LinkML Registry
For more information on LinkML:
Registry Entries
| Title | Topics | Stars | GitHub URL |
|---|---|---|---|
| cs249r_book Machine Learning Systems |
24204 (details) | harvard-edge/cs249r_book | |
| ontogpt LLM-based ontological extraction tools, including SPIRES |
880 (details) | monarch-initiative/ontogpt | |
| semantic-python-overview (subjective) overview of projects which are related both to python and semantic technologies (RDF, O... |
550 (details) | pysemtec/semantic-python-overview | |
| ontology-development-kit Ontology lifecycle management |
330 (details) | INCATools/ontology-development-kit | |
| mondo Mondo Disease Ontology |
300 (details) | monarch-initiative/mondo | |
| biolink-model Schema and generated objects for biolink data model and upper ontology |
ai4curation, biolink, datamodel... | 240 (details) | biolink/biolink-model |
| sssom Simple Standard for Sharing Ontology Mappings |
linkml, mapping, mapping-commons... | 200 (details) | mapping-commons/sssom |
| ontology-access-kit Ontology Access Kit: A python library and command line application for working with ontologies |
168 (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... | 126 (details) | cidgoh/DataHarmonizer |
| obo-relations RO is an ontology of relations for use with biological ontologies |
112 (details) | oborel/obo-relations | |
| kg-covid-19 An instance of KG Hub to produce a knowledge graph for COVID-19 response. |
84 (details) | Knowledge-Graph-Hub/kg-covid-19 | |
| CoreMS CoreMS is a comprehensive mass spectrometry software framework |
65 (details) | EMSL-Computing/CoreMS | |
| koza Data transformation framework for LinkML data models |
etl, knowledge-graph, koza... | 64 (details) | monarch-initiative/koza |
| mixs Minimum Information about any (X) Sequence” (MIxS) specification |
63 (details) | GenomicsStandardsConsortium/mixs | |
| sssom-py Python toolkit for SSSOM mapping format |
linkml, mappings, obofoundry... | 62 (details) | mapping-commons/sssom-py |
| semantic-sql SQL and SQLite builds of OWL ontologies |
ai4curation, linkml, monarchinitiative... | 61 (details) | INCATools/semantic-sql |
| go-site A collection of metadata, tools, and files associated with the Gene Ontology public web presence. |
49 (details) | geneontology/go-site | |
| artificial-intelligence-ontology An ontology modeling classes and relationships describing deep learning networks, their component la... |
48 (details) | berkeleybop/artificial-intelligence-ontology | |
| specification Margo Specification |
48 (details) | margo/specification | |
| nmdc-schema National Microbiome Data Collaborative (NMDC) unified data model |
ecoinformatics, fair-data, genomics... | 46 (details) | microbiomedata/nmdc-schema |
| matrix | 43 (details) | everycure-org/matrix | |
| semantic-llama A knowledge extraction tool that uses a large language model to extract semantic information from te... |
ai, knowledge-extraction, language-models... | 30 (details) | cmungall/semantic-llama |
| COSMoS CDISC Conceptual and Operational Standards Metadata Services (COSMoS) |
26 (details) | cdisc-org/COSMoS | |
| kg-registry A registry of Knowledge Graphs, their data sources, and the ways they fit together. |
26 (details) | Knowledge-Graph-Hub/kg-registry | |
| nwb_hackathons Repository for collecting materials from nwb hackathons |
25 (details) | NeurodataWithoutBorders/nwb_hackathons | |
| dismech Disease Mechanisms KB |
24 (details) | monarch-initiative/dismech | |
| monarch-ingest Data ingest application for Monarch Initiative knowledge graph using Koza |
kgx, knowledge-graphs, linkml... | 24 (details) | monarch-initiative/monarch-ingest |
| chemrof Schema for chemistry ontology classes |
chebi, chemistry, linkml... | 23 (details) | chemkg/chemrof |
