get_drugs: Get antineoplastic drugs and drug regimens

In sigven/oncoPharmaDB: Molecularly targeted cancer drugs and biomarkers

Get antineoplastic drugs and drug regimens

Description

Downloads preprocessed datasets to a local cache directory and returns a selected set of drugs based on various criteria set by the user.

The dataset comes as a list object, with two elements:

• metadata - a data frame with metadata regarding drug resources used

• records - a data frame with drug records

Usage

get_drugs(
  cache_dir = NA,
  force_download = FALSE,
  exclude_salt_forms = TRUE,
  exclude_adc = FALSE,
  treatment_category = c("targeted_therapy_classified", "targeted_therapy_unclassified",
    "chemo_therapy_classified", "hormone_therapy_classified",
    "immuno_suppressants_classified", "other"),
  drug_is_approved = FALSE,
  drug_target = NULL,
  drug_action_type = NULL,
  drug_indication_main = NULL,
  drug_source_opentargets = FALSE,
  drug_cancer_indication = TRUE,
  drug_classified_cancer = TRUE,
  drug_has_blackbox_warning = FALSE,
  drug_approval_year = 1939,
  drug_minimum_phase_any_indication = 0,
  output_resolution = "drug2target2indication",
  drug_action_inhibition = F
)

Arguments

cache_dir	local cache directory for data retrieval
force_download	force download data from remote repository even if data exists in cache
exclude_salt_forms	exclude salt forms of drugs
exclude_adc	exclude antibody-drug conjugates (ADCs)
treatment_category	main treatment category, classified according to ATC or not ('targeted_therapy_classified', 'targeted_therapy_unclassified','chemo_therapy_classified','hormone_therapy_classified', 'immuno_suppressants_classified','other')
drug_is_approved	logical indicating if resulting drug records should contain approved drugs only
drug_target	character vector with drug targets (gene symbols) for drug records included in results
drug_action_type	character vector with drug action types to include in drug record list - possible values "INHIBITOR","AGONIST","MODULATOR","ANTAGONIST", "BLOCKER","ACTIVATOR","BINDING AGENT","OPENER", "STABILISER","CROSS-LINKING AGENT",DISRUPTING AGENT","OTHER"
drug_indication_main	character vector with main tumor types for which drug(s) are indicated. Possible values: "Adrenal Gland","Biliary Tract", "Bladder/Urinary Tract","Bone","Breast","Cervix","CNS/Brain", "Colon/Rectum","Esophagus/Stomach","Eye","Head and Neck","Kidney", "Liver","Lung","Lymphoid","Myeloid","Ovary/Fallopian Tube", "Pancreas","Penis","Peripheral Nervous System","Peritoneum", "Pleura","Prostate","Skin","Soft Tissue","Testis","Thymus", "Thyroid","Uterus","Vulva/Vagina"
drug_source_opentargets	logical indicating if resulting drug records should contain drug records from Open Targets Platform/ChEMBL only
drug_cancer_indication	logical indicating if resulting drug records should be for those indicated for cancer conditions only (from approved conditions, found in clinical trials etc.)
drug_classified_cancer	logical indicating if resulting drug records should be for those classified only in the "L" class of ATC ( "ANTINEOPLASTIC AND IMMUNOMODULATING AGENTS") only
drug_has_blackbox_warning	logical indicating if resulting drug records should contain drugs with black box warnings only
drug_approval_year	only include records for drugs approved later than this date (year)
drug_minimum_phase_any_indication	only include drug records that are in a clinical phase (any indication) greater or equal than this phase
output_resolution	dictate output record resolution ('drug','drug2target','drug2target2indication')
drug_action_inhibition	logical indicating to only return drug records with inhibitory mechanism-of-action

Value

The records data frame contains the following columns (only selected columns will be shown based on the value of output_resolution)

• drug_id - drug identifier (pharmaOncoX)

• drug_name - primary drug name (upper case, NCI Thesaurus)

• drug_type - type of drug molecule (Antibody, small molecule etc)

• molecule_chembl_id - ChEMBL compound identifier

• drug_action_type - main action elicited by drug (antagonist, inhibitor, stabiliser etc)

• drug_alias - collection of unambiguous drug aliases (separated by '|')

• nci_concept_definition - detailed description of drug mechanism-of-action (NCI Thesaurus)

• opentargets - logical - drug is found in the Open Targets Platform resource

• is_salt - logical - drug record represents a salt form (excluded by default)

• is_adc - logical - drug record represents an antibody-drug conjugate (ADC - excluded by default)

• drug_blacbox_warning - logical indicating if drug has blackbox warning

• nci_t - NCI thesaurus identifier

• target_symbol - gene symbol of drug target

• target_entrezgene - Entrez gene identifier of drug target

• target_genename - gene name/description of drug target

• target_ensembl_gene_id - Ensembl gene identifier of drug target

• target_type - type of drug target (single protein, protein family etc.)

• drug_max_phase_indication - maximum clinical phase for drug (given indication)

• drug_approved_indication - logical indicating if drug has an approved indication

• drug_frac_cancer_indications - fraction of drug indications that are for cancers

• drug_approved_noncancer - logical indicating if drug is approved for a non-cancer disease

• drug_n_indications - number of indications for the given drug (from approved indications, clinical trials etc)

• drug_year_first_approval - year drug was first approved

• drug_max_ct_phase - maximum clinical phase for drug (any indication)

• disease_efo_id - EFO (Experimental Factor Ontology) identifier for drug indication

• disease_efo_label - EFO (Experimental Factor Ontology) label for drug indication

• primary_site - primary tumor site/type (obtained through https://github.com/sigven/oncoPhenoMap)

• drug_clinical_id - drug clinical identifier (clinicaltrials.gov, DailyMed, FDA etc.)

• drug_clinical_source - underlying source for drug entry (DailyMed, clinicaltrials.gov, FDA etc.)

• atc_code_level1 - drug identifier ATC (level 1)

• atc_level1 - drug label ATC (level 1)

• atc_code_level1 - drug identifier ATC (level 2)

• atc_level2 - drug label ATC (level 2)

• atc_code_level3 - drug identifier ATC (level 3)

• atc_level3 - drug label ATC (level 3)

• atc_treatment_category - treatment category (targeted/chemo/hormone, cancer/other etc)

sigven/oncoPharmaDB documentation built on Dec. 24, 2024, 9:46 p.m.