LinkML Registry
For more information on LinkML:
Registry Entries
| Title | Topics | Stars | GitHub URL |
|---|---|---|---|
| ontogpt LLM-based ontological extraction tools, including SPIRES |
738 (details) | monarch-initiative/ontogpt | |
| semantic-python-overview (subjective) overview of projects which are related both to python and semantic technologies (RDF, O... |
532 (details) | pysemtec/semantic-python-overview | |
| mondo Mondo Disease Ontology |
272 (details) | monarch-initiative/mondo | |
| ontology-development-kit Ontology lifecycle management |
271 (details) | INCATools/ontology-development-kit | |
| go-ontology Source ontology files for the Gene Ontology |
238 (details) | geneontology/go-ontology | |
| ITK-Wasm High performance spatial analysis in a web browser and across programming languages and hardware arc... |
219 (details) | InsightSoftwareConsortium/ITK-Wasm | |
| biolink-model Schema and generated objects for biolink data model and upper ontology |
ai4curation, biolink, datamodel... | 207 (details) | biolink/biolink-model |
| sssom Simple Standard for Sharing Ontology Mappings |
linkml, mapping, mapping-commons... | 174 (details) | mapping-commons/sssom |
| ontology-access-kit Ontology Access Kit: A python library and command line application for working with ontologies |
152 (details) | INCATools/ontology-access-kit | |
| kgx KGX is a Python library for exchanging Knowledge Graphs |
133 (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 |
| risk-atlas-nexus Risk Atlas Nexus: tooling to bring together resources related to governance of foundation models. |
101 (details) | IBM/risk-atlas-nexus | |
| obo-relations RO is an ontology of relations for use with biological ontologies |
99 (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 |
82 (details) | psych-ds/psych-DS | |
| CoreMS CoreMS is a comprehensive mass spectrometry software framework |
60 (details) | EMSL-Computing/CoreMS | |
| koza Data transformation framework for LinkML data models |
etl, knowledge-graph, koza... | 57 (details) | monarch-initiative/koza |
| sssom-py Python toolkit for SSSOM mapping format |
linkml, mappings, obofoundry... | 55 (details) | mapping-commons/sssom-py |
| mixs Minimum Information about any (X) Sequence” (MIxS) specification |
53 (details) | GenomicsStandardsConsortium/mixs | |
| SEPIO-ontology Ontology for representing scientific evidence and provenance information |
51 (details) | monarch-initiative/SEPIO-ontology | |
| semantic-sql SQL and SQLite builds of OWL ontologies |
linkml, oaklib, obofoundry... | 49 (details) | INCATools/semantic-sql |
| go-site A collection of metadata, tools, and files associated with the Gene Ontology public web presence. |
46 (details) | geneontology/go-site | |
| enola Enola 🕵🏾♀️ Holmes was an SRE. |
44 (details) | enola-dev/enola | |
| nmdc-schema National Microbiome Data Collaborative (NMDC) unified data model |
ecoinformatics, fair-data, genomics... | 44 (details) | microbiomedata/nmdc-schema |
| specification Margo Specification |
41 (details) | margo/specification | |
| artificial-intelligence-ontology An ontology modeling classes and relationships describing deep learning networks, their component la... |
35 (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 |
| COSMoS CDISC Conceptual and Operational Standards Metadata Services (COSMoS) |
24 (details) | cdisc-org/COSMoS | |
| nwb_hackathons Repository for collecting materials from nwb hackathons |
24 (details) | NeurodataWithoutBorders/nwb_hackathons | |
| chemrof Schema for chemistry ontology classes |
chebi, chemistry, linkml... | 20 (details) | chemkg/chemrof |
| 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 |
| kg-registry A simple registry for KGHub projects |
18 (details) | Knowledge-Graph-Hub/kg-registry | |
| 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 |
| neat-ml Network Embedding All the Things |
18 (details) | Knowledge-Graph-Hub/neat-ml | |
| 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 |
| political-affairs-ech-group The working repository to develop standards for the swiss political system. |
14 (details) | swiss/political-affairs-ech-group | |
| py-typedlogic Logic plus python types |
answer-set-programming, clif, clingo... | 14 (details) | py-typedlogic/py-typedlogic |
| 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 |
| nmdc-server Data portal client and server for NMDC. |
12 (details) | microbiomedata/nmdc-server | |
| agr_curation_schema Schema repository for the Alliance of Genome Resources persistent data store |
11 (details) | alliance-genome/agr_curation_schema | |
| 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 |
| ontorunner | 11 (details) | monarch-initiative/ontorunner | |
