Literature Review

Core Workflow

Illustrative workflow; example queries, dates, counts, and numerical findings are not executed review results. Run commands from this skill directory, using paths to your review workspace.

All seven phases in full: planning and scoping, systematic search, screening and selection, data extraction and quality assessment, synthesis and analysis, citation verification, and document generation.

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 complementary bibliographic databases and registries appropriate to the question

   • Optionally use parallel-web (parallel-cli search) for initial scoping to quickly gauge the landscape before formal database searches

4. Set Inclusion/Exclusion Criteria:

   • Date range (e.g., the explicitly historical interval 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 bibliographic databases and registries appropriate for the domain. Use optional web search for scoping and supplementary discovery; record it separately from database exports.

   Supplementary web discovery (parallel-web):

   • Use parallel-cli search with academic domain filtering for broad scholarly coverage

   • Consider academic-focused and general searches; ranked samples do not guarantee complete retrieval

   Copy

   mkdir -p sources
   # Illustrative ranked sample; not a complete search
   parallel-cli search "your research topic" -q "keyword1" -q "keyword2" \
     --json --max-results 10 --excerpt-max-chars-total 27000 \
     --include-domains "scholar.google.com,arxiv.org,pubmed.ncbi.nlm.nih.gov,semanticscholar.org,biorxiv.org,medrxiv.org,ncbi.nlm.nih.gov,nature.com,science.org,ieee.org,acm.org,springer.com,wiley.com,cell.com,pnas.org,nih.gov" \
     -o sources/litreview_<topic>-academic.json
   
   # General search for supplementary sources
   parallel-cli search "your research topic" -q "keyword1" -q "keyword2" \
     --json --max-results 10 --excerpt-max-chars-total 27000 \
     -o sources/litreview_<topic>-general.json

   • Use parallel-cli extract --full-content to request content from accessible paper URLs; check for truncation and retrieval errors

   Copy

   parallel-cli extract "https://arxiv.org/abs/1706.03762" --full-content --json

   Biomedical & Life Sciences:

   • Search PubMed via its interface or E-utilities; PMC has different full-text coverage

   • Search bioRxiv/medRxiv interfaces, or retrieve date-range API metadata and explicitly filter it

   • See database_strategies.md for exact requests, authentication, and export limits

   General Scientific Literature:

   • Search arXiv via direct API (preprints in physics, math, CS, q-bio)

   • Search Semantic Scholar using its documented relevance or bulk API as appropriate

   • Use Google Scholar manually for supplementary discovery and citation chaining; preserve search and screening limits

   Biological entity databases can inform background, but do not count as bibliographic sources simply because they contain references.

2. Document Search Parameters:

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   ## 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 ("Anemia, Sickle Cell"[MeSH Terms] OR "SCD"[Title/Abstract]) AND 2015:2024[Publication Date]

   Copy

   - **Results**: 247 articles

   Repeat for each database searched.

3. Export and Aggregate Results:

   • Export results in JSON format from each database

   • Normalize raw provider responses into a JSON array, preserving raw exports and provenance separately

   • Use scripts/search_databases.py for post-processing:

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     python scripts/search_databases.py combined_results.json \
       --deduplicate \
       --format markdown \
       --output aggregated_results.md

Phase 3: Screening and Selection

1. Deduplication:

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   python scripts/search_databases.py results.json --deduplicate --format json --output unique_results.json

   • Keeps first normalized DOI; title fallback compares DOI-less records only. Review matches and retain raw duplicates for enrichment

   • Document number of duplicates removed

2. Title Screening:

   • Review all titles against inclusion/exclusion criteria

   • Exclude obviously irrelevant studies

   • Document number excluded at this stage

3. Abstract Screening:

   • Read abstracts of remaining studies

   • Apply inclusion/exclusion criteria rigorously

   • Document reasons for exclusion

4. Full-Text Screening:

   • Obtain full texts of remaining studies

   • Conduct detailed review against all criteria

   • Document specific reasons for exclusion

   • Record final number of included studies

5. Create PRISMA Flow Diagram:

   • Use the official template matching new/updated review and source types.

   • Track records identified and removed before screening, records screened and excluded, reports sought/not retrieved/assessed, excluded reports with reasons, and included studies plus reports of those studies.

   • Reconcile counts at each transition; do not invent one included-study count from the number of publications. Maintain a study-to-report map.

