--- name: biomed-outline-generator description: Generates structured biomedical outlines for review articles, discussion sections, and thesis proposals. Use when a user provides biomedical keywords, results/discussion text, or a proposal title plus background and needs a directly usable academic writing scaffold. license: MIT author: aipoch --- > **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills) # Biomedical Research Outline Generator This is an **Academic Writing** skill for producing manuscript-grade biomedical outlines with deterministic headings and clear section logic. ## Optional Validation Shortcut If you want to confirm the local helper path exists before use: ```bash python scripts/validate_skill.py --check ``` This helper is optional. The primary workflow is still direct outline generation from user input. ## When to Use Use this skill in biomedical contexts when the user wants one of these three outputs: - **Type I: Review Outline** Input pattern: research directions, disease area, pathway keywords, or field description - **Type II: Discussion Outline** Input pattern: results or discussion paragraphs containing observations, models, markers, statistics, or mechanisms - **Type III: Thesis / Proposal Outline** Input pattern: `Title:` plus background, methods expectations, cohort notes, timeline, or validation requirements ## When Not to Use - The request is clearly non-biomedical. - The user wants fabricated results, unsupported claims, or invented citations. - The request is for a complete manuscript draft rather than an outline. ## Required Inputs - A biomedical topic, result paragraph, or proposal title with enough context to determine one of the three supported types. Recommended: - disease model or population - key molecules, pathways, or interventions - study aim or proposal objective - any special formatting or institutional requirements ## Type Recognition Rules ### Type I: Review Outline Use this type when the input is mostly: - topic keywords - field description - research direction Signals: - no explicit `Title:` - no detailed result paragraph - no proposal/timeline language ### Type II: Discussion Outline Use this type when the input contains: - observations or findings - effect sizes or p-values - model systems such as cell, mouse, cohort, or patient data - mechanistic hints and limitations ### Type III: Thesis / Proposal Outline Use this type when the input contains: - `Title:` - proposal framing - background and aims - plan, feasibility, timeline, or expected outcomes If the request is off-domain, stop and use the refusal contract in `## Fallback and Refusal Contract`. ## Output Contract ### Type I: Review Outline Must include: - title - abstract - keywords - introduction - `4-6` major chapters - `2-3` subchapters under each major chapter where appropriate - conclusion / outlook ### Type II: Discussion Outline Must include: - summary of key findings - interpretation blocks - literature integration - limitations - future directions - conclusion ### Type III: Thesis / Proposal Outline Must include: - project review / background - purpose and significance - research plan - feasibility / risk or ethics considerations - innovation - timeline - expected outcomes ## Formatting Rules - Markdown headings only: `#`, `##`, `###` - Stable numeric hierarchy - concise, field-appropriate wording - no placeholder text like `to be added` - no fabricated results or unsupported claims ## Workflow ### 1. Validate domain and sufficiency Confirm that: - the topic is biomedical - there is enough information to classify the request - the requested output is an outline, not a full manuscript ### 2. Detect type Assign Type I, II, or III using the rules above. ### 3. Build the section skeleton Use the output contract for the detected type and keep section order deterministic. ### 4. Enrich with academic logic For each section, add actionable subpoints that reflect: - mechanism - evidence structure - limitations - validation or future work ### 5. Final safety and writing pass Check that: - the outline remains an outline - the tone is biomedical and academic - no claims exceed the source material ## Fallback and Refusal Contract If the input is non-biomedical or too weak to classify, respond with: ```text Cannot generate a biomedical outline yet. Reason: Accepted retry formats: - Review: biomedical keywords or topic direction - Discussion: biomedical results/discussion paragraph - Proposal: `Title:` plus background and objectives ``` ## Validation and Safety Rules - Do not fabricate citations, statistics, or findings. - Do not convert associative findings into causal conclusions unless the source clearly supports that level of language. - For clinically adjacent topics, remain at academic-writing level rather than diagnostic or treatment advice. - Surface ethics, consent, privacy, or cohort-compliance considerations when the prompt clearly implies them. ## Deterministic Output Rules - Keep section order fixed for each type. - Use stable section labels across repeated runs. - If an expected item is missing, ask for it or leave the section high-level; do not hallucinate details. ## Examples of Accepted Inputs ### Type I ```text Research direction: tumor microenvironment, macrophage polarization, immune checkpoint resistance Please generate a review outline. ``` ### Type II ```text In our mouse model, anti-PD-1 reduced tumor burden, but the effect was lost after CSF1 overexpression. Please draft a discussion outline. ``` ### Type III ```text Title: Exosomal miRNAs as early diagnostic biomarkers for Alzheimer's disease Background: include plasma exosomes, qPCR versus small RNA-seq, validation cohort, and neuroinflammation markers. ``` ## Completion Checklist - Type detection is explicit. - Output matches the correct outline contract. - The result is directly usable for academic drafting. - Any limitation or missing-input warning is surfaced clearly.