Epic: resolve disorder entries missing top-level MONDO disease_term anchors

[cmungall]

Summary

Follow-up from the June 2026 audit of current, non-.history.yaml disorder entries lacking a top-level disease_term.term.id with a MONDO identifier.

This is an anchor-placement / upstream-status tracking epic, not a claim that every listed entry lacks any MONDO-relevant concept. Several entries already have close/related MONDO mappings or upstream requests; the question is whether there is a safe exact top-level disease_term anchor now.

Only one implementation task appears actionable right now: plug in the newly minted RNU12 MONDO ID that is already present in the local dismech OAK/MONDO snapshot.

For the remaining entries, wait for MONDO curator response / upstream term availability or explicit maintainer direction before filing additional MONDO requests or changing disease anchors.

Immediate actionable task

• Update kb/disorders/RNU12-related_Minor_Spliceopathy.yaml to use the newly minted MONDO anchor:
  • MONDO:1060223
  • label: RNU12-related minor spliceopathy disorder
  • verified locally with runoak -i sqlite:obo:mondo info MONDO:1060223 -O obo
• Remove or revise stale notes saying the RNU12 umbrella term is not yet available in MONDO.
• Run validation:
  • just validate kb/disorders/RNU12-related_Minor_Spliceopathy.yaml
  • just validate-references kb/disorders/RNU12-related_Minor_Spliceopathy.yaml
  • just validate-terms-file kb/disorders/RNU12-related_Minor_Spliceopathy.yaml

Upstream / deferred items

These are not immediate dismech edit tasks unless MONDO changes land or maintainers decide otherwise.

Existing MONDO requests or work

• AIP-related pituitary adenoma predisposition

  • Current file: kb/disorders/AIP-related_pituitary_adenoma_predisposition.yaml
  • MONDO NTR open: AIP-related pituitary adenoma predisposition mondo#10131
  • Current local MONDO mappings:
    • MONDO:0007052 / growth hormone secreting pituitary adenoma 1 as skos:closeMatch
    • MONDO:0017824 / familial isolated pituitary adenoma as skos:relatedMatch
  • Important nuance: MONDO:0007052 is not a random GH adenoma term. It carries OMIM:102200, exact synonyms including pituitary adenoma predisposition, autosomal dominant, somatic mutation, and is_a MONDO:0017824 familial isolated pituitary adenoma. OMIM:102200 includes AIP-related PITA1 / PAP / FIPA and explicitly covers non-GH tumor types in the AIP spectrum.
  • Open question: should dismech promote MONDO:0007052 to the top-level disease_term despite its GH-skewed primary label and parentage, or wait for MONDO curators to resolve #10131 by renaming/splitting/adding a more precise AIP-related syndrome anchor?
  • Defer exact disease_term anchor until MONDO curators respond or maintainers explicitly choose the MONDO:0007052 close-match anchor.

• CKD-mineral and bone disorder (CKD-MBD)

  • Current file: kb/disorders/CKD-Mineral_Bone_Disorder.yaml
  • MONDO NTR open: Request term for chronic kidney disease-mineral and bone disorder (CKD-MBD) mondo#10128
  • Related dismech cleanup issue: Tighten CKD-MBD page: distinguish CKD-MBD from renal osteodystrophy and clean up ontology/evidence issues #978
  • Existing MONDO renal osteodystrophy mapping is only a close match to the bone component, not the full CKD-MBD syndrome.
  • Defer exact disease_term anchor until MONDO curators resolve the NTR.

• Green tobacco sickness / nicotine poisoning

  • Current file: kb/disorders/Green_Tobacco_Sickness.yaml
  • MONDO NTR open: Request for new term green tobacco sickness mondo#10054
  • Defer exact disease_term anchor until MONDO curators resolve the NTR.

• MCM9-related gametogenic failure

  • Current file: kb/disorders/MCM9-related_gametogenic_failure.yaml
  • MONDO NTR closed/merged: Request for new term [MCM9 - related gametogenic failure] mondo#10022
  • MONDO PR merged: NT MCM9-related gametogenic failure mondo#10278
  • New term: MONDO:1060226 / MCM9-related gametogenic failure
  • Existing dismech follow-up: Update MCM9-related gametogenic failure to exact Mondo anchor MONDO:1060226 #3324
  • Still blocked as of this audit because local sqlite:obo:mondo does not yet resolve MONDO:1060226. Do not duplicate Update MCM9-related gametogenic failure to exact Mondo anchor MONDO:1060226 #3324.

