Adding MassBank (#77)

taxonomicallyinformedannotation · Sep 6, 2023 · 06a0ff4 · 06a0ff4
1 parent 2c71f31
commit 06a0ff4
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Showing 12 changed files with 240 additions and 69 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -15,6 +15,7 @@ BugReports: https://github.com/taxonomicallyinformedannotation/tima-r/issues
 Depends:
     R (>= 4.3.0)
 Imports:
+    AnnotationHub (>= 3.8.0),
     crayon (>= 1.5.2),
     docopt (>= 0.7.1),
     dplyr (>= 1.1.3),
@@ -98,6 +99,7 @@ Collate:
     'get_example_sirius.R'
     'get_gnps_tables.R'
     'get_last_version_from_zenodo.R'
+    'get_massbank_spectra.R'
     'get_organism_taxonomy_ott.R'
     'parse_yaml_paths.R'
     'parse_yaml_params.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -31,6 +31,7 @@ export(get_example_sirius)
 export(get_file)
 export(get_gnps_tables)
 export(get_last_version_from_zenodo)
+export(get_massbank_spectra)
 export(get_organism_taxonomy_ott)
 export(get_params)
 export(harmonize_names_sirius)

diff --git a/R/annotate_spectra.R b/R/annotate_spectra.R
@@ -50,7 +50,7 @@ annotate_spectra <- function(input = params$files$spectral$raw,
 
   params <<- parameters
   if (length(library) > 1) {
-    library <- library[[polarity]]
+    library <- library[grepl(polarity, library)]
   }
 
   log_debug("Loading spectra...")
@@ -64,6 +64,7 @@ annotate_spectra <- function(input = params$files$spectral$raw,
 
   df_empty <- data.frame(
     feature_id = NA,
+    candidate_library = NA,
     candidate_error_mz = NA,
     candidate_structure_name = NA,
     candidate_structure_inchikey_no_stereo = NA,
@@ -146,7 +147,8 @@ annotate_spectra <- function(input = params$files$spectral$raw,
       lib_precursors * (1 + (10^-6 * ppm))
     )
 
-    lib_id <- spectral_library@backend@spectraData$spectrum_id
+    lib_id <- seq_along(1:length(spectral_library))
+    spectral_library$spectrum_id <- lib_id
     lib_spectra <- spectral_library@backend@peaksData
 
     calculate_entropy_score <-
@@ -259,15 +261,15 @@ annotate_spectra <- function(input = params$files$spectral$raw,
       lib_inchikey <- rep(NA_character_, length(spectral_library))
     }
     lib_inchikey2D <-
-      spectral_library@backend@spectraData$inchikey_no_stereo
+      spectral_library@backend@spectraData$inchikey_2D
     if (is.null(lib_inchikey2D)) {
       lib_inchikey2D <- rep(NA_character_, length(spectral_library))
     }
     lib_smiles <- spectral_library@backend@spectraData$smiles
     if (is.null(lib_smiles)) {
       lib_smiles <- rep(NA_character_, length(spectral_library))
     }
-    lib_smiles2D <- spectral_library@backend@spectraData$smiles_no_stereo
+    lib_smiles2D <- spectral_library@backend@spectraData$smiles_2D
     if (is.null(lib_smiles2D)) {
       lib_smiles2D <- rep(NA_character_, length(spectral_library))
     }
@@ -310,7 +312,6 @@ annotate_spectra <- function(input = params$files$spectral$raw,
       tidytable::select(-target_id)
 
     df_final <- df_final |>
-      tidytable::rowwise() |>
       tidytable::mutate(
         candidate_structure_error_mz = target_precursorMz - precursorMz,
         candidate_structure_inchikey_no_stereo = ifelse(

