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¶

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

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¶

linkml-datalog allows rule-based reasoning over linkml data

Data Transformation¶

linkml-transformer allows data to be transformed between linkml models

Data Rendering¶

linkml-renderer allows linkml data to be rendered as markdowm or HTML.

Semantic DSL¶

semdsl allows for grammars to be embedded in LinkML models

SOLR¶

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¶

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