literature-review

name	literature-review
description	Search and review ecosystem and biogeochemical literature using MCP tools (PubMed, arXiv, bioRxiv, Google Scholar), with optional full-text reading and citation snowballing. Use when the user needs evidence, citations, methods comparison, or novelty checks for EcoSIM and warming-nitrogen hypotheses.
allowed-tools	Bash, Read, Write, WebSearch, Agent
user-invocable	true

Literature Review Skill

Search, read, and synthesize literature relevant to EcoSIM modeling, warming experiments, nitrogen cycling, and related ecosystem biogeochemistry.

Compatibility Modes

• Full mode: MCP servers available (pubmed, paper-search) for richer search and full text.
• Limited mode: WebSearch + DOI fallback with explicit reduced-coverage note.

Prerequisites

Preferred servers are configured in .claude/.mcp.json:

• pubmed for rich biomedical search and PMC full text
• paper-search for arXiv, bioRxiv, medRxiv, and Google Scholar search/read

If MCP servers are unavailable, fall back to WebSearch and DOI landing pages.

Scope

Prioritize evidence for:

• Experimental warming impacts on nitrogen processes
• Soil moisture-temperature interactions
• N2O emissions, nitrification, denitrification, mineralization
• EcoSIM-relevant forcing/parameterization methods
• Ecosystem-specific effects (tundra, forest, grassland, agricultural)

Review Tiers

Tier	Papers	Full text	Citation expansion	When to use
Quick scan	5-10	No	No	Fast orientation
Standard review	20-30	Top 10	Yes	Default for project work
Deep review	50+	Top 20	Yes	Comprehensive synthesis

Default: quick for ad-hoc questions, standard for project work, deep only when explicitly requested.

Workflow

Step 1: Clarify the Question

Capture:

• Topic and hypothesis
• Organisms/ecosystems
• Time horizon (recent vs historical)
• Whether methods comparison is required

Step 2: Build Query Set

Construct 3 query families:

• Core process query (for example: warming + nitrification)
• Ecosystem query (for example: tundra + soil nitrogen)
• Methods query (for example: incubation, isotope tracing, flux chamber)

Step 3: Discover, Deduplicate, Rank

Search across PubMed, bioRxiv, arXiv, and Google Scholar. Deduplicate by DOI/PMID. Rank by EcoSIM relevance:

• HIGH: directly measures N-cycling or climate-soil controls used in EcoSIM workflows
• MEDIUM: adjacent mechanisms or methods transferable to EcoSIM
• LOW: tangential background

Step 4: Optional Deep Reading

For standard/deep tiers, read top papers in full text where available. Extract:

• Study design and sample sizes
• Quantitative outcomes (effect sizes, p-values, uncertainty)
• Limitations and caveats
• Variables that map to EcoSIM or BERVO terms

Step 5: Summarize

Produce:

• Thematic findings
• Methods comparison table
• Key quantitative results table
• Evidence quality notes
• Knowledge gaps and contested findings

Use this structure:

## Literature Review: <topic>

Review depth: <quick|standard|deep>
Papers found: <N>
Full text read: <N>
Sources searched: <list>

### Summary
<2-3 sentence synthesis>

### Key Findings by Theme
- <Author Year>: <finding> (DOI/PMID)

### Methods Comparison
| Study | Ecosystem | Method | Sample size | Key metric |
|---|---|---|---|---|

### Key Quantitative Results
| Finding | Value | Study | Evidence quality |
|---|---|---|---|

### Gaps in Current Knowledge
- <gap>

### Relevance to EcoSIM
- <variables, parameters, forcing constraints, benchmark opportunities>

Step 6: Store References

If a project location is known, append references to a repo-local file such as:

• docs/references/<topic>.md or
• derived/<study-id>/summary.md (when extending an existing study packet)

Do not require a BERIL projects/{id} layout.

Integration

• Called by: suggest-research, synthesize
• Inputs from: derived/*.tsv, study summaries, user hypotheses
• Outputs: a citation-backed review and optional reference file updates

Fallback

If MCP is unavailable:

• Use WebSearch with source constraints (site:pubmed.ncbi.nlm.nih.gov, DOI URLs)
• Note reduced coverage and lack of robust full-text retrieval