if not input_genes: raise RuntimeError("GeneToTissueBiclusters ERROR: missing mandatory input_genes parameter") input_gene_set = self.get_simple_input_identifier_list(input_genes) most_common_tissues = asyncio.run(self.module.gene_to_tissue_biclusters_async(input_gene_set)) self.results = pd.DataFrame.from_records(most_common_tissues) GeneToTissueBiclusters.set_metadata( ModuleMetaData( name="Mod9A - Gene-to-Tissue Bicluster", source='RNAseqDB Biclustering', association=GeneToExpressionSiteAssociation, domain=ConceptSpace(Gene, ['ENSEMBL']), relationship='related_to', range=ConceptSpace(AnatomicalEntity, ['MONDO', 'DOID', 'UBERON']), ) ) def metadata(): """ Retrieve Module Metadata """ return GeneToTissueBiclusters.get_metadata() def main(): fire.Fire(GeneToTissueBiclusters)
if not input_diseases: raise RuntimeError("DiseaseToPhenotypeBiclusters ERROR: missing mandatory input_diseases parameter") input_disease_ids = self.get_simple_input_identifier_list(input_diseases) most_common_phenotype = asyncio.run(self.module.disease_to_phenotype_biclusters_async(input_disease_ids)) self.results = pd.DataFrame.from_records(most_common_phenotype, columns=["hit_id", "score"]) DiseaseToPhenotypeBiclusters.set_metadata( ModuleMetaData( name="Mod2.0 - Disease Associated Genes", source='RNAseqDB Biclustering', association=DiseaseToPhenotypicFeatureAssociation, domain=ConceptSpace(Disease, ['MONDO']), relationship='has_phenotype', range=ConceptSpace(PhenotypicFeature, ['HP']), ) ) def metadata(): """ Retrieve Module Metadata """ return DiseaseToPhenotypeBiclusters.get_metadata() def main(): fire.Fire(DiseaseToPhenotypeBiclusters)
input_gene_set = self.get_simple_input_identifier_list(input_genes) asyncio.run(self.module.gene_to_gene_biclusters_async(input_gene_set)) sorted_list_of_output_genes = self.module.gene_to_gene_bicluster_summarize( input_gene_set, keep_input_id) self.results = pd.DataFrame.from_records(sorted_list_of_output_genes) GeneToGeneDepMapBiclusters.set_metadata( ModuleMetaData(name="Mod9B - Gene-to-Gene Bicluster", source='DepMap Biclustering', association=GeneToGeneAssociation, domain=ConceptSpace(Gene, ['NCBI']), relationship='related_to', range=ConceptSpace(Gene, ['NCBI']))) def metadata(): """ Retrieve Module Metadata """ return GeneToGeneDepMapBiclusters.get_metadata() def main(): fire.Fire(GeneToGeneDepMapBiclusters)
disease_identifier, disease_label, query_biolink) if not self.results.empty: self.disease_associated_genes = self.results[[ 'hit_id', 'hit_symbol' ]].to_dict(orient='records') else: self.disease_associated_genes = [] DiseaseAssociatedGeneSet.set_metadata( ModuleMetaData( name="Mod2.0 - Disease Associated Genes", source='Monarch Biolink', association=GeneToDiseaseAssociation, domain=ConceptSpace(Disease, ['MONDO']), relationship='gene_associated_with_condition', range=ConceptSpace(Gene, ['HGNC']), )) def metadata(): """ Retrieve Module Metadata """ return DiseaseAssociatedGeneSet.get_metadata() def main(): fire.Fire(DiseaseAssociatedGeneSet)
raise RuntimeError( "GeneToChemicalInteractionPayload ERROR: missing mandatory input_genes parameter" ) input_gene_set = self.get_simple_input_identifier_list( input_genes, object_id_only=True) self.results = self.module.get_chemicals_interacting_with_genes( input_gene_set, rows) GeneToChemicalInteractionPayload.set_metadata( ModuleMetaData(name="Module 1B: Gene to Chemical Interactions", source='Chemical Toxicology Database (CTD)', association=ChemicalToGeneAssociation, domain=ConceptSpace(Gene, ['NCBIGene']), relationship='interacts_with', range=ConceptSpace(ChemicalSubstance, ['CTD']))) def metadata(): """ Retrieve Module Metadata """ return GeneToChemicalInteractionPayload.get_metadata() def main(): fire.Fire(GeneToChemicalInteractionPayload)
input_gene_set = self.get_simple_input_identifier_list(input_genes) asyncio.run(self.module.gene_to_gene_biclusters_async(input_gene_set)) sorted_list_of_output_genes = self.module.gene_to_gene_bicluster_summarize( input_gene_set, keep_input_id) self.results = pd.DataFrame.from_records(sorted_list_of_output_genes) DepMapBiclusters.set_metadata( ModuleMetaData(name="Mod9B - Gene-to-CellLine Bicluster", source='DepMap Biclustering', association=GeneToGeneAssociation, domain=ConceptSpace(Gene, ['NCBI']), relationship='related_to', range=ConceptSpace(CellLine, ['ACH']))) def metadata(): """ Retrieve Module Metadata """ return DepMapBiclusters.get_metadata() def main(): fire.Fire(DepMapBiclusters)
input_tissue_ids = self.get_simple_input_identifier_list(input_tissues) most_common_tissues = asyncio.run( self.module.tissue_to_tissue_biclusters_async(input_tissue_ids)) self.results = pd.DataFrame.from_records(most_common_tissues, columns=["hit_id", "score"]) TissueToTissueBicluster.set_metadata( ModuleMetaData( name="Mod9A - Tissue-to-Tissue Bicluster", source='RNAseqDB Biclustering', association=AnatomicalEntityToAnatomicalEntityAssociation, domain=ConceptSpace(AnatomicalEntity, ['UBERON']), relationship='related_to', range=ConceptSpace(AnatomicalEntity, ['UBERON']), )) def metadata(): """ Retrieve Module Metadata """ return TissueToTissueBicluster.get_metadata() def main(): fire.Fire(TissueToTissueBicluster)
def mock_concept_space(): cs = ConceptSpace( category=mock_concept_space_category, id_prefixes=[mock_concept_space_id_prefixes] ) return cs
super(GeneInteractionSet, self).__init__(module=GeneInteractions()) if not input_genes: raise RuntimeError("GeneInteractionSet ERROR: missing mandatory input_genes parameter") input_gene_data_frame = self.get_input_data_frame(input_genes) self.results = self.module.get_interactions(input_gene_data_frame, threshold) GeneInteractionSet.set_metadata( ModuleMetaData( name="Module 1E - Gene Interaction", source='Monarch Biolink', association=GeneToGeneAssociation, domain=ConceptSpace(Gene, ['HGNC']), relationship='interacts_with', range=ConceptSpace(Gene, ['HGNC']), ) ) def metadata(): """ Retrieve Module Metadata """ return GeneInteractionSet.get_metadata() def main(): fire.Fire(GeneInteractionSet)