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https://github.com/thanaraklee/herbhub
Herb Hub Platform, developed for DSI314, is a web app for exploring, analyzing, and managing herbal knowledge. It integrates a knowledge graph, Streamlit dashboards, and database tools for efficient herbal data management and research.
https://github.com/thanaraklee/herbhub
docker-compose llm minio neo4j openai pipeline python scraping streamlit
Last synced: 7 days ago
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Herb Hub Platform, developed for DSI314, is a web app for exploring, analyzing, and managing herbal knowledge. It integrates a knowledge graph, Streamlit dashboards, and database tools for efficient herbal data management and research.
- Host: GitHub
- URL: https://github.com/thanaraklee/herbhub
- Owner: Thanaraklee
- License: mit
- Created: 2024-11-21T15:15:25.000Z (about 1 month ago)
- Default Branch: main
- Last Pushed: 2024-12-15T09:34:36.000Z (9 days ago)
- Last Synced: 2024-12-15T10:21:17.772Z (9 days ago)
- Topics: docker-compose, llm, minio, neo4j, openai, pipeline, python, scraping, streamlit
- Language: JavaScript
- Homepage:
- Size: 8.68 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
[](https://github.com/Thanaraklee/HerbHub/actions/workflows/main.yml)
[](https://github.com/Thanaraklee/HerbHub/actions/workflows/dependabot/dependabot-updates)
[](https://github.com/Thanaraklee/HerbHub/actions/workflows/checkstatus.yml)
# Herb Hub Platform
## Overview
**Herb Hub Platform** is a web-based application designed to facilitate the exploration, analysis, and management of herbal knowledge. The platform integrates various tools, including a knowledge graph, Streamlit dashboards, and database management systems, to provide users with a comprehensive solution for managing herbal data and research.
## Features
- **Streamlit Interface:** A user-friendly dashboard for visualizing and analyzing herbal data.
- **Neo4j Integration:** A graph database to store and query relationships between herbs, compounds, and their effects.
- **MinIO Storage:** A scalable object storage system for managing supplementary data.
- **Dockerized Services:** Simplified deployment and scaling using Docker containers.
## Project Structure (*Sample*)
```bash
HerbHub/
├── backend/ # Handles scraping, transformation, loading, and database management
│
├── frontend/ # Hosts the Streamlit application and contains its configuration files
│
├── docker-compose.yml # Docker Compose file for orchestrating services
├── .env # Environment variables file
└── README.md # Project documentation
```
## Prerequisites
Ensure the following tools are installed:
- [Docker](https://www.docker.com/)
## Installation
1. **Clone the Repository**
Clone the repository and navigate to the project directory:
```bash
git clone https://github.com/your-repository/herb-hub.git
cd herb-hub
```
2. **Set Up Environment Variables**
- Create a `.env` file in the root directory by referencing the `example.env` file provided in the `frontend/` folder.
- Make sure to update the API keys for OpenAI and other credentials as needed:
```bash
# Example for OpenAI
OPENAI_API_1=your_api_key_1
```
Replace the placeholder values (`your_api_key_1`, etc.) with your actual API keys.
3. **Start the Required Services**
Use the following command to build and start the Neo4j and MinIO containers:
```bash
docker-compose up neo4j minio -d --build
```
4. **Run the Scraping and Loading Process**
**Important:** To prevent clearing the database, ensure you comment out line 50 in the `master_pipe.py` file:
```python
# neo4j_pipe.clear_database()
```
Then, execute the following command to start the scraping and loading process (this may take approximately 1 hour):
```bash
python backend/data_pipeline/pipeline/master_pipe.py
```
5. **Start Streamlit**
Launch the Streamlit application using the following command:
```bash
docker compose up streamlit -d
```
6. **Access the Platform**
- Streamlit Dashboard: Navigate to http://localhost:8503
- Neo4j Browser: Navigate to http://localhost:7474
- MinIO Console: Navigate to http://localhost:9001
# Workflow
# Example
# References
- Herb images: [GBIF](https://www.gbif.org)
- Species names, synonyms, and taxonomy: [WFO Plant List](https://www.wfoplantlist.org)
- Plant parts and medicinal uses: [Kew Science - Medicinal Plant Names Services](https://mpns.science.kew.org)
- Plant parts and chemical properties: [USDA Phytochemical Database](https://phytochem.nal.usda.gov)
- Common names, local names, and pharmacological data: [CosmeHerb Database](https://cosmeherb.nbt.or.th)