from biothings_explorer.hint import Hint from biothings_explorer.user_query_dispatcher import FindConnection ht = Hint() ace2 = ht.query("ACE2")['Gene'][0] # print(ace2) fc = FindConnection(input_obj=ace2, output_obj='DiseaseOrPhenotypicFeature', intermediate_nodes='ChemicalSubstance') fc.connect(verbose=True) # save graphml file to test.graphml output = fc.to_graphml("test.graphml")
fc = FindConnection(input_obj=depression, output_obj=tbi, intermediate_nodes="BiologicalEntity") # BTE finding connection fc.connect(verbose=True) print() print("Displaying and filter results") # Displaying and filter results df = fc.display_table_view() # because UMLS is not currently well-integrated in our ID-to-object translation system, removing UMLS-only entries here patternDel = "^UMLS:C\d+" filter = df.node1_id.str.contains(patternDel) df = df[~filter] fc.to_graphml("TBI.graphml") fc.to_reasoner_std() print(df.shape) df.sample(10) # Which diseases are mentioned the most mentioned = df.node1_name.value_counts().head(10) print(mentioned) print() print( "fetch all articles connecting 'unipolar depression' and 'OBESITY DISORDER'" ) # fetch all articles connecting 'unipolar depression' and 'OBESITY DISORDER' articles = []