Index

Symbols

-e <edges> kg-covid-19-holdouts command line option -i kg-covid-19-download command line option -i <input_dir> kg-covid-19-transform command line option -n <nodes> kg-covid-19-holdouts command line option -o <output_dir> kg-covid-19-download command line option kg-covid-19-holdouts command line option kg-covid-19-query command line option kg-covid-19-transform command line option

-p <processes> kg-covid-19-merge command line option -s <sources> kg-covid-19-transform command line option -t <train_fraction> kg-covid-19-holdouts command line option -v kg-covid-19-holdouts command line option -y <yaml> kg-covid-19-merge command line option kg-covid-19-query command line option -y <yaml_file> kg-covid-19-download command line option

C

CantFindPharmGKBKey ChemblTransform (class in kg_covid_19.transform_utils.chembl) (class in kg_covid_19.transform_utils.chembl.chembl_transform)

collapse_uniprot_curie() (in module kg_covid_19.utils.transform_utils) contract_uri() (kg_covid_19.transform_utils.scibite_cord.scibite_cord.ScibiteCordTransform method) (kg_covid_19.transform_utils.scibite_cord.ScibiteCordTransform method)

D

data_to_dict() (in module kg_covid_19.utils.transform_utils) DEFAULT_INPUT_DIR (kg_covid_19.transform_utils.transform.Transform attribute) DEFAULT_OUTPUT_DIR (kg_covid_19.transform_utils.transform.Transform attribute) df_to_tsv() (in module kg_covid_19.make_holdouts) download() (in module kg_covid_19) (in module kg_covid_19.download)

download_from_api() (in module kg_covid_19.utils.download_utils) download_from_yaml() (in module kg_covid_19.utils) (in module kg_covid_19.utils.download_utils) DrugCentralTransform (class in kg_covid_19.transform_utils.drug_central) (class in kg_covid_19.transform_utils.drug_central.drug_central)

E

elastic_search_query() (in module kg_covid_19.utils.download_utils)

extract_termite_hits() (kg_covid_19.transform_utils.scibite_cord.scibite_cord.ScibiteCordTransform method) (kg_covid_19.transform_utils.scibite_cord.ScibiteCordTransform method)

G

get_gene_name() (kg_covid_19.transform_utils.ttd.ttd.TTDTransform method) get_header_items() (in module kg_covid_19.utils.transform_utils) get_identifier_by_prefix() (kg_covid_19.transform_utils.scibite_cord.scibite_cord.ScibiteCordTransform static method) (kg_covid_19.transform_utils.scibite_cord.ScibiteCordTransform static method) get_item_by_priority() (in module kg_covid_19.utils.transform_utils) get_targ_type() (kg_covid_19.transform_utils.ttd.ttd.TTDTransform method) get_uniproids() (kg_covid_19.transform_utils.ttd.ttd.TTDTransform method) get_uniprot_id() (kg_covid_19.transform_utils.pharmgkb.PharmGKB method) (kg_covid_19.transform_utils.pharmgkb.pharmgkb.PharmGKB method)

GocamTransform (class in kg_covid_19.transform_utils.gocam_transform) (class in kg_covid_19.transform_utils.gocam_transform.gocam_transform) gpa_to_edge_data() (kg_covid_19.transform_utils.sars_cov_2_gene_annot.sars_cov_2_gene_annot.SARSCoV2GeneAnnot method) (kg_covid_19.transform_utils.sars_cov_2_gene_annot.SARSCoV2GeneAnnot method) gpi_to_gene_node_data() (kg_covid_19.transform_utils.sars_cov_2_gene_annot.sars_cov_2_gene_annot.SARSCoV2GeneAnnot method) (kg_covid_19.transform_utils.sars_cov_2_gene_annot.SARSCoV2GeneAnnot method) guess_bl_category() (in module kg_covid_19.utils.transform_utils)

I

IntAct (class in kg_covid_19.transform_utils.intact.intact) interaction_to_edge() (kg_covid_19.transform_utils.intact.intact.IntAct method) interactor_to_node() (kg_covid_19.transform_utils.intact.intact.IntAct method) is_curie() (kg_covid_19.transform_utils.scibite_cord.scibite_cord.ScibiteCordTransform static method) (kg_covid_19.transform_utils.scibite_cord.ScibiteCordTransform static method)

is_iri() (kg_covid_19.transform_utils.scibite_cord.scibite_cord.ScibiteCordTransform static method) (kg_covid_19.transform_utils.scibite_cord.ScibiteCordTransform static method) ItemInDictNotFound items_dict_to_protein_data_dict() (in module kg_covid_19.transform_utils.drug_central.drug_central)

