obophenotype/upheno

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

Stars: 87
Forks: 21
Open beginner issues: 0
Indexed issues: 282

Dominant language: Jupyter Notebook
License: CC0-1.0
Last GitHub push: Sep 16, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: help wanted
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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282 open issues indexed

GO:0098734 macromolecule depalmitoylation term is being obsoleted Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

obophenotype/upheno#1032 · 1 comment · Opened Aug 11, 2026
Add Abnormal morphology of part of cellular component Open

pattern-request

obophenotype/upheno#1030 · 1 assignee · Opened Jul 17, 2026
review pattern names and text in response to PATO changes Open

pattern

Difficulty 3/5 1-2 days Newbie friendliness 52/100

obophenotype/upheno#1029 · Opened Jul 6, 2026
Abnormal volume of anatomical entity Open

pattern-request

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

obophenotype/upheno#1028 · Opened Jun 15, 2026
Identify patterns that need a normal alternate Open

editors-call help wanted pattern

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

obophenotype/upheno#1027 · 3 comments · Opened Apr 17, 2026
broken pattern link Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 78/100

obophenotype/upheno#1018 · Opened Apr 3, 2026
Grouping classes mix unspecified and directional phenotypes Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

obophenotype/upheno#1015 · Opened Apr 3, 2026
developmental markers in lab rodentshello! Open

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

obophenotype/upheno#1014 · 7 comments · Opened Mar 26, 2026
incorporate new MP-HP mappings Open

obophenotype/upheno#1013 · 1 assignee · Opened Mar 23, 2026
obsolete UPHENO terms using obsolete terms from other ontologies Open

quality control

Difficulty 4/5 3-5 days Newbie friendliness 45/100

obophenotype/upheno#1011 · Opened Mar 20, 2026
large unstained cell number phenotype Open

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

obophenotype/upheno#1010 · 1 comment · Opened Mar 20, 2026
Examples in ReadMe throwing error Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 38/100

obophenotype/upheno#1008 · Opened Feb 2, 2026
misalignment of some UPHENO terms with BFO? Open

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

obophenotype/upheno#1006 · 7 comments · Opened Jan 3, 2026
dilated vs enlarged Open

pattern-request

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

obophenotype/upheno#1002 · 2 comments · Opened Sep 15, 2025
UPHENO_0056750 and UPHENO_0016048 are dangling Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

obophenotype/upheno#1000 · Opened Jul 21, 2025
Congestion pattern? Open

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

obophenotype/upheno#989 · 11 comments · Opened May 15, 2025
Embryonic development-related phenotype terms should be grouped together - UPHENO:0050108, UPHENO:3000001 Open

obophenotype/upheno#988 · 1 assignee · Opened May 13, 2025
Can anatomical entity patterns be used for fungal anatomy? Open

question

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

obophenotype/upheno#987 · 8 comments · Opened May 13, 2025
Zebrafish phenotype neoplasm terms not connected to Upheno neoplasm term Open

obophenotype/upheno#986 · 2 comments · 1 assignee · Opened May 9, 2025
Add more synonyms to patterns Open

enhancement pattern

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

obophenotype/upheno#985 · 1 comment · Opened May 5, 2025
create pattern for abnormal morphology of cellular component in cell type Open

pattern-request

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

obophenotype/upheno#984 · 3 comments · Opened May 5, 2025
Restrict the abnormalLevelOfChemicalEntity pattern to anatomical entities Open

dosdp pattern

obophenotype/upheno#981 · 6 comments · 1 reaction · 1 assignee · Opened Apr 11, 2025
Write a short report with the main outcomes of the uPheno workshop Open

obophenotype/upheno#980 · 3 comments · 1 reaction · 1 assignee · Opened Apr 7, 2025
Incorrect classification of ‘lung morphology phenotype’ in uPheno Open

obophenotype/upheno#979 · 1 comment · 1 assignee · Opened Apr 4, 2025
Integration/classification of mortality/aging phenotypes in uPheno Open

