https://github.com/ebodshojaei/sentinel_ai
Retrieve PubMed publications using phi3.5 with phidata to generate and run a Mesh search on NCBI Entrez.
https://github.com/ebodshojaei/sentinel_ai
biopython dotenv entrez ncbi ollama pandas phi3 phidata pubmed python sqlalchemy xlsx
Last synced: 6 months ago
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Retrieve PubMed publications using phi3.5 with phidata to generate and run a Mesh search on NCBI Entrez.
- Host: GitHub
- URL: https://github.com/ebodshojaei/sentinel_ai
- Owner: EbodShojaei
- License: mit
- Created: 2025-03-28T23:06:59.000Z (6 months ago)
- Default Branch: master
- Last Pushed: 2025-03-28T23:25:57.000Z (6 months ago)
- Last Synced: 2025-03-29T00:24:51.955Z (6 months ago)
- Topics: biopython, dotenv, entrez, ncbi, ollama, pandas, phi3, phidata, pubmed, python, sqlalchemy, xlsx
- Language: Python
- Homepage:
- Size: 12.7 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Sentinel | Terminal-Based AI Agent for PubMed Search
This application is a terminal-based AI agent that:
- Accepts a natural language search query from the user.
- Uses a local phi3.5 model (via Ollama and phidata) to generate a research purpose and a detailed MeSH search strategy.
- Executes the search on PubMed using a free API (via Entrez from Biopython).
- Retrieves the top 250 relevant articles, sorted by relevance and publication year.
- Stores the search results and metadata in a relational SQL database.
- Allows the user to export the search results and metadata to an Excel file with two tabs.
## File Structure
```plaintext
sentinel/
├── src/
│ ├── __init__.py
│ ├── agent.py
│ ├── config.py
│ └── utils/
│ ├── __init__.py
│ ├── xlsx_export.py
│ ├── database.py
│ ├── extract_values.py
│ └── pubmed_search.py
├── tests/
│ ├── __init__.py
│ └── test_pubmed_search.py
├── main.py
├── requirements.txt
└── setup.sh
```
## Requirements
The application uses the following Python packages:
- phidata
- ollama
- sqlalchemy
- requests
- biopython
- openpyxl
- pandas
- python-dotenv
Setup virtual Python environment and install all dependencies with:
```bash
./setup.sh
```
## Configuration
Create a `.env` file (make a copy of `.env.example`) in the project root with your configuration. For example:
```dotenv
# .env file
ENTREZ_EMAIL=your.email@example.com
PUBMED_API_KEY=your_pubmed_api_key
MODEL_ID=phi3.5
```
## Usage
Run the application from the terminal:
```bash
python main.py --query "efficacy of placebo injections in knee osteoarthritis patients between 2000 and 2025" --export
```
- If `--query` is not provided, you will be prompted to enter it interactively.
- Optionally specify `--min_year` and `--max_year` for the publication date range (defaults to the last 5 years).
- The `--export` flag will export the results to an Excel file (`output.xlsx`).
## Example Output
See the below example for running a custom query:
```bash
python main.py
Using PubMed API key for enhanced rate limits.
Enter your search query: efficacy of placebo injections in knee osteoarthritis patients
2025-03-28 20:58:24,835 [WARNING] No date range found in the query. Using default values: 2020 to 2025
2025-03-28 20:58:33,472 [INFO] HTTP Request: POST http://127.0.0.1:11434/api/chat "HTTP/1.1 200 OK"
2025-03-28 20:58:33,834 [INFO] HTTP Request: POST https://api.phidata.com/v1/telemetry/agent/run/create "HTTP/1.1 200 OK"
2025-03-28 20:58:41,921 [INFO] HTTP Request: POST http://127.0.0.1:11434/api/chat "HTTP/1.1 200 OK"
2025-03-28 20:58:42,270 [INFO] HTTP Request: POST https://api.phidata.com/v1/telemetry/agent/run/create "HTTP/1.1 200 OK"
2025-03-28 20:58:42,272 [INFO] To assess whether placebo injections offer measurable improvements beyond psychological effects on physical health outcomes such as pain management and functional mobility among adults suffering from knee osteoarthritis, this study will evaluate their efficacy.
2025-03-28 20:59:02,339 [INFO] HTTP Request: POST http://127.0.0.1:11434/api/chat "HTTP/1.1 200 OK"
2025-03-28 20:59:02,680 [INFO] HTTP Request: POST https://api.phidata.com/v1/telemetry/agent/run/create "HTTP/1.1 200 OK"
2025-03-28 20:59:07,426 [INFO] HTTP Request: POST http://127.0.0.1:11434/api/chat "HTTP/1.1 200 OK"
2025-03-28 20:59:07,777 [INFO] HTTP Request: POST https://api.phidata.com/v1/telemetry/agent/run/create "HTTP/1.1 200 OK"
2025-03-28 20:59:07,778 [INFO] (osteoarthritis knee) AND ((placebo injection treatment) AND (pain relief OR analgesia OR symptom improvement)) AND (functionality OR mobility)
2025-03-28 20:59:07,778 [INFO] Executing PubMed search...
Final query for PubMed: (osteoarthritis knee) AND ((placebo injection treatment) AND (pain relief OR analgesia OR symptom improvement)) AND (functionality OR mobility) AND "2020/01/01"[dp] : "2025/12/31"[dp]
Found 74 PubMed IDs
2025-03-28 20:59:19,417 [INFO] Retrieved 74 search results
2025-03-28 20:59:19,460 [INFO] Data stored successfully in the database.
```
## License
This project is released under the MIT License.