K

kg-covid-19-download command line option -i -o <output_dir> -y <yaml_file> kg-covid-19-holdouts command line option -e <edges> -n <nodes> -o <output_dir> -t <train_fraction> -v kg-covid-19-merge command line option -p <processes> -y <yaml> kg-covid-19-query command line option -o <output_dir> -y <yaml> kg-covid-19-transform command line option -i <input_dir> -o <output_dir> -s <sources> kg_covid_19 module kg_covid_19.download module kg_covid_19.make_holdouts module kg_covid_19.query module kg_covid_19.transform module kg_covid_19.transform_utils module kg_covid_19.transform_utils.chembl module kg_covid_19.transform_utils.chembl.chembl_transform module kg_covid_19.transform_utils.drug_central module kg_covid_19.transform_utils.drug_central.drug_central module kg_covid_19.transform_utils.gocam_transform module

kg_covid_19.transform_utils.gocam_transform.gocam_transform module kg_covid_19.transform_utils.intact module kg_covid_19.transform_utils.intact.intact module kg_covid_19.transform_utils.ontology module kg_covid_19.transform_utils.ontology.ontology_transform module kg_covid_19.transform_utils.pharmgkb module kg_covid_19.transform_utils.pharmgkb.pharmgkb module kg_covid_19.transform_utils.sars_cov_2_gene_annot module kg_covid_19.transform_utils.sars_cov_2_gene_annot.sars_cov_2_gene_annot module kg_covid_19.transform_utils.scibite_cord module kg_covid_19.transform_utils.scibite_cord.scibite_cord module kg_covid_19.transform_utils.string_ppi module kg_covid_19.transform_utils.string_ppi.string_ppi module kg_covid_19.transform_utils.transform module kg_covid_19.transform_utils.ttd module kg_covid_19.transform_utils.ttd.ttd module kg_covid_19.transform_utils.zhou_host_proteins module kg_covid_19.transform_utils.zhou_host_proteins.zhou_transform module kg_covid_19.utils module kg_covid_19.utils.download_utils module kg_covid_19.utils.transform_utils module

L

load_country_code() (kg_covid_19.transform_utils.scibite_cord.scibite_cord.ScibiteCordTransform method) (kg_covid_19.transform_utils.scibite_cord.ScibiteCordTransform method) load_gene_info() (kg_covid_19.transform_utils.scibite_cord.scibite_cord.ScibiteCordTransform method) (kg_covid_19.transform_utils.scibite_cord.ScibiteCordTransform method) (kg_covid_19.transform_utils.string_ppi.string_ppi.StringTransform method) (kg_covid_19.transform_utils.string_ppi.StringTransform method)

load_mapping() (kg_covid_19.transform_utils.string_ppi.string_ppi.StringTransform method) (kg_covid_19.transform_utils.string_ppi.StringTransform method) load_obj() (in module tests.test_query)

