civic/mitelman db update

Author: sigven

NEWS.md

@@ -1,3 +1,8 @@
+# Version 2.1.8
+
+* CIViC update (20260119)
+* MitelmanDB update (20260115)
+
 # Version 2.1.7
 
 * CIViC update (20260101)

R/sysdata.rda

@@ -5,8 +5,8 @@ RMC-9085|Fulzerasib|RG6620|VS-7375|Olomorasib	KRAS
 Rofecoxib|MTI-301	SCD
 ALTA2618|ATV-1601	AKT1
 Elironrasib	KRAS
-Rineterkib	ERK1
-Rineterkib	ERK2
+Rineterkib	MAPK3
+Rineterkib	MAPK1
 Zoligratinib	FGFR1
 Zoligratinib	FGFR2
 Zoligratinib	FGFR3
@@ -16,8 +16,10 @@ Navicixizumab	DLL4
 Osunprotafib	PTPN2
 Tigozertinib	EGFR
 Acasunlimab	CD274
-ABD-3001	ALDH1
-ABD-3001	ALDH3
+ABD-3001	ALDH1A1
+ABD-3001	ALDH3A1
+GSK2879552	KDM1A
+AZD5153	BRD4
 OATD-02	ARG1
 OATD-02	ARG2
 Glecirasib	KRAS
@@ -38,7 +40,7 @@ Fexagratinib	FGFR4
 Firmonertinib	EGFR
 HIF-2alpha Inhibitor	EPAS1
 HMGB1 Inhibitor	HMGB1
-Izalontamab	HER1
+Izalontamab	EGFR
 Izalontamab	ERBB3
 DGK-alpha Inhibitor	DGKH
 DGKalpha Inhibitor	DGKH
@@ -102,7 +104,7 @@ Tinengotinib	FLT3
 Tinengotinib	FLT4
 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
+pan-RAF Inhibitor|pan-RAF Kinase Inhibitor|BDTX-4933|DCC-3084	RAF1
 Ebvaciclib|Tagtociclib|Certociclib	CDK2
 Ebvaciclib|Atirmociclib	CDK4
 Ebvaciclib	CDK6
@@ -285,15 +287,13 @@ HS-10502|GS-0201|HRS-1167|IMP1734|SNV1521	PARP1
 ORIC-944	PRC2
 NPX267	KIR3DL3
 ADA-011	LILRB1
-ABD-3001	ALDH1
-ABD-3001	ALDH3
 Ivonescimab	PDCD1
 (FASN )	FASN
 Glutaminase	GLS
 GSK-3	GSK3A
 GSK-3	GSK3B
 belvarafenib|exarafenib	BRAF
-belvarafenib	CRAF
+belvarafenib	RAF1
 nhibitor of 6-phosphofructo-2-kinase	PFKFB3
 belumosudil binds to and inhibits	ROCK2
 protein kinase C (PKC) inhibitor	PRKCA
@@ -338,6 +338,9 @@ QLC1101|KQB365|QTX3544|Elisrasib	KRAS
 Amdizalisib	PIK3CD
 Trodusquemine	PTP1B
 Mahatinib	TNK2
+MAK683	EED
+ERAS-801	EGFR
+GSK4418959|MOMA-341|NDI-219216|HRO761	WRN
 Razuprotafib	PTPRB
 Zunsemetinib	MAP2K2
 CPB/p300 Bromodomain Inhibitor	CREB1
@@ -475,7 +478,7 @@ Apomab	TNFRSF10B
 Astegolimab	ST2
 Burosumab	FGF23
 BCL-2|Bcl-2	BCL2
-Empesertib	MPS1
+Empesertib	TTK
 Enavatuzumab	TNFRSF12A
 Enokizumab	IL9
 Enoticumab	DLL4

data-raw/custom_drug_target_regex_nci.tsv

@@ -51,14 +51,18 @@ gene_info <- dplyr::bind_rows(
                   symbol, name, gene_biotype),
     dplyr::select(gene_gencode$records$grch38, 
                   entrezgene, ensembl_gene_id),
-    by = c("entrezgene"), multiple = "all"),
+    by = c("entrezgene"), 
+    relationship = "many-to-many"),
   dplyr::inner_join(
     dplyr::select(gene_basic$records, entrezgene, 
                   symbol, name, gene_biotype),
     dplyr::select(gene_gencode$records$grch37, 
                   entrezgene, ensembl_gene_id),
-    by = c("entrezgene"), multiple = "all")) |>
-  dplyr::filter(gene_biotype == "protein_coding") |>
+    by = c("entrezgene"), 
+    relationship = "many-to-many")) |>
+  dplyr::filter(
+    gene_biotype == "protein_coding" |
+      gene_biotype == "unknown") |>
   dplyr::distinct() |>
   dplyr::mutate(association_sourceID = "nci_thesaurus_custom",
                 target_type = "single_protein") |>
@@ -213,7 +217,7 @@ biomarkers[['metadata']] <- metadata$biomarkers
 #  substr(as.character(packageVersion("pharmOncoX")),1,4),
 #  as.character(as.integer(substr(as.character(packageVersion("pharmOncoX")),5,5)) + 1))
 
-version_bump <- "2.1.7"
+version_bump <- "2.1.8"
 
 db <- list()
 db[['biomarkers']] <- biomarkers

data-raw/data-raw.R

@@ -1049,7 +1049,8 @@ map_curated_targets <- function(gene_info = NULL,
       sep = "\t", header = T, 
       stringsAsFactors = F, quote = "") |>
     dplyr::inner_join(
-      gene_info, by = "symbol", multiple = "all", 
+      gene_info, by = "symbol", 
+      multiple = "all", 
       relationship = "many-to-many") |>
     dplyr::distinct()
 
@@ -1163,11 +1164,16 @@ map_curated_targets <- function(gene_info = NULL,
       "(A|a)ntibody(-| )drug conjugate \\(ADC\\)"
     )) |>
     dplyr::filter(!stringr::str_detect(
-      tolower(nci_cd_name),"^(allogeneic|regimen |copper |fluorine f |indium |iodine |carbon c|autologous |recombinant |lutetium |yttrium |y 90)|vaccine$"
+      tolower(nci_cd_name),
+      paste0(
+        "^(allogeneic|regimen |copper |fluorine f |",
+        "indium |iodine |carbon c|autologous |",
+        "recombinant |lutetium |yttrium |y 90)|vaccine$")
     )) |>
     dplyr::filter(
       stringr::str_detect(
-        nci_concept_definition, "antineoplastic|tumor|cancer"
+        nci_concept_definition, 
+        "antineoplastic|tumor|cancer"
       )
     ) |>
     dplyr::select(nci_cd_name,