# Seerai > AI Research assistant plugin for Zotero 9. Chat with your library, run federated scholarly search, RAG, OCR, systematic reviews, and manage cloud storage. Includes standalone MCP, Agentic capabilities, and skills library. - **Type:** MCP server - **Install:** `agentstack add mcp-dralkh-seerai` - **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior - **Seller:** [dralkh](https://agentstack.voostack.com/s/dralkh) - **Installs:** 0 - **Category:** [AI & ML](https://agentstack.voostack.com/c/ai-and-ml) - **Latest version:** 0.1.0 - **License:** MIT - **Upstream author:** [dralkh](https://github.com/dralkh) - **Source:** https://github.com/dralkh/seerai ## Install ```sh agentstack add mcp-dralkh-seerai ``` Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent. ## About # seerai — AI Research Assistant Plugin for Zotero **seerai** is an intelligent research assistant plugin for Zotero 9 that integrates AI-powered chat, advanced search, structured data extraction, and systematic review workflows directly into your research workflow. Chat with your papers, extract structured data, run PRISMA-style reviews, and accelerate your literature review with a local-first, privacy-focused design. --- ## Installation ### From GitHub (Recommended) 1. Download the latest release (`.xpi` file) from [Releases](https://github.com/dralkh/seerai/releases). 2. In Zotero, go to **Tools → Add-ons**. 3. Click the gear icon ⚙️ and select **Install Add-on From File...**. 4. Select the downloaded `.xpi` file. 5. Restart Zotero. ### From Source ```bash # Clone the repository git clone https://github.com/dralkh/seerai.git cd seerai # Install dependencies npm install # Build the plugin npm run build # The .xpi file will be generated in the root directory ``` --- ## Features ### AI-Powered Chat Interface - **Contextual Conversations**: Chat with AI about your selected papers with full context awareness. - **Smart Context Priority**: Automatically prioritizes content sources: 1. **Zotero Notes** (OCR note, and other notes for highest priority) 2. **Indexed PDF Text** (Fast, efficient, however consumes a lot of tokens and may cause limit issues) 3. **OCR** (Fallback for scanned documents with no indexed text) - **Multi-paper Support**: Add multiple papers to a single conversation for comparative analysis. - **Streaming Responses**: Real-time, token-by-token response rendering. - **Markdown & Math**: Responses are formatted with syntax highlighting and LaTeX math support. - **Vision Support**: Paste images directly into chat for multimodal analysis. - **Multimodal Generation**: Generate images, videos, speech-to-text, and text-to-speech directly from chat. - **Attachments Upload**: Add files to conversations via the context menu. - **Interactive Follow-ups**: Deepen the conversation with streaming follow-up questions. - **Configurable Citations**: Choose your preferred citation style for AI insights and chat. - **Smart Copy**: Select and copy text with preserved formatting (Markdown) directly from chat bubbles. - **Enhanced Keybindings**: - `Enter`: Insert new line - `Shift+Enter`: Send message - `Ctrl+Shift+S`: Toggle/Focus detachable window - **Detachable Window**: Pop out the SeerAI interface into a standalone resizable floating window to maintain chat access while navigating your library. - **Themed UI**: Enhanced dialogs and components with full theme support for a consistent look across Zotero's Light and Dark modes. - **Responsive Layout**: Chat, tables, and search tabs dynamically adapt to panel width changes. ### Semantic Search & Discovery - **RAG (Retrieval-Augmented Generation)**: Per-context embeddings with chunking, vector store, and semantic retrieval for large documents. - **Web Search**: Integrated Firecrawl, Tavily, and You.com support for finding high-quality full-text content. - **Federated Scholarly Search**: Search across 11 providers at once — Semantic Scholar, arXiv, PubMed, bioRxiv, medRxiv, IACR, Europe PMC, CORE, BASE, Zenodo, and HAL — with cross-source deduplication and rank fusion. - **Smart Modes**: One-click presets (Broad, Biomedical, Preprints, Cryptography, Repositories) target the right provider sets, or pick sources manually. - **AI Query Refinement**: An AI step extracts your concepts and synonyms once, then compiles them into each provider's native query syntax — so you get precise results without