M

make_holdouts() (in module kg_covid_19.make_holdouts) make_id_mapping_file() (kg_covid_19.transform_utils.pharmgkb.PharmGKB method) (kg_covid_19.transform_utils.pharmgkb.pharmgkb.PharmGKB method) make_negative_edges() (in module kg_covid_19.make_holdouts) make_pharmgkb_chemical_node() (kg_covid_19.transform_utils.pharmgkb.PharmGKB method) (kg_covid_19.transform_utils.pharmgkb.pharmgkb.PharmGKB method) make_pharmgkb_edge() (kg_covid_19.transform_utils.pharmgkb.PharmGKB method) (kg_covid_19.transform_utils.pharmgkb.pharmgkb.PharmGKB method) make_pharmgkb_gene_node() (kg_covid_19.transform_utils.pharmgkb.PharmGKB method) (kg_covid_19.transform_utils.pharmgkb.pharmgkb.PharmGKB method) make_positive_edges() (in module kg_covid_19.make_holdouts) make_preferred_drug_id() (kg_covid_19.transform_utils.pharmgkb.PharmGKB method) (kg_covid_19.transform_utils.pharmgkb.pharmgkb.PharmGKB method) module kg_covid_19 kg_covid_19.download kg_covid_19.make_holdouts kg_covid_19.query kg_covid_19.transform kg_covid_19.transform_utils kg_covid_19.transform_utils.chembl kg_covid_19.transform_utils.chembl.chembl_transform kg_covid_19.transform_utils.drug_central kg_covid_19.transform_utils.drug_central.drug_central kg_covid_19.transform_utils.gocam_transform kg_covid_19.transform_utils.gocam_transform.gocam_transform kg_covid_19.transform_utils.intact kg_covid_19.transform_utils.intact.intact kg_covid_19.transform_utils.ontology kg_covid_19.transform_utils.ontology.ontology_transform kg_covid_19.transform_utils.pharmgkb kg_covid_19.transform_utils.pharmgkb.pharmgkb kg_covid_19.transform_utils.sars_cov_2_gene_annot kg_covid_19.transform_utils.sars_cov_2_gene_annot.sars_cov_2_gene_annot kg_covid_19.transform_utils.scibite_cord kg_covid_19.transform_utils.scibite_cord.scibite_cord kg_covid_19.transform_utils.string_ppi kg_covid_19.transform_utils.string_ppi.string_ppi kg_covid_19.transform_utils.transform kg_covid_19.transform_utils.ttd kg_covid_19.transform_utils.ttd.ttd kg_covid_19.transform_utils.zhou_host_proteins kg_covid_19.transform_utils.zhou_host_proteins.zhou_transform kg_covid_19.utils kg_covid_19.utils.download_utils kg_covid_19.utils.transform_utils tests tests.test_chembl tests.test_download tests.test_download_from_yaml tests.test_drug_central tests.test_gocams tests.test_gpi_file tests.test_holdouts tests.test_intact tests.test_pharmgkb tests.test_query tests.test_run tests.test_sars_cov_2_gene_annot tests.test_scibite_cord tests.test_string tests.test_transform_class tests.test_transform_utils tests.test_ttd_transform tests.test_version

multi_page_table_to_list() (in module kg_covid_19.utils) (in module kg_covid_19.utils.transform_utils)

O

OntologyTransform (class in kg_covid_19.transform_utils.ontology) (class in kg_covid_19.transform_utils.ontology.ontology_transform)

P

parse() (kg_covid_19.transform_utils.gocam_transform.gocam_transform.GocamTransform method) (kg_covid_19.transform_utils.gocam_transform.GocamTransform method) (kg_covid_19.transform_utils.ontology.ontology_transform.OntologyTransform method) (kg_covid_19.transform_utils.ontology.OntologyTransform method) parse_annotation_doc() (kg_covid_19.transform_utils.scibite_cord.scibite_cord.ScibiteCordTransform method) (kg_covid_19.transform_utils.scibite_cord.ScibiteCordTransform method) parse_annotations() (kg_covid_19.transform_utils.scibite_cord.scibite_cord.ScibiteCordTransform method) (kg_covid_19.transform_utils.scibite_cord.ScibiteCordTransform method) parse_chembl_activity() (kg_covid_19.transform_utils.chembl.chembl_transform.ChemblTransform method) (kg_covid_19.transform_utils.chembl.ChemblTransform method) parse_chembl_assay() (kg_covid_19.transform_utils.chembl.chembl_transform.ChemblTransform method) (kg_covid_19.transform_utils.chembl.ChemblTransform method) parse_chembl_document() (kg_covid_19.transform_utils.chembl.chembl_transform.ChemblTransform method) (kg_covid_19.transform_utils.chembl.ChemblTransform method) parse_chembl_molecules() (kg_covid_19.transform_utils.chembl.chembl_transform.ChemblTransform method) (kg_covid_19.transform_utils.chembl.ChemblTransform method) parse_cooccurrence() (kg_covid_19.transform_utils.scibite_cord.scibite_cord.ScibiteCordTransform method) (kg_covid_19.transform_utils.scibite_cord.ScibiteCordTransform method) parse_cooccurrence_record() (kg_covid_19.transform_utils.scibite_cord.scibite_cord.ScibiteCordTransform method) (kg_covid_19.transform_utils.scibite_cord.ScibiteCordTransform method)

parse_doc_fields() (kg_covid_19.transform_utils.chembl.chembl_transform.ChemblTransform method) (kg_covid_19.transform_utils.chembl.ChemblTransform method) parse_drug_central_line() (in module kg_covid_19.transform_utils.drug_central.drug_central) parse_experiment_info() (kg_covid_19.transform_utils.intact.intact.IntAct method) parse_header() (in module kg_covid_19.transform_utils.string_ppi.string_ppi) (in module kg_covid_19.utils.transform_utils) parse_line() (kg_covid_19.transform_utils.ttd.ttd.TTDTransform method) parse_pharmgkb_line() (kg_covid_19.transform_utils.pharmgkb.PharmGKB method) (kg_covid_19.transform_utils.pharmgkb.pharmgkb.PharmGKB method) parse_query_rq() (in module kg_covid_19.query) parse_stringdb_interactions() (in module kg_covid_19.transform_utils.string_ppi.string_ppi) parse_ttd_file() (kg_covid_19.transform_utils.ttd.ttd.TTDTransform method) parse_xml_to_nodes_edges() (kg_covid_19.transform_utils.intact.intact.IntAct method) participant_experimental_role() (kg_covid_19.transform_utils.intact.intact.IntAct method) participant_to_node() (kg_covid_19.transform_utils.intact.intact.IntAct method) PharmGKB (class in kg_covid_19.transform_utils.pharmgkb) (class in kg_covid_19.transform_utils.pharmgkb.pharmgkb) PharmGKBFileError PharmGKBInvalidEdge PharmKGBInvalidNodeType

R

read_json() (kg_covid_19.transform_utils.chembl.chembl_transform.ChemblTransform method) (kg_covid_19.transform_utils.chembl.ChemblTransform method) result_dict_to_tsv() (in module kg_covid_19.query) run() (kg_covid_19.transform_utils.chembl.chembl_transform.ChemblTransform method) (kg_covid_19.transform_utils.chembl.ChemblTransform method) (kg_covid_19.transform_utils.drug_central.drug_central.DrugCentralTransform method) (kg_covid_19.transform_utils.drug_central.DrugCentralTransform method) (kg_covid_19.transform_utils.gocam_transform.gocam_transform.GocamTransform method) (kg_covid_19.transform_utils.gocam_transform.GocamTransform method) (kg_covid_19.transform_utils.intact.intact.IntAct method) (kg_covid_19.transform_utils.ontology.ontology_transform.OntologyTransform method) (kg_covid_19.transform_utils.ontology.OntologyTransform method) (kg_covid_19.transform_utils.pharmgkb.PharmGKB method) (kg_covid_19.transform_utils.pharmgkb.pharmgkb.PharmGKB method) (kg_covid_19.transform_utils.sars_cov_2_gene_annot.sars_cov_2_gene_annot.SARSCoV2GeneAnnot method) (kg_covid_19.transform_utils.sars_cov_2_gene_annot.SARSCoV2GeneAnnot method) (kg_covid_19.transform_utils.scibite_cord.scibite_cord.ScibiteCordTransform method) (kg_covid_19.transform_utils.scibite_cord.ScibiteCordTransform method) (kg_covid_19.transform_utils.string_ppi.string_ppi.StringTransform method) (kg_covid_19.transform_utils.string_ppi.StringTransform method) (kg_covid_19.transform_utils.transform.Transform method) (kg_covid_19.transform_utils.ttd.ttd.TTDTransform method) (kg_covid_19.transform_utils.zhou_host_proteins.zhou_transform.ZhouTransform method)

run_query() (in module kg_covid_19.query)

S

SARSCoV2GeneAnnot (class in kg_covid_19.transform_utils.sars_cov_2_gene_annot) (class in kg_covid_19.transform_utils.sars_cov_2_gene_annot.sars_cov_2_gene_annot) save_obj() (in module tests.test_query) ScibiteCordTransform (class in kg_covid_19.transform_utils.scibite_cord) (class in kg_covid_19.transform_utils.scibite_cord.scibite_cord) setUp() (tests.test_chembl.TestChembl method) (tests.test_download.TestDownload method) (tests.test_drug_central.TestDrugCentral method) (tests.test_gocams.TestGOCams method) (tests.test_gpi_file.TestGpiFile method) (tests.test_holdouts.TestEdges method) (tests.test_intact.TestIntAct method) (tests.test_pharmgkb.TestPharmGKB method) (tests.test_query.TestQuery method) (tests.test_run.TestRun method) (tests.test_sars_cov_2_gene_annot.TestSarsGeneAnnot method) (tests.test_string.TestString method) (tests.test_transform_class.TestTransform method) (tests.test_ttd_transform.TestTTD method)

setUpClass() (tests.test_chembl.TestChembl class method) (tests.test_holdouts.TestEdges class method) (tests.test_scibite_cord.TestScibiteCord class method) StringTransform (class in kg_covid_19.transform_utils.string_ppi) (class in kg_covid_19.transform_utils.string_ppi.string_ppi)

