Phenotype to gene search finds similar phenotypes and diseases across various ontology sources, independent of the underlying vocabulary in each source. If an equivalent concept does not exist across the sources, BaseSpace Variant Interpreter calculates the distance between nodes in the ontological hierarchies and assigns a score from 0–1, where:
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Values closer to 0 indicate that the concepts are more equivalent. A value of 0 indicates that the concepts are the same. |
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Values closer to 1 indicate that the concepts are more dissimilar. A value of 1 indicates that the concepts can only be connected at the root node and are therefore excluded from query results. |
The determination of distance accounts for the fact that sibling concepts on leaf nodes (eg, hypertrophic cardiomyopathy and dilated cardiomyopathy) are more closely related to each other than siblings close to the root (eg, abnormal vascular morphology and abnormal heart morphology).