linkml/linkml-owl

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

Language: Python - Size: 6.49 MB - Last synced: about 3 hours ago - Pushed: about 3 hours ago - Stars: 11 - Forks: 1

eecavanna/refscan

Command-line program that scans a LinkML schema-compliant MongoDB database for referential integrity issues

Language: Python - Size: 103 KB - Last synced: about 9 hours ago - Pushed: about 10 hours ago - Stars: 0 - Forks: 0

linkml/linkml-runtime

Runtime support for linkml generated models

Language: Python - Size: 2.39 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 21 - Forks: 21

linkml/linkml-store

ALPHA wrapper for multiple linkml storage engines

Language: Python - Size: 7.11 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 3 - Forks: 0

linkml/linkml-map

Mapping between LinkML schemas

Language: Python - Size: 4.92 MB - Last synced: 2 days ago - Pushed: 4 days ago - Stars: 13 - Forks: 2

biolink/biolink-model

Schema and generated objects for biolink data model and upper ontology

Language: Python - Size: 291 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 167 - Forks: 71

mapping-commons/sssom-py

Python toolkit for SSSOM mapping format

Language: Python - Size: 16.2 MB - Last synced: 5 days ago - Pushed: 7 days ago - Stars: 45 - Forks: 9

monarch-initiative/ontogpt

LLM-based ontological extraction tools, including SPIRES

Language: Jupyter Notebook - Size: 58.7 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 516 - Forks: 64

microbiomedata/nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

Language: Python - Size: 115 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 27 - Forks: 8

linkml/linkml-model

Link Modeling Language (LinkML) model

Language: Python - Size: 11.4 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 29 - Forks: 14

linkml/semantic-dsl

Easy Domain Specific Languages for your Schemas

Language: Python - Size: 288 KB - Last synced: 5 days ago - Pushed: about 1 year ago - Stars: 4 - Forks: 0

cmungall/obo-metadata

EXPERIMENTAL obo metadata repo

Language: Jupyter Notebook - Size: 1.2 MB - Last synced: 5 days ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

cmungall/mixs-source

Language: Python - Size: 34.5 MB - Last synced: 5 days ago - Pushed: over 2 years ago - Stars: 2 - Forks: 3

cmungall/human-cell-atlas

EXPERIMENTAL translation of HCA json schema to LinkML

Language: Python - Size: 1.6 MB - Last synced: 5 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

cmungall/edd-schema

Language: Perl - Size: 6.06 MB - Last synced: 5 days ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

cmungall/data-manifesto

semantic modeling of data manifests

Language: Python - Size: 847 KB - Last synced: 5 days ago - Pushed: about 2 years ago - Stars: 2 - Forks: 0

cmungall/basin3d_schema

EXPERIMENTAL

Language: Python - Size: 884 KB - Last synced: 5 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

biodatamodels/ontology-associations

schema for ontology associations

Language: Python - Size: 6.38 MB - Last synced: 5 days ago - Pushed: over 2 years ago - Stars: 4 - Forks: 1

nfdi4cat/pid4cat-model

LinkML model for handle-based PIDs for resources in catalysis (PID4Cat)

Language: Python - Size: 1.05 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 1 - Forks: 1

linkml/linkml

Linked Open Data Modeling Language

Language: Python - Size: 86.4 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 280 - Forks: 85

mapping-commons/sssom

Simple Standard for Sharing Ontology Mappings

Language: Python - Size: 13.7 MB - Last synced: 5 days ago - Pushed: 7 days ago - Stars: 135 - Forks: 24

linkml/schema-automator

Automated assistance for the schema development lifecycle

Language: Python - Size: 8 MB - Last synced: 5 days ago - Pushed: about 2 months ago - Stars: 32 - Forks: 12

monarch-initiative/monarch-ingest

Data ingest application for Monarch Initiative knowledge graph using Koza

Language: Python - Size: 9.13 MB - Last synced: about 5 hours ago - Pushed: 19 days ago - Stars: 14 - Forks: 1

saved-models/ext

Generated documentation for SAVED data model. Due to the interaction between LinkML, JSON-LD contexts and yet-to-be-generated RDF (turtle/n-triples), this is manually compiled.