| chem-dcat-ap | 10 (details) | nfdi-de/chem-dcat-ap | |
| kg-bioportal BioPortal, as a Knowledge Graph |
9 (details) | ncbo/kg-bioportal | |
| 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 |
| datalad-concepts | 7 (details) | psychoinformatics-de/datalad-concepts | |
| gx-credential-generator Tools for creating Gaia-X Credentials (OpenStack, k8s, ...) |
7 (details) | SovereignCloudStack/gx-credential-generator | |
| Hestia Hestia is an API for function calling on the OMOP CDM. |
7 (details) | OHDSI/Hestia | |
| 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 | |
| SemanticDataLink The Semantic Data Link repository hosts a Streamlit-based web application designed for managing and ... |
7 (details) | GX4FM-Base-X/SemanticDataLink | |
| DCAT-ap_as_LinkML_template | 6 (details) | HendrikBorgelt/DCAT-ap_as_LinkML_template | |
| define-json A metadata exchange model for Data Contracts and specs. Simplified successor to Define-XML that link... |
6 (details) | TeMeta/define-json | |
| gff-schema LinkML schema for GFF3, the Genome Feature Format |
bioinformatics, formats, genomics... | 6 (details) | biodatamodels/gff-schema |
| rarelink RareLink - A REDCap-based framework linking international registries to FHIR and Phenopackets |
6 (details) | BIH-CEI/rarelink | |
| 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 | |
| mtg_ontology An ontology describing cards in Magic The Gathering. |
linkml, mtg, ontology... | 5 (details) | cmdoret/mtg_ontology |
| sample-annotator NMDC Sample Annotator |
annotator, environment-ontology, environmentontology... | 5 (details) | microbiomedata/sample-annotator |
| 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 | |
| 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 |
| 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 | |
| structsense | 4 (details) | sensein/structsense | |
| bertron-schema LinkML schema for BERtron project. |
3 (details) | ber-data/bertron-schema | |
| cde-harmonization Initial private repo for P1 CDE harmonization |
3 (details) | monarch-initiative/cde-harmonization | |
| 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 | |
| hprc-data-explorer | 3 (details) | human-pangenomics/hprc-data-explorer | |
| 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 | |
| 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 |
| mixs-source | 3 (details) | cmungall/mixs-source | |
| model-card-schema LinkML rendering of model cards |
ai, bridge2ai, deep-learning... | 3 (details) | bridge2ai/model-card-schema |
| 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 | |
| translator-ingests NCATS Biomedical Data Translator Data INGest and Operations WG consolidated data ingest pipeline pro... |
3 (details) | NCATSTranslator/translator-ingests | |
| universalizer The KG-Hub Universalizer provides functions for knowledge graph cleanup and identifier normalization... |
3 (details) | Knowledge-Graph-Hub/universalizer | |
| 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 |
| cgmes-to-linkml Generate a LinkML schema from a CIM RDF schema (conforming IEC 61970-501). |
2 (details) | Netbeheer-Nederland/cgmes-to-linkml | |
| CIM4Diagram CIM use of LinkML for creating vocabulary and profile for Diagram |
2 (details) | Sveino/CIM4Diagram | |
| 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 |
| Explanatory-Agent | 2 (details) | NCATSTranslator/Explanatory-Agent | |
| external-metadata-awareness Tools for fetching and processing external schemas, ontologies and metadata records. Includes value ... |
2 (details) | microbiomedata/external-metadata-awareness | |
| gaganyatri.in Gaganyatri - Space Operations for Mars Transfer |
2 (details) | slabstech/gaganyatri.in | |
| metldata A framework for handling metadata based on ETL, CQRS, and event sourcing. |
2 (details) | ghga-de/metldata | |
| 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 | |
| PandaSaurus Supporting simple queries over ontology annotations in dataframes, using UberGraph queries |
2 (details) | INCATools/PandaSaurus | |
| 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 | |
| all-about-me Metadata for the people |
1 (details) | cmungall/all-about-me | |
| alpha-repos | 1 (details) | krishnapraveen7/alpha-repos | |
| asctb-tables LinkML schema for ASCB-T tables |
1 (details) | obophenotype/asctb-tables | |
| cas-tools Cell Annotation Schema Tools |
1 (details) | cellannotation/cas-tools | |
| comet | 1 (details) | cmungall/comet | |
| ctd_ingest | 1 (details) | sierra-moxon/ctd_ingest | |
| github-helperbot AI Agent to research and search for projects on GitHub |
1 (details) | tallboy17/github-helperbot | |
| hca-validation-tools | 1 (details) | clevercanary/hca-validation-tools | |