learning 11 query dialects. - **Advanced Filters**: Fine-tune results by Year, Venue, and Citation Count. - **AI Insights Config**: Configure insight generation directly from the search panel. - **Export**: Export results to BibTeX or CSV. - **Smart Import**: - **Federated Imports**: Import papers from Semantic Scholar, arXiv, PubMed, Europe PMC, repositories, and preprint sources using provider IDs, DOI, PMID/PMCID, URLs, or search results. - **Fast Agent Imports**: Agent imports return as soon as a Zotero item is created or reused, then queue PDF discovery in the background. - **PDF Discovery**: Automatically finds and attaches PDFs during import with bounded background concurrency. - **Configurable Import OCR**: Auto-OCR is enabled by default for imports and can be disabled in Chat Settings to skip OCR completely. - **Source Link**: Fallback to source links if PDFs are unavailable. - **Status Indicators**: Clear feedback on import status (⬇️ Importing, ✅ Imported, ⚠️ Failed). - **Global Search Scope**: Searching now extends across all libraries, including personal and group collections. - **Advanced Boolean Search**: Robust support for nested logic (AND/OR/NOT), implicit phrasing, and markdown-aware matching. - **Smart Regex matching**: Improved search precision with intelligent handling of word boundaries and special characters. ### Agentic Chat & Tool Use - **Autonomous Agents**: AI can use tools to interact with your Zotero library, the web, and your workspace. - **Research Mode**: You.com research mode for multi-source answer synthesis. - **Rich Tool Suite**: - **Search Tool**: Search through your library with advanced filters. - **Collection Tool**: Manage collections and move items. - **Note Tools**: Read, create, and **edit existing** item notes for seamless research updates. - **Tag Tool**: Automatically generate and apply relevant tags to your research. - **Read Tool**: Extract text from PDFs and items for deep analysis. - **Citation Tool**: Generate citations and bibliographies. - **Table Tool**: Interact with and generate data for your Paper Tables. - **Web Tool**: Search the web and fetch content using Firecrawl, Tavily, or You.com. - **Workspace Tools**: Create, read, edit, and delete files directly in your workspace. - **Todo Tool**: Create and manage task lists for complex multi-step research workflows. - **Skills Tool**: Discover and load on-demand instructions from a bundled library of ~148 agent skills. - **Systematic Review Tool**: Create and update review protocols, sources, and screening decisions from chat. - **Agent Skills Library**: A curated library of self-contained skill packages (scientific computing, bioinformatics, document generation, search, and more) that the agent loads only when relevant — sourced from [K-Dense-AI/scientific-agent-skills](https://github.com/K-Dense-AI/scientific-agent-skills). Add your own bundled, workspace, or custom skills. - **Tool Activity Notices**: Inline status indicators show when the agent is invoking tools, running workspace commands, or waiting on external results. - **Task Completion Signaling**: Agents signal completion explicitly for clean multi-step workflows. - **Advanced Orchestration**: Improved tool calling logic with tool filtering, iteration tracking, and observability tracing. - **Model-as-a-Tool**: Seamless integration with LLM tool-calling capabilities. ### Papers Tables - **Structured Extraction**: Extract specific data points from multiple papers into a comparative table. - **AI-Powered Columns**: Define custom columns with AI prompts (e.g., "Methodology", "Sample Size"). - **Inline Editing**: innovative inline editor for column titles and prompts. - **One-Click Generation**: Generate data for individual cells or entire columns instantly. - **Bulk Actions**: Regenerate content or add selected papers to collections in bulk. - **Side Strip Actions**: Unified controls for adding, removing columns, generating triggers, and settings. ### Systematic Review End-to-end systematic review workflow built directly into Zotero: - **Protocol Builder**: Define your research question and choose a structured framework — PICO, PICOS, PICOT, PICOTS, PICOTT, PECO, PICo, PEO, SPIDER, SPICE, or PCC. - **Eligibility Criteria**: AI-assisted inclusion/exclusion rules with keyword aids, rationale, and a full revision history. - **Search Strategy**: Compile a