OBO Ontology Editor

About

This skill provides a comprehensive toolkit for bio-curators and developers working with Open Biomedical Ontologies (OBO). It enables efficient term discovery, bulk editing via a robust checkout/checkin mechanism, and strict adherence to logical and metadata standards. By automating complex tasks like ID verification, citation management via PMID/DOI, and syntax validation using the ROBOT tool, it ensures that ontology modifications are consistent, well-documented, and error-free without requiring the manual handling of massive development files.

Key Features

• Automated citation support with PMID and DOI full-text retrieval capabilities
• Built-in syntax checking and OBO format validation via ROBOT integration
• 14 GitHub stars
• Streamlined checkout/checkin workflow for editing individual terms in large files
• Standardized logical definition and relationship validation patterns
• Optimized OBO term searching using specialized high-speed grep scripts

Use Cases

• Managing complex term obsoletion while maintaining logical consistency and replacement paths
• Curating new biomedical terms and cross-references within existing OBO ontologies
• Standardizing metadata and scientific citations for large-scale knowledge engineering projects