Index

A

add_compound_node() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) add_creator_node() (in module pyBiodatafuse.graph.rdf.metadata)

add_data_source_node() (in module pyBiodatafuse.graph.rdf.utils) add_gene_node() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) add_metadata() (in module pyBiodatafuse.graph.rdf.metadata)

B

BDFGraph (class in pyBiodatafuse.graph.rdf.rdf)

bridgedb_xref() (in module pyBiodatafuse.id_mapper) build_networkx_graph() (in module pyBiodatafuse.graph.generator)

C

check_columns_against_constants() (in module pyBiodatafuse.utils) check_endpoint_ensembl() (in module pyBiodatafuse.human_homologs) check_smiles() (in module pyBiodatafuse.id_mapper) check_version_ensembl() (in module pyBiodatafuse.human_homologs) cid2chembl() (in module pyBiodatafuse.id_mapper) collapse_data_sources() (in module pyBiodatafuse.utils) collect_disease_data() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) combine_sources() (in module pyBiodatafuse.utils) combine_with_homologs() (in module pyBiodatafuse.utils)

connect_db() (in module pyBiodatafuse.graph.neo4j) construct_uri() (in module pyBiodatafuse.graph.rdf.utils) convert_graph_to_json() (in module pyBiodatafuse.graph.cytoscape) count_triples() (pyBiodatafuse.graph.rdf.graphdb.GraphDBManager static method) create_df_from_dea() (in module pyBiodatafuse.data_loader) create_df_from_file() (in module pyBiodatafuse.data_loader) create_df_from_text() (in module pyBiodatafuse.data_loader) create_harmonized_input_file() (in module pyBiodatafuse.utils) create_or_append_to_metadata() (in module pyBiodatafuse.utils) create_repository() (pyBiodatafuse.graph.rdf.graphdb.GraphDBManager static method)

D

delete_repository() (pyBiodatafuse.graph.rdf.graphdb.GraphDBManager static method)

discover_prefixes_from_graph() (in module pyBiodatafuse.graph.rdf.utils)

E

exporter() (in module pyBiodatafuse.graph.neo4j)

extract_curie() (in module pyBiodatafuse.graph.rdf.utils)

F

filter_dea() (in module pyBiodatafuse.data_loader)

G

generate_rdf() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) get_aops() (in module pyBiodatafuse.annotators.aopwiki) get_aops_compound() (in module pyBiodatafuse.annotators.aopwiki) get_aops_gene() (in module pyBiodatafuse.annotators.aopwiki) get_cid_from_data() (in module pyBiodatafuse.id_mapper) get_cid_from_pugrest() (in module pyBiodatafuse.id_mapper) get_compound_annotations() (in module pyBiodatafuse.annotators.compoundwiki) get_compound_gene_inhibitor() (in module pyBiodatafuse.annotators.molmedb) get_compound_interactions() (in module pyBiodatafuse.annotators.intact) get_compounds() (in module pyBiodatafuse.annotators.kegg) get_disease_compound_interactions() (in module pyBiodatafuse.annotators.opentargets) get_gene_cellular_component() (in module pyBiodatafuse.annotators.wikidata) get_gene_compound_inhibitor() (in module pyBiodatafuse.annotators.molmedb) get_gene_compound_interactions() (in module pyBiodatafuse.annotators.opentargets) get_gene_disease() (in module pyBiodatafuse.annotators.disgenet) get_gene_enrichment() (in module pyBiodatafuse.annotators.gprofiler) get_gene_expression() (in module pyBiodatafuse.annotators.bgee) get_gene_go_process() (in module pyBiodatafuse.annotators.opentargets) get_gene_interactions() (in module pyBiodatafuse.annotators.intact) get_gene_mito_pathways() (in module pyBiodatafuse.annotators.mitocarta)

