Choosing a column mapper
pyphetools defines several ColumnMapper's that map the contents of a specific column to HPO annotations. In addition, there are AgeMapper, SexMapper, and VariantMapper classes that help to ingest this type of data but are not covered here.
To choose a ColumnMapper for a specific column, see the following table. Detailed documentation about each mapper is linked.
| Column Mapper | Scope |
|---|---|
| Simple column mapper | A column describes a single abnormality (HPO term) and contains symbols that represent observed, excluded, and not measured/not available |
| Constant column mapper | A column for which all individuals (i.e., all rows) have a given HPO term (or the exclusion of the term) |
| Option column mapper | A column that contains several phentypic abnormalities, usually all in one organ system. |
| Threshold column mapper | A column that contains a number that implies an abnormality (HPO term) if the number is above (or below) a given threshold. |
It is advisable to review several notebooks in the Phenopacket-Store project to get a feeling for how and when to use the various mappers.