sdrf:terms

What problem does it solve?

This Skill helps annotators and AI assistants select, verify, and map controlled-vocabulary ontology terms and accessions for SDRF columns, reducing ambiguity and ensuring values conform to the SDRF specification and accepted ontologies.

Core Features & Use Cases

• Spec-driven ontology selection: Reads the TERMS.tsv mapping to determine which ontology or database to search for each column and applies primary and fallback choices.
• OLS-powered lookup and specificity checks: Demonstrates how to use OLS searches, embedding searches, and ancestor/child navigation to evaluate term specificity and choose appropriate terms.
• Cross-ontology mapping and special databases: Provides procedures for mapping terms across EFO/MONDO/DOID, enforcing UNIMOD accessions for modifications, and consulting Cellosaurus for cell line accessions.
• Use Case: Convert a vague user label like "cancer" or "HeLa" into validated ontology accessions, SDRF-formatted values, and alternatives for more or less specificity before validation.

Quick Start

Find the most appropriate ontology term and accession for the SDRF column characteristics[disease] given the search "breast cancer".