LinkML Registry
For more information on LinkML:
Registry Entries
| Title | Topics | Stars | GitHub URL |
|---|---|---|---|
| ontogpt LLM-based ontological extraction tools, including SPIRES |
762 (details) | monarch-initiative/ontogpt | |
| semantic-python-overview (subjective) overview of projects which are related both to python and semantic technologies (RDF, O... |
536 (details) | pysemtec/semantic-python-overview | |
| ontology-development-kit Ontology lifecycle management |
279 (details) | INCATools/ontology-development-kit | |
| mondo Mondo Disease Ontology |
278 (details) | monarch-initiative/mondo | |
| biolink-model Schema and generated objects for biolink data model and upper ontology |
ai4curation, biolink, datamodel... | 211 (details) | biolink/biolink-model |
| pydna Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination,... |
208 (details) | pydna-group/pydna | |
| sssom Simple Standard for Sharing Ontology Mappings |
linkml, mapping, mapping-commons... | 177 (details) | mapping-commons/sssom |
| ontology-access-kit Ontology Access Kit: A python library and command line application for working with ontologies |
155 (details) | INCATools/ontology-access-kit | |
| DataHarmonizer A standardized browser-based spreadsheet editor and validator that can be run offline and locally, a... |
application, data, harmonization... | 116 (details) | cidgoh/DataHarmonizer |
| risk-atlas-nexus Risk Atlas Nexus: tooling to bring together resources related to governance of foundation models. |
107 (details) | IBM/risk-atlas-nexus | |
| obo-relations RO is an ontology of relations for use with biological ontologies |
103 (details) | oborel/obo-relations | |
| autopilot Distributed behavioral experiments |
95 (details) | auto-pi-lot/autopilot | |
| 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 | |
| koza Data transformation framework for LinkML data models |
etl, knowledge-graph, koza... | 59 (details) | monarch-initiative/koza |
| sssom-py Python toolkit for SSSOM mapping format |
linkml, mappings, obofoundry... | 57 (details) | mapping-commons/sssom-py |
| mixs Minimum Information about any (X) Sequence” (MIxS) specification |
55 (details) | GenomicsStandardsConsortium/mixs | |
| hdmf The Hierarchical Data Modeling Framework |
54 (details) | hdmf-dev/hdmf | |
| semantic-sql SQL and SQLite builds of OWL ontologies |
ai4curation, linkml, monarchinitiative... | 51 (details) | INCATools/semantic-sql |
| optinist calcium imaging pipeline tool |
48 (details) | oist/optinist | |
| nmdc-schema National Microbiome Data Collaborative (NMDC) unified data model |
ecoinformatics, fair-data, genomics... | 44 (details) | microbiomedata/nmdc-schema |
| specification Margo Specification |
43 (details) | margo/specification | |
| artificial-intelligence-ontology An ontology modeling classes and relationships describing deep learning networks, their component la... |
38 (details) | berkeleybop/artificial-intelligence-ontology | |
| alhazen AI agents + toolkits for scientific knowledge |
33 (details) | chanzuckerberg/alhazen | |
| 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 | |
| cogs Convention-based Ontology Generation System |
21 (details) | Colectica/cogs | |
| chemrof Schema for chemistry ontology classes |
chebi, chemistry, linkml... | 20 (details) | chemkg/chemrof |
| kgcl Datamodel for KGCL (Knowledge Graph Change Language) |
kgcl, linkml, ontology-changes... | 20 (details) | INCATools/kgcl |
| monarch-ingest Data ingest application for Monarch Initiative knowledge graph using Koza |
kgx, knowledge-graphs, linkml... | 20 (details) | monarch-initiative/monarch-ingest |
| kg-registry A simple registry for KGHub projects |
19 (details) | Knowledge-Graph-Hub/kg-registry | |
| kgcl-rdflib Tools for working with KGCL |
diff, diffs, kg... | 18 (details) | INCATools/kgcl-rdflib |
| comp-loinc Computational LOINC in OWL. |
17 (details) | loinc/comp-loinc | |
| ccdhmodel CRDC-H model in LinkML, developed by the Center for Cancer Data Harmonization (CCDH) |
google-sheets, linkml | 16 (details) | cancerDHC/ccdhmodel |
| political-affairs-ech-group The working repository to develop standards for the swiss political system. |
15 (details) | swiss/political-affairs-ech-group | |
| py-typedlogic Logic plus python types |
answer-set-programming, clif, clingo... | 15 (details) | py-typedlogic/py-typedlogic |
| b2ai-standards-registry Bridge2AI Standards Registry data models, API specification, and other documentation. |
14 (details) | bridge2ai/b2ai-standards-registry | |
| ghga-metadata-schema Metadata schema for the German Human Genome-Phenome Archive (GHGA) |
fega, ghga, linkml... | 14 (details) | ghga-de/ghga-metadata-schema |
| 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 |
ai4curation, chromosomes, etl... | 13 (details) | monarch-initiative/monochrom |
| translator-openpredict 🔮🐍 A package to help serve predictions of biomedical concepts associations as Translator Reasoner AP... |
12 (details) | MaastrichtU-IDS/translator-openpredict | |
| 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 |
| chem-dcat-ap This is an extension of the DCAT Application Profile PLUS LinkML schema. It is intended to be used b... |
linkml-schema | 10 (details) | nfdi-de/chem-dcat-ap |
| im-tc57cim The CIM information model represented as LinkML schemas. |
9 (details) | Netbeheer-Nederland/im-tc57cim | |
| linkml-phenopackets EXPERIMENTAL rendering of phenopackets in linkml |
human-phenotype-ontology, linkml, metadata... | 9 (details) | cmungall/linkml-phenopackets |
| starrynight A toolkit for processing, analyzing, and managing optical pooled screening (OPS) image data. |
9 (details) | broadinstitute/starrynight | |
| rd-cdm Repo for the ontology-based rare disease common data model harmonising international registries, FHI... |
