Literature Review

Processes user-provided PDFs one at a time using isolated subagents to prevent context overflow, then synthesizes findings and drafts the Introduction section.

CRITICAL CONSTRAINTS

┌────────────────────────────────────────────────────────────────────┐ │ ⛔ ORCHESTRATOR MUST NEVER READ PDF FILES DIRECTLY ⛔ │ │ │ │ The orchestrator (you, running this skill) may ONLY read: │ │ - scope.md │ │ - inventory.md │ │ - notes/ethics-summary.md │ │ - notes/papers/*.md (the condensed notes, NOT PDFs) │ │ - notes/bibliography.md │ │ - notes/literature-synthesis.md │ │ │ │ If you find yourself about to use the Read tool on a .pdf file, │ │ STOP. Spawn a subagent instead. │ ├────────────────────────────────────────────────────────────────────┤ │ ⛔ EACH SUBAGENT PROCESSES EXACTLY ONE PAPER ⛔ │ │ │ │ - One Task tool call = One PDF │ │ - Never pass multiple PDFs to a single subagent │ │ - Never ask a subagent to "process the remaining papers" │ │ - Wait for each subagent to complete before spawning the next │ │ │ │ WRONG: Task("Process papers/a.pdf, papers/b.pdf, papers/c.pdf") │ │ RIGHT: Task("Process papers/a.pdf") → wait → Task("Process b.pdf")│ └────────────────────────────────────────────────────────────────────┘

Architecture: Subagent Pattern

Each paper is processed by an isolated subagent to prevent context overflow:

┌─────────────────────────────────────────────────────────────────┐ │ LITERATURE REVIEW WORKFLOW │ ├─────────────────────────────────────────────────────────────────┤ │ │ │ [ORCHESTRATOR] │ │ │ │ │ ├──► Read scope.md (extract research context) │ │ │ │ │ ├──► List papers/.pdf │ │ │ │ │ ├──► For each PDF, spawn isolated subagent: │ │ │ │ │ │ │ ├──► [Subagent] Read ONE PDF │ │ │ ├──► [Subagent] Generate notes/papers/.md │ │ │ └──► [Subagent] Exit (context cleared) │ │ │ │ │ ├──► Read all notes/papers/*.md (small files) │ │ │ │ │ ├──► Generate bibliography + synthesis │ │ │ │ │ └──► Draft Introduction │ │ │ └─────────────────────────────────────────────────────────────────┘

Why subagents?

• Each PDF can be 10-50 pages of dense content

• Processing 30 papers in one context overflows limits

• Subagents process one paper, write condensed notes, then exit

• Orchestrator only reads small markdown note files

Prerequisites

• scope.md must exist (from scoping step)

• notes/ethics-summary.md may exist (provides study objectives and population context)

• papers/ folder with PDF files to process

• Create directories: notes/papers/ , notes/papers-library/ , drafts/

Workflow Overview

[Step 1: Read scope.md for context] │ ▼ [Step 2: Inventory papers/ folder] │ ▼ [Step 3: Process each PDF via subagent] ─── One at a time │ └── notes/papers/*.md ▼ [Step 4: Generate bibliography] ─── From all notes │ └── notes/bibliography.md ▼ [Step 5: Synthesize literature] ─── Aggregate findings │ └── notes/literature-synthesis.md ▼ [Step 6: Draft Introduction] │ ▼ [Output] ─── drafts/introduction.md

Step 1: Read Scope Context

From scope.md , extract comprehensive context to pass to each subagent:

• Research question (frames how to evaluate relevance)

• Key findings (what results need literature context)

• Target journal (determines citation depth)

• Hypothesis (what the manuscript argues)

• Population/methods (for identifying comparable studies)

Create a detailed scope summary to pass to each subagent:

Manuscript Context

You are helping write a scientific research manuscript. Your job is to read ONE paper and extract information most relevant to this manuscript.

Our Research Question

[Full research question from scope.md]

Our Hypothesis

[What we expect to find / are arguing]

Our Key Findings

[Summary of main results - what we found]

Our Methods

[Brief description of study design, population, techniques used]

Target Journal

[Journal name] - [word limit] words - [citation style]

What to Look For in This Paper

As you read, focus on extracting:

1. Background claims we can cite to establish the problem's importance
2. Methodological precedents that justify our approach
3. Comparable results we can compare our findings against
4. Contradictory findings we need to address in Discussion
5. Gaps identified that our study fills
6. Quotable statements that frame the field well

If notes/ethics-summary.md exists, also include:

• Study objectives from ethics document

• Target population details

• Approved procedures

Step 2: Inventory Papers

List all PDFs in the papers/ folder:

ls papers/*.pdf

Create processing queue:

Papers to Process

Copy PDFs to central library:

mkdir -p notes/papers-library cp papers/*.pdf notes/papers-library/

Step 3: Process Each PDF via Subagent

CRITICAL: Process ONE paper at a time using the Task tool.

For each PDF in the queue:

3a. Spawn Subagent

Use the Task tool to spawn an isolated subagent.

IMPORTANT: Each Task call must specify exactly ONE PDF file. Do not batch.

