OMIM (Online Mendelian Inheritance in Man) is a comprehensive database of human genes and genetic phenotypes, with a particular focus on the molecular relationship between genetic variation and phenotypic expression.
Data is downloaded from OMIM's data portal (requires access key): the morbidmap.txt file which maps diseases to their associated genes.
Each row in morbidmap represents a disease-gene association with a confidence level (1-4) and an optional susceptibility marker {}. These are used to determine the association type and predicate:
| Confidence Level | Susceptibility | Association Type | Predicate |
|---|---|---|---|
| 3 (molecular basis known) | No | CausalGeneToDiseaseAssociation |
biolink:causes |
| 1 or 2 (mapped gene/phenotype) | No | CorrelatedGeneToDiseaseAssociation |
biolink:contributes_to |
| Any | Yes {} |
CorrelatedGeneToDiseaseAssociation |
biolink:contributes_to |
| 4 (chromosomal abnormality) | — | Skipped | — |
Biolink Captured:
-
biolink:CausalGeneToDiseaseAssociation- id (UUID)
- subject (
OMIM:{gene_mim}) - predicate (
biolink:causes) - object (
OMIM:{disease_mim}) - knowledge_level (
not_provided) - agent_type (
not_provided)
-
biolink:CorrelatedGeneToDiseaseAssociation- id (UUID)
- subject (
OMIM:{gene_mim}) - predicate (
biolink:contributes_to) - object (
OMIM:{disease_mim}) - knowledge_level (
not_provided) - agent_type (
not_provided)
Amberger JS, Bocchini CA, Scott AF, Hamosh A. OMIM.org: leveraging knowledge across phenotype-gene relationships. Nucleic Acids Research. 2019;47(D1):D1038-D1043. doi: 10.1093/nar/gky1151. PMID: 30445645
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