kg_covid_19.transform_utils.intact package¶
Submodules¶
kg_covid_19.transform_utils.intact.intact module¶
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class
kg_covid_19.transform_utils.intact.intact.IntAct(input_dir: str = None, output_dir: str = None)¶ Bases:
kg_covid_19.transform_utils.transform.Transform-
interaction_to_edge(interaction: object, nodes_dict: dict, exp_dict: dict) → list¶
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interactor_to_node(interactor) → List[Union[int, list]]¶
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parse_experiment_info(xmldoc: object) → Dict[int, str]¶ Extract info about experiment from miXML doc
- Parameters
self – IntAct instance
xmldoc – a minidom object containing a miXML doc
- Returns
dictionary with parsed info about experiments (publication, exp type)
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parse_xml_to_nodes_edges(xml_file: str) → dict¶
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participant_experimental_role(participant: object) → str¶
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participant_to_node(participant: object, nodes_dict: dict) → Optional[str]¶
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run(data_file: Optional[str] = None)¶ Method to run transform to ingest data from IntAct for viral/human PPIs
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