Skip to content

LinkML Registry

For more information on LinkML:

Registry Entries

Title Topics Stars GitHub URL
ontogpt
LLM-based ontological extraction tools, including SPIRES
709 (details) monarch-initiative/ontogpt
semantic-python-overview
(subjective) overview of projects which are related both to python and semantic technologies (RDF, O...
528 (details) pysemtec/semantic-python-overview
awesome-ontology
A curated list of ontology things
397 (details) ozekik/awesome-ontology
ontology-development-kit
Ontology lifecycle management
263 (details) INCATools/ontology-development-kit
mondo
Mondo Disease Ontology
261 (details) monarch-initiative/mondo
ITK-Wasm
High performance spatial analysis in a web browser and across programming languages and hardware arc...
217 (details) InsightSoftwareConsortium/ITK-Wasm
biolink-model
Schema and generated objects for biolink data model and upper ontology
biolink, datamodel, gene-ontology... 201 (details) biolink/biolink-model
sssom
Simple Standard for Sharing Ontology Mappings
linkml, mapping, mapping-commons... 168 (details) mapping-commons/sssom
kgx
KGX is a Python library for exchanging Knowledge Graphs
130 (details) biolink/kgx
DataHarmonizer
A standardized browser-based spreadsheet editor and validator that can be run offline and locally, a...
application, data, harmonization... 112 (details) cidgoh/DataHarmonizer
obo-relations
RO is an ontology of relations for use with biological ontologies
96 (details) oborel/obo-relations
kg-covid-19
An instance of KG Hub to produce a knowledge graph for COVID-19 response.
82 (details) Knowledge-Graph-Hub/kg-covid-19
psych-DS
YAML-based schema model for the Psych-DS project and its tools
80 (details) psych-ds/psych-DS
risk-atlas-nexus
Risk Atlas Nexus: tooling to bring together resources related to governance of foundation models.
72 (details) IBM/risk-atlas-nexus
CoreMS
CoreMS is a comprehensive mass spectrometry software framework
59 (details) EMSL-Computing/CoreMS
koza
Data transformation framework for LinkML data models
etl, knowledge-graph, koza... 54 (details) monarch-initiative/koza
sssom-py
Python toolkit for SSSOM mapping format
linkml, mappings, obofoundry... 54 (details) mapping-commons/sssom-py
hdmf
The Hierarchical Data Modeling Framework
52 (details) hdmf-dev/hdmf
mixs
Minimum Information about any (X) Sequence” (MIxS) specification
48 (details) GenomicsStandardsConsortium/mixs
go-site
A collection of metadata, tools, and files associated with the Gene Ontology public web presence.
47 (details) geneontology/go-site
optinist
calcium imaging pipeline tool
47 (details) oist/optinist
semantic-sql
SQL and SQLite builds of OWL ontologies
linkml, oaklib, obofoundry... 47 (details) INCATools/semantic-sql
nmdc-schema
National Microbiome Data Collaborative (NMDC) unified data model
ecoinformatics, fair-data, genomics... 43 (details) microbiomedata/nmdc-schema
specification
Margo Specification
39 (details) margo/specification
enola
Enola 🕵🏾‍♀️ Holmes was an SRE.
35 (details) enola-dev/enola
artificial-intelligence-ontology
An ontology modeling classes and relationships describing deep learning networks, their component la...
34 (details) berkeleybop/artificial-intelligence-ontology
semantic-llama
A knowledge extraction tool that uses a large language model to extract semantic information from te...
ai, knowledge-extraction, language-models... 28 (details) cmungall/semantic-llama
nwb_hackathons
Repository for collecting materials from nwb hackathons
24 (details) NeurodataWithoutBorders/nwb_hackathons
RNA-KG 23 (details) AnacletoLAB/RNA-KG
cogs
Convention-based Ontology Generation System
20 (details) Colectica/cogs
monarch-ingest
Data ingest application for Monarch Initiative knowledge graph using Koza
kgx, knowledge-graphs, linkml... 19 (details) monarch-initiative/monarch-ingest
kgcl
Datamodel for KGCL (Knowledge Graph Change Language)
kgcl, linkml, ontology-changes... 18 (details) INCATools/kgcl
kgcl-rdflib
Tools for working with KGCL
diff, diffs, kg... 18 (details) INCATools/kgcl-rdflib
openstudybuilder-solution 17 (details) NovoNordisk-OpenSource/openstudybuilder-solution
ccdhmodel
CRDC-H model in LinkML, developed by the Center for Cancer Data Harmonization (CCDH)
google-sheets, linkml 16 (details) cancerDHC/ccdhmodel
comp-loinc
Computational LOINC in OWL.
