NCI 24.09e, OTP 2024.09, skip DGIDB chembl map

sigven · Nov 2, 2024 · 20b04da · 20b04da
1 parent e39a5f4
commit 20b04da
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Showing 7 changed files with 178 additions and 1,365 deletions.
diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/data-raw/custom_drug_target_regex_nci.tsv b/data-raw/custom_drug_target_regex_nci.tsv
@@ -74,7 +74,7 @@ Tolinapant|Xevinapant|Smac Mimetic	BIRC2
 Xevinapant|(Smac|SMAC) Mimetic	BIRC3
 Tolinapant|Idronoxil|Xevinapant|Smac Mimetic	XIAP
 hSTC810	BTN1A1
-Divarasib|Opnurasib	KRAS
+Divarasib|Opnurasib|INCB161734|QTX3046|RMC-9805|TSN1611|QTX3034|RMC-6236	KRAS
 Ras Inhibitor LUNA18	KRAS
 Ras Inhibitor LUNA18	NRAS
 Ras Inhibitor LUNA18	HRAS
@@ -90,11 +90,11 @@ Tinengotinib	FLT1
 Tinengotinib	KDR
 Tinengotinib	FLT3
 Tinengotinib	FLT4
-pan-RAF Inhibitor|pan-RAF Kinase Inhibitor	BRAF
-pan-RAF Inhibitor|pan-RAF Kinase Inhibitor	ARAF
-pan-RAF Inhibitor|pan-RAF Kinase Inhibitor	CRAF
+pan-RAF Inhibitor|pan-RAF Kinase Inhibitor|Brimarafenib|BDTX-4933|DCC-3084	BRAF
+pan-RAF Inhibitor|pan-RAF Kinase Inhibitor|BDTX-4933|DCC-3084	ARAF
+pan-RAF Inhibitor|pan-RAF Kinase Inhibitor|BDTX-4933|DCC-3084	CRAF
 Ebvaciclib|Tagtociclib	CDK2
-Ebvaciclib	CDK4
+Ebvaciclib|Atirmociclib	CDK4
 Ebvaciclib	CDK6
 Utatrectinib	NTRK1
 Utatrectinib	NTRK2

diff --git a/data-raw/data-raw.R b/data-raw/data-raw.R
@@ -21,7 +21,7 @@ opentargets_version <-
   metadata$compounds[metadata$compounds$source_abbreviation == "opentargets", 
                      "source_version"]
 package_datestamp <- stringr::str_replace_all(Sys.Date(),"-","")
-chembl_pubchem_datestamp <- '20240708' 
+chembl_pubchem_datestamp <- '20241024' 
 
 ## set logging layout
 lgr::lgr$appenders$console$set_layout(
@@ -81,7 +81,7 @@ drug_sets[['nci']] <- get_nci_drugs(
 #### -- Open Targets Platform - drugs ---####
 ## Get all targeted anticancer/other drugs from Open Targets Platform
 drug_sets[['otp']] <-
-  get_opentargets_cancer_drugs(
+  get_otp_cancer_drugs(
     path_data_raw = path_data_raw,
     ot_version = opentargets_version)
 
@@ -101,7 +101,7 @@ drug_sets[['nci_otp_curated']] <- map_curated_targets(
   gene_info = gene_info,
   path_data_raw = path_data_raw,
   drug_df = drug_sets[['nci_otp']]
-)
+)$curated
 
 ####-- Cancer drugs classified into categories (ATC) ---####
 drug_sets[['nci_otp_curated_classified']] <- assign_drug_category(
@@ -194,19 +194,20 @@ raw_biomarkers[['depmap']] <-
 raw_biomarkers[['custom_fusions']]$variant <- 
   raw_biomarkers[['custom_fusions']]$variant |>
   dplyr::anti_join(
-    raw_biomarkers[["mitelmandb"]][['variant']], by = "variant_alias")
+    raw_biomarkers[["mitelmandb"]][['variant']], 
+    by = "variant_alias")
 
 biomarkers <- list()
 biomarkers[['data']] <- raw_biomarkers
 biomarkers[['metadata']] <- metadata$biomarkers
 #rm(biomarkers_all)
 
 ## upload to Google Drive
-version_bump <- paste0(
-  substr(as.character(packageVersion("pharmOncoX")),1,4),
-  as.character(as.integer(substr(as.character(packageVersion("pharmOncoX")),5,5)) + 1))
+#version_bump <- paste0(
+#  substr(as.character(packageVersion("pharmOncoX")),1,4),
+#  as.character(as.integer(substr(as.character(packageVersion("pharmOncoX")),5,5)) + 1))
 
-
+version_bump <- "1.8.0"
 
 db <- list()
 db[['biomarkers']] <- biomarkers
@@ -221,7 +222,7 @@ db[['drug_map_basic']][['records']] <- drug_index_map[['id2basic']]
 db[['drug_map_alias']] <- list()
 db[['drug_map_alias']][['records']] <- drug_index_map[['id2alias']]
 
-googledrive::drive_auth_configure(api_key = Sys.getenv("GD_KEY"))
+#googledrive::drive_auth_configure(api_key = Sys.getenv("GD_KEY"))
 
 gd_records <- list()
 db_id_ref <- data.frame()

diff --git a/data-raw/drug_name_black_list.txt b/data-raw/drug_name_black_list.txt
@@ -9,6 +9,7 @@ Sodium Caseinate
 AXL-1717
 AZD-7451
 TAS-115
+RAC-3-N-BUTYLPHTHALIDE
 Lenperone Hydrochloride
 ABT-126
 AZD-3759