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obophenotype

13 indexed repositories · View on GitHub

human-phenotype-ontology
Ontology for the description of human clinical features

Makefile · 373 stars
cell-ontology
An ontology of cell types

Makefile · 212 stars
uberon
An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology

Emacs Lisp · 163 stars
upheno
The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.

Jupyter Notebook · 87 stars
ncbitaxon
Build for NCBITaxon

Python · 31 stars
bio-attribute-ontology
source files for OBA (Ontology of Biological Attributes)

Jupyter Notebook · 31 stars
biological-spatial-ontology
An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces

Makefile · 13 stars
hpo-translations
This repo will contain the Human Phenotype Ontology language profiles

Makefile · 9 stars
chiro
CHEBI Integrated Role Ontology

Makefile · 6 stars
porifera-ontology
An ontology covering the anatomy of Porifera (sponges)

Vue · 6 stars
planaria-ontology
PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea.

Makefile · 6 stars
developmental-mouse-anatomy-ontology
Ontologies for mouse anatomy and development

Makefile · 5 stars
chebi_obo_slim
A slimmed down version of CHEBI sufficient to cover 99% of the term needs across OBO ontologies

Makefile · 4 stars

Beginner friendly Everything

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[Fix] UBERON:0003351 'pharyngeal epithelium' is chordate-restricted but generically labelled Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

obophenotype/uberon#3776 · Opened Sep 18, 2026
[NTR] cloaca outside Vertebrata, or generalise UBERON:0000162 Open

new term request

Difficulty 5/5 Over a week Newbie friendliness 42/100

obophenotype/uberon#3775 · Opened Sep 18, 2026
[NTR] respiratory tree (Holothuroidea) Open

new term request

Difficulty 3/5 1-2 days Newbie friendliness 70/100

obophenotype/uberon#3774 · Opened Sep 18, 2026
11 definitions in the 2026-06-19 release promise a `part_of` the axioms do not state, and 21 HPO phenotype definitions rest on those terms, and 20 automatic definitions place a metapodial element inside a digit the axioms declare disjoint from it Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

obophenotype/uberon#3773 · Opened Sep 18, 2026
Hypoplastic facial nerve Open

new term request

obophenotype/human-phenotype-ontology#11771 · 1 assignee · Opened Sep 17, 2026
Term Request: Corneal ectasia Open

new term request

obophenotype/human-phenotype-ontology#11770 · 1 assignee · Opened Sep 17, 2026
bone nose Open

textual definition

obophenotype/human-phenotype-ontology#11769 · 1 assignee · Opened Sep 16, 2026
Term Request: Cellular deposits on intraocular lens Open

new term request

obophenotype/human-phenotype-ontology#11768 · 1 assignee · Opened Sep 16, 2026
asymptomatic elevated creatine kinase Open

new term request

obophenotype/human-phenotype-ontology#11767 · 1 assignee · Opened Sep 16, 2026
Term Request: Corneal graft suture complication Open

new term request

obophenotype/human-phenotype-ontology#11766 · 1 assignee · Opened Sep 16, 2026
Term Request: Corneal graft failure Open

new term request

obophenotype/human-phenotype-ontology#11765 · 1 assignee · Opened Sep 16, 2026
Term Request: Descemet membrane endothelial keratoplasty graft detachment Open

new term request

obophenotype/human-phenotype-ontology#11764 · 1 assignee · Opened Sep 16, 2026
Term Request: Corneal graft rejection Open

new term request

obophenotype/human-phenotype-ontology#11763 · 1 assignee · Opened Sep 16, 2026
Term Request: Corneal endothelial pigment deposits Open

new term request

obophenotype/human-phenotype-ontology#11762 · 1 assignee · Opened Sep 16, 2026
Term Request: Dendritic keratitis Open

new term request

obophenotype/human-phenotype-ontology#11761 · 1 assignee · Opened Sep 16, 2026
Herpetic skin vesicle Open

new term request

obophenotype/human-phenotype-ontology#11760 · 1 assignee · Opened Sep 16, 2026
Update crustacea references to pancrustacea Open

Difficulty 2/5 1-3 hours Newbie friendliness 75/100

obophenotype/uberon#3771 · 3 comments · Opened Sep 15, 2026
new term request: hemiplegic migraine Open

new term request

obophenotype/human-phenotype-ontology#11759 · 1 assignee · Opened Sep 15, 2026
Missing has_part relations to CL: systematic scan of term definitions (33 evidence-backed candidates) Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

obophenotype/uberon#3769 · Opened Sep 14, 2026
Term Request: Filamentary keratitis Open

new term request

obophenotype/human-phenotype-ontology#11758 · 1 assignee · Opened Sep 14, 2026
Term Request: Hutchinson sign of herpes zoster Open

new term request

obophenotype/human-phenotype-ontology#11757 · 1 assignee · Opened Sep 13, 2026
"thigh" may not be an appropriate exact synonym of `hindlimb stylopod` Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

obophenotype/uberon#3768 · 5 comments · Opened Sep 11, 2026
Definitions vs axioms in the 2026-06-19 release: a tooth both inside the head and disjoint from it, three terms whose definition and axiom disagree, and 12 candidate `part_of` axioms Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

