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OBO Foundry

The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants follow and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Operations Committee with Editorial, Technical and Outreach working groups.

https://github.com/ontodev/robot

ROBOT is an OBO Tool

obo obofoundry ontology owl

Last synced: 18 Feb 2026

https://github.com/BFO-ontology/BFO

BFO repository including source code and latest documents

obofoundry

Last synced: 03 Apr 2025

https://github.com/althonos/pronto

A Python frontend to (Open Biomedical) Ontologies.

bioinformatics obo obo-graphs obofoundry ontology owl parser python semantic-web

Last synced: 16 May 2025

https://github.com/callahantiff/pheknowlator

PheKnowLator: Heterogeneous Biomedical Knowledge Graphs and Benchmarks Constructed Under Alternative Semantic Models

benchmarks biolink-model biomedical-applications bioregistry hacktoberfest knowledge-graph linked-open-data mechanisms obofoundry ontologies owl semantic-web translational-research

Last synced: 05 Apr 2025

https://github.com/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.

agriculture food obofoundry ontology owl

Last synced: 03 Apr 2025

https://github.com/incatools/ontology-access-kit

Ontology Access Kit: A python library and command line application for working with ontologies

apis geneontology monarchinitiative oaklib obofoundry ontology ontology-api owl python rdf semantic-web

Last synced: 12 Apr 2026

https://github.com/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

Last synced: 16 May 2025

https://github.com/oborel/obo-relations

RO is an ontology of relations for use with biological ontologies

bfo knowledge-graph obo-relations obofoundry ontologies owl relations

Last synced: 27 Jan 2026

https://github.com/EBISPOT/OLS

Ontology Lookup Service from SPOT at EBI

java neo4j obofoundry owl owl-api

Last synced: 09 May 2025

https://github.com/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

Last synced: 20 Jun 2025

https://github.com/obi-ontology/obi

The Ontology for Biomedical Investigations

bioinformatics obo obofoundry ontology owl semantic-web

Last synced: 11 Mar 2025

https://github.com/information-artifact-ontology/IAO

information artifact ontology

obofoundry ontologies

Last synced: 03 Apr 2025

https://github.com/biopragmatics/pyobo

📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures

bioinformatics biopragmatics bioregistry obo obofoundry ontologies

Last synced: 04 Apr 2025

https://github.com/jannahastings/emotion-ontology

Ontology for emotions and affective phenomena

affective-sciences emotion-ontology obofoundry

Last synced: 14 Jul 2025

https://github.com/monarch-initiative/sepio-ontology

Ontology for representing scientific evidence and provenance information

evidence monarchinitiative obofoundry provenance

Last synced: 21 Jan 2026

https://github.com/monarch-initiative/koza

Data transformation framework for LinkML data models

etl knowledge-graph koza linkml monarchinitiative obofoundry ontology

Last synced: 07 May 2026

https://github.com/incatools/ubergraph

Integrated OBO ontology store

knowledge-graph ncats-translator obofoundry owl rdf

Last synced: 05 Mar 2026

https://github.com/planteome/plant-trait-ontology

Explore the Plant Trait Ontology on the Planteome site.

obo obofoundry owl phenotype plant-trait-ontology plant-traits

Last synced: 16 Jan 2026

https://github.com/evidenceontology/evidenceontology

Evidence & Conclusion Ontology development site: Use ISSUES to request terms. See WIKI for how to request terms. See README for how to cite ECO. Visit our website for more project info.

annotation evidence obo obofoundry ontology owl

Last synced: 11 Mar 2025

https://github.com/incatools/dead_simple_owl_design_patterns

A simple system for specifying OWL class design patterns for OBO-ish ontologies.

obofoundry odp ontology templates

Last synced: 19 Jun 2025

https://github.com/incatools/semantic-sql

SQL and SQLite builds of OWL ontologies

linkml oaklib obofoundry ontologies owl relation-graph sparql sql

Last synced: 05 Apr 2025

https://github.com/vemonet/shapes-of-you

💠 An index for linked open data & standard knowledge descriptions (ontologies, vocabularies, shapes, queries, mappings)

git grlc index mappings obofoundry ontologies owl registry shacl shacl-shapes shapes shex skos sparql

Last synced: 15 Jun 2025

https://github.com/allysonlister/swo

The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, licences, provenance and associated data.

obofoundry

Last synced: 03 Apr 2025

https://github.com/ISA-tools/stato

This is the development repository for the STATistics Ontology (STATO). For more information and demonstration on the ontology content, please visit its website:

obofoundry ontology owl statistics

Last synced: 11 Mar 2025

https://github.com/fastobo/fastobo-py

Faultless AST for Open Biomedical Ontologies in Python.

ast obo obofoundry ontology parser python-bindings python-extension rust

Last synced: 17 Mar 2026

https://github.com/knowledge-graph-hub/kg-obo

A package to transform all OBO ontologies into KGX TSV format and OBO json, and put the transformed graph in KGhub

biolink knowledge-graph monarchinitiative obo obofoundry ontology-infrastructure

Last synced: 25 Jan 2026

https://github.com/fastobo/fastobo

Faultless AST for Open Biomedical Ontologies.

ast obo obofoundry ontology

Last synced: 11 Mar 2025

https://github.com/cmungall/semantic-llama

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

ai knowledge-extraction language-models linkml oaklib obofoundry

Last synced: 05 May 2025

https://github.com/incatools/dosdp-tools

Utility for working with DOSDP design patterns and OWL ontologies

design-patterns dosdp-pattern monarchinitiative obofoundry odp ontology owl

Last synced: 03 Sep 2025

https://github.com/jannahastings/mental-functioning-ontology

Ontology for all aspects of human mental functioning

mentalfunctioning obofoundry ontologies ontology

Last synced: 08 Jan 2026

https://github.com/INCATools/obographviz

Customizable translation of OBO graphs to dot for visualization using graphviz and other tools

graph-visualization graphviz javascript json node obofoundry obographs

Last synced: 11 Mar 2025

https://github.com/incatools/obographviz

Customizable translation of OBO graphs to dot for visualization using graphviz and other tools

graph-visualization graphviz javascript json node obofoundry obographs

Last synced: 11 Apr 2025

https://github.com/biopragmatics/curies

🐸 Idiomatic conversion between URIs and compact URIs (CURIEs) in Python

curies obofoundry semantic-web uris

Last synced: 07 Apr 2025

https://github.com/BiodiversityOntologies/bco

Biological Collections Ontology

obofoundry

Last synced: 11 Mar 2025

https://github.com/CIDO-ontology/cido

CIDO: Coronavirus Infectious Disease Ontology

coronavirus covid-19 infectious-diseases mers-cov obofoundry ontology sars-cov sars-cov-2

Last synced: 11 Mar 2025

https://github.com/OBOFoundry/OBO-Dashboard

Summary Dashboard for Open Biological and Biomedical Ontologies

obofoundry

Last synced: 11 Mar 2025

https://github.com/chemkg/chemrof

Schema for chemistry ontology classes

chebi chemistry linkml metaclass obo obofoundry ontology owl schema

Last synced: 28 Feb 2026

https://github.com/mgijax/mammalian-phenotype-ontology

Standard terms for annotating mammalian phenotypic data

json mammals obo obofoundry ontology owl phenotype phenotyping

Last synced: 05 Feb 2026

https://github.com/data2health/contributor-role-ontology

This ontology provides contribution roles for use in crediting persons or organizations.

data2health obofoundry pea

Last synced: 11 Mar 2025

https://github.com/OGMS/ogms

Automatically exported from code.google.com/p/ogms

obofoundry

Last synced: 11 Mar 2025

https://github.com/monarch-initiative/GENO-ontology

Repository for representing genotypes and their association with phenotypes

monarchinitiative obofoundry ontology

Last synced: 11 Mar 2025

https://github.com/planteome/plant-stress-ontology

An ontology containing biotic and abiotic plant stresses. Part of the Planteome suite of reference ontologies. Formerly called the Ontology of Plant Stress

abiotic-stresses biotic-stresses obo obofoundry ontology plant-stress

Last synced: 12 Jan 2026

https://github.com/monarch-initiative/geno-ontology

Repository for representing genotypes and their association with phenotypes

monarchinitiative obofoundry ontology

Last synced: 22 Jan 2026

https://github.com/BFO-ontology/BFO2

BFO 2 classes with relations commonly used by OBO Foundry ontologies defined in RO core

obofoundry

Last synced: 11 Mar 2025

https://github.com/pcastellanoescuder/FoodBiomarkerOntology

:rocket: Food-Biomarker Ontology defines the relationships between foods and their associated metabolites (biomarkers) through a formal ontology

biomarkers foods knowledge-graph metabolomics nutrition obofoundry ontologies ontology

Last synced: 11 Mar 2025

https://github.com/pcastellanoescuder/foodbiomarkerontology

:rocket: Food-Biomarker Ontology defines the relationships between foods and their associated metabolites (biomarkers) through a formal ontology

biomarkers foods knowledge-graph metabolomics nutrition obofoundry ontologies ontology