get_gene_pathways() (in module pyBiodatafuse.annotators.minerva) get_gene_reactome_pathways() (in module pyBiodatafuse.annotators.opentargets) get_gene_wikipathways() (in module pyBiodatafuse.annotators.wikipathways) get_homologs() (in module pyBiodatafuse.human_homologs) get_human_homologs() (in module pyBiodatafuse.human_homologs) get_identifier_of_interest() (in module pyBiodatafuse.utils) get_minerva_components() (in module pyBiodatafuse.annotators.minerva) get_node_label() (in module pyBiodatafuse.graph.rdf.utils) get_pathways() (in module pyBiodatafuse.annotators.kegg) get_ppi() (in module pyBiodatafuse.annotators.stringdb) get_protein_compound_screened() (in module pyBiodatafuse.annotators.pubchem) get_repository_info() (pyBiodatafuse.graph.rdf.graphdb.GraphDBManager static method) get_shacl_prefixes() (in module pyBiodatafuse.graph.rdf.utils) get_shapes() (in module pyBiodatafuse.graph.rdf.utils) get_tf_target() (in module pyBiodatafuse.annotators.tflink) get_version_datasource_bridgedb() (in module pyBiodatafuse.id_mapper) get_version_webservice_bridgedb() (in module pyBiodatafuse.id_mapper) get_wikidata_gene_literature() (in module pyBiodatafuse.analyzer.explorer.literature) give_annotator_warning() (in module pyBiodatafuse.utils) GraphDBManager (class in pyBiodatafuse.graph.rdf.graphdb)

L

list_repositories() (pyBiodatafuse.graph.rdf.graphdb.GraphDBManager static method) load_dataframe_from_pickle() (in module pyBiodatafuse.graph.generator)

load_graph() (in module pyBiodatafuse.graph.cytoscape) (in module pyBiodatafuse.graph.neo4j)

M

match_input_datasource() (in module pyBiodatafuse.id_mapper) module pyBiodatafuse pyBiodatafuse.analyzer pyBiodatafuse.annotators pyBiodatafuse.graph

P

plot_hbarplot_chart() (in module pyBiodatafuse.analyzer.utils) plot_pie_chart() (in module pyBiodatafuse.analyzer.utils) plotly_barplot_chart() (in module pyBiodatafuse.analyzer.utils) plotly_pie_chart() (in module pyBiodatafuse.analyzer.utils) process_aop_data() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) process_compound_data() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) process_compoundwiki_data() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) process_disease_data() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) process_expression_data() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) process_inhibitor_transporter_data() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) process_literature_data() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) process_molecular_pathway() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) process_pathways() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method)

process_ppi_data() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) process_processes_data() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) process_pubchem_assay_data() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) process_row() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) process_transporter_inhibitor_data() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) pubchem_xref() (in module pyBiodatafuse.id_mapper) pyBiodatafuse module pyBiodatafuse.analyzer module pyBiodatafuse.annotators module pyBiodatafuse.graph module

Q

query_graphdb() (pyBiodatafuse.graph.rdf.graphdb.GraphDBManager static method)

R

read_datasource_file() (in module pyBiodatafuse.id_mapper) record_datasource() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method)

replace_na_none() (in module pyBiodatafuse.graph.rdf.utils) restart_repository() (pyBiodatafuse.graph.rdf.graphdb.GraphDBManager static method) run_gene_selected_sources() (in module pyBiodatafuse.id_annotator)

S

save_cytoscape_json() (in module pyBiodatafuse.graph.saver) save_graph() (in module pyBiodatafuse.graph.saver) save_graph_to_edgelist() (in module pyBiodatafuse.graph.saver) save_graph_to_graphml() (in module pyBiodatafuse.graph.saver)

save_graph_to_tsv() (in module pyBiodatafuse.graph.saver) shacl() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) shacl_prefixes() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method) shex() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method)

U

upload_to_graphdb() (pyBiodatafuse.graph.rdf.graphdb.GraphDBManager static method)

V

valid_indices() (pyBiodatafuse.graph.rdf.rdf.BDFGraph method)