Index

A

add_atc_codes() (in module CanGraph.GraphifyDrugBank.build_database) add_biological_properties() (in module CanGraph.GraphifyHMDB.build_database) add_cancer_associations() (in module CanGraph.ExposomeExplorer.build_database) add_categories() (in module CanGraph.GraphifyDrugBank.build_database) add_causes() (in module CanGraph.QueryWikidata.build_database) add_chem_isom() (in module CanGraph.MeSHandMetaNetX.build_database) add_chem_prop() (in module CanGraph.MeSHandMetaNetX.build_database) add_chem_xref() (in module CanGraph.MeSHandMetaNetX.build_database) add_comp_prop() (in module CanGraph.MeSHandMetaNetX.build_database) add_comp_xref() (in module CanGraph.MeSHandMetaNetX.build_database) add_components() (in module CanGraph.ExposomeExplorer.build_database) add_concentrations_abnormal() (in module CanGraph.GraphifyHMDB.build_database) add_concentrations_normal() (in module CanGraph.GraphifyHMDB.build_database) add_correlations() (in module CanGraph.ExposomeExplorer.build_database) add_disease_info() (in module CanGraph.QueryWikidata.build_database) add_diseases() (in module CanGraph.GraphifyHMDB.build_database) add_dosages() (in module CanGraph.GraphifyDrugBank.build_database) add_drug_external_ids() (in module CanGraph.QueryWikidata.build_database) add_drug_interactions() (in module CanGraph.GraphifyDrugBank.build_database) add_drugs() (in module CanGraph.GraphifyDrugBank.build_database) (in module CanGraph.QueryWikidata.build_database) add_experimental_properties() (in module CanGraph.GraphifyDrugBank.build_database) (in module CanGraph.GraphifyHMDB.build_database) add_external_equivalents() (in module CanGraph.GraphifyDrugBank.build_database) add_external_identifiers() (in module CanGraph.GraphifyDrugBank.build_database) add_gene_info() (in module CanGraph.QueryWikidata.build_database) add_gene_properties() (in module CanGraph.GraphifyHMDB.build_database) add_general_references() (in module CanGraph.GraphifyDrugBank.build_database) (in module CanGraph.GraphifyHMDB.build_database) add_genes() (in module CanGraph.QueryWikidata.build_database) add_go_classifications() (in module CanGraph.GraphifyHMDB.build_database) add_manufacturers() (in module CanGraph.GraphifyDrugBank.build_database) add_measurements_stuff() (in module CanGraph.ExposomeExplorer.build_database) add_mesh_and_metanetx() (in module CanGraph.main) add_mesh_by_name() (in module CanGraph.MeSHandMetaNetX.build_database) add_metabolite_associations() (in module CanGraph.GraphifyHMDB.build_database) add_metabolite_info() (in module CanGraph.QueryWikidata.build_database) add_metabolite_references() (in module CanGraph.GraphifyHMDB.build_database) add_metabolites() (in module CanGraph.GraphifyHMDB.build_database) (in module CanGraph.GraphifySMPDB.build_database) add_metabolomic_associations() (in module CanGraph.ExposomeExplorer.build_database)

