Scientific thinking literature review

Literature Review

Use this skill when the task is to find, screen, synthesize, and cite a body of academic or technical literature.

When to Use

• Building a systematic, scoping, or narrative literature review.
• Synthesizing the state of the art for a research question.
• Finding gaps, contradictions, or future-work directions.
• Preparing citation-backed background sections for papers or reports.
• Comparing evidence across peer-reviewed papers, preprints, patents, and technical reports.

Review Types

• Narrative review: broad synthesis; useful for orientation.
• Scoping review: maps concepts, methods, and evidence gaps.
• Systematic review: predefined protocol, reproducible search, explicit screening and exclusion.
• Meta-analysis: systematic review plus quantitative effect aggregation.

Ask the user which level of rigor is needed. If unspecified, default to a scoping review for exploratory work and a systematic review for publication or clinical claims.

Workflow

1. Define the Question

Convert the prompt into a searchable research question.

For clinical or biomedical work, use PICO:

• Population
• Intervention or exposure
• Comparator
• Outcome

For technical work, use:

• system or domain
• method or intervention
• comparison baseline
• evaluation metric

2. Plan the Search

Create a search protocol before collecting sources:

• databases to search
• date range
• languages
• publication types
• inclusion criteria
• exclusion criteria
• exact search strings

Minimum useful database set:

• PubMed for biomedical and life-sciences literature.
• arXiv for CS, math, physics, quantitative biology, and preprints.
• Semantic Scholar or Crossref for broad academic discovery.
• Domain-specific sources when relevant, such as clinical-trial registries, patent databases, standards bodies, or official technical docs.

3. Search and Log Evidence

Keep a search log that makes the review reproducible:

| Database | Date searched | Query | Filters | Results | Export |
| --- | --- | --- | --- | ---: | --- |
| PubMed | 2026-05-11 | `("CRISPR"[tiab] OR "Cas9"[tiab]) AND "sickle cell"[tiab]` | 2020:2026, English | 86 | PMID list |
| arXiv | 2026-05-11 | `CRISPR sickle cell gene editing` | q-bio, 2020:2026 | 9 | BibTeX |

Save raw IDs, URLs, DOIs, abstracts, and notes separately from the final prose.

4. Deduplicate

Deduplicate in this order:

1. DOI
2. PMID or arXiv ID
3. exact title
4. normalized title plus first author and year

Record how many duplicates were removed.

5. Screen Sources

Screen in stages:

1. title
2. abstract
3. full text

For systematic work, record exclusion reasons:

• wrong population
• wrong intervention
• wrong outcome
• not primary research
• duplicate
• unavailable full text
• outside date range

6. Extract Data

Use a structured extraction table:

| Study | Design | Population/Data | Method | Comparator | Outcome | Key finding | Limitations |
| --- | --- | --- | --- | --- | --- | --- | --- |
| Author Year | RCT/cohort/review/etc. | sample or corpus | method | baseline | measured outcome | result | caveat |

For technical papers, include dataset, benchmark, metric, baseline, and reproducibility notes.

7. Synthesize

Group evidence by theme rather than summarizing papers one by one.

Useful synthesis lenses:

• strongest evidence
• conflicting evidence
• methodological weaknesses
• population or dataset limits
• recency and replication
• practical implications
• unanswered questions

Separate claims by confidence:

• High confidence: replicated, high-quality evidence across sources.
• Medium confidence: plausible but limited by sample, method, or recency.
• Low confidence: early, speculative, single-source, or weakly measured.

8. Verify Citations

Before finalizing:

• verify DOI, PMID, arXiv ID, or official URL
• check author names and publication year
• do not cite a paper for a claim it does not make
• mark preprints as preprints
• distinguish reviews from primary evidence

Output Template

# Literature Review: <Topic>

Generated: <date>
Review type: <narrative | scoping | systematic | meta-analysis>
Search window: <dates>
Databases: <list>

## Research Question

## Search Strategy

## Inclusion and Exclusion Criteria

## Evidence Summary

## Thematic Synthesis

## Gaps and Limitations

## References

## Search Log

Pitfalls

• Do not treat search snippets as evidence.
• Do not mix preprints, reviews, and primary studies without labeling them.
• Do not omit negative or conflicting findings.
• Do not claim systematic-review rigor without a reproducible protocol.
• Do not use a single database for a broad claim unless the scope is explicitly limited to that database.