Citation Management

Citation Management

Overview

Manage citations systematically throughout the research and writing process. This skill provides tools and strategies for searching academic databases (Google Scholar, PubMed), extracting accurate metadata from multiple sources (CrossRef, PubMed, arXiv), validating citation information, and generating properly formatted BibTeX entries.

Critical for maintaining citation accuracy, avoiding reference errors, and ensuring reproducible research. Integrates seamlessly with the literature-review skill for comprehensive research workflows.

When to Use This Skill

Use this skill when:

• Searching for specific papers on Google Scholar or PubMed
• Converting DOIs, PMIDs, or arXiv IDs to properly formatted BibTeX
• Extracting complete metadata for citations (authors, title, journal, year, etc.)
• Validating existing citations for accuracy
• Cleaning and formatting BibTeX files
• Finding highly cited papers in a specific field
• Verifying that citation information matches the actual publication
• Building a bibliography for a manuscript or thesis
• Checking for duplicate citations
• Ensuring consistent citation formatting

Visual Enhancement with Scientific Schematics

When creating documents with this skill, always consider adding scientific diagrams and schematics to enhance visual communication.

If your document does not already contain schematics or diagrams:

• Use the scientific-schematics skill to generate AI-powered publication-quality diagrams
• Simply describe your desired diagram in natural language
• Nano Banana Pro will automatically generate, review, and refine the schematic

For new documents: Scientific schematics should be generated by default to visually represent key concepts, workflows, architectures, or relationships described in the text.

How to generate schematics:

python scripts/generate_schematic.py "your diagram description" -o figures/output.png

The AI will automatically:

• Create publication-quality images with proper formatting
• Review and refine through multiple iterations
• Ensure accessibility (colorblind-friendly, high contrast)
• Save outputs in the figures/ directory

When to add schematics:

• Citation workflow diagrams
• Literature search methodology flowcharts
• Reference management system architectures
• Citation style decision trees
• Database integration diagrams
• Any complex concept that benefits from visualization

For detailed guidance on creating schematics, refer to the scientific-schematics skill documentation.

---

Core Workflow

Citation management follows a systematic process:

Phase 1: Paper Discovery and Search

Goal: Find relevant papers using academic search engines.

Google Scholar Search

Google Scholar provides the most comprehensive coverage across disciplines.

Basic Search:

# Search for papers on a topic
python scripts/search_google_scholar.py "CRISPR gene editing" \
  --limit 50 \
  --output results.json

# Search with year filter
python scripts/search_google_scholar.py "machine learning protein folding" \
  --year-start 2020 \
  --year-end 2024 \
  --limit 100 \
  --output ml_proteins.json

Advanced Search Strategies (see references/google_scholar_search.md):

• Use quotation marks for exact phrases: "deep learning"
• Search by author: author:LeCun
• Search in title: intitle:"neural networks"
• Exclude terms: machine learning -survey
• Find highly cited papers using sort options
• Filter by date ranges to get recent work

Best Practices:

• Use specific, targeted search terms
• Include key technical terms and acronyms
• Filter by recent years for fast-moving fields
• Check "Cited by" to find seminal papers
• Export top results for further analysis

PubMed Search

PubMed specializes in biomedical and life sciences literature (35+ million citations).

Basic Search:

# Search PubMed
python scripts/search_pubmed.py "Alzheimer's disease treatment" \
  --limit 100 \
  --output alzheimers.json

# Search with MeSH terms and filters
python scripts/search_pubmed.py \
  --query '"Alzheimer Disease"[MeSH] AND "Drug Therapy"[MeSH]' \
  --date-start 2020 \
  --date-end 2024 \
  --publication-types "Clinical Trial,Review" \
  --output alzheimers_trials.json

Advanced PubMed Queries (see references/pubmed_search.md):

• Use MeSH terms: "Diabetes Mellitus"[MeSH]
• Field tags: "cancer"[Title], "Smith J"[Author]
• Boolean operators: AND, OR, NOT
• Date filters: 2020:2024[Publication Date]
• Publication types: "Review"[Publication Type]
• Combine with E-utilities API for automation

Best Practices:

• Use MeSH Browser to find correct controlled vocabulary
• Construct complex queries in PubMed Advanced Search Builder first
• Include multiple synonyms with OR
• Retrieve PMIDs for easy metadata extraction
• Export to JSON or directly to BibTeX

Phase 2: Metadata Extraction

Goal: Convert paper identifiers (DOI, PMID, arXiv ID) to complete, accurate metadata.

Quick DOI to BibTeX Conversion

For single DOIs, use the quick conversion tool:

# Convert single DOI
python scripts/doi_to_bibtex.py 10.1038/s41586-021-03819-2

# Convert multiple DOIs from a file
python scripts/doi_to_bibtex.py --input dois.txt --output references.bib

# Different output formats
python scripts/doi_to_bibtex.py 10.1038/nature12345 --format json

Comprehensive Metadata Extraction

For DOIs, PMIDs, arXiv IDs, or URLs:

# Extract from DOI
python scripts/extract_metadata.py --doi 10.1038/s41586-021-03819-2

# Extract from PMID
python scripts/extract_metadata.py --pmid 34265844

# Extract from arXiv ID
python scripts/extract_metadata.py --arxiv 2103.14030

# Extract from URL
python scripts/extract_metadata.py --url "https://www.nature.com/articles/s41586-021-03819-2"

# Batch extraction from file (mixed identifiers)
python scripts/extract_metadata.py --input identifiers.txt --output citations.bib

Metadata Sources (see references/metadata_extraction.md):

1. CrossRef API: Primary source for DOIs

• Comprehensive metadata for journal articles
• Publisher-provided information
• Includes authors, title, journal, volume, pages, dates
• Free, no API key required

2. PubMed E-utilities: Biomedical literature

• Official NCBI metadata
• Includes MeSH terms, abstracts
• PMID and PMCID identifiers
• Free, API key recommended for high volume

3. arXiv API: Preprints in physics, math, CS, q-bio

• Complete metadata for preprints
• Version tracking
• Author affiliations
• Free, open access

4. DataCite API: Research datasets, software, other resources

• Metadata for non-traditional scholarly outputs
• DOIs for datasets and code
• Free access

What Gets Extracted:

• Required fields: author, title, year
• Journal articles: journal, volume, number, pages, DOI
• Books: publisher, ISBN, edition
• Conference papers: booktitle, conference location, pages
• Preprints: repository (arXiv, bioRxiv), preprint ID
• Additional: abstract, keywords, URL

Phase 2.5: Metadata Enrichment via Web Search (MANDATORY)

Goal: Detect and fill in any missing metadata fields using web search. This phase runs AFTER extraction and BEFORE formatting to ensure every BibTeX entry is complete.

Why This Is Critical: Metadata extraction from APIs (CrossRef, PubMed, arXiv) sometimes returns incomplete records — missing volume, pages, issue number, or DOI. These gaps must be filled before the bibliography is considered ready.

Step 1: Scan for Incomplete Entries

After extracting metadata, scan the BibTeX file for entries missing key fields:

Fields to check per entry type:

Any @article entry missing volume, pages, or doi is considered incomplete and must be enriched.

Step 2: Web Search for Missing Metadata

For each incomplete entry, use the parallel-web skill to search for the missing information:

Option A — Search by title and author (best for finding DOI):

parallel-cli search "FIRST_AUTHOR TITLE JOURNAL_NAME volume pages DOI" \
  --json --max-results 10 \
  -o sources/search_citation_CITATIONKEY.json

Option B — Extract from DOI page (best when DOI is known but volume/pages missing):

parallel-cli extract "https://doi.org/10.XXXX/YYYY" --json \
  --objective "extract complete citation metadata: volume, issue, pages, publication date" \
  -o sources/extract_doi_CITATIONKEY.json

Option C — Search CrossRef API directly (programmatic, fast):

parallel-cli search "crossref DOI metadata FIRST_AUTHOR TITLE" \
  --json --max-results 10 \
  -o sources/search_crossref_CITATIONKEY.json

Option D — Search Google Scholar (fallback for hard-to-find papers):

parallel-cli search "google scholar FIRST_AUTHOR TITLE YEAR complete citation" \
  --json --max-results 10 \
  -o sources/search_scholar_CITATIONKEY.json

Step 3: Update BibTeX Entries

After finding the missing metadata:

1. Open references.bib 2. Add the missing fields to the incomplete entry 3. Verify the found metadata is consistent with existing fields (same author, title, year) 4. Log each fix:

   [HH:MM:SS] METADATA ENRICHED: [CitationKey] - added volume={X}, pages={Y--Z}, doi={10.XXX/YYY} ✅

Step 4: Handle Unfindable Metadata

If metadata genuinely cannot be found after web search (very old paper, obscure conference, etc.):

1. Add a note field to the BibTeX entry explaining the gap:

   note = {Volume and pages not available — published online only}

2. Log the exception:

   [HH:MM:SS] METADATA INCOMPLETE: [CitationKey] - pages unavailable (online-only publication) ⚠️

3. These exceptions should be rare — most modern papers have complete metadata findable via web search.

Quick Reference: Common Missing Fields and Where to Find Them

---

Phase 3: BibTeX Formatting

Goal: Generate clean, properly formatted BibTeX entries.

Understanding BibTeX Entry Types

See references/bibtex_formatting.md for complete guide.

Common Entry Types:

• @article: Journal articles (most common)
• @book: Books
• @inproceedings: Conference papers
• @incollection: Book chapters
• @phdthesis: Dissertations
• @misc: Preprints, software, datasets

Required Fields by Type:

@article{citationkey,
  author  = {Last1, First1 and Last2, First2},
  title   = {Article Title},
  journal = {Journal Name},
  year    = {2024},
  volume  = {10},
  number  = {3},
  pages   = {123--145},
  doi     = {10.1234/example}
}

@inproceedings{citationkey,
  author    = {Last, First},
  title     = {Paper Title},
  booktitle = {Conference Name},
  year      = {2024},
  pages     = {1--10}
}

@book{citationkey,
  author    = {Last, First},
  title     = {Book Title},
  publisher = {Publisher Name},
  year      = {2024}
}

Formatting and Cleaning

Use the formatter to standardize BibTeX files:

# Format and clean BibTeX file
python scripts/format_bibtex.py references.bib \
  --output formatted_references.bib

# Sort entries by citation key
python scripts/format_bibtex.py references.bib \
  --sort key \
  --output sorted_references.bib

# Sort by year (newest first)
python scripts/format_bibtex.py references.bib \
  --sort year \
  --descending \
  --output sorted_references.bib

# Remove duplicates
python scripts/format_bibtex.py references.bib \
  --deduplicate \
  --output clean_references.bib

# Validate and report issues
python scripts/format_bibtex.py references.bib \
  --validate \
  --report validation_report.txt

Formatting Operations:

• Standardize field order
• Consistent indentation and spacing
• Proper capitalization in titles (protected with {})
• Standardized author name format
• Consistent citation key format
• Remove unnecessary fields
• Fix common errors (missing commas, braces)

Phase 4: Citation Validation

Goal: Verify all citations are accurate and complete.

