pathway-introduction-expert

name	pathway-introduction-expert
description	Generates comprehensive academic introductions for biological pathways, including signaling processes, markers, and inhibitors. Use when the user asks to introduce a pathway, molecule, or gene.
license	MIT
author	AIPOCH

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

When to Use

• Use this skill when the request matches its documented task boundary.
• Use it when the user can provide the required inputs and expects a structured deliverable.
• Prefer this skill for repeatable, checklist-driven execution rather than open-ended brainstorming.

Key Features

• Scope-focused workflow aligned to: Generates comprehensive academic introductions for biological pathways, including signaling processes, markers, and inhibitors. Use when the user asks to introduce a pathway, molecule, or gene.
• Packaged executable path(s): scripts/validate_skill.py.
• Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

• Python: 3.10+. Repository baseline for current packaged skills.
• Third-party packages: not explicitly version-pinned in this skill package. Add pinned versions if this skill needs stricter environment control.

Example Usage

cd "20260316/scientific-skills/Evidence Insight/pathway-introduction-expert"
python -m py_compile scripts/validate_skill.py
python scripts/validate_skill.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/validate_skill.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/validate_skill.py.
• 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.

Validation Shortcut

Run this minimal command first to verify the supported execution path:

python scripts/validate_skill.py --help

Pathway Introduction Expert

Workflow

1. Analyze the Request: Identify if the user is asking about a specific Pathway, Molecule, or Gene.
2. Generate Report:
   • Follow the Content Requirements and Output Format below strictly.
   • If the input is a Molecule/Gene, list 5 related pathways first, then choose the most relevant one to introduce.
   • If the input is a Pathway, introduce it directly.

Content Requirements

1. General Introduction

• Focus: Protein interactions and signaling processes.
• Length: No less than 500 words.
• Logic:
  • Pathway Input: Introduce directly.
  • Molecule/Gene Input: List 5 related pathways, then CHOOSE 1 most relevant pathway to introduce.

2. Markers and Key Genes

• List all markers and key genes.
• Provide brief introductions for each.
• Crucial: Describe their detection forms.

3. Agonists and Inhibitors

• List all known agonists.
• List all known inhibitors.

Output Format (Strict)

You MUST answer in Chinese. Translate the following structure and headers into Chinese for the final output:

I. Pathway Introduction
(Content...)

II. Markers and Key Genes
1. Molecule Name; Introduction; Detection Form
2. Molecule Name; Introduction; Detection Form
...
n. Molecule Name; Introduction; Detection Form

III. Agonists and Inhibitors
1. Agonists:
   a.
   b.
   ...
2. Inhibitors:
   a.
   b.
   ...

Example (Structure Reference)

I. Pathway Introduction: The MAPK (Mitogen-Activated Protein Kinase) pathway is a signaling pathway widely present in cells... (Content continues)...

II. Markers: a) ERK1/2 pathway: Ras, Raf... Name Detection Form ERK1/2 Phosphorylation ...

III. Agonists and Inhibitors

1. Agonists: a) Growth factors...
2. Inhibitors: a) ERK1/2 pathway inhibitors: U0126...

When Not to Use

• Do not use this skill when the required source data, identifiers, files, or credentials are missing.
• Do not use this skill when the user asks for fabricated results, unsupported claims, or out-of-scope conclusions.
• Do not use this skill when a simpler direct answer is more appropriate than the documented workflow.

Required Inputs

• A clearly specified task goal aligned with the documented scope.
• All required files, identifiers, parameters, or environment variables before execution.
• Any domain constraints, formatting requirements, and expected output destination if applicable.

Output Contract

• Return a structured deliverable that is directly usable without reformatting.
• If a file is produced, prefer a deterministic output name such as pathway_introduction_expert_result.md unless the skill documentation defines a better convention.
• Include a short validation summary describing what was checked, what assumptions were made, and any remaining limitations.

Validation and Safety Rules

• Validate required inputs before execution and stop early when mandatory fields or files are missing.
• Do not fabricate measurements, references, findings, or conclusions that are not supported by the provided source material.
• Emit a clear warning when credentials, privacy constraints, safety boundaries, or unsupported requests affect the result.
• Keep the output safe, reproducible, and within the documented scope at all times.

Failure Handling

• If validation fails, explain the exact missing field, file, or parameter and show the minimum fix required.
• If an external dependency or script fails, surface the command path, likely cause, and the next recovery step.
• If partial output is returned, label it clearly and identify which checks could not be completed.

Quick Validation

Run this minimal verification path before full execution when possible:

No local script validation step is required for this skill.

Expected output format:

Result file: pathway_introduction_expert_result.md
Validation summary: PASS/FAIL with brief notes
Assumptions: explicit list if any

Deterministic Output Rules

• Use the same section order for every supported request of this skill.
• Keep output field names stable and do not rename documented keys across examples.
• If a value is unavailable, emit an explicit placeholder instead of omitting the field.

Completion Checklist

• Confirm all required inputs were present and valid.
• Confirm the supported execution path completed without unresolved errors.
• Confirm the final deliverable matches the documented format exactly.
• Confirm assumptions, limitations, and warnings are surfaced explicitly.