✅ Features

• Speed Commands - Single-key commands when cursor is at the start of an entry

• Entry Operations - Clean, format, and transform individual entries

• File Operations - Sort entries, apply batch transformations, validate files

• Smart Author Parsing - Proper handling of particles (von, van der), suffixes (Jr., III), and corporate authors

• Journal Abbreviations - Toggle journal names between full and abbreviated forms using 50,000+ abbreviation database

✅ When to Use This

This document covers editing .bib files directly. For inserting and managing citations in org/markdown/LaTeX documents, see References and Citations.

✅ Enabling Speed Commands

Speed commands are enabled by default for BibTeX files. The context scimax.atBibtexEntryStart is automatically set when appropriate.

✅ Available Speed Commands

✅ Using Speed Commands

1. Open a .bib file

2. Move cursor to column 0 of an @entry{ line

3. Press a single key from the tables above

4. Press ? to see available commands

Example:

@article{smith2020machine,    <-- cursor at column 0 here
  author = {John Smith},
  title = {Machine Learning},
  year = {2020}
}

✅ Clean Entry

Command: scimax.bibtex.cleanEntry (speed key: c)

Cleans the current entry by:

• Normalizing whitespace (single spaces, trimmed)

• Lowercasing field names

• Sorting fields in standard BibTeX order

• Removing duplicate outer braces ({{Title}} → {Title})

• Preserving inner braces for case protection ({DNA} stays as-is)

Before:

@Article{Smith2020,
  AUTHOR = {  John   Smith  },
  TITLE = {{A Machine Learning Approach}},
  Year = {2020},
  Journal = {Nature}
}

After:

@article{Smith2020,
  author = {John Smith},
  title = {A Machine Learning Approach},
  journal = {Nature},
  year = {2020},
}

✅ Title Case

Command: scimax.bibtex.titleCase (speed key: T)

Converts the title field to Title Case while preserving:

• Braced content ({DNA}, {NASA})

• Small words (a, an, the, and, but, or, for, in, of, on, to, etc.)

Example:

• "the effects of machine learning on {DNA} analysis" → "The Effects of Machine Learning on {DNA} Analysis"

Sentence Case

Command: scimax.bibtex.sentenceCase (speed key: t)

Converts the title field to sentence case (only first word capitalized) while preserving braced content.

Example:

• "The Effects Of Machine Learning" → "The effects of machine learning"

• "Analysis of {DNA} Sequences" → "Analysis of {DNA} sequences"

✅ Generate Key

Command: scimax.bibtex.generateKey (speed key: K)

Generates a citation key based on a configurable pattern. The pattern is set via the scimax.bibtex.keyPattern setting.

Sort Fields

Command: scimax.bibtex.sortFields (speed key: s)

Reorders fields in standard BibTeX order:

1. author, title, journaltitle/journal, booktitle

2. editor, edition, volume, number, issue, pages

3. publisher, location/address, year, date, month

4. doi, url, urldate, isbn, issn

5. eprint, eprinttype, archiveprefix, primaryclass

6. note, annote, abstract, keywords, file

7. Any remaining fields

Downcase Entry

Command: scimax.bibtex.downcaseEntry (speed key: d)

Lowercases the entry type and all field names:

• @Article → @article

• =Author = = → =author ==

• =JOURNAL = = → =journal ==

Wrap in Braces

Command: scimax.bibtex.wrapBraces (speed key: b, keybinding: Cmd+Shift+])

Wraps the current selection or word in curly braces for case protection.

Use this to protect:

• Acronyms: DNA → {DNA}

• Proper nouns: Python → {Python}

• Chemical formulas: H2O → {H2O}

✅ Strip Braces

Command: scimax.bibtex.stripBraces (speed key: B, keybinding: Cmd+Shift+[)

Strips all internal braces from the current entry. Useful for cleaning up entries where braces have been overused.

Before:

@article{smith2024,
  author = {John Smith},
  title = {{A} {Study} of {Machine} {Learning}},
  journal = {{Nature}},
  year = {2024}
}

After:

@article{smith2024,
  author = {John Smith},
  title = {A Study of Machine Learning},
  journal = {Nature},
  year = {2024}
}

Note: This removes ALL internal braces. If you need to preserve specific braces (like {DNA}), you'll need to re-add them after running this command.

