Documentation / Phenotype Matching / HPO Term Selection Guide
HPO Term Selection Guide
A focused, accurate patient phenotype is more useful than a long list of uncertain or repetitive terms. Select findings that are present, clinically meaningful, and as specific as the available evidence supports.
Selection Principles
Record observed findings
Use findings documented in the patient rather than suspected diagnoses or features copied from a candidate syndrome.
Choose the most specific supported term
Prefer a specific seizure type, structural finding, or biochemical abnormality when the record supports it. Do not infer detail that was not observed.
Cover the whole presentation
Include relevant findings across organ systems, not only the referral complaint. The combination is often more discriminating than any single feature.
Avoid parent-child duplication
If a specific child term fully represents a finding, usually omit its broad ancestor so one feature is not counted twice.
Keep absent findings separate
Do not select a negated feature as present. Negative phenotypes are not currently used as exclusion evidence in the similarity score.
Useful Clinical Detail
Onset and course
Use onset- or progression-specific HPO concepts when those concepts exist and are documented.
Morphology and anatomy
Prefer the precise structural or imaging finding over a broad organ-system abnormality.
Laboratory phenotype
A specific metabolite, enzyme, hematologic, or biochemical abnormality may be more informative than a general symptom.
Neurodevelopment
Capture the affected domain, seizure type, tone, behavior, imaging, and developmental trajectory where observed.
Multisystem findings
Include secondary organ-system features that help distinguish syndromic from isolated disease.
Age-appropriate absence
Do not add a feature that cannot yet be assessed because of the patient's age as though it were present or absent.
Using Folklore's Input Tools
HPO Search
Search by clinical wording, synonym, or HPO identifier. Review the preferred name and choose the most specific current concept supported by the record.
Free-Text Extraction
Paste relevant clinical text to obtain proposed terms, then review every proposal. Confirm the mapping, remove duplicates and generic findings, and check negation manually before analysis.
Pre-Run Checklist
Every selected term describes a finding that is present in this patient.
The term is as specific as the clinical evidence allows.
Broad ancestors and duplicate synonyms have been removed.
Important findings outside the primary organ system are included.
Automatically extracted terms and possible negation have been reviewed.
Refine and Re-Run
Phenotype matching can be repeated after the clinical profile changes. Re-run when new findings are confirmed or when a corrected term set materially changes the patient phenotype used for prioritization.