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LinkML Registry

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Registry Entries

Title Topics Stars GitHub URL
ontogpt
LLM-based ontological extraction tools, including SPIRES
703 (details) monarch-initiative/ontogpt
semantic-python-overview
(subjective) overview of projects which are related both to python and semantic technologies (RDF, O...
526 (details) pysemtec/semantic-python-overview
awesome-ontology
A curated list of ontology things
389 (details) ozekik/awesome-ontology
ontology-development-kit
Ontology lifecycle management
260 (details) INCATools/ontology-development-kit
mondo
Mondo Disease Ontology
259 (details) monarch-initiative/mondo
ITK-Wasm
High performance spatial analysis in a web browser and across programming languages and hardware arc...
215 (details) InsightSoftwareConsortium/ITK-Wasm
biolink-model
Schema and generated objects for biolink data model and upper ontology
biolink, datamodel, gene-ontology... 198 (details) biolink/biolink-model
sssom
Simple Standard for Sharing Ontology Mappings
linkml, mapping, mapping-commons... 167 (details) mapping-commons/sssom
kgx
KGX is a Python library for exchanging Knowledge Graphs
128 (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
95 (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.
67 (details) IBM/risk-atlas-nexus
CoreMS
CoreMS is a comprehensive mass spectrometry software framework
59 (details) EMSL-Computing/CoreMS
sssom-py
Python toolkit for SSSOM mapping format
linkml, mappings, obofoundry... 54 (details) mapping-commons/sssom-py
koza
Data transformation framework for LinkML data models
etl, knowledge-graph, koza... 53 (details) monarch-initiative/koza
hdmf
The Hierarchical Data Modeling Framework
52 (details) hdmf-dev/hdmf
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
mixs
Minimum Information about any (X) Sequence” (MIxS) specification
46 (details) GenomicsStandardsConsortium/mixs
semantic-sql
SQL and SQLite builds of OWL ontologies
linkml, oaklib, obofoundry... 46 (details) INCATools/semantic-sql
nmdc-schema
National Microbiome Data Collaborative (NMDC) unified data model
ecoinformatics, fair-data, genomics... 42 (details) microbiomedata/nmdc-schema
specification
Margo Specification
39 (details) margo/specification
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
monarch-app
Monarch Initiative website and API
27 (details) monarch-initiative/monarch-app
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
COSMoS
CDISC Conceptual and Operational Standards Metadata Services (COSMoS)
20 (details) cdisc-org/COSMoS
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
monarch-ingest
Data ingest application for Monarch Initiative knowledge graph using Koza
kgx, knowledge-graphs, linkml... 17 (details) monarch-initiative/monarch-ingest
ccdhmodel
CRDC-H model in LinkML, developed by the Center for Cancer Data Harmonization (CCDH)
google-sheets, linkml 16 (details) cancerDHC/ccdhmodel
ghga-metadata-schema
Metadata schema for the German Human Genome-Phenome Archive (GHGA)
fega, ghga, linkml... 14 (details) ghga-de/ghga-metadata-schema
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... 12 (details) py-typedlogic/py-typedlogic
translator-openpredict
🔮🐍 A package to help serve predictions of biomedical concepts associations as Translator Reasoner AP...
12 (details) MaastrichtU-IDS/translator-openpredict
b2ai-standards-registry
Bridge2AI Standards Registry data models, API specification, and other documentation.
11 (details) bridge2ai/b2ai-standards-registry
metadata
Collation of metadata examples and notes for the project
linkml, metadata, physical-specimen 11 (details) isamplesorg/metadata
political-affairs-ech-group
The working repository to develop standards for the swiss political system.
11 (details) swiss/political-affairs-ech-group
json-flattener
Python library for denormalizing nested dicts or json objects to tables and back
dataframes, denormalization, linkml... 10 (details) cmungall/json-flattener
kg-registry
A simple registry for KGHub projects
9 (details) Knowledge-Graph-Hub/kg-registry
Hestia
Hestia is an API for function calling on the OMOP CDM.
8 (details) OHDSI/Hestia
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
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
platformics
Codegen Python GraphQL Entity Framework
6 (details) chanzuckerberg/platformics
srpAnalytics
This repository contains the code necessary to process any new data for the Superfund Research Progr...
6 (details) PNNL-CompBio/srpAnalytics
data-vocab
Vocabulary and schemas for digital identity
5 (details) govuk-one-login/data-vocab
knowledge-graph-hub.github.io 5 (details) Knowledge-Graph-Hub/knowledge-graph-hub.github.io
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
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
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
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
microbial-lims
Metadata definitions for microbial strain research at NIST
3 (details) usnistgov/microbial-lims
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
models
BICAN data models
3 (details) brain-bican/models
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
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-analytics 2 (details) galaxyproject/brc-analytics
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
collections2efi
Code used at Stiftung Deutsche Kinemathek to register AVefi compliant PIDs for collections on record...
