https://github.com/vida-nyu/bdi-viz
https://github.com/vida-nyu/bdi-viz
bdf-toolbox data-harmonization data-integration
Last synced: 20 days ago
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- Host: GitHub
- URL: https://github.com/vida-nyu/bdi-viz
- Owner: VIDA-NYU
- License: apache-2.0
- Created: 2024-09-25T19:18:42.000Z (8 months ago)
- Default Branch: main
- Last Pushed: 2025-05-01T04:43:25.000Z (24 days ago)
- Last Synced: 2025-05-05T03:46:13.289Z (20 days ago)
- Topics: bdf-toolbox, data-harmonization, data-integration
- Language: Python
- Homepage:
- Size: 734 KB
- Stars: 2
- Watchers: 10
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# bdi-viz
[](https://github.com/VIDA-NYU/bdi-viz/actions/workflows/build.yml)
[](https://github.com/VIDA-NYU/bdi-viz/actions/workflows/lint.yml)
[](https://bdi-viz.readthedocs.io/en/latest/)
## Contents
- [1. Introduction](#sparkle-1-introduction)
- [2. Installation](#package-2-installation)
- [3. Quick Start](#rocket-3-quick-start)
- [4. Documentation](#page_facing_up-4-documentation)
- [4.1 Read the Docs](#41-read-the-docs)
- [4.2 Demo Video](#42-demo-video)
## :sparkle: 1. Introduction
BDIViz is a powerful, interactive tool designed as an extension to [BDIKit](https://github.com/VIDA-NYU/bdi-kit) to assist biomedical researchers and domain experts in performing schema matching tasks. Built to address the challenges of matching complex biomedical datasets, BDIViz leverages a visual approach to streamline the process and enhance both speed and accuracy.
Key features of BDIViz include:
- **Interactive Heatmap** for exploring and comparing matching candidates.
- **Value Comparisons** Panel for analyzing similarities between attributes.
- **Detailed Analysis** Panel offering in-depth insights into attribute value distributions.
- **Filtering & Refinement Tools** to customize and adjust matching candidates based on datatype and similarity scores.
- **Expert-in-the-Loop Workflow** allowing users to iteratively accept, reject, or refine matches, keeping the expert in control of decision-making.
BDIViz is designed to be integrated with Python notebooks, providing a flexible and easy-to-use tool for domain-specific schema matching in biomedical research and beyond.
## :package: 2. Installation
To use ``BDI-Viz``, install it using pip:
```bash
pip install bdi-viz
```
## :rocket: 3. Quick Start
``BDI-Viz 1.0`` is built leveraging [Panel](https://panel.holoviz.org/). The application is designed to provide a user-friendly interface on jupyter notebooks. Where users can explore the schema matching recommandations, interact with the result, and pass them to the next step of the data integration process.
```python
import pandas as pd
from bdiviz import BDISchemaMatchingHeatMap
# Load the data
source_df = pd.read_csv('data/source.csv')
target_df = pd.read_csv('data/target.csv')
# Render the BDI-Viz Heatmap
heatmap_manager = BDISchemaMatchingHeatMap(
source=source_df,
target=target_df,
top_k=20,
)
heatmap_manager.plot_heatmap()
```
The following interface will be displayed in the jupyter notebook:
## :page_facing_up: 4. Documentation
### 4.1 Read the Docs
For more information, please refer to the [documentation](https://bdi-viz.readthedocs.io/en/latest/).
### 4.2 Demo Video
[BDIViz Demo](https://drive.google.com/file/d/1eAbDicO0oXIbbVg56m3H8xdNDDsBGBLI/view?usp=drive_link)