Documentation / Phenotype Matching / Using HPO Terms
How HPO Terms Support Phenotype Matching
HPO terms turn observed clinical abnormalities into standardized identifiers. Folklore compares the reviewed positive findings in a patient profile with gene-associated phenotype profiles; the score prioritizes review and does not by itself diagnose a condition or classify a variant.
Record specific observed findings, check automatically extracted terms, and keep absent or negated features out of the positive profile. Qualified professionals remain responsible for the clinical profile and interpretation.
Create a Folklore accountTerms and Relationships
Each HPO concept has an identifier, a preferred name, synonyms, and relationships to broader or more specific concepts. For example, a specific seizure type sits below the broader term "Seizure". These relationships allow clinically related findings to contribute to a match without requiring identical wording.
A specific, observed finding is usually more informative than a broad ancestor term. HPO is a vocabulary for phenotype description, not a diagnosis code and not a substitute for clinical interpretation.
How Terms Enter Folklore
Search by name, synonym, or identifier
The clinical profile search resolves current HPO terms and excludes obsolete entries from suggestions.
Extract findings from free text
Folklore can propose clinical findings from pasted text and map them to HPO. If that path is unavailable, a local ontology-based fallback is used.
Review before analysis
Automatic extraction is an aid, not a final clinical profile. Confirm the concept, specificity, and whether the finding is actually present before accepting it.
Reuse gene associations
Variant Analysis attaches gene-associated HPO profiles to eligible variants. Phenotype Matching compares the patient profile against those annotations.
Negated Findings Need Manual Review
Do not add an absent or explicitly negated feature as a present HPO term. Automatic extraction can miss contextual negation, especially in complex clinical text. Folklore's phenotype score currently evaluates selected positive findings; it does not use absent findings as exclusion evidence.
Data Boundaries
Ontology coverage
Matching is limited to HPO concepts and gene-phenotype associations available to the analysis environment.
Annotation maturity
Recently described genes and phenotypes may have incomplete profiles and can be under-ranked.
Unresolved identifiers
HPO identifiers that cannot be resolved are omitted from the similarity calculation.
Clinical context
Age, onset, severity, and inheritance remain important even when they are not fully represented by the selected terms.
Reference
Kohler S, et al. "The Human Phenotype Ontology in 2024: phenotypes around the world." Nucleic Acids Research. 2024;52(D1):D1333-D1346. PMID: 37953324.
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