literature-review

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---
name: literature-review
description: Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).
---

# Literature Review

## Overview

Conduct systematic, comprehensive literature reviews following rigorous academic methodology. Search multiple literature databases, synthesize findings thematically, verify all citations for accuracy, and generate professional output documents in markdown and PDF formats.

This skill integrates with multiple scientific skills for database access (gget, bioservices, datacommons-client) and provides specialized tools for citation verification, result aggregation, and document generation.

## When to Use This Skill

Use this skill when:
- Conducting a systematic literature review for research or publication
- Synthesizing current knowledge on a specific topic across multiple sources
- Performing meta-analysis or scoping reviews
- Writing the literature review section of a research paper or thesis
- Investigating the state of the art in a research domain
- Identifying research gaps and future directions
- Requiring verified citations and professional formatting

## Core Workflow

Literature reviews follow a structured, multi-phase workflow:

### Phase 1: Planning and Scoping

1. **Define Research Question**: Use PICO framework (Population, Intervention, Comparison, Outcome) for clinical/biomedical reviews
   - Example: "What is the efficacy of CRISPR-Cas9 (I) for treating sickle cell disease (P) compared to standard care (C)?"

2. **Establish Scope and Objectives**:
   - Define clear, specific research questions
   - Determine review type (narrative, systematic, scoping, meta-analysis)
   - Set boundaries (time period, geographic scope, study types)

3. **Develop Search Strategy**:
   - Identify 2-4 main concepts from research question
   - List synonyms, abbreviations, and related terms for each concept
   - Plan Boolean operators (AND, OR, NOT) to combine terms
   - Select minimum 3 complementary databases

4. **Set Inclusion/Exclusion Criteria**:
   - Date range (e.g., last 10 years: 2015-2024)
   - Language (typically English, or specify multilingual)
   - Publication types (peer-reviewed, preprints, reviews)
   - Study designs (RCTs, observational, in vitro, etc.)
   - Document all criteria clearly

### Phase 2: Systematic Literature Search

1. **Multi-Database Search**:

   Select databases appropriate for the domain:

   **Biomedical & Life Sciences:**
   - Use `gget` skill: `gget search pubmed "search terms"` for PubMed/PMC
   - Use `gget` skill: `gget search biorxiv "search terms"` for preprints
   - Use `bioservices` skill for ChEMBL, KEGG, UniProt, etc.

   **General Scientific Literature:**
   - Search arXiv via direct API (preprints in physics, math, CS, q-bio)
   - Search Semantic Scholar via API (200M+ papers, cross-disciplinary)
   - Use Google Scholar for comprehensive coverage (manual or careful scraping)

   **Specialized Databases:**
   - Use `gget alphafold` for protein structures
   - Use `gget cosmic` for cancer genomics
   - Use `datacommons-client` for demographic/statistical data
   - Use specialized databases as appropriate for the domain

2. **Document Search Parameters**:
   ```markdown
   ## Search Strategy

   ### Database: PubMed
   - **Date searched**: 2024-10-25
   - **Date range**: 2015-01-01 to 2024-10-25
   - **Search string**:
     ```
     ("CRISPR"[Title] OR "Cas9"[Title])
     AND ("sickle cell"[MeSH] OR "SCD"[Title/Abstract])
     AND 2015:2024[Publication Date]
     ```
   - **Results**: 247 articles
   ```

   Repeat for each database se