Comprehensive Validation

# Validate BibTeX file
python scripts/validate_citations.py references.bib

# Validate against a venue standard (e.g., Nature, NeurIPS, Literature Review)
python scripts/validate_citations.py references.bib --venue nature
python scripts/validate_citations.py references.bib --venue neurips
python scripts/validate_citations.py references.bib --venue review

# Validate with custom minimum citation count
python scripts/validate_citations.py references.bib --min-count 40

# Check references against a written manuscript file (detect missing or unused citations)
python scripts/validate_citations.py references.bib --manuscript paper.md

# Generate detailed validation report
python scripts/validate_citations.py references.bib \
  --venue nature \
  --manuscript paper.md \
  --report validation_report.json \
  --verbose

Validation Checks (see references/citation_validation.md):

1. DOI Verification:

• DOI resolves correctly via doi.org
• Metadata matches between BibTeX and CrossRef
• No broken or invalid DOIs

2. Required Fields:

• All required fields present for entry type
• No empty or missing critical information
• Author names properly formatted

3. Data Consistency:

• Year is valid (4 digits, reasonable range)
• Volume/number are numeric
• Pages formatted correctly (e.g., 123--145)
• URLs are accessible

4. Duplicate Detection:

• Same DOI used multiple times
• Similar titles (possible duplicates)
• Same author/year/title combinations

5. Format Compliance:

• Valid BibTeX syntax
• Proper bracing and quoting
• Citation keys are unique
• Special characters handled correctly

Validation Output:

{
  "total_entries": 150,
  "valid_entries": 145,
  "errors": [
    {
      "citation_key": "Smith2023",
      "error_type": "missing_field",
      "field": "journal",
      "severity": "high"
    },
    {
      "citation_key": "Jones2022",
      "error_type": "invalid_doi",
      "doi": "10.1234/broken",
      "severity": "high"
    }
  ],
  "warnings": [
    {
      "citation_key": "Brown2021",
      "warning_type": "possible_duplicate",
      "duplicate_of": "Brown2021a",
      "severity": "medium"
    }
  ]
}

Citation Count Standards by Venue

Citations must always be high in number based on standards for journal and conference publications in the venue of choice or recommendation. Never settle for a sparse reference list; establish an authoritative, rich context with dense, verified citations.

Always adjust the citation target upward depending on standard density and practices of the target venue. Avoid 'lazy' citation over-repetition — do not repeatedly cite the same 1 or 2 papers to support multiple unrelated claims; draw from a diverse, high-quality set of reputable references.

Enforce these standards programmatically with validate_citations.py --venue <venue> or --min-count <N>.

Mandatory Post-Writing Reference Checks (Non-Negotiable)

Once the entire scientific report or paper has been drafted and written, perform a comprehensive post-writing verification of all citations before compiling the final deliverables:

1. Verify No Missing or Unresolved Citations: Check the draft or compiled document to ensure that every in-text citation correctly resolves to a reference in references.bib. There must be ZERO broken citation keys, missing identifiers, or unresolved references (e.g., [?] or [citation needed]). 2. Verify No Unused (Dangling) Bibliography Entries: Check that every entry in references.bib is actually cited in the body of the report. Remove any unused entries to keep the bibliography perfectly clean. 3. Verify Citation Quantity Against Target Standards: Ensure the final citation count meets or exceeds the high standard of the chosen or recommended venue (see table above). If the count is below standard, perform additional literature search first, find high-quality papers, and integrate them into appropriate sections. 4. Verify Metadata Completeness: Confirm that all cited entries contain complete, fully-verified fields (all author names, complete journal/conference names, exact year, volume, issue, page range, and valid DOI).

Run all of these checks in one command:

python scripts/validate_citations.py references.bib \
  --venue <venue> \
  --manuscript paper.md \
  --report post_writing_check.json

Phase 5: Integration with Writing Workflow

Building References for Manuscripts

Complete workflow for creating a bibliography:

# 1. Search for papers on your topic
python scripts/search_pubmed.py \
  '"CRISPR-Cas Systems"[MeSH] AND "Gene Editing"[MeSH]' \
  --date-start 2020 \
  --limit 200 \
  --output crispr_papers.json

# 2. Extract DOIs from search results and convert to BibTeX
python scripts/extract_metadata.py \
  --input crispr_papers.json \
  --output crispr_refs.bib

# 3. Add specific papers by DOI
python scripts/doi_to_bibtex.py 10.1038/nature12345 >> crispr_refs.bib
python scripts/doi_to_bibtex.py 10.1126/science.abcd1234 >> crispr_refs.bib

# 4. Format and clean the BibTeX file
python scripts/format_bibtex.py crispr_refs.bib \
  --deduplicate \
  --sort year \
  --descending \
  --output references.bib

# 5. Validate all citations
python scripts/validate_citations.py references.bib \
  --auto-fix \
  --report validation.json \
  --output final_references.bib

# 6. Review validation report and fix any remaining issues
cat validation.json

# 7. Use in your LaTeX document
# \bibliography{final_references}

Integration with Literature Review Skill

This skill complements the literature-review skill:

Literature Review Skill → Systematic search and synthesis Citation Management Skill → Technical citation handling

Combined Workflow: 1. Use literature-review for comprehensive multi-database search 2. Use citation-management to extract and validate all citations 3. Use literature-review to synthesize findings thematically 4. Use citation-management to verify final bibliography accuracy

# After completing literature review
# Verify all citations in the review document
python scripts/validate_citations.py my_review_references.bib --report review_validation.json

# Format for specific citation style if needed
python scripts/format_bibtex.py my_review_references.bib \
  --style nature \
  --output formatted_refs.bib

Search Strategies

Google Scholar Best Practices

Finding Seminal and High-Impact Papers (CRITICAL):

Always prioritize papers based on citation count, venue quality, and author reputation:

Citation Count Thresholds:

Venue Quality Tiers:

• Tier 1 (Prefer): Nature, Science, Cell, NEJM, Lancet, JAMA, PNAS
• Tier 2 (High Priority): Impact Factor >10, top conferences (NeurIPS, ICML, ICLR)
• Tier 3 (Good): Specialized journals (IF 5-10)
• Tier 4 (Sparingly): Lower-impact peer-reviewed venues

Author Reputation Indicators:

• Senior researchers with h-index >40
• Multiple publications in Tier-1 venues
• Leadership at recognized institutions
• Awards and editorial positions

Search Strategies for High-Impact Papers:

• Sort by citation count (most cited first)
• Look for review articles from Tier-1 journals for overview
• Check "Cited by" for impact assessment and recent follow-up work
• Use citation alerts for tracking new citations to key papers
• Filter by top venues using source:Nature or source:Science
• Search for papers by known field leaders using author:LastName

Advanced Operators (full list in references/google_scholar_search.md):

"exact phrase"           # Exact phrase matching
author:lastname          # Search by author
intitle:keyword          # Search in title only
source:journal           # Search specific journal
-exclude                 # Exclude terms
OR                       # Alternative terms
2020..2024              # Year range

Example Searches:

# Find recent reviews on a topic
"CRISPR" intitle:review 2023..2024

# Find papers by specific author on topic
author:Church "synthetic biology"

# Find highly cited foundational work
"deep learning" 2012..2015 sort:citations

# Exclude surveys and focus on methods
"protein folding" -survey -review intitle:method

PubMed Best Practices

Using MeSH Terms: MeSH (Medical Subject Headings) provides controlled vocabulary for precise searching.

1. Find MeSH terms at https://meshb.nlm.nih.gov/search 2. Use in queries: "Diabetes Mellitus, Type 2"[MeSH] 3. Combine with keywords for comprehensive coverage

Field Tags:

[Title]              # Search in title only
[Title/Abstract]     # Search in title or abstract
[Author]             # Search by author name
[Journal]            # Search specific journal
[Publication Date]   # Date range
[Publication Type]   # Article type
[MeSH]              # MeSH term

Building Complex Queries:

# Clinical trials on diabetes treatment published recently
"Diabetes Mellitus, Type 2"[MeSH] AND "Drug Therapy"[MeSH] 
AND "Clinical Trial"[Publication Type] AND 2020:2024[Publication Date]

# Reviews on CRISPR in specific journal
"CRISPR-Cas Systems"[MeSH] AND "Nature"[Journal] AND "Review"[Publication Type]

# Specific author's recent work
"Smith AB"[Author] AND cancer[Title/Abstract] AND 2022:2024[Publication Date]

E-utilities for Automation: The scripts use NCBI E-utilities API for programmatic access:

• ESearch: Search and retrieve PMIDs
• EFetch: Retrieve full metadata
• ESummary: Get summary information
• ELink: Find related articles

See references/pubmed_search.md for complete API documentation.

Tools and Scripts

search_google_scholar.py

Search Google Scholar and export results.

Features:

• Automated searching with rate limiting
• Pagination support
• Year range filtering
• Export to JSON or BibTeX
• Citation count information

Usage:

# Basic search
python scripts/search_google_scholar.py "quantum computing"

# Advanced search with filters
python scripts/search_google_scholar.py "quantum computing" \
  --year-start 2020 \
  --year-end 2024 \
  --limit 100 \
  --sort-by citations \
  --output quantum_papers.json

# Export directly to BibTeX
python scripts/search_google_scholar.py "machine learning" \
  --limit 50 \
  --format bibtex \
  --output ml_papers.bib

search_pubmed.py

Search PubMed using E-utilities API.

Features:

• Complex query support (MeSH, field tags, Boolean)
• Date range filtering
• Publication type filtering
• Batch retrieval with metadata
• Export to JSON or BibTeX

Usage:

# Simple keyword search
python scripts/search_pubmed.py "CRISPR gene editing"

# Complex query with filters
python scripts/search_pubmed.py \
  --query '"CRISPR-Cas Systems"[MeSH] AND "therapeutic"[Title/Abstract]' \
  --date-start 2020-01-01 \
  --date-end 2024-12-31 \
  --publication-types "Clinical Trial,Review" \
  --limit 200 \
  --output crispr_therapeutic.json

# Export to BibTeX
python scripts/search_pubmed.py "Alzheimer's disease" \
  --limit 100 \
  --format bibtex \
  --output alzheimers.bib

extract_metadata.py

Extract complete metadata from paper identifiers.

Features:

• Supports DOI, PMID, arXiv ID, URL
• Queries CrossRef, PubMed, arXiv APIs
• Handles multiple identifier types
• Batch processing
• Multiple output formats

Usage:

# Single DOI
python scripts/extract_metadata.py --doi 10.1038/s41586-021-03819-2

# Single PMID
python scripts/extract_metadata.py --pmid 34265844

# Single arXiv ID
python scripts/extract_metadata.py --arxiv 2103.14030

# From URL
python scripts/extract_metadata.py \
  --url "https://www.nature.com/articles/s41586-021-03819-2"

# Batch processing (file with one identifier per line)
python scripts/extract_metadata.py \
  --input paper_ids.txt \
  --output references.bib

# Different output formats
python scripts/extract_metadata.py \
  --doi 10.1038/nature12345 \
  --format json  # or bibtex, yaml

validate_citations.py

Validate BibTeX entries for accuracy, completeness, citation count standard compliance, and manuscript integration.

Features:

• DOI verification via doi.org and CrossRef
• Required field checking
• Duplicate detection
• Format validation
• Publication standard citation count checks against specified venues (Nature, NeurIPS, review, etc.) or custom thresholds.
• Mandatory post-writing checks matching manuscript citations (Markdown or LaTeX) with defined BibTeX entries to detect unresolved/missing or unused references.
• Detailed reporting

Usage:

# Basic validation
python scripts/validate_citations.py references.bib

# Validate against a venue standard (e.g., Nature, NeurIPS, Literature Review)
python scripts/validate_citations.py references.bib --venue nature
python scripts/validate_citations.py references.bib --venue neurips
python scripts/validate_citations.py references.bib --venue review

# Validate with custom minimum citation count
python scripts/validate_citations.py references.bib --min-count 40

# Check references against a written manuscript file (detect missing or unused citations)
python scripts/validate_citations.py references.bib --manuscript paper.md

# Combined full validation
python scripts/validate_citations.py references.bib \
  --venue nature \
  --manuscript paper.md \
  --report validation_report.json \
  --verbose

format_bibtex.py

Format and clean BibTeX files.