T

test_api_download() (tests.test_download.TestDownload method) test_attributes (tests.test_transform_class.TestTransform attribute) test_attributes_0_source_name() (tests.test_transform_class.TestTransform method) test_attributes_1_node_header() (tests.test_transform_class.TestTransform method) test_attributes_2_edge_header() (tests.test_transform_class.TestTransform method) test_attributes_3_output_base_dir() (tests.test_transform_class.TestTransform method) test_attributes_4_input_base_dir() (tests.test_transform_class.TestTransform method) test_attributes_5_output_dir() (tests.test_transform_class.TestTransform method) test_attributes_6_output_node_file() (tests.test_transform_class.TestTransform method) test_attributes_7_output_edge_file() (tests.test_transform_class.TestTransform method) test_attributes_8_output_json_file() (tests.test_transform_class.TestTransform method) test_collapse_uniprot_curie (tests.test_transform_utils.TestTransformUtils attribute) test_collapse_uniprot_curie_0_foobar() (tests.test_transform_utils.TestTransformUtils method) test_collapse_uniprot_curie_1_ENSEMBL_ENSG00000178607() (tests.test_transform_utils.TestTransformUtils method) test_collapse_uniprot_curie_2_UniprotKB_P63151_1() (tests.test_transform_utils.TestTransformUtils method) test_collapse_uniprot_curie_3_uniprotkb_P63151_1() (tests.test_transform_utils.TestTransformUtils method) test_collapse_uniprot_curie_4_UniprotKB_P63151_2() (tests.test_transform_utils.TestTransformUtils method) test_default_dir (tests.test_transform_class.TestTransform attribute) test_default_dir_0_DEFAULT_INPUT_DIR() (tests.test_transform_class.TestTransform method) test_default_dir_1_DEFAULT_OUTPUT_DIR() (tests.test_transform_class.TestTransform method) test_df_to_tsv() (tests.test_holdouts.TestEdges method) test_edges_file() (tests.test_drug_central.TestDrugCentral method) (tests.test_string.TestString method) test_fix_for_chebi_id() (tests.test_intact.TestIntAct method) test_gpa_to_edge_data() (tests.test_sars_cov_2_gene_annot.TestSarsGeneAnnot method) test_gpi12iterator_instance (tests.test_sars_cov_2_gene_annot.TestSarsGeneAnnot attribute) test_gpi12iterator_instance_0_DB() (tests.test_sars_cov_2_gene_annot.TestSarsGeneAnnot method) test_gpi12iterator_instance_1_DB_Object_ID() (tests.test_sars_cov_2_gene_annot.TestSarsGeneAnnot method) test_gpi12iterator_instance_2_DB_Object_Symbol() (tests.test_sars_cov_2_gene_annot.TestSarsGeneAnnot method) test_gpi12iterator_instance_3_DB_Object_Name() (tests.test_sars_cov_2_gene_annot.TestSarsGeneAnnot method) test_gpi12iterator_instance_4_DB_Object_Synonym() (tests.test_sars_cov_2_gene_annot.TestSarsGeneAnnot method) test_gpi12iterator_instance_5_DB_Object_Type() (tests.test_sars_cov_2_gene_annot.TestSarsGeneAnnot method) test_gpi12iterator_instance_6_DB_Xref() (tests.test_sars_cov_2_gene_annot.TestSarsGeneAnnot method) test_gpi12iterator_instance_7_Taxon() (tests.test_sars_cov_2_gene_annot.TestSarsGeneAnnot method) test_gpi_file_exists() (tests.test_gpi_file.TestGpiFile method) test_gpi_parsing() (tests.test_gpi_file.TestGpiFile method) test_gpi_to_gene_node() (tests.test_sars_cov_2_gene_annot.TestSarsGeneAnnot method) test_guess_bl_category (tests.test_transform_utils.TestTransformUtils attribute) test_guess_bl_category_0_() (tests.test_transform_utils.TestTransformUtils method) test_guess_bl_category_1_UniProtKB() (tests.test_transform_utils.TestTransformUtils method) test_guess_bl_category_2_ComplexPortal() (tests.test_transform_utils.TestTransformUtils method) test_guess_bl_category_3_GO() (tests.test_transform_utils.TestTransformUtils method) test_input_dir() (tests.test_string.TestString method) test_instance_vars (tests.test_string.TestString attribute) test_instance_vars_0_ensembl2ncbi_map() (tests.test_string.TestString method) test_instance_vars_1_gene_info_map() (tests.test_string.TestString method) test_instance_vars_2_protein_gene_map() (tests.test_string.TestString method) test_intact_instance() (tests.test_intact.TestIntAct method) test_make_edges_check_edge_output_files (tests.test_holdouts.TestEdges attribute) test_make_edges_check_edge_output_files_0_pos_train_edges_tsv() (tests.test_holdouts.TestEdges method) test_make_edges_check_edge_output_files_1_pos_test_edges_tsv() (tests.test_holdouts.TestEdges method) test_make_edges_check_edge_output_files_2_pos_test_edges_tsv() (tests.test_holdouts.TestEdges method) test_make_edges_check_edge_output_files_3_pos_valid_edges_tsv() (tests.test_holdouts.TestEdges method) test_make_edges_check_edge_output_files_4_pos_valid_edges_tsv() (tests.test_holdouts.TestEdges method) test_make_edges_check_edge_output_files_5_neg_train_edges_tsv() (tests.test_holdouts.TestEdges method) test_make_edges_check_edge_output_files_6_neg_test_edges_tsv() (tests.test_holdouts.TestEdges method) test_make_edges_check_edge_output_files_7_neg_test_edges_tsv() (tests.test_holdouts.TestEdges