obophenotype/uberon#3767 · 1 comment · Opened Sep 11, 2026
[Bug] chromaffin cell (CL:0000166) is inferred to be a neuron via the neuroendocrine cell equivalence, and inherits a hidden develops_from restriction Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 48/100

obophenotype/cell-ontology#3741 · Opened Sep 10, 2026
[Bug] Hidden GCI: epithelial cell of thyroid gland (CL:0002257) gives parafollicular cell an endodermal origin, contradicting its neural crest derivation Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 68/100

obophenotype/cell-ontology#3740 · Opened Sep 10, 2026
[Bug] Hidden GCI: lamp5 GABAergic interneuron (CL:4023011) puts a caudal ganglionic eminence origin on the MGE-derived Lamp5 Lhx6 neuron Open

bug

obophenotype/cell-ontology#3739 · 1 assignee · Opened Sep 10, 2026
Term Request: Marginal keratitis Open

new term request

obophenotype/human-phenotype-ontology#11756 · 1 assignee · Opened Sep 10, 2026
Peripheral retinal degeneration is not Progressive loss of peripheral retinal pigment epithelium... Open

textual definition

obophenotype/human-phenotype-ontology#11755 · 1 assignee · Opened Sep 9, 2026
Term Request: Beaten metal appearance of corneal endothelium Open

new term request

obophenotype/human-phenotype-ontology#11754 · 1 assignee · Opened Sep 8, 2026
Term Request: Moon crater-like corneal endothelial lesions Open

new term request

obophenotype/human-phenotype-ontology#11753 · 1 assignee · Opened Sep 8, 2026
Term Request: Railroad-track corneal endothelial bands Open

new term request

obophenotype/human-phenotype-ontology#11752 · 1 assignee · Opened Sep 8, 2026
Term Request: Vesicular lesions of corneal endothelium Open

new term request

obophenotype/human-phenotype-ontology#11751 · 1 assignee · Opened Sep 8, 2026
Term Request: Panstromal corneal lipid haze Open

new term request

obophenotype/human-phenotype-ontology#11750 · 1 assignee · Opened Sep 8, 2026
Term Request: Polychromatic pre-Descemet corneal opacities Open

new term request

obophenotype/human-phenotype-ontology#11749 · 1 assignee · Opened Sep 8, 2026
Term Request: Sheet-like posterior corneal stromal opacities Open

new term request

obophenotype/human-phenotype-ontology#11748 · 1 assignee · Opened Sep 8, 2026
Term Request: Dandruff-like corneal stromal flecks Open

new term request

obophenotype/human-phenotype-ontology#11747 · 1 assignee · Opened Sep 8, 2026
Term Request: Spiky corneal stromal opacities Open

new term request

obophenotype/human-phenotype-ontology#11746 · 1 assignee · Opened Sep 8, 2026
Term Request: Granular corneal stromal deposits Open

new term request

obophenotype/human-phenotype-ontology#11745 · 1 assignee · Opened Sep 8, 2026
Term Request: Corneal lattice lines Open

new term request

obophenotype/human-phenotype-ontology#11744 · 1 assignee · Opened Sep 8, 2026
Term Request: Mulberry-like corneal subepithelial deposits Open

new term request

obophenotype/human-phenotype-ontology#11743 · 1 assignee · Opened Sep 8, 2026
Term Request: Sawtooth pattern of Bowman layer Open

new term request

obophenotype/human-phenotype-ontology#11742 · 1 assignee · Opened Sep 8, 2026
Term Request: Honeycomb-shaped subepithelial corneal opacities Open

new term request

obophenotype/human-phenotype-ontology#11741 · 1 assignee · Opened Sep 8, 2026
Term Request: Corneal epithelial microcysts Open

new term request

obophenotype/human-phenotype-ontology#11740 · 1 assignee · Opened Sep 8, 2026
State publicly where specimen / sample-type terms belong (organoid, cell culture, PBMC, biopsy) Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

obophenotype/uberon#3766 · Opened Sep 7, 2026
Track Uberon/CL single-cell coverage as a recurring report Open

Difficulty 3/5 1-2 days Newbie friendliness 72/100

obophenotype/uberon#3765 · Opened Sep 7, 2026
Create a single-cell sampling-site subset from observed usage Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

obophenotype/uberon#3764 · Opened Sep 7, 2026
CL_0020059 serous demilune cell of salivary gland → every salivary serous cell becomes a demilune cell Open

Difficulty 3/5 1-2 days Newbie friendliness 15/100

obophenotype/cell-ontology#3728 · Opened Sep 7, 2026
Kernicterus = Chronic bilirubin encephalopathy Open

synonyms

obophenotype/human-phenotype-ontology#11739 · 1 assignee · Opened Sep 7, 2026
Term Request: Fingerprint-like corneal lines Open

new term request

obophenotype/human-phenotype-ontology#11738 · 1 assignee · Opened Sep 7, 2026
Term Request: Map-like corneal epithelial opacities Open

new term request

obophenotype/human-phenotype-ontology#11737 · 1 assignee · Opened Sep 7, 2026

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