citation-management

Malicious tool definition detected

Tool: SKILL.md [1/4] Description: --- name: citation-management description: Comprehensive citation management for academic research.

Tool: SKILL.md [2/4] Description: 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**: ```bibtex @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} } @

Tool: SKILL.md [3/4] Description: Export to JSON or BibTeX - Citation count information **Usage**: ```bash # 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 \ --

Tool: SKILL.md [4/4] Description: submission**: Submitting with citation errors - **Solution**: Always run validation as final check 10.

Malicious tool definition detected

Tool: assets/bibtex_template.bib Description: % BibTeX Template File % Examples of properly formatted entries for all common types % ============================================================================= % JOURNAL ARTICLES % ============================================================================= @article{Jumper2021, author = {Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf and Tunyasuvunakool, Kathryn and Bates, Russ

Malicious tool definition detected

Tool: assets/citation_checklist.md [1/2]

Tool: assets/citation_checklist.md [2/2] Description: - [ ] LaTeX compilation successful with no warnings - [ ] PDF renders all citations correctly - [ ] Bibliography appears in correct format - [ ] No placeholder citations (Smith et al.

Malicious tool definition detected

Tool: references/bibtex_formatting.md [1/3] Description: # BibTeX Formatting Guide Comprehensive guide to BibTeX entry types, required fields, formatting conventions, and best practices.

Tool: references/bibtex_formatting.md [2/3] Description: {2024}, type = {Technical Report}, number = {TR-2024-01} } ``` ### @unpublished - Unpublished Work **For unpublished works** (not preprints - use @misc for those).

Tool: references/bibtex_formatting.md [3/3] Description: nouns: `{AlphaFold}` - Acronyms: `{DNA}`, `{CRISPR}` - Formulas: `{H2O}` - Names: `{Python}`, `{R}` ### 4.

Malicious tool definition detected

Tool: references/citation_validation.md [1/3] Description: # Citation Validation Guide Comprehensive guide to validating citation accuracy, completeness, and formatting in BibTeX files.

Tool: references/citation_validation.md [2/3] Description: 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 **Autom

Tool: references/citation_validation.md [3/3] Description: **Cause**: - Online-first vs print publication - Correction/update - Extraction error **Solution**: 1.

Malicious tool definition detected

Tool: references/google_scholar_search.md [1/3] Description: # Google Scholar Search Guide Comprehensive guide to searching Google Scholar for academic papers, including advanced search operators, filtering strategies, and metadata extraction.

Tool: references/google_scholar_search.md [2/3] Description: **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.

Tool: references/google_scholar_search.md [3/3] Description: Exclude common irrelevant terms 5.

Malicious tool definition detected

Tool: references/metadata_extraction.md [1/3] Description: # Metadata Extraction Guide Comprehensive guide to extracting accurate citation metadata from DOIs, PMIDs, arXiv IDs, and URLs using various APIs and services.

Tool: references/metadata_extraction.md [2/3] Description: = {10}, isbn = {978-0-323-53113-9} } ``` ### @inproceedings (Conference Papers) **Required**: - `author`: Author names - `title`: Paper title - `booktitle`: Conference/proceedings name - `year`: Year **Optional but recommended**: - `pages`: Page range - `organization`: Organizing body - `publisher`: Publisher - `address`: Conference location - `month`: Conference month - `doi`: DOI if available **Example**: ```bibtex @inproceedings{Vaswa

Tool: references/metadata_extraction.md [3/3] Description: year = {2024} } ``` ### Book Chapters vs Edited Collections **Extract correctly**: - Chapter: Use `@incollection` - Whole book: Use `@book` - Book editor: List in `editor` field - Chapter author: List in `author` field ### Datasets and Software **Use @misc** with appropriate fields: ```bibtex @misc{DatasetName2024, author = {Author, Name}, title = {Dataset Title}, year = {2024}, howpublished = {Zenodo}, doi = {10.5281/zenodo.123456}, not

Malicious tool definition detected

Tool: references/pubmed_search.md [1/3] Description: # PubMed Search Guide Comprehensive guide to searching PubMed for biomedical and life sciences literature, including MeSH terms, field tags, advanced search strategies, and E-utilities API usage.

Tool: references/pubmed_search.md [2/3] Description: } ``` ### EFetch - Retrieve Records Get full metadata for PMIDs.

Tool: references/pubmed_search.md [3/3] Description: Save search - Receive email updates - Daily, weekly, or monthly 2.

Malicious tool definition detected

Tool: scripts/doi_to_bibtex.py Description: #!/usr/bin/env python3 """ DOI to BibTeX Converter Quick utility to convert DOIs to BibTeX format using CrossRef API.

Malicious tool definition detected

Tool: scripts/extract_metadata.py [1/2] Description: #!/usr/bin/env python3 """ Metadata Extraction Tool Extract citation metadata from DOI, PMID, arXiv ID, or URL using various APIs.

Tool: scripts/extract_metadata.py [2/2] Description: _format_authors_crossref(self, authors: List[Dict]) -> str: """Format author list from CrossRef data.""" if not authors: return '' formatted = [] for author in authors: given = author.get('given', '') family = author.get('family', '') if family: if given: formatted.append(f'{family}, {given}') else: formatted.append(family) return ' and '.join(formatted) def _format_authors_pubmed(self, authors: List) -> str: """Format author list from PubMed

Malicious tool definition detected

Tool: scripts/format_bibtex.py Description: #!/usr/bin/env python3 """ BibTeX Formatter and Cleaner Format, clean, sort, and deduplicate BibTeX files.

Malicious tool definition detected

Tool: scripts/search_google_scholar.py Description: #!/usr/bin/env python3 """ Google Scholar Search Tool Search Google Scholar and export results.

Malicious tool definition detected

Tool: scripts/search_pubmed.py Description: #!/usr/bin/env python3 """ PubMed Search Tool Search PubMed using E-utilities API and export results.

Malicious tool definition detected

Tool: scripts/validate_citations.py [1/2] Description: #!/usr/bin/env python3 """ Citation Validation Tool Validate BibTeX files for accuracy, completeness, and format compliance.

Tool: scripts/validate_citations.py [2/2] Description: DOI {i+1}: {doi}', file=sys.stderr) is_valid, metadata = self.verify_doi(doi) if not is_valid: doi_errors.append({ 'type': 'invalid_doi', 'entry': entry['key'], 'doi': doi, 'severity': 'high', 'message': f'Entry {entry["key"]}: DOI does not resolve: {doi}' }) all_errors.extend(doi_errors) return { 'filepath': filepath, 'total_entries': len(entries), 'valid_entries': len(entries) - len([e for e in all_errors if e['severity'] == 'high']), 'err