Agent-Skills.md

Agent Skills: Synthesis

Synthesize all accumulated notes and drafts to generate the Discussion and Abstract sections. Sixth step of writer workflow. Requires all notes/*.md files and drafts/introduction.md, methods.md, results.md.

UncategorizedID: sxg/biomedical-science-writer/synthesis

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pnpm dlx add-skill https://github.com/sxg/science/tree/HEAD/plugins/writer/skills/synthesis

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plugins/writer/skills/synthesis/SKILL.md

Skill Metadata

Name
synthesis
Description
Synthesize all accumulated notes and drafts to generate the Discussion and Abstract sections. Sixth step of writer workflow. Requires all notes/*.md files and drafts/introduction.md, methods.md, results.md.

Synthesis

Integrates all accumulated notes and prior drafts to generate the Discussion and Abstract sections, connecting findings to the broader literature.

Prerequisites

Required files:

  • scope.md - Research question and key findings
  • notes/papers/*.md - Literature notes (from user-provided PDFs)
  • notes/literature-synthesis.md - Aggregated themes and findings (key input!)
  • notes/code-analysis.md - Methods context
  • notes/data-analysis.md - Results context
  • drafts/introduction.md - For narrative continuity
  • drafts/methods.md - For methodological context
  • drafts/results.md - Findings to discuss

Workflow

[Load all notes and drafts]
     │
     ▼
[Map findings to literature] ─── What supports/contradicts
     │
     ▼
[Draft Discussion] ─── Interpret, compare, contextualize
     │
     ▼
[Draft Abstract] ─── Structured summary
     │
     ▼
[Output] ─── drafts/discussion.md, drafts/abstract.md

Step 1: Load and Organize Materials

Read Literature Synthesis (Primary Reference)

Start with notes/literature-synthesis.md - this document already contains:

  • Paper Citation Tracker — Shows which papers have planned citations and which need review
  • Source inventory with relationships to our work
  • Key themes identified across all papers
  • Findings that support our hypothesis
  • Contradictory findings to address
  • Methodological patterns
  • Gaps our study addresses
  • Citation map showing foundational papers
  • Implications for Discussion section

This synthesis is the primary guide for drafting the Discussion.

Review Paper Citation Tracker

Check the Paper Citation Tracker table to see which papers have natural fits planned. Use these as your citation guide.

Important: Only cite papers where they contribute meaningfully. Do not:

  • Add sentences solely to include a citation
  • Force parenthetical references that interrupt flow
  • Stretch to make a paper seem relevant when it isn't

Papers marked "Not Applicable" in the tracker should remain uncited. A focused manuscript with relevant citations is better than a cluttered one that forces every paper.

Read All Notes

ls notes/papers/*.md notes/*.md

Use individual paper notes for specific quotes and statistics.

Mapping from Literature Synthesis

The synthesis document provides:

  • Which sources support our findings
  • Which sources provide contrasting results
  • Which sources explain mechanisms
  • Which sources address limitations

Extract Key Results

From drafts/results.md and notes/data-analysis.md:

  • Primary finding (statistic and interpretation)
  • Secondary findings
  • Unexpected results
  • Null findings (if any)

Review Scope

From scope.md:

  • Research question being answered
  • Hypothesis (was it supported?)
  • Limitations to address

Step 2: Map Findings to Literature

Use notes/literature-synthesis.md as the starting point - it already contains:

  • "Findings That Support Our Hypothesis" table
  • "Contradictory or Conflicting Findings" table
  • "Implications for Discussion" section

Extend this mapping with our actual results from drafts/results.md:

| Our Finding | Supporting Literature | Contrasting Literature | Notes | |-------------|----------------------|------------------------|-------| | [Primary result] | [from synthesis] | [from synthesis] | [why contrast] | | [Secondary result] | [from synthesis] | None | |

For each finding, the synthesis document identifies:

  1. Agreement: Papers with similar findings
  2. Disagreement: Papers with different findings (explain why)
  3. Mechanism: Papers that explain why this occurs
  4. Clinical relevance: Papers that contextualize importance

Step 3: Draft Discussion

Create drafts/discussion.md following this structure:

Discussion Structure (6-7 paragraphs)

# Discussion

## Principal Findings (Paragraph 1)

[Open with main finding - interpret, don't just restate]

This study demonstrates that [interpretation of primary finding]. 
[Connect to research question from scope.md].
[One sentence on significance].

## Comparison with Literature (Paragraphs 2-3)

[Compare findings to existing work]

Our findings are consistent with [Author et al.], who reported [finding] [citation]. 
Similarly, [Author2 et al.] demonstrated [related finding] [citation].

[Address any discrepancies]

In contrast to [Author3 et al.], who found [different result] [citation], our study suggests [explanation]. 
This difference may be attributed to [methodological differences, population differences, etc.].

