pypath.inputs.hmdb.common.raw

pypath.inputs.hmdb.common.raw(dataset: Literal['metabolites', 'proteins'], schema: dict | None = None, head: int | None = None) → list[dict]

Parse data from HMDB XML files.

Parameters:

• dataset – Either “metabolites” or “proteins”.

• schema – The schema defines the fields to be parsed. By default, a schema covering nearly all fields in the HMDB XML is used. Likely you don’t need all the fields within one task: in this case see pypath.inputs.hmdb.METABOLITE_SCHEMA or pypath.inputs.hmdb.PROTEINS_SCHEMA to see the full schema, and create your own that is restricted to your fields of interest.

• head – Process the first N records only. Useful for peeking into the data.

Returns:

A list of dicts, each dict containing the data extracted from one record. These dicts might be deeply nested, and the structure depends on the schema used.