Source: 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:
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 chapters2-3 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:
Cannot generate a biomedical outline yet.
Reason: <non-biomedical input / insufficient context / unsupported request>
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
Research direction: tumor microenvironment, macrophage polarization, immune checkpoint resistance
Please generate a review outline.
Type II
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
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.