managing-bibliography

Managing Bibliography

Read scientific papers and manage citations. Two capabilities:

1. Read papers — Download arXiv LaTeX source to read full text, verify claims, understand methodology
2. Cite papers — Fetch BibTeX from NASA ADS and add to bibliography

Reading Papers

Download arXiv LaTeX source to read full paper text:

# Download source (replace ID as needed)
curl -L -o /tmp/2503.19441.tar.gz "https://arxiv.org/src/2503.19441"

# Extract
mkdir -p /tmp/2503.19441 && cd /tmp/2503.19441 && tar -xzf /tmp/2503.19441.tar.gz

# Find the main tex file
ls *.tex

Available after extraction:

• Full paper text (not just abstract), equations, methodology details
• Exact author phrasing for verification
• Their bibliography (.bib or .bbl files) for cross-referencing

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ADS API Setup

Before using citation features, verify $ADS_API_TOKEN is set:

echo $ADS_API_TOKEN

If missing, direct the user to create one at https://ui.adsabs.harvard.edu/user/settings/token and export it. Do not proceed with ADS API calls until the token is available.

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Citing Papers

When adding a paper to the bibliography:

1. Web search for the paper using description + "arxiv"

   • Look for arXiv ID in format YYMM.NNNNN
   • If multiple results, show options and ask user to select

2. Query ADS API to get bibcode using arXiv ID

   curl -H "Authorization: Bearer $ADS_API_TOKEN" \
     'https://api.adsabs.harvard.edu/v1/search/query?q=arXiv:YYMM.NNNNN&fl=bibcode'
   

3. Fetch BibTeX entry with abstract from ADS

   curl -H "Authorization: Bearer $ADS_API_TOKEN" \
     'https://api.adsabs.harvard.edu/v1/export/bibtexabs/{bibcode}'
   

4. Parse BibTeX to extract author names and year:

   • Parse author = {...} field for last names
   • Parse year = YYYY field for publication year
   • Generate citation key based on author count:
     • 1 author: firstauthor{YY} (e.g., asgari17)
     • 2 authors: firstauthor.secondauthor{YY} (e.g., schneider.kilbinger12)
     • 3+ authors: firstauthor.etal{YY} (e.g., wright.etal25)
   • Use only last names, lowercase, final 2 digits of year

5. Replace citation key in BibTeX entry

   • Update the entry key on the first line (before the opening brace)
   • Keep all other fields unchanged

6. Append to bibliography file

   • Add the modified entry to the project's .bib file
   • Check for duplicate keys first and warn if found

7. Report success

   • Show the user the complete entry that was added
   • Confirm file location

Citation Key Generation

Examples from BibTeX parsing:

• author = {{Wright}, Angus H. and {Stölzner}, Benjamin and ...} + year = 2025 → wright.etal25
• author = {{Schneider}, Peter and {Kilbinger}, Martin} + year = 2012 → schneider.kilbinger12
• author = {{Asgari}, Marika} + year = 2017 → asgari17

Notes

• Always use the bibtexabs endpoint (not bibtex) to include abstracts
• ADS author format: author = {{LastName}, FirstName and {LastName}, FirstName ...}