| cogs Convention-based Ontology Generation System |
22 (details) | Colectica/cogs | |
| kgcl Datamodel for KGCL (Knowledge Graph Change Language) |
kgcl, linkml, ontology-changes... | 22 (details) | INCATools/kgcl |
| PyNIDM | 22 (details) | incf-nidash/PyNIDM | |
| py-typedlogic Logic plus python types |
answer-set-programming, clif, clingo... | 21 (details) | py-typedlogic/py-typedlogic |
| bilayers | 20 (details) | bilayer-containers/bilayers | |
| kgcl-rdflib Tools for working with KGCL |
diff, diffs, kg... | 20 (details) | INCATools/kgcl-rdflib |
| ccdhmodel CRDC-H model in LinkML, developed by the Center for Cancer Data Harmonization (CCDH) |
google-sheets, linkml | 18 (details) | cancerDHC/ccdhmodel |
| comp-loinc Computational LOINC in OWL. |
18 (details) | loinc/comp-loinc | |
| ai-gene-review Demonstration of AI review of existing functional annotations |
17 (details) | ai4curation/ai-gene-review | |
| ddimodel Model for DDI Lifecycle |
16 (details) | ddialliance/ddimodel | |
| ghga-metadata-schema Metadata schema for the German Human Genome-Phenome Archive (GHGA) |
fega, ghga, linkml... | 16 (details) | ghga-de/ghga-metadata-schema |
| monochrom Standardized identifiers and OWL classes for chromosomes and chromosomal parts across species |
ai4curation, chromosomes, etl... | 16 (details) | monarch-initiative/monochrom |
| political-affairs-ech-group The working repository to develop standards for the swiss political system. |
16 (details) | swiss/political-affairs-ech-group | |
| namo | ai4curation, artificial-intelligence, linkml... | 15 (details) | monarch-initiative/namo |
| chem-dcat-ap This is an extension of the DCAT Application Profile PLUS LinkML schema. It is intended to be used b... |
linkml, linkml-schema, shacl... | 14 (details) | nfdi-de/chem-dcat-ap |
| reusabledata The home repository for the (Re)usable Data Project. |
14 (details) | reusabledata/reusabledata | |
| 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 | |
| agr_curation_schema Schema repository for the Alliance of Genome Resources persistent data store |
12 (details) | alliance-genome/agr_curation_schema | |
| InfDB InfDB (Energy and Infrastructure Database) provides a modular and easy-to-configure open-source data... |
12 (details) | tum-ens/InfDB | |
| json-flattener Python library for denormalizing nested dicts or json objects to tables and back |
dataframes, denormalization, linkml... | 12 (details) | cmungall/json-flattener |
| metadata Collation of metadata examples and notes for the project |
12 (details) | isamplesorg/metadata | |
| translator-openpredict 🔮🐍 A package to help serve predictions of biomedical concepts associations as Translator Reasoner AP... |
12 (details) | MaastrichtU-IDS/translator-openpredict | |
| dcat-ap-plus A domain-agnostic extension of the DCAT Application Profile. It allow providing domain-specific meta... |
dcat-ap, linkml, linkml-schema... | 11 (details) | nfdi-de/dcat-ap-plus |
| linkml-phenopackets EXPERIMENTAL rendering of phenopackets in linkml |
human-phenotype-ontology, linkml, metadata... | 11 (details) | cmungall/linkml-phenopackets |
| mondo-ingest Coordinating the mondo-ingest with external sources |
11 (details) | monarch-initiative/mondo-ingest | |
| cgmes ENTSO-E CGMES profiles represented as LinkML schemas. |
cgmes, cim, documentation | 10 (details) | Netbeheer-Nederland/cgmes |
| kg-bioportal BioPortal, as a Knowledge Graph |
10 (details) | ncbo/kg-bioportal | |
| reactome-ontology Ontology-first LinkML schema for Reactome with generated Python models, ontology artifacts, mappings... |
10 (details) | cair2015/reactome-ontology | |
| tc57cim The CIM information model represented as LinkML schemas. |
cim, documentation | 10 (details) | Netbeheer-Nederland/tc57cim |