diff --git a/R/get_massbank_spectra.R b/R/get_massbank_spectra.R
@@ -0,0 +1,48 @@
+#' @title Get MassBank spectra
+#'
+#' @description This function gets MassBank spectra
+#'
+#' @param output_dir Output where to store the spectra
+#'
+#' @return NULL
+#'
+#' @export
+#'
+#' @examples NULL
+get_massbank_spectra <-
+  function(output_dir = "data/source/libraries/spectra/exp/") {
+    log_debug("Loading last AnnotationHub version ...")
+    ah <- AnnotationHub::AnnotationHub()
+
+    log_debug("Querying for most recent MassBank version available ...")
+    ahmb <- AnnotationHub::query(ah, "MassBank")
+    mb_last <- ahmb$ah_id |> tail(1)
+
+    export <- file.path(output_dir, paste0(mb_last, ".mgf"))
+
+    log_debug("Checking if a previous MassBank version already exists")
+    if (!file.exists(export)) {
+      log_debug("Downloading most recent MassBank version available ...")
+      mb_sp <- AnnotationHub::AnnotationHub()[[mb_last]] |>
+        Spectra::Spectra()
+      log_debug("Removing faulty columns")
+      mb_sp_2 <- mb_sp |>
+        Spectra::selectSpectraVariables(
+          Spectra::spectraVariables(mb_sp)[!grepl(
+            pattern = "synonym",
+            x = Spectra::spectraVariables(mb_sp)
+          )]
+        ) |>
+        log_pipe("Exporting") |>
+        Spectra::export(
+          backend = MsBackendMgf::MsBackendMgf(),
+          file = export
+        )
+    } else {
+      log_debug(
+        "It appears you already have",
+        "the most recent MassBank version available!"
+      )
+    }
+    return(export)
+  }
diff --git a/codemeta.json b/codemeta.json
@@ -304,6 +304,19 @@
       "version": ">= 4.3.0"
     },
     "2": {
+      "@type": "SoftwareApplication",
+      "identifier": "AnnotationHub",
+      "name": "AnnotationHub",
+      "version": ">= 3.8.0",
+      "provider": {
+        "@id": "https://www.bioconductor.org",
+        "@type": "Organization",
+        "name": "Bioconductor",
+        "url": "https://www.bioconductor.org"
+      },
+      "sameAs": "https://bioconductor.org/packages/release/bioc/html/AnnotationHub.html"
+    },
+    "3": {
       "@type": "SoftwareApplication",
       "identifier": "crayon",
       "name": "crayon",
@@ -316,7 +329,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=crayon"
     },
-    "3": {
+    "4": {
       "@type": "SoftwareApplication",
       "identifier": "docopt",
       "name": "docopt",
@@ -329,7 +342,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=docopt"
     },
-    "4": {
+    "5": {
       "@type": "SoftwareApplication",
       "identifier": "dplyr",
       "name": "dplyr",
@@ -342,7 +355,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=dplyr"
     },
-    "5": {
+    "6": {
       "@type": "SoftwareApplication",
       "identifier": "httr2",
       "name": "httr2",
@@ -355,7 +368,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=httr2"
     },
-    "6": {
+    "7": {
       "@type": "SoftwareApplication",
       "identifier": "igraph",
       "name": "igraph",
@@ -368,7 +381,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=igraph"
     },
-    "7": {
+    "8": {
       "@type": "SoftwareApplication",
       "identifier": "jsonlite",
       "name": "jsonlite",
@@ -381,7 +394,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=jsonlite"
     },
-    "8": {
+    "9": {
       "@type": "SoftwareApplication",
       "identifier": "MsBackendMgf",
       "name": "MsBackendMgf",
@@ -394,7 +407,7 @@
       },
       "sameAs": "https://bioconductor.org/packages/release/bioc/html/MsBackendMgf.html"
     },
-    "9": {
+    "10": {
       "@type": "SoftwareApplication",
       "identifier": "msentropy",
       "name": "msentropy",
@@ -407,7 +420,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=msentropy"
     },
-    "10": {
+    "11": {
       "@type": "SoftwareApplication",
       "identifier": "pbapply",
       "name": "pbapply",
@@ -420,7 +433,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=pbapply"
     },
-    "11": {
+    "12": {
       "@type": "SoftwareApplication",
       "identifier": "R.utils",
       "name": "R.utils",
@@ -433,7 +446,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=R.utils"
     },
-    "12": {
+    "13": {
       "@type": "SoftwareApplication",
       "identifier": "rotl",
       "name": "rotl",
@@ -446,7 +459,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=rotl"
     },
-    "13": {
+    "14": {
       "@type": "SoftwareApplication",
       "identifier": "Spectra",
       "name": "Spectra",
@@ -459,12 +472,12 @@
       },
       "sameAs": "https://bioconductor.org/packages/release/bioc/html/Spectra.html"
     },
-    "14": {
+    "15": {
       "@type": "SoftwareApplication",
       "identifier": "stats",
       "name": "stats"
     },
-    "15": {
+    "16": {
       "@type": "SoftwareApplication",
       "identifier": "stringi",
       "name": "stringi",
@@ -477,7 +490,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=stringi"
     },
-    "16": {
+    "17": {
       "@type": "SoftwareApplication",
       "identifier": "tidytable",
       "name": "tidytable",
@@ -490,7 +503,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=tidytable"
     },
-    "17": {
+    "18": {
       "@type": "SoftwareApplication",
       "identifier": "tidyfst",
       "name": "tidyfst",
@@ -503,12 +516,12 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=tidyfst"
     },
-    "18": {
+    "19": {
       "@type": "SoftwareApplication",
       "identifier": "utils",
       "name": "utils"
     },
-    "19": {
+    "20": {
       "@type": "SoftwareApplication",
       "identifier": "yaml",
       "name": "yaml",

