Agent skill

Protocol Extraction From PDF

Extract laboratory protocols from PDF documents using Thoth-Plan to convert experimental procedures into structured text.

MITAuto-check passedDocuments & Office

Install Protocol Extraction From PDF

skills CLI

$ npx skills add InternScience/scp --skill protocol-extraction-from-pdf -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install InternScience/scp protocol-extraction-from-pdf --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/protocol-extraction-from-pdf .claude/skills/protocol-extraction-from-pdf && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "protocol-extraction-from-pdf" agent skill from https://github.com/InternScience/scp/tree/main/skills/protocol-extraction-from-pdf into .claude/skills/protocol-extraction-from-pdf/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protocol-extraction-from-pdf", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/InternScience/scp/tree/main/skills/protocol-extraction-from-pdf

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add InternScience/scp --skill protocol-extraction-from-pdf -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install InternScience/scp protocol-extraction-from-pdf --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/protocol-extraction-from-pdf .agents/skills/protocol-extraction-from-pdf && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "protocol-extraction-from-pdf" agent skill from https://github.com/InternScience/scp/tree/main/skills/protocol-extraction-from-pdf into .agents/skills/protocol-extraction-from-pdf/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protocol-extraction-from-pdf", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add InternScience/scp --skill protocol-extraction-from-pdf -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install InternScience/scp protocol-extraction-from-pdf --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/protocol-extraction-from-pdf .cursor/skills/protocol-extraction-from-pdf && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "protocol-extraction-from-pdf" agent skill from https://github.com/InternScience/scp/tree/main/skills/protocol-extraction-from-pdf into .cursor/skills/protocol-extraction-from-pdf/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protocol-extraction-from-pdf", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/InternScience/scp.git --path skills/protocol-extraction-from-pdf

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add InternScience/scp --skill protocol-extraction-from-pdf -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install InternScience/scp protocol-extraction-from-pdf --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/protocol-extraction-from-pdf .gemini/skills/protocol-extraction-from-pdf && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "protocol-extraction-from-pdf" agent skill from https://github.com/InternScience/scp/tree/main/skills/protocol-extraction-from-pdf into .gemini/skills/protocol-extraction-from-pdf/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protocol-extraction-from-pdf", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install InternScience/scp protocol-extraction-from-pdf

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add InternScience/scp --skill protocol-extraction-from-pdf -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/protocol-extraction-from-pdf .github/skills/protocol-extraction-from-pdf && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "protocol-extraction-from-pdf" agent skill from https://github.com/InternScience/scp/tree/main/skills/protocol-extraction-from-pdf into .github/skills/protocol-extraction-from-pdf/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protocol-extraction-from-pdf", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add InternScience/scp --skill protocol-extraction-from-pdf -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install InternScience/scp protocol-extraction-from-pdf --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/protocol-extraction-from-pdf .opencode/skills/protocol-extraction-from-pdf && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "protocol-extraction-from-pdf" agent skill from https://github.com/InternScience/scp/tree/main/skills/protocol-extraction-from-pdf into .opencode/skills/protocol-extraction-from-pdf/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protocol-extraction-from-pdf", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: protocol-extraction-from-pdf
GitHub stars: 169
Used in: 1 other repo
Token cost: ~589 tokens
SKILL.md length: 32 words
Files: 1
Skills in repo: 73
Repo updated: Jun 3, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Extract laboratory protocols from PDF documents using Thoth-Plan to convert experimental procedures into structured text.

Tasks that involve PDF
Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Protocol Extraction From PDF is an agent skill from InternScience/scp. Extract laboratory protocols from PDF documents using Thoth-Plan to convert experimental procedures into structured text.

Its SKILL.md is about 590 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Documents & Office, covering PDF. The licence is MIT.

When your agent uses it

Tasks that involve PDF

Example prompts

“/protocol-extraction-from-pdf”

Requirements

Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit cea5398. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md (its code samples are python).
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Protocol Extraction From PDF loads about 589 tokens when it runs. Until then it costs about 38 tokens; SKILL.md has 32 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~38
When it runs · the whole SKILL.md, loaded when a task matches: ~589

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from InternScience/scp at commit cea5398, republished under its MIT licence (© InternScience). 32 words, ~589 tokens.

Download SKILL.mdSave it as .claude/skills/protocol-extraction-from-pdf/SKILL.md (or your agent's skills folder).

name: protocol-extraction-from-pdf
description: Extract laboratory protocols from PDF documents using Thoth-Plan to convert experimental procedures into structured text.
license: MIT license
metadata.skill-author: PJLab

Protocol Extraction from PDF

Usage

python

import asyncio
import json
from mcp.client.streamable_http import streamablehttp_client
from mcp import ClientSession

class ThothClient:
    def __init__(self, server_url: str):
        self.server_url = server_url
        self.session = None

    async def connect(self):
        try:
            self.transport = streamablehttp_client(url=self.server_url, sse_read_timeout=60 * 10)
            self.read, self.write, self.get_session_id = await self.transport.__aenter__()
            self.session_ctx = ClientSession(self.read, self.write)
            self.session = await self.session_ctx.__aenter__()
            await self.session.initialize()
            return True
        except Exception as e:
            return False

    async def disconnect(self):
        if self.session:
            await self.session_ctx.__aexit__(None, None, None)
        if hasattr(self, 'transport'):
            await self.transport.__aexit__(None, None, None)

    def parse_result(self, result):
        try:
            if hasattr(result, 'content') and result.content:
                content = result.content[0]
                if hasattr(content, 'text'):
                    return json.loads(content.text)
            return str(result)
        except:
            try:
                return result.content[0].text
            except:
                return {"error": "parse error", "raw": str(result)}