| CultureMech Microbial Culture Media Knowledge Graph - Comprehensive collection of 10,000+ culture media recipes ... |
cultivation, growth-media, media... | 9 (details) | CultureBotAI/CultureMech |
| cdm Altium Common Data Model |
8 (details) | AltiumDeveloper/cdm | |
| define-json A metadata exchange model for Data Contracts and specs. Simplified successor to Define-XML that link... |
8 (details) | TeMeta/define-json | |
| knowledge-graph-hub.github.io | 8 (details) | Knowledge-Graph-Hub/knowledge-graph-hub.github.io | |
| linkml-qudt Conversion of QUDT ontology to LinkML |
knowledge-graph, linkml, linkml-schema... | 8 (details) | vladistan/linkml-qudt |
| monarch-documentation Technical documentation for all Monarch applications, packages, services and related projects. |
8 (details) | monarch-initiative/monarch-documentation | |
| propstore Propositional knowledge store — compiler, argumentation engine, and query system for structured clai... |
8 (details) | ctoth/propstore | |
| structsense | 8 (details) | sensein/structsense | |
| wot-thing-description-toolchain-tmp work area for WoT Thing Description toolchain |
8 (details) | w3c/wot-thing-description-toolchain-tmp | |
| data-vocab Vocabulary and schemas for digital identity |
7 (details) | govuk-one-login/data-vocab | |
| gff-schema LinkML schema for GFF3, the Genome Feature Format |
bioinformatics, formats, genomics... | 7 (details) | biodatamodels/gff-schema |
| nmdc-runtime Runtime system for NMDC data management and orchestration |
7 (details) | microbiomedata/nmdc-runtime | |
| sample-annotator NMDC Sample Annotator |
annotator, environment-ontology, environmentontology... | 7 (details) | microbiomedata/sample-annotator |
| SemanticDataLink The Semantic Data Link repository hosts a Streamlit-based web application designed for managing and ... |
7 (details) | GX4FM-Base-X/SemanticDataLink | |
| sepio-linkml LinkML-based specification of the SEPIO information model. |
7 (details) | sepio-framework/sepio-linkml | |
| srpAnalytics This repository contains the code necessary to process any new data for the Superfund Research Progr... |
7 (details) | PNNL-CompBio/srpAnalytics | |
| data-sheets-schema Datasheets for Datasets, as LinkML Schema |
6 (details) | bridge2ai/data-sheets-schema | |
| linkml-omop-tutorial | 6 (details) | alabarga/linkml-omop-tutorial | |
| mtg_ontology An ontology describing cards in Magic The Gathering. |
6 (details) | cmdoret/mtg_ontology | |
| dppkb DEMO example knowledge base created using DRAGON-AI |
5 (details) | monarch-initiative/dppkb | |
| information-resource-registry The information resource registry is a listing of data sources present in the NCATS Data Translator ... |
5 (details) | biolink/information-resource-registry | |
| linkml-java LinkML runtime library for Java |
linkml, semantic-web | 5 (details) | gouttegd/linkml-java |
| mianct-schema Minimal Information About a New Cell Type |
5 (details) | cmungall/mianct-schema | |
| model-card-schema LinkML rendering of model cards |
ai, bridge2ai, deep-learning... | 5 (details) | bridge2ai/model-card-schema |
| obograph | 5 (details) | biodatamodels/obograph | |
| pid4cat-model Handle-based PIDs with a rich LinkML metadata model for resources in catalysis (PID4Cat) |
handles, linkml, linkml-schema... | 5 (details) | nfdi4cat/pid4cat-model |
| prefixcommons-py Prefix commons python utlities |
5 (details) | prefixcommons/prefixcommons-py | |
| regen-data-standards | 5 (details) | regen-network/regen-data-standards | |
| TermCI-model The Terminology Code Index Entry model |
5 (details) | timsbiomed/TermCI-model | |
| cde-harmonization Initial private repo for P1 CDE harmonization |
4 (details) | monarch-initiative/cde-harmonization | |
| cim-to-linkml Generates LinkML schemas for packages in the CIM information model. |
