dunnlab-biblio

name	dunnlab-biblio
description	Standards and workflow for managing bibliographic references in manuscripts. Covers BibTeX formatting conventions, author lists, title capitalization, and conservative editing rules.

Bibliographic Reference Management

Standards for managing .bib files and bibliographic references in Dunn Lab manuscripts.

Core principle: be conservative

Never guess or fabricate bibliographic data. If information is missing or uncertain, flag it for the user rather than filling in a plausible value. This applies to:

• DOIs
• Full author lists
• Titles
• Journal names
• Volume/issue/page numbers
• Publication years

If a field is missing from the source material, leave it out and add a comment (% TODO: missing <field>) rather than guessing.

BibTeX file conventions

Entry keys

Use the format AuthorYear for entry keys (e.g., Dunn2008, HejnolMartindale2009). For multiple papers by the same first author in the same year, append lowercase letters: Dunn2008a, Dunn2008b.

Author lists

Always retain the full author list. Never abbreviate with "and others", "et al.", or truncate the list. Every author must be listed in the author field exactly as published.

% CORRECT
author = {Dunn, Casey W. and Hejnol, Andreas and Matus, David Q. and Pang, Kevin and Browne, William E. and Smith, Stephen A. and Seaver, Elaine and Rouse, Greg W. and Obst, Matthias and Edgecombe, Gregory D. and S{\o}rensen, Martin V. and Haddock, Steven H. D. and Schmidt-Rhaesa, Andreas and Okusu, Akiko and Kristensen, Reinhardt M{\o}bjerg and Wheeler, Ward C. and Martindale, Mark Q. and Giribet, Gonzalo},

% WRONG — do not truncate
author = {Dunn, Casey W. and others},

Title capitalization

Protect words with non-standard capitalization by wrapping them in curly braces {}. This prevents BibTeX styles from down-casing them. Words that need protection include:

• Proper nouns: {Bayesian}, {Darwin}, {Atlantic}
• Tool and software names: {RAxML}, {BLAST}, {Python}, {GitHub}
• Acronyms and initialisms: {DNA}, {RNA}, {HIV}, {MCMC}, {HPC}
• Species names (when in the title): {Nematostella}, {Drosophila}
• Other words with intentional capitalization: {pH}, {mRNA}

Wrap only the individual words, not the entire title:

% CORRECT
title = {Broad phylogenomic sampling improves resolution of the animal tree of life using {Bayesian} methods},

% WRONG — wrapping entire title prevents style-driven formatting
title = {{Broad phylogenomic sampling improves resolution of the animal tree of life using Bayesian methods}},

Fields to exclude

Do not include the following fields, as they add bulk without value for our use cases:

• abstract
• keywords
• file
• local-url
• url (unless it is the only way to locate the work, e.g., for preprints without DOIs)

Required and recommended fields

For articles:

• Required: author, title, journal, year
• Recommended: volume, number, pages, doi

For books:

• Required: author or editor, title, publisher, year
• Recommended: edition, doi, isbn

For incollection (book chapters):

• Required: author, title, booktitle, publisher, year
• Recommended: editor, pages, doi

For unpublished/preprints:

• Required: author, title, year
• Recommended: doi, note (e.g., "Preprint on bioRxiv")

Formatting conventions

• Use standard BibTeX entry types: @article, @book, @incollection, @inproceedings, @phdthesis, @misc, @unpublished
• Use and to separate authors in the author field
• Use LaTeX-encoded special characters: {\"o} for ö, {\o} for ø, {\'e} for é, etc.
• Keep one field per line, with consistent indentation
• End each field line with a comma
• Use double braces for the journal field only when needed to preserve exact capitalization

Example of a well-formatted entry:

@article{Dunn2008,
  author  = {Dunn, Casey W. and Hejnol, Andreas and Matus, David Q. and Pang, Kevin and Browne, William E. and Smith, Stephen A. and Seaver, Elaine and Rouse, Greg W. and Obst, Matthias and Edgecombe, Gregory D. and S{\o}rensen, Martin V. and Haddock, Steven H. D. and Schmidt-Rhaesa, Andreas and Okusu, Akiko and Kristensen, Reinhardt M{\o}bjerg and Wheeler, Ward C. and Martindale, Mark Q. and Giribet, Gonzalo},
  title   = {Broad phylogenomic sampling improves resolution of the animal tree of life},
  journal = {Nature},
  year    = {2008},
  volume  = {452},
  number  = {7188},
  pages   = {745--749},
  doi     = {10.1038/nature06614},
}

Workflow for adding references

1. Obtain the reference from a reliable source — publisher website, PubMed, or CrossRef. Do not reconstruct citations from memory.
2. Verify the full author list — check the original publication. If the source only provides abbreviated authors, look up the full list before adding the entry.
3. Apply title capitalization rules — identify words needing curly-brace protection.
4. Remove excluded fields — strip abstract, keywords, file, and other unnecessary fields.
5. Verify entry key uniqueness — ensure the key doesn't conflict with existing entries in the .bib file.
6. Check for duplicates — search the .bib file for the same DOI or a similar author/year/title combination before adding.

Workflow for editing existing references

When editing entries already in a .bib file:

• Do not modify fields you are not specifically asked to change. Even if formatting differs slightly from these conventions, leave existing correct data alone unless the user requests cleanup.
• Never replace a full author list with an abbreviated one.
• Never add a DOI, title, or other substantive field by guessing. If you believe a field is wrong or missing, flag it with a % TODO comment and inform the user.
• When fixing capitalization, only add curly braces around words that clearly need protection — do not wrap ambiguous cases without confirming.

Checking and validating .bib files

When asked to review a .bib file, check for:

1. Truncated author lists (look for "and others", "et al", or suspiciously short lists for multi-author papers)
2. Missing curly braces on proper nouns, tool names, and acronyms in titles
3. Presence of abstract or other excluded fields
4. Missing required fields for each entry type
5. Duplicate entries (same DOI or very similar author/title/year)
6. Malformed LaTeX special characters
7. Inconsistent entry key formatting