Unstructured Medical Text Miner (ID: 213)

When to Use

• Use this skill when the task needs Mine unstructured clinical text from MIMIC-IV to extract diagnostic logic.
• 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

See ## Features above for related details.

• Scope-focused workflow aligned to: Mine unstructured clinical text from MIMIC-IV to extract diagnostic logic.
• Packaged executable path(s): scripts/__init__.py plus 1 additional script(s).
• Reference material available in references/ for task-specific guidance.
• Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

pandas>=1.3.0
spacy>=3.4.0
scispacy>=0.5.1
radlex (for radiology terminology)
negspacy (for negation detection)

Example Usage

See ## Usage above for related details.

cd "20260318/scientific-skills/Evidence Insight/unstructured-medical-text-miner"
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/__init__.py with additional helper scripts under scripts/.
• 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
python scripts/main.py -h

Workflow

1. Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work.