14 (details) loinc/comp-loinc
ghga-metadata-schema
Metadata schema for the German Human Genome-Phenome Archive (GHGA)
fega, ghga, linkml... 14 (details) ghga-de/ghga-metadata-schema
political-affairs-ech-group
The working repository to develop standards for the swiss political system.
14 (details) swiss/political-affairs-ech-group
ukgov-metadata-exchange-model
A metadata model for describing data assets for exchanging between UK government organisations.
14 (details) co-cddo/ukgov-metadata-exchange-model
markdown-corpus
Many markdown files taken from around github
13 (details) tcr/markdown-corpus
monochrom
Standardized identifiers and OWL classes for chromosomes and chromosomal parts across species
chromosomes, etl, genomics... 13 (details) monarch-initiative/monochrom
py-typedlogic
Logic plus python types
answer-set-programming, clif, clingo... 13 (details) py-typedlogic/py-typedlogic
json-flattener
Python library for denormalizing nested dicts or json objects to tables and back
dataframes, denormalization, linkml... 11 (details) cmungall/json-flattener
metadata
Collation of metadata examples and notes for the project
linkml, metadata, physical-specimen 11 (details) isamplesorg/metadata
kg-registry
A simple registry for KGHub projects
9 (details) Knowledge-Graph-Hub/kg-registry
babelon
A format for language profiles for ontologies
8 (details) monarch-initiative/babelon
im-tc57cim
The CIM information model represented as LinkML schemas.
8 (details) Netbeheer-Nederland/im-tc57cim
linkml-phenopackets
EXPERIMENTAL rendering of phenopackets in linkml
human-phenotype-ontology, linkml, metadata... 8 (details) cmungall/linkml-phenopackets
SemanticDataLink
The Semantic Data Link repository hosts a Streamlit-based web application designed for managing and ...
8 (details) GX4FM-Base-X/SemanticDataLink
agr_curation_schema
Schema repository for the Alliance of Genome Resources persistent data store
7 (details) alliance-genome/agr_curation_schema
dcat-4C-ap 7 (details) StroemPhi/dcat-4C-ap
go-fastapi 7 (details) geneontology/go-fastapi
gx-credential-generator
Tools for creating Gaia-X Credentials (OpenStack, k8s, ...)
7 (details) SovereignCloudStack/gx-credential-generator
knowledge-graph-hub.github.io 7 (details) Knowledge-Graph-Hub/knowledge-graph-hub.github.io
monarch-documentation
Technical documentation for all Monarch applications, packages, services and related projects.
7 (details) monarch-initiative/monarch-documentation
mondo-ingest
Coordinating the mondo-ingest with external sources
7 (details) monarch-initiative/mondo-ingest
nmdc-runtime
Runtime system for NMDC data management and orchestration
7 (details) microbiomedata/nmdc-runtime
DCAT-ap_as_LinkML_template 6 (details) HendrikBorgelt/DCAT-ap_as_LinkML_template
gff-schema
LinkML schema for GFF3, the Genome Feature Format
bioinformatics, formats, genomics... 6 (details) biodatamodels/gff-schema
starrynight
A toolkit for processing, analyzing, and managing optical pooled screening (OPS) image data.
6 (details) broadinstitute/starrynight
data-vocab
Vocabulary and schemas for digital identity
5 (details) govuk-one-login/data-vocab
oakx-grape
Experimental OAK plugin for Grape
5 (details) INCATools/oakx-grape
sample-annotator
NMDC Sample Annotator
annotator, environment-ontology, environmentontology... 5 (details) microbiomedata/sample-annotator
ConfIDent_schema
The data schema for the ConfIDent project.
4 (details) TIBHannover/ConfIDent_schema
cryoet-data-portal-backend
CryoET Data Portal API server & ingestion scripts
4 (details) chanzuckerberg/cryoet-data-portal-backend
data-sheets-schema
Datasheets for Datasets, as LinkML Schema
4 (details) bridge2ai/data-sheets-schema
data-utilities
SAVED project - data processing tools for fish farms
4 (details) saved-models/data-utilities
gen-linkml-profile
LinkML schema profiler.
4 (details) Netbeheer-Nederland/gen-linkml-profile
im-cgmes
ENTSO-E CGMES profiles represented as LinkML schemas.
4 (details) Netbeheer-Nederland/im-cgmes
information-resource-registry
The information resource registry is a listing of data sources present in the NCATS Data Translator ...