| kg-envpolyreg | 1 (details) | Knowledge-Graph-Hub/kg-envpolyreg | |
| knowledge-graph | 1 (details) | genophenoenvo/knowledge-graph | |
| 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-map-example | 1 (details) | sierra-moxon/linkml-map-example | |
| metadata_converter Conversion of schemas/templates/metadata to biolinkml |
1 (details) | microbiomedata/metadata_converter | |
| modos-schema Metadata schema for the Multi-Omics Digital-Object |
1 (details) | sdsc-ordes/modos-schema | |
| mofdscribe-schema | 1 (details) | kjappelbaum/mofdscribe-schema | |
| monarch-project-copier New template for monarch repos, replaces old cookiecutter |
1 (details) | monarch-initiative/monarch-project-copier | |
| 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 | |
| noctua-py Python tools for programmatically manipulating GO-CAM (Gene Ontology Causal Activity Models) via the... |
1 (details) | geneontology/noctua-py | |
| oae-data-protocol Base ontology and data schemas for ocean alkalinity enhancement projects, experiments, and field tra... |
1 (details) | clevinson/oae-data-protocol | |
| oakx-oger OGER plugin for oaklib. |
1 (details) | hrshdhgd/oakx-oger | |
| OSCEM_Schemas | 1 (details) | osc-em/OSCEM_Schemas | |
| scxa_2_cxg | 1 (details) | EBISPOT/scxa_2_cxg | |
| sheet2linkml Python package for conversion of Google Sheet to LinkML for CCDH |
1 (details) | cancerDHC/sheet2linkml | |
| 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 | |
| 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 | |
| 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 | |
| dcat-ms-ap A dcat ap implementing the recommondations fo the MS MIChI |
0 (details) | NFDI4Chem/dcat-ms-ap | |
| edd-schema | 0 (details) | cmungall/edd-schema | |
| EssDiveSampleRF | 0 (details) | heycatwonton/EssDiveSampleRF | |
| EssDiveSampleRFOld | 0 (details) | heycatwonton/EssDiveSampleRFOld | |
| foo-model | 0 (details) | hsolbrig/foo-model | |
| ftd-dd Tools to help create research data-dictionaries |
0 (details) | carrollaboratory/ftd-dd | |
| ghp-vocab Vocabulary for Good Health Pass |
0 (details) | mukundanps/ghp-vocab | |
| go-ingest gene ontology ingest from gene association formatted files |
0 (details) | monarch-initiative/go-ingest | |
| idr_metadata_model | 0 (details) | German-BioImaging/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 | |
| legacy_cogat_linkml LinkML representation of the neo4j based data. |
0 (details) | CognitiveAtlas/legacy_cogat_linkml | |
| 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-gen-something-functional Fragments of schemas including features that may not work with all genrated artifacts |
0 (details) | turbomam/linkml-gen-something-functional | |
| linkml-playground linkml-playground |
0 (details) | manulera/linkml-playground | |
| linkml-toolkit | 0 (details) | genomewalker/linkml-toolkit | |
| linkml-tutorial-2024 | 0 (details) | hoodriverheather/linkml-tutorial-2024 | |
| linkml-tutorial-2024 | 0 (details) | robsyme/linkml-tutorial-2024 | |
| monarch-kg-qc-schema Schema for QC Reports on the Monarch KG |
0 (details) | amc-corey-cox/monarch-kg-qc-schema | |
| music-library-jsonld-poc PoC: From JSON to JSON-LD with LinkML and my music library data. |
0 (details) | bartkl/music-library-jsonld-poc | |
| omni-schema Data model for omnibenchmark. |
0 (details) | omnibenchmark/omni-schema | |
| ontology_to_schema | 0 (details) | liuji1031/ontology_to_schema | |
| oregon-water-samples Sample LinkML project setup for 2024 paper figures |
0 (details) | sierra-moxon/oregon-water-samples | |
| 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 | |
| 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 | |
| pynmdc Python library and tools to work on NMDC data. |
0 (details) | microbiomedata/pynmdc | |
| 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 | |
| stoplight_harmonization_project A toy model for prototyping and demonstrating LinkML based data harmonization |
0 (details) | hsolbrig/stoplight_harmonization_project | |
| synbio-schema A schema for synthetic biology, inspired by IARPA FELIX |
0 (details) | iarpa-felix/synbio-schema | |
| tccm-api | 0 (details) | timsbiomed/tccm-api | |
| template-fun-model Demo |
0 (details) | hsolbrig/template-fun-model | |
| 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 | |
| tum-bc | 0 (details) | saezlab/tum-bc | |
| vega-scverse Vega specifications used for visualization in the scverse ecosystem. |
0 (details) | melonora/vega-scverse | |
| vrs_linkml LinkML Version of the GA4GH Variation Representation Specification |
0 (details) | sierra-moxon/vrs_linkml | |
| water-sample-schema Sample LinkML project setup for 2024 paper figures |
0 (details) | sierra-moxon/water-sample-schema |