Update example and metal_list

R/extract_metal_binders.R

@@ -90,7 +90,8 @@
 #'   columns = c(
 #'     "ft_binding",
 #'     "cc_cofactor",
-#'     "cc_catalytic_activity"
+#'     "cc_catalytic_activity",
+#'     "keyword"
 #'   )
 #' )
 #'
@@ -690,11 +691,14 @@ extract_metal_binders <- function(data_uniprot,
     )) %>%
     dplyr::mutate(chebi_id = str_split(.data$chebi_id, pattern = ";")) %>%
     tidyr::unnest("chebi_id") %>%
+    # Use the atom id if chebi ion ID is not present
     dplyr::mutate(chebi_id = ifelse(is.na(.data$chebi_id),
       stats::setNames(metal_list$chebi_id, metal_list$name)[.data$keyword],
       .data$chebi_id
     )) %>%
+    # first use uniprot data to directly annotate IDs that don't have a formula with the correct metal
     dplyr::mutate(metal_id_part = stats::setNames(metal_chebi_uniprot$metal_atom_id, as.character(metal_chebi_uniprot$id))[.data$chebi_id]) %>%
+    # then use the metal_list to annotate the rest
     dplyr::mutate(metal_id_part = ifelse(is.na(.data$metal_id_part),
       stats::setNames(unlisted_metal_list$chebi_id, as.character(unlisted_metal_list$chebi_ion_id))[.data$chebi_id],
       .data$metal_id_part

data-raw/metal_list.R

@@ -513,25 +513,25 @@ metal_list <- data.frame(
     "33610",
     "29101",
     "39127",
-    "60272",
+    "63062",
     "37763", # elemental
     "29103",
-    "39124",
+    "39123",
     "155869", # elemental
     "190496",
     "35172",
-    "61310",
+    "33516",
     "25155",
     "24875",
     "23336",
-    "60248",
+    "25516",
     "23378",
-    "27365",
+    "63056",
     "84043",
     "30549;30550",
     "35826", # elemental
     "49847",
-    "39130",
+    "39129",
     "49978;49962",
     NA, # no zirconium ion
     "155922", # elemental
@@ -540,22 +540,22 @@ metal_list <- data.frame(
     "30686;49862",
     NA, # no Rhodium ion
     NA, # no Palladium ion
-    "60247",
+    "60253",
     "63063",
     "49664",
     "30475;30476",
     "49867",
     "36660", # elemental
     "60270",
-    "39126",
+    "39125",
     "37317;49701",
-    "37265", # elemental
+    "37265", # elemental submitted: CHEBI:231845
     "229784",
     "229785",
     NA, # no Promethium ion
     "49890",
     "49588;49591",
-    "37285", # elemental
+    "37285", # elemental submitted: CHEBI:231846
     "49902",
     NA, # no Dysprosium ion
     "49650",
@@ -573,8 +573,8 @@ metal_list <- data.frame(
     "33970", # elemental
     "25197",
     "49920;30439",
-    "60249",
-    "85543",
+    "60252",
+    "85544",
     NA, # no Polonium ion
     NA, # no Astatine ion
     "33502",