obophenotype

All

64 repositories

cell-ontology
Public
An ontology of cell types
genomics semantic-web owl ontology transcriptomics anatomy metazoa monarchinitiative obofoundry cell-ontology
Makefile
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Creative Commons Attribution 4.0 International
•53•180•305•27•Updated Aug 8, 2025Aug 8, 2025
upheno
Public
The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
obofoundry
Jupyter Notebook
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Creative Commons Zero v1.0 Universal
•19•79•269•20•Updated Aug 7, 2025Aug 7, 2025
uberon
Public
An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
ontology anatomy uberon metazoa geneontology monarchinitiative obofoundry anatomy-ontology gross-anatomy
Emacs Lisp
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Other
•34•141•304•33•Updated Aug 6, 2025Aug 6, 2025
developmental-stage-ontologies
Public
Source files for various species-specific stage ontologies
owl ontology anatomy obofoundry anatomy-ontology developmental-stages
Makefile
•5•10•54•0•Updated Aug 6, 2025Aug 6, 2025
pro_obo_slim
Public
A repo to generate a pro slim for the OBO phenotype organisation
Makefile
•1•1•0•0•Updated Aug 5, 2025Aug 5, 2025
ascomycete-phenotype-ontology
Public
ontology phenotype fungal obofoundry phenotype-ontology ascomycete
Shell
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Creative Commons Attribution 4.0 International
•3•4•1•0•Updated Aug 1, 2025Aug 1, 2025
bio-attribute-ontology
Public
source files for OBA (Ontology of Biological Attributes)
traits phenotypes monarchinitiative phenotype-ontologies obofoundry
Jupyter Notebook
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Creative Commons Zero v1.0 Universal
•12•27•83•7•Updated Aug 1, 2025Aug 1, 2025
upheno-dev
Public archive
Framework for the automated construction of uPheno 2.0
Jupyter Notebook
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MIT License
•5•5•0•7•Updated Jul 31, 2025Jul 31, 2025
human-phenotype-ontology
Public
Ontology for the description of human clinical features
semantic-web owl ontology obo phenotyping phenotype ontologies hpo monarchinitiative obofoundry
Makefile
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Other
•56•315•286•9•Updated Jul 31, 2025Jul 31, 2025
xenopus-phenotype-ontology
Public
XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and X. tropicalis.
phenotype xpo obofoundry xenopus ontology xenopus-phenotype-ontology
Makefile
•3•11•17•0•Updated Jul 25, 2025Jul 25, 2025
ncbitaxon
Public
Build for NCBITaxon
taxonomy ontology ncbi-taxonomy obofoundry
Python
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BSD 3-Clause "New" or "Revised" License
•7•29•30•3•Updated Jul 23, 2025Jul 23, 2025
chebi_obo_slim
Public
A slimmed down version of CHEBI sufficient to cover 99% of the term needs across OBO ontologies
obofoundry
Ruby
•1•3•2•2•Updated Jul 23, 2025Jul 23, 2025
c-elegans-gross-anatomy-ontology
Public
C. elegans Gross Anatomy Ontology
anatomy obofoundry caenorhabditis-elegans ontology
Makefile
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Creative Commons Attribution 4.0 International
•2•7•6•0•Updated Jul 16, 2025Jul 16, 2025
fungal-anatomy-ontology
Public
A structured controlled vocabulary for the anatomy of fungi
fungi anatomy obofoundry anatomy-ontology ontology
Makefile
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Creative Commons Zero v1.0 Universal
•4•9•8•0•Updated Jul 15, 2025Jul 15, 2025
provisional_cell_ontology
Public
Draft cell type definitions from data - candidates for inclusion in CL
transcriptomics single-cell-rna-seq single-cell-analysis obofoundry cell-ontology cell-types ontology
Makefile
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Creative Commons Attribution 4.0 International
•1•12•19•0•Updated Jul 8, 2025Jul 8, 2025
brain_data_standards_ontologies
Public
A repository for co-ordinating work on ontologies for the Brain Data Standards Project
metadata neuron brain neuroanatomy obofoundry cell-types brain-data anatomy-ontology ontology
Python
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Apache License 2.0
•3•11•28•4•Updated Jul 4, 2025Jul 4, 2025
uberon-robot-plugin
Public
Extra ROBOT commands for Uberon
Java
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Jul 2, 2025Jul 2, 2025
hpo-translations
Public
This repo will contain the Human Phenotype Ontology language profiles
localisation ontologies hpo obofoundry i18n localization
Makefile
•3•4•10•0•Updated Jun 19, 2025Jun 19, 2025
zebrafish-phenotype-ontology
Public
A vocabulary for describing Zebrafish Phenotypes
ontology anatomy zebrafish obofoundry anatomy-ontology developmental-stages
Python
•4•9•21•3•Updated Jun 18, 2025Jun 18, 2025
c-elegans-development-ontology
Public
C. elegans Development Ontology
development obofoundry caenorhabditis-elegans ontology nematodes wormbase
Makefile
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Creative Commons Attribution 4.0 International
•2•5•0•0•Updated Apr 1, 2025Apr 1, 2025
c-elegans-phenotype-ontology
Public
Ontology for phenotypes pertaining to the nematode Caenorhabditis elegans and related nematodes used by the nematode genome database WormBase
phenotypes phenotype-ontologies obofoundry caenorhabditis-elegans ontology elegans nematodes elegans-phenotype-ontology phenotype-term
Makefile
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Creative Commons Attribution 4.0 International
•4•11•3•0•Updated Apr 1, 2025Apr 1, 2025
sibo
Public
Social Insect Behavior Ontology
ontology obofoundry
2•2•7•0•Updated Nov 13, 2024Nov 13, 2024
test-actions
Public
0•0•0•1•Updated Nov 13, 2024Nov 13, 2024
CCF_graphs
Public
Python
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MIT License
•0•0•0•0•Updated Oct 11, 2024Oct 11, 2024
vccf-ontology
Public
Makefile
•0•1•6•0•Updated Jun 4, 2024Jun 4, 2024
pattern-review
Public
Python
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MIT License
•0•1•4•3•Updated Mar 1, 2024Mar 1, 2024
cephalopod-ontology
Public
An ontology of cephalopod anatomy and traits
semantic-web owl ontology nautilus squid anatomy octopus obofoundry cuttlefish cephalopod
Makefile
•6•5•7•0•Updated Feb 29, 2024Feb 29, 2024
human-developmental-anatomy-ontology
Public
Ontology of human developmental anatomy
human ontology anatomy uberon metazoa developmental-biology obofoundry anatomy-ontology developmental-stages
Makefile
•4•5•12•0•Updated Jan 12, 2024Jan 12, 2024
dicty-phenotype-ontology
Public
Dicty Phenotype Ontology
obofoundry ontology phenotypes
Makefile
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Creative Commons Zero v1.0 Universal
•3•6•2•3•Updated Dec 14, 2023Dec 14, 2023
mouse-anatomy-ontology
Public
Ontologies for mouse anatomy and development
mouse anatomy obofoundry
Makefile
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Other
•3•5•57•3•Updated Nov 14, 2023Nov 14, 2023