Rare Disease ICD Coverage Gaps (MONDO)

Overview

Catalog rare MONDO diseases that lack ICD mappings, with priority on missing ICD-11 Foundation (icd11f / icd11.foundation) mappings.

Scope and Method

• Source ontology cache: sqlite:obo:mondo (~/.data/oaklib/mondo.db)
• Independent target vocabulary: sqlite:obo:icd11f (~/.data/oaklib/icd11f.db)
• Rare disease set: terms with oio:inSubset = obo:mondo#rare
• Exclusions: deprecated MONDO terms
• ICD-11 Foundation coverage check: oio:hasDbXref values matching icd11.foundation:% or icd11f:%
• Any-ICD coverage check: xrefs matching icd11.foundation:%, icd11f:%, ICD10CM:%, ICD10WHO:%, or ICD9:%
• Independent search candidates: exact normalized MONDO label + hasExactSynonym matches against ICD-11F rdfs:label

Catalog Artifacts

Added Columns for Review

• Metadata: definition, ordo_mappings, orphanet_mappings, omim_mappings, omimps_mappings
• MONDO mapping status: has_icd11f, icd11f_xrefs, has_any_icd, any_icd_xrefs
• Independent candidate search: independent_candidate_icd11f_*
• Manual tracking flags in review queues:
• search_status (NOT_REVIEWED, IN_PROGRESS, MATCH_CONFIRMED, NO_MATCH_CONFIRMED)
• search_method, search_date, searched_by
• selected_icd11f_id, selected_icd11f_label, search_confidence, search_notes

Regeneration

• Run: scripts/generate_rare_disease_no_icd_catalog.py
• The generator preserves existing manual review fields when rerun.
• In this MONDO cache snapshot, ORDO:* xrefs are absent; use orphanet_mappings as the practical ORDO-adjacent mapping field.

Summary Counts

• Active MONDO rare terms analyzed: 15,938
• With ICD-11 Foundation mapping: 3,356
• Without ICD-11 Foundation mapping: 12,582
• With any ICD mapping (ICD11F/ICD10/ICD9): 4,846
• Without any ICD mapping: 11,092

STATUS

Baseline Catalog Build (5/5) ✓

• [x] Identified active MONDO rare term universe
• [x] Computed ICD-11 Foundation coverage for all terms
• [x] Computed any-ICD coverage for all terms
• [x] Added definition, ORDO, and OMIM mapping columns
• [x] Exported full and filtered CSV catalogs with manual search-status fields under projects/RARE_DISEASE_NO_ICD_CODE/

Next Pass Curation (0/3)

• [ ] Triage rare_without_icd11f_but_with_other_icd.csv for ICD11F bridge candidates
• [ ] Partition rare_without_any_icd.csv by MONDO superclasses for batch review
• [ ] Add automated refresh workflow so counts track MONDO releases

NOTES

2026-02-20

• Initialized project RARE_DISEASE_NO_ICD_CODE.
• Built baseline catalog from local MONDO SQLite cache.
• Generated full dataset plus ICD-gap subsets for project tracking and downstream curation.
• Added independent ICD-11F candidate search (exact normalized MONDO label/synonym match against ICD11F labels).
• Added per-term review status fields so each disease can be manually searched and tracked.
• Added reproducible generator: scripts/generate_rare_disease_no_icd_catalog.py.