Features:

• Standardize formatting
• Sort entries (by key, year, author)
• Remove duplicates
• Validate syntax
• Fix common errors
• Enforce citation key conventions

Usage:

# Basic formatting
python scripts/format_bibtex.py references.bib

# Sort by year (newest first)
python scripts/format_bibtex.py references.bib \
  --sort year \
  --descending \
  --output sorted_refs.bib

# Remove duplicates
python scripts/format_bibtex.py references.bib \
  --deduplicate \
  --output clean_refs.bib

# Complete cleanup
python scripts/format_bibtex.py references.bib \
  --deduplicate \
  --sort year \
  --validate \
  --auto-fix \
  --output final_refs.bib

doi_to_bibtex.py

Quick DOI to BibTeX conversion.

Features:

• Fast single DOI conversion
• Batch processing
• Multiple output formats
• Clipboard support

Usage:

# Single DOI
python scripts/doi_to_bibtex.py 10.1038/s41586-021-03819-2

# Multiple DOIs
python scripts/doi_to_bibtex.py \
  10.1038/nature12345 \
  10.1126/science.abc1234 \
  10.1016/j.cell.2023.01.001

# From file (one DOI per line)
python scripts/doi_to_bibtex.py --input dois.txt --output references.bib

# Copy to clipboard
python scripts/doi_to_bibtex.py 10.1038/nature12345 --clipboard

Best Practices

Search Strategy

1. Start broad, then narrow:

• Begin with general terms to understand the field
• Refine with specific keywords and filters
• Use synonyms and related terms

2. Use multiple sources:

• Google Scholar for comprehensive coverage
• PubMed for biomedical focus
• arXiv for preprints
• Combine results for completeness

3. Leverage citations:

• Check "Cited by" for seminal papers
• Review references from key papers
• Use citation networks to discover related work

4. Document your searches:

• Save search queries and dates
• Record number of results
• Note any filters or restrictions applied

Metadata Extraction

1. Always use DOIs when available:

• Most reliable identifier
• Permanent link to the publication
• Best metadata source via CrossRef

2. Verify extracted metadata:

• Check author names are correct
• Verify journal/conference names
• Confirm publication year
• Validate page numbers and volume

3. Handle edge cases:

• Preprints: Include repository and ID
• Preprints later published: Use published version
• Conference papers: Include conference name and location
• Book chapters: Include book title and editors

4. Maintain consistency:

• Use consistent author name format
• Standardize journal abbreviations
• Use same DOI format (URL preferred)

BibTeX Quality

1. Follow conventions:

• Use meaningful citation keys (FirstAuthor2024keyword)
• Protect capitalization in titles with {}
• Use -- for page ranges (not single dash)
• Include DOI field for all modern publications

2. Keep it clean:

• Remove unnecessary fields
• No redundant information
• Consistent formatting
• Validate syntax regularly

3. Organize systematically:

• Sort by year or topic
• Group related papers
• Use separate files for different projects
• Merge carefully to avoid duplicates

Validation

1. Validate early and often:

• Check citations when adding them
• Validate complete bibliography before submission
• Re-validate after any manual edits

2. Fix issues promptly:

• Broken DOIs: Find correct identifier
• Missing fields: Extract from original source
• Duplicates: Choose best version, remove others
• Format errors: Use auto-fix when safe

3. Manual review for critical citations:

• Verify key papers cited correctly
• Check author names match publication
• Confirm page numbers and volume
• Ensure URLs are current

Common Pitfalls to Avoid

1. Single source bias: Only using Google Scholar or PubMed

• Solution: Search multiple databases for comprehensive coverage

2. Accepting metadata blindly: Not verifying extracted information

• Solution: Spot-check extracted metadata against original sources

3. Ignoring DOI errors: Broken or incorrect DOIs in bibliography

• Solution: Run validation before final submission

4. Inconsistent formatting: Mixed citation key styles, formatting

• Solution: Use format_bibtex.py to standardize

5. Duplicate entries: Same paper cited multiple times with different keys

• Solution: Use duplicate detection in validation

6. Missing required fields: Incomplete BibTeX entries (volume, pages, DOI missing)

• Solution: Run Phase 2.5 metadata enrichment — web search for every missing field before proceeding. NEVER leave an @article entry without volume, pages, and DOI.

7. Outdated preprints: Citing preprint when published version exists

• Solution: Check if preprints have been published, update to journal version

8. Special character issues: Broken LaTeX compilation due to characters

• Solution: Use proper escaping or Unicode in BibTeX

9. No validation before submission: Submitting with citation errors

• Solution: Always run validation as final check

10. Manual BibTeX entry: Typing entries by hand

• Solution: Always extract from metadata sources using scripts

Example Workflows

Example 1: Building a Bibliography for a Paper

# Step 1: Find key papers on your topic
python scripts/search_google_scholar.py "transformer neural networks" \
  --year-start 2017 \
  --limit 50 \
  --output transformers_gs.json

python scripts/search_pubmed.py "deep learning medical imaging" \
  --date-start 2020 \
  --limit 50 \
  --output medical_dl_pm.json

# Step 2: Extract metadata from search results
python scripts/extract_metadata.py \
  --input transformers_gs.json \
  --output transformers.bib

python scripts/extract_metadata.py \
  --input medical_dl_pm.json \
  --output medical.bib

# Step 3: Add specific papers you already know
python scripts/doi_to_bibtex.py 10.1038/s41586-021-03819-2 >> specific.bib
python scripts/doi_to_bibtex.py 10.1126/science.aam9317 >> specific.bib

# Step 4: Combine all BibTeX files
cat transformers.bib medical.bib specific.bib > combined.bib

# Step 5: Format and deduplicate
python scripts/format_bibtex.py combined.bib \
  --deduplicate \
  --sort year \
  --descending \
  --output formatted.bib

# Step 6: Validate
python scripts/validate_citations.py formatted.bib \
  --auto-fix \
  --report validation.json \
  --output final_references.bib

# Step 7: Review any issues
cat validation.json | grep -A 3 '"errors"'

# Step 8: Use in LaTeX
# \bibliography{final_references}

Example 2: Converting a List of DOIs

# You have a text file with DOIs (one per line)
# dois.txt contains:
# 10.1038/s41586-021-03819-2
# 10.1126/science.aam9317
# 10.1016/j.cell.2023.01.001

# Convert all to BibTeX
python scripts/doi_to_bibtex.py --input dois.txt --output references.bib

# Validate the result
python scripts/validate_citations.py references.bib --verbose

Example 3: Cleaning an Existing BibTeX File

# You have a messy BibTeX file from various sources
# Clean it up systematically

# Step 1: Format and standardize
python scripts/format_bibtex.py messy_references.bib \
  --output step1_formatted.bib

# Step 2: Remove duplicates
python scripts/format_bibtex.py step1_formatted.bib \
  --deduplicate \
  --output step2_deduplicated.bib

# Step 3: Validate and auto-fix
python scripts/validate_citations.py step2_deduplicated.bib \
  --auto-fix \
  --output step3_validated.bib

# Step 4: Sort by year
python scripts/format_bibtex.py step3_validated.bib \
  --sort year \
  --descending \
  --output clean_references.bib

# Step 5: Final validation report
python scripts/validate_citations.py clean_references.bib \
  --report final_validation.json \
  --verbose

# Review report
cat final_validation.json

Example 4: Finding and Citing Seminal Papers

# Find highly cited papers on a topic
python scripts/search_google_scholar.py "AlphaFold protein structure" \
  --year-start 2020 \
  --year-end 2024 \
  --sort-by citations \
  --limit 20 \
  --output alphafold_seminal.json

# Extract the top 10 by citation count
# (script will have included citation counts in JSON)

# Convert to BibTeX
python scripts/extract_metadata.py \
  --input alphafold_seminal.json \
  --output alphafold_refs.bib

# The BibTeX file now contains the most influential papers

Integration with Other Skills

Literature Review Skill

Citation Management provides the technical infrastructure for Literature Review:

• Literature Review: Multi-database systematic search and synthesis
• Citation Management: Metadata extraction and validation

Combined workflow: 1. Use literature-review for systematic search methodology 2. Use citation-management to extract and validate citations 3. Use literature-review to synthesize findings 4. Use citation-management to ensure bibliography accuracy

Scientific Writing Skill

Citation Management ensures accurate references for Scientific Writing:

• Export validated BibTeX for use in LaTeX manuscripts
• Verify citations match publication standards
• Format references according to journal requirements

Venue Templates Skill

Citation Management works with Venue Templates for submission-ready manuscripts:

• Different venues require different citation styles
• Generate properly formatted references
• Validate citations meet venue requirements

Resources

Bundled Resources

References (in references/):

• google_scholar_search.md: Complete Google Scholar search guide
• pubmed_search.md: PubMed and E-utilities API documentation
• metadata_extraction.md: Metadata sources and field requirements
• citation_validation.md: Validation criteria and quality checks
• bibtex_formatting.md: BibTeX entry types and formatting rules

Scripts (in scripts/):

• search_google_scholar.py: Google Scholar search automation
• search_pubmed.py: PubMed E-utilities API client
• extract_metadata.py: Universal metadata extractor
• validate_citations.py: Citation validation and verification
• format_bibtex.py: BibTeX formatter and cleaner
• doi_to_bibtex.py: Quick DOI to BibTeX converter

Assets (in assets/):

• bibtex_template.bib: Example BibTeX entries for all types
• citation_checklist.md: Quality assurance checklist

External Resources

Search Engines:

• Google Scholar: https://scholar.google.com/
• PubMed: https://pubmed.ncbi.nlm.nih.gov/
• PubMed Advanced Search: https://pubmed.ncbi.nlm.nih.gov/advanced/

Metadata APIs:

• CrossRef API: https://api.crossref.org/
• PubMed E-utilities: https://www.ncbi.nlm.nih.gov/books/NBK25501/
• arXiv API: https://arxiv.org/help/api/
• DataCite API: https://api.datacite.org/

Tools and Validators:

• MeSH Browser: https://meshb.nlm.nih.gov/search
• DOI Resolver: https://doi.org/
• BibTeX Format: http://www.bibtex.org/Format/

Citation Styles:

• BibTeX documentation: http://www.bibtex.org/
• LaTeX bibliography management: https://www.overleaf.com/learn/latex/Bibliography_management

Dependencies

Required Python Packages

# Core dependencies
pip install requests  # HTTP requests for APIs
pip install bibtexparser  # BibTeX parsing and formatting
pip install biopython  # PubMed E-utilities access

# Optional (for Google Scholar)
pip install scholarly  # Google Scholar API wrapper
# or
pip install selenium  # For more robust Scholar scraping

Optional Tools

# For advanced validation
pip install crossref-commons  # Enhanced CrossRef API access
pip install pylatexenc  # LaTeX special character handling

Summary

The citation-management skill provides:

1. Comprehensive search capabilities for Google Scholar and PubMed 2. Automated metadata extraction from DOI, PMID, arXiv ID, URLs 3. Citation validation with DOI verification and completeness checking 4. BibTeX formatting with standardization and cleaning tools 5. Quality assurance through validation and reporting 6. Integration with scientific writing workflow 7. Reproducibility through documented search and extraction methods

Use this skill to maintain accurate, complete citations throughout your research and ensure publication-ready bibliographies.

Citation Quality Checklist

Use this checklist to ensure your citations are accurate, complete, and properly formatted before final submission.

