Medical-research-skills bib-formatter

Source: https://github.com/aipoch/medical-research-skills

When to Use

• You have a bibliography in RIS/BibTeX/plain text/CSL-JSON and must reformat it to a journal style (e.g., NEJM, The Lancet, Nature) before submission.
• You need to switch in-text citation formatting (e.g., generating formatted citations for specific cite keys/IDs).
• You are consolidating references from multiple sources and want a single consistent output style.
• You want a before/after comparison to verify formatting changes and spot missing metadata.
• You need to validate and repair incomplete entries (missing authors, year, journal, pages, DOI/URL) prior to final export.

Key Features

• Supports input formats: RIS, BibTeX, plain text, CSL-JSON.
• Outputs bibliography entries compatible with CSL styles (including NEJM/Lancet/Nature or any custom

  .csl

  ).
• Journal-name driven style selection with automatic CSL retrieval (exact match preferred; download first, then search fallback).
• Batch conversion via

  scripts/format_bibliography.py

  .
• In-text citation generation mode for specified cite keys/IDs.
• Produces a Markdown Before/After table (minimum 2 examples) for quick review.
• Detects entries that cannot be reliably parsed and requests missing fields.

Dependencies

• Python 3.10+
• Citation Style Language (CSL) style files (

  .csl

  ) for target formatting (e.g.,

  styles/nature.csl

  ,

  styles/the-lancet.csl

  ,

  styles/new-england-journal-of-medicine.csl

  )

Example Usage

1) Auto-retrieve a journal style (recommended)

python scripts/format_bibliography.py \
  --input refs.bib \
  --input-format bibtex \
  --journal "Nature"

2) Use a local CSL style file for bibliography formatting

python scripts/format_bibliography.py \
  --input refs.bib \
  --input-format bibtex \
  --style "styles/nature.csl" \
  --output formatted.txt

3) RIS input example

python scripts/format_bibliography.py \
  --input refs.ris \
  --input-format ris \
  --style "styles/the-lancet.csl"

4) In-text citations mode (format citations for specific IDs)

python scripts/format_bibliography.py \
  --input refs.json \
  --input-format csljson \
  --style "styles/new-england-journal-of-medicine.csl" \
  --mode citations \
  --cite-keys "ITEM-1,ITEM-2"

Implementation Details

• Workflow

  1. Collect input text/files and identify the input format:

     ris | bibtex | plain | csljson

     .
  2. Choose the target style by either:
     • providing

       --journal "<Journal Name>"

       (auto-retrieval; exact match prioritized; download first, then search), or
     • providing

       --style "<path/to/style.csl>"

       (local CSL file).
  3. Run batch conversion using

     scripts/format_bibliography.py

     .
  4. Validate completeness of critical fields and rerun after fixing missing metadata:
     • author(s), year, title, journal/container title, volume/issue, pages, DOI/URL.
  5. After formatting, append a Markdown comparison table with at least two Before/After examples.

• Input parsing and field mapping

  • Refer to

    references/input-formats.md

    for parsing rules, field mapping, and format-specific details.

• Output requirements

  • All instructions/prompts shown to the user must be in Chinese.
  • Clearly state the target CSL style and the source input format.
  • For entries that cannot be reliably parsed, prompt in Chinese and list the missing fields that must be completed.
  • Always include a Markdown Before/After comparison table (≥ 2 examples) at the end.

• Quality checklist

  • Output matches the target journal style (NEJM/Lancet/Nature/custom CSL).
  • Required metadata is complete: author, year, journal, volume/issue/pages, DOI/URL.
  • Sorting, punctuation, and capitalization follow the CSL style rules.