Poster ID
P-03
Poster Title
Mondo as the Integrative Interface for Genetic-Disease Knowledge: An OMIM Cross-Validation Use Case Toward ICD-11
Authors
Xiaohan Tanner Zhang1, Ada Hamosh1,Nicolas Matentzoglu2 Christopher J Mungall3, Sabrina Toro4 Melissa A. Haendel4
1 Johns Hopkins University, US
2 Semanticly Ltd, UK
3 Lawrence Berkeley National Laboratory, US
4 University of North Carolina at Chapel Hill, US
1 Johns Hopkins University, US
2 Semanticly Ltd, UK
3 Lawrence Berkeley National Laboratory, US
4 University of North Carolina at Chapel Hill, US
Abstract
Background. Authoritative disease knowledge is fragmented across independently curated resources, limiting reuse in genomic medicine. Mondo (Monarch Initiative, a GA4GH Driver Project) - the first resource recognised under GA4GH's endorsement programme for externally developed standards (2026) - unifies many curated sources through explicit, provenanced cross-references, so users reach and cross-validate each authority through one interoperable interface rather than replacing it. We use OMIM - the comprehensive, authoritative compendium of human genes and Mendelian phenotypes, expert-curated from the primary literature since 1966 and depended on across genomics - as the demonstrator, quantifying how faithfully Mondo integrates it and how far that knowledge reaches WHO ICD-11.
Methods. Using only formal cross-references (oboInOwl:hasDbXref, OMIM to Mondo; skos:exactMatch, Mondo to ICD-11) from the June 2026 Mondo release and the OMIM API, we classified all 6,921 OMIM molecularized phenotypes (molecular basis known) as DELIVERED (reaching ICD-11), READY (in Mondo, not yet ICD-11), or UNBRIDGED (OMIM only). Only derived aggregate statistics are reported; IDs verified against sources.
Results. Mondo represents 98.7% of OMIM's molecularized phenotypes (6,833/6,921) while faithfully preserving OMIM's curation: every mapped OMIM entry aligns to a single Mondo class (no erroneous splits) and 99.1% of Mondo classes map to one OMIM entry. Alignment is by identity, not absorption - Mondo aligns identity and adds computable logic for a third of entries, while OMIM's clinical descriptions, allelic variants, and literature remain in OMIM by design. The 88 outside Mondo (1.3%) are non-disease entities (blood groups, QTLs, susceptibility loci), correctly excluded. Onward, 734 (10.6%) reach ICD-11; 6,099 are READY (1,827 machine-actionable) across 354 expert-curated phenotypic series prioritized for delivery.
Significance. National efforts already build on this pattern: the Monarch-US CDC collaboration is bringing Mondo into ICD-10-CM, and ClinGen requires Mondo IDs to name diseases in curation. The same source-to-Mondo-to-classification route yields a roadmap of 6,099 READY diseases for WHO ICD-11, giving initiatives one GA4GH-endorsed interface to that knowledge. OMIM remains the definitive authority for Mendelian disease; Mondo makes that knowledge findable, computable, and deliverable at global scale without replacing or altering it.
Methods. Using only formal cross-references (oboInOwl:hasDbXref, OMIM to Mondo; skos:exactMatch, Mondo to ICD-11) from the June 2026 Mondo release and the OMIM API, we classified all 6,921 OMIM molecularized phenotypes (molecular basis known) as DELIVERED (reaching ICD-11), READY (in Mondo, not yet ICD-11), or UNBRIDGED (OMIM only). Only derived aggregate statistics are reported; IDs verified against sources.
Results. Mondo represents 98.7% of OMIM's molecularized phenotypes (6,833/6,921) while faithfully preserving OMIM's curation: every mapped OMIM entry aligns to a single Mondo class (no erroneous splits) and 99.1% of Mondo classes map to one OMIM entry. Alignment is by identity, not absorption - Mondo aligns identity and adds computable logic for a third of entries, while OMIM's clinical descriptions, allelic variants, and literature remain in OMIM by design. The 88 outside Mondo (1.3%) are non-disease entities (blood groups, QTLs, susceptibility loci), correctly excluded. Onward, 734 (10.6%) reach ICD-11; 6,099 are READY (1,827 machine-actionable) across 354 expert-curated phenotypic series prioritized for delivery.
Significance. National efforts already build on this pattern: the Monarch-US CDC collaboration is bringing Mondo into ICD-10-CM, and ClinGen requires Mondo IDs to name diseases in curation. The same source-to-Mondo-to-classification route yields a roadmap of 6,099 READY diseases for WHO ICD-11, giving initiatives one GA4GH-endorsed interface to that knowledge. OMIM remains the definitive authority for Mendelian disease; Mondo makes that knowledge findable, computable, and deliverable at global scale without replacing or altering it.