XzhLoongSkills/skills/academic/citation-management/references/bibtex_formatting.md

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!