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: ```bash # 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 --- ## ADS API Setup Before using citation features, verify `$ADS_API_TOKEN` is set: ```bash 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. --- ## 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 ```bash 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 ```bash 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 ...}`