Last synced: 28 Oct 2025

https://github.com/pombase/fypo

Fission Yeast Phenotype Ontology

fission-yeast obofoundry phenotypes pombase

Last synced: 16 Jan 2026

https://github.com/incatools/relation-graph

Materialize OWL existential relations

obofoundry ontology owl rdf

Last synced: 01 Mar 2025

https://github.com/PopulationAndCommunityOntology/pco

An ontology about groups of interacting organisms such as populations and communities

obofoundry

Last synced: 11 Mar 2025

https://github.com/monarch-initiative/monochrom

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

ai4curation chromosomes etl genomics linkml monarchinitiative obofoundry owl

Last synced: 29 Oct 2025

https://github.com/DIDEO/DIDEO

The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology (DIDEO)

obofoundry

Last synced: 11 Mar 2025

https://github.com/planteome/plant-experimental-conditions-ontology

Repository for the Plant Experimental Conditions Ontology

exposures obo obofoundry owl plant-treatments

Last synced: 28 Jan 2026

https://github.com/linkml/prefixmaps

Semantic prefix map registry

bioregistry linkml obofoundry prefixmaps

Last synced: 23 Apr 2025

https://github.com/obophenotype/biological-spatial-ontology

An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces

anatomy anatomy-ontology metazoa obofoundry spatial

Last synced: 16 Apr 2026

https://github.com/speciesfilegroup/nomen

A nomenclatural ontology for names (not concepts).

nomen nomenclature obofoundry ontology taxa taxon taxonomy web-ontology-language

Last synced: 09 Feb 2026

https://github.com/obophenotype/provisional_cell_ontology

Draft cell type definitions from data - candidates for inclusion in CL

cell-ontology cell-types obofoundry ontology single-cell-analysis single-cell-rna-seq transcriptomics

Last synced: 16 Apr 2026

https://github.com/obophenotype/brain_data_standards_ontologies

A repository for co-ordinating work on ontologies for the Brain Data Standards Project

anatomy-ontology brain brain-data cell-types metadata neuroanatomy neuron obofoundry ontology

Last synced: 16 Apr 2026

https://github.com/ClinicalTrialOntology/CTO

CTO: Core Ontology of Clinical Trials

clinical-trials obofoundry ontology

Last synced: 11 Mar 2025

https://github.com/obophenotype/c-elegans-phenotype-ontology

Ontology for phenotypes pertaining to the nematode Caenorhabditis elegans and related nematodes used by the nematode genome database WormBase

caenorhabditis-elegans elegans elegans-phenotype-ontology nematodes obofoundry ontology phenotype-ontologies phenotype-term phenotypes

Last synced: 16 Apr 2026

https://github.com/cthoyt/curies4j

🐸 Idiomatic conversion between URIs and compact URIs (CURIEs)

curies java obofoundry semantic-web uris

Last synced: 10 Apr 2025

https://github.com/cmungall/sweet-obo-alignment

Alignment between ESIP SWEET and Open Bio Ontologies

environment environment-variables mapping obo obofoundry ontology sssom sweet

Last synced: 08 Jan 2026

https://github.com/evoinfo/miapa

Minimum Information About a Phylogenetic Analysis (MIAPA) vocabularies and tools

information-exchange minimum-information obofoundry phylogenetics standard

Last synced: 11 Mar 2025

https://github.com/ebi-biomodels/sbo

The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling.

biosimulators computational-biology mathematical-modeling numerical-simulation obofoundry ontology sbml systems-biology

Last synced: 25 Apr 2026

https://github.com/obophenotype/fungal-anatomy-ontology

A structured controlled vocabulary for the anatomy of fungi

anatomy anatomy-ontology fungi obofoundry ontology

Last synced: 16 Apr 2026

https://github.com/EBI-BioModels/SBO

The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling.

biosimulators computational-biology mathematical-modeling numerical-simulation obofoundry ontology sbml systems-biology

Last synced: 11 Mar 2025

https://github.com/IHCC-cohorts/GECKO

Genomics Cohorts Knowledge Ontology

cohort genomics obofoundry ontology

Last synced: 11 Mar 2025

https://github.com/glygen-glycan-data/gnome

GNOme - Glycan Naming and Subsumption Ontology.

glycans obofoundry subsumption

Last synced: 11 Feb 2026

https://github.com/biopragmatics/obo-db-ingest

🗄️ Conversion of biomedical nomenclatures like HGNC to OBO

biocuration obo obofoundry obographs obographviz ontologies owl rdf

Last synced: 14 Jul 2025

https://github.com/obophenotype/porifera-ontology

An ontology covering the anatomy of Porifera (sponges)

anatomy anatomy-ontology evodevo metazoa obofoundry ontology porifera sponges

Last synced: 16 Apr 2026

https://github.com/phenoscape/taxrank

Taxonomic rank ontology

obofoundry

Last synced: 28 Jan 2026

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