The LinkML Ecosystem

LinkML is part of a growing ecosystem of tools; these may be at varying levels of maturity

Tools that build off LinkML

Data Harmonizer

  • DataHarmonizer is a ontology-based curation tool that is being adapter to LinkML

Koza

  • Koza is a data transformation framework for LinkML models

Schemasheets

  • Schemasheets allows the specification of schemas via excel and google sheets

Bootstrapping Models

  • schema-automator bootstraps schemas from existing structured and semi-structured sources

Templated OWL generation

  • linkml-owl allows schemas to be used as templates for generating OWL ontologies from LinkML data

Datalog reasoning

SPARQL templates

  • sparqlfun is a framework for generating and executing queries against sparql endpoints

Ontology Access Kit

  • OAK is a Python library for accessing ontologies and vocabularies

SSSOM-py

  • sssom-py is a toolkit for managing mappings and is driven by a linkml schema