add_microbial_metabolite_identifications() (in module CanGraph.ExposomeExplorer.build_database) add_mixtures() (in module CanGraph.GraphifyDrugBank.build_database) add_more_drug_info() (in module CanGraph.QueryWikidata.build_database) add_packagers() (in module CanGraph.GraphifyDrugBank.build_database) add_pathways() (in module CanGraph.GraphifySMPDB.build_database) add_pathways_and_relations() (in module CanGraph.GraphifyDrugBank.build_database) add_pept() (in module CanGraph.MeSHandMetaNetX.build_database) add_predicted_properties() (in module CanGraph.GraphifyHMDB.build_database) add_prefixes() (in module CanGraph.MeSHandMetaNetX.build_database) add_products() (in module CanGraph.GraphifyDrugBank.build_database) add_protein_associations() (in module CanGraph.GraphifyHMDB.build_database) add_protein_properties() (in module CanGraph.GraphifyHMDB.build_database) add_proteins() (in module CanGraph.GraphifyHMDB.build_database) (in module CanGraph.GraphifySMPDB.build_database) add_reproducibilities() (in module CanGraph.ExposomeExplorer.build_database) add_samples() (in module CanGraph.ExposomeExplorer.build_database) add_sequence() (in module CanGraph.GraphifySMPDB.build_database) add_sequences() (in module CanGraph.GraphifyDrugBank.build_database) add_subjects() (in module CanGraph.ExposomeExplorer.build_database) add_targets_enzymes_carriers_and_transporters() (in module CanGraph.GraphifyDrugBank.build_database) add_taxonomy() (in module CanGraph.GraphifyDrugBank.build_database) (in module CanGraph.GraphifyHMDB.build_database) add_toomuch_metabolite_info() (in module CanGraph.QueryWikidata.build_database) add_wikidata_and_mesh_by_name() (in module CanGraph.QueryWikidata.build_database) add_yet_more_drug_info() (in module CanGraph.QueryWikidata.build_database) annotate_auto_units() (in module CanGraph.ExposomeExplorer.build_database) annotate_cancers() (in module CanGraph.ExposomeExplorer.build_database) annotate_cohorts() (in module CanGraph.ExposomeExplorer.build_database) annotate_experimental_methods() (in module CanGraph.ExposomeExplorer.build_database) annotate_measurements() (in module CanGraph.ExposomeExplorer.build_database) annotate_microbial_metabolite_info() (in module CanGraph.ExposomeExplorer.build_database) annotate_publications() (in module CanGraph.ExposomeExplorer.build_database) annotate_reproducibilities() (in module CanGraph.ExposomeExplorer.build_database) annotate_samples() (in module CanGraph.ExposomeExplorer.build_database) annotate_specimens() (in module CanGraph.ExposomeExplorer.build_database) annotate_subjects() (in module CanGraph.ExposomeExplorer.build_database) annotate_units() (in module CanGraph.ExposomeExplorer.build_database) annotate_using_wikidata() (in module CanGraph.main) args_parser() (in module CanGraph.deploy) (in module CanGraph.main) (in module CanGraph.setup)

B

build_from_file() (in module CanGraph.ExposomeExplorer.build_database) (in module CanGraph.GraphifyDrugBank.build_database) (in module CanGraph.GraphifySMPDB.build_database) (in module CanGraph.main) (in module CanGraph.MeSHandMetaNetX.build_database)

build_from_metabolite_file() (in module CanGraph.GraphifyHMDB.build_database) build_from_protein_file() (in module CanGraph.GraphifyHMDB.build_database)

C

call_db_schema_visualization() (in module CanGraph.miscelaneous) CanGraph.deploy module CanGraph.ExposomeExplorer.build_database module CanGraph.ExposomeExplorer.main module CanGraph.GraphifyDrugBank.build_database module CanGraph.GraphifyDrugBank.main module CanGraph.GraphifyHMDB.build_database module CanGraph.GraphifyHMDB.main module CanGraph.GraphifySMPDB.build_database module CanGraph.GraphifySMPDB.main module CanGraph.main module

CanGraph.MeSHandMetaNetX.build_database module CanGraph.MeSHandMetaNetX.main module CanGraph.miscelaneous module CanGraph.QueryWikidata.build_database module CanGraph.QueryWikidata.main module CanGraph.setup module change_neo4j_password() (in module CanGraph.setup) check_exposome_files() (in module CanGraph.setup) check_file() (in module CanGraph.miscelaneous) check_neo4j_protocol() (in module CanGraph.miscelaneous) clean_database() (in module CanGraph.miscelaneous) configure_neo4j() (in module CanGraph.setup) connect_to_neo4j() (in module CanGraph.miscelaneous) countlines() (in module CanGraph.miscelaneous) create_n10s_graphconfig() (in module CanGraph.miscelaneous)

D

deploy_code() (in module CanGraph.deploy) deploy_pdf_manual() (in module CanGraph.deploy) deploy_webdocs() (in module CanGraph.deploy)

download() (in module CanGraph.miscelaneous) download_and_untargz() (in module CanGraph.miscelaneous) download_and_unzip() (in module CanGraph.miscelaneous)

E

export_graphml() (in module CanGraph.miscelaneous)

F

final_message() (in module CanGraph.setup) find_instance_of_disease() (in module CanGraph.QueryWikidata.build_database) find_metabolites_related_to_mesh() (in module CanGraph.MeSHandMetaNetX.build_database) find_neo4j_installation_status() (in module CanGraph.setup) find_protein_data_in_metanetx() (in module CanGraph.MeSHandMetaNetX.build_database)

find_protein_interactions_in_metanetx() (in module CanGraph.MeSHandMetaNetX.build_database) find_reasons_to_import_all_files() (in module CanGraph.main) find_reasons_to_import_inchi() (in module CanGraph.main) find_subclass_of_disease() (in module CanGraph.QueryWikidata.build_database) find_synonyms_in_cts() (in module CanGraph.MeSHandMetaNetX.build_database)

