Academic Paper Finder

Search biomedical literature, get citation counts, and import to Zotero/EndNote. Use when: (1) User asks to search for papers/literature by DOI, title, autho...

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

python3 scripts/pubmed_search.py --doi "10.1016/j.cell.2014.07.013"

2. Search by Title

python3 scripts/pubmed_search.py --title "circulating tumor cell clusters"

3. Search by Author

python3 scripts/pubmed_search.py --author "Aceto N" --year 2014

4. Add to Zotero

# 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)

python3 scripts/batch_import.py --pmids "25171411,30728496,41212905"

6. Generate RIS for EndNote

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:

# 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.