cim | 4 (details) | Netbeheer-Nederland/cim-to-linkml |
| ConfIDent_schema The data schema for the ConfIDent project. |
4 (details) | TIBHannover/ConfIDent_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 | |
| linkml-activitypub LinkML Schema representation of ActivityPub |
4 (details) | p2p-ld/linkml-activitypub | |
| miiid-schema A metadata schema for the Minimum Information about Intermicrobial Interaction Data (MIIID) using Li... |
fair-data, linkml, linkml-schema... | 4 (details) | FAIR-MI/miiid-schema |
| mixs-source | 4 (details) | cmungall/mixs-source | |
| nwb-linkml Translating NWB schema language to linkml |
4 (details) | p2p-ld/nwb-linkml | |
| oae-data-protocol A data standards initiative for ocean alkalinity enhancement projects, experiments, and field trails... |
4 (details) | submarine-mrv/oae-data-protocol | |
| translator-ingests NCATS Biomedical Data Translator Data INGest and Operations WG consolidated data ingest pipeline pro... |
4 (details) | NCATSTranslator/translator-ingests | |
| bertron-schema LinkML schema for BERtron project. |
3 (details) | ber-data/bertron-schema | |
| eco-kg | 3 (details) | Knowledge-Graph-Hub/eco-kg | |
| hprc-data-explorer | 3 (details) | human-pangenomics/hprc-data-explorer | |
| include-linkml LinkML Schema for INCLUDE DCC |
3 (details) | include-dcc/include-linkml | |
| KGQA-COVID | 3 (details) | MrBearWithHisSword/KGQA-COVID | |
| linkml-aop A LinkML schema for Adverse Outcome Pathways |
3 (details) | EHS-Data-Standards/linkml-aop | |
| linkml-pokemon Adaptation of Pokemon Knowledge Graph as LinkML Schema |
agentic-ai, knowledge-graph, linked-data... | 3 (details) | vladistan/linkml-pokemon |
| monarch-project-copier New template for monarch repos, replaces old cookiecutter |
3 (details) | monarch-initiative/monarch-project-copier | |
| ome-nbo-formatter | 3 (details) | ome-nbo-tools/ome-nbo-formatter | |
| OpenCloning_LinkML A LinkML data model for OpenCloning |
3 (details) | OpenCloning/OpenCloning_LinkML | |
| oscem-schemas | 3 (details) | osc-em/oscem-schemas | |
| PPODLinkML A LinkML representation of the PPOD schema |
3 (details) | adhollander/PPODLinkML | |
| rnacentral-probing-metadata Metadata for structural chemical probing experiments for RNAcentral |
3 (details) | RNAcentral/rnacentral-probing-metadata | |
| ak-schema AIRR Knowledge Schema |
2 (details) | airr-knowledge/ak-schema | |
| BDP-Ontology | 2 (details) | hsolbrig/BDP-Ontology | |
| biobricks-schema BioBricks data dictionary schema |
2 (details) | biobricks-ai/biobricks-schema | |
| dragon-ai-cookiecutter Cookiecutter for DRAGON-AI projects |
2 (details) | monarch-initiative/dragon-ai-cookiecutter | |
| 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 | |
| htan2-data-model Data Model for HTAN Phase 2 |
2 (details) | ncihtan/htan2-data-model | |
| idr_metadata_model | 2 (details) | German-BioImaging/idr_metadata_model | |
| ingest-metadata | 2 (details) | biolink/ingest-metadata | |
| linkml-toolkit | 2 (details) | genomewalker/linkml-toolkit | |
| metadata-schema Metadata schema describing electrochemical data |
2 (details) | echemdb/metadata-schema | |
| monarch-provenance | 2 (details) | matentzn/monarch-provenance | |
| nmdc-metadata Managing metadata and policy around metadata in NMDC |
2 (details) | microbiomedata/nmdc-metadata | |
| NMRspec Prototype to semantify NMR spectroscopy research data |
2 (details) | StroemPhi/NMRspec | |
| bdfkb-schema | 1 (details) | ARPA-H-BDF/bdfkb-schema | |
| bridge-schemas | 1 (details) | cmungall/bridge-schemas | |
| cas-tools Cell Annotation Schema Tools |
1 (details) | cellannotation/cas-tools | |
| comet | 1 (details) | cmungall/comet | |
| edd-schema | 1 (details) | cmungall/edd-schema | |
| ga4gh-va-schema Data model for variant annotation in the GA4GH consortium. |
