Navigating the HPO Website: Hints and Solutions
This page provides the worked solutions for the introductory exercises. Use these to check your work or if you get stuck during the module.
Exercise 1: Solution
To determine the number of genes associated with Pulmonary insufficiency (HP:0010444), the most reliable method is using the Export associations feature.
Answer
At the time of this writing, there were 18 genes associated with Pulmonary insufficiency.
When you download the Excel file, your data should look similar to the screenshot below. Each row represents a unique gene-disease-phenotype relationship.
Exercise 2: Solution
The goal was to determine the "depth" of the term Sutural cataract (HP:0010695) relative to the root term Phenotypic abnormality (HP:0000118).
While you can click through the parents on the HPO website, using the Ontology Lookup Service (OLS) provides a much clearer visual path.
Answer
There are 7 links (or "hops") between Sutural cataract and Phenotypic abnormality. Therefore, we say the depth of this term is 7.
Why Depth Matters
In computational phenotyping, the depth of a term is often used as a proxy for Information Content (IC). Generally, the deeper a term is in the hierarchy, the more specific it is, and the more power it has to help reach a specific diagnosis.
Next Module: Other HPO Browsers