diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 700bbed..0b4aa59 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, jermiah]
   pull_request:
     branches: [main, master]
 
@@ -31,18 +31,18 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: rcmdcheck
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
         with:
           error-on: '"error"'
\ No newline at end of file
diff --git a/DESCRIPTION b/DESCRIPTION
index bce9f5c..4a578fd 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -5,6 +5,8 @@ Version: 0.0.5.9001
 Authors@R: c(
     person("Christopher", "Eeles", role = c("aut"),
         email = "christopher.eeles@uhnresearch.ca"),
+    person("Jermiah", "Joseph", role = c("aut"),
+        email = "jermiah.joseph@uhn.ca"),
     person("Sisira", "Nair", role = c("aut"),
         email="sisira.nair@uhnresearch.ca"),
     person("Petr", "Smirnov", role=c("aut")),
@@ -30,7 +32,6 @@ Imports:
     qs,
     checkmate,
     rlang,
-    CoreGx,
     crayon,
     memoise,
     R6,
diff --git a/NAMESPACE b/NAMESPACE
index 2f6d128..14e2b30 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(.buildURL)
+export(.createQueryURLs)
 export(.groupListByName)
 export(addAnnotationColumnToDrugs)
 export(characterToNamedVector)
@@ -13,9 +14,10 @@ export(downloadAndExtract)
 export(downloadFDAOrangeBook)
 export(find_remote_files_recursive)
 export(fsquash)
+export(getAllPubChemAnnotations)
 export(getBrainArrayTable)
-export(getCellApi)
 export(getCellosaurus)
+export(getCellosaurusAPI)
 export(getCellosaurusDataFrame)
 export(getCelloxml)
 export(getChemblAllMechanisms)
@@ -31,7 +33,7 @@ export(getGencodeFilesTable)
 export(getGencodeGRangesAnnotated)
 export(getGuideToPharm)
 export(getInfoFromCelllineInput)
-export(getPubChemAnnotations)
+export(getPubChemAnnotation)
 export(getPubChemCompound)
 export(getPubChemFromNSC)
 export(getPubChemSubstance)
@@ -55,7 +57,6 @@ export(scrapeRemoteFTPFilesTable)
 export(zenodoMetadata)
 import(R6)
 import(checkmate)
-import(httr)
 importFrom(BiocParallel,"bplog<-")
 importFrom(BiocParallel,"bpprogressbar<-")
 importFrom(BiocParallel,"bpworkers<-")
@@ -66,8 +67,6 @@ importFrom(BiocParallel,bpparam)
 importFrom(BiocParallel,bpprogressbar)
 importFrom(BiocParallel,bptry)
 importFrom(BiocParallel,bpworkers)
-importFrom(CoreGx,.errorMsg)
-importFrom(CoreGx,.warnMsg)
 importFrom(R6P,Singleton)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,mcols)
diff --git a/R/getCellosaurus.R b/R/getCellosaurus.R
index eab15e1..981149b 100644
--- a/R/getCellosaurus.R
+++ b/R/getCellosaurus.R
@@ -19,54 +19,58 @@
 #' @md
 #' @importFrom xml2 read_xml
 #' @export
-getCelloxml <-
-    memoise::memoise(function(url = "https://ftp.expasy.org/databases/cellosaurus/cellosaurus.xml", verbose = TRUE) {
-      if (verbose) {
-        message(paste(
-          "xml read started from",
-          url,
-          format(Sys.time(), "%Y-%m-%d %H:%M:%S")
-        ))
-      }
-      main_xml <- read_xml(url)
-      if (verbose) {
-        message(paste(
-          "xml read completed at",
-          format(Sys.time(), "%Y-%m-%d %H:%M:%S")
-        ))
-      }
-      return(main_xml)
-    })
-
-#' @md
-#' @importFrom xml2 read_xml xml_find_all
-#' @export
-#########ADD DOCS
-cleanCellnames <-
-  function(main_xml, verbose = TRUE) {
+getCelloxml <- memoise::memoise(function(url = "https://ftp.expasy.org/databases/cellosaurus/cellosaurus.xml", verbose = TRUE) {
     if (verbose) {
       message(paste(
-        "Started removing special characters from cell line names in the xml",
+        "xml read started from",
+        url,
         format(Sys.time(), "%Y-%m-%d %H:%M:%S")
       ))
     }
-    matching <- xml_find_all(main_xml, "//cell-line/name-list/name/text()")
-    # A raw string, added in R 4.0 will excape characters for you: r"{ <string> }"
-    badchars <- r"{[\xb5]|[]|[ ,]|[;]|[:]|[-]|[+]|[*]|[%]|[$]|[#]|[{]|[}]|[[]|[]]|[|]|[^]|[/]|[\]|[.]|[_]|[ ]|[(]|[)]}"
-    for(i in 1:length(matching)){
-      node1 <- matching[[i]]
-      node1text <- xml_text(node1)
-      xml_par <- xml_find_first(node1, "parent::*")
-      xml_set_attr(xml_par, "cleanname", gsub(badchars,"",ignore.case = TRUE, node1text))
-    }
+    main_xml <- read_xml(url)
     if (verbose) {
       message(paste(
