MONDO-DOID 12K: Disease Ontology Entity Alignment Benchmark

MONDO-DOID Entity Alignment 12K is a biomedical benchmark for aligning disease entities between the Mondo Disease Ontology (MONDO) and the Human Disease Ontology (DOID). It contains 12,000 manually curated exact-match mappings distributed by MONDO in SSSOM format. The dataset was created by vaibhavalakshmiravideshik and was last updated on 2026-05-29.

Use Cases

• Benchmarking entity alignment models based on manually curated disease mappings.
• Training models for realistic ontology matching tasks beyond simple dictionary lookups.
• Evaluating the performance of knowledge graph integration techniques on biomedical ontologies.
• Researching semantic interoperability between the MONDO and DOID disease classification systems.

Strengths

• Contains 12,000 manually curated exact-match mappings between two major disease ontologies.
• Uses a standard SSSOM format for representing mappings, which suggests interoperability.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Last updated 2026-05-29 21:42:56; freshness should be verified.

Provenance

Source

Mappings are distributed by the Mondo Disease Ontology (MONDO).

Collection Method

Manually curated exact-match mappings.

Freshness

Last updated 2026-05-29 21:42:56.