How do I install the Linkml Valuesets Pv Mapping skill?

Run npx skillmds@latest add tomevault-io/linkml-valuesets-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.

What does the Linkml Valuesets Pv Mapping skill do?

Permissible Value Ontology Mapping It is listed under Coding & Dev Tools on SkillMD.

Is Linkml Valuesets Pv Mapping safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Linkml Valuesets 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 Linkml Valuesets Pv Mapping free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Linkml Valuesets Pv Mapping?

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

Linkml Valuesets Pv Mapping by tomevault-io

Name: Linkml Valuesets Pv Mapping
Author: tomevault-io

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

Converted and distributed by TomeVault — claim your Tome and manage your conversions.

---name: linkml-valuesets-pv-mappingdescription: Permissible Value Ontology Mapping---# Permissible Value Ontology Mapping## Core Rules1. **Never change PERMISSIBLE_VALUE names** - Keep uppercase names like `NUCLEIC_ACID`2. **Use `title:` for ontology label** - Match the ontology term's label3. **Use `meaning:` for CURIE** - Always verify via runoak before adding4. **Never guess CURIEs** - Wrong mappings are worse than no mappings## Workflow### 1. Look up term via runoak```bash# Search for termsrunoak -i sqlite:obo:ncit search "nucleic acid"# Verify a CURIE exists and get its labelrunoak -i sqlite:obo:ncit info NCIT:C706```### 2. Add mapping```yamlNUCLEIC_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 aliasesshould 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:```yamlNUCLEIC_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```bashjust 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 SelectionSee [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 MappingsRemove `meaning:` when:- No appropriate ontology term exists- CURIE consistently fails validation- Mapped term is semantically incorrect or not the same concept---> Converted and distributed by [TomeVault](https://tomevault.io/claim/linkml) — claim your Tome and manage your conversions.

Frequently asked questions

Linkml Valuesets Pv Mapping