linkml

There are 12 repositories under linkml topic.

• monarch-initiative / ontogpt

  LLM-based ontological extraction tools, including SPIRES

  aigpt-3language-modelslinkmlnlpoaklibrelation-extractionmonarchinitiativechat-gptlarge-language-modelsobofoundrydata-modelinginformation-extractionllmnamed-entity-recognitionner
  Language:Jupyter Notebook 525
• linkml

  linkml / linkml

  Linked Open Data Modeling Language

  rdfmodelinglinkmljson-schemalinkml-schemasemantic-webschemadata-modelingjson-ld-contextowldata-dictionarieslinked-datahacktoberfeststandardsshexshacl
  Language:Python 288
• biolink-model

  biolink / biolink-model

  Schema and generated objects for biolink data model and upper ontology

  biolinkmonarchinitiativegene-ontologydatamodelstandardspecificationyamljson-apiowlncats-translatorlinkmlobofoundryrdfneo4jknowledge-graphsncats
  Language:Python 167
• sssom

  mapping-commons / sssom

  Simple Standard for Sharing Ontology Mappings

  sssomowltsvmappingmapping-toolsmapping-standardsmetadata-elementslinkmlobofoundrymapping-commons
  Language:Python 136

• cidgoh / DataHarmonizer

  A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the Centre for Infectious Disease Genomics and One Health (CIDGOH), at Simon Fraser University, is now an open-source collaboration with contributions from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.

  dataharmonizationspreadsheetjavascriptapplicationlinkmllinkml-schema
  Language:JavaScript 87

• mapping-commons / sssom-py

  Python toolkit for SSSOM mapping format

  sssomobofoundrypythonmappingsontology-mappingslinkml
  Language:Python 45

• monarch-initiative / koza

  Data transformation framework for LinkML data models

  kozalinkmlobofoundryetlknowledge-graphontologymonarchinitiative
  Language:Python 43

• linkml / schemasheets

  Structure your data in a FAIR way using google sheets or TSVs. These are then converted to LinkML, and from there other formats

  linkmlschemasspreadsheetsfair-datashape-languagesshaclshexsheets2linkmlmetadata
  Language:Python 38

• INCATools / semantic-sql

  SQL and SQLite builds of OWL ontologies

  owlrelation-graphsqlsparqlontologieslinkmlobofoundryoaklib
  Language:Python 33

• linkml / schema-automator

  Automated assistance for the schema development lifecycle

  linkmldata-modelingowlcsvsspreadsheetsschema-inferencetoolspythonlinked-dataincatoolsintelligent-concept-assistant
  Language:Python 32

• linkml / linkml-model

  Link Modeling Language (LinkML) model

  linkmlsemantic-webjsonjson-schemagraph-qlmetamodelyamldata-integrationmetadataumlschema-languagedata-modelingshaclshexlinked-data
  Language:Python 29

• microbiomedata / nmdc-schema

  National Microbiome Data Collaborative (NMDC) unified data model

  nmdcmicrobiomestandardslinkmlgenomicsproteomicsmetabolomicstranscriptomicsschemamicrobiomedatasamplesmetadatamixsecoinformaticsfair-data
  Language:Python 26

• cmungall / semantic-llama

  A knowledge extraction tool that uses a large language model to extract semantic information from text

  aiknowledge-extractionlanguage-modelslinkmloaklibobofoundry
  Language:Python 22

• linkml / linkml-runtime

  Runtime support for linkml generated models

  linkml-runtimelinkmlpythonobject-modelinstancesconversionhacktoberfest
  Language:Python 21

• cancerDHC / ccdhmodel

  CRDC-H model in LinkML, developed by the Center for Cancer Data Harmonization (CCDH)

  google-sheetslinkmlpython
  Language:Python 16

• INCATools / kgcl-rdflib

  Tools for working with KGCL

  ontologyknowledge-graphdiffowlrdfkgsemantic-difflinkmldiffsontology-change-languageobofoundry
  Language:Python 15