Pre-Submission Checklist

✓ Metadata Accuracy

• [ ] All author names are correct and properly formatted
• [ ] Article titles match the actual publication
• [ ] Journal/conference names are complete (not abbreviated unless required)
• [ ] Publication years are accurate
• [ ] Volume and issue numbers are correct
• [ ] Page ranges are accurate

✓ Required Fields

• [ ] All @article entries have: author, title, journal, year
• [ ] All @book entries have: author/editor, title, publisher, year
• [ ] All @inproceedings entries have: author, title, booktitle, year
• [ ] Modern papers (2000+) include DOI when available
• [ ] All entries have unique citation keys

✓ DOI Verification

• [ ] All DOIs are properly formatted (10.XXXX/...)
• [ ] DOIs resolve correctly to the article
• [ ] No DOI prefix in the BibTeX field (no "doi:" or "https://doi.org/")
• [ ] Metadata from CrossRef matches your BibTeX entry
• [ ] Run: python scripts/validate_citations.py references.bib --check-dois

✓ Formatting Consistency

• [ ] Page ranges use double hyphen (--) not single (-)
• [ ] No "pp." prefix in pages field
• [ ] Author names use "and" separator (not semicolon or ampersand)
• [ ] Capitalization protected in titles ({AlphaFold}, {CRISPR}, etc.)
• [ ] Month names use standard abbreviations if included
• [ ] Citation keys follow consistent format

✓ Duplicate Detection

• [ ] No duplicate DOIs in bibliography
• [ ] No duplicate citation keys
• [ ] No near-duplicate titles
• [ ] Preprints updated to published versions when available
• [ ] Run: python scripts/validate_citations.py references.bib

✓ Special Characters

• [ ] Accented characters properly formatted (e.g., {\"u} for ü)
• [ ] Mathematical symbols use LaTeX commands
• [ ] Chemical formulas properly formatted
• [ ] No unescaped special characters (%, &, $, #, etc.)

✓ BibTeX Syntax

• [ ] All entries have balanced braces {}
• [ ] Fields separated by commas
• [ ] No comma after last field in each entry
• [ ] Valid entry types (@article, @book, etc.)
• [ ] Run: python scripts/validate_citations.py references.bib

✓ File Organization

• [ ] Bibliography sorted in logical order (by year, author, or key)
• [ ] Consistent formatting throughout
• [ ] No formatting inconsistencies between entries
• [ ] Run: python scripts/format_bibtex.py references.bib --sort year

Automated Validation

Step 1: Format and Clean

python scripts/format_bibtex.py references.bib \
  --deduplicate \
  --sort year \
  --descending \
  --output clean_references.bib

What this does:

• Removes duplicates
• Standardizes formatting
• Fixes common issues (page ranges, DOI format, etc.)
• Sorts by year (newest first)

Step 2: Validate

python scripts/validate_citations.py clean_references.bib \
  --check-dois \
  --report validation_report.json \
  --verbose

What this does:

• Checks required fields
• Verifies DOIs resolve
• Detects duplicates
• Validates syntax
• Generates detailed report

Step 3: Review Report

cat validation_report.json

Address any:

• Errors: Must fix (missing fields, broken DOIs, syntax errors)
• Warnings: Should fix (missing recommended fields, formatting issues)
• Duplicates: Remove or consolidate

Step 4: Final Check

python scripts/validate_citations.py clean_references.bib --verbose

Goal: Zero errors, minimal warnings

Manual Review Checklist

Critical Citations (Top 10-20 Most Important)

For your most important citations, manually verify:

• [ ] Visit DOI link and confirm it's the correct article
• [ ] Check author names against the actual publication
• [ ] Verify year matches publication date
• [ ] Confirm journal/conference name is correct
• [ ] Check that volume/pages match

Common Issues to Watch For

Missing Information:

• [ ] No DOI for papers published after 2000
• [ ] Missing volume or page numbers for journal articles
• [ ] Missing publisher for books
• [ ] Missing conference location for proceedings

Formatting Errors:

• [ ] Single hyphen in page ranges (123-145 → 123--145)
• [ ] Ampersands in author lists (Smith & Jones → Smith and Jones)
• [ ] Unprotected acronyms in titles (DNA → {DNA})
• [ ] DOI includes URL prefix (https://doi.org/10.xxx → 10.xxx)

Metadata Mismatches:

• [ ] Author names differ from publication
• [ ] Year is online-first instead of print publication
• [ ] Journal name abbreviated when it should be full
• [ ] Volume/issue numbers swapped

Duplicates:

• [ ] Same paper cited with different citation keys
• [ ] Preprint and published version both cited
• [ ] Conference paper and journal version both cited

Field-Specific Checks

Biomedical Sciences

• [ ] PubMed Central ID (PMCID) included when available
• [ ] MeSH terms appropriate (if using)
• [ ] Clinical trial registration number included (if applicable)
• [ ] All references to treatments/drugs accurately cited

Computer Science

• [ ] arXiv ID included for preprints
• [ ] Conference proceedings properly cited (not just "NeurIPS")
• [ ] Software/dataset citations include version numbers
• [ ] GitHub links stable and permanent

General Sciences

• [ ] Data availability statements properly cited
• [ ] Retracted papers identified and removed
• [ ] Preprints checked for published versions
• [ ] Supplementary materials referenced if critical

Final Pre-Submission Steps

1 Week Before Submission

• [ ] Run full validation with DOI checking
• [ ] Fix all errors and critical warnings
• [ ] Manually verify top 10-20 most important citations
• [ ] Check for any retracted papers

3 Days Before Submission

• [ ] Re-run validation after any manual edits
• [ ] Ensure all in-text citations have corresponding bibliography entries
• [ ] Ensure all bibliography entries are cited in text
• [ ] Check citation style matches journal requirements

1 Day Before Submission

• [ ] Final validation check
• [ ] LaTeX compilation successful with no warnings
• [ ] PDF renders all citations correctly
• [ ] Bibliography appears in correct format
• [ ] No placeholder citations (Smith et al. XXXX)

Submission Day

• [ ] One final validation run
• [ ] No last-minute edits without re-validation
• [ ] Bibliography file included in submission package
• [ ] Figures/tables referenced in text match bibliography

Quality Metrics

Excellent Bibliography

• ✓ 100% of entries have DOIs (for modern papers)
• ✓ Zero validation errors
• ✓ Zero missing required fields
• ✓ Zero broken DOIs
• ✓ Zero duplicates
• ✓ Consistent formatting throughout
• ✓ All citations manually spot-checked

Acceptable Bibliography

• ✓ 90%+ of modern entries have DOIs
• ✓ Zero high-severity errors
• ✓ Minor warnings only (e.g., missing recommended fields)
• ✓ Key citations manually verified
• ✓ Compilation succeeds without errors

Needs Improvement

• ✗ Missing DOIs for recent papers
• ✗ High-severity validation errors
• ✗ Broken or incorrect DOIs
• ✗ Duplicate entries
• ✗ Inconsistent formatting
• ✗ Compilation warnings or errors

Emergency Fixes

If you discover issues at the last minute:

Broken DOI

# Find correct DOI
# Option 1: Search CrossRef
# https://www.crossref.org/

# Option 2: Search on publisher website
# Option 3: Google Scholar

# Re-extract metadata
python scripts/extract_metadata.py --doi CORRECT_DOI

Missing Information

# Extract from DOI
python scripts/extract_metadata.py --doi 10.xxxx/yyyy

# Or from PMID (biomedical)
python scripts/extract_metadata.py --pmid 12345678

# Or from arXiv
python scripts/extract_metadata.py --arxiv 2103.12345

Duplicate Entries

# Auto-remove duplicates
python scripts/format_bibtex.py references.bib \
  --deduplicate \
  --output fixed_references.bib

Formatting Errors

# Auto-fix common issues
python scripts/format_bibtex.py references.bib \
  --output fixed_references.bib

# Then validate
python scripts/validate_citations.py fixed_references.bib

Long-Term Best Practices

During Research

• [ ] Add citations to bibliography file as you find them
• [ ] Extract metadata immediately using DOI
• [ ] Validate after every 10-20 additions
• [ ] Keep bibliography file under version control

During Writing

• [ ] Cite as you write
• [ ] Use consistent citation keys
• [ ] Don't delay adding references
• [ ] Validate weekly

Before Submission

• [ ] Allow 2-3 days for citation cleanup
• [ ] Don't wait until the last day
• [ ] Automate what you can
• [ ] Manually verify critical citations

Tool Quick Reference

Extract Metadata

# From DOI
python scripts/doi_to_bibtex.py 10.1038/nature12345

# From multiple sources
python scripts/extract_metadata.py \
  --doi 10.1038/nature12345 \
  --pmid 12345678 \
  --arxiv 2103.12345 \
  --output references.bib

Validate

# Basic validation
python scripts/validate_citations.py references.bib

# With DOI checking (slow but thorough)
python scripts/validate_citations.py references.bib --check-dois

# Generate report
python scripts/validate_citations.py references.bib \
  --report validation.json \
  --verbose

Format and Clean

# Format and fix issues
python scripts/format_bibtex.py references.bib

# Remove duplicates and sort
python scripts/format_bibtex.py references.bib \
  --deduplicate \
  --sort year \
  --descending \
  --output clean_refs.bib

Summary

Minimum Requirements: 1. Run format_bibtex.py --deduplicate 2. Run validate_citations.py 3. Fix all errors 4. Compile successfully

Recommended: 1. Format, deduplicate, and sort 2. Validate with --check-dois 3. Fix all errors and warnings 4. Manually verify top citations 5. Re-validate after fixes

Best Practice: 1. Validate throughout research process 2. Use automated tools consistently 3. Keep bibliography clean and organized 4. Document any special cases 5. Final validation 1-3 days before submission

Remember: Citation errors reflect poorly on your scholarship. Taking time to ensure accuracy is worthwhile!

BibTeX Formatting Guide

Comprehensive guide to BibTeX entry types, required fields, formatting conventions, and best practices.

Overview

BibTeX is the standard bibliography format for LaTeX documents. Proper formatting ensures:

• Correct citation rendering
• Consistent formatting
• Compatibility with citation styles
• No compilation errors

This guide covers all common entry types and formatting rules.

Entry Types

@article - Journal Articles

Most common entry type for peer-reviewed journal articles.

Required fields:

• author: Author names
• title: Article title
• journal: Journal name
• year: Publication year

Optional fields:

• volume: Volume number
• number: Issue number
• pages: Page range
• month: Publication month
• doi: Digital Object Identifier
• url: URL
• note: Additional notes

Template:

@article{CitationKey2024,
  author  = {Last1, First1 and Last2, First2},
  title   = {Article Title Here},
  journal = {Journal Name},
  year    = {2024},
  volume  = {10},
  number  = {3},
  pages   = {123--145},
  doi     = {10.1234/journal.2024.123456},
  month   = jan
}

Example:

@article{Jumper2021,
  author  = {Jumper, John and Evans, Richard and Pritzel, Alexander and others},
  title   = {Highly Accurate Protein Structure Prediction with {AlphaFold}},
  journal = {Nature},
  year    = {2021},
  volume  = {596},
  number  = {7873},
  pages   = {583--589},
  doi     = {10.1038/s41586-021-03819-2}
}

@book - Books

For entire books.

Required fields:

• author OR editor: Author(s) or editor(s)
• title: Book title
• publisher: Publisher name
• year: Publication year

Optional fields:

• volume: Volume number (if multi-volume)
• series: Series name
• address: Publisher location
• edition: Edition number
• isbn: ISBN
• url: URL

Template:

@book{CitationKey2024,
  author    = {Last, First},
  title     = {Book Title},
  publisher = {Publisher Name},
  year      = {2024},
  edition   = {3},
  address   = {City, Country},
  isbn      = {978-0-123-45678-9}
}

Example:

@book{Kumar2021,
  author    = {Kumar, Vinay and Abbas, Abul K. and Aster, Jon C.},
  title     = {Robbins and Cotran Pathologic Basis of Disease},
  publisher = {Elsevier},
  year      = {2021},
  edition   = {10},
  address   = {Philadelphia, PA},
  isbn      = {978-0-323-53113-9}
}

@inproceedings - Conference Papers

For papers in conference proceedings.