• FICUS syndrome / PICS-F ambiguity

  • Current file: kb/disorders/FICUS_syndrome.yaml
  • MONDO issue open: Disambiguate current FICUS syndrome entry mondo#9902
  • MONDO PR open: Disambiguate FICUS syndrome with LSM1-prefixed name mondo#9903
  • Important: the existing MONDO FICUS term is the LSM1-related genetic syndrome, not the psychiatric PICS-F / Family ICU Syndrome concept modeled in dismech.
  • Defer any disease anchor change until MONDO curators resolve the disambiguation / scope question.

No relevant open MONDO work found in audit

• Transient neonatal pustular melanosis

  • Current file: kb/disorders/Transient_Neonatal_Pustular_Melanosis.yaml
  • No exact MONDO class found by local OAK, OLS exact MONDO search, or MONDO source-code search.
  • Other terminology coverage exists:
    • NCIT:C116771 — Transient Neonatal Pustular Melanosis
    • SNOMED:239092005 — Transient neonatal pustulosis
    • MedGen / UMLS concept C0406782
  • Possible future direction: add ncit_mappings and/or file a MONDO NTR using NCIT/SNOMED/MedGen support. Do not do this from this epic without maintainer direction.

• Arsenic poisoning

  • Current file: kb/disorders/Arsenic_Poisoning.yaml
  • No relevant MONDO issue/PR found by audit.
  • Defer until there is a MONDO curator response or maintainer direction on whether to request an exact term or use a close/proxy mapping.

• Chemotherapy-induced nausea and vomiting (CINV)

  • Current file: kb/disorders/Chemotherapy_Induced_Nausea_and_Vomiting.yaml
  • No relevant MONDO issue/PR found by audit.
  • Defer until there is a MONDO curator response or maintainer direction.

• Spaceflight associated neuro-ocular syndrome (SANS)

  • Current file: kb/disorders/Spaceflight_Associated_Neuro-Ocular_Syndrome.yaml
  • No relevant MONDO issue/PR found by audit; acronym-only SANS hits were unrelated.
  • Defer until there is a MONDO curator response or maintainer direction.

Acceptance criteria for this epic

• RNU12 is updated to MONDO:1060223 and validates.
• Existing deferred items remain linked here with clear upstream status and mapping nuance.
• No duplicate work is created for MCM9, which is already tracked in Update MCM9-related gametogenic failure to exact Mondo anchor MONDO:1060226 #3324.
• No new MONDO NTRs are filed from this issue unless maintainers explicitly decide that is the next course of action.

Notes

Audit scope was current kb/disorders/*.yaml entries excluding .history.yaml files. The goal is to avoid conflating local dismech work with upstream ontology curation while still keeping the missing-top-level-anchor inventory visible.

[github-actions]

Epic Summary — Upstream Status Audit (2026-06-02)

This comment audits the status of every tracked item in this epic against live upstream state.

---

✅ Immediately Actionable

RNU12-related Minor Spliceopathy → MONDO:1060223

Current file (kb/disorders/RNU12-related_Minor_Spliceopathy.yaml, lines 362–370) has a notes: block stating:

"The broader umbrella is not yet available as a stable MONDO term in the local ontology snapshot, so no disease_term mapping is asserted here."

This note is now stale. The epic correctly identifies that MONDO:1060223 (RNU12-related minor spliceopathy disorder) is verified present in the local sqlite:obo:mondo snapshot. The file has no top-level disease_term block at all — it needs one added, and the stale note revised.

@dragon-ai-agent please update kb/disorders/RNU12-related_Minor_Spliceopathy.yaml:

1. Add a top-level disease_term block with MONDO:1060223 / RNU12-related minor spliceopathy disorder (verify the exact label first with uv run runoak -i sqlite:obo:mondo info MONDO:1060223 -O obo)
2. Remove or revise the notes: paragraph that says the umbrella term is not yet available in MONDO
3. Run validation: just validate kb/disorders/RNU12-related_Minor_Spliceopathy.yaml, just validate-references kb/disorders/RNU12-related_Minor_Spliceopathy.yaml, just validate-terms-file kb/disorders/RNU12-related_Minor_Spliceopathy.yaml
4. Open a PR for this focused change only — do not modify other disorder files

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⏳ Deferred — Open MONDO NTRs (Awaiting Curator Response)

Disorder	MONDO issue	Status	Notes
AIP-related pituitary adenoma predisposition	mondo#10131	🟡 OPEN — 0 comments	Filed 2026-04-07 by @keparis (ClinGen affiliation). No MONDO curator response yet.
CKD-Mineral Bone Disorder	mondo#10128	🟡 OPEN — 0 comments	Filed 2026-04-07 by @cmungall. Proposed definition and parent (MONDO:0029000 poisoning… wait, no — parent renal osteodystrophy as narrower). No response yet. Related dismech cleanup tracked in #978.
Green tobacco sickness	mondo#10054	🟡 OPEN — 1 comment	Filed 2026-03-23 by @sierra-moxon. Last activity 2026-03-30; 1 comment but NTR unresolved.