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -20,6 +20,7 @@ InChI
 InChIKey
 Lifecycle
 MatchForwardReverseParam
+MassBank
 MGF
 MegaLinter
 MsCoreUtils

diff --git a/inst/app/server.R b/inst/app/server.R
@@ -117,10 +117,11 @@ server <- function(input, output, session) {
             "benchmark_ann_pre_ms2_b_c_pos",
             "benchmark_ann_pre_ms2_b_neg",
             "benchmark_ann_pre_ms2_b_pos",
-            "benchmark_ann_spe_is_lot_neg",
-            "benchmark_ann_spe_is_lot_pos",
-            "benchmark_ann_spe_is_pre_neg",
-            "benchmark_ann_spe_is_pre_pos",
+            "benchmark_ann_sir_pre",
+            "benchmark_ann_spe_neg",
+            "benchmark_ann_spe_pos",
+            "benchmark_ann_spe_pre_neg",
+            "benchmark_ann_spe_pre_pos",
             "benchmark_com_neg",
             "benchmark_com_pos",
             "benchmark_com_pre_neg",
@@ -132,6 +133,7 @@ server <- function(input, output, session) {
             "benchmark_def_cre_edg_com",
             "benchmark_def_cre_edg_spe",
             "benchmark_def_fil_ann",
+            "benchmark_def_pre_ann_sir",
             "benchmark_def_pre_ann_spe",
             "benchmark_def_pre_fea_com",
             "benchmark_def_pre_fea_edg",

diff --git a/inst/params/default/annotate_spectra.yaml b/inst/params/default/annotate_spectra.yaml
@@ -29,11 +29,13 @@ files:
       exp:
         #' List of negative experimental spectral libraries. STRING
         neg:
-          - data/interim/libraries/spectra/exp/internal_neg.rds
+          - data/interim/libraries/spectra/exp/massbank_neg.rds
+          # - data/interim/libraries/spectra/exp/internal_neg.rds
 
         #' List of positive experimental spectral libraries. STRING
         pos:
-          - data/interim/libraries/spectra/exp/internal_pos.rds
+          - data/interim/libraries/spectra/exp/massbank_pos.rds
+          # - data/interim/libraries/spectra/exp/internal_pos.rds
 
       #' In silico libraries
       is:

diff --git a/inst/params/default/params.yaml b/inst/params/default/params.yaml
@@ -152,11 +152,13 @@ files:
       exp:
         #' List of negative experimental spectral libraries. STRING
         neg:
-          - data/interim/libraries/spectra/exp/internal_neg.rds
+          - data/interim/libraries/spectra/exp/massbank_neg.rds
+          # - data/interim/libraries/spectra/exp/internal_neg.rds
 
         #' List of positive experimental spectral libraries. STRING
         pos:
-          - data/interim/libraries/spectra/exp/internal_pos.rds
+          - data/interim/libraries/spectra/exp/massbank_pos.rds
+          # - data/interim/libraries/spectra/exp/internal_pos.rds
 
       #' In silico libraries
       is: