obofoundry

There are 26 repositories under obofoundry topic.

monarch-initiative / ontogpt
LLM-based ontological extraction tools, including SPIRES
ai chat-gpt data-modeling gpt-3 information-extraction language-models large-language-models linkml llm monarchinitiative named-entity-recognition ner nlp oaklib obofoundry relation-extraction
Language:Jupyter Notebook 628
DiseaseOntology / HumanDiseaseOntology
Repository for the Human Disease Ontology.
disease obofoundry ontology
Language:Makefile 350
human-phenotype-ontology
obophenotype / human-phenotype-ontology
Ontology for the description of human clinical features
hpo ontology phenotype phenotyping ontologies obo owl semantic-web obofoundry monarchinitiative
Language:Makefile 295
BFO-ontology / BFO
BFO repository including source code and latest documents
obofoundry
Language:HTML 267
ontodev / robot
ROBOT is an OBO Tool
ontology owl obo obofoundry
Language:Java 264
mondo
monarch-initiative / mondo
Mondo Disease Ontology
monarchinitiative ontology obofoundry mondo disease disease-classification owl
Language:Jupyter Notebook 237
althonos / pronto
A Python frontend to (Open Biomedical) Ontologies.
obo owl ontology parser python bioinformatics semantic-web obofoundry obo-graphs
Language:Python 231
ontology-development-kit
INCATools / ontology-development-kit
Bootstrap an OBO Library ontology
obo ontology continuous-integration owl protege travis robot obofoundry monarchinitiative
Language:Jinja 231
go-ontology
geneontology / go-ontology
Source ontology files for the Gene Ontology
ontology go owl obo obofoundry gene-ontology geneontology functional-annotation
Language:Makefile 225
FoodOntology / foodon
The core repository for the FOODON food ontology project. This holds the key classes of the ontology; larger files and the results of text-mining projects will be stored in other repos.
obofoundry ontology owl food agriculture
Language:Python 186
biolink-model
biolink / biolink-model
Schema and generated objects for biolink data model and upper ontology
biolink monarchinitiative gene-ontology datamodel standard specification yaml json-api owl ncats-translator linkml obofoundry rdf neo4j knowledge-graphs ncats
Language:Python 181
callahantiff / PheKnowLator
PheKnowLator: Heterogeneous Biomedical Knowledge Graphs and Benchmarks Constructed Under Alternative Semantic Models
knowledge-graph ontologies biomedical-applications mechanisms translational-research linked-open-data owl semantic-web benchmarks obofoundry bioregistry biolink-model hacktoberfest
Language:Python 173
OBOFoundry / OBOFoundry.github.io
Metadata and website for the Open Bio Ontologies Foundry Ontology Registry
ontology-registry obo ontology semantic-web bioinformatics life-sciences metadata open-science open-source annotation biocuration obofoundry
Language:Python 166
sssom
mapping-commons / sssom
Simple Standard for Sharing Ontology Mappings
sssom owl tsv mapping mapping-tools mapping-standards metadata-elements linkml obofoundry mapping-commons monarchinitiative
Language:Python 156
cell-ontology
obophenotype / cell-ontology
An ontology of cell types
obofoundry cell-ontology ontology anatomy cell-types owl anatomy-ontology semantic-web genomics transcriptomics metazoa monarchinitiative
Language:Makefile 151
envo
EnvironmentOntology / envo
A community-driven ontology for the representation of environments
obofoundry environment ecology ontology ecoinformatics data-science data-management sustainable-development-goals esip earth-science planetary-science semantics
Language:Makefile 137
uberon
obophenotype / uberon
An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
obofoundry uberon ontology anatomy monarchinitiative gross-anatomy metazoa anatomy-ontology geneontology
Language:Emacs Lisp 135
INCATools / ontology-access-kit
Ontology Access Kit: A python library and command line application for working with ontologies
obofoundry owl apis ontology rdf python ontology-api semantic-web monarchinitiative geneontology oaklib
Language:Python 127
biolink / ontobio
python library for working with ontologies and ontology associations
bioinformatics gene-ontology graph obo obofoundry ontology ontology-tools python rdf semantic-web sparql
Language:Python 125
EBISPOT / OLS
Ontology Lookup Service from SPOT at EBI
java neo4j obofoundry owl owl-api
Language:JavaScript 98
OBOAcademy / obook
OBO Organized Knowledge: Training materials for becoming an OBO engineer
obofoundry
Language:Makefile 98
The-Sequence-Ontology / SO-Ontologies
Collect of SO Ontologies
obofoundry
Language:Makefile 96
oborel / obo-relations
RO is an ontology of relations for use with biological ontologies
obofoundry obo-relations ontologies relations bfo owl knowledge-graph
Language:Jupyter Notebook 94
callahantiff / OMOP2OBO
OMOP2OBO: A Python Library for mapping OMOP standardized clinical terminologies to Open Biomedical Ontologies
clinical-terminologies hacktoberfest obofoundry omop omop-cdm open-biomedical-ontologies translational-research
Language:Jupyter Notebook 84
information-artifact-ontology / IAO
information artifact ontology
obofoundry ontologies
Language:Common Lisp 80
OBOFoundry / purl.obolibrary.org
A system for managing OBO PURLs
obo-services obofoundry ontology ontology-infrastructure purls
Language:Python 78
upheno
obophenotype / upheno
The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
obofoundry
Language:Makefile 78
obi-ontology / obi
The Ontology for Biomedical Investigations
bioinformatics obo obofoundry ontology owl semantic-web
Language:Python 75
monarch-initiative / curategpt
LLM-driven curation assist tool
ai curation gpt llm monarchinitiative obofoundry ontogpt ontologies ontology-tools biocuration
Language:Jupyter Notebook 71
DUO
EBISPOT / DUO
Ontology for consent codes and data use requirements
obofoundry ontology datasets-tagged biomedical-informatics biomedical-applications genomics-data owl
Language:Makefile 67
geneontology / obographs
Basic and Advanced OBO Graphs: specification and reference implementation
obofoundry owl json ontology-standards ontologies graphs gene-ontology geneontology ontology
Language:Java 64
biopragmatics / pyobo
📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures
obo ontologies obofoundry biopragmatics bioinformatics bioregistry
Language:Python 61
Planteome / plant-ontology
Repository for the Plant Ontology
obofoundry plant-ontology owl obo-format plants plant-anatomy plant-development
Language:Perl 60
pato-ontology / pato
PATO - the Phenotype And Trait Ontology
obo obofoundry ontology phenotypes qualities quantities semantic-web standards trait-ontology units
Language:Makefile 58
jannahastings / emotion-ontology
Ontology for emotions and affective phenomena
obofoundry emotion-ontology affective-sciences
Language:Java 53
monarch-initiative / MAxO
Medical action ontology
monarchinitiative medical treatments interventions diagnostics medicine treatment owl ontology obofoundry
Language:HTML 52

Related Topics

owl owl-ontology web-ontology-language