Language: HTML - Size: 657 KB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

INCATools/semantic-sql

SQL and SQLite builds of OWL ontologies

Language: Python - Size: 7.65 MB - Last synced: 4 days ago - Pushed: 13 days ago - Stars: 33 - Forks: 3

monarch-initiative/babelon

A format for language profiles for ontologies

Language: Python - Size: 21.3 MB - Last synced: 5 days ago - Pushed: 13 days ago - Stars: 8 - Forks: 0

monarch-initiative/koza

Data transformation framework for LinkML data models

Language: Python - Size: 4.63 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 42 - Forks: 3

alliance-genome/agr_curation_schema

Schema repository for the Alliance of Genome Resources persistent data store

Language: Makefile - Size: 13.3 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 6 - Forks: 1

cmungall/linkml-phenopackets

EXPERIMENTAL rendering of phenopackets in linkml

Language: Python - Size: 11.2 MB - Last synced: 4 days ago - Pushed: 18 days ago - Stars: 7 - Forks: 0

isamplesorg/metadata

Collation of metadata examples and notes for the project

Language: Python - Size: 39.6 MB - Last synced: 4 days ago - Pushed: 23 days ago - Stars: 7 - Forks: 2

linkml/template-config-model 📦

Lightweight model for the linkml-model-template configuration parameters

Language: Python - Size: 5.14 MB - Last synced: 27 days ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0

linkml/linkml-schemaorg

Automated linkml rendering of schema.org

Language: Makefile - Size: 28.6 MB - Last synced: 27 days ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

linkml/linkml-sparql

Maps LinkML queries to SPARQL and back (ALPHA)

Language: Python - Size: 10.7 KB - Last synced: 27 days ago - Pushed: almost 3 years ago - Stars: 3 - Forks: 0

linkml/linkml-prov

LinkML rendering of PROV

Language: Python - Size: 5.32 MB - Last synced: 27 days ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

linkml/linkml-project-template 📦

A template for LinkML projects using poetry and gen-project

Language: Jinja - Size: 202 KB - Last synced: 27 days ago - Pushed: over 1 year ago - Stars: 9 - Forks: 2

cidgoh/DataHarmonizer

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.

Language: JavaScript - Size: 47.6 MB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 87 - Forks: 23

biobricks-ai/biobricks-schema

BioBricks data dictionary schema

Language: Python - Size: 1.22 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

linkml/linkml-solr

Simple wrapper for using Solr with LinkML schemas

Language: Python - Size: 315 KB - Last synced: 5 days ago - Pushed: 2 months ago - Stars: 3 - Forks: 0

linkml/schemasheets

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

Language: Python - Size: 1.27 MB - Last synced: 27 days ago - Pushed: about 2 months ago - Stars: 38 - Forks: 5

cmungall/semantic-llama

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

Language: Python - Size: 1.52 MB - Last synced: 5 days ago - Pushed: over 1 year ago - Stars: 22 - Forks: 1

INCATools/kgcl

Datamodel for KGCL (Knowledge Graph Change Language)

Language: Python - Size: 9.12 MB - Last synced: 4 days ago - Pushed: about 1 month ago - Stars: 10 - Forks: 3

chemkg/chemrof

Schema for chemistry ontology classes

Language: Prolog - Size: 13.1 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 13 - Forks: 3

biodatamodels/gff-schema

LinkML schema for GFF3, the Genome Feature Format

Language: Python - Size: 5.2 MB - Last synced: 5 days ago - Pushed: over 2 years ago - Stars: 6 - Forks: 0

linkml/linkml-runtime.js

An implementation of the linkml-runtime in javascript ALPHA VERSION

Language: TypeScript - Size: 310 KB - Last synced: 5 days ago - Pushed: 11 months ago - Stars: 6 - Forks: 3

obophenotype/asctb-tables

LinkML schema for ASCB-T tables

Language: Python - Size: 5.16 MB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

linkml/prefixmaps

Semantic prefix map registry

Language: Python - Size: 5.61 MB - Last synced: 5 days ago - Pushed: 28 days ago - Stars: 9 - Forks: 3

linkml/rda-crosswalk

Example schema: RDA crosswalk

Language: Python - Size: 5.19 MB - Last synced: 27 days ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0

