metakb.transformers.civic#

A module for to transform CIViC.

class metakb.transformers.civic.CivicTransformer(src_data_store, normalizers=None)[source]#

A class for transforming CIViC to the common data model.

async transform(harvested_data_path)[source]#

Transform CIViC evidence and assertions to common data model.

Store result in transformed_data instance variable.

For each statement: * Build its base GKS equivalent :rtype: TransformedData

  • Try to normalize variant, disease, gene(, drug)

  • If they all normalize, also build the aggregate statement, supported by an evidence line to the base statement

class metakb.transformers.civic.MolecularProfileNameComponents(*args, **kwargs)[source]#

Define components for molecular profile name

__init__(*args, **kwargs)[source]#
c_change: Optional[str][source]#
gene: str[source]#
p_change: Optional[str][source]#