method) test_make_edges_check_edge_output_files_8_neg_valid_edges_tsv() (tests.test_holdouts.TestEdges method) test_make_edges_check_edge_output_files_9_neg_valid_edges_tsv() (tests.test_holdouts.TestEdges method) test_make_edges_check_node_output_file() (tests.test_holdouts.TestEdges method) test_make_edges_exists() (tests.test_holdouts.TestEdges method) test_make_edges_pos_train_test_valid_edges_distinct (tests.test_holdouts.TestEdges attribute) test_make_edges_pos_train_test_valid_edges_distinct_0_pos_train_edges_tsv() (tests.test_holdouts.TestEdges method) test_make_edges_pos_train_test_valid_edges_distinct_1_neg_train_edges_tsv() (tests.test_holdouts.TestEdges method) test_make_id_mapping_file() (tests.test_pharmgkb.TestPharmGKB method) test_make_negative_edges_check_column_names() (tests.test_holdouts.TestEdges method) test_make_negative_edges_check_edge_label_column() (tests.test_holdouts.TestEdges method) test_make_negative_edges_check_instance_type() (tests.test_holdouts.TestEdges method) test_make_negative_edges_check_neg_nodes() (tests.test_holdouts.TestEdges method) test_make_negative_edges_check_num_edges_returned() (tests.test_holdouts.TestEdges method) test_make_negative_edges_check_relation_column() (tests.test_holdouts.TestEdges method) test_make_negative_edges_ensure_neg_edges_are_actually_negative() (tests.test_holdouts.TestEdges method) test_make_negative_edges_no_reflexive_edges() (tests.test_holdouts.TestEdges method) test_make_negative_edges_test_repeated_edges() (tests.test_holdouts.TestEdges method) test_make_positive_edges_check_nodes() (tests.test_holdouts.TestEdges method) test_make_positive_edges_check_num_test_edges_returned() (tests.test_holdouts.TestEdges method) test_make_positive_edges_check_num_train_edges_returned() (tests.test_holdouts.TestEdges method) test_make_positive_edges_check_test_edge_label_column() (tests.test_holdouts.TestEdges method) test_make_positive_edges_check_test_edge_relation_column() (tests.test_holdouts.TestEdges method) test_make_positive_edges_check_test_edges_column_names() (tests.test_holdouts.TestEdges method) test_make_positive_edges_check_train_edges_column_num() (tests.test_holdouts.TestEdges method) test_make_positive_edges_check_train_edges_columns() (tests.test_holdouts.TestEdges method) test_make_positive_edges_test_pos_edges_are_in_input_edge_df() (tests.test_holdouts.TestEdges method) test_make_positive_edges_test_pos_edges_are_removed_from_train_edges() (tests.test_holdouts.TestEdges method) test_make_positive_edges_test_repeated_edges() (tests.test_holdouts.TestEdges method) test_make_positives_edges_check_new_edges_instance_type() (tests.test_holdouts.TestEdges method) test_make_positives_edges_check_test_edge_instance_type() (tests.test_holdouts.TestEdges method) test_make_preferred_drug_id (tests.test_pharmgkb.TestPharmGKB attribute) test_make_preferred_drug_id_0_PA164712302() (tests.test_pharmgkb.TestPharmGKB method) test_make_preferred_drug_id_1_PA131887008() (tests.test_pharmgkb.TestPharmGKB method) test_merge_missing_file_error() (tests.test_run.TestRun method) test_nodes_are_not_repeated() (tests.test_drug_central.TestDrugCentral method) test_nodes_file() (tests.test_drug_central.TestDrugCentral method) (tests.test_string.TestString method) test_nodes_parse_xml_to_nodes_edges (tests.test_intact.TestIntAct attribute) test_nodes_parse_xml_to_nodes_edges_0_tests_resources_intact_test_xml() (tests.test_intact.TestIntAct method) test_nodes_parse_xml_to_nodes_edges_1_tests_resources_intact_3_participants_xml() (tests.test_intact.TestIntAct method) test_output_dir() (tests.test_string.TestString method) test_output_edge_file() (tests.test_string.TestString method) test_output_node_file() (tests.test_string.TestString method) test_parse_chembl_activity() (tests.test_chembl.TestChembl method) test_parse_drug_central_line (tests.test_drug_central.TestDrugCentral attribute) test_parse_drug_central_line_00_STRUCT_ID() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_01_TARGET_NAME() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_02_TARGET_CLASS() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_03_ACCESSION() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_04_GENE() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_05_SWISSPROT() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_06_ACT_VALUE() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_07_ACT_UNIT() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_08_ACT_TYPE() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_09_ACT_COMMENT() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_10_ACT_SOURCE() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_11_RELATION() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_12_MOA() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_13_MOA_SOURCE() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_14_ACT_SOURCE_URL() (tests.test_drug_central.TestDrugCentral method)

