Resolve ontology terms and accessions for SDRF columns via OLS and databases.
npx skills add https://github.com/bigbio/sdrf-skills --skill sdrf-terms
Please help me install this Agent Skill. Skill: sdrf:terms Source: https://github.com/bigbio/sdrf-skills/tree/main/skills/sdrf-terms Command: npx skills add https://github.com/bigbio/sdrf-skills --skill sdrf-terms
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.
Find the most appropriate ontology term and accession for the SDRF column characteristics[disease] given the search "breast cancer".
High-intent search queries and answers about installing and using this skill.
To find ontology terms for SDRF columns, this Skill reads the TERMS.tsv mapping to determine the correct source, then uses OLS search and hierarchy navigation to select and verify the appropriate accession for your annotation workflow.
The best way to resolve cell line accessions for SDRF annotation is using Cellosaurus cross-references. This Skill consults Cellosaurus to convert vague labels like HeLa into validated cell line accessions conforming to SDRF specifications.
Mapping disease ontology terms across EFO, MONDO, and DOID for SDRF involves cross-ontology mapping procedures. This Skill applies these mappings to convert user labels like cancer into validated, SDRF-formatted ontology accessions.
Yes, SDRF annotation enforces UNIMOD accessions for modifications. This Skill enforces UNIMOD accession requirements during annotation workflows, ensuring modification values conform to the SDRF specification.
You can check ontology term specificity using OLS searches, embedding searches, and ancestor/child navigation. This Skill demonstrates these OLS techniques to evaluate term specificity and choose appropriate terms for SDRF columns.
SDRF validation fails with vague labels because the specification requires controlled-vocabulary ontology terms. This Skill reduces ambiguity by selecting, verifying, and mapping user labels into validated accessions before validation.
bigbioPlan SDRF annotation by defining metadata strategy and selecting templates.
bigbioValidate SDRF files for structural, template, and ontology issues.
nahisahoIntegrate EFO, OLS, Enrichr, and UMLS to map experimental factors and enrich gene lists.
bigbioAnswer SDRF specification questions using official spec data files.