review-wide strategy into native queries for each scholarly source, or refine it with AI and push it straight into the search input. - **Sources**: Import papers from Zotero collections as review sources; track per-source counts, overlap, and deduplication. - **PRISMA Flow Diagram**: Visualize title/abstract → full-text → final screening flow with live counts. - **Screening**: Title/abstract and full-text screening with include/exclude/maybe decisions, reasons, confidence scores, and AI recommendations. - **Data Extraction**: AI-powered structured extraction with customizable templates, outcomes, effect measures (OR, RR, HR, MD, SMD), confidence intervals, timepoints, and a proposed → verified → rejected workflow. - **Evidence Synthesis**: Random-effects and common-effect meta-analysis, forest plots, I² heterogeneity, and pooled effect sizes. - **Gap Analysis**: AI-generated research gap identification with severity scoring. - **Extraction Health Checks**: Automatic warnings for missing effect sizes, missing CIs, missing timepoints, negative variances, extreme effect sizes, low sample sizes, and potential duplicate extractions. - **Review Export**: Export systematic review data and synthesis outputs for reporting and downstream analysis. - **Async Jobs**: Run extraction and analysis jobs in the background with progress tracking and cancellation. ### Workspace & File Management - **Built-in File Workspace**: A persistent file system workspace accessible to you and your AI agent. - **File Tree Navigation**: Sidebar with full file tree for browsing, creating, and organizing files and folders. - **Code Editor**: Built-in Monaco-inspired editor with syntax highlighting, line numbers, and auto-save. - **Git Integration**: Initialize repos, stage changes, commit, and view diffs directly within the workspace. - **Diff Viewer**: Side-by-side or unified diff view for reviewing file changes. - **File Viewer**: Render workspace files with syntax highlighting across multiple formats. - **DOCX Converter**: Convert documents to/from DOCX format for interoperability with word processors. - **Custom Workspace Paths**: Configure a custom directory for your workspace files. ### Cloud Storage Integration - **Multi-Provider Support**: Connect to Google Drive, Dropbox, Box, OneDrive, or Nextcloud. - **OAuth 2.0 + PKCE**: Secure authentication flow for all cloud providers. - **Cloud Drive Tab**: Browse, search, and manage cloud files directly within Zotero. - **Cloud Context**: Include cloud-stored files as context in your AI conversations. - **File Sync**: Upload and download files between workspace and cloud storage seamlessly. ### OCR & Text Extraction - **Flexible OCR Options**: - **Mistral OCR**: High-quality cloud OCR (Recommended). - **DataLab.to**: Reliable cloud-based extraction. - **Local Marker**: Run your own local OCR server for free, private processing. - **Auto-Processing**: Automatically processes unindexed PDFs when needed. ### Customizable AI - **Persistent API Keys**: API keys are saved and persisted across all configured providers. - **Model Presets**: Pre-configured settings for popular providers: - OpenAI, Anthropic, Google, xAI - DeepSeek, Mistral, Groq, Together, Fireworks, Cohere, OpenRouter - Local Models (Openai compatible endpoint) - 4-8g Vram - Qwen3.5 2B / Qwen3.5 4B - 12-16g Vram - Qwen3.5 9B / Gemma 4 12B - 24-32g Vram - Qwen3.6 27B / Qwen3.6 35B A3B / Gemma 4 31B / Gemma 4 26B A4B - 48-96g Vram - Qwen3.5 122B A10B / Mistral Medium 3.5 / NVIDIA Nemotron 3 Super / - 128g Vram - MiniMax-M3 / MiMo-V2.5-Pro / GLM-5.2 / Kimi K2.6 / DeepSeek V4 Pro / Nemotron 3 Ultra / Qwen3.5 397B A17B / DeepSeek-V4-Flash - **Local CLI Agents**: Route chat through a CLI you already have installed and logged in — **Codex**, **Claude Code**, **Antigravity**, or **GitHub Copilot**. seerai stores no credentials; it reuses the CLI's own session. - **CLI MCP Harness**: Local CLI agents can optionally connect to the bundled seerai MCP server so they can read and act on your Zotero library while you chat. - **Capability-Based Routing**: Assign separate models per capability — chat, embeddings, image, video, text-to-speech, and speech-to-text — and route each request to the right endpoint automatically. - **Smart Rate Limiting**: Per-model configuration for concurrency, RPM, and TPM to prevent provider errors. - **Per-Conversation Models**: