What is reaction-data-extraction?

A chemistry document-extraction tool that reads research-paper PDFs and turns reaction details into structured CSV or JSON data. It can extract substances, catalysts, solvents, temperatures, times, pressures, and yields.

Use it to extract and organize reaction conditions from one or many chemistry papers, with reaction types and a confidence score for each result.

It reduces the manual work of copying reaction conditions from paragraphs and optimization tables into spreadsheets.

reaction-data-extraction — Skill for Claude Code and Codex by InternScience: A chemistry document-extraction tool that reads research-paper

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.

agentmods

npx agentmods add skills/internscience/chemclaw/reaction-data-extraction

Any agent

npx skills add InternScience/ChemClaw --skill reaction-data-extraction

Clone the repo

git clone --depth 1 https://github.com/InternScience/ChemClaw

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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/internscience/chemclaw/reaction-data-extraction.svg)](https://agentmods.dev/skills/internscience/chemclaw/reaction-data-extraction)

Your own site

<a href="https://agentmods.dev/skills/internscience/chemclaw/reaction-data-extraction"><img src="https://agentmods.dev/badge/skills/internscience/chemclaw/reaction-data-extraction.svg" alt="Measured on agentmods" height="20"></a>

Per session 75 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 4,554 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 1 finding. Scan, not verified.

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	$0.00075	$0.04554
Opus 5	$0.00037	$0.02277
Sonnet 5	$0.00015	$0.00911
Haiku 4.5	$0.00007	$0.00455

Measured 5d ago against content hash f0c4aa1b9d71, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

reaction-data-extraction scanned grade A with 1 finding 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 5d ago.

The scan reads SKILL.md. This mod also ships 3 executable files (scripts/extract_jacs_paper.py, scripts/reaction_data_extraction.py, scripts/test_extraction.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.

Runs shell commandslowCapability

Expected in a hook, worth knowing in a rule or an instructions file.

result = subprocess.run(cmd, capture_output=True, text=True, timeout=600)

skills/reaction-data-extraction/SKILL.md · 476 lines

How it starts

The opening of the file, as written. The whole thing — 476 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Reaction Data Extraction

从化学文献 PDF 中精确提取化学反应数据，特别是反应条件优化信息。支持提取反应物、产物、催化剂、溶剂、温度、时间、产率等关键信息，并输出结构化的 CSV/JSON 文件。

触发条件

用户提供 PDF 文献并要求提取反应数据
提到"提取反应条件"、"反应优化数据"
说"extract reaction conditions"、"reaction data from PDF"
需要从文献中整理反应表格
需要批量提取多篇文献的反应数据

功能特性

✅ 反应物/产物识别 - 自动提取反应物和产物的 SMILES/名称
✅ 反应条件提取 - 催化剂、配体、溶剂、添加剂
✅ 参数提取 - 温度、时间、压力、浓度
✅ 产率提取 - 分离产率、GC 产率、NMR 产率
✅ 反应类型识别 - 偶联、氧化、还原、环化等
✅ 表格数据提取 - 从反应条件优化表格中提取数据
✅ 支持体内容 - 从正文段落中提取反应描述
✅ 结构化输出 - CSV/JSON 格式，便于后续分析
✅ 批量处理 - 支持多篇文献批量提取
✅ 置信度评分 - 每个提取结果附带置信度

核心技术

组件	用途
MinerU	PDF 解析和文本提取 (命令行调用)
正则表达式	反应条件模式匹配
Rule-based Parser	反应句子解析
表格解析器	Markdown 表格→反应数据

提取的数据字段

字段	说明	示例
`reaction_id`	反应唯一标识	`RXN_001`
`entry`	表格中的条目号	`1`, `2`, `3`
`reactants`	反应物 (SMILES 或名称)	`c1ccccc1Br`
`products`	产物 (SMILES 或名称)	`c1ccccc1-c2ccccc2`
`catalyst`	催化剂	`Pd(PPh3)4`
`ligand`	配体	`PPh3`
`base`	碱	`K2CO3`
`solvent`	溶剂	`DMF`, `Toluene`
`temperature`	温度	`80 °C`, `rt`, `reflux`
`time`	反应时间	`12 h`, `30 min`
`pressure`	压力 (如有)	`1 atm`, `10 bar`
`concentration`	浓度	`0.1 M`
`yield_value`	产率数值	`85`
`yield_type`	产率类型	`isolated`, `GC`, `NMR`
`ee_value`	对映选择性	`99%`, `>99%`
`reaction_type`	反应类型	`Suzuki coupling`
`scheme_number`	反应式编号	`Scheme 1`, `Table 2`
`page_number`	页码	`5`
`confidence`	提取置信度	`0.95`
`notes`	备注	`optimized condition`

使用方法

对话框中使用

从这篇 PDF 提取所有反应条件
提取反应优化数据并生成 CSV
extract reaction data from this paper
把文献中的反应表格整理成 Excel
提取 Suzuki 偶联反应的条件

命令行使用

# 基本提取（自动模式）
python3 scripts/reaction_data_extraction.py -i paper.pdf -o ./output

# 只提取表格数据
python3 scripts/reaction_data_extraction.py -i paper.pdf -o ./output --tables-only

# 只提取体内容反应
python3 scripts/reaction_data_extraction.py -i paper.pdf -o ./output --text-only

# 批量处理
python3 scripts/reaction_data_extraction.py -i ./papers/ -o ./output --batch

# JSON 输出
python3 scripts/reaction_data_extraction.py -i paper.pdf -o ./output --output-format json

# 详细模式
python3 scripts/reaction_data_extraction.py -i paper.pdf -o ./output -v

# 使用 OCR 处理扫描版
python3 scripts/reaction_data_extraction.py -i scanned.pdf -o ./output --method ocr

Read the full file on GitHub · 476 lines

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.

5d ago First seen · 476 lines · 75 tokens per session scan A f0c4aa1b9d71

Subscribe to this mod's changes

reaction-data-extraction is a skill published in the GitHub repository InternScience/ChemClaw (52 stars, last pushed 5mo ago), licensed MIT. It adds 75 tokens to every session and 4,554 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 1 finding (runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Documents PDF Scientific

pydicom

Use pydicom to read, inspect, write, transform, and safely preflight local DICOM datasets and pixel data. Applies to DICOM metadata, transfer syntaxes, compression plugins, frames, private elements, JSON, and bounded de-identification review.

K-Dense-AI/scientific-agent-skills · 56 tokens

pptx-posters

Create and audit editable scientific posters in macro-free PowerPoint (.pptx) from author-approved local content and assets. Use when the requested deliverable is a PowerPoint research/conference poster and exact physical, printer, accessibility, provenance, and package-security checks are required.

K-Dense-AI/scientific-agent-skills · 59 tokens

extracting-lab-tables

Detects and extracts tabular laboratory panels from PDFs, scans, and images into structured rows ready for OpenMed and FHIR. Use when the user has a CBC, CMP, lipid panel, or other lab report as a scanned image / PDF / spreadsheet and needs the test name, value, unit, reference range, and abnormal flag as clean rows.…

maziyarpanahi/openmed · 210 tokens

reaction-data-extraction