Academic Agent

Work-in-progress academic agent for paper workflows: Zotero integration, tag-scoped RAG search, and writing-oriented citation support.

Why this project

Academic reading and writing usually spans multiple tools: literature management, search, notes, and citation-heavy drafting. This repo brings those workflows together in one local agent setup centered on Zotero as the source of truth.

Core Modules

1) Zotero Integration

• Import papers from DOI, title search, or local PDFs
• Organize papers with structured tags (area/*, project/*, topic/*, status/*)
• Generate concise paper summaries as Zotero child notes
• Manage project workspaces with scoped bibliography exports

2) RAG Integration

• Tag-scoped semantic search over your paper collection
• Retrieval powered by PaperQA2
• Scope-aware indexing and source-grounded answers for research exploration

3) Writing Integration

• Citation-oriented workflows for markdown writing
• Citation key lookup from your Zotero library
• Writing pipeline direction for bibliography + style-based document builds

Architecture (high level)

User/agent commands flow through a local MCP server (zotero-companion) and service modules for import, metadata enrichment, summaries, workspace operations, and RAG queries.

Primary integrations:

• Zotero Web API + local Zotero data access
• Semantic Scholar (metadata enrichment)
• OpenAI models (summaries and retrieval workflows)
• PaperQA2 (paper-focused retrieval)

Tech Stack

• Python 3.12+
• uv
• Ruff
• Pyright
• Pytest
• Nox
• MCP SDK

Setup

uv sync
cp .env.example .env
# Fill required keys in .env

Run validation:

uv run nox

Run the MCP server:

uv run zotero-companion

Notes

• This repository is intentionally maintained as a pragmatic, portfolio-oriented project.
• Scope is focused on academic agent workflows rather than a broad general-purpose platform.