Task( subagent_type: "general-purpose", prompt: """ ⛔ YOU ARE PROCESSING EXACTLY ONE PAPER. DO NOT READ ANY OTHER PDFs. ⛔

Your Role

You are a research assistant helping write a scientific manuscript. Your job is to:

1. Read ONE paper
2. Extract information most relevant to our manuscript
3. Write condensed notes highlighting what's useful for our paper
4. Exit immediately after

Your ONE Paper

PDF to read: papers/{filename}.pdf Output file: notes/papers/{filename}.md

Manuscript Context (What We're Writing)

{scope_summary}

Instructions

1. Read ONLY the PDF file specified above
2. Extract citation metadata (authors, title, journal, DOI, PMID)
3. Summarize the paper's main contribution
4. Focus on relevance: What from this paper helps our manuscript?
   • Background claims we can cite?
   • Methods similar to ours?
   • Results we can compare against?
   • Contradictions we need to address?
   • Quotes that frame the problem well?
5. Recommend inclusion: Should this paper be cited in our manuscript?
6. Write condensed notes to the output file
7. Return a summary with your recommendation
8. EXIT - Do not process any other papers

Note Template

[First Author] et al., [Year]

Processed: [timestamp]

Citation

• Authors: [full author list]
• Title: [title]
• Journal: [journal]
• Year: [year]
• DOI: [doi or "not found"]
• PMID: [pmid or "not found"]

Paper Summary

[2-3 sentences on what this paper is about]

Study Design

• Type: [RCT, cohort, retrospective, etc.]
• Population: [N, key characteristics]
• Methods: [key techniques used]

Key Findings

Relevance to Our Manuscript

Relationship: [Supports / Contradicts / Provides Context / Methodological Reference]

For Introduction

• [Claims or context we can cite to frame our problem]
• [Gaps this paper identifies that we address]

For Methods

• [Methodological precedents that justify our approach]

For Discussion

• [Results to compare against ours]
• [Contradictions we need to explain]

Key Quotes

"[Quotable statement that frames the field or problem well]" (p. X)

"[Another useful quote if available]" (p. X)

Recommendation

Include in draft?: [Yes / No] Rationale: [1-2 sentences - Is this paper directly relevant? Would citing it feel natural or forced?]

Tags

#[topic1] #[topic2] #[methodology] """ )

3b. Wait for Completion

Wait for the subagent to complete before processing the next paper.

3c. Update Status

Track the subagent's recommendation for each paper:

3d. Handle Errors

If a subagent fails:

• Log the error

• Mark as "Needs manual review"

• Continue with next paper

Step 4: Generate Bibliography

After ALL papers are processed, read the notes and compile bibliography.

Read each notes/papers/*.md and extract citations:

Create notes/bibliography.md :

Master Bibliography

Generated: [timestamp] Total References: [n]

References

Papers Needing Attention

Step 5: Synthesize Literature

Read all notes/papers/*.md files and create synthesis.

Note: At this point you're only reading small markdown files, not full PDFs.

Create notes/literature-synthesis.md :

Literature Synthesis

Generated: [timestamp] Research Question: [from scope.md] Papers Reviewed: [n]

Paper Citation Tracker

Use the subagent recommendations from Step 3 to populate this table. Papers recommended for exclusion by the subagent should be marked "Not Applicable."

Status Legend:

• Planned: Subagent recommended inclusion and paper has a natural place
• Not Applicable: Subagent recommended exclusion or paper doesn't fit naturally

Guidance: Trust the subagent's assessment of relevance. The goal is a coherent manuscript, not maximum citations.

Source Inventory

Key Themes

Theme 1: [Theme Name]

Summary: [2-3 sentences]

Sources: Smith 2023, Jones 2022

Relevance: [connection to our study]

Theme 2: [Theme Name]

[repeat pattern]

Supporting Findings

Contradictory Findings

Gaps in Literature

Implications for Manuscript

Introduction

• Paragraph 1 (Problem): Cite [sources]
• Paragraph 2 (Knowledge): Cite [sources]
• Paragraph 3 (Gap): Cite [sources]
• Paragraph 4 (This Study): Reference scope.md

Discussion

• Comparisons: [sources for comparing results]
• Interpretation: [sources for mechanisms]

Step 6: Draft Introduction

Using notes/literature-synthesis.md , draft the Introduction.

Structure (4 paragraphs)

Paragraph 1: The Problem

• Significance of the clinical/scientific problem

• Epidemiology, impact, importance

Paragraph 2: Current Knowledge

• What is currently known

• Existing approaches and successes

Paragraph 3: The Gap

• What remains unknown

• Limitations of current approaches

Paragraph 4: This Study

• Purpose and approach

• What this paper contributes

Writing Guidelines

• Present tense for established facts ("MRI provides...")

• Past tense for specific findings ("Smith et al. found...")

• Every claim needs a citation [1]

• Numbered citations in order of appearance

• Aim for ~500-800 words

Draft Format

Create drafts/introduction.md :

Introduction

[Paragraph 1 - Problem and significance]

[Paragraph 2 - Current knowledge]

[Paragraph 3 - Gap and limitations]

[Paragraph 4 - This study's purpose]

References Used

1. [Citation] - notes/papers/smith-2023.md
2. [Citation] - notes/papers/jones-2022.md ...

Output

Save to:

• notes/papers-library/*.pdf

• Central PDF storage

• notes/papers/*.md

• Condensed notes per paper

• notes/bibliography.md

• Master reference list

• notes/literature-synthesis.md

• Aggregated synthesis

• drafts/introduction.md

• Introduction draft

Return summary:

• Papers processed: [n]

• Papers recommended for inclusion: [n]

• Papers recommended for exclusion: [n]

• Papers with issues: [n]

• Key themes identified: [n]

• Introduction word count: [n]