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Core Workflow

skills/literature-review/references/core_workflow.md

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Core Workflow

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 minimum 3 complementary databases
    • Use the parallel-web skill (parallel-cli search) for initial scoping to quickly gauge the landscape before formal database searches

  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

  1. Multi-Database Search:

    Select databases appropriate for the domain. Always start with parallel-web for broad academic coverage, then supplement with domain-specific databases.

    Web-Based Academic Search (parallel-web skill — START HERE):

    • Use parallel-cli search with academic domain filtering for broad scholarly coverage
    • Run two searches: academic-focused + general to catch all relevant sources
    bash
    # Academic-focused search across scholarly sources
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 to fetch full content from specific paper URLs or PDFs found in search results
    bash
    parallel-cli extract "https://arxiv.org/abs/XXXX.XXXXX" --json

    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 searched.

  3. Export and Aggregate Results:

    • Export results in JSON format from each database
    • Combine all results into a single file
    • Use scripts/search_databases.py for post-processing:
      bash
      python search_databases.py combined_results.json \
  --deduplicate \
  --format markdown \
  --output aggregated_results.md

Phase 3: Screening and Selection

  1. Deduplication:

    bash
    python search_databases.py results.json --deduplicate --output unique_results.json
    • Removes duplicates by DOI (primary) or title (fallback)
    • 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:

    Initial search: n = X
├─ After deduplication: n = Y
├─ After title screening: n = Z
├─ After abstract screening: n = A
└─ Included in review: n = B

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 Study Quality:

    • For RCTs: Use Cochrane Risk of Bias tool
    • For observational studies: Use Newcastle-Ottawa Scale
    • For systematic reviews: Use AMSTAR 2
    • Rate each study: High, Moderate, Low, or Very Low quality
    • Consider excluding very low-quality studies

  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:

    bash
    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

    Example structure:

    markdown
    #### 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:

    bash
    python scripts/verify_citations.py my_literature_review.md

    This script:

    • Extracts all DOIs from the document
    • Verifies each DOI resolves correctly
    • Retrieves metadata from CrossRef
    • Generates verification report
    • Outputs properly formatted citations

  2. Review Verification Report:

    • Check for any failed DOIs
    • Verify author names, titles, and publication details match
    • Correct any errors in the original document
    • Re-run verification until all citations pass

  3. Format Citations Consistently:

    • Choose one citation style and use throughout (see references/citation_styles.md)
    • Common styles: APA, Nature, Vancouver, Chicago, IEEE
    • Use verification script output to format citations correctly
    • Ensure in-text citations match reference list format

Phase 7: Document Generation

  1. Generate PDF:

    bash
    python scripts/generate_pdf.py my_literature_review.md \
  --citation-style apa \
  --output my_review.pdf

    Options:

    • --citation-style: apa, nature, chicago, vancouver, ieee
    • --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:

    • All DOIs verified with verify_citations.py
    • 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