Citation Management

Source: https://github.com/aipoch/medical-research-skills

When to Use

• You need to find relevant or highly cited papers on a topic using Google Scholar or PubMed.
• You have identifiers (e.g., DOI, PMID, arXiv ID, URL) and must convert them into correct BibTeX.
• You want to verify citation accuracy (DOI resolution, required fields, consistency with CrossRef/PubMed).
• You need to clean, deduplicate, sort, and standardize an existing .bib file before submission.
• You are preparing a thesis/manuscript and need a reproducible workflow from search → extraction → formatting → validation.

Key Features

• Paper discovery
  • Google Scholar search with year filtering, pagination, and citation-count sorting.
  • PubMed search with MeSH terms, field tags, publication-type filters, and date ranges.
• Metadata extraction
  • Resolve DOI/PMID/arXiv/URL to structured metadata via CrossRef, PubMed E-utilities, and arXiv APIs.
  • Batch processing from files containing mixed identifiers.
• BibTeX generation & cleanup
  • Generate BibTeX entries with appropriate entry types and required fields.
  • Format, sort (key/year/author), and deduplicate BibTeX libraries.
• Citation validation
  • DOI resolution checks and metadata cross-checking.
  • Required-field checks by entry type, syntax validation, duplicate detection, and optional auto-fix.
• Workflow integration
  • Produces submission-ready .bib files for LaTeX/Overleaf workflows and complements literature review pipelines.

Dependencies

• Python: 3.10+ (recommended)
• Python packages:
  • requests>=2.31.0
  • scholarly>=1.7.11 (optional; required only for Google Scholar automation)

Example Usage

A complete, end-to-end workflow that searches, extracts metadata, formats, deduplicates, and validates a bibliography:

# 1) Search PubMed (biomedical focus)
python scripts/search_pubmed.py \
  --query '"CRISPR-Cas Systems"[MeSH] AND "Gene Editing"[MeSH]' \
  --date-start 2020-01-01 \
  --date-end 2024-12-31 \
  --limit 200 \
  --output crispr_pubmed.json

# 2) Search Google Scholar (broad coverage)
python scripts/search_google_scholar.py "CRISPR gene editing therapeutics" \
  --year-start 2020 \
  --year-end 2024 \
  --limit 100 \
  --output crispr_scholar.json

# 3) Extract metadata from search outputs (or mixed identifiers)
cat crispr_pubmed.json crispr_scholar.json > combined_results.json
python scripts/extract_metadata.py \
  --input combined_results.json \
  --output combined.bib

# 4) Add known papers by DOI (append)
python scripts/doi_to_bibtex.py 10.1038/s41586-021-03819-2 >> combined.bib
python scripts/doi_to_bibtex.py 10.1126/science.aam9317 >> combined.bib

# 5) Format + deduplicate + sort (newest first)
python scripts/format_bibtex.py combined.bib \
  --deduplicate \
  --sort year \
  --descending \
  --output formatted.bib

# 6) Validate + auto-fix common issues + emit report
python scripts/validate_citations.py formatted.bib \
  --auto-fix \
  --report validation.json \
  --output final_references.bib

# 7) Inspect validation results
cat validation.json

Implementation Details

1) Search (Discovery)

• Google Scholar (scripts/search_google_scholar.py)

  • Supports query operators such as exact phrases ("deep learning"), author filters (author:LeCun), title-only (intitle:"neural networks"), exclusions (-survey), and year ranges.
  • Typical parameters:
    • --year-start, --year-end: constrain publication years
    • --limit: cap results
    • --sort-by citations: prioritize highly cited papers (when supported by the script)

• PubMed (scripts/search_pubmed.py)

  • Uses NCBI E-utilities (e.g., ESearch/EFetch/ESummary) to retrieve PMIDs and metadata.
  • Typical parameters:
    • --query: supports MeSH terms, field tags, and Boolean logic
    • --date-start, --date-end: publication date filtering
    • --publication-types: e.g., Clinical Trial,Review
    • --format: JSON or BibTeX output (if supported)

(See: references/google_scholar_search.md, references/pubmed_search.md)

2) Metadata Extraction (Normalization)

• Identifier inputs: DOI, PMID, arXiv ID, URL, or mixed lists/files.
• Primary sources:
  • CrossRef API for DOI-centric journal metadata
  • PubMed E-utilities for biomedical records (PMID/PMCID, MeSH, abstracts)
  • arXiv API for preprints and versioned records
  • DataCite API for datasets/software DOIs (if implemented/used)
• Field mapping goals:
  • Required: author, title, year
  • Articles: journal, volume, number, pages, doi
  • Conferences: booktitle, pages
  • Preprints: repository + identifier (e.g., eprint, archivePrefix)

(See: references/metadata_extraction.md)

3) BibTeX Formatting (Quality & Consistency)

• Entry types commonly produced: @article, @inproceedings, @book, @misc.
• Formatting rules enforced/encouraged:
  • Page ranges use -- (e.g., 123--145)
  • Protect capitalization in titles with braces (e.g., {CRISPR})
  • Consistent author formatting (Last, First and Last, First)
  • Stable citation keys (project convention; often FirstAuthorYearKeyword)

(See: references/bibtex_formatting.md)

4) Validation (Correctness)

Validation typically checks:

• DOI validity: resolves via doi.org and matches CrossRef metadata.
• Required fields: present per entry type; no empty critical fields.
• Consistency: year format, numeric volume/issue, page-range syntax, URL accessibility.
• Duplicates: same DOI, near-identical titles, or same author/year/title combinations.
• BibTeX syntax: braces/quotes, commas, unique keys, special character handling.

Outputs may include a machine-readable report (e.g., JSON) with errors and warnings. (See: references/citation_validation.md)

When Not to Use

• Do not proceed when required input files, identifiers, parameters, or context are missing — ask the user to provide them first.
• Do not assume capabilities beyond this skill's declared scope when the user requests external operations or inferences.
• Do not proceed without user confirmation when overwriting existing results, executing high-cost batch operations, or expanding task scope.