def _add_component_pathway_association(self, gene_curie, pathway_curie, pathway_label, eco_curie): pathway = Pathway(self.graph) pathway.addPathway(pathway_curie, pathway_label) pathway.addComponentToPathway(gene_curie, pathway_curie) association = Assoc(self.graph, self.name) association.sub = gene_curie association.rel = self.globaltt['involved in'] association.obj = pathway_curie association.set_association_id() association.add_evidence(eco_curie) association.add_association_to_graph()
def _add_component_pathway_association( self, eco_map, component, component_prefix, pathway_id, pathway_prefix, pathway_label, go_ecode): pathway = Pathway(self.graph) pathway_curie = "{}:{}".format(pathway_prefix, pathway_id) gene_curie = "{}:{}".format(component_prefix, component.strip()) eco_curie = eco_map[go_ecode] pathway.addPathway(pathway_curie, pathway_label) pathway.addComponentToPathway(gene_curie, pathway_curie) association = Assoc(self.graph, self.name) association.sub = gene_curie association.rel = pathway.object_properties['involved_in'] association.obj = pathway_curie association.set_association_id() association.add_evidence(eco_curie) association.add_association_to_graph() return
def _add_component_pathway_association( self, eco_map, component, component_prefix, pathway_id, pathway_prefix, pathway_label, go_ecode): pathway = Pathway(self.graph) pathway_curie = "{}:{}".format(pathway_prefix, pathway_id) gene_curie = "{}:{}".format(component_prefix, component.strip()) eco_curie = eco_map[go_ecode] pathway.addPathway(pathway_curie, pathway_label) pathway.addComponentToPathway(gene_curie, pathway_curie) association = Assoc(self.graph, self.name) association.sub = gene_curie association.rel = self.globaltt['involved in'] association.obj = pathway_curie association.set_association_id() association.add_evidence(eco_curie) association.add_association_to_graph() return