test_parse_drug_central_line_15_MOA_SOURCE_URL() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_16_ACTION_TYPE() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_17_TDL() (tests.test_drug_central.TestDrugCentral method) test_parse_drug_central_line_18_ORGANISM() (tests.test_drug_central.TestDrugCentral method) test_parse_experiment_info (tests.test_intact.TestIntAct attribute) test_parse_experiment_info_0_tests_resources_intact_test_xml() (tests.test_intact.TestIntAct method) test_parse_experiment_info_1_tests_resources_intact_test_xml() (tests.test_intact.TestIntAct method) test_parse_pharmgkb_line() (tests.test_pharmgkb.TestPharmGKB method) test_parse_query_rq() (tests.test_query.TestQuery method) test_parse_query_rq_parameterized (tests.test_query.TestQuery attribute) test_parse_query_rq_parameterized_0_title() (tests.test_query.TestQuery method) test_parse_query_rq_parameterized_1_description() (tests.test_query.TestQuery method) test_parse_query_rq_parameterized_2_endpoint() (tests.test_query.TestQuery method) test_parse_query_rq_parameterized_3_query() (tests.test_query.TestQuery method) test_parse_query_rq_should_return_dict() (tests.test_query.TestQuery method) test_parse_ttd_file_fxn() (tests.test_ttd_transform.TestTTD method) test_parse_ttd_file_values (tests.test_ttd_transform.TestTTD attribute) test_parse_ttd_file_values_0_T47101() (tests.test_ttd_transform.TestTTD method) test_parse_ttd_file_values_1_T47101() (tests.test_ttd_transform.TestTTD method) test_parse_ttd_file_values_2_T47101() (tests.test_ttd_transform.TestTTD method) test_parse_ttd_file_values_3_T17514() (tests.test_ttd_transform.TestTTD method) test_reality() (tests.test_transform_class.TestTransform method) test_result_dict_to_tsv_makes_correct_file() (tests.test_query.TestQuery method) test_result_dict_to_tsv_makes_file() (tests.test_query.TestQuery method) test_run() (tests.test_chembl.TestChembl method) (tests.test_drug_central.TestDrugCentral method) (tests.test_gocams.TestGOCams method) (tests.test_pharmgkb.TestPharmGKB method) (tests.test_sars_cov_2_gene_annot.TestSarsGeneAnnot method) (tests.test_scibite_cord.TestScibiteCord method) (tests.test_string.TestString method) (tests.test_ttd_transform.TestTTD method) test_run_exists() (tests.test_gocams.TestGOCams method) test_source_name() (tests.test_chembl.TestChembl method) (tests.test_string.TestString method) test_struct_parse_xml_to_nodes_edges() (tests.test_intact.TestIntAct method) test_transform() (tests.test_run.TestRun method) test_transform_child_classes (tests.test_transform_class.TestTransform attribute) test_transform_child_classes_00_ZhouTransform() (tests.test_transform_class.TestTransform method) test_transform_child_classes_01_DrugCentralTransform() (tests.test_transform_class.TestTransform method) test_transform_child_classes_02_TTDTransform() (tests.test_transform_class.TestTransform method) test_transform_child_classes_03_StringTransform() (tests.test_transform_class.TestTransform method) test_transform_child_classes_04_ScibiteCordTransform() (tests.test_transform_class.TestTransform