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Get antineoplastic drugs and drug regimens

Source: R/pharm_oncox.R
get_drugs.Rd

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)