• monarch-initiative / monarch-ingest

  Data ingest application for Monarch Initiative knowledge graph using Koza

  kgxknowledge-graphslinkmllinkml-schemamonarchinitiativeneo4jpythonsemantic-websolrsqlite
  Language:Python 14

• chemkg / chemrof

  Schema for chemistry ontology classes

  chemistryontologyoboowlmetaclassschemachebilinkmlobofoundry
  Language:Prolog 13

• ghga-de / ghga-metadata-schema

  Metadata schema for the German Human Genome-Phenome Archive (GHGA)

  metadata-schemaghgalinkmlfega
  Language:Python 13

• linkml / linkml-map

  Mapping between LinkML schemas

  data-model-mappingetllinkmlmapping
  Language:Python 13

• monarch-initiative / monochrom

  Standardized identifiers and OWL classes for chromosomes and chromosomal parts across species

  obofoundryowllinkmlgenomicschromosomesetl
  Language:Python 12

• linkml / linkml-datalog

  Translates LinkML schemas into Datalog programs and executes them using Souffle, enabling advanced validation and inference over instance data. ALPHA.

  constraintsdataloglinkmllogic-programmingrdfreasoningrule-languagerulessemantic-websemanticssouffle-datalog-languagevalidation
  Language:Python 11

• linkml / linkml-owl

  Extension of LinkML runtime for converting instances of LinkML classes to OWL (classes or instances)

  linkmlowldesign-patternstemplatesontologiesontology-generationontology-design-patternsmetaclassesjson2owlyaml2owltsv2owlontology-mapping
  Language:Python 11

• linkml / linkml-registry

  Registry of schemas that use LinkML

  linkmlregistryschema-registryschemas
  Language:Python 11

• INCATools / kgcl

  Datamodel for KGCL (Knowledge Graph Change Language)

  linkmlontology-changesontology-diffsrdfsemantic-webkgcl
  Language:Python 10

• linkml / linkml-project-template

  A template for LinkML projects using poetry and gen-project

  linkmllinkml-model-template
  Language:Jinja 9

• linkml / prefixmaps

  Semantic prefix map registry

  bioregistrylinkmlobofoundryprefixmaps
  Language:Python 9

• cmungall / json-flattener

  Python library for denormalizing nested dicts or json objects to tables and back

  jsonyamldenormalizationdataframeslinkmlpandas
  Language:Python 8

• linkml / sparqlfun

  sparql templates for linkml (alpha)

  linked-datalinkmlobofoundryontobeeontologiesrdflibsparqlsparql-templatesubergraph
  Language:Python 8

• monarch-initiative / babelon

  A format for language profiles for ontologies

  language-translationlinkmlmonarchinitiativeobofoundryowlsemantic-webinternationalization
  Language:Python 8

• cmungall / linkml-phenopackets

  EXPERIMENTAL rendering of phenopackets in linkml

  linkmlphenopacketsmonarchinitiativemetadatardfsemwebphenotypeshuman-phenotype-ontology
  Language:Python 7

• isamplesorg / metadata

  Collation of metadata examples and notes for the project

  linkmlmetadataphysical-specimen
  Language:Python 7

• alliance-genome / agr_curation_schema

  Schema repository for the Alliance of Genome Resources persistent data store

  linkmlalliance-curationalliance-of-genome-resources
  Language:Makefile 6

• biodatamodels / gff-schema

  LinkML schema for GFF3, the Genome Feature Format

  linkmlgenomicsbioinformaticsgffstandardsformatssequences
  Language:Python 6

• linkml / linkml-runtime.js

  An implementation of the linkml-runtime in javascript ALPHA VERSION

  data-harmonizerlinkml
  Language:TypeScript 6

• linkml / linkml-tutorial

  linkmltutorial
  Language:Python 6