What is the main benefit of using OAK over standard OLS search?

OAK handles complex operations like graph traversals, boolean logic queries, and local file manipulation that standard search APIs cannot easily perform.

Do I need to install external dependencies for visualization?

Yes, to use the visualization features (the 'viz' command), you must have Graphviz and the og2dot package installed on your system.

Can I use this skill with my own local ontology files?

Yes, the skill supports the impleobo adapter, allowing you to work directly with local .obo files for custom data curation.

Can OAK search across multiple ontologies simultaneously?

Yes, by using the BioPortal or OLS adapters, you can perform global searches across their entire hosted collections of ontologies.

Which OAK adapter is recommended for the best performance?

The sqlite adapter is generally the fastest as it provides rapid access to ontologies indexed in semantic-sql.

Ontology Access Kit (OAK)

Name: Ontology Access Kit (OAK)
Author: ai4curation

byai4curation

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Data Science & ML

Queries and manipulates biological and medical ontologies using the powerful OAK library for complex semantic operations.

About

This skill integrates the Ontology Access Kit (OAK) into Claude's environment, enabling advanced interactions with structured knowledge bases. It goes beyond simple searches by providing tools for complex graph traversals, relationship extraction, and multi-ontology queries via SQLite, OLS, and BioPortal adapters. Ideal for bioinformatics, data curation, and knowledge engineering, it allows Claude to programmatically explore ontological hierarchies, visualize subgraphs, and manage local OBO files with high precision and speed.

Key Features

Visualize ontology subgraphs and relationships using Graphviz integration
Perform high-performance metadata extraction and lexical matching
4 GitHub stars
Access diverse data sources including local OBO files, SQLite, BioPortal, and OLS
Execute complex ontology queries with boolean logic and subclass reasoning
Manage and filter ontology subsets or 'slims' for specific domain needs

Use Cases

Extracting hierarchical relationships and part-of chains for knowledge graph enrichment
Comparing and aligning different ontologies using automated lexical matching and statistics
Mapping clinical terms or research data to standardized ontology IDs like CL, Uberon, or MONDO

About

Key Features

Visualize ontology subgraphs and relationships using Graphviz integration
Perform high-performance metadata extraction and lexical matching
4 GitHub stars
Access diverse data sources including local OBO files, SQLite, BioPortal, and OLS
Execute complex ontology queries with boolean logic and subclass reasoning
Manage and filter ontology subsets or 'slims' for specific domain needs

Use Cases

Extracting hierarchical relationships and part-of chains for knowledge graph enrichment
Comparing and aligning different ontologies using automated lexical matching and statistics
Mapping clinical terms or research data to standardized ontology IDs like CL, Uberon, or MONDO