zotero-rag

zotero-rag is a skill for Claude Code from nealcaren/social-data-analysis. It costs 45 tokens per session (1,380 once invoked), scanned A, original, MIT.

A local research-library search tool for markdown versions of papers. It indexes registered papers and finds passages by meaning rather than exact words.

In plain words
What is it for?
Use it to index papers, search topics such as educational attainment, find similar passages, and retrieve surrounding context.
Why use it?
It helps you locate relevant evidence when you do not know the paper's exact wording. It also flags library files that are not linked to your reference list.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin. Also seen: mentions Claude Code.

Part of the zotero-rag plugin — 1 skill shipped together

Good fit Use it to index papers, search topics such as educational attainment, find similar passages, and retrieve surrounding context.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/nealcaren/social-data-analysis/zotero-rag
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add nealcaren/social-data-analysis --skill zotero-rag
Clone the repo
git clone --depth 1 https://github.com/nealcaren/social-data-analysis

Made for: Claude Code.

Or install zotero-rag, the plugin that ships this one along with the rest of its 1 skill.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for zotero-rag

README.md
[![agentmods](https://agentmods.dev/badge/skills/nealcaren/social-data-analysis/zotero-rag/github.svg)](https://agentmods.dev/skills/nealcaren/social-data-analysis/zotero-rag)
Your own site
<a href="https://agentmods.dev/skills/nealcaren/social-data-analysis/zotero-rag"><img src="https://agentmods.dev/badge/skills/nealcaren/social-data-analysis/zotero-rag/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for zotero-rag

Your own site · 80×15
<a href="https://agentmods.dev/skills/nealcaren/social-data-analysis/zotero-rag"><img src="https://agentmods.dev/badge/skills/nealcaren/social-data-analysis/zotero-rag.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 45 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,380 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00045 $0.01380
Opus 5.5 $0.00018 $0.00552
Sonnet 5.5 $0.00009 $0.00276
Haiku 4.5 $0.00005 $0.00138

Measured yesterday against content hash 3ad65ac30985, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

zotero-rag scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured yesterday.

The scan reads SKILL.md. This mod also ships 2 executable files (scripts/ingest.py, scripts/rag.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

plugins/zotero-rag/skills/zotero-rag/SKILL.md · 153 lines

How it starts

The opening of the file, as written. The whole thing — 153 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Script paths below are relative to this skill's base directory ($SKILL_DIR), which Claude Code reports when the skill loads.

Semantic search over your local library of markdown-converted papers using sentence-transformers embeddings and ChromaDB.

Prerequisites

  • uv installed (standard in this project)
  • Papers ingested via ingest.py (which converts to markdown, organizes files, and adds metadata to references.bib)
  • references.bib with md_path fields linking citation keys to markdown files

Important: Only files registered in references.bib are indexed. Loose markdown files in library/markdown/ without a bib entry will be flagged as "unlinked" during indexing. Run ingest.py to register them.

Quick Start

# Index your library (first time or after adding papers)
uv run "$SKILL_DIR"/scripts/rag.py index

# Search by meaning
uv run "$SKILL_DIR"/scripts/rag.py search "cultural capital and educational attainment"

Script Location

All commands use:

uv run "$SKILL_DIR"/scripts/rag.py <command>

Dependencies (sentence-transformers, chromadb) are auto-installed by uv on first run via PEP 723 inline metadata. No manual installation needed.

Commands

Index

Build or update the vector index from library/markdown/ files.

# Index all markdown files (incremental — skips unchanged files)
uv run "$SKILL_DIR"/scripts/rag.py index

# Index specific citation keys only
uv run "$SKILL_DIR"/scripts/rag.py index --keys Smith2020_Cultural Jones2019_Institutional

The index is stored at library/.rag-index/. First run downloads the all-MiniLM-L6-v2 embedding model (~80MB, cached by sentence-transformers).

Run this after adding new papers to keep the index current.

Search

Semantic search across all indexed documents. Returns JSON lines ranked by similarity.

uv run "$SKILL_DIR"/scripts/rag.py search "social movements and collective identity"
uv run "$SKILL_DIR"/scripts/rag.py search "interview methodology" --top-k 5
uv run "$SKILL_DIR"/scripts/rag.py search "Bourdieu field theory" --min-score 0.3

Read the full file on GitHub · 153 lines

Files

What ships with it

2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. yesterday First seen · 153 lines · 45 tokens per session scan A 3ad65ac30985

Subscribe to this mod's changes

zotero-rag is a skill published in the GitHub repository nealcaren/social-data-analysis (90 stars, last pushed 2d ago), licensed MIT. It adds 45 tokens to every session and 1,380 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-10-17.

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