8 (details) | BIH-CEI/rd-cdm | |
| define-json A metadata exchange model for Data Contracts and specs. Simplified successor to Define-XML that link... |
7 (details) | TeMeta/define-json | |
| Hestia Hestia is an API for function calling on the OMOP CDM. |
7 (details) | OHDSI/Hestia | |
| 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 | |
| SemanticDataLink The Semantic Data Link repository hosts a Streamlit-based web application designed for managing and ... |
7 (details) | GX4FM-Base-X/SemanticDataLink | |
| structsense | 7 (details) | sensein/structsense | |
| cryoet-data-portal-backend CryoET Data Portal API server & ingestion scripts |
6 (details) | chanzuckerberg/cryoet-data-portal-backend | |
| 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 |
| linkml-qudt Conversion of QUDT ontology to LinkML |
knowledge-graph, linkml, linkml-schema... | 6 (details) | vladistan/linkml-qudt |
| rarelink RareLink - A REDCap-based framework linking international registries to FHIR and Phenopackets |
6 (details) | BIH-CEI/rarelink | |
| 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 |
| regen-data-standards | 5 (details) | regen-network/regen-data-standards | |
| 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 | |
| hra-do-processor hra-do-processor: HRA Digital Objects Processor |
4 (details) | hubmapconsortium/hra-do-processor | |
| 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 |
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 |
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 | |
| prefixcommons-py Prefix commons python utlities |
4 (details) | prefixcommons/prefixcommons-py | |
| bertron-schema LinkML schema for BERtron project. |
3 (details) | ber-data/bertron-schema | |
| brc-analytics | 3 (details) | galaxyproject/brc-analytics | |
| 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 | |
| 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 |
| ome-nbo-formatter | 3 (details) | Efertugrul/ome-nbo-formatter | |
| 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 |
| PPODLinkML A LinkML representation of the PPOD schema |
3 (details) | adhollander/PPODLinkML | |
| pyMetaModel migrates https://wiki.bitplan.com/index.php/MetaModel#tab=Model to python |
3 (details) | WolfgangFahl/pyMetaModel | |
| sepio-linkml LinkML-based specification of the SEPIO information model. |
3 (details) | sepio-framework/sepio-linkml | |
| 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 | |
| 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 |
| cdm-schema Schema files for the KBase CDM |
2 (details) | kbase/cdm-schema | |
| 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 |
| 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 | |
| ingest-metadata | 2 (details) | biolink/ingest-metadata | |
| linkml-initializer | 2 (details) | pkalita-lbl/linkml-initializer | |
| 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 | |
| refscan Command-line program that scans NMDC database for referential integrity violations |
2 (details) | microbiomedata/refscan | |
| 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 | |
| alpha-repos | 1 (details) | krishnapraveen7/alpha-repos | |
| cas-tools Cell Annotation Schema Tools |
1 (details) | cellannotation/cas-tools | |
| comet | 1 (details) | cmungall/comet | |
| github-helperbot AI Agent to research and search for projects on GitHub |
1 (details) | tallboy17/github-helperbot | |
| go-library | 1 (details) | geneontology/go-library | |
| 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 | |
| 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 | |
| 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 | |
| ai_data | 0 (details) | BioImage-Archive/ai_data | |
| 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 | |
| biolink-model-doc | 0 (details) | sierra-moxon/biolink-model-doc | |
| biotic-interactions LinkML model for biotic interactions - designed for use with OntoGPT |
0 (details) | diatomsRcool/biotic-interactions | |
| cell-annotation-schema A general, open-standard schema for cell annotations and related metadata. |
0 (details) | Cellular-Semantics/cell-annotation-schema | |
| CPKG Translation tools for ClinicalProfile to Knowledge Graphs |
0 (details) | NCATS-Tangerine/CPKG | |
| crystalia-collector | 0 (details) | Ebiquity/crystalia-collector | |
| data-model | 0 (details) | behaverse/data-model | |
| 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 | |
| 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 | |
| hdmf-term-lists | 0 (details) | rly/hdmf-term-lists | |
| 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 | |
| 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 | 0 (details) | 4lirastegar/linkml-tutorial | |
| LinkMLFormBuilder A Python3.8 CLI tool to transform LinkML models (yaml) into PDF, and additionally HTML, forms |
0 (details) | AmsterdamUMC/LinkMLFormBuilder | |
| omop-link linkML model of OMOP Common Data Model |
0 (details) | SPHERE-Cancer-CAG/omop-link | |
| 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 | |
| operando-catalysis-metadata-schema [HZB] operando Catalysis (meta)data schema |
0 (details) | anak-velazquez/operando-catalysis-metadata-schema | |
| OSLO2LINKML | 0 (details) | samuvack/OSLO2LINKML | |
| PCDMLinkML Portland Common Data Model, in LinkML |
0 (details) | multimeric/PCDMLinkML | |
| 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 | |
| research-paper-schema | 0 (details) | liuji1031/research-paper-schema | |
| 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 | |
| SRI_testing | 0 (details) | TranslatorSRI/SRI_testing | |
| 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 | |
| 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 |