-        "Removed special characters from cell line names in the xml",
+        "xml read completed at",
         format(Sys.time(), "%Y-%m-%d %H:%M:%S")
       ))
     }
     return(main_xml)
   }
+)
+
+#' Clean Cell Names
+#' 
+#' @description 
+#' TODO::
+#' 
+#' @md
+#' @importFrom xml2 read_xml xml_find_all
+#' @export
+#########ADD DOCS
+cleanCellnames <- function(main_xml, verbose = TRUE) {
+  if (verbose) {
+    message(paste(
+      "Started removing special characters from cell line names in the xml",
+      format(Sys.time(), "%Y-%m-%d %H:%M:%S")
+    ))
+  }
+  matching <- xml_find_all(main_xml, "//cell-line/name-list/name/text()")
+  # A raw string, added in R 4.0 will excape characters for you: r"{ <string> }"
+  badchars <- r"{[\xb5]|[]|[ ,]|[;]|[:]|[-]|[+]|[*]|[%]|[$]|[#]|[{]|[}]|[[]|[]]|[|]|[^]|[/]|[\]|[.]|[_]|[ ]|[(]|[)]}"
+  for(i in 1:length(matching)){
+    node1 <- matching[[i]]
+    node1text <- xml_text(node1)
+    xml_par <- xml_find_first(node1, "parent::*")
+    xml_set_attr(xml_par, "cleanname", gsub(badchars,"",ignore.case = TRUE, node1text))
+  }
+  if (verbose) {
+    message(paste(
+      "Removed special characters from cell line names in the xml",
+      format(Sys.time(), "%Y-%m-%d %H:%M:%S")
+    ))
+  }
+  return(main_xml)
+}
 
 #' Filter parent node cell-line and parse child nodes for required annotations
 #' @param cell_ip is either cell name or cvcl id.
diff --git a/R/getCellosaurusAPI.R b/R/getCellosaurusAPI.R
new file mode 100644
index 0000000..cdb6a2b
--- /dev/null
+++ b/R/getCellosaurusAPI.R
@@ -0,0 +1,164 @@
+
+#' Create a list of query URLS for Cellosaurus API
+#'
+#' @description
+#' This function creates a queryURL for the cellosaurus API using a list of cell line names
+#'
+#' @details 
+#' Function to create a URL query for Cellosaurus to search for a cell-line using its name 
+#' An example call:   computedURLs <- .createQueryURLs(api = "https://api.cellosaurus.org/", cl_names = c("22rv1", "Hela"), fields = c("id", "ac"))
+#' @return A list of URLS
+#' @param api is the link to the API to build the URL. i.e "https://api.cellosaurus.org/"
+#' @param cl_names is a list of the cell line names
+#' @param format is the type of format to return from the API. Can be "txt" or "json" 
+#' @param num_results is the number of of items to return, DEFAULT=1
+#' @param GETfxn is the function to use on the cellosaurus website. Currently only supports "search/cell-line?"
+#' @param fields is a list of desired fields to include in the response 
+#' 
+#' @md
+#' @export
+.createQueryURLs <- 
+    function(api = "https://api.cellosaurus.org/",
+             cl_names,
+             format = "txt",
+             num_results = 1,
+             GETfxn = c("search/cell-line?", "cell-line/"),
+             fields,
+             q = "idsy:") {
+        
+        if (GETfxn == "search/cell-line?") {
+                # create urls 
+            computedURLs <- paste0(
+                api,
+                GETfxn,
+                "q=", q,
+                gsub(" ", "%20",cl_names),
+                "&rows=", num_results,
+                "&format=", format,
+                "&fields=", paste(fields, collapse=",")
+            )
+            return(computedURLs)
+        } else if (GETfxn == "cell-line/") {
+            computedURLs <- paste0(
+                api,
+                GETfxn,
+                gsub(" ", "%20",cl_names),
+                "?",
+                "format=",format,
+                "&fields=", paste(fields, collapse=",")
+            )
+            return(computedURLs)
+        } else {
+            stop("GETfxn must be either 'search/cell-line?' or 'cell-line/'")
+        }
+        
+        return(computedURLs)
+}
+
+#' Query Cellosaurus
+#' 
+#' @description
+#' This function takes a list of cell line names and interested fields and gets responses from the Cellosaurus API 
+#'
+#' @details 
+#' Function to get responses from Cellosaurus API
+#' 
+#' @return A list of responses
+#' @param cl_names is a list of the cell line names
+#' @param fields is a list of desired fields to obtain for each cell line in the API query, i.e if only trying to get synonynms and primary accesssion then fields=c("sy", "ac"). see https://api.cellosaurus.org/static/fields_help.html for all fields.