linkml/linkml-registry

Registry of schemas that use LinkML

Language: Python - Size: 5.35 MB - Last synced: 5 days ago - Pushed: 3 months ago - Stars: 11 - Forks: 3

linkml/linkml-tutorial

Language: Python - Size: 1.96 MB - Last synced: 27 days ago - Pushed: 10 months ago - Stars: 5 - Forks: 2

linkml/linkml-common

ALPHA common modeling patterns

Language: Python - Size: 1.97 MB - Last synced: 27 days ago - Pushed: about 1 month ago - Stars: 5 - Forks: 0

linkml/linkml-arrays

Support for N-dimensional arrays in LinkML.

Language: Python - Size: 2.82 MB - Last synced: 27 days ago - Pushed: about 2 months ago - Stars: 3 - Forks: 1

vemonet/ontogpt-api

⛏️ An API to extract informations from text using OntoGPT

Language: Python - Size: 33.2 KB - Last synced: 26 days ago - Pushed: 6 months ago - Stars: 2 - Forks: 0

linkml/sparqlfun

sparql templates for linkml (alpha)

Language: Python - Size: 6.13 MB - Last synced: 13 days ago - Pushed: about 2 years ago - Stars: 8 - Forks: 0

ghga-de/ghga-metadata-schema

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

Language: Python - Size: 5.31 MB - Last synced: 20 days ago - Pushed: 21 days ago - Stars: 13 - Forks: 4

cancerDHC/ccdhmodel

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

Language: Python - Size: 25.6 MB - Last synced: 11 days ago - Pushed: over 2 years ago - Stars: 16 - Forks: 8

monarch-initiative/monochrom

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

Language: Python - Size: 7.56 MB - Last synced: 4 months ago - Pushed: about 1 year ago - Stars: 12 - Forks: 2

linkml/linkml-datalog

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

Language: Python - Size: 705 KB - Last synced: 17 days ago - Pushed: 3 months ago - Stars: 11 - Forks: 0

FAIR-MI/miiid-schema

A metadata schema for the Minimum Information about Intermicrobial Interaction Data (MIIID) using LinkML

Language: Python - Size: 715 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 2 - Forks: 0

microbiomedata/sample-annotator

NMDC Sample Annotator

Language: Python - Size: 8.33 MB - Last synced: 5 days ago - Pushed: about 1 year ago - Stars: 5 - Forks: 9

bridge2ai/model-card-schema

LinkML rendering of model cards

Language: Python - Size: 618 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 3 - Forks: 1

cmungall/mianct-schema

Minimal Information About a New Cell Type

Language: Python - Size: 6.06 MB - Last synced: 5 days ago - Pushed: almost 3 years ago - Stars: 4 - Forks: 1

StroemPhi/NMRspec

Prototype to semantify NMR spectroscopy research data

Language: Python - Size: 194 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 0

linkml/linkml.github.io

Website/splash page for main LinkML project

Language: HTML - Size: 5.37 MB - Last synced: 5 days ago - Pushed: 12 months ago - Stars: 1 - Forks: 3

linkml/linkml-renderer

Rendering of instance data as HTML, Markdown, Mermaid

Language: Python - Size: 2.92 MB - Last synced: 9 days ago - Pushed: 9 months ago - Stars: 1 - Forks: 0

cmungall/json-flattener

Python library for denormalizing nested dicts or json objects to tables and back

Language: Python - Size: 98.6 KB - Last synced: 5 days ago - Pushed: about 2 months ago - Stars: 7 - Forks: 3

INCATools/kgcl-rdflib

Tools for working with KGCL

Language: Python - Size: 6.96 MB - Last synced: 4 days ago - Pushed: about 1 year ago - Stars: 15 - Forks: 6

sujaypatil96/ga4gh-va-schema

Data model for variant annotation in the GA4GH consortium.

