Ontology Access Kit (OAK)

About

The Ontology Access Kit (OAK) skill empowers Claude to perform sophisticated bio-ontology operations that go beyond basic search. While standard tools handle simple lookups, this skill enables recursive graph traversal, complex boolean logic (conjunctions, disjunctions, and subtractions), and detailed relationship mapping. It supports multiple backends including SQLite for high-speed local access to OBO ontologies, as well as remote access via BioPortal and OLS. It is an essential utility for bioinformaticians and knowledge engineers needing to automate data curation, analyze hierarchical structures, or visualize term subgraphs.

Key Features

• Complex query support using boolean logic (e.g., .sub, .and, .minus) for precise term filtering.
• Lexical matching and alignment tools for mapping terms across different ontologies.
• High-performance local ontology access using the semantic-sql SQLite adapter.
• Subgraph visualization and metadata extraction in multiple formats including OBO.
• 14 GitHub stars
• Advanced graph traversal for exploring is-a and part-of relationships in ontologies like GO, CL, and Uberon.

Use Cases

• Analyzing term dependencies and definitions to ensure consistency in large-scale metadata annotation projects.
• Extracting specific hierarchical subgraphs for biological data curation and knowledge graph construction.
• Automating the mapping of clinical or biological terms across SNOMEDCT, EFO, and other major ontologies.