LLM-based ontological extraction tools, including SPIRES

Linked Open Data Modeling Language

Schema and generated objects for biolink data model and upper ontology

Simple Standard for Sharing Ontology Mappings

A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the Centre for Infectious Disease Genomics and One Health (CIDGOH), at Simon Fraser University, is now an open-source collaboration with contributions from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.

Link Modeling Language (LinkML) model

Data transformation framework for LinkML data models

Python toolkit for SSSOM mapping format

SQL and SQLite builds of OWL ontologies

Automated assistance for the schema development lifecycle

Structure your data in a FAIR way using google sheets or TSVs. These are then converted to LinkML, and from there other formats

National Microbiome Data Collaborative (NMDC) unified data model

Runtime support for linkml generated models

Mapping between LinkML schemas

A knowledge extraction tool that uses a large language model to extract semantic information from text

wrapper for multiple linkml storage engines

Data ingest application for Monarch Initiative knowledge graph using Koza

Datamodel for KGCL (Knowledge Graph Change Language)

Schema for chemistry ontology classes

Logic plus python types

Tools for working with KGCL

CRDC-H model in LinkML, developed by the Center for Cancer Data Harmonization (CCDH)

Translates LinkML schemas into Datalog programs and executes them using Souffle, enabling advanced validation and inference over instance data. ALPHA.

Extension of LinkML runtime for converting instances of LinkML classes to OWL (classes or instances)

Standardized identifiers and OWL classes for chromosomes and chromosomal parts across species

Registry of schemas that use LinkML

Metadata schema for the German Human Genome-Phenome Archive (GHGA)

Semantic prefix map registry

sparql templates for linkml (alpha)

Common value sets (enums) for science, biomedicine, computing, and other areas