The LinkML Ecosystem#

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

Tools that build off or enhance LinkML#

Data Harmonizer#

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


  • Koza is a data transformation framework for LinkML models


  • 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

Large Language Models#

  • OntoGPT extracts LinkML-compliant data from unstructured text.

Valve and Nanobot#

Valve and Nanobot are Rust-based tools for validating and editing data. valve2linkml provides a layer of interoperability between these frameworks.

See this presentation from the LinkML community meeting.

Datalog reasoning#

Data Transformation#

Data Rendering#

Semantic DSL#

  • semdsl allows for grammars to be embedded in LinkML models


  • linkml-solr allows linkml data to be indexed and queried from SOLR

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 is a toolkit for managing mappings and is driven by a linkml schema