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pv-mapping

@linkml/valuesets
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SKILL.md

name pv-mapping
description Map permissible values in LinkML enums to ontology terms. Use this skill when: (1) Adding or updating ontology mappings (meaning: field) for enum permissible values, (2) Fixing validation errors from linkml-term-validator, (3) User asks to map enums to ontology terms or fix CURIE mappings. This skill covers OAK/runoak lookup, CURIE verification, and validation workflows.

Permissible Value Ontology Mapping

Core Rules

  1. Never change PERMISSIBLE_VALUE names - Keep uppercase names like NUCLEIC_ACID
  2. Use title: for ontology label - Match the ontology term's label
  3. Use meaning: for CURIE - Always verify via runoak before adding
  4. Never guess CURIEs - Wrong mappings are worse than no mappings

Workflow

1. Look up term via runoak

# Search for terms
runoak -i sqlite:obo:ncit search "nucleic acid"

# Verify a CURIE exists and get its label
runoak -i sqlite:obo:ncit info NCIT:C706

2. Add mapping

NUCLEIC_ACID:
  title: Nucleic Acids          # matches ontology term label
  description: DNA or RNA sample
  meaning: NCIT:C706            # verified CURIE

Note that either the permissible value key, the title, or one of the aliases should be a (case insensitive) match to the ontology term.

If there is already a canonical meaning field, OR the concept is not a close map, then linkml close/narrow/broad/exact mappings can be used:

NUCLEIC_ACID:
  title: Nucleic Acids          # matches ontology term label
  description: DNA or RNA sample
  meaning: NCIT:C706            # verified CURIE
  close_mappings:
    - SO:0000348.               # label is nucleic_acid
  aliases:
    - nucleic_acid              # to match SO

3. Validate

just validate

Interpreting Validation Errors

Error Type Action
"resolves to [wrong concept]" Fix immediately - CURIE points to wrong term
"label mismatch" Usually OK - add title: to match label if needed, or use an aliases
"Could not retrieve" Check CURIE format or remove if term doesn't exist

Ontology Selection

See references/ontologies.md for:

  • Domain-to-ontology mapping (which ontology for which concept type)
  • CURIE format patterns for each ontology
  • Additional runoak commands

When to Remove Mappings

Remove meaning: when:

  • No appropriate ontology term exists
  • CURIE consistently fails validation
  • Mapped term is semantically incorrect or not the same concept