Phase 4: Data Extraction and Quality Assessment

1. Extract Key Data from each included study:

   • Study metadata (authors, year, journal, DOI)

   • Study design and methods

   • Sample size and population characteristics

   • Key findings and results

   • Limitations noted by authors

   • Funding sources and conflicts of interest

2. Assess Risk of Bias and Certainty:

   • Use a tool appropriate to the design and question: RoB 2 for randomized trial results; ROBINS-I for nonrandomized intervention results; AMSTAR 2 for systematic reviews of healthcare interventions. Other designs require their own appraisal tool.

   • Preserve domain judgments and rationale. RoB 2 uses low risk, some concerns, or high risk; do not force every tool onto a common numerical scale.

   • GRADE assesses a body of evidence for each outcome (high/moderate/low/very low), not a generic grade for each individual study. See the Cochrane certainty guidance.

   • Pre-specify how bias affects synthesis; do not invent post-hoc exclusions.

3. Organize by Themes:

   • Identify 3-5 major themes across studies

   • Group studies by theme (studies may appear in multiple themes)

   • Note patterns, consensus, and controversies

Phase 5: Synthesis and Analysis

1. Create Review Document from template:

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   cp assets/review_template.md my_literature_review.md

2. Write Thematic Synthesis (NOT study-by-study summaries):

   • Organize Results section by themes or research questions

   • Synthesize findings across multiple studies within each theme

   • Compare and contrast different approaches and results

   • Identify consensus areas and points of controversy

   • Highlight the strongest evidence

   Fictitious structure example (replace every count and percentage with extracted evidence):

   Copy

   #### 3.3.1 Theme: CRISPR Delivery Methods
   
   Multiple delivery approaches have been investigated for therapeutic
   gene editing. Viral vectors (AAV) were used in 15 studies^1-15^ and
   showed high transduction efficiency (65-85%) but raised immunogenicity
   concerns^3,7,12^. In contrast, lipid nanoparticles demonstrated lower
   efficiency (40-60%) but improved safety profiles^16-23^.

3. Critical Analysis:

   • Evaluate methodological strengths and limitations across studies

   • Assess quality and consistency of evidence

   • Identify knowledge gaps and methodological gaps

   • Note areas requiring future research

4. Write Discussion:

   • Interpret findings in broader context

   • Discuss clinical, practical, or research implications

   • Acknowledge limitations of the review itself

   • Compare with previous reviews if applicable

   • Propose specific future research directions

Phase 6: Citation Verification

CRITICAL: All citations must be verified for accuracy before final submission.

1. Verify All DOIs:

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   python scripts/verify_citations.py my_literature_review.md

   This script:

   • Extracts all DOIs from the document

   • Checks DOI registration via the Handle API

   • Retrieves available Crossref metadata and preserves unresolved errors

   • Generates verification report

   • Does not verify claim support, publisher accessibility, or final citation style

2. Review Verification Report:

   • Check for any failed DOIs

   • Verify author names, titles, and publication details match

   • Correct any errors in the original document

   • Resolve errors against the source; do not delete a reference solely because a service timed out or lacks its metadata

3. Format Citations Consistently:

   • Choose one citation style and use throughout (see references/citation_styles.md)

   • Common styles: APA, Nature, Vancouver, Chicago, IEEE

   • Use complete metadata with a CSL processor; the script only provides metadata previews

   • Ensure in-text citations match reference list format

Phase 7: Document Generation

1. Generate PDF:

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   python scripts/generate_pdf.py my_literature_review.md \
     --bibliography my_literature_review.bib --csl styles/apa.csl \
     --output my_review.pdf

   Supply an existing .bib and .csl for that example; they are not bundled. [@key] citations are formatted, while manually typed references remain unchanged.

   Options:

   • --csl / --citation-style: existing local CSL path/name; omitted uses Pandoc default

   • --bibliography: bibliography file; sibling .bib also auto-detected

   • --output: PDF destination

   • --no-toc: Disable table of contents

   • --no-numbers: Disable section numbering

   • --check-deps: Check if pandoc/xelatex are installed

2. Review Final Output:

   • Check PDF formatting and layout

   • Verify all sections are present

   • Ensure citations render correctly

   • Check that figures/tables appear properly

   • Verify table of contents is accurate

3. Quality Checklist:

   • [ ] DOI registration checked; metadata identity and claim support reviewed manually

   • [ ] Citations formatted consistently

   • [ ] PRISMA flow diagram included (for systematic reviews)

   • [ ] Search methodology fully documented

   • [ ] Inclusion/exclusion criteria clearly stated

   • [ ] Results organized thematically (not study-by-study)

   • [ ] Quality assessment completed

   • [ ] Limitations acknowledged

   • [ ] References complete and accurate

   • [ ] PDF generates without errors