4 (details) biolink/information-resource-registry
kgviz-model
Schema for configurations / stylesheets for visualizing ontology and KGs
graphviz, javascript, kgs... 4 (details) berkeleybop/kgviz-model
linkml-activitypub
LinkML Schema representation of ActivityPub
4 (details) p2p-ld/linkml-activitypub
mianct-schema
Minimal Information About a New Cell Type
anatomy, cell-ontology, cell-types... 4 (details) cmungall/mianct-schema
mtg_ontology
An ontology describing cards in Magic The Gathering.
linkml, mtg, ontology... 4 (details) cmdoret/mtg_ontology
nwb-linkml
Translating NWB schema language to linkml
4 (details) p2p-ld/nwb-linkml
obograph 4 (details) biodatamodels/obograph
omnibenchmark
The omnibenchmark CLI
4 (details) omnibenchmark/omnibenchmark
ontology-associations
schema for ontology associations
annotation, bioinformatics, datamodels... 4 (details) biodatamodels/ontology-associations
prefixcommons-py
Prefix commons python utlities
4 (details) prefixcommons/prefixcommons-py
rarelink
RareLink - A REDCap-based framework linking international registries toFHIR and Phenopackets
4 (details) BIH-CEI/rarelink
av-efi-schema 3 (details) AV-EFI/av-efi-schema
cim-to-linkml
Generates LinkML schemas for packages in the CIM information model.
3 (details) Netbeheer-Nederland/cim-to-linkml
eco-kg 3 (details) Knowledge-Graph-Hub/eco-kg
hra-do-processor
hra-do-processor: HRA Digital Objects Processor
3 (details) hubmapconsortium/hra-do-processor
include-linkml
LinkML Schema for INCLUDE DCC
3 (details) include-dcc/include-linkml
KGQA-COVID 3 (details) MrBearWithHisSword/KGQA-COVID
llm-matrix
Run multiple AI prompts in batch
3 (details) monarch-initiative/llm-matrix
mifc
A minimum information standard checklist formalizing the description of food composition data and re...
3 (details) kaiiam/mifc
miiid-schema
A metadata schema for the Minimum Information about Intermicrobial Interaction Data (MIIID) using Li...
fair-data, linkml, linkml-schema... 3 (details) FAIR-MI/miiid-schema
model-card-schema
LinkML rendering of model cards
ai, bridge2ai, deep-learning... 3 (details) bridge2ai/model-card-schema
mondolib
Python library for mondo QC
3 (details) monarch-initiative/mondolib
pid4cat-model
Handle-based PIDs with a rich LinkML metadata model for resources in catalysis (PID4Cat)
handles, linkml, linkml-schema... 3 (details) nfdi4cat/pid4cat-model
standards-schemas
Data schema for Bridge2AI Standards.
3 (details) bridge2ai/standards-schemas
structsense 3 (details) sensein/structsense
TermCI-model
The Terminology Code Index Entry model
3 (details) timsbiomed/TermCI-model
alpha-repos 2 (details) krishnapraveen7/alpha-repos
BDP-Ontology 2 (details) hsolbrig/BDP-Ontology
brc-schema
LinkML schema repo for bioenergy.org data integration
linkml-schema 2 (details) bioenergy-research-centers/brc-schema
CIM4Diagram
CIM use of LinkML for creating vocabulary and profile for Diagram
2 (details) Sveino/CIM4Diagram
cohd_api 2 (details) WengLab-InformaticsResearch/cohd_api
data-models
data models for the elite project
2 (details) eliteportal/data-models
DataExchange-ODM-LinkML
LinkML related work for ODMv2
data-exchange-standard 2 (details) cdisc-org/DataExchange-ODM-LinkML
DEPRECATED_agr_persistent_schema
Repository using linkml templating system for generating Alliance of Genome Resources persistent dat...
linkml 2 (details) alliance-genome/DEPRECATED_agr_persistent_schema
Efe-Will-OME-Research 2 (details) Efertugrul/Efe-Will-OME-Research
Explanatory-Agent 2 (details) NCATSTranslator/Explanatory-Agent
gaganyatri.in
Gaganyatri - Space Operations for Mars Transfer
2 (details) slabstech/gaganyatri.in
mixs-source 2 (details) cmungall/mixs-source
monarch-provenance 2 (details) matentzn/monarch-provenance
neat-ml-schema
A repository that contains the LinkML model for specifying graph ML pipelines
2 (details) Knowledge-Graph-Hub/neat-ml-schema
NIST-GEC_Lexicon
NIST Genome Editing Consortium Lexicon Schema Repository
2 (details) usnistgov/NIST-GEC_Lexicon
nmdc-metadata
Managing metadata and policy around metadata in NMDC
2 (details) microbiomedata/nmdc-metadata
OpenCloning_LinkML
A LinkML data model for OpenCloning
2 (details) OpenCloning/OpenCloning_LinkML
PPODLinkML
A LinkML representation of the PPOD schema
2 (details) adhollander/PPODLinkML
refscan
Command-line program that scans NMDC database for referential integrity violations
2 (details) microbiomedata/refscan
sepio-linkml
LinkML-based specification of the SEPIO information model.