G

get_identifiers() (in module CanGraph.MeSHandMetaNetX.build_database) get_import_path() (in module CanGraph.miscelaneous)

get_kegg_pathways_for_metabolites() (in module CanGraph.MeSHandMetaNetX.build_database) git_push() (in module CanGraph.deploy)

I

import_based_on_all_files() (in module CanGraph.main) import_based_on_index() (in module CanGraph.main) import_csv() (in module CanGraph.ExposomeExplorer.build_database) import_genomic_seqs() (in module CanGraph.GraphifySMPDB.main) import_graphml() (in module CanGraph.miscelaneous) import_metabolites() (in module CanGraph.GraphifySMPDB.main) import_pathways() (in module CanGraph.GraphifySMPDB.main) import_proteic_seqs() (in module CanGraph.GraphifySMPDB.main)

import_proteins() (in module CanGraph.GraphifySMPDB.main) improve_search_terms() (in module CanGraph.main) improve_search_terms_with_cts() (in module CanGraph.main) improve_search_terms_with_metanetx() (in module CanGraph.main) initial_cancer_discovery() (in module CanGraph.QueryWikidata.build_database) initial_message() (in module CanGraph.setup) install_neo4j() (in module CanGraph.setup) install_packages() (in module CanGraph.setup)

K

kill_neo4j() (in module CanGraph.miscelaneous)

L

link_to_original_data() (in module CanGraph.main)

M

main() (in module CanGraph.deploy) (in module CanGraph.ExposomeExplorer.main) (in module CanGraph.GraphifyDrugBank.main) (in module CanGraph.GraphifyHMDB.main) (in module CanGraph.GraphifySMPDB.main) (in module CanGraph.main) (in module CanGraph.MeSHandMetaNetX.main) (in module CanGraph.QueryWikidata.main) (in module CanGraph.setup) make_sphinx_prechecks() (in module CanGraph.deploy) manage_transaction() (in module CanGraph.miscelaneous) merge_duplicate_nodes() (in module CanGraph.miscelaneous) module CanGraph.deploy CanGraph.ExposomeExplorer.build_database CanGraph.ExposomeExplorer.main CanGraph.GraphifyDrugBank.build_database CanGraph.GraphifyDrugBank.main CanGraph.GraphifyHMDB.build_database CanGraph.GraphifyHMDB.main CanGraph.GraphifySMPDB.build_database CanGraph.GraphifySMPDB.main CanGraph.main CanGraph.MeSHandMetaNetX.build_database CanGraph.MeSHandMetaNetX.main CanGraph.miscelaneous CanGraph.QueryWikidata.build_database CanGraph.QueryWikidata.main CanGraph.setup

O

old_sleep_with_counter() (in module CanGraph.miscelaneous)

P

purge_database() (in module CanGraph.miscelaneous)

R

read_synonyms_in_metanetx() (in module CanGraph.MeSHandMetaNetX.build_database) remove_counts_and_displayeds() (in module CanGraph.ExposomeExplorer.build_database) remove_cross_properties() (in module CanGraph.ExposomeExplorer.build_database)

remove_duplicate_relationships() (in module CanGraph.miscelaneous) remove_ExternalEquivalent() (in module CanGraph.miscelaneous) remove_n10s_graphconfig() (in module CanGraph.miscelaneous) restart_neo4j() (in module CanGraph.miscelaneous)

S

scan_folder() (in module CanGraph.miscelaneous) setup_database_index() (in module CanGraph.setup) setup_databases() (in module CanGraph.setup) setup_drugbank() (in module CanGraph.setup) setup_exposome() (in module CanGraph.setup) setup_folders() (in module CanGraph.setup)

setup_git() (in module CanGraph.setup) setup_hmdb() (in module CanGraph.setup) setup_neo4j() (in module CanGraph.setup) setup_smpdb() (in module CanGraph.setup) sleep_with_counter() (in module CanGraph.miscelaneous) split_csv() (in module CanGraph.miscelaneous) split_xml() (in module CanGraph.miscelaneous)

U

untargz() (in module CanGraph.miscelaneous)

unzip() (in module CanGraph.miscelaneous) update_neo4j_confs() (in module CanGraph.setup)

W

write_synonyms_in_metanetx() (in module CanGraph.MeSHandMetaNetX.build_database)