Required fields:

• author: Author names
• title: Paper title
• booktitle: Conference/proceedings name
• year: Year

Optional fields:

• editor: Proceedings editor(s)
• volume: Volume number
• series: Series name
• pages: Page range
• address: Conference location
• month: Conference month
• organization: Organizing body
• publisher: Publisher
• doi: DOI

Template:

@inproceedings{CitationKey2024,
  author    = {Last, First},
  title     = {Paper Title},
  booktitle = {Proceedings of Conference Name},
  year      = {2024},
  pages     = {123--145},
  address   = {City, Country},
  month     = jun
}

Example:

@inproceedings{Vaswani2017,
  author    = {Vaswani, Ashish and Shazeer, Noam and Parmar, Niki and others},
  title     = {Attention is All You Need},
  booktitle = {Advances in Neural Information Processing Systems 30 (NeurIPS 2017)},
  year      = {2017},
  pages     = {5998--6008},
  address   = {Long Beach, CA}
}

Note: @conference is an alias for @inproceedings.

@incollection - Book Chapters

For chapters in edited books.

Required fields:

• author: Chapter author(s)
• title: Chapter title
• booktitle: Book title
• publisher: Publisher name
• year: Publication year

Optional fields:

• editor: Book editor(s)
• volume: Volume number
• series: Series name
• type: Type of section (e.g., "chapter")
• chapter: Chapter number
• pages: Page range
• address: Publisher location
• edition: Edition
• month: Month

Template:

@incollection{CitationKey2024,
  author    = {Last, First},
  title     = {Chapter Title},
  booktitle = {Book Title},
  editor    = {Editor, Last and Editor2, Last},
  publisher = {Publisher Name},
  year      = {2024},
  pages     = {123--145},
  chapter   = {5}
}

Example:

@incollection{Brown2020,
  author    = {Brown, Peter O. and Botstein, David},
  title     = {Exploring the New World of the Genome with {DNA} Microarrays},
  booktitle = {DNA Microarrays: A Molecular Cloning Manual},
  editor    = {Eisen, Michael B. and Brown, Patrick O.},
  publisher = {Cold Spring Harbor Laboratory Press},
  year      = {2020},
  pages     = {1--45},
  address   = {Cold Spring Harbor, NY}
}

@phdthesis - Doctoral Dissertations

For PhD dissertations and theses.

Required fields:

• author: Author name
• title: Thesis title
• school: Institution
• year: Year

Optional fields:

• type: Type (e.g., "PhD dissertation", "PhD thesis")
• address: Institution location
• month: Month
• url: URL
• note: Additional notes

Template:

@phdthesis{CitationKey2024,
  author = {Last, First},
  title  = {Dissertation Title},
  school = {University Name},
  year   = {2024},
  type   = {{PhD} dissertation},
  address = {City, State}
}

Example:

@phdthesis{Johnson2023,
  author  = {Johnson, Mary L.},
  title   = {Novel Approaches to Cancer Immunotherapy Using {CRISPR} Technology},
  school  = {Stanford University},
  year    = {2023},
  type    = {{PhD} dissertation},
  address = {Stanford, CA}
}

Note: @mastersthesis is similar but for Master's theses.

@mastersthesis - Master's Theses

For Master's theses.

Required fields:

• author: Author name
• title: Thesis title
• school: Institution
• year: Year

Template:

@mastersthesis{CitationKey2024,
  author = {Last, First},
  title  = {Thesis Title},
  school = {University Name},
  year   = {2024}
}

@misc - Miscellaneous

For items that don't fit other categories (preprints, datasets, software, websites, etc.).

Required fields:

• author (if known)
• title
• year

Optional fields:

• howpublished: Repository, website, format
• url: URL
• doi: DOI
• note: Additional information
• month: Month

Template for preprints:

@misc{CitationKey2024,
  author       = {Last, First},
  title        = {Preprint Title},
  year         = {2024},
  howpublished = {bioRxiv},
  doi          = {10.1101/2024.01.01.123456},
  note         = {Preprint}
}

Template for datasets:

@misc{DatasetName2024,
  author       = {Last, First},
  title        = {Dataset Title},
  year         = {2024},
  howpublished = {Zenodo},
  doi          = {10.5281/zenodo.123456},
  note         = {Version 1.2}
}

Template for software:

@misc{SoftwareName2024,
  author       = {Last, First},
  title        = {Software Name},
  year         = {2024},
  howpublished = {GitHub},
  url          = {https://github.com/user/repo},
  note         = {Version 2.0}
}

@techreport - Technical Reports

For technical reports.

Required fields:

• author: Author name(s)
• title: Report title
• institution: Institution
• year: Year

Optional fields:

• type: Type of report
• number: Report number
• address: Institution location
• month: Month

Template:

@techreport{CitationKey2024,
  author      = {Last, First},
  title       = {Report Title},
  institution = {Institution Name},
  year        = {2024},
  type        = {Technical Report},
  number      = {TR-2024-01}
}

@unpublished - Unpublished Work

For unpublished works (not preprints - use @misc for those).

Required fields:

• author: Author name(s)
• title: Work title
• note: Description

Optional fields:

• month: Month
• year: Year

Template:

@unpublished{CitationKey2024,
  author = {Last, First},
  title  = {Work Title},
  note   = {Unpublished manuscript},
  year   = {2024}
}

@online/@electronic - Online Resources

For web pages and online-only content.

Note: Not standard BibTeX, but supported by many bibliography packages (biblatex).

Required fields:

• author OR organization
• title
• url
• year

Template:

@online{CitationKey2024,
  author = {{Organization Name}},
  title  = {Page Title},
  url    = {https://example.com/page},
  year   = {2024},
  note   = {Accessed: 2024-01-15}
}

Formatting Rules

Citation Keys

Convention: FirstAuthorYEARkeyword

Examples:

Smith2024protein
Doe2023machine
JohnsonWilliams2024cancer  % Multiple authors, no space
NatureEditorial2024        % No author, use publication
WHO2024guidelines          % Organization author

Rules:

• Alphanumeric plus: -, _, ., :
• No spaces
• Case-sensitive
• Unique within file
• Descriptive

Avoid:

• Special characters: @, #, &, %, $
• Spaces: use CamelCase or underscores
• Starting with numbers: 2024Smith (some systems disallow)

Author Names

Recommended format: Last, First Middle

Single author:

author = {Smith, John}
author = {Smith, John A.}
author = {Smith, John Andrew}

Multiple authors - separate with and:

author = {Smith, John and Doe, Jane}
author = {Smith, John A. and Doe, Jane M. and Johnson, Mary L.}

Many authors (10+):

author = {Smith, John and Doe, Jane and Johnson, Mary and others}

Special cases:

% Suffix (Jr., III, etc.)
author = {King, Jr., Martin Luther}

% Organization as author
author = {{World Health Organization}}
% Note: Double braces keep as single entity

% Multiple surnames
author = {Garc{\'i}a-Mart{\'i}nez, Jos{\'e}}

% Particles (van, von, de, etc.)
author = {van der Waals, Johannes}
author = {de Broglie, Louis}

Wrong formats (don't use):

author = {Smith, J.; Doe, J.}  % Semicolons (wrong)
author = {Smith, J., Doe, J.}  % Commas (wrong)
author = {Smith, J. & Doe, J.} % Ampersand (wrong)
author = {Smith J}             % No comma

Title Capitalization

Protect capitalization with braces:

% Proper nouns, acronyms, formulas
title = {{AlphaFold}: Protein Structure Prediction}
title = {Machine Learning for {DNA} Sequencing}
title = {The {Ising} Model in Statistical Physics}
title = {{CRISPR-Cas9} Gene Editing Technology}

Reason: Citation styles may change capitalization. Braces protect.

Examples:

% Good
title = {Advances in {COVID-19} Treatment}
title = {Using {Python} for Data Analysis}
title = {The {AlphaFold} Protein Structure Database}

% Will be lowercase in title case styles
title = {Advances in COVID-19 Treatment}  % covid-19
title = {Using Python for Data Analysis}  % python

Whole title protection (rarely needed):

title = {{This Entire Title Keeps Its Capitalization}}

Page Ranges

Use en-dash (double hyphen --):

pages = {123--145}     % Correct
pages = {1234--1256}   % Correct
pages = {e0123456}     % Article ID (PLOS, etc.)
pages = {123}          % Single page

Wrong:

pages = {123-145}      % Single hyphen (don't use)
pages = {pp. 123-145}  % "pp." not needed
pages = {123–145}      % Unicode en-dash (may cause issues)

Month Names

Use three-letter abbreviations (unquoted):

month = jan
month = feb
month = mar
month = apr
month = may
month = jun
month = jul
month = aug
month = sep
month = oct
month = nov
month = dec

Or numeric:

month = {1}   % January
month = {12}  % December

Or full name in braces:

month = {January}

Standard abbreviations work without quotes because they're defined in BibTeX.

Journal Names

Full name (not abbreviated):

journal = {Nature}
journal = {Science}
journal = {Cell}
journal = {Proceedings of the National Academy of Sciences}
journal = {Journal of the American Chemical Society}

Bibliography style will handle abbreviation if needed.

Avoid manual abbreviation:

% Don't do this in BibTeX file
journal = {Proc. Natl. Acad. Sci. U.S.A.}

% Do this instead
journal = {Proceedings of the National Academy of Sciences}

Exception: If style requires abbreviations, use full abbreviated form:

journal = {Proc. Natl. Acad. Sci. U.S.A.}  % If required by style

DOI Formatting

URL format (preferred):

doi = {10.1038/s41586-021-03819-2}

Not:

doi = {https://doi.org/10.1038/s41586-021-03819-2}  % Don't include URL
doi = {doi:10.1038/s41586-021-03819-2}              % Don't include prefix

LaTeX will format as URL automatically.

Note: No period after DOI field!

URL Formatting

url = {https://www.example.com/article}

Use:

• When DOI not available
• For web pages
• For supplementary materials

Don't duplicate:

% Don't include both if DOI URL is same as url
doi = {10.1038/nature12345}
url = {https://doi.org/10.1038/nature12345}  % Redundant!

Special Characters

Accents and diacritics:

author = {M{\"u}ller, Hans}        % ü
author = {Garc{\'i}a, Jos{\'e}}    % í, é
author = {Erd{\H{o}}s, Paul}       % ő
author = {Schr{\"o}dinger, Erwin}  % ö

Or use UTF-8 (with proper LaTeX setup):

author = {Müller, Hans}
author = {García, José}

Mathematical symbols:

title = {The $\alpha$-helix Structure}
title = {$\beta$-sheet Prediction}

Chemical formulas:

title = {H$_2$O Molecular Dynamics}
% Or with chemformula package:
title = {\ce{H2O} Molecular Dynamics}

Field Order

Recommended order (for readability):

@article{Key,
  author  = {},
  title   = {},
  journal = {},
  year    = {},
  volume  = {},
  number  = {},
  pages   = {},
  doi     = {},
  url     = {},
  note    = {}
}

Rules:

• Most important fields first
• Consistent across entries
• Use formatter to standardize

Best Practices

1. Consistent Formatting

Use same format throughout:

• Author name format
• Title capitalization
• Journal names
• Citation key style

2. Required Fields

Always include:

• All required fields for entry type
• DOI for modern papers (2000+)
• Volume and pages for articles
• Publisher for books

3. Protect Capitalization

Use braces for:

• Proper nouns: {AlphaFold}
• Acronyms: {DNA}, {CRISPR}
• Formulas: {H2O}
• Names: {Python}, {R}

4. Complete Author Lists

Include all authors when possible:

• All authors if <10
• Use "and others" for 10+
• Don't abbreviate to "et al." manually

5. Use Standard Entry Types

Choose correct entry type:

• Journal article → @article
• Book → @book
• Conference paper → @inproceedings
• Preprint → @misc

6. Validate Syntax

Check for:

• Balanced braces
• Commas after fields
• Unique citation keys
• Valid entry types

7. Use Formatters

Use automated tools:

python scripts/format_bibtex.py references.bib

Benefits:

• Consistent formatting
• Catch syntax errors
• Standardize field order
• Fix common issues

Common Mistakes

1. Wrong Author Separator

Wrong:

author = {Smith, J.; Doe, J.}    % Semicolon
author = {Smith, J., Doe, J.}    % Comma
author = {Smith, J. & Doe, J.}   % Ampersand