2 (details) sepio-framework/sepio-linkml
valve-linkml
Convert LinkML schema + data to VALVE tables and vice versa
2 (details) tmprd/valve-linkml
abacus
Functions for data dictionary validation and summaries
1 (details) NIH-NCPI/abacus
acr-harmonized-data-model
ACR Data Model
1 (details) anvilproject/acr-harmonized-data-model
ak-schema
AIRR Knowledge Schema
1 (details) airr-knowledge/ak-schema
bdfkb-schema 1 (details) ARPA-H-BDF/bdfkb-schema
beril-model
A proposed LinkML schema in support of sample interoperability at the Department of Energy's Biologi...
1 (details) beril-model/beril-model
bertron-schema
LinkML schema for BERtron project.
1 (details) ber-data/bertron-schema
bkbit
Brain Knowledge Interaction Toolkit
1 (details) brain-bican/bkbit
cas-tools
Cell Annotation Schema Tools
1 (details) cellannotation/cas-tools
comet 1 (details) cmungall/comet
go-db
TEST bulk loading of go into duckdb
1 (details) cmungall/go-db
kg-envpolyreg 1 (details) Knowledge-Graph-Hub/kg-envpolyreg
knowledge-graph 1 (details) genophenoenvo/knowledge-graph
linkml-aind-model
Translate pydantic-based schemas from python modules to LinkML.
1 (details) DailyDreaming/linkml-aind-model
linkml-data-dictionary
Define the data dictionary using LinkML for data validation and reusable artifacts. (Proof of concep...
1 (details) chicagopcdc/linkml-data-dictionary
linkml-project-copier
A copier template for your next LinkML project
copier, linkml, schema... 1 (details) dalito/linkml-project-copier
metadata_converter
Conversion of schemas/templates/metadata to biolinkml
1 (details) microbiomedata/metadata_converter
modos-schema
Metadata schema for the SMOC Multi-Omics Digital-Object
1 (details) sdsc-ordes/modos-schema
mofdscribe-schema 1 (details) kjappelbaum/mofdscribe-schema
nmdc-client
A Python client for the National Microbiome Data Collaborative
1 (details) jeffbaumes/nmdc-client
NMRspec
Prototype to semantify NMR spectroscopy research data
1 (details) StroemPhi/NMRspec
SketchML
:whale: SketchML - distributed Machine Leaning framework for Apache Flink :star:
1 (details) axenov/SketchML
smpdb-beacon 1 (details) NCATS-Tangerine/smpdb-beacon
tccm-model-lite 1 (details) timsbiomed/tccm-model-lite
trano
Automate building energy simulation implementation in Modelica
1 (details) andoludo/trano
alspac-data-catalogue-schema
This repo is for the schema of alspac data catalogues and meta data for alspac data sets
0 (details) alspac/alspac-data-catalogue-schema
arcZcode
Architecture as Code
0 (details) Sveino/arcZcode
automate_mappings 0 (details) sierra-moxon/automate_mappings
basin3d_schema
EXPERIMENTAL
0 (details) cmungall/basin3d_schema
biotic-interactions
LinkML model for biotic interactions - designed for use with OntoGPT
0 (details) diatomsRcool/biotic-interactions
cell-annotation-schema 0 (details) Cellular-Semantics/cell-annotation-schema
CellCard-Schema
CellCard-LinkML: Cell Card LinkML project
0 (details) CellCards/CellCard-Schema
CPKG
Translation tools for ClinicalProfile to Knowledge Graphs
0 (details) NCATS-Tangerine/CPKG
DataMetadataWorkflowDocs
Documentation for In2PrimateBrains Data and Metadata Workflows
0 (details) In2PrimateBrains/DataMetadataWorkflowDocs
edd-schema 0 (details) cmungall/edd-schema
external-metadata-awareness
Tools for fetching and processing external schemas, ontologies and metadata records. Includes value ...
