phenopacket_mapper.data_standards.code_system module

class phenopacket_mapper.data_standards.code_system.CodeSystem(name: str, namespace_prefix: str, url: str = None, iri_prefix: str = None, version: str = '0.0.0', synonyms: ~typing.List[str] = <factory>)[source]

Bases: object

Data class for a CodeSystem

A CodeSystem is a resource that defines a set of codes and their meanings. It could be a terminology, an ontology, a nomenclature, etc. Popular examples include SNOMED CT, HPO, MONDO, OMIM, ORDO, LOINC, etc.

This class is necessary to fill the resources parameter in the Phenopacket later.

Variables:

  • name – The name of the CodeSystem

  • namespace_prefix – The namespace prefix of the CodeSystem

  • url – The URL of the CodeSystem

  • iri_prefix – The IRI prefix of the CodeSystem

  • version – The version of the CodeSystem

name: str
namespace_prefix: str
url: str
iri_prefix: str
version: str

List typical alternative abbreviations or names for the resource, to better parse its usage (e.g. ‘HPO’ for the Human Phenotype Ontology, even if its name space prefix is commonly ‘HP’)

synonyms: List[str]
set_version(value) → CodeSystem[source]