Ib Summarizer

Source: https://github.com/aipoch/medical-research-skills

IB Summarizer

When to Use

• Use this skill when the task is to Summarize core safety information from Investigator's Brochures for clinical.
• Use this skill for evidence insight tasks that require explicit assumptions, bounded scope, and a reproducible output format.
• Use this skill when you need a documented fallback path for missing inputs, execution errors, or partial evidence.

Key Features

• Scope-focused workflow aligned to: Summarize core safety information from Investigator's Brochures for clinical.
• Packaged executable path(s): scripts/main.py.
• Reference material available in references/ for task-specific guidance.
• Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

• Python 3.8+
• PyPDF2 / pdfplumber (PDF parsing)
• python-docx (Word parsing)
• Optional: openai / anthropic (for AI-enhanced extraction)

Example Usage

See ## Usage above for related details.

cd "20260318/scientific-skills/Evidence Insight/ib-summarizer"
python -m py_compile scripts/main.py
python scripts/main.py --help

Example run plan:

1. Confirm the user input, output path, and any required config values.
2. Edit the in-file CONFIG block or documented parameters if the script uses fixed settings.
3. Run python scripts/main.py with the validated inputs.
4. Review the generated output and return the final artifact with any assumptions called out.

Implementation Details

See ## Workflow above for related details.

• Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
• Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
• Primary implementation surface: scripts/main.py.
• Reference guidance: references/ contains supporting rules, prompts, or checklists.
• Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
• Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.

Quick Check

Use this command to verify that the packaged script entry point can be parsed before deeper execution.

python -m py_compile scripts/main.py

Audit-Ready Commands

Use these concrete commands for validation. They are intentionally self-contained and avoid placeholder paths.

python -m py_compile scripts/main.py
python scripts/main.py --help

Workflow

1. Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work.
2. Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions.
3. Use the packaged script path or the documented reasoning path with only the inputs that are actually available.
4. Return a structured result that separates assumptions, deliverables, risks, and unresolved items.
5. If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.

Description

Summarize core safety information from Investigator's Brochures (IB), helping clinical researchers quickly obtain key drug safety data.

Functions

• Extract Core Safety Information (CSI) from IB documents
• Identify and summarize:
  • Known Adverse Drug Reactions (ADRs) and their incidence rates
  • Contraindications
  • Warnings and Precautions
  • Drug Interactions
  • Special population precautions
  • Overdose Management
  • Important safety updates

Usage

python scripts/main.py <input_file> [options]

Parameters

Examples

# Basic usage
python scripts/main.py /path/to/IB.pdf

# Output to JSON file
python scripts/main.py /path/to/IB.pdf -o summary.json -f json

# English output
python scripts/main.py /path/to/IB.docx -l en -o summary.md

Output Structure

Markdown Format

# IB Safety Information Summary

## Basic Drug Information
- **Drug Name**: XXX
- **Version**: X.X
- **Date**: YYYY-MM-DD

## Core Safety Information

### Known Adverse Reactions
| System Organ Class | Adverse Reaction | Incidence | Severity |
|-------------|---------|--------|---------|
| ... | ... | ... | ... |

### Contraindications
- ...

### Warnings and Precautions
- ...

### Drug Interactions
- ...

### Special Populations
| Population | Precautions |
|-----|---------|
| Pregnant women | ... |
| Lactating women | ... |
| Children | ... |
| Elderly | ... |
| Hepatic/renal impairment | ... |

### Overdose
- Symptoms: ...
- Management: ...

### Safety Update History
| Version | Date | Update Content |
|-----|------|---------|
| ... | ... | ... |

JSON Format

{
  "drug_info": {
    "name": "Drug Name",
    "version": "Version Number",
    "date": "Date"
  },
  "core_safety_info": {
    "adverse_reactions": [...],
    "contraindications": [...],
    "warnings": [...],
    "drug_interactions": [...],
    "special_populations": {...},
    "overdose": {...},
    "safety_updates": [...]
  }
}

Installation

pip install -r requirements.txt

Notes

1. Input documents should be readable PDF or Word format
2. Scanned PDFs require OCR processing first
3. For complex table structures, manual verification may be needed
4. Information extracted by this tool is for reference only and does not constitute medical advice

Risk Assessment