Pathway Introduction Expert

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.