What is paper-glossary?

A workflow for turning research papers into shared glossary notes in Obsidian, a note-taking app. It proposes terms for review before creating notes or linking them to an article.

Building a reviewed list of terms from paper files, creating glossary notes, and adding links from an Obsidian article.

It helps keep technical definitions grounded in a paper and prevents glossary changes from being made without review.

paper-glossary — Skill for Claude Code and Codex by 917Dhj

About the project

DeepPaperNote is an agent skill that reads one research paper and turns its content into a structured Obsidian research note. It is for researchers and learners who want to preserve a paper’s question, methods, evidence, results, and figures in an academic knowledge base. The catalogue entries are its agent skills, instructions, and plugin packaging for use with coding agents.

917Dhj/DeepPaperNote · 1,051 stars · on GitHub · 917dhj.github.io

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 917Dhj/DeepPaperNote --skill paper-glossary

Clone the repo

git clone --depth 1 https://github.com/917Dhj/DeepPaperNote

Made for: Claude Code, Codex.

Or install deeppapernote, the plugin that ships this one along with the rest of its 2 skills.

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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/917dhj/deeppapernote/paper-glossary/github.svg)](https://agentmods.dev/skills/917dhj/deeppapernote/paper-glossary)

Your own site

<a href="https://agentmods.dev/skills/917dhj/deeppapernote/paper-glossary"><img src="https://agentmods.dev/badge/skills/917dhj/deeppapernote/paper-glossary/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/917dhj/deeppapernote/paper-glossary"><img src="https://agentmods.dev/badge/skills/917dhj/deeppapernote/paper-glossary.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 46 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,276 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. Third-party audits

NVIDIA SkillSpector warn 7 Sept 2026

SkillSpector: 1 finding, up to medium

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

medium Rogue Agent · line 12
Skill establishes unauthorized persistence across sessions via cron jobs, startup scripts, or state files. Session persistence allows an attacker to maintain access beyond the current interaction.

Fix: Remove any persistence mechanisms (cron jobs, startup scripts, state files). Skills should not maintain state across sessions without explicit user consent.

How audits are shown

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.

Model	Per session	Once invoked
Fable 5.1	$0.00046	$0.01276
Opus 5	$0.00023	$0.00638
Sonnet 5	$0.00009	$0.00255
Haiku 4.5	$0.00005	$0.00128

Measured 10d ago against content hash ae87ec9e2353, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

paper-glossary 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 10d ago.

The scan reads SKILL.md. This mod also ships 18 executable files (scripts/configure_glossary.py, scripts/glossary_common.py, scripts/glossary_config.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.

skills/paper-glossary/SKILL.md · 44 lines

How it starts

The opening of the file, as written. The whole thing — 44 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Paper Glossary

Build shared glossary notes from *_source_manifest.json. --source-manifest is always required; --raw-sections only overrides its raw_sections_path with an explicit *_raw_sections.jsonl. This skill never runs or modifies a paper-reading workflow; the manifest and raw-sections file are its only paper-content boundary. See references/file-contract.md for JSON and CLI contracts.

Preview And Wait (Default)

Show saved configuration on first use per person/device. If absent, ask for a term directory inside an Obsidian vault and configure it; reuse valid configuration later. Setup may create ~/.paper-glossary/config.json.
Require an explicit article Markdown path when article links are requested. Validate it and the configured term directory are in the same Obsidian vault; never infer an article path.
Run deterministic proposal from the effective body.
Perform exactly one grounded host semantic review, bounded by shortlist_limit. It may only drop or reorder candidates and must preserve each retained proposal candidate's exact term string.
Record the reviewed shortlist with plan_glossary.py --review-proposal PROPOSAL --reviewed-terms NAMES; this validates the saved proposal against the current paper source and preserves each full candidate, ordered surface_forms, and provenance. If review produces an empty reviewed shortlist, report no_candidates and stop without presenting a selector.
Present every retained term from that reviewed artifact as a numbered Markdown list. This is the terminal, Codex, and Claude Code interaction. Show the resolved term directory, the article Markdown path (or that none was requested), and that selection authorizes glossary writes/enrichment plus first-safe-occurrence article links when an article was supplied.
State: No glossary notes or article Markdown have been written before selection. End the response and wait. Do not triage, inventory, generate, link, or lint during preview.

Read the full file on GitHub · 44 lines

Files

What ships with it

23 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.

10d ago First seen · 44 lines · 46 tokens per session scan A ae87ec9e2353

Subscribe to this mod's changes

paper-glossary is a skill published in the GitHub repository 917Dhj/DeepPaperNote (1,051 stars, last pushed 3d ago), licensed MIT. It adds 46 tokens to every session and 1,276 once invoked, about $0.0002 per session on Opus 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 2026-08-30.

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paper-glossary