## Mechanistic Interpretation (Paragraph 4)

[Explain WHY these results might occur]

These findings may reflect [biological/clinical mechanism]. 
[Author et al.] previously showed that [mechanistic evidence] [citation], 
which supports the hypothesis that [explanation].

[If speculative, use appropriate hedging: "may", "might", "could potentially"]

## Clinical/Practical Implications (Paragraph 5)

[What does this mean for practice?]

These results have several implications for [clinical practice / research / etc.].
First, [implication 1].
Second, [implication 2].
[If applicable: These findings suggest that clinicians should consider...]

## Limitations (Paragraph 6)

[Honest but constructive discussion of limitations]

This study has several limitations that should be considered.
First, [limitation 1 with mitigation if possible].
Second, [limitation 2].
[Frame constructively: "While [limitation], [mitigating factor]..."]

Common limitations to address:
- Sample size
- Single-center
- Retrospective design
- Selection bias
- Technical limitations
- Generalizability

## Future Directions (Paragraph 7)

[What should come next?]

Future studies should [specific actionable suggestion].
Prospective validation in [population] is warranted.
Additionally, [another future direction].

---

## Discussion References

[List all citations used in Discussion with note references]

Writing Guidelines

  • Present tense: General truths ("MRI enables...")
  • Past tense: Specific studies ("Smith et al. found...")
  • Hedging: Match to evidence strength
  • No new data: All statistics should be in Results

Literature Integration Phrases

Agreement:

  • "Consistent with prior work [X], we found..."
  • "Our findings support those of [X], who demonstrated..."
  • "In line with [X], our results indicate..."

Disagreement:

  • "In contrast to [X], our study suggests..."
  • "Unlike [X], who reported..., we found..."
  • "Our results differ from [X], possibly due to..."

Extension:

  • "Our findings extend those of [X] by demonstrating..."
  • "Building on work by [X], we show..."
  • "While [X] established..., our study further demonstrates..."

Step 4: Draft Abstract

Create drafts/abstract.md:

# Abstract

## Background/Purpose
[2-3 sentences: Gap in knowledge + study objective]

[Clinical/scientific problem]. [What is unknown]. The purpose of this study was to [objective].

## Methods
[3-4 sentences: Design, population, key methods, statistics]

This [study design] included [n] patients from [setting]. [Key methods]. [Primary outcome measure]. [Statistical approach].

## Results  
[3-4 sentences: Key findings with numbers]

[Primary finding with statistics]. [Secondary finding]. [Additional notable result].

## Conclusion
[1-2 sentences: Main takeaway + implication]

[Main conclusion]. [Clinical/research implication].

---

**Word Count**: [count]
**Keywords**: [keyword1], [keyword2], [keyword3], [keyword4], [keyword5]

Abstract Guidelines

  • Standalone: Understandable without reading paper
  • Specific: Include key numbers (n, primary statistic, p-value)
  • Consistent: Match paper content exactly
  • Past tense: Throughout (this study was conducted)
  • No citations: Never cite in abstract
  • No abbreviations: Or define on first use

Word Count Targets

| Section | Target | |---------|--------| | Background | 50-75 words | | Methods | 75-100 words | | Results | 75-100 words | | Conclusion | 25-50 words | | Total | ~250-300 words |

Adjust based on scope.md target journal requirements.

Step 5: Generate Title Options

Based on synthesis, suggest 2-3 title options:

## Suggested Titles

1. [Descriptive]: "[Method/Approach] for [Application]: [Key Finding]"
   
2. [Question-answer]: "[Research Question]? A [Study Type]"
   
3. [Finding-focused]: "[Key Finding] in [Population] Using [Method]"

Title guidelines:

  • 10-15 words maximum
  • No abbreviations (usually)
  • Informative > clever
  • Include key method and finding if possible

Step 6: Document Paper Usage

Record which papers were cited and which were not.

Update Citation Summary

Update notes/literature-synthesis.md with final citation status:

## Citation Summary

**Generated**: [timestamp]
**Total Papers Provided**: [n]
**Papers Cited**: [n]
**Papers Not Used**: [n]

### Cited Papers

| # | Citation | Section | Purpose |
|---|----------|---------|---------|
| 1 | Smith et al., 2023 | Introduction | Establishes prevalence |
| 2 | Jones et al., 2022 | Discussion | Comparable methodology |

### Papers Not Used

| Paper | Reason |
|-------|--------|
| Brown et al., 2020 | Different population; not directly comparable |
| Lee et al., 2019 | Tangential to our research question |

Note: Not using a paper is acceptable when it doesn't naturally fit. The goal is manuscript quality, not citation count.

Output

Save to:

  • drafts/discussion.md - Discussion section
  • drafts/abstract.md - Structured abstract with title options
  • notes/literature-synthesis.md - Updated with Citation Summary

Return to parent skill with summary:

  • Discussion word count: [n]
  • Abstract word count: [n]
  • Papers cited: [n] of [n] provided
  • Title options: [n]