Does this skill support local files?

Yes, OAK can interact with local .obo files using the impleobo adapter for direct manipulation of local ontology resources.

What is the difference between this OAK skill and the OLS MCP?

The OLS MCP is designed for basic external ontology searching, while the OAK skill is meant for complex operations like subgraph traversal, boolean queries, and working with local OBO files.

Which ontologies can I access with this skill?

You can access any ontology available in OBO, BioPortal, or OLS, including specialized ones like SNOMEDCT, GO, CL, and Uberon.

Can I visualize ontology structures with this tool?

Yes, OAK includes a visualization command that can generate subgraphs from specific terms, provided og2dot is installed.

Ontology Access Kit (OAK)

Name: Ontology Access Kit (OAK)
Author: ai4curation

byai4curation

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数据科学与机器学习

Provides advanced capabilities for querying, visualizing, and manipulating complex ontologies through the Ontology Access Kit (OAK).

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.

主要功能

01Complex query support using boolean logic (e.g., .sub, .and, .minus) for precise term filtering.

02Lexical matching and alignment tools for mapping terms across different ontologies.

03High-performance local ontology access using the semantic-sql SQLite adapter.

04Subgraph visualization and metadata extraction in multiple formats including OBO.

0514 GitHub stars

06Advanced graph traversal for exploring is-a and part-of relationships in ontologies like GO, CL, and Uberon.

使用场景

01Analyzing term dependencies and definitions to ensure consistency in large-scale metadata annotation projects.

02Extracting specific hierarchical subgraphs for biological data curation and knowledge graph construction.

03Automating the mapping of clinical or biological terms across SNOMEDCT, EFO, and other major ontologies.

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add ai4curation/curation-skills ontology-access-kit

For use in Claude.ai and ChatGPT

Download Skill