civic update and fusion alias filtering

data-raw/biomarker_utilities.R

@@ -2530,10 +2530,22 @@ load_mitelman_db <- function(cache_dir = NA,
                     evidence_id, 
                     source_id) |>
       tidyr::separate_rows(variant_alias, sep = "@@@") |>
-      #dplyr::rename(variant_alias = alias) |>
+
+      ## Remove aliases where fusion partners are mentioned in reverse order
+      #dplyr::filter(
+        # !stringr::str_detect(
+        #   variant_alias,
+        #   paste0(
+        #     "RARA::PML|ABL1::BCR|ERG::TMPRSS2|RUNX1T1::RUNX1|NSD1::NUP98|",
+        #     "MYH11::CBFB|RET::KIF5B|RET::CCDC6|ROS1::CD74|CAMTA1::WWTR1|",
+        #     "NPM1::MLF1|BRAF::KIAA1549|CREBBP::KAT6A|MLF1::NPM1"))) |>
       dplyr::filter(
         !stringr::str_detect(
-          variant_alias,"RARA::PML|ABL1::BCR|ERG::TMPRSS2")) |>
+          variant_name_primary,
+          paste0(
+            "RARA::PML|ABL1::BCR|ERG::TMPRSS2|RUNX1T1::RUNX1|NSD1::NUP98|",
+            "MYH11::CBFB|RET::KIF5B|RET::CCDC6|ROS1::CD74|CAMTA1::WWTR1|",
+            "NPM1::MLF1|BRAF::KIAA1549|CREBBP::KAT6A|MLF1::NPM1"))) |>
 
       dplyr::bind_rows(
         bcr_abl_custom

data-raw/data-raw.R

@@ -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 <- "1.8.8"
+version_bump <- "1.8.9"
 
 db <- list()
 db[['biomarkers']] <- biomarkers

data-raw/salts.tsv

@@ -0,0 +1,45 @@
+(M|m)aleate
+(S|s)uccinate
+(T|t)risodium
+(B|b)enzoate
+(B|b)esylate
+(G|g)luconate
+(D|d)ifumarate
+(D|d)iacetate
+(T|t)romethamide
+(T|t)romethamine
+(A|a)nhydrous
+(T|t)osylate
+(D|d)imesylate
+(D|d)imeglumine
+(S|s)uccinate
+(M|m)eglumine
+(H|h)ydrobromide
+(S|s)ulfate
+(F|f)umarate
+(D|d)imaleate
+(D|d)itosylate
+(L|l)actate
+(P|p)otassium
+(H|h)ydrochloride (M|m)onohydrate
+(D|d)ihydrochloride
+(S|s)-malate
+(D|d)isodium
+(T|t)risodium
+(C|c)amsylate
+(C|c)hloride
+(A|a)cetate
+(S|s)odium (P|p)hosphate
+(S|s)odium
+(P|p)hosphate
+(D|d)iphosphate
+(C|c)itrate
+(M|m)esylate
+(A|a)cetate
+(C|c)alcium
+(T|t)osylate
+(T|t)artrate
+(H|h)ydrochloride
+(P|p)ropionate
+(M|m)onosodium
+(N|n)itrate

pharmOncoX.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 61133395-cd0c-4413-abc6-2666b9c039c1
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

pkgdown/index.md

@@ -10,14 +10,14 @@ Drug-target associations from the Open Targets Platform have furthermore been in
 
 _pharmOncoX_ provides anti-cancer drug classification through existing entries in the [Anatomical Therapeutic Chemical (ATC) Classification System](https://www.whocc.no/atc_ddd_index/), and these have been extended significantly with manual curation, also by establishing novel drug categories that are presently missing in the ATC classificiation tree (examples include _AURK inhibitors_, _MET inhibitors_, _BET inhibitors_, _AKT inhibitors_, _PLK inhibitors_, _IAP inhibitors_, _RAS inhibitors_, _BCL2 inhibitors_ etc.) enabling a filtering of drugs according to their main mechanisms of action.
 
-Currently (as of early December 2024), `pharmOncoX` is built upon the following 
+Currently (as of early January 2025), `pharmOncoX` is built upon the following 
 releases of external databases:
 
  - Open Targets Platform (2024.09)
  - ChEMBL (v34)
- - NCI Thesaurus (24.11d)
+ - NCI Thesaurus (24.12e)
  - MitelmanDB (20241015)
- - CIViC (20241221)
+ - CIViC (20250105)
 
 ### Getting started