How do I install the Pv Mapping skill?

Run npx skillmds@latest add majiayu000/pv-mapping in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Pv Mapping safe to use?

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Which AI agents work with Pv Mapping?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Pv Mapping free to use?

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Who published Pv Mapping?

majiayu000 (@majiayu000) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Pv Mapping by majiayu000 — Agent Skill

Name: Pv Mapping
Rating: 4.2 (5 reviews)
Author: majiayu000

Pv Mapping

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.

majiayu000 Updated Sep 9, 2026 567 repo stars

File contents

Permissible Value Ontology Mapping

Core Rules

Never change PERMISSIBLE_VALUE names - Keep uppercase names like NUCLEIC_ACID
Use title: for ontology label - Match the ontology term's label
Use meaning: for CURIE - Always verify via runoak before adding
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

---name: pv-mappingdescription: 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 ```bash # 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 ```yaml 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: ```yaml 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 ```bash 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](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

Frequently asked questions