Sort Entries

Command: scimax.bibtex.sortEntries

Sorts all entries in the file. Shows a menu to choose sort order:

The command preserves any preamble content (comments, @string definitions) at the top of the file.

Apply Operation to All Entries

Command: scimax.bibtex.applyToAllEntries

Applies a transformation to every entry in the file. Shows a menu of operations:

Validate File

Command: scimax.bibtex.validateFile

Validates the BibTeX file and reports:

• Total number of entries

• Entry types and counts

• Syntax style (BibTeX vs BibLaTeX vs mixed)

• Duplicate keys

• Missing required fields

• Syntax errors

Results are shown in an output channel with severity indicators:

• ❌ Errors (must fix)

• ⚠️ Warnings (should fix)

Show Statistics

Command: scimax.bibtex.showStatistics

Shows a quick overview of the BibTeX file:

• Total entries

• Entries by type (article, book, etc.)

• Syntax style detection

• Field usage statistics

✅ Supported Formats

Key Generation with Authors

When generating citation keys, the first author's last name is used:

• Particles are stripped for the key (van der Berg → berg)

• Corporate names are cleaned (NASA → nasa)

• Accents are normalized (Müller → muller)

✅ Entry Formatting

1. Use consistent case - Run "Downcase Entries" on your file

2. Sort fields consistently - Use "Clean Entries" or "Sort Fields"

3. Protect case-sensitive text - Wrap in braces: {DNA}, {Python}, {NASA}

4. Include DOIs - Enables OpenAlex integration and hover previews

✅ Key Naming

Recommended format: author-year-keyword or authoryearkeyword

Good keys:

• smith-2024-machine or smith2024machine

• vandenberg-2023-neural (note: particle stripped)

• nasa-2022-report

Bad keys:

• ref1, paper2 (not memorable)

• ML_Paper_2024 (inconsistent format)

✅ File Organization

• One bibliography file per project or topic

• Use @string definitions for common journals

• Keep entries in consistent order (by key or year)

• Regularly validate files for errors

✅ Before Sharing

1. Run scimax.bibtex.validateFile to check for errors

2. Run "Clean Entries" via scimax.bibtex.applyToAllEntries

3. Optionally sort entries by key or year

Data Sources

The abbreviation database is sourced from the JabRef Abbreviation Repository, which aggregates abbreviations from multiple authoritative sources:

Total: approximately 50,000 abbreviation entries.

✅ Important: Use Version Control

Before making batch changes to your bibliography files, ensure your files are under version control (git). This allows you to:

• Review changes with git diff

• Undo changes with git checkout if something goes wrong

• Track the history of modifications

Tip: Commit your .bib file before running batch abbreviation operations. If anything goes wrong, you can always revert.

✅ Toggling Journal Names

@article{smith2024,
  author = {John Smith},
  title = {A Great Paper},
  journal = {Journal of the American Chemical Society},
  year = {2024}
}

@article{smith2024,
  author = {John Smith},
  title = {A Great Paper},
  journal = {J. Am. Chem. Soc.},
  year = {2024}
}

✅ Searching Abbreviations

Command: scimax.bibtex.searchJournalAbbreviations

Search the abbreviation database by full name or abbreviation:

1. Enter search query (e.g., "chemistry", "J. Am.")

2. Browse matching results

3. Select an entry to copy the abbreviation to clipboard

✅ Custom Abbreviations

You can add your own journal abbreviations that override the built-in database.

✅ Updating the Database

Command: scimax.bibtex.updateJournalAbbreviations

Downloads the latest abbreviation lists from the JabRef repository:

1. Select which sources to download (multi-select)

2. Wait for downloads to complete

3. Abbreviations are immediately available

Use this to get the latest additions and corrections.

✅ Statistics

Command: scimax.bibtex.journalAbbreviationStats

Shows the number of abbreviations loaded from each source.

✅ Speed Command

✅ Related Standards

• ISO 4 - International standard for abbreviating serial titles

• ISSN LTWA - List of Title Word Abbreviations (56,000+ words in 65 languages)

• CASSI - Chemical Abstracts Service Source Index (chemistry-specific)

✅ Entry Commands (require cursor in entry)

✅ File Commands (operate on entire file)