Scientific research

Scientific Research

Two sequential phases. Run Phase 1 to find and synthesize literature. Run Phase 2 to evaluate the quality of a specific scholarly work.

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Phase 1 — Literature Review

Use 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.

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 which level of rigor is needed. Default to scoping for exploratory work and systematic 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: 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 and languages
• publication types
• inclusion and exclusion criteria
• exact search strings

Minimum useful database set: PubMed (biomedical/life-sciences), arXiv (CS, math, physics, preprints), Semantic Scholar or Crossref (broad academic). Add domain-specific sources as needed.

3. Search and Log Evidence

Keep a search log for reproducibility:

| Database | Date searched | Query | Filters | Results | Export |
| --- | --- | --- | --- | ---: | --- |
| PubMed | 2026-05-11 | `("CRISPR"[tiab]) AND "sickle cell"[tiab]` | 2020:2026, English | 86 | PMID list |

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

4. Deduplicate

Order: DOI → PMID or arXiv ID → exact title → normalized title plus first author and year. Record how many duplicates were removed.

5. Screen Sources

Screen in stages: title → abstract → 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

| Study | Design | Population/Data | Method | Comparator | Outcome | Key finding | Limitations |
| --- | --- | --- | --- | --- | --- | --- | --- |

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 lenses: strongest evidence, conflicting evidence, methodological weaknesses, population or dataset limits, recency and replication, practical implications, unanswered questions.

Separate claims by confidence:

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

8. Verify Citations

Before finalizing: verify DOI, PMID, arXiv ID, or official URL; check author names and 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.

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Phase 2 — Scholar Evaluation

Use to evaluate academic or scientific work with a repeatable rubric.

When to Use

• Reviewing a research paper, proposal, thesis chapter, or literature review.
• Checking whether claims are supported by cited evidence.
• Evaluating methodology, study design, analysis, or limitations.
• Comparing two or more papers for quality or relevance.
• Producing structured feedback for revision.

Evaluation Scope

Identify the artifact type: empirical paper, theoretical paper, technical report, systematic or narrative literature review, research proposal, thesis chapter, conference abstract.

Choose scope:

• Comprehensive: all rubric dimensions.
• Targeted: one or two dimensions (e.g., method or citations).
• Comparative: rank multiple works against the same rubric.

Rubric (score 1–5 per dimension)

• 5: excellent; clear, rigorous, publication-ready.
• 4: good; minor improvements needed.
• 3: adequate; meaningful gaps but usable.
• 2: weak; substantial revision needed.
• 1: poor; major validity or clarity problems.
• N/A: dimension does not apply.

1. Problem and Research Question

Is the problem clear and specific? Is the contribution meaningful? Are scope and assumptions explicit? Does the question match the claimed contribution?

2. Literature and Context

Is relevant prior work covered? Does the work synthesize rather than merely list? Are gaps accurately identified? Are recent and foundational sources balanced?

3. Methodology

Does the method answer the research question? Are design choices justified? Are variables, datasets, participants, or materials described clearly? Could another researcher reproduce the work?

4. Data and Evidence

Are data sources credible and appropriate? Is sample size or corpus coverage adequate? Are inclusion, exclusion, and preprocessing decisions documented? Are missing data and bias risks discussed?

5. Analysis

Are statistical, qualitative, or computational methods appropriate? Are baselines and controls fair? Are uncertainty, sensitivity, or robustness checks included when needed? Are alternative explanations considered?

6. Results and Interpretation

Are results clearly presented? Do claims stay within the evidence? Are figures, tables, and metrics understandable? Are negative or null results handled honestly?

7. Limitations and Threats to Validity

Are limitations specific rather than generic? Are internal, external, construct, and conclusion-validity risks addressed? Does the paper distinguish speculation from demonstrated results?

8. Writing and Structure

Is the argument easy to follow? Are sections organized around the research question? Are definitions and notation clear? Is the tone precise and scholarly?

9. Citations

Do cited papers support the claims attached to them? Are primary sources used where possible? Are reviews and preprints labeled? Are citation metadata and links correct?

Review Process

1. Read the abstract, introduction, figures, and conclusion for claimed contribution.
2. Read methods and results for evidence quality.
3. Check the strongest claims against cited sources.
4. Score each applicable dimension.
5. Separate critical blockers from revision suggestions.
6. End with concrete next edits.

Output Template

# Scholar Evaluation: <Artifact>

## Overall Assessment
- Overall score: <1-5 or N/A>
- Confidence: <high | medium | low>
- Summary: <3-5 sentences>

## Dimension Scores

| Dimension | Score | Evidence | Revision priority |
| --- | ---: | --- | --- |
| Problem and question |  |  |  |
| Literature and context |  |  |  |
| Methodology |  |  |  |
| Data and evidence |  |  |  |
| Analysis |  |  |  |
| Results and interpretation |  |  |  |
| Limitations |  |  |  |
| Writing and structure |  |  |  |
| Citations |  |  |  |

## Critical Issues
## Recommended Revisions
## Evidence Checks Needed

Pitfalls

• Do not use the score as a substitute for concrete feedback.
• Do not penalize a paper for omitting a dimension outside its scope.
• Do not treat citation count, venue, or author reputation as proof of quality.
• Do not accept unsupported claims just because they appear in the abstract.

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Migration Notes

Deprecated skill	Replaced by	Phase
scientific-thinking-literature-review	scientific-research	Phase 1
scientific-thinking-scholar-evaluation	scientific-research	Phase 2