obophenotype/upheno#978 · 1 assignee · Opened Apr 4, 2025
Review cycles in mappings Open

obophenotype/upheno#977 · 9 comments · 1 assignee · Opened Mar 30, 2025
Lost lexical matches and other odditities in uPheno Open

bug

obophenotype/upheno#999 · 4 comments · 2 assignees · Opened Mar 28, 2025
create a version of uPheno_Reordered with SSPOs included Open

obophenotype/upheno#998 · 1 assignee · Opened Feb 21, 2025
examples with same label, similar or identical eq but different placement Open

obophenotype/upheno#975 · 1 assignee · Opened Feb 10, 2025
Add 'Elevated urine biliverdin level HP:0025743' Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

obophenotype/upheno#992 · 5 comments · Opened Jan 28, 2025
cell nucleus phenotype - descendant term labels and defintions Open

obophenotype/upheno#972 · 4 comments · 2 assignees · Opened Jan 13, 2025
placement of fertilization phenotypes under cell nucleus phenotype Open

obophenotype/upheno#971 · 2 comments · 1 assignee · Opened Jan 13, 2025
incomplete organelle organization integration in upheno release 1-12-2025 Open

obophenotype/upheno#970 · 1 assignee · Opened Jan 13, 2025
Ensure that pattern apply to unicellular organisms as well Open

obophenotype/upheno#968 · 1 assignee · Opened Jan 8, 2025
Difficulties in the selection of top-level terms for organ systems Open

obophenotype/upheno#967 · 1 assignee · Opened Dec 18, 2024
Uncovered cardio terms below top-level term `UPHENO:0004507: cardiovascular system phenotype` Open

obophenotype/upheno#966 · 4 comments · 1 assignee · Opened Dec 18, 2024
uPheno integration issues Open

editors-call pattern

Difficulty 5/5 Over a week Newbie friendliness 30/100

obophenotype/upheno#965 · 7 comments · Opened Dec 17, 2024
Create an MP -> OBA mapping Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

obophenotype/upheno#964 · Opened Nov 18, 2024
Documentation: Many stub markdown articles with little or no content Open

documentation

Difficulty 4/5 3-5 days Newbie friendliness 25/100

obophenotype/upheno#954 · 1 comment · Opened Jul 8, 2024
Consider creating all Uberon system level phenotype classes manually for uPheno Open

obophenotype/upheno#949 · 1 reaction · 1 assignee · Opened May 30, 2024
Ensure that all TOP level HPO and MP terms have corresponding uPheno classes Open

obophenotype/upheno#948 · 10 comments · 1 assignee · Opened May 30, 2024
Investigate why "uPheno:circulatory system phenotype" and "uPheno: integumental system phenotype" do not exist.. Open

obophenotype/upheno#947 · 2 comments · 1 assignee · Opened May 30, 2024
CHEBI IDs used by HPO and other phenotype ontologies do not match those used by GO, RHEA, UniProt Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

obophenotype/upheno#946 · 2 comments · Opened May 27, 2024
Some plural labels do not work Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

obophenotype/upheno#943 · 1 comment · Opened Apr 24, 2024
RPPR stats OBA Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

obophenotype/upheno#935 · Opened Mar 28, 2024
Create a uPheno release product for data analysis Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

obophenotype/upheno#932 · 2 comments · Opened Mar 7, 2024
Request new pattern for Incomplete structure Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

obophenotype/upheno#931 · 4 comments · Opened Feb 22, 2024
Failure importing http://purl.obolibrary.org/obo/upheno/upheno_root_alignments.owl Open

obophenotype/upheno#929 · 4 comments · 1 assignee · Opened Feb 5, 2024
Map APO entities to OBA / GO (or whatever else) Open

obophenotype/upheno#928 · 5 comments · 1 assignee · Opened Jan 30, 2024
Map APO modifiers to PATO Open

obophenotype/upheno#927 · 10 comments · 1 assignee · Opened Jan 30, 2024

obophenotype/upheno

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