Does this skill support local ontology files?

Yes, OAK can work with local OBO files using the impleobo adapter, allowing you to query and manage private datasets.

Can I visualize ontology hierarchies with this skill?

Yes, OAK provides tree views and graph visualization tools (via the viz command) to help understand the hierarchical structure of terms.

When should I use OAK instead of the OLS MCP?

Use OAK for complex operations such as relationship mapping, visualization, and boolean queries. Use the OLS MCP for basic external ontology searches.

What external ontology databases are supported?

OAK supports major adapters including SQLite (semantic-sql), BioPortal, and OLS, providing access to hundreds of ontologies.

Does it support complex logical queries?

Yes, OAK supports conjunctions (AND), disjunctions (OR), and exclusions (MINUS) for filtering ontology terms based on their relationships and ancestors.

Ontology Access Kit (OAK)

Name: Ontology Access Kit (OAK)
Author: ai4curation

byai4curation

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Data Science & ML

Enables complex ontology querying, mapping, and visualization using the Ontology Access Kit (OAK) library.

About

The Ontology Access Kit (OAK) skill provides a comprehensive suite of tools for interacting with semantic ontologies like GO, CL, and Uberon. It allows users to perform sophisticated operations beyond simple searches, including relational mapping, tree visualization, subset analysis, and complex boolean queries across local OBO files or external databases like BioPortal and OLS. This skill is essential for bioinformatics, knowledge engineering, and data curation workflows that require deep structural insights into hierarchical data models and semantic relationships.

Key Features

Advanced semantic search and lookup across major ontology databases
Complex boolean query support (AND, OR, MINUS) for term sets
Relationship and mapping retrieval between diverse ontological terms
14 GitHub stars
Integration with multiple adapters including SQLite, BioPortal, and OLS
Hierarchical tree visualization and subgraph generation

Use Cases

Data curators generating subset summaries and statistical reports on ontology structures
Bioinformatics researchers analyzing gene or cell type ontologies for data enrichment
Knowledge engineers mapping local OBO files to global semantic standards

About

Key Features

Advanced semantic search and lookup across major ontology databases
Complex boolean query support (AND, OR, MINUS) for term sets
Relationship and mapping retrieval between diverse ontological terms
14 GitHub stars
Integration with multiple adapters including SQLite, BioPortal, and OLS
Hierarchical tree visualization and subgraph generation

Use Cases

Data curators generating subset summaries and statistical reports on ontology structures
Bioinformatics researchers analyzing gene or cell type ontologies for data enrichment
Knowledge engineers mapping local OBO files to global semantic standards