2 (details) AV-EFI/collections2efi
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
dragon-ai-cookiecutter
Cookiecutter for DRAGON-AI projects
2 (details) monarch-initiative/dragon-ai-cookiecutter
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
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
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
ak-schema
AIRR Knowledge Schema
1 (details) airr-knowledge/ak-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
cas-tools
Cell Annotation Schema Tools
1 (details) cellannotation/cas-tools
comet 1 (details) cmungall/comet
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
meta-disco 1 (details) DataBiosphere/meta-disco
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
oae-data-protocol
Base ontology and data schemas for ocean alkalinity enhancement projects, experiments, and field tra...
1 (details) clevinson/oae-data-protocol
OSCEM_Schemas 1 (details) osc-em/OSCEM_Schemas
scxa_2_cxg 1 (details) EBISPOT/scxa_2_cxg
SketchML
:whale: SketchML - distributed Machine Leaning framework for Apache Flink :star:
1 (details) axenov/SketchML
smpdb-beacon 1 (details) NCATS-Tangerine/smpdb-beacon
structsense 1 (details) sensein/structsense
submission-schema 1 (details) microbiomedata/submission-schema
tccm-model-lite 1 (details) timsbiomed/tccm-model-lite
arcZcode
Architecture as Code
0 (details) Sveino/arcZcode
automate_mappings 0 (details) sierra-moxon/automate_mappings
bdf-mock-tool
Mock BDF Tool Used for consuming content
0 (details) alico-cra/bdf-mock-tool
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
cellmark_schema 0 (details) Cellular-Semantics/cellmark_schema
clinical-studies-schema 0 (details) sierra-moxon/clinical-studies-schema
CPKG
Translation tools for ClinicalProfile to Knowledge Graphs
0 (details) NCATS-Tangerine/CPKG
datalab-schemas
Core schemas for datalab.
0 (details) ml-evs/datalab-schemas
DataMetadataWorkflowDocs
Documentation for In2PrimateBrains Data and Metadata Workflows
0 (details) In2PrimateBrains/DataMetadataWorkflowDocs
edd-schema 0 (details) cmungall/edd-schema
EssDiveSampleRFOld 0 (details) heycatwonton/EssDiveSampleRFOld
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
ga4gh-va-schema
Data model for variant annotation in the GA4GH consortium.
0 (details) sujaypatil96/ga4gh-va-schema
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
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
kg-envpolyreg 0 (details) Knowledge-Graph-Hub/kg-envpolyreg
link-ml-sandbox
LinkML sandbox
0 (details) digital-botanical-gardens-initiative/link-ml-sandbox
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-learn
Playing around with LinkML Stuff to check whether it's a good choice to use for Bilayers
0 (details) rajavishah/linkml-learn
linkml-playground
linkml-playground
0 (details) manulera/linkml-playground
linkml-toolkit 0 (details) genomewalker/linkml-toolkit
linkml-tutorial 0 (details) 4lirastegar/linkml-tutorial
linkml-tutorial-1
my new linkml project!
0 (details) sierra-moxon/linkml-tutorial-1
linkml_test 0 (details) alschaap/linkml_test
LinkMLFormBuilder
A Python3.8 CLI tool to transform LinkML models (yaml) into PDF, and additionally HTML, forms
0 (details) AmsterdamUMC/LinkMLFormBuilder
microscopemetrics-schema 0 (details) MontpellierRessourcesImagerie/microscopemetrics-schema
monarch-kg-qc-schema
Schema for QC Reports on the Monarch KG
0 (details) amc-corey-cox/monarch-kg-qc-schema
omni-schema
Data model for omnibenchmark.
0 (details) omnibenchmark/omni-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
OpenCloning-submission
An API to submit ShareYourCloning templates
0 (details) OpenCloning/OpenCloning-submission
oregon-water-samples
Sample LinkML project setup for 2024 paper figures
0 (details) sierra-moxon/oregon-water-samples
OSLO2LINKML 0 (details) samuvack/OSLO2LINKML
pantherdb-orthologs-ingest
orthologs ingest from pantherdb
0 (details) monarch-initiative/pantherdb-orthologs-ingest
PCDMLinkML
Portland Common Data Model, in LinkML
0 (details) multimeric/PCDMLinkML
pfhub-cli
PFHub CLI tool
0 (details) usnistgov/pfhub-cli
pfhub-cli-old 0 (details) wd15/pfhub-cli-old
pfhub-schema
Phase-field simulation and benchmark schema in LinkML
0 (details) usnistgov/pfhub-schema
portable-microhaplotype-object
A schema to define the minimum amount of data needed to export a microhaplotype calling pipeline ana...
0 (details) PlasmoGenEpi/portable-microhaplotype-object
psyndex2linkeddata
A set of python tools for describing PSYNDEX data in RDF and for converting from STARXML to Linked D...
0 (details) leibniz-psychology/psyndex2linkeddata
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
synbio-schema
A schema for synthetic biology, inspired by IARPA FELIX
0 (details) iarpa-felix/synbio-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_predicates 0 (details) sierra-moxon/test_predicates
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
vrs_linkml
LinkML Version of the GA4GH Variation Representation Specification
0 (details) sierra-moxon/vrs_linkml
zfin-genotype-to-phenotype-ingest 0 (details) monarch-initiative/zfin-genotype-to-phenotype-ingest