Correct:

author = {Smith, John and Doe, Jane}

2. Missing Commas

Wrong:

@article{Smith2024,
  author = {Smith, John}    % Missing comma!
  title = {Title}
}

Correct:

@article{Smith2024,
  author = {Smith, John},   % Comma after each field
  title = {Title}
}

3. Unprotected Capitalization

Wrong:

title = {Machine Learning with Python}
% "Python" will become "python" in title case

Correct:

title = {Machine Learning with {Python}}

4. Single Hyphen in Pages

Wrong:

pages = {123-145}   % Single hyphen

Correct:

pages = {123--145}  % Double hyphen (en-dash)

5. Redundant "pp." in Pages

Wrong:

pages = {pp. 123--145}

Correct:

pages = {123--145}

6. DOI with URL Prefix

Wrong:

doi = {https://doi.org/10.1038/nature12345}
doi = {doi:10.1038/nature12345}

Correct:

doi = {10.1038/nature12345}

Example Complete Bibliography

% Journal article
@article{Jumper2021,
  author  = {Jumper, John and Evans, Richard and Pritzel, Alexander and others},
  title   = {Highly Accurate Protein Structure Prediction with {AlphaFold}},
  journal = {Nature},
  year    = {2021},
  volume  = {596},
  number  = {7873},
  pages   = {583--589},
  doi     = {10.1038/s41586-021-03819-2}
}

% Book
@book{Kumar2021,
  author    = {Kumar, Vinay and Abbas, Abul K. and Aster, Jon C.},
  title     = {Robbins and Cotran Pathologic Basis of Disease},
  publisher = {Elsevier},
  year      = {2021},
  edition   = {10},
  address   = {Philadelphia, PA},
  isbn      = {978-0-323-53113-9}
}

% Conference paper
@inproceedings{Vaswani2017,
  author    = {Vaswani, Ashish and Shazeer, Noam and Parmar, Niki and others},
  title     = {Attention is All You Need},
  booktitle = {Advances in Neural Information Processing Systems 30 (NeurIPS 2017)},
  year      = {2017},
  pages     = {5998--6008}
}

% Book chapter
@incollection{Brown2020,
  author    = {Brown, Peter O. and Botstein, David},
  title     = {Exploring the New World of the Genome with {DNA} Microarrays},
  booktitle = {DNA Microarrays: A Molecular Cloning Manual},
  editor    = {Eisen, Michael B. and Brown, Patrick O.},
  publisher = {Cold Spring Harbor Laboratory Press},
  year      = {2020},
  pages     = {1--45}
}

% PhD thesis
@phdthesis{Johnson2023,
  author  = {Johnson, Mary L.},
  title   = {Novel Approaches to Cancer Immunotherapy},
  school  = {Stanford University},
  year    = {2023},
  type    = {{PhD} dissertation}
}

% Preprint
@misc{Zhang2024,
  author       = {Zhang, Yi and Chen, Li and Wang, Hui},
  title        = {Novel Therapeutic Targets in {Alzheimer}'s Disease},
  year         = {2024},
  howpublished = {bioRxiv},
  doi          = {10.1101/2024.01.001},
  note         = {Preprint}
}

% Dataset
@misc{AlphaFoldDB2021,
  author       = {{DeepMind} and {EMBL-EBI}},
  title        = {{AlphaFold} Protein Structure Database},
  year         = {2021},
  howpublished = {Database},
  url          = {https://alphafold.ebi.ac.uk/},
  doi          = {10.1093/nar/gkab1061}
}

Summary

BibTeX formatting essentials:

✓ Choose correct entry type (@article, @book, etc.) ✓ Include all required fields ✓ Use `and` for multiple authors ✓ Protect capitalization with braces ✓ Use `--` for page ranges ✓ Include DOI for modern papers ✓ Validate syntax before compilation

Use formatting tools to ensure consistency:

python scripts/format_bibtex.py references.bib

Properly formatted BibTeX ensures correct, consistent citations across all bibliography styles!

Citation Validation Guide

Comprehensive guide to validating citation accuracy, completeness, and formatting in BibTeX files.

Overview

Citation validation ensures:

• All citations are accurate and complete
• DOIs resolve correctly
• Required fields are present
• No duplicate entries
• Proper formatting and syntax
• Links are accessible

Validation should be performed:

• After extracting metadata
• Before manuscript submission
• After manual edits to BibTeX files
• Periodically for maintained bibliographies

Validation Categories

1. DOI Verification

Purpose: Ensure DOIs are valid and resolve correctly.

What to Check

DOI format:

Valid:   10.1038/s41586-021-03819-2
Valid:   10.1126/science.aam9317
Invalid: 10.1038/invalid
Invalid: doi:10.1038/... (should omit "doi:" prefix in BibTeX)

DOI resolution:

• DOI should resolve via https://doi.org/
• Should redirect to actual article
• Should not return 404 or error

Metadata consistency:

• CrossRef metadata should match BibTeX
• Author names should align
• Title should match
• Year should match

How to Validate

Manual check: 1. Copy DOI from BibTeX 2. Visit https://doi.org/10.1038/nature12345 3. Verify it redirects to correct article 4. Check metadata matches

Automated check (recommended):

python scripts/validate_citations.py references.bib --check-dois

Process: 1. Extract all DOIs from BibTeX file 2. Query doi.org resolver for each 3. Query CrossRef API for metadata 4. Compare metadata with BibTeX entry 5. Report discrepancies

Common Issues

Broken DOIs:

• Typos in DOI
• Publisher changed DOI (rare)
• Article retracted
• Solution: Find correct DOI from publisher site

Mismatched metadata:

• BibTeX has old/incorrect information
• Solution: Re-extract metadata from CrossRef

Missing DOIs:

• Older articles may not have DOIs
• Acceptable for pre-2000 publications
• Add URL or PMID instead

2. Required Fields

Purpose: Ensure all necessary information is present.

Required by Entry Type

@article:

author   % REQUIRED
title    % REQUIRED
journal  % REQUIRED
year     % REQUIRED
volume   % Highly recommended
pages    % Highly recommended
doi      % Highly recommended for modern papers

@book:

author OR editor  % REQUIRED (at least one)
title            % REQUIRED
publisher        % REQUIRED
year             % REQUIRED
isbn             % Recommended

@inproceedings:

author     % REQUIRED
title      % REQUIRED
booktitle  % REQUIRED (conference/proceedings name)
year       % REQUIRED
pages      % Recommended

@incollection (book chapter):

author     % REQUIRED
title      % REQUIRED (chapter title)
booktitle  % REQUIRED (book title)
publisher  % REQUIRED
year       % REQUIRED
editor     % Recommended
pages      % Recommended

@phdthesis:

author  % REQUIRED
title   % REQUIRED
school  % REQUIRED
year    % REQUIRED

@misc (preprints, datasets, etc.):

author  % REQUIRED
title   % REQUIRED
year    % REQUIRED
howpublished  % Recommended (bioRxiv, Zenodo, etc.)
doi OR url    % At least one required

Validation Script

python scripts/validate_citations.py references.bib --check-required-fields

Output:

Error: Entry 'Smith2024' missing required field 'journal'
Error: Entry 'Doe2023' missing required field 'year'
Warning: Entry 'Jones2022' missing recommended field 'volume'

3. Author Name Formatting

Purpose: Ensure consistent, correct author name formatting.

Proper Format

Recommended BibTeX format:

author = {Last1, First1 and Last2, First2 and Last3, First3}

Examples:

% Correct
author = {Smith, John}
author = {Smith, John A.}
author = {Smith, John Andrew}
author = {Smith, John and Doe, Jane}
author = {Smith, John and Doe, Jane and Johnson, Mary}

% For many authors
author = {Smith, John and Doe, Jane and others}

% Incorrect
author = {John Smith}  % First Last format (not recommended)
author = {Smith, J.; Doe, J.}  % Semicolon separator (wrong)
author = {Smith J, Doe J}  % Missing commas

Special Cases

Suffixes (Jr., III, etc.):

author = {King, Jr., Martin Luther}

Multiple surnames (hyphenated):

author = {Smith-Jones, Mary}

Van, von, de, etc.:

author = {van der Waals, Johannes}
author = {de Broglie, Louis}

Organizations as authors:

author = {{World Health Organization}}
% Double braces treat as single author

Validation Checks

Automated validation:

python scripts/validate_citations.py references.bib --check-authors

Checks for:

• Proper separator (and, not &, ; , etc.)
• Comma placement
• Empty author fields
• Malformed names

4. Data Consistency

Purpose: Ensure all fields contain valid, reasonable values.

Year Validation

Valid years:

year = {2024}    % Current/recent
year = {1953}    % Watson & Crick DNA structure (historical)
year = {1665}    % Hooke's Micrographia (very old)

Invalid years:

year = {24}      % Two digits (ambiguous)
year = {202}     % Typo
year = {2025}    % Future (unless accepted/in press)
year = {0}       % Obviously wrong

Check:

• Four digits
• Reasonable range (1600-current+1)
• Not all zeros

Volume/Number Validation

volume = {123}      % Numeric
volume = {12}       % Valid
number = {3}        % Valid
number = {S1}       % Supplement issue (valid)

Invalid:

volume = {Vol. 123}  % Should be just number
number = {Issue 3}   % Should be just number

Page Range Validation

Correct format:

pages = {123--145}    % En-dash (two hyphens)
pages = {e0123456}    % PLOS-style article ID
pages = {123}         % Single page

Incorrect format:

pages = {123-145}     % Single hyphen (use --)
pages = {pp. 123-145} % Remove "pp."
pages = {123–145}     % Unicode en-dash (may cause issues)

URL Validation

Check:

• URLs are accessible (return 200 status)
• HTTPS when available
• No obvious typos
• Permanent links (not temporary)

Valid:

url = {https://www.nature.com/articles/nature12345}
url = {https://arxiv.org/abs/2103.14030}

Questionable:

url = {http://...}  % HTTP instead of HTTPS
url = {file:///...} % Local file path
url = {bit.ly/...}  % URL shortener (not permanent)

5. Duplicate Detection

Purpose: Find and remove duplicate entries.

Types of Duplicates

Exact duplicates (same DOI):

@article{Smith2024a,
  doi = {10.1038/nature12345},
  ...
}

@article{Smith2024b,
  doi = {10.1038/nature12345},  % Same DOI!
  ...
}

Near duplicates (similar title/authors):

@article{Smith2024,
  title = {Machine Learning for Drug Discovery},
  ...
}

@article{Smith2024method,
  title = {Machine learning for drug discovery},  % Same, different case
  ...
}

Preprint + Published:

@misc{Smith2023arxiv,
  title = {AlphaFold Results},
  howpublished = {arXiv},
  ...
}

@article{Smith2024,
  title = {AlphaFold Results},  % Same paper, now published
  journal = {Nature},
  ...
}
% Keep published version only

Detection Methods

By DOI (most reliable):

• Same DOI = exact duplicate
• Keep one, remove other

By title similarity:

• Normalize: lowercase, remove punctuation
• Calculate similarity (e.g., Levenshtein distance)
• Flag if >90% similar

By author-year-title:

• Same first author + year + similar title
• Likely duplicate

Automated detection:

python scripts/validate_citations.py references.bib --check-duplicates

Output:

Warning: Possible duplicate entries:
  - Smith2024a (DOI: 10.1038/nature12345)
  - Smith2024b (DOI: 10.1038/nature12345)
  Recommendation: Keep one entry, remove the other.

6. Format and Syntax

Purpose: Ensure valid BibTeX syntax.

