protocol-extraction-from-pdf
Extract laboratory protocols from PDF documents using Thoth-Plan to convert experimental procedures into structured text.
Best use case
protocol-extraction-from-pdf is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
Extract laboratory protocols from PDF documents using Thoth-Plan to convert experimental procedures into structured text.
Teams using protocol-extraction-from-pdf should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/protocol-extraction-from-pdf/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How protocol-extraction-from-pdf Compares
| Feature / Agent | protocol-extraction-from-pdf | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
Extract laboratory protocols from PDF documents using Thoth-Plan to convert experimental procedures into structured text.
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
SKILL.md Source
# Protocol Extraction from PDF
## Usage
```python
import asyncio
import json
from contextlib import AsyncExitStack
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._stack = AsyncExitStack()
await self._stack.__aenter__()
self.read, self.write, self.get_session_id = await self._stack.enter_async_context(self.transport)
self.session_ctx = ClientSession(self.read, self.write)
self.session = await self._stack.enter_async_context(self.session_ctx)
await self.session.initialize()
return True
except Exception as e:
return False
async def disconnect(self):
"""Disconnect from server"""
try:
if hasattr(self, '_stack'):
await self._stack.aclose()
print("✓ already disconnect")
except Exception as e:
print(f"✗ disconnect error: {e}")
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
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- Lab protocol digitization, SOP extraction, experimental workflow documentationRelated Skills
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