agentmods.dev

scientific-papers-to-dataset

scientific-papers-to-dataset is a skill for Claude Code, Codex from eamag/papers2dataset. It costs 47 tokens per session (1,246 once invoked), scanned C, original, no licence file.

A tool for turning scientific papers into structured datasets. It can search OpenAlex, follow citation links between papers, and extract data from PDF documents; bioRxiv, for example, is a public website for sharing biology research papers before formal peer review.

In plain words
What is it for?
Collecting paper metadata, traversing citation networks, and extracting structured information from scientific literature.
Why use it?
Research information is often spread across papers, PDFs, and citation lists. This helps organize that material into data that can be searched or analyzed.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

not rated 22repo 9mo ago C scan 47 tokens no licence

Good fit Collecting paper metadata, traversing citation networks, and extracting structured information from scientific literature.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/eamag/papers2dataset/skill
View source ↗ eamag/papers2dataset eamag.me
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 eamag/papers2dataset --skill skill
Clone the repo
git clone --depth 1 https://github.com/eamag/papers2dataset

Made for: Claude Code, Codex.

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 scientific-papers-to-dataset

README.md
[![agentmods](https://agentmods.dev/badge/skills/eamag/papers2dataset/skill/github.svg)](https://agentmods.dev/skills/eamag/papers2dataset/skill)
Your own site
<a href="https://agentmods.dev/skills/eamag/papers2dataset/skill"><img src="https://agentmods.dev/badge/skills/eamag/papers2dataset/skill/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 scientific-papers-to-dataset

Your own site · 80×15
<a href="https://agentmods.dev/skills/eamag/papers2dataset/skill"><img src="https://agentmods.dev/badge/skills/eamag/papers2dataset/skill.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 47 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,246 The whole file, excluding the scripts and references it only reads on demand.
Security scan C 2 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown 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 $0.00047 $0.01246
Opus 5.5 $0.00019 $0.00498
Sonnet 5.5 $0.00009 $0.00249
Haiku 4.5 $0.00005 $0.00125

Measured 2mo ago against content hash c223ab7fa0d5, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade C, and why

scientific-papers-to-dataset scanned grade C with 2 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 2mo ago.

The scan reads SKILL.md. This mod also ships 3 executable files (scripts/bfs_queue.py, scripts/download_pdf.py, scripts/search_openalex.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.

Downloads and executes remote codehighSupply chain

curl | sh runs whatever the server returns today, which is not necessarily what it returned when this was reviewed.

- Install uv (`curl -LsSf https://astral.sh/uv/install.sh | sh`) and use Python directly

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

- Install uv (`curl -LsSf https://astral.sh/uv/install.sh | sh`) and use Python directly
skill/SKILL.md · 167 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

Read it on GitHub

Files

What ships with it

5 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. 2mo ago First seen · 167 lines · 47 tokens per session scan C c223ab7fa0d5

Subscribe to this mod's changes

scientific-papers-to-dataset is a skill published in the GitHub repository eamag/papers2dataset (22 stars, last pushed 9mo ago), with no licence file. It adds 47 tokens to every session and 1,246 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it C with 2 findings (downloads and executes remote code, makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

ResearchScienceScientificai-agentsai4science
Related

scientific-papers-to-dataset compared with skills from other repositories

scientific-papers-to-dataset next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
scientific-papers-to-dataseteamag/papers2datasetSkill229mo agononeC47Claude Code, Codex
bio-ortholog-inferencePKU-YuanGroup/OpenAI4SSkill6623d agoMITA141Claude Code, Codex
bioprobenchPKU-YuanGroup/OpenAI4SSkill6623d agoMITA46Claude Code, Codex
paper-planningEvoScientist/EvoSkillsSkill48610d agoApache-2.0A166Claude Code
evo-memoryEvoScientist/EvoSkillsSkill48610d agoApache-2.0A186Claude Code
paper-reviewEvoScientist/EvoSkillsSkill48610d agoApache-2.0A200Claude Code
onescience-research-workflowonescience-ai/OneSkillsSkill24yesterdayMITA95Claude Code