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metadata

The vocabulary with which the fit mappings of the models are described.

Every fit mapping of an experiment carries metadata which says what its curve is: the tissue, the route, the application form, the dosing, the fasting, the health of the subjects and what was coadministered. The fits select their data by these values (see pkpdsim.fit.metadata_filter), so a model describes its studies with the same words as the other models:

  • the closed vocabularies are shared, the enums of this module;
  • the open vocabularies (the health of the subjects, the coadministered substances, the genotypes) are the model's own StrEnums, which grow with its studies. Their conventional members are HEALTHY, NONE (nothing coadministered) and NR (not reported), and a member has the same name and value in every model.

A model derives the metadata of its mappings from PKPDMappingMetaData and adds its own fields:

# not executed
@dataclass(kw_only=True)
class HctzMappingMetaData(PKPDMappingMetaData):
    health: Health
    coadministration: Coadministration = Coadministration.NONE

The tables of sbmlsim show the metadata by member name (to_dict); no code reads the values, which are readable text.

Tissue

Bases: StrEnum

The tissue of a measurement.

Route

Bases: StrEnum

The route of the administration of a substance.

Not pkpdutils.Route (ORAL, IV_BOLUS), the route of a dose in the non-compartmental analysis; a module which needs both imports one under an alias.

Dosing

Bases: StrEnum

The dosing of a substance.

Fasting

Bases: StrEnum

The fasting state of the subjects at the administration.

ApplicationForm

Bases: StrEnum

The pharmaceutical form of the administered substance.

DataType

Bases: StrEnum

What the values of a curve are.

PKPDData

Bases: StrEnum

Whether a curve is pharmacokinetic or pharmacodynamic data.

PKPDMappingMetaData dataclass 

PKPDMappingMetaData(
    *,
    tissue,
    route,
    application_form=NR,
    dosing,
    fasting=NR,
)

Bases: MappingMetaData

The metadata of a fit mapping: the facets every model describes.

The metadata describes the curve; what a fit does with it is decided by the filters of the fits. The fields are keyword-only, so a model adds fields without a default after the defaults of this class.

Attributes:

Name Type Description
tissue Tissue

the tissue of the measurement.
route Route

the route of the administration.
application_form ApplicationForm

the pharmaceutical form, not reported by default.
dosing Dosing

the dosing.
fasting Fasting

the fasting state, not reported by default.

to_dict 

to_dict()

Get the metadata by field: the member names of the enums.

Any other value is its string ("None" for None). The order is that of the fields, the fields of this class first.