obophenotype / obophenotype/uberon

State publicly where specimen / sample-type terms belong (organoid, cell culture, PBMC, biopsy)

Open Beginner friendly
#3,766 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Emacs Lisp
Stars
163
Forks
43
Avg merge
1d 17h
Merged PRs (30d)
5

Description

Problem

Single-cell schemas need to describe what kind of material was sampled, not just where it came from. Uberon has essentially none of this vocabulary:

Term sought Matches in uberon-edit.obo
organoid 0
cell culture 0
biopsy 0
explant 0
tissue block 0
peripheral blood mononuclear cell 0
buffy coat 0
bone marrow aspirate 0
whole blood 1

Because nobody owns the join, every schema improvises its own escape hatch. CELLxGENE and scFAIR both carry a tissue_type enum alongside the Uberon term:

tissue_type CELLxGENE datasets
tissue 8,250
organoid 80
primary cell culture 28
cell line 5

scFAIR 7.1.0 is explicit about the consequence: when tissue_type is cell line the tissue_ontology_term_id field takes a Cellosaurus ID, and when it is primary cell culture it takes a CL ID. One field holds three different kinds of entity, disambiguated by a sibling field.

Proposal

Much of this legitimately belongs to OBI (specimen and sampling process) and Cellosaurus (cell lines), not to Uberon. That is a defensible position — but it is not written down anywhere, so downstream schemas keep reinventing the workaround.

Publish a short statement in the Uberon docs saying where each of these belongs, and coordinate with OBI on anything genuinely missing. Deciding and documenting the boundary is worth more here than minting terms.

Why this is actionable now

This is a scope/ownership statement, not a modelling change. It needs no new relations.

Context

Single-cell coverage gap report §6, modernization strategy §3.2.

Possibly related: #2898 (data element harmonization).

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Read §6 of docs/single-cell/gap-report.md and §3.2 of docs/single-cell/modernization-strategy.md, then review the examples in the issue. Document where organoid, culture, biopsy, blood, and related terms belong across Uberon, OBI, and Cellosaurus, and identify anything needing OBI coordination.

Written by the indexing model from the issue text.

Assessment

Domain
documentation
Issue type
Documentation
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Active
Clarity
Mostly clear
Newbie friendliness
68/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.