0.6.1 release

Author: sigven

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: oncoPharmaDB
 Type: Package
 Title: Dataset with targeted and non-targeted anticancer drugs
-Version: 0.6.0
-Date: 2021-09-30
+Version: 0.6.1
+Date: 2021-10-28
 Authors@R: 
     c(person(given = "Sigve",
              family = "Nakken",

NEWS.md

@@ -1,3 +1,19 @@
+# Version 0.6.1 (October 28th 2021)
+
+* Data update: NCI Thesaurus (21.10d)
+* Removed some redundant/non-informative columns of main data frame (**oncopharmadb**)
+  * `target_chembl_id`
+  * `drug_synonyms`
+  * `drug_description`
+  * `drug_moa`
+  * `drug_tradenames`
+  * `cancer_drug`
+* Documented exported data objects (**oncopharmadb** and **oncopharma_synonyms**)
+* Annotated gonadotropin releasing hormone analogues with *hormone_therapy*  label
+* Added *platinum_compound* as a dedicated drug category (and as a column in **oncopharmadb**) 
+  * New argument `is_platinum_compound` to `get_onco_drugs()`
+
+
 # Version 0.6.0 (September 30th 2021)
 
 * Data update: Open Targets Platform (2021.09)

R/data.R

@@ -0,0 +1,77 @@
+#' Dataset of targeted and non-targeted cancer drugs
+#'
+#' A dataset containing an extensive collection of anti-cancer drugs, i.e. targeted compounds, chemotherapy regimens etc. The
+#' data has been harvested from the Open Targets Platform, the NCI Thesaurus, and ChEMBL. Note that each entry corresponds
+#' to a "drug synonym-target-indication association"
+#'
+#' @format \bold{oncopharmadb} - A data frame with 418,620 rows and 49 columns:
+#' \itemize{
+#'   \item \emph{drug_name} - Primary drug name (upper case, NCI Thesaurus)
+#'   \item \emph{nci_concept_display_name} - Primary drug name (NCI Thesaurus)
+#'   \item \emph{drug_type} - type of drug molecule (Antibody, small molecule etc)
+#'   \item \emph{drug_action_type} - main action elicited by drug (antagonist, inhibitor, stabiliser etc)
+#'   \item \emph{molecule_chembl_id} - ChEMBL compound identifier
+#'   \item \emph{drug_max_phase_indication} - maximum clinical phase for drug (given indication)
+#'   \item \emph{drug_max_ct_phase} - maximum clinical phase for drug (any indication)
+#'   \item \emph{target_genename} - name/description of drug target
+#'   \item \emph{target_symbol} - symbol of drug target
+#'   \item \emph{target_type} - type of drug target (single protein, protein family etc.)
+#'   \item \emph{target_ensembl_gene_id} - Ensembl gene identifier of drug target
+#'   \item \emph{target_entrezgene} - Entrez gene identifier of drug target
+#'   \item \emph{target_uniprot_id} - UniProt identifier of drug target
+#'   \item \emph{disease_efo_id} - EFO (Experimental Factor Ontology) identifier for drug indication
+#'   \item \emph{disease_efo_label} - EFO (Experimental Factor Ontology) label for drug indication
+#'   \item \emph{cui} - UMLS metathesaurus identifier (concept unique identifier) for drug indication
+#'   \item \emph{cui_name} - UMLS metahesaurus name for drug indication
+#'   \item \emph{primary_site} - primary tumor site/type (obtained through https://github.com/sigven/oncoPhenoMap)
+#'   \item \emph{nci_concept_synonym} - drug synonym (NCI, Open Targets Platform)
+#'   \item \emph{nci_concept_synonym_all} - all drug synonyms (NCI Thesurus, Open Targets Platform)
+#'   \item \emph{drug_clinical_source} - underlying source for drug entry (DailyMed, clinicaltrials.gov, FDA etc.)
+#'   \item \emph{drug_approved_indication} - logical indicating if drug has an approved indication
+#'   \item \emph{drug_blacbox_warning} - logical indicating if drug has blackbox warning
+#'   \item \emph{drug_year_first_approval} - year drug was first approved
+#'   \item \emph{drug_clinical_id} - drug clinical identifier (clinicaltrials.gov, DailyMed, FDA etc.)
+#'   \item \emph{nci_t} - NCI Thesaurus identifier
+#'   \item \emph{nci_concept_definition} - detailed description of drug mechanism-of-action (NCI Thesaurus)
+#'   \item \emph{nci_version} - version of NCI used for this version of oncoPharmaDB
+#'   \item \emph{chembl_version} - version of ChEMBL used for this version of oncoPharmaDB
+#'   \item \emph{opentargets_version} - version of Open Target Platform used for this version of oncoPharmaDB
+#'   \item \emph{comb_regimen_indication} - type of drug molecule (Antibody, small molecule etc)
+#'   \item \emph{immune_checkpoint_inhibitor} - logical indicating if drug is an immune checkpoint inhibitor
+#'   \item \emph{topoisomerase_inhibitor} - logical indicating if drug is a topoisomerase inhibitor
+#'   \item \emph{tubulin_inhibitor} - logical indicating if drug is a tubulin inhibitor
+#'   \item \emph{kinase_inhibitor} - logical indicating if drug is a kinase inhibitor
+#'   \item \emph{hdac_inhibitor} - logical indicating if drug is a HDAC inhibitor
+#'   \item \emph{parp_inhibitor} - logical indicating if drug is a PARP inhibitor
+#'   \item \emph{bet_inhibitor} - logical indicating if drug is a BET inhibitor
+#'   \item \emph{ar_antagonist} - logical indicating if drug is an androgen receptor antagonist
+#'   \item \emph{monoclonal_antibody} - logical indicating if drug is an antibody
+#'   \item \emph{antimetabolite} - logical indicating if drug is an antimetabolite
+#'   \item \emph{angiogenesis_inhibitor} - logical indicating if drug is an angiogenesis inhibitor
+#'   \item \emph{alkylating_agent} - logical indicating if drug is an alkylating agent
+#'   \item \emph{platinum_compound} - logical indicating if drug is a platinum compound
+#'   \item \emph{anthracycline} - logical indicating if drug is an anthracycline
+#'   \item \emph{proteasome_inhibitor} - logical indicating if drug is a proteasome inhibitor
+#'   \item \emph{hormone_therapy} - logical indicating if drug is a hormone therapy
+#'   \item \emph{hedgehog_antagonist} - logical indicating if drug is a hedgehog pathway antagonist
+#' }
+#'
+#'
+#' @source \url{https://targetvalidation.org/}
+#' @source \url{https://www.ebi.ac.uk/chembl/}
+#' @source \url{https://ncithesaurus.nci.nih.gov/ncitbrowser/}
+"oncopharmadb"
+
+#' Dataset of drug synonyms - linking known drug aliases to a primary identifier
+#'
+#' @format \bold{oncopharma_synonyms} - A data frame with 9,946 rows and 52 columns:
+#' \itemize{
+#'   \item \emph{alias} - drug alias
+#'   \item \emph{nci_concept_display_name} - Primary drug name (NCI Thesaurus)
+#'   \item \emph{molecule_chembl_id} - ChEMBL compound identifier
+#' }
+#'
+#' @source \url{https://targetvalidation.org/}
+#' @source \url{https://www.ebi.ac.uk/chembl/}
+#' @source \url{https://ncithesaurus.nci.nih.gov/ncitbrowser/}
+"oncopharma_synonyms"