Switch models dynamically based on the task complexity. --- ## Configuration Go to **Zotero → Settings → seerai** to configure your AI providers and services. ### 1. AI Models Use the **Add Configuration** button to set up your AI models. - **Presets**: Select from built-in presets (OpenAI, Anthropic, Ollama, etc.) for quick setup. - **Custom**: Manually configure API URL, Key, and Model ID for any OpenAI-compatible provider. - **Default**: Set a preferred model as your default for new conversations. ### 2. OCR Services Choose your preferred text extraction engine: - **Mistral OCR**: Requires [Mistral API Key](https://console.mistral.ai/). Best for accuracy. - **Cloud (DataLab.to)**: Requires DataLab API Key. - **Local Marker Server**: Requires running a local Python server. - URL: `http://localhost:8001` (Default) - See [Marker Project](https://github.com/VikParuchuri/marker) for setup. ### 3. Search Integrations - **Semantic Scholar**: Add your [API Key](https://www.semanticscholar.org/product/api) for higher rate limits and faster searches. - **Firecrawl**: Add [API Key](https://firecrawl.dev) to enable deep web search capabilities - local instance with ([GitHub](https://github.com/firecrawl/firecrawl)). - **Tavily**: Add [API Key](https://tavily.com/) for optimized search results tailored for AI agents. - **You.com**: Add [API Key](https://api.you.com) for web search and research mode. ### 4. Workspace - **Local Path**: Configure a custom directory path for your workspace files (Settings → seerai → Workspace). - **Git Integration**: Enable Git version control for automatic versioning and collaboration. - Files created in the workspace are accessible to your AI agent via workspace tools. ### 5. Cloud Storage - **Supported Providers**: Google Drive, Dropbox, Box, OneDrive, Nextcloud. - **Authentication**: Secure OAuth 2.0 with PKCE flow — no passwords stored. - Connect via the **Cloud tab** in the workspace sidebar to browse, sync, and use cloud files as AI context. ### 6. MCP Server & API Seer-AI now includes a Model Context Protocol (MCP) server and a local API for external integrations. - **MCP Server**: Located in [`mcp-server/`](mcp-server/README.md). Allows external LLMs (like Claude Desktop) to interact with your Zotero library. See the [MCP Setup Guide](mcp-server/README.md) for configuration instructions. - **Local API**: Provides endpoints for chat, tool execution, and library management. - **Settings → seerai → API**. - Default Port: `23119` This mode requires sophisticated models with strong tool/function-calling capabilities to function properly. --- ## Usage Guide ### Chatting with Papers 1. Select a paper (or multiple) in your library. 2. Open the **SeerAI** sidebar tab. 3. (Optional) Customize context inclusions via the settings icon (Abstracts, Notes). 4. Type your question or use templates from the **Prompt Library** (Book icon). ### Detachable Window - **Pop-out**: Click the `⇱` button in the SeerAI tab bar to open a floating window. - **Hotkey**: Press `Ctrl+Shift+S` to instantly detach, toggle, or focus the window. - **Auto-Sync**: The detached window automatically updates its context when you select different items in Zotero. - **Attach**: Close the floating window or click the dock button (within the sidebar placeholder) to return to the sidebar. ### Creating Data Tables 1. Open the **Tables** ta … ## Source & license This open-source MCP server is cataloged on AgentStack and links to its original source — we do not rehost the code. - **Author:** [dralkh](https://github.com/dralkh) - **Source:** [dralkh/seerai](https://github.com/dralkh/seerai) - **License:** MIT Install and usage instructions live in the source repository linked above. ## Pricing - **Free** — Free ## Security capabilities Automated source analysis of v0.1.0 — what this tool can access: - **Network access:** no - **Filesystem access:** no - **Shell / process execution:** no - **Environment & secrets:** no - **Dynamic code execution:** no *"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.* ## Versions - **0.1.0** — security scan: passed — Imported from the upstream source. ## Links - Listing page: https://agentstack.voostack.com/l/mcp-dralkh-seerai - Seller: https://agentstack.voostack.com/s/dralkh - Browse the marketplace: https://agentstack.voostack.com/browse --- Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.