Deep Literature Research

Conduct a thorough literature search on a topic with verified citations. CRITICAL: Never fabricate citations. Every claim must have a verifiable source.

When to Use

• Starting a new project (research core concepts)

• Exploring methodology options

• Understanding the current state of a field

• Finding prior work on a specific technique

Usage

/deep_research [topic] /deep_research normalization methods for RNA-seq /deep_research machine learning in proteomics

The 5-Step Literature Review Process

Follow this framework for rigorous, reproducible literature reviews:

1. DEFINE SCOPE → What are we looking for? Set boundaries.
2. SEARCH → Systematic, documented search across databases.
3. EVALUATE → Assess source quality and relevance.
4. SYNTHESIZE → Identify themes, patterns, and gaps.
5. DOCUMENT → Write findings with proper citations.

Execution Steps

1. Understand the Research Need (Define Scope)

If topic is vague, ask clarifying questions:

• "What specific aspect of [topic] are you most interested in?"

• "Are you looking for methodological approaches, theoretical background, or applications?"

• "Any specific time range? (e.g., last 5 years, seminal works)"

2. Generate Search Strategy

Break the topic into searchable concepts:

Search Strategy for: [Topic]

Core Concepts

1. [Primary concept] - synonyms: [alternatives]
2. [Secondary concept] - synonyms: [alternatives]
3. [Methodological aspect]

Search Queries

• "[concept1] AND [concept2]"
• "[method] in [application domain]"
• "review [topic]" (for overview papers)

Key Databases

• PubMed (biomedical)
• arXiv (computational, preprints)
• Google Scholar (broad)
• Semantic Scholar (AI-enhanced)

3. Evaluate Sources

Apply the ACRAP criteria to each source:

Criterion Questions to Ask

Authority Who wrote it? What are their credentials? Institutional affiliation?

Currency When published? Is it current for this field? (Generally <5 years, seminal works excepted)

Relevance Does it directly address the research question?

Accuracy Is it peer-reviewed? Are claims supported by evidence?

Purpose Why was it written? Any funding bias or conflicts of interest?

Quick Assessment:

• ✅ High quality: Peer-reviewed, reputable journal, clear methodology

• ⚠️ Use with caution: Preprints, conference papers, older works

• ❌ Avoid: Non-peer-reviewed, predatory journals, unsupported claims

4. Conduct Research

CRITICAL RULES:

• ✅ Only include claims with verifiable sources

• ✅ Format citations properly (Author et al., Year)

• ✅ Include DOI or URL when available

• ❌ NEVER fabricate or guess citations

• ❌ NEVER make up author names, years, or findings

• ✅ If no source exists, explicitly state: "Gap identified: No literature found on [specific topic]"

• ✅ If uncertain, say: "Limited sources found. Manual verification recommended."

5. Organize Findings

Structure the output as:

Literature Review: [Topic]

Executive Summary

[2-3 sentence overview of the field]

Current State of the Field

[Theme 1]

[Synthesized findings with citations]

Key findings:

• Finding 1 (Author et al., Year)
• Finding 2 (Author et al., Year)

[Theme 2]

[Synthesized findings]

Methodological Approaches

[What methods are commonly used]

Gaps in the Literature

• Gap 1: [What's missing or unexplored]
• Gap 2: [Contradictions or debates]

Seminal Works

[Important foundational papers that should be cited]

Recent Advances (Last 2-3 years)

[Most current developments]

Implications for This Project

[How this literature relates to the user's aims]

References

[Full BibTeX entries for all citations]

6. Save Outputs

Save to .research/literature/ :

• [topic-slug].md

• The literature summary

• [topic-slug].bib

• BibTeX citations

Example:

.research/literature/ ├── rna-seq-normalization.md └── rna-seq-normalization.bib

7. Prompt Next Steps

After completing:

Literature review saved to .research/literature/[topic].md

Suggested next steps: A) Run /write_background to draft your background section B) Run /deep_research on another topic: [suggest related topic] C) Review the findings and refine your project aims

Would you like to explore any of these sources in more detail?

Citation Format Standards

In-Text Citations

• Single author: (Smith, 2023)

• Two authors: (Smith & Jones, 2023)

• Three+ authors: (Smith et al., 2023)

• Multiple citations: (Smith, 2023; Jones, 2022)

BibTeX Format

@article{smith2023keyword, author = {Smith, John and Jones, Jane and Williams, Bob}, title = {Title of the Paper}, journal = {Journal Name}, year = {2023}, volume = {10}, number = {2}, pages = {123-145}, doi = {10.1234/example.doi} }

Handling Uncertainty

When sources are limited:

⚠️ Limited sources found on [specific topic]. Available sources cover [related area] but not [specific aspect]. Recommend:

• Manual search in [specific database]
• Consultation with domain expert
• This may represent a gap in the field

When sources conflict:

📊 Conflicting findings in the literature:

• Position A: [claim] (Author1, Year)
• Position B: [opposing claim] (Author2, Year) Current consensus appears to favor [position] based on [evidence].

When no sources found:

🔍 Gap identified: No peer-reviewed literature found on [topic]. This could mean:

• Novel research opportunity
• Need for different search terms
• Topic may be covered under different terminology Suggested alternative searches: [alternatives]

Quality Checks

Before finalizing, verify:

• Every factual claim has a citation

• All citations are real and verifiable

• BibTeX entries are complete

• DOIs are included where available

• No made-up author names or publication details

• Gaps and limitations are explicitly stated

Related Skills

• write-background

• Use literature to draft background section

• next

• Get next suggested step