1 (details) | sujaypatil96/ga4gh-va-schema | |
| hca-validation-tools | 1 (details) | clevercanary/hca-validation-tools | |
| infoextract-cidoc Heritage Information Extraction to Markdown, JSON-LD, and Property Graphs (OpenCypher) |
1 (details) | DecisionNerd/infoextract-cidoc | |
| 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-tutorial-2024 | 1 (details) | hoodriverheather/linkml-tutorial-2024 | |
| 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 | |
| NHLBI-BDC-DMC-HV BDC Harmonized Variables |
1 (details) | RTIInternational/NHLBI-BDC-DMC-HV | |
| nmdc-client A Python client for the National Microbiome Data Collaborative |
1 (details) | jeffbaumes/nmdc-client | |
| oak-api | 1 (details) | pkalita-lbl/oak-api | |
| oakx-robot robot plugin for OAK |
1 (details) | INCATools/oakx-robot | |
| resume-model m30ml example project for rendering a resume |
1 (details) | Open-Ecological-Technology/resume-model | |
| SketchML :whale: SketchML - distributed Machine Leaning framework for Apache Flink :star: |
1 (details) | axenov/SketchML | |
| smpdb-beacon | 1 (details) | NCATS-Tangerine/smpdb-beacon | |
| stoplight_harmonization_project A toy model for prototyping and demonstrating LinkML based data harmonization |
1 (details) | hsolbrig/stoplight_harmonization_project | |
| submission-schema The NMDC submission schema |
1 (details) | microbiomedata/submission-schema | |
| tccm-model-lite | 1 (details) | timsbiomed/tccm-model-lite | |
| trowel TROWEL - a Tool for Retrieving, Organizing, and Wrangling Earth science data and Labels |
1 (details) | bioepic-data/trowel | |
| 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 | |
| bashtown bash town |
0 (details) | groenewt/bashtown | |
| 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 | |
| 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 | |
| EssDiveSampleRF | 0 (details) | heycatwonton/EssDiveSampleRF | |
| foo-model | 0 (details) | hsolbrig/foo-model | |
| ghp-vocab Vocabulary for Good Health Pass |
0 (details) | mukundanps/ghp-vocab | |
| graph-validation-test-runners This repository provides the implementation of some Translator knowledge graph validation Test Runne... |
0 (details) | TranslatorSRI/graph-validation-test-runners | |
| hdmf-term-lists | 0 (details) | rly/hdmf-term-lists | |
| hoopla | 0 (details) | cmungall/hoopla | |
| 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-playground linkml-playground |
0 (details) | manulera/linkml-playground | |
| LinkML-Project-Cookiecutter This project is from the LinkML tutorial at ISMB 2024 |
0 (details) | lmnb2055/LinkML-Project-Cookiecutter | |
| linkml-tutorial | 0 (details) | 4lirastegar/linkml-tutorial | |
| microscopemetrics-schema | 0 (details) | MontpellierRessourcesImagerie/microscopemetrics-schema | |
| minimal-metab A LinkML cookiecutter repo for modelling metabolomics from the ground up |
0 (details) | microbiomedata/minimal-metab | |
| monarch-kg-qc-schema Schema for QC Reports on the Monarch KG |
0 (details) | amc-corey-cox/monarch-kg-qc-schema | |
| nmdc-lakehouse | 0 (details) | microbiomedata/nmdc-lakehouse | |
| ontology_to_schema | 0 (details) | liuji1031/ontology_to_schema | |
| OpenCloning-submission An API to submit ShareYourCloning templates |
0 (details) | OpenCloning/OpenCloning-submission | |
| parkerslinkmltest | 0 (details) | plbremer/parkerslinkmltest | |
| PCDMLinkML Portland Common Data Model, in LinkML |
0 (details) | multimeric/PCDMLinkML | |
| pfhub-cli-old | 0 (details) | wd15/pfhub-cli-old | |
| pfhub-schema Phase-field simulation and benchmark schema in LinkML |
0 (details) | usnistgov/pfhub-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 | |
| 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 | |
| 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 |