glygen-glycan-data/GNOme

GNOme - Glycan Naming and Subsumption Ontology.

Language: JavaScript - Size: 223 MB - Last synced: about 3 hours ago - Pushed: about 4 hours ago - Stars: 7 - Forks: 2

Radiobiology-Informatics-Consortium/RBO

Radiation Biology Ontology development

Language: Makefile - Size: 52.6 MB - Last synced: about 3 hours ago - Pushed: about 4 hours ago - Stars: 4 - Forks: 3

INCATools/ubergraph

Integrated OBO ontology store

Language: Makefile - Size: 187 KB - Last synced: about 4 hours ago - Pushed: about 5 hours ago - Stars: 41 - Forks: 3

OBOFoundry/OBOFoundry.github.io

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

Language: Python - Size: 31.6 MB - Last synced: about 6 hours ago - Pushed: 1 day ago - Stars: 159 - Forks: 199

obophenotype/upheno

The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.

Language: Makefile - Size: 38.2 MB - Last synced: about 11 hours ago - Pushed: about 11 hours ago - Stars: 76 - Forks: 16

biolink/ontobio

python library for working with ontologies and ontology associations

Language: Python - Size: 58.8 MB - Last synced: about 19 hours ago - Pushed: 2 days ago - Stars: 117 - Forks: 30

DiseaseOntology/HumanDiseaseOntology

Repository for the Human Disease Ontology.

Language: Makefile - Size: 886 MB - Last synced: about 6 hours ago - Pushed: 1 day ago - Stars: 324 - Forks: 109

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

Language: Makefile - Size: 52.2 MB - Last synced: about 19 hours ago - Pushed: 1 day ago - Stars: 13 - Forks: 9

AnimalGenome/vertebrate-trait-ontology

Terms for annotation of vertebrate trait data

Size: 8.02 MB - Last synced: about 16 hours ago - Pushed: 1 day ago - Stars: 6 - Forks: 2

obophenotype/bio-attribute-ontology

source files for OBA (Ontology of Biological Attributes)

Language: Jupyter Notebook - Size: 223 MB - Last synced: about 18 hours ago - Pushed: 1 day ago - Stars: 26 - Forks: 10

obophenotype/brain_data_standards_ontologies

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

Language: Python - Size: 274 MB - Last synced: 9 days ago - Pushed: 19 days ago - Stars: 9 - Forks: 3

monarch-initiative/koza

Data transformation framework for LinkML data models

Language: Python - Size: 4.63 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 42 - Forks: 3

ontodev/robot

ROBOT is an OBO Tool

Language: Java - Size: 5.06 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 252 - Forks: 68

mgijax/mammalian-phenotype-ontology

Standard terms for annotating mammalian phenotypic data

Language: Makefile - Size: 632 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 19 - Forks: 6

enpadasi/Ontology-for-Nutritional-Studies

The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies.

Size: 15.7 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 10 - Forks: 5

INCATools/ontology-development-kit

Bootstrap an OBO Library ontology

Language: Jinja - Size: 4.97 MB - Last synced: about 19 hours ago - Pushed: 3 days ago - Stars: 206 - Forks: 53

OBOAcademy/obook

OBO Organized Knowledge: Training materials for becoming an OBO engineer

Language: Makefile - Size: 68 MB - Last synced: 9 days ago - Pushed: 16 days ago - Stars: 83 - Forks: 38

insect-morphology/aism

This repository contains the ontology for the Anatomy of the Insect SkeletoMuscular system (AISM), which contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research.

Language: Makefile - Size: 36.2 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 10 - Forks: 9

Planteome/plant-trait-ontology

Explore the Plant Trait Ontology on the Planteome site.

Language: Python - Size: 15.1 MB - Last synced: about 9 hours ago - Pushed: 6 days ago - Stars: 36 - Forks: 12

biolink/biolink-model

Schema and generated objects for biolink data model and upper ontology

Language: Python - Size: 291 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 167 - Forks: 71

mapping-commons/sssom-py

Python toolkit for SSSOM mapping format

Language: Python - Size: 16.2 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 45 - Forks: 9

monarch-initiative/ontogpt

LLM-based ontological extraction tools, including SPIRES

Language: Jupyter Notebook - Size: 58.7 MB - Last synced: 2 days ago - Pushed: 6 days ago - Stars: 516 - Forks: 64

HUPO-PSI/psi-ms-CV

HUPO-PSI mass spectrometry CV

Language: Python - Size: 83.1 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 26 - Forks: 33

monarch-initiative/MAxO

Medical action ontology

Language: HTML - Size: 236 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 46 - Forks: 5

monarch-initiative/mondo

Mondo Disease Ontology

Language: Jupyter Notebook - Size: 10.2 GB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 216 - Forks: 48

INCATools/ontology-access-kit

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

Language: Jupyter Notebook - Size: 49.2 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 103 - Forks: 22

mcwdsi/OMRSE

The Ontology for Modeling and Representation of Social Entities

Language: Makefile - Size: 3.76 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 14 - Forks: 7

obophenotype/ncbitaxon

Build for NCBITaxon

Language: Python - Size: 5 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 24 - Forks: 6

EBISPOT/DUO

Ontology for consent codes and data use requirements

Language: Makefile - Size: 6.43 MB - Last synced: 9 days ago - Pushed: over 1 year ago - Stars: 59 - Forks: 15

cmungall/obo-metadata

EXPERIMENTAL obo metadata repo

Language: Jupyter Notebook - Size: 1.2 MB - Last synced: 9 days ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

cmungall/obi-mappings

Language: Prolog - Size: 17.6 KB - Last synced: 9 days ago - Pushed: about 3 years ago - Stars: 2 - Forks: 0

cmungall/agrovoc-obo

Agrovoc alignment to OBO Ontologies

Language: Prolog - Size: 2.41 MB - Last synced: 9 days ago - Pushed: almost 8 years ago - Stars: 2 - Forks: 0

mapping-commons/microbial-trait-mappings

Size: 3.15 MB - Last synced: 9 days ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0

rat-genome-database/XCO-Experimental-Condition-Ontology

Experimental Condition Ontology maintained by RGD

Size: 991 KB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 2 - Forks: 2

rat-genome-database/MMO-Measurement-Method-Ontology

Measurement method ontology maintained by RGD

Size: 2.24 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 1 - Forks: 2

rat-genome-database/CMO-Clinical-Measurement-Ontology

Clinical Measurement Ontology (CMO) maintained by RGD

Size: 1.97 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 3 - Forks: 4

vaccineontology/VO

Vaccine Ontology

Language: Makefile - Size: 13.1 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 15 - Forks: 9

rat-genome-database/RS-Rat-Strain-Ontology

Rat strain ontology maintained by RGD

Size: 17.6 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 0 - Forks: 2

NCI-Thesaurus/thesaurus-obo-edition

OBO Library edition of NCIt

Language: Makefile - Size: 7.62 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 22 - Forks: 8

oral-health-and-disease-ontologies/ohd-ontology

The OHD is an ontology for representing the diagnosis and treatment of dental maladies.

Language: Common Lisp - Size: 29.5 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 7 - Forks: 6

mapping-commons/sssom

Simple Standard for Sharing Ontology Mappings

Language: Python - Size: 13.7 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 135 - Forks: 24

monarch-initiative/curate-gpt

LLM-driven curation assist tool (pre-alpha)

Language: Jupyter Notebook - Size: 4.27 MB - Last synced: 9 days ago - Pushed: 2 months ago - Stars: 40 - Forks: 9

xenopus-anatomy/xao

XAO represents the anatomy and development of the African frogs Xenopus laevis and X. tropicalis.

Language: Python - Size: 4.94 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 5 - Forks: 3

cthoyt/obo-community-health

🫀 Check the OBO Foundry repositories to see what's going on

Language: Python - Size: 19 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 2 - Forks: 0

Planteome/plant-ontology

Repository for the Plant Ontology

Language: Perl - Size: 29.9 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 54 - Forks: 17

callahantiff/PheKnowLator

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

Language: Python - Size: 43.5 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 139 - Forks: 25

pato-ontology/pato

PATO - the Phenotype And Trait Ontology

Language: Makefile - Size: 35.5 MB - Last synced: 9 days ago - Pushed: about 2 months ago - Stars: 58 - Forks: 18

FlyBase/flybase-controlled-vocabulary

The home of the FlyBase miscellaneous ontologies - incorporating the Drosophila Phenotype Ontology (see also FlyBase/drosophila-phenotype-ontology)

Language: Shell - Size: 31.1 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 9 - Forks: 5

biopragmatics/curies

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

Language: Python - Size: 466 KB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 18 - Forks: 6

biopragmatics/pyobo

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

Language: Python - Size: 23.1 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 57 - Forks: 11

fastobo/fastobo-syntax

PEG Syntax and pest parser for the OBO flat file format 1.4

Language: Rust - Size: 72.3 KB - Last synced: 14 days ago - Pushed: 3 months ago - Stars: 3 - Forks: 0

cthoyt/curies4j

🐸 Idiomatic conversion between URIs and compact URIs (CURIEs)

Language: Java - Size: 37.1 KB - Last synced: 15 days ago - Pushed: 7 months ago - Stars: 9 - Forks: 0

biopragmatics/oquat

🎬 Ontology Quality Assesment Toolkit

Language: Python - Size: 63.3 MB - Last synced: 15 days ago - Pushed: 5 months ago - Stars: 5 - Forks: 1

oborel/obo-relations

RO is an ontology of relations for use with biological ontologies

Language: Jupyter Notebook - Size: 23.5 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 88 - Forks: 46

INCATools/semantic-sql

SQL and SQLite builds of OWL ontologies

Language: Python - Size: 7.65 MB - Last synced: 8 days ago - Pushed: 17 days ago - Stars: 33 - Forks: 3

monarch-initiative/babelon

A format for language profiles for ontologies

Language: Python - Size: 21.3 MB - Last synced: 9 days ago - Pushed: 17 days ago - Stars: 8 - Forks: 0

obi-ontology/obi

The Ontology for Biomedical Investigations

Language: Python - Size: 33.9 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 74 - Forks: 24

obophenotype/ascomycete-phenotype-ontology

Language: Shell - Size: 872 KB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 4 - Forks: 3

FlyBase/drosophila-phenotype-ontology

The home of the Drosophila phenotype ontology

Language: Makefile - Size: 37.8 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 4 - Forks: 1

EBISPOT/hancestro

Language: Makefile - Size: 85.6 MB - Last synced: 20 days ago - Pushed: 21 days ago - Stars: 6 - Forks: 2

fastobo/fastobo

Faultless AST for Open Biomedical Ontologies.

Language: Rust - Size: 1.25 MB - Last synced: 16 days ago - Pushed: 3 months ago - Stars: 22 - Forks: 3

althonos/pronto

A Python frontend to (Open Biomedical) Ontologies.

Language: Python - Size: 10.1 MB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 217 - Forks: 46

callahantiff/OMOP2OBO

OMOP2OBO: A Python Library for mapping OMOP standardized clinical terminologies to Open Biomedical Ontologies

Language: Jupyter Notebook - Size: 92 MB - Last synced: 17 days ago - Pushed: 8 months ago - Stars: 78 - Forks: 12

drseb/boqa

Bayesian ontology querying from Bauer et al.

Language: Java - Size: 202 KB - Last synced: 23 days ago - Pushed: over 5 years ago - Stars: 5 - Forks: 6

OBOFoundry/purl.obolibrary.org

A system for managing OBO PURLs

Language: Python - Size: 1.56 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 70 - Forks: 123

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

Language: Python - Size: 6.12 MB - Last synced: 9 days ago - Pushed: about 2 months ago - Stars: 28 - Forks: 2

biopragmatics/debio

🥮 Decentralized Biomedical Ontology

Language: Python - Size: 195 KB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 0 - Forks: 0

obophenotype/uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology

Language: Emacs Lisp - Size: 1.89 GB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 129 - Forks: 30

FlyBase/drosophila-developmental-ontology

The home of the Drosophila developmental ontology, an ontology of Drosophila melanogaster developmental stages.

Language: Makefile - Size: 12.3 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 4 - Forks: 0

FlyBase/drosophila-anatomy-developmental-ontology

The home of the Drosophila anatomy ontology

Language: Jupyter Notebook - Size: 469 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 18 - Forks: 6

PlantPhenoOntology/ppo

An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales.

Language: Makefile - Size: 35.9 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 16 - Forks: 7

GenEpiO/genepio

The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information required to support data sharing and integration for foodborne infectious disease surveillance and outbreak investigations.

