dipper.models.Pathway module

class dipper.models.Pathway.Pathway(graph)

Bases: object

This provides convenience methods to deal with gene and protein collections in the context of pathways.

addComponentToPathway(component_id, pathway_id)

This can be used directly when the component is directly involved in the pathway. If a transforming event is performed on the component first, then the addGeneToPathway should be used instead.

Parameters:

• pathway_id –
• component_id –

Returns:

addGeneToPathway(gene_id, pathway_id)

When adding a gene to a pathway, we create an intermediate ‘gene product’ that is involved in the pathway, through a blank node.

gene_id RO:has_gene_product _gene_product _gene_product RO:involved_in pathway_id

Parameters:

• pathway_id –
• gene_id –

Returns:

addPathway(pathway_id, pathway_label, pathway_type=None, pathway_description=None)

Adds a pathway as a class. If no specific type is specified, it will default to a subclass of “GO:cellular_process” and “PW:pathway”. :param pathway_id: :param pathway_label: :param pathway_type: :param pathway_description: :return:

object_properties = {'gene_product_of': 'RO:0002204', 'has_gene_product': 'RO:0002205', 'involved_in': 'RO:0002331'}

pathway_parts = {'cellular_process': 'GO:0009987', 'gene_product': 'CHEBI:33695', 'pathway': 'PW:0000001', 'signal_transduction': 'GO:0007165'}

properties = {'gene_product_of': 'RO:0002204', 'has_gene_product': 'RO:0002205', 'involved_in': 'RO:0002331'}