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🔴 Deferred — MONDO Term Merged But OAK Release Lag

MCM9-related gametogenic failure → MONDO:1060226

• MONDO NTR #10022 CLOSED 2026-05-26 (completed by @sabrinatoro)
• MONDO PR #10278 MERGED 2026-05-26 by @MeeSiing / @sabrinatoro
• Term MONDO:1060226 / MCM9-related gametogenic failure exists upstream in MONDO but NOT YET propagated to the local sqlite:obo:mondo OAK release (verified 2026-05-31 in dismech#3324 — 5 automated scanner comments confirm the gate is still closed)
• Provenance metadata (NTR tracking status, notes about pending state) already cleaned up in merged PR MCM9 gametogenic failure: refresh stale Mondo NTR provenance (#3324) #3331
• Core re-anchor (skos:relatedMatch MONDO:0014520 → skos:exactMatch MONDO:1060226) remains blocked on the next monthly Mondo OBO sqlite build
• Detection command: uv run runoak -i sqlite:obo:mondo info MONDO:1060226 -O obo — non-empty output = unblocked
• Tracked separately in dismech#3324; do not duplicate

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🟠 Deferred — MONDO Disambiguation PR Open

FICUS syndrome

• MONDO issue #9902 OPEN — 7 comments; the original issue (by @cmungall) noted that the existing MONDO:0978296 FICUS syndrome (LSM1-related genetic syndrome) was being conflated with the unrelated Family ICU Syndrome (PICS-F)
• MONDO PR #9903 OPEN — created by @dragon-ai-agent; proposes renaming MONDO:0978296 to LSM1-related facial dysmorphism-impaired intellectual development-cardiovascular-urogenital-skeletal anomalies syndrome, keeping FICUS syndrome as an exact synonym, and explicitly deciding that Family ICU Syndrome falls outside MONDO scope
• PR is awaiting MONDO curator review; dismech disease_term anchor for FICUS_syndrome.yaml cannot be updated until MONDO's canonical label is settled

---

🔵 Deferred — No MONDO Term / NTR Found

Disorder	Status	Possible future path
Transient neonatal pustular melanosis	No MONDO class found. External coverage: NCIT:C116771, SNOMED:239092005, MedGen C0406782	File MONDO NTR using NCIT/SNOMED cross-refs; or add ncit_mappings as an interim measure
Arsenic poisoning	No relevant MONDO issue found	Needs maintainer decision on exact vs. close mapping
Chemotherapy-induced nausea and vomiting (CINV)	No relevant MONDO issue found	Needs maintainer decision
Spaceflight associated neuro-ocular syndrome (SANS)	No relevant MONDO issue found	Needs maintainer decision

---

Summary Table

Item	Upstream state	dismech action
RNU12	MONDO:1060223 ✅ in local OAK	Actionable now — add disease_term, revise notes
MCM9	MONDO:1060226 merged upstream; ❌ not in local OAK	Blocked on OAK release; tracked in #3324
FICUS	MONDO PR #9903 open	Blocked on MONDO PR merge
AIP-pituitary	MONDO NTR open, no response	Blocked on MONDO curators
CKD-MBD	MONDO NTR open, no response	Blocked on MONDO curators
Green tobacco sickness	MONDO NTR open, 1 comment	Blocked on MONDO curators
TNPM, Arsenic, CINV, SANS	No MONDO NTR	Needs maintainer direction

[cmungall]

Clarification from follow-up review: this epic is about entries missing a top-level disease_term.term.id, not necessarily entries with no MONDO-relevant concept anywhere.

AIP-related pituitary adenoma predisposition is the subtle case to keep in view. The current YAML already records:

• MONDO:0007052 / growth hormone secreting pituitary adenoma 1 as skos:closeMatch
• MONDO:0017824 / familial isolated pituitary adenoma as skos:relatedMatch
• upstream NTR: AIP-related pituitary adenoma predisposition mondo#10131

MONDO:0007052 is not just a random GH adenoma term: it carries OMIM:102200, exact synonyms including pituitary adenoma predisposition, autosomal dominant, somatic mutation, and is_a MONDO:0017824 familial isolated pituitary adenoma. OMIM:102200 includes AIP-related pituitary adenoma predisposition / PITA1 / FIPA / PAP and explicitly notes non-GH tumor types as part of the AIP spectrum.

So the unresolved question for AIP is narrower than "no MONDO link exists": should dismech promote MONDO:0007052 to the top-level disease_term despite its GH-skewed primary label and parentage, or wait for MONDO curators to resolve #10131 by renaming/splitting/adding a more precise AIP-related syndrome anchor? For now, keep this deferred pending MONDO curator response or maintainer direction.