Documentation / Phenotype Matching / Semantic Similarity
HPO Semantic Similarity
Folklore compares HPO concepts through their position in the ontology rather than by label alone. It uses the established Lin similarity measure with information content derived from OMIM disease annotations.
From Individual Terms to One Score
Resolve the selected patient HPO identifiers and the HPO profile associated with the variant gene.
For each valid patient term, compare it with every valid term in the gene profile.
Keep the strongest semantic match for that patient term.
Average those patient-term matches and convert the result to a 0-100 phenotype match score.
Why Specific Terms Matter
Information content reflects how informative a term is in disease annotations. A broad finding shared by many disorders contributes less discrimination than a specific finding associated with a smaller set of disorders. Exact term matches receive the highest individual similarity, while closely related terms can still score strongly through a shared informative ancestor.
The Comparison Is Directional
The final score asks how well the gene profile explains each selected patient term. Extra phenotypes in the gene profile are not penalized. By contrast, an additional patient term with no close match can lower the average. This is why confirmed, relevant term selection matters.
How to Read the Output
Phenotype match score
A 0-100 semantic similarity summary for the patient-to-gene comparison.
Individual matches
The strongest gene-profile match for every valid patient HPO term.
Matched-term count
The number of individual term similarities above the service threshold.
Unresolved terms
Identifiers that are not present in the loaded ontology do not contribute to the average.
Limitations
Absent or negated findings are not used as negative evidence in the similarity score.
Redundant parent and child terms can over-represent one clinical feature because each selected patient term contributes to the average.
A low score can reflect incomplete gene annotation or an atypical presentation, not only biological irrelevance.