# 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](https://github.com/Public-Health-Bioinformatics/DataHarmonizer) is a ontology-based curation tool that is being adapter to LinkML

### Koza

 - [Koza](https://github.com/monarch-initiative/koza) is a data transformation framework for LinkML models

### Schemasheets

 - [Schemasheets](https://github.com/linkml/schemasheets) allows the specification of schemas via excel and google sheets

### Bootstrapping Models

 - [schema-automator](https://github.com/linkml/schema-automator) bootstraps schemas from existing structured and semi-structured sources

### Templated OWL generation

 - [linkml-owl](https://github.com/linkml/linkml-owl) allows schemas to be used as templates for generating OWL ontologies from LinkML data

### Large Language Models

 - [OntoGPT](https://github.com/monarch-initiative/ontogpt) extracts LinkML-compliant data from unstructured text.

### Valve and Nanobot

 - [Valve](https://github.com/ontodev/valve.rs)
 - [Nanobot](https://github.com/ontodev/nanobot.rs)

Valve and Nanobot are Rust-based tools for validating and editing data.
[valve2linkml](https://github.com/tmprd/valve-linkml/blob/master/valve_linkml/linkml2valve.py)
provides a layer of interoperability between these frameworks.

See [this presentation](https://lbnl.zoom.us/rec/share/chiJad2dFzJcnvHWnMXjVLOhuTv9z9izp5wcdvfc_EEdXDgpD9EcUiEHot4d8jVk.-qE8OtMpb-06lVi2?startTime=1686841814000)
from the LinkML community meeting.

### Datalog reasoning

 - [linkml-datalog](https://github.com/linkml/linkml-datalog) allows rule-based reasoning over linkml data

### Data Transformation

 - [linkml-transformer](https://github.com/linkml/linkml-transformer) allows data to be transformed between linkml models

### Data Rendering

 - [linkml-renderer](https://github.com/linkml/linkml-renderer) allows linkml data to be rendered as markdowm or HTML.
 - [plugin-link](https://github.com/plugin-healthcare/plugin-link) allows linkml to be viewed interactively using Svelte Flow.

### Semantic DSL

 - [semdsl](https://github.com/linkml/semantic-dsl) allows for grammars to be embedded in LinkML models

### SOLR

 - [linkml-solr](https://github.com/linkml/linkml-solr) allows linkml data to be indexed and queried from SOLR

### SPARQL templates

 - [sparqlfun](https://github.com/linkml/sparqlfun) is a framework for generating and executing queries against sparql endpoints

### Ontology Access Kit

 - [OAK](https://incatools.github.io/ontology-access-kit/) is a Python library for accessing ontologies and vocabularies

### SSSOM-py

 - [sssom-py](https://github.com/mapping-commons/sssom-py) is a toolkit for managing mappings and is driven by a linkml schema