically.app>) account.
- Internet access (messages are sent to Logically’s API).

## Installation Guide

### Option A - Community Plugins

1. **Inside Obsidian**, open **Settings → Community plugins**
2. Select **Browse** and search for **Logically AI Research Assistant**
3. Install, then enable the plugin

### Option B - How to install the Beta version directly

If you don’t see Logically listed in the Community Plugins browser, you can install the plugin directly via this guide instead https://github.com/afforai/obsidian-logically-plugin/blob/master/how-to-install-beta.md

## Set Up

1. **Inside Obsidian**, Open **Settings → Logically AI Research Assistant**
2. Sign in with your Logically email and password (or paste a token under **Advanced → Login with token**)
3. (Optional) Use **Verify connection** to test your login/API

<img alt="image" src="https://github.com/user-attachments/assets/b9c122a4-e4c5-421e-879c-e6b6d8f674ba" />

## Using The Plugin

1. Open the AI Research Assistant by clicking the Logically ribbon icon or using the command palette (if using the command palette, type: **Logically: Open Research Assistant** / **Logically: Toggle Research Assistant)**
2. Select a search mode (Document Retrieval, Google, Semantic Scholar).
3. Select an AI model.
4. Ask your question.

<img alt="image" src="https://github.com/user-attachments/assets/c6a73d1b-4ec1-4121-a467-48df85e20b2f" />

### Using Document Retrieval Mode

- When in Document Retrieval mode, click **"Files"** to open the file picker. From here, you can (search your vault and select notes) or drag a note from Obsidian’s file explorer into the assistant panel.

<img alt="image" src="https://github.com/user-attachments/assets/6752ee43-dd73-4287-a59a-1e8749829819" />

**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.
- Messages with sources included show a **Sources table** where you can:
  - Open external links (Google / Scholar).
  - Open vault notes used as reference files.

<img alt="image" src="https://github.com/user-attachments/assets/e11d8f1a-ad9a-4cb5-9d8f-40b75eb43672" />

### Inserting an Answer into Your Note

Press the ”**Insert into active note”** icon button to add a chat output to your note.

- Citation markers are converted into Obsidian **footnotes** (`[^1]`, `[^2]`, …).
- Footnote definitions will appear at the bottom of your note.
- A dedicated **Sources** section will be added with links to reference files and/or external URLs.

<img alt="image" src="https://github.com/user-attachments/assets/b75ca7de-c7ab-4f31-9b54-8328549aa0c4" />

### Settings panel (in the AI Research Assistant Header)

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

<img alt="image" src="https://github.com/user-attachments/assets/8f1c0429-e78f-4ba4-919e-63f13ffac637" />

## 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 from external sources, the contents of those selected notes are included with the request.
- Avoid adding sensitive/private content you don’t want processed remotely.

## Account switching & history

- If you sign in to a **different Logically account** than the one you used last time, the plugin will **clear the existing chat history** to protect your privacy.
- If after logging out, you log back in to your account, your chat history will be preserved.

## Troubleshooting

- **Google Sign-In**: the button is visible, but Google Sign-In isn’t available in Obsidian yet. For now, please sign in using **email + password** (you can set this up at <https://logically.app> under **Account Details**) or use a **login token** (see **Advanced → Log in with token** in plugin settings).
- **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>