## Initialize and use
client = ThothClient("https://scp.intern-ai.org.cn/api/v1/mcp/19/Thoth-Plan")
await client.connect()

# PDF URL (must be publicly accessible)
pdf_url = "https://example.com/protocol.pdf"

result = await client.session.call_tool("extract_protocol_from_pdf", arguments={"pdf_url": pdf_url})
protocol = client.parse_result(result)
print("Extracted Protocol:")
print(protocol)

await client.disconnect()

Tool: `extract_protocol_from_pdf`

Args: pdf_url (str) - Public URL to PDF file
Returns: Structured protocol text with numbered steps

Use Cases

Lab protocol digitization, SOP extraction, experimental workflow documentation

Files

Just SKILL.md in skills/protocol-extraction-from-pdf of InternScience/scp.

Open the folder on GitHubat commit cea5398

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in InternScience/scp, which our catalogue first saw on October 7, 2026.

SpectrAI-Initiative/InnoClaw.claude/skills/protocol-extraction-from-pdf

Compare with similar skills

Protocol Extraction From PDF next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Protocol Extraction From PDF compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Protocol Extraction From PDF this skillInternScience/scp	169	1 repos	~589	Automated safety check: Pass	MIT	4 mo ago
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Gzh Designisjiamu/gzh-design-skill	3.9k	1 repos	~2.2k	Automated safety check: Pass	AGPL-3.0	4 days ago
GenOffice Document CLIgenspark-ai/genoffice	8.8k	—	~19k	Automated safety check: Pass	Apache-2.0	yesterday
Harness Book Best Practicewquguru/harness-books	3.2k	—	~4.1k	Automated safety check: Pass	None	5 mo ago
Bookforge Korean Ebook PDF Makergongnyang/bookforge	314	1 repos	~1.7k	Automated safety check: Pass	MIT	1 mo ago

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Questions about Protocol Extraction From PDF

What does Protocol Extraction From PDF do?

Extract laboratory protocols from PDF documents using Thoth-Plan to convert experimental procedures into structured text. Protocol Extraction From PDF is an agent skill from InternScience/scp. Extract laboratory protocols from PDF documents using Thoth-Plan to convert experimental procedures into structured text.

When should I use Protocol Extraction From PDF?

Protocol Extraction From PDF fits situations like: tasks that involve PDF.

How do I install Protocol Extraction From PDF in Claude Code?

Run `npx skills add InternScience/scp --skill protocol-extraction-from-pdf -a claude-code`. Or copy the skill folder (skills/protocol-extraction-from-pdf in InternScience/scp) into .claude/skills/protocol-extraction-from-pdf in your project. Claude Code loads it when a task matches its description.

How do I install Protocol Extraction From PDF in Codex?

Run `npx skills add InternScience/scp --skill protocol-extraction-from-pdf -a codex`. Or copy the skill folder (skills/protocol-extraction-from-pdf in InternScience/scp) into .agents/skills/protocol-extraction-from-pdf in your project. Codex loads it when a task matches its description.

Can I use Protocol Extraction From PDF in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add InternScience/scp --skill protocol-extraction-from-pdf -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/protocol-extraction-from-pdf, .gemini/skills/protocol-extraction-from-pdf, .github/skills/protocol-extraction-from-pdf and .opencode/skills/protocol-extraction-from-pdf in your project.

What does Protocol Extraction From PDF need to run?

SKILL.md names no scripts, command-line tools or credentials: Protocol Extraction From PDF is instructions for the agent only. Our summary lists: Python 3.

Does Protocol Extraction From PDF access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Protocol Extraction From PDF safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Protocol Extraction From PDF use?

Protocol Extraction From PDF is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Protocol Extraction From PDF use?

About 589 tokens (SKILL.md is roughly 2.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Protocol Extraction From PDF?

Skills that share tags, products or a category with Protocol Extraction From PDF: Markitdown (ImCa0/just-laws, 781 stars), Gzh Design (isjiamu/gzh-design-skill, 3.9k stars), GenOffice Document CLI (genspark-ai/genoffice, 8.8k stars) and Harness Book Best Practice (wquguru/harness-books, 3.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Protocol Extraction From PDF?

InternScience (a GitHub organization) maintains it in InternScience/scp, which has 169 GitHub stars. The repository holds 73 skills in this directory. The repository was last updated on June 3, 2026.

Source: InternScience/scp on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Protocol Extraction From PDF

Install Protocol Extraction From PDF

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Protocol Extraction from PDF

Usage

Tool: `extract_protocol_from_pdf`

Use Cases

Files

Used in 1 other repository

Compare with similar skills

Similar skills

Markitdown

Gzh Design

GenOffice Document CLI

Harness Book Best Practice

Bookforge Korean Ebook PDF Maker

Instrument Data To Allotrope

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Questions about Protocol Extraction From PDF

Install Protocol Extraction From PDF

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Protocol Extraction from PDF

Usage

Tool: extract_protocol_from_pdf

Use Cases

Files

Used in 1 other repository

Compare with similar skills

Similar skills

More from InternScience/scp

Related

Questions about Protocol Extraction From PDF

Tool: `extract_protocol_from_pdf`