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linkml-schema

Generate LinkML schema YAML from markdown, Excel, or text descriptions.

14|11|Updated Jan 15, 2026
Search Tags:#data modeling#yaml#project scaffolding#schema generation#linkml#excel parsing
One-click install
npx skills add https://github.com/kbaseincubator/BERIL-research-observatory --skill linkml-schema
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: linkml-schema
Source: https://github.com/kbaseincubator/BERIL-research-observatory/tree/main/.claude/skills/linkml-schema
Command: npx skills add https://github.com/kbaseincubator/BERIL-research-observatory --skill linkml-schema

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires linkml, openpyxl, copier, gh, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the creation of formal data schemas (LinkML YAML) from informal descriptions, streamlining data modeling and project setup.

Core Features & Use Cases

  • Schema Inference: Automatically generates LinkML schema YAML from markdown tables, Excel files, or plain text descriptions.
  • Project Scaffolding: Optionally scaffolds a complete LinkML project repository, including build tools and GitHub integration.
  • Use Case: You have a collection of spreadsheets describing biological samples. This Skill can infer a LinkML schema from them, ensuring data consistency and enabling programmatic access.

Quick Start

Use the linkml-schema skill to generate a LinkML schema from the provided Excel file 'samples.xlsx'.

Frequently Asked Questions about linkml-schema

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I generate a LinkML schema from an Excel file?▼

To generate a LinkML schema from an Excel file, you provide the spreadsheet to the schema inference process, which automatically infers classes, slots, types, and relationships to produce the required YAML data model.

Can I create a LinkML project repository and push it to GitHub automatically?▼

Yes, you can scaffold a complete LinkML project repository using copier and automatically push it to GitHub via the gh dependency, automating the project setup and GitHub integration.

What is the best way to convert markdown tables into a formal data schema?▼

The best way to convert markdown tables into a formal data schema is using schema inference, which reads informal markdown data descriptions and automatically generates a structured LinkML YAML representation.

Do I need openpyxl to parse Excel files for YAML schema generation?▼

Yes, openpyxl is required as a dependency to parse Excel files, enabling the extraction of data structures needed to infer and generate the corresponding LinkML YAML schema.

Does LinkML schema generation support interactive review before scaffolding a project?▼

Yes, the schema generation process offers interactive review and validation of the inferred classes and slots before optionally scaffolding the LinkML project repository.

Why use LinkML YAML for FAIR data initiatives?▼

LinkML YAML ensures data consistency and enables programmatic access for FAIR data initiatives by providing a formal, standardized schema generated directly from informal data descriptions.

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