method) test_transform_child_classes_05_PharmGKB() (tests.test_transform_class.TestTransform method) test_transform_child_classes_06_SARSCoV2GeneAnnot() (tests.test_transform_class.TestTransform method) test_transform_child_classes_07_IntAct() (tests.test_transform_class.TestTransform method) test_transform_child_classes_08_GoTransform() (tests.test_transform_class.TestTransform method) test_transform_child_classes_09_HpTransform() (tests.test_transform_class.TestTransform method) test_transform_child_classes_10_MondoTransform() (tests.test_transform_class.TestTransform method) test_transform_child_classes_11_ChebiTransform() (tests.test_transform_class.TestTransform method) test_transform_child_classes_12_GocamTransform() (tests.test_transform_class.TestTransform method) test_transform_child_classes_13_ChemblTransform() (tests.test_transform_class.TestTransform method) test_tsv_to_df() (tests.test_holdouts.TestEdges method) test_version() (in module tests.test_version) TestChembl (class in tests.test_chembl) TestDownload (class in tests.test_download) TestDownloadFromYaml (class in tests.test_download_from_yaml) TestDrugCentral (class in tests.test_drug_central) TestEdges (class in tests.test_holdouts) TestGOCams (class in tests.test_gocams) TestGpiFile (class in tests.test_gpi_file) TestIntAct (class in tests.test_intact) TestPharmGKB (class in tests.test_pharmgkb) TestQuery (class in tests.test_query) TestRun (class in tests.test_run) tests module tests.test_chembl module tests.test_download module tests.test_download_from_yaml module tests.test_drug_central module tests.test_gocams module tests.test_gpi_file module tests.test_holdouts module tests.test_intact module tests.test_pharmgkb module tests.test_query module tests.test_run module tests.test_sars_cov_2_gene_annot module tests.test_scibite_cord module tests.test_string module tests.test_transform_class module tests.test_transform_utils module tests.test_ttd_transform module tests.test_version module TestSarsGeneAnnot (class in tests.test_sars_cov_2_gene_annot) TestScibiteCord (class in tests.test_scibite_cord) TestString (class in tests.test_string) TestTransform (class in tests.test_transform_class) TestTransformUtils (class in tests.test_transform_utils) TestTTD (class in tests.test_ttd_transform) Transform (class in kg_covid_19.transform_utils.transform) transform() (in module kg_covid_19) (in module kg_covid_19.transform) TransformChildClass (class in tests.test_transform_class) TransformError tsv_to_df() (in module kg_covid_19.make_holdouts) TTDNotEnoughFields TTDTransform (class in kg_covid_19.transform_utils.ttd.ttd)

U

ungzip_to_tempdir() (in module kg_covid_19.utils.transform_utils) uniprot_make_name_to_id_mapping() (in module kg_covid_19.utils.transform_utils)

uniprot_name_to_id() (in module kg_covid_19.utils.transform_utils) unzip_to_tempdir() (in module kg_covid_19.utils.transform_utils)

W

write_node_edge_item() (in module kg_covid_19.utils) (in module kg_covid_19.utils.transform_utils)

Z

ZhouTransform (class in kg_covid_19.transform_utils.zhou_host_proteins.zhou_transform)