🧩 KNIME OBO Reader Extension

📖 Description

The KNIME OBO Reader Extension is a custom KNIME node that enables users to read and process OBO (Ontology) files efficiently. It leverages obonet, polars, and networkx to extract nodes and edges from ontology files and convert them into KNIME-compatible tables.

This extension allows users to:

• Browse and select .obo files for parsing.
• Automatically detect available columns or manually specify them.
• Process and transform ontology data into tabular format.

---

🚀 Features

✅ OBO File Selection: Browse and select files instead of manually entering paths.
✅ Automatic Column Detection: Choose to auto-detect columns or specify them manually.
✅ Node & Edge Extraction: Extracts ontology terms as nodes and relationships as edges.
✅ Flexible Schema: Supports different OBO structures dynamically.

---

📌 Usage Instructions

🎯 Adding the Node

• Open KNIME and navigate to the Community section.
• Drag & drop OBO NetworkX Reader into your workflow.

---

🏗 Configuration

1. Select the OBO file using the Browse button.
2. Choose column detection mode:
   • 🔍 Automatic: Detects all available columns.
   • 📝 Manual: Allows specifying columns (e.g., id, name, synonym).
3. Run the node to extract data into two KNIME tables:
   • Nodes Table (id, name, synonym, xref, etc.).
   • Edges Table (source, target, type).

---

🤝 Contributing

We welcome contributions! Feel free to:

• 🛠 Improve the node functionality.
• 🐞 Report issues in the GitHub Issues.
• 📖 Improve documentation.

---

🏆 Credits

Developed by De Sousa Mathis at CIAD.
Special thanks to the KNIME community, especially Martin from the KNIME forum, for guidance!

---