Language: Python - Size: 1.16 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

lmodel/uco-analysis

Unofficial, Linkml schema characterizing analytic actions and results in Unified Cyber Ontology 1.1.0

Language: Python - Size: 2.58 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

lmodel/uco-action

Unofficial, Linkml schema characterizing Actions in Unified Cyber Ontology 1.1.0

Language: Python - Size: 2.62 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

lmodel/uco-configuration

Unofficial, Linkml schema characterizing Configurations in Unified Cyber Ontology 1.1.0

Language: Python - Size: 2.35 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

lmodel/uco-core

Unofficial, Linkml schema characterizing Core in Unified Cyber Ontology 1.1.0

Language: Python - Size: 2.53 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

lmodel/uco-identity

Unofficial, Linkml schema characterizing Identities in Unified Cyber Ontology 1.1.0

Language: Python - Size: 2.55 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

lmodel/uco-location

Unofficial, Linkml schema characterizing Locations in Unified Cyber Ontology 1.1.0

Language: Python - Size: 2.37 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

lmodel/uco-marking

Unofficial, Linkml schema characterizing Markings in the Unified Cyber Ontology 1.1.0

Language: Python - Size: 2.33 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

lmodel/uco-pattern

Unofficial, Linkml schema characterizing Patterns in Unified Cyber Ontology 1.1.0

Language: Python - Size: 2.28 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

lmodel/uco-role

Unofficial, Linkml schema characterizing Roles in Unified Cyber Ontology 1.1.0

Language: TypeScript - Size: 1.89 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

lmodel/uco-time

Unofficial, Linkml schema characterizing Time in Unified Cyber Ontology 1.1.0

Language: Makefile - Size: 1.5 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

lmodel/uco-types

Unofficial, Linkml schema characterizing Types in Unified Cyber Ontology

Language: Python - Size: 2.74 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

lmodel/uco-victim

Unofficial, Linkml schema for Victim in Unified Cyber Ontology 1.1.0

Language: TypeScript - Size: 1.85 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

lmodel/collections

Unofficial, Linkml schema for Collections Ontology (CO) 2.0

Language: Python - Size: 1.3 MB - Last synced: 5 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

lmodel/uco-tool

Unofficial, Linkml Schema characterizing Tools in Unified Cyber Ontology 1.1.0

Language: Python - Size: 1.65 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

lmodel/uco-observable

Unoffiical, Linkml schema characterizing Observables in Unified Cyber Ontology 1.1.0

Language: Python - Size: 6.31 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

lmodel/uco-master

Unofficial, merged Linkml schema for Master Universal Cyber Ontology 1.1.0

Language: Python - Size: 6.54 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

linkml/linkml-csv 📦

LinkML to CSV conversion

Language: Python - Size: 22.5 KB - Last synced: 16 days ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0

cmungall/owl-schema

schema for OWL in LinkML

Language: Python - Size: 757 KB - Last synced: 5 days ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

cmungall/all-about-me

Metadata for the people

Language: Python - Size: 68.4 KB - Last synced: 5 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1

berkeleybop/kgviz-model

Schema for configurations / stylesheets for visualizing ontology and KGs

Language: Python - Size: 6.29 MB - Last synced: 5 days ago - Pushed: over 1 year ago - Stars: 4 - Forks: 0

sujaypatil96/ga4gh-va

LinkML schema for GA4GH variant annotation

Language: Jinja - Size: 1.67 MB - Last synced: 5 days ago - Pushed: about 2 years ago - Stars: 0 - Forks: 1

biodatamodels/obograph

Language: Makefile - Size: 978 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 4 - Forks: 0

alliance-genome/DEPRECATED_agr_persistent_schema

Repository using linkml templating system for generating Alliance of Genome Resources persistent database schema

Language: Python - Size: 5.88 MB - Last synced: 26 days ago - Pushed: about 2 years ago - Stars: 2 - Forks: 1

linkml/linkml-dataops

Data API for LinkML instance data

Language: Python - Size: 125 KB - Last synced: 9 days ago - Pushed: 3 months ago - Stars: 4 - Forks: 1

biodatamodels/domestic-animal-diversity

LinkML rendering of FAO domestic-animal-diversity schema EXPERIMENTAL

Language: Python - Size: 6.86 MB - Last synced: 3 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

timsbiomed/TermCI-model

The Terminology Code Index Entry model

Language: Python - Size: 147 KB - Last synced: 5 days ago - Pushed: about 3 years ago - Stars: 3 - Forks: 1