Language: Python - Size: 26.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 16 - Forks: 10

geneontology/go-ontology

Source ontology files for the Gene Ontology

Language: Makefile - Size: 1.49 GB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 205 - Forks: 39

obophenotype/human-phenotype-ontology

Ontology for the description of human clinical features

Language: Makefile - Size: 1.54 GB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 278 - Forks: 53

pombase/fypo

Fission Yeast Phenotype Ontology

Language: Makefile - Size: 905 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 14 - Forks: 6

obophenotype/cell-ontology

An ontology of cell types

Language: Makefile - Size: 316 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 130 - Forks: 47

psiotwo/ontology-version-extractor

A heuristic-based extractor of ontology version without downloading the whole ontology.

Language: Java - Size: 692 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

EnvironmentOntology/envo

A community-driven ontology for the representation of environments

Language: Makefile - Size: 94.2 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 124 - Forks: 53

semanticchemistry/semanticchemistry

Chemical Information Ontology

Language: Java - Size: 16.6 MB - Last synced: 26 days ago - Pushed: 27 days ago - Stars: 15 - Forks: 9

obophenotype/c-elegans-phenotype-ontology

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

Language: Makefile - Size: 95.7 MB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 10 - Forks: 4

BiodiversityOntologies/bco

Biological Collections Ontology

Language: Makefile - Size: 4.83 MB - Last synced: 9 days ago - Pushed: over 2 years ago - Stars: 21 - Forks: 3

OBOFoundry/obo-nor.github.io

Repo to manage the dashboard for new term requests

Language: HTML - Size: 10 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 6 - Forks: 6

cmungall/semantic-llama

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

Language: Python - Size: 1.52 MB - Last synced: 9 days ago - Pushed: over 1 year ago - Stars: 22 - Forks: 1

geneontology/obographs

Basic and Advanced OBO Graphs: specification and reference implementation

Language: Java - Size: 13 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 62 - Forks: 12

OBOFoundry/obo-dash.github.io

Development version of OBO dashboard

Language: HTML - Size: 26.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 8 - Forks: 0

chemkg/chemrof

Schema for chemistry ontology classes

Language: Prolog - Size: 13.1 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 13 - Forks: 3

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:

Language: Java - Size: 6.25 MB - Last synced: 29 days ago - Pushed: 30 days ago - Stars: 26 - Forks: 8

ebi-chebi/ChEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.

Size: 10.7 KB - Last synced: 29 days ago - Pushed: about 2 years ago - Stars: 39 - Forks: 10

The-Sequence-Ontology/SO-Ontologies

Collect of SO Ontologies

Language: Makefile - Size: 32.6 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 89 - Forks: 37

CompositionalDietaryNutritionOntology/cdno

Compositional Dietary Nutrition Ontology

Language: Makefile - Size: 17.2 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 11 - Forks: 2

ProperNameOntology/proper-name-ontology

Automatically exported from code.google.com/p/proper-name-ontology

Size: 110 KB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 2

OpenLHS/LABO

An ontology of informational entities about laboratory tests prescriptions and reports.

Size: 1.89 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 2 - Forks: 2

AgriculturalSemantics/agro

AgrO describes agronomic practices, techniques, and variables used in agronomic experiments.

Language: Python - Size: 5.49 MB - Last synced: about 2 months ago - Pushed: 12 months ago - Stars: 45 - Forks: 16

obophenotype/planarian-phenotype-ontology

Planarian Phenotype Ontology

Language: Makefile - Size: 11.9 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 6 - Forks: 1

obophenotype/spider-ontology

An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing), and products (e.g. silk, web, burrow).

Size: 172 KB - Last synced: about 2 months ago - Pushed: 9 months ago - Stars: 3 - Forks: 1

obophenotype/sibo

Social Insect Behavior Ontology

Language: Web Ontology Language - Size: 207 KB - Last synced: about 2 months ago - Pushed: almost 9 years ago - Stars: 2 - Forks: 1

obophenotype/xenopus-phenotype-ontology

XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and X. tropicalis.

Language: Makefile - Size: 60.5 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 8 - Forks: 3

obophenotype/caro

Working repository for v2 of CARO

Language: Makefile - Size: 10.5 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 3 - Forks: 2

obophenotype/mouse-anatomy-ontology

Ontologies for mouse anatomy and development

Language: Makefile - Size: 15.2 MB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 5 - Forks: 3

obophenotype/human-developmental-anatomy-ontology

Ontology of human developmental anatomy

Language: Makefile - Size: 798 KB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 5 - Forks: 4