Setting HPO Terms

What Are HPO Terms

The Human Phenotype Ontology (HPO) is a standardized clinical vocabulary for phenotypic abnormalities observed in human disease. It contains over 17,000 terms organized in a hierarchical structure where specific terms (such as "Focal clonic seizure", HP:0002266) are children of broader terms (such as "Seizure", HP:0001250). Using standardized HPO terms enables computational comparison across patients, diseases, and databases.

Why HPO Terms Matter

Providing HPO terms enables three platform features that significantly improve the clinical relevance of results. First, the PP4 ACMG criterion activates when patient phenotype matches a gene with a known disease association, adding supporting pathogenic evidence. Second, the Phenotype Matching service scores every candidate gene against the patient's presentation, producing a 0-100 similarity score and clinical tier assignment. Third, the Screening service uses phenotype correlation to boost prioritization of variants in phenotype-relevant genes.

Selecting HPO Terms

Be specific. "Seizure" (HP:0001250) provides more discrimination than "Abnormality of the nervous system" (HP:0012638). Include findings from all affected organ systems, not just the primary complaint. Negative findings with clinical significance should also be included -- the platform handles negation. Five to fifteen specific terms is optimal for most cases.

The platform provides two input methods: manual HPO term search and selection with real-time autocomplete, and free-text clinical description where the platform automatically extracts HPO terms using ontology matching with negation detection.

HPO Term Selection by Clinical Domain