0 (details) microbiomedata/external-metadata-awareness
foo-model 0 (details) hsolbrig/foo-model
ghga-validator 0 (details) ghga-de/ghga-validator
ghp-vocab
Vocabulary for Good Health Pass
0 (details) mukundanps/ghp-vocab
github-helperbot
AI Agent to research and search for projects on GitHub
0 (details) tallboy17/github-helperbot
h2scm-supply-demand
The Hydrogen Supply Chain Testbed reference application which matches supply to demand.
0 (details) hydrologiq/h2scm-supply-demand
hca-validation-tools 0 (details) clevercanary/hca-validation-tools
hoopla 0 (details) cmungall/hoopla
idr_metadata_model 0 (details) khaledk2/idr_metadata_model
in2pb-linkml-test 0 (details) ree-gupta/in2pb-linkml-test
jsonasobj
Extension to the python json library that represents JSON as first class python objects.
0 (details) hsolbrig/jsonasobj
link-ml-sandbox
LinkML sandbox
0 (details) digital-botanical-gardens-initiative/link-ml-sandbox
linkml-asciidoc-generator
LinkML generator for Antora documentation in AsciiDoc.
0 (details) Netbeheer-Nederland/linkml-asciidoc-generator
linkml-cfde
EXPERIMENTAL rendering of Common Fund Data Ecocystem as LinkML
0 (details) cmungall/linkml-cfde
linkml-enhanced-template
Linkml template playground
0 (details) hsolbrig/linkml-enhanced-template
linkml-playground
linkml-playground
0 (details) manulera/linkml-playground
linkml-toolkit 0 (details) genomewalker/linkml-toolkit
linkml-tutorial-1
my new linkml project!
0 (details) sierra-moxon/linkml-tutorial-1
linkml-tutorial-2024 0 (details) sumirp/linkml-tutorial-2024
linkml-tutorial-2024
LinkML tutorial from ISMB 2024
0 (details) cwseidel/linkml-tutorial-2024
matrix-schema 0 (details) everycure-org/matrix-schema
omop_to_rdf
test repo for automating conversion from omop tables to rdf via linkml-schema-automator and linkml-c...
0 (details) sierra-moxon/omop_to_rdf
Ontology-Metadata
A schema for ontology metadata (WIP)
0 (details) StroemPhi/Ontology-Metadata
ontology_to_schema 0 (details) liuji1031/ontology_to_schema
OSLO2LINKML 0 (details) samuvack/OSLO2LINKML
parco-hbm 0 (details) eu-parc/parco-hbm
PCDMLinkML
Portland Common Data Model, in LinkML
0 (details) multimeric/PCDMLinkML
pfhub-cli-old 0 (details) wd15/pfhub-cli-old
rhea-beacon
Knowledge Beacon wrapper for the Rhea Annotated Reactions database (https://www.rhea-db.org)
0 (details) NCATS-Tangerine/rhea-beacon
schema-automator-monarch 0 (details) sierra-moxon/schema-automator-monarch
semanticscience-model
LinkML model for the SemanticScience Integrated Ontology
0 (details) vemonet/semanticscience-model
sepio-models
Shared SEPIO models based on the bioLinkML modeling language supporting the metakb and clingen sepio...
0 (details) clingen-data-model/sepio-models
slides
collectin my slides instead of having them be all over everywhere
0 (details) sneakers-the-rat/slides
synbio-schema
A schema for synthetic biology, inspired by IARPA FELIX
0 (details) iarpa-felix/synbio-schema
synbio-sheets
schemasheets & cogs based synthetic biology schema
0 (details) turbomam/synbio-sheets
synthetic-population-schema
A LinkML version of RTI's synthetic population schema
0 (details) EHS-Data-Standards/synthetic-population-schema
tank-schema 0 (details) turbomam/tank-schema
tccm-api 0 (details) timsbiomed/tccm-api
template-fun-model
Demo
0 (details) hsolbrig/template-fun-model
test-linkml-cookiecutter
test linkml cookiecutter
0 (details) yibeichan/test-linkml-cookiecutter
tkg-beacon
Knowledge Beacon wrapper of a Translator Knowledge Graph data model compliant Neo4j Database
0 (details) NCATS-Tangerine/tkg-beacon
tmpl-cm
Template repository for conceptual models.
0 (details) Netbeheer-Nederland/tmpl-cm
ubergraph2asct
ubergraph2asct: generate simple ASCT+B Tables via Ubergraph
0 (details) hubmapconsortium/ubergraph2asct
vrs_linkml
LinkML Version of the GA4GH Variation Representation Specification
0 (details) sierra-moxon/vrs_linkml
zzz
Reference model forked from csolink/biolink
0 (details) lmodel/zzz