paper-bib

Generate properly formatted BibTeX entries from DOI, paper title, or /paper-ref output. Verify metadata via Crossref API and optionally append to an existing .bib file.

Input formats

The user may provide one or more of the following:

1. DOI — e.g. 10.1038/s41929-023-01045-5
2. Paper title — e.g. "Unravelling the role of metal–support interactions..."
3. paper-ref-hunter output — a markdown table with columns like Title, DOI, Year, etc.
4. Mixed list — multiple DOIs/titles, one per line or comma-separated

Workflow

Step 1. Extract DOIs

• If input is a DOI string (matches 10.\d{4,}/\S+), use directly.
• If input is a title, search Crossref: https://api.crossref.org/works?query.title=<URL-encoded-title>&rows=3
  • Pick the top result whose title fuzzy-matches (>80% overlap).
  • If no match, warn and ask user to provide DOI manually.
• If input is a /paper-ref table, extract DOI column values.

Step 2. Fetch metadata from Crossref

For each DOI, fetch:

https://api.crossref.org/works/{DOI}

Extract from the message object:

• type → determines BibTeX entry type (see mapping below)
• title[0] → title
• author[] → list of {given, family} pairs
• container-title[0] → journal name
• volume, issue, page → standard fields
• published-print.date-parts[0] or published-online.date-parts[0] → year
• DOI → doi field
• publisher → publisher (for books/proceedings)
• URL → url field

Step 3. Determine entry type

Step 4. Format BibTeX entry

Citation key

Format: {FirstAuthorLastName}{Year}{FirstTitleWord}

• FirstAuthorLastName: ASCII-only, lowercase. Remove diacritics. E.g. müller → muller.
• Year: 4-digit year.
• FirstTitleWord: first significant word of title (skip articles: a, an, the, on, in, of, for).
• Example: choung2023unravelling

Author format

author = {LastName, FirstName and LastName, FirstName and ...},

• Use family and given from Crossref.
• If given is missing, use initials or just family name.
• For consortium/group authors, use {Organization Name} with braces.

Template

@article{key,
  author    = {LastName1, FirstName1 and LastName2, FirstName2},
  title     = {{Title with Braces for Capitalization}},
  journal   = {Journal Name},
  volume    = {V},
  number    = {N},
  pages     = {start--end},
  year      = {YYYY},
  doi       = {10.xxxx/yyyy},
  url       = {https://doi.org/10.xxxx/yyyy},
}

Notes:

• Title wrapped in double braces {{...}} to preserve capitalization.
• Pages use en-dash --.
• Trailing comma after last field (BibTeX tolerates this).
• Two-space indentation for fields.

Step 5. Handle edge cases

ArXiv preprints

• If DOI is missing but arXiv ID is available, use:

  @misc{key,
    author       = {...},
    title        = {{...}},
    year         = {YYYY},
    eprint       = {XXXX.XXXXX},
    archiveprefix = {arXiv},
    primaryclass = {cond-mat.mtrl-sci},
  }

• Try Crossref first; if 404, try https://export.arxiv.org/api/query?id_list=XXXX.XXXXX

Missing fields

• If volume, number, or pages are missing, omit those fields (do NOT insert placeholders).
• If year is missing from both published-print and published-online, check created.date-parts.
• Always warn the user about missing fields: ⚠ Missing: volume, pages

Preprints / posted-content

• Use @misc with note = {Preprint} and howpublished = {\url{...}} if no journal.

Duplicate detection

• Before appending to a .bib file, read the file and check if any existing entry has the same DOI.
• If duplicate found, warn and skip (do not overwrite).

Step 6. Output

Default (no .bib file specified)

Print the BibTeX entry to the conversation. Format as a code block.

Append to .bib file

If user specifies a .bib file path (or one is found in the current project):

1. Read the existing file.
2. Check for duplicate DOIs.
3. Append new entries at the end, separated by a blank line.
4. Report what was added.

Auto-detect: look for *.bib files in the project root or archive/06_references/.

Batch mode

When multiple DOIs/titles are provided:

1. Process each sequentially.
2. Collect all entries.
3. Print or append all at once.
4. Report summary: N entries generated, M skipped (duplicates), K warnings (missing fields).

Error handling

• Crossref 404: DOI not found. Ask user to verify.
• Crossref rate limit: Wait and retry once. If still failing, report.
• Network error: Report and suggest user check connectivity.
• Malformed DOI: Regex-validate before calling API. Strip leading https://doi.org/ if present.

Integration with paper-ref

When receiving output from /paper-ref, parse the markdown table:

• Extract DOI column values.
• Process each DOI through the standard workflow.
• Return BibTeX entries in the same order as the table rows.

Examples

User: /paper-bib 10.1038/s41929-023-01045-5

Output:

@article{choung2023unravelling,
  author    = {Choung, Seokhyun and Park, Jeong-Myeong and ...},
  title     = {{Unravelling the role of metal--support interactions ...}},
  journal   = {Nature Catalysis},
  volume    = {6},
  pages     = {1082--1093},
  year      = {2023},
  doi       = {10.1038/s41929-023-01045-5},
  url       = {https://doi.org/10.1038/s41929-023-01045-5},
}

User: /paper-bib "machine learning interatomic potentials" --file refs.bib

→ Search title on Crossref → fetch top match → format → append to refs.bib.