Common Syntax Errors

Missing commas:

@article{Smith2024,
  author = {Smith, John}   % Missing comma!
  title = {Title}
}
% Should be:
  author = {Smith, John},  % Comma after each field

Unbalanced braces:

title = {Title with {Protected} Text  % Missing closing brace
% Should be:
title = {Title with {Protected} Text}

Missing closing brace for entry:

@article{Smith2024,
  author = {Smith, John},
  title = {Title}
  % Missing closing brace!
% Should end with:
}

Invalid characters in keys:

@article{Smith&Doe2024,  % & not allowed in key
  ...
}
% Use:
@article{SmithDoe2024,
  ...
}

BibTeX Syntax Rules

Entry structure:

@TYPE{citationkey,
  field1 = {value1},
  field2 = {value2},
  ...
  fieldN = {valueN}
}

Citation keys:

• Alphanumeric and some punctuation (-, _, ., :)
• No spaces
• Case-sensitive
• Unique within file

Field values:

• Enclosed in {braces} or "quotes"
• Braces preferred for complex text
• Numbers can be unquoted: year = 2024

Special characters:

• { and } for grouping
• \ for LaTeX commands
• Protect capitalization: {AlphaFold}
• Accents: {\"u}, {\'e}, {\aa}

Validation

python scripts/validate_citations.py references.bib --check-syntax

Checks:

• Valid BibTeX structure
• Balanced braces
• Proper commas
• Valid entry types
• Unique citation keys

Validation Workflow

Step 1: Basic Validation

Run comprehensive validation:

python scripts/validate_citations.py references.bib

Checks all:

• DOI resolution
• Required fields
• Author formatting
• Data consistency
• Duplicates
• Syntax

Step 2: Review Report

Examine validation report:

{
  "total_entries": 150,
  "valid_entries": 140,
  "errors": [
    {
      "entry": "Smith2024",
      "error": "missing_required_field",
      "field": "journal",
      "severity": "high"
    },
    {
      "entry": "Doe2023",
      "error": "invalid_doi",
      "doi": "10.1038/broken",
      "severity": "high"
    }
  ],
  "warnings": [
    {
      "entry": "Jones2022",
      "warning": "missing_recommended_field",
      "field": "volume",
      "severity": "medium"
    }
  ],
  "duplicates": [
    {
      "entries": ["Smith2024a", "Smith2024b"],
      "reason": "same_doi",
      "doi": "10.1038/nature12345"
    }
  ]
}

Step 3: Fix Issues

High-priority (errors): 1. Add missing required fields 2. Fix broken DOIs 3. Remove duplicates 4. Correct syntax errors

Medium-priority (warnings): 1. Add recommended fields 2. Improve author formatting 3. Fix page ranges

Low-priority: 1. Standardize formatting 2. Add URLs for accessibility

Step 4: Auto-Fix

Use auto-fix for safe corrections:

python scripts/validate_citations.py references.bib \
  --auto-fix \
  --output fixed_references.bib

Auto-fix can:

• Fix page range format (- to --)
• Remove "pp." from pages
• Standardize author separators
• Fix common syntax errors
• Normalize field order

Auto-fix cannot:

• Add missing information
• Find correct DOIs
• Determine which duplicate to keep
• Fix semantic errors

Step 5: Manual Review

Review auto-fixed file:

# Check what changed
diff references.bib fixed_references.bib

# Review specific entries that had errors
grep -A 10 "Smith2024" fixed_references.bib

Step 6: Re-Validate

Validate after fixes:

python scripts/validate_citations.py fixed_references.bib --verbose

Should show:

✓ All DOIs valid
✓ All required fields present
✓ No duplicates found
✓ Syntax valid
✓ 150/150 entries valid

Validation Checklist

Use this checklist before final submission:

DOI Validation

• [ ] All DOIs resolve correctly
• [ ] Metadata matches between BibTeX and CrossRef
• [ ] No broken or invalid DOIs

Completeness

• [ ] All entries have required fields
• [ ] Modern papers (2000+) have DOIs
• [ ] Authors properly formatted
• [ ] Journals/conferences properly named

Consistency

• [ ] Years are 4-digit numbers
• [ ] Page ranges use -- not -
• [ ] Volume/number are numeric
• [ ] URLs are accessible

Duplicates

• [ ] No entries with same DOI
• [ ] No near-duplicate titles
• [ ] Preprints updated to published versions

Formatting

• [ ] Valid BibTeX syntax
• [ ] Balanced braces
• [ ] Proper commas
• [ ] Unique citation keys

Final Checks

• [ ] Bibliography compiles without errors
• [ ] All citations in text appear in bibliography
• [ ] All bibliography entries cited in text
• [ ] Citation style matches journal requirements

Best Practices

1. Validate Early and Often

# After extraction
python scripts/extract_metadata.py --doi ... --output refs.bib
python scripts/validate_citations.py refs.bib

# After manual edits
python scripts/validate_citations.py refs.bib

# Before submission
python scripts/validate_citations.py refs.bib --strict

2. Use Automated Tools

Don't validate manually - use scripts:

• Faster
• More comprehensive
• Catches errors humans miss
• Generates reports

3. Keep Backup

# Before auto-fix
cp references.bib references_backup.bib

# Run auto-fix
python scripts/validate_citations.py references.bib \
  --auto-fix \
  --output references_fixed.bib

# Review changes
diff references.bib references_fixed.bib

# If satisfied, replace
mv references_fixed.bib references.bib

4. Fix High-Priority First

Priority order: 1. Syntax errors (prevent compilation) 2. Missing required fields (incomplete citations) 3. Broken DOIs (broken links) 4. Duplicates (confusion, wasted space) 5. Missing recommended fields 6. Formatting inconsistencies

5. Document Exceptions

For entries that can't be fixed:

@article{Old1950,
  author = {Smith, John},
  title = {Title},
  journal = {Obscure Journal},
  year = {1950},
  volume = {12},
  pages = {34--56},
  note = {DOI not available for publications before 2000}
}

6. Validate Against Journal Requirements

Different journals have different requirements:

• Citation style (numbered, author-year)
• Abbreviations (journal names)
• Maximum reference count
• Format (BibTeX, EndNote, manual)

Check journal author guidelines!

Common Validation Issues

Issue 1: Metadata Mismatch

Problem: BibTeX says 2023, CrossRef says 2024.

Cause:

• Online-first vs print publication
• Correction/update
• Extraction error

Solution: 1. Check actual article 2. Use more recent/accurate date 3. Update BibTeX entry 4. Re-validate

Issue 2: Special Characters

Problem: LaTeX compilation fails on special characters.

Cause:

• Accented characters (é, ü, ñ)
• Chemical formulas (H₂O)
• Math symbols (α, β, ±)

Solution:

% Use LaTeX commands
author = {M{\"u}ller, Hans}  % Müller
title = {Study of H\textsubscript{2}O}  % H₂O
% Or use UTF-8 with proper LaTeX packages

Issue 3: Incomplete Extraction (REQUIRES WEB SEARCH)

Problem: Extracted metadata missing fields (volume, pages, DOI, issue number).

Cause:

• Source API doesn't provide all metadata
• Extraction error
• Incomplete database record
• Online-first publication without final pagination

Solution — MANDATORY web search to fill gaps:

1. Identify the missing fields by scanning the BibTeX entry for empty or absent volume, pages, number, doi fields.

2. Search for the missing metadata using web search (parallel-web skill):

   # Search by author + title to find complete citation info
   parallel-cli search "AUTHOR_NAME PAPER_TITLE JOURNAL volume pages DOI" \
     --json --max-results 10 \
     -o sources/search_citation_CITATIONKEY.json

3. If DOI is known, extract from DOI resolver page:

   parallel-cli extract "https://doi.org/DOI_HERE" --json \
     --objective "extract volume, issue number, page range, publication date" \
     -o sources/extract_doi_CITATIONKEY.json

4. If DOI is unknown, search for it:

   parallel-cli search "AUTHOR_NAME PAPER_TITLE JOURNAL_NAME DOI" \
     --json --max-results 10 \
     -o sources/search_find_doi_CITATIONKEY.json

5. Try alternative metadata sources:

• CrossRef API (via DOI): Most reliable for volume/pages
• PubMed (via PMID): Good for biomedical papers
• Google Scholar: Fallback for hard-to-find papers
• Publisher website: Last resort

6. Update the BibTeX entry with the found metadata and log:

   [HH:MM:SS] METADATA ENRICHED: [CitationKey] - added volume, pages, doi ✅

7. If truly unfindable (rare), add a note field:

   note = {Complete pagination not yet assigned — online-first publication}

CRITICAL: Never leave an @article entry without volume, pages, and doi unless you have exhausted all search options and documented the reason.

Issue 4: Cannot Find Duplicate

Problem: Same paper appears twice, not detected.

Cause:

• Different DOIs (should be rare)
• Different titles (abbreviated, typo)
• Different citation keys

Solution:

• Manual search for author + year
• Check for similar titles
• Remove manually

Summary

Validation ensures citation quality:

✓ Accuracy: DOIs resolve, metadata correct ✓ Completeness: All required fields present ✓ Consistency: Proper formatting throughout ✓ No duplicates: Each paper cited once ✓ Valid syntax: BibTeX compiles without errors

Always validate before final submission!

Use automated tools:

python scripts/validate_citations.py references.bib

Follow workflow: 1. Extract metadata 2. Validate 3. Fix errors 4. Re-validate 5. Submit

Google Scholar Search Guide

Comprehensive guide to searching Google Scholar for academic papers, including advanced search operators, filtering strategies, and metadata extraction.

Overview

Google Scholar provides the most comprehensive coverage of academic literature across all disciplines:

• Coverage: 100+ million scholarly documents
• Scope: All academic disciplines
• Content types: Journal articles, books, theses, conference papers, preprints, patents, court opinions
• Citation tracking: "Cited by" links for forward citation tracking
• Accessibility: Free to use, no account required

Basic Search

Simple Keyword Search

Search for papers containing specific terms anywhere in the document (title, abstract, full text):

CRISPR gene editing
machine learning protein folding
climate change impact agriculture
quantum computing algorithms

Tips:

• Use specific technical terms
• Include key acronyms and abbreviations
• Start broad, then refine
• Check spelling of technical terms

Exact Phrase Search

Use quotation marks to search for exact phrases:

"deep learning"
"CRISPR-Cas9"
"systematic review"
"randomized controlled trial"

When to use:

• Technical terms that must appear together
• Proper names
• Specific methodologies
• Exact titles

Advanced Search Operators

Author Search

Find papers by specific authors:

author:LeCun
author:"Geoffrey Hinton"
author:Church synthetic biology

Variations:

• Single last name: author:Smith
• Full name in quotes: author:"Jane Smith"
• Author + topic: author:Doudna CRISPR

Tips:

• Authors may publish under different name variations
• Try with and without middle initials
• Consider name changes (marriage, etc.)
• Use quotation marks for full names

Title Search

Search only in article titles:

intitle:transformer
intitle:"attention mechanism"
intitle:review climate change

Use cases:

• Finding papers specifically about a topic
• More precise than full-text search
• Reduces irrelevant results
• Good for finding reviews or methods

Source (Journal) Search

Search within specific journals or conferences:

source:Nature
source:"Nature Communications"
source:NeurIPS
source:"Journal of Machine Learning Research"

Applications:

• Track publications in top-tier venues
• Find papers in specialized journals
• Identify conference-specific work
• Verify publication venue

Exclusion Operator

Exclude terms from results:

machine learning -survey
CRISPR -patent
climate change -news
deep learning -tutorial -review

Common exclusions:

• -survey: Exclude survey papers
• -review: Exclude review articles
• -patent: Exclude patents
• -book: Exclude books
• -news: Exclude news articles
• -tutorial: Exclude tutorials

OR Operator

Search for papers containing any of multiple terms:

"machine learning" OR "deep learning"
CRISPR OR "gene editing"
"climate change" OR "global warming"

Best practices:

• OR must be uppercase
• Combine synonyms
• Include acronyms and spelled-out versions
• Use with exact phrases

Wildcard Search

Use asterisk (*) as wildcard for unknown words:

"machine * learning"
"CRISPR * editing"
"* neural network"

Note: Limited wildcard support in Google Scholar compared to other databases.

