academic-paper-finder

# Academic Paper Finder Search PubMed and import papers to Zotero or generate RIS file for EndNote. ## Setup Requires environment variables: - `ZOTERO_API_KEY` - Zotero API key (from https://www.zotero.org/settings/keys/new) - `ZOTERO_USER_ID` - Your Zotero user ID ## Quick Start ### 1. Search Paper by DOI ```bash python3 scripts/pubmed_search.py --doi "10.1016/j.cell.2014.07.013" ``` ### 2. Search by Title ```bash python3 scripts/pubmed_search.py --title "circulating tumor cell clusters" ``` ### 3. Search by Author ```bash python3 scripts/pubmed_search.py --author "Aceto N" --year 2014 ``` ### 4. Add to Zotero ```bash # By PMID python3 scripts/zotero_add.py --pmid 25171411 # By DOI python3 scripts/zotero_add.py --doi "10.1016/j.cell.2014.07.013" ``` ### 5. Batch Import (Multiple PMIDs) ```bash python3 scripts/batch_import.py --pmids "25171411,30728496,41212905" ``` ### 6. Generate RIS for EndNote ```bash python3 scripts/generate_ris.py --pmids "25171411,30728496" --output literature.ris ``` ## Scripts - `pubmed_search.py` - Search PubMed by DOI/title/author - `zotero_add.py` - Add paper to Zotero by PMID/DOI - `batch_import.py` - Batch add multiple papers - `generate_ris.py` - Generate RIS file for EndNote ## Examples ### Get PMID from Citation When user provides a citation like: ``` Aceto, N.; Bardia, A.; Miyamoto, D. T.; Donaldson, M. C.; Wittner, B. S.; Spencer, J. A.; Yu, M.; Pely, A.; Ting, K.; Haber, D. A.; Maheswaran, S. Circulating Tumor Cell Clusters Are Oligoclonal Precursors of Breast Cancer Metastasis. Cell 2014, 158 (5), 1110–1122. https://doi.org/10.1016/j.cell.2014.07.013. ``` 1. Extract DOI: `10.1016/j.cell.2014.07.013` 2. Search: `python3 scripts/pubmed_search.py --doi "10.1016/j.cell.2014.07.013"` 3. Result: PMID 25171411 4. Add to Zotero: `python3 scripts/zotero_add.py --pmid 25171411` ### Batch Import for EndNote User has multiple papers and wants to import to EndNote: ```bash # List all PMIDs python3 scripts/generate_ris.py --pmids "25171411,30728496,41212905,41651843,19945376" --output my_papers.ris ``` Then import the RIS file to EndNote: File → Import → Select .ris file.