Does it support mappings other than 'exact' matches?

Yes, if the concept is not a direct match, you can use linkml fields for close, narrow, or broad mappings alongside the primary meaning.

Which tools does this skill interact with?

The skill utilizes the runoak (Ontology Access Kit) CLI for lookups and the linkml-term-validator for verifying mapping accuracy.

What is the primary purpose of the pv-mapping skill?

It is designed to map permissible values in LinkML enums to specific ontology terms using verified CURIEs and labels to ensure data standards.

What happens if a CURIE fails validation?

The skill provides a workflow to interpret validation errors, such as label mismatches or retrieval failures, allowing you to fix the CURIE or update the title/alias.

Can I change the permissible value names while mapping?

No, the skill enforces a rule to keep the original uppercase permissible value names (e.g., NUCLEIC_ACID) and uses the 'title' field for the ontology label.

Ontology Permissible Value Mapper

Name: Ontology Permissible Value Mapper
Author: linkml

bylinkml

•

データサイエンスとML

Maps LinkML enum permissible values to verified ontology terms and CURIEs using the Ontology Access Kit (OAK).

The pv-mapping skill streamlines the process of linking LinkML permissible values to standardized ontology terms, ensuring data interoperability in scientific and biomedical domains. It provides a structured workflow for searching ontologies via runoak, verifying CURIEs, and managing semantic mappings (including exact, close, narrow, and broad) while maintaining strict naming conventions and validation standards. This skill is essential for developers and data scientists working with LinkML schemas who need to maintain high-quality, validated semantic metadata.

主な機能

01Automated ontology term lookup using runoak search and info commands

02Integrated validation workflow with linkml-term-validator to catch mapping errors

03Semantic label synchronization using the title and meaning fields

04Verified CURIE mapping for LinkML enum permissible values

05Support for complex mapping relationships including close, narrow, and broad mappings

0610 GitHub stars

ユースケース

01Mapping scientific enums like cell types or chemical compounds to NCIT, SO, or other OBO ontologies

02Standardizing data models to ensure semantic interoperability across biomedical databases

03Resolving and fixing CURIE validation errors in LinkML schema repositories

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add linkml/valuesets pv-mapping

For use in Claude.ai and ChatGPT

Download Skill