Advanced Filtering

Year Range

Filter by publication year:

Using interface:

• Click "Since [year]" on left sidebar
• Select custom range

Using search operators:

# Not directly in search query
# Use interface or URL parameters

In script:

python scripts/search_google_scholar.py "quantum computing" \
  --year-start 2020 \
  --year-end 2024

Sorting Options

By relevance (default):

• Google's algorithm determines relevance
• Considers citations, author reputation, publication venue
• Generally good for most searches

By date:

• Most recent papers first
• Good for fast-moving fields
• May miss highly cited older papers
• Click "Sort by date" in interface

By citation count (via script):

python scripts/search_google_scholar.py "transformers" \
  --sort-by citations \
  --limit 50

Language Filtering

In interface:

• Settings → Languages
• Select preferred languages

Default: English and papers with English abstracts

Search Strategies

Finding Seminal Papers

Identify highly influential papers in a field:

1. Search by topic with broad terms 2. Sort by citations (most cited first) 3. Look for review articles for comprehensive overviews 4. Check publication dates for foundational vs recent work

Example:

"generative adversarial networks"
# Sort by citations
# Top results: original GAN paper (Goodfellow et al., 2014), key variants

Finding Recent Work

Stay current with latest research:

1. Search by topic 2. Filter to recent years (last 1-2 years) 3. Sort by date for newest first 4. Set up alerts for ongoing tracking

Example:

python scripts/search_google_scholar.py "AlphaFold protein structure" \
  --year-start 2023 \
  --year-end 2024 \
  --limit 50

Finding Review Articles

Get comprehensive overviews of a field:

intitle:review "machine learning"
"systematic review" CRISPR
intitle:survey "natural language processing"

Indicators:

• "review", "survey", "perspective" in title
• Often highly cited
• Published in review journals (Nature Reviews, Trends, etc.)
• Comprehensive reference lists

Citation Chain Search

Forward citations (papers citing a key paper): 1. Find seminal paper 2. Click "Cited by X" 3. See all papers that cite it 4. Identify how field has developed

Backward citations (references in a key paper): 1. Find recent review or important paper 2. Check its reference list 3. Identify foundational work 4. Trace development of ideas

Example workflow:

# Find original transformer paper
"Attention is all you need" author:Vaswani

# Check "Cited by 120,000+"
# See evolution: BERT, GPT, T5, etc.

# Check references in original paper
# Find RNN, LSTM, attention mechanism origins

Comprehensive Literature Search

For thorough coverage (e.g., systematic reviews):

1. Generate synonym list:

• Main terms + alternatives
• Acronyms + spelled out
• US vs UK spelling

2. Use OR operators:

   ("machine learning" OR "deep learning" OR "neural networks")

3. Combine multiple concepts:

   ("machine learning" OR "deep learning") ("drug discovery" OR "drug development")

4. Search without date filters initially:

• Get total landscape
• Filter later if too many results

5. Export results for systematic analysis:

   python scripts/search_google_scholar.py \
     '"machine learning" OR "deep learning" drug discovery' \
     --limit 500 \
     --output comprehensive_search.json

Extracting Citation Information

From Google Scholar Results Page

Each result shows:

• Title: Paper title (linked to full text if available)
• Authors: Author list (often truncated)
• Source: Journal/conference, year, publisher
• Cited by: Number of citations + link to citing papers
• Related articles: Link to similar papers
• All versions: Different versions of the same paper

Export Options

Manual export: 1. Click "Cite" under paper 2. Select BibTeX format 3. Copy citation

Limitations:

• One paper at a time
• Manual process
• Time-consuming for many papers

Automated export (using script):

# Search and export to BibTeX
python scripts/search_google_scholar.py "quantum computing" \
  --limit 50 \
  --format bibtex \
  --output quantum_papers.bib

Metadata Available

From Google Scholar you can typically extract:

• Title
• Authors (may be incomplete)
• Year
• Source (journal/conference)
• Citation count
• Link to full text (when available)
• Link to PDF (when available)

Note: Metadata quality varies:

• Some fields may be missing
• Author names may be incomplete
• Need to verify with DOI lookup for accuracy

Rate Limiting and Access

Rate Limits

Google Scholar has rate limiting to prevent automated scraping:

Symptoms of rate limiting:

• CAPTCHA challenges
• Temporary IP blocks
• 429 "Too Many Requests" errors

Best practices: 1. Add delays between requests: 2-5 seconds minimum 2. Limit query volume: Don't search hundreds of queries rapidly 3. Use scholarly library: Handles rate limiting automatically 4. Rotate User-Agents: Appear as different browsers 5. Consider proxies: For large-scale searches (use ethically)

In our scripts:

# Automatic rate limiting built in
time.sleep(random.uniform(3, 7))  # Random delay 3-7 seconds

Ethical Considerations

DO:

• Respect rate limits
• Use reasonable delays
• Cache results (don't re-query)
• Use official APIs when available
• Attribute data properly

DON'T:

• Scrape aggressively
• Use multiple IPs to bypass limits
• Violate terms of service
• Burden servers unnecessarily
• Use data commercially without permission

Institutional Access

Benefits of institutional access:

• Access to full-text PDFs through library subscriptions
• Better download capabilities
• Integration with library systems
• Link resolver to full text

Setup:

• Google Scholar → Settings → Library links
• Add your institution
• Links appear in search results

Tips and Best Practices

Search Optimization

1. Start simple, then refine:

   # Too specific initially
   intitle:"deep learning" intitle:review source:Nature 2023..2024
   
   # Better approach
   deep learning review
   # Review results
   # Add intitle:, source:, year filters as needed

2. Use multiple search strategies:

• Keyword search
• Author search for known experts
• Citation chaining from key papers
• Source search in top journals

3. Check spelling and variations:

• Color vs colour
• Optimization vs optimisation
• Tumor vs tumour
• Try common misspellings if few results

4. Combine operators strategically:

   # Good combination
   author:Church intitle:"synthetic biology" 2015..2024
   
   # Find reviews by specific author on topic in recent years

Result Evaluation

1. Check citation counts:

• High citations indicate influence
• Recent papers may have low citations but be important
• Citation counts vary by field

2. Verify publication venue:

• Peer-reviewed journals vs preprints
• Conference proceedings
• Book chapters
• Technical reports

3. Check for full text access:

• [PDF] link on right side
• "All X versions" may have open access version
• Check institutional access
• Try author's website or ResearchGate

4. Look for review articles:

• Comprehensive overviews
• Good starting point for new topics
• Extensive reference lists

Managing Results

1. Use citation manager integration:

• Export to BibTeX
• Import to Zotero, Mendeley, EndNote
• Maintain organized library

2. Set up alerts for ongoing research:

• Google Scholar → Alerts
• Get emails for new papers matching query
• Track specific authors or topics

3. Create collections:

• Save papers to Google Scholar Library
• Organize by project or topic
• Add labels and notes

4. Export systematically:

   # Save search results for later analysis
   python scripts/search_google_scholar.py "your topic" \
     --output topic_papers.json
   
   # Can re-process later without re-searching
   python scripts/extract_metadata.py \
     --input topic_papers.json \
     --output topic_refs.bib

Advanced Techniques

Boolean Logic Combinations

Combine multiple operators for precise searches:

# Highly cited reviews on specific topic by known authors
intitle:review "machine learning" ("drug discovery" OR "drug development")
author:Horvath OR author:Bengio 2020..2024

# Method papers excluding reviews
intitle:method "protein folding" -review -survey

# Papers in top journals only
("Nature" OR "Science" OR "Cell") CRISPR 2022..2024

Finding Open Access Papers

# Search with generic terms
machine learning

# Filter by "All versions" which often includes preprints
# Look for green [PDF] links (often open access)
# Check arXiv, bioRxiv versions

In script:

python scripts/search_google_scholar.py "topic" \
  --open-access-only \
  --output open_access_papers.json

Tracking Research Impact

For a specific paper: 1. Find the paper 2. Click "Cited by X" 3. Analyze citing papers:

• How is it being used?
• What fields cite it?
• Recent vs older citations?

For an author: 1. Search author:LastName 2. Check h-index and i10-index 3. View citation history graph 4. Identify most influential papers

For a topic: 1. Search topic 2. Sort by citations 3. Identify seminal papers (highly cited, older) 4. Check recent highly-cited papers (emerging important work)

Finding Preprints and Early Work

# arXiv papers
source:arxiv "deep learning"

# bioRxiv papers
source:biorxiv CRISPR

# All preprint servers
("arxiv" OR "biorxiv" OR "medrxiv") your topic

Note: Preprints are not peer-reviewed. Always check if published version exists.

Common Issues and Solutions

Too Many Results

Problem: Search returns 100,000+ results, overwhelming.

Solutions: 1. Add more specific terms 2. Use intitle: to search only titles 3. Filter by recent years 4. Add exclusions (e.g., -review) 5. Search within specific journals

Too Few Results

Problem: Search returns 0-10 results, suspiciously few.

Solutions: 1. Remove restrictive operators 2. Try synonyms and related terms 3. Check spelling 4. Broaden year range 5. Use OR for alternative terms

Irrelevant Results

Problem: Results don't match intent.

Solutions: 1. Use exact phrases with quotes 2. Add more specific context terms 3. Use intitle: for title-only search 4. Exclude common irrelevant terms 5. Combine multiple specific terms

CAPTCHA or Rate Limiting

Problem: Google Scholar shows CAPTCHA or blocks access.

Solutions: 1. Wait several minutes before continuing 2. Reduce query frequency 3. Use longer delays in scripts (5-10 seconds) 4. Switch to different IP/network 5. Consider using institutional access

Missing Metadata

Problem: Author names, year, or venue missing from results.

Solutions: 1. Click through to see full details 2. Check "All versions" for better metadata 3. Look up by DOI if available 4. Extract metadata from CrossRef/PubMed instead 5. Manually verify from paper PDF

Duplicate Results

Problem: Same paper appears multiple times.

Solutions: 1. Click "All X versions" to see consolidated view 2. Choose version with best metadata 3. Use deduplication in post-processing:

   python scripts/format_bibtex.py results.bib \
     --deduplicate \
     --output clean_results.bib

Integration with Scripts

search_google_scholar.py Usage

Basic search:

python scripts/search_google_scholar.py "machine learning drug discovery"

With year filter:

python scripts/search_google_scholar.py "CRISPR" \
  --year-start 2020 \
  --year-end 2024 \
  --limit 100

Sort by citations:

python scripts/search_google_scholar.py "transformers" \
  --sort-by citations \
  --limit 50

Export to BibTeX:

python scripts/search_google_scholar.py "quantum computing" \
  --format bibtex \
  --output quantum.bib

Export to JSON for later processing:

python scripts/search_google_scholar.py "topic" \
  --format json \
  --output results.json

# Later: extract full metadata
python scripts/extract_metadata.py \
  --input results.json \
  --output references.bib

Batch Searching

For multiple topics:

# Create file with search queries (queries.txt)
# One query per line

# Search each query
while read query; do
  python scripts/search_google_scholar.py "$query" \
    --limit 50 \
    --output "${query// /_}.json"
  sleep 10  # Delay between queries
done < queries.txt

Summary

Google Scholar is the most comprehensive academic search engine, providing:

✓ Broad coverage: All disciplines, 100M+ documents ✓ Free access: No account or subscription required ✓ Citation tracking: "Cited by" for impact analysis ✓ Multiple formats: Articles, books, theses, patents ✓ Full-text search: Not just abstracts

Key strategies:

• Use advanced operators for precision
• Combine author, title, source searches
• Track citations for impact
• Export systematically to citation manager
• Respect rate limits and access policies
• Verify metadata with CrossRef/PubMed

For biomedical research, complement with PubMed for MeSH terms and curated metadata.