obophenotype / obophenotype/uberon

Completing HRA branches

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new term request
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Emacs Lisp
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Avg merge
1d 17h
Merged PRs (30d)
5

Description

Progress report:

Status: HRA / bulk-NTR PRs from @zhengj2007 — layout compliance & blockers

Tracking issue for the batch of open HRA / bulk-NTR PRs from @zhengj2007 (plus the reference muscular PR). Assesses each against the agreed rules and captures blockers.

Agreed rules (from prior review)

  1. Large batches → ROBOT template registered as an ODK component (components/*.owl + uberon-odk.yaml + Makefile + catalog). Tooling/instructions on main (bulk_ntr_workflow/CLAUDE.md Stage 5, register_templates.py).
  2. Small additions → added by hand (or via a local template) directly into uberon-edit.obo; no ODK component.
  3. Reports must NOT live under src/templates/. Canonical location is bulk_ntr_workflow/outputs/<name>-reports/.

⚠️ Root-cause finding

The corrected "reports → bulk_ntr_workflow/outputs/<name>-reports/" instruction currently lives only on the muscular branch (add-hra-muscular-ntr, PR #3700), not on master. Master's bulk_ntr_workflow/CLAUDE.md/README.md still direct reports to src/templates/<name>-reports/. Every @zhengj2007 PR below branched off master, so they all followed the old layout. Merging the corrected docs to master (or cherry-picking them) is the key unblock.

Reference exemplar

  • #3700 — muscular (@dosumis): the model layout. Reports under bulk_ntr_workflow/outputs/hra-muscular-reports/; templates clean under src/templates/; fully ODK-registered. Also carries the corrected docs.

Status of @zhengj2007 PRs

On the right track (ODK-registered)
PR Terms State Notes
#3715 fallopian tube 58 CI green, blocked on review Fully ODK-registered (best zhengj2007 example). Reports relocated to bulk_ntr_workflow/outputs/.
#3714 capillary 31 CI failing Registration attempted (odk.yaml + import), but build breakage. Also 2 sparse defs + 1 generic parent flagged.
Small addition, correctly hand-edited
PR Terms State Notes
#3713 eye 2 1 CI failure Converted to 2 stanzas in uberon-edit.obo per review. Remaining failure = leftover import: …/hra_eye.owl line.
Not yet converted — old layout (unregistered templates; reports being relocated)

None of these touch uberon-odk.yaml/Makefile/catalog, so nothing actually enters the ontology; CI is "green" only because the build ignores them.

PR Terms Suggested route
#3717 kidney 2 hand-edit into -edit.obo (kidney "papillary tip epithelium" still needs a real PMID)
#3716 intestine/liver/skin 4 hand-edit
#3719 palatine-tonsil 7 hand-edit (borderline)
#3712 brain 12 ODK-register — also: @RiveraAndrea83 asked to drop ifs1-4 and weak transition-zone terms
#3720 small-intestine — ODK-register
#3721 placenta — ODK-register
#3722 spleen — ODK-register
#3723 uterus — ODK-register
#3718 lymph 41 ODK-register (largest batch)
Separate concern
PR Notes
#3704 added_by_HRA annotations (163 terms) Direct -edit.obo edit; 3 CI failures — needs diagnosis, independent of the layout question.

Blockers summary

  1. Corrected reports-location docs not on master (only on #3700) — merge/cherry-pick to unblock.
  2. 9 PRs still use the pre-instruction layout and need rework: small → hand-edit; large → ODK-register.
  3. CI red: #3714 (registration build), #3713 (stray import), #3704 (annotations).
  4. Curator judgment needed: #3712 brain term pruning.
  5. All PRs are MERGEABLE but BLOCKED on review approval; most past the 1-week-inactivity threshold for author self-merge.

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

Start with bulk_ntr_workflow/CLAUDE.md and README.md on master, then compare the corrected instructions and layout in PR #3700. Review the listed PRs, their CI failures, and the relevant uberon-edit.obo, uberon-odk.yaml, Makefile, and catalog changes. Done means the affected branches follow the agreed route and their blockers are resolved.

Written by the indexing model from the issue text.

Assessment

Domain
build-system, documentation, tooling
Issue type
Refactor
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Needs clarification
Newbie friendliness
28/100

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