NCI 24.10d & CIVIC 20241108

Author: sigven

NEWS.md

@@ -1,3 +1,8 @@
+# Version 1.8.1
+
+* CIViC update (20241107)
+* NCI Thesaurus update (24.10d)
+
 # Version 1.8.0
 
 * CIViC update (20241102)

R/sysdata.rda

@@ -271,7 +271,7 @@ CENP-E	CENPE
 CYP17	CYP17A1
 EBNA-1	EBNA1
 STP938	CTPS1
-HS-10502	PARP1
+HS-10502|GS-0201|HRS-1167|IMP1734|SNV1521	PARP1
 ORIC-944	PRC2
 NPX267	KIR3DL3
 ADA-011	LILRB1
@@ -376,6 +376,7 @@ DNMT1	DNMT1
 CTX-712	CLK1
 CTX-712	CLK2
 STC-15	METTL3
+RO7589831|HRO761	WRN
 ATI-2231	MAPKAPK2
 NLRP3 Inhibitor	NLRP3
 Epidermal Growth Factor Receptor|Anti-[A-Za-z]{1,}[0-9]{0,}/EGFR|EGFR (.+)?Antagonist	EGFR
@@ -420,6 +421,7 @@ CDC7	CDC7
 HIF-1alpha	HIF1A
 (FAK )	PTK2
 (Fascin )	FSCN1
+FX-909	PPARG
 (Gamma-Secretase )	GSAP
 Uridine Phosphorylase Inhibitor	UPP1
 EZH2	EZH2
@@ -432,6 +434,7 @@ NEDD8 Activating Enzyme E1	NAE1
 MetAP2	METAP2
 (Mps1 )	TTK
 MKNK1	MKNK1
+Tegtociclib	CDK2
 MNK1/2	MKNK1
 MNK1/2	MKNK2
 (CDK4/6)	CDK4
@@ -471,7 +474,6 @@ Menin Inhibitor	MEN1
 FGF Receptor Antagonist HGS1036	FGFR1
 Gunagratinib	FGFR1
 Gunagratinib	FGFR2
-
 Gunagratinib|LOXO-435	FGFR3
 Gunagratinib	FGFR4
 Vofatamab	FGFR3
@@ -481,7 +483,7 @@ Anti-NY-ESO(-)?1	CTAG1B
 Anti-GITR|Anti-human GITR	TNFRSF18
 Anti-BCMA	TNFRSF17
 17beta-Hydroxysteroid Dehydrogenase Type 5 Inhibitor	AKR1C3
-Adagrasib	KRAS
+Adagrasib|AZD0022|LY3962673	KRAS
 Anti-CD123	IL3RA
 Anti-CD33(-|/| )	CD33
 Anti-CD38(-|/| )	CD38

data-raw/custom_drug_target_regex_nci.tsv

@@ -74,7 +74,7 @@ drug_sets <- list()
 ## Get all anticancer drugs, NCI thesaurus + DGIdb
 drug_sets[['nci']] <- get_nci_drugs(
   nci_db_release = nci_db_release,
-  overwrite = F,
+  overwrite = T,
   path_data_raw = path_data_raw,
   path_data_processed = path_data_tmp_processed)
 
@@ -207,7 +207,7 @@ biomarkers[['metadata']] <- metadata$biomarkers
 #  substr(as.character(packageVersion("pharmOncoX")),1,4),
 #  as.character(as.integer(substr(as.character(packageVersion("pharmOncoX")),5,5)) + 1))
 
-version_bump <- "1.8.0"
+version_bump <- "1.8.1"
 
 db <- list()
 db[['biomarkers']] <- biomarkers

data-raw/data-raw.R

@@ -586,7 +586,7 @@ get_nci_drugs <- function(nci_db_release = nci_db_release,
 
     ## parse all entries in nci thesaurus where the 
     ## semantic concept type is treatment-related
-    nci_antineo_thesaurus_raw2 <- as.data.frame(
+    nci_antineo_thesaurus_raw <- as.data.frame(
       read.table(file = file.path(path_data_raw, "nci_thesaurus", "Thesaurus.txt"),
                  header = F, stringsAsFactors = F, sep="\t",
                  comment.char="", quote = "") |>

data-raw/drug_utilities.R

@@ -15,9 +15,9 @@ releases of external databases:
 
  - Open Targets Platform (2024.09)
  - ChEMBL (v35)
- - NCI Thesaurus (24.09e)
+ - NCI Thesaurus (24.10d)
  - MitelmanDB (20241015)
- - CIViC (20241102)
+ - CIViC (20241108)
 
 ### Getting started