+#'  
+#' @md
+#' @export
+#' 
+getCellosaurusAPI <-
+    function(
+            cl_names,                       # List of cell line names 
+            fields = c(
+                "id",               # Recommended name. Most frequently the name of the cell line as provided in the original publication.
+                "ac",           # Primary accession. It is the unique identifier of the cell line. It is normally stable across Cellosaurus versions ...
+                "sy",           # List of synonyms.
+                "misspelling",  # Identified misspelling(s) of the cell line name
+                "din",          # Disease(s) suffered by the individual from which the cell line originated with its NCI Thesaurus or ORDO identifier.
+                "ca",           # Category to which a cell line belongs, one of 14 defined terms. Example: cancer cell line, hybridoma, transformed cell line.
+                "sx",           # Sex
+                "ag",           # Age at sampling time of the individual from which the cell line was established.
+                "sampling-site", # Body part, organ, cell-type the cell line is derived from
+                "metastatic-site" # Body part, organ the cell line is derived from in the case of a cell line originating from a cancer metastasis.
+                ),
+            GETfxn = c("search/cell-line?", "cell-line/"), # Function to use on the cellosaurus website
+            querydomain = "ac:"
+            ){
+        cellosaurus_api_url <- "https://api.cellosaurus.org/"
+        
+        computedURLs <- .createQueryURLs(api = cellosaurus_api_url, GETfxn = GETfxn, cl_names = cl_names, fields = fields, q = querydomain)
+
+        responseList <- BiocParallel::bplapply(computedURLs, function(x) GET(x)) 
+        names(responseList) <- cl_names
+        return(responseList)
+}
+
+#' Clean cellosaurus responses
+#'
+#' @description
+#' This function takes a list of Cellosaurus Responses and cleans them for use 
+#'
+#' @details This function takes a list of Cellosaurus Responses and cleans them for use 
+#' @return A list of responses
+#' @param responseList is a list of responses
+#' 
+#' @md
+#' @export
+#' 
+cleanCellosaurusResponse <- 
+    function(
+        responseList, 
+        GETfxn = c("search/cell-line?", "cell-line/")
+        ){
+        # Get content of each response, then separate content on newline character
+        responseContent <- lapply(lapply(responseList, httr::content),
+                                    function(x) strsplit(x=x, split="\n"))
+        
+        if (GETfxn == "search/cell-line?") {
+            #Remove first 15 rows of content
+            responseContent_sub <- lapply(responseContent, function(x) x[[1]][-(1:15)]) 
+            # Split on first "  " appearance
+            responseContent_sub_split <- lapply(responseContent_sub, function(x) strsplit(x, split = "  ."))
+                    # rbind responses (do.call returns as one large matrix instead of dataframe)
+            df_ <- lapply(responseContent_sub_split, function(x) do.call(rbind, x))
+
+            # convert each response from matrix to data.table
+            df_2 <- lapply(df_, function(x) data.table(x))
+
+            # rbinds all responses (creates new column so all of cell line x will have its name in col cellLine)
+            df_3<- rbindlist(df_2, idcol = "cellLine")
+            df_3 <- df_3[V1!="//"]
+
+            # Collapse all rows with the same cellLine & V1 (most often rows for cc) and separate by "; "
+            df_4 <- df_3[, list(data = paste0(unique(na.omit(V2)), collapse ="; ")), by = c("cellLine", "V1")]
+
+            # transpose 
+            df_5 <- data.table::dcast(df_4, cellLine ~ ...)
+
+            return(df_5) 
+        } else if (GETfxn == "cell-line/") {
+            #Remove first 15 rows of content
+            # responseContent_sub <- lapply(responseContent, function(x) x[[1]][-(1:15)])
+            responseContent_sub <- responseContent
+            responseContent_sub_split <- lapply(responseContent_sub, function(x) strsplit(x[[1]], split = "  ."))
+
+            result <- rbindlist(lapply(responseContent_sub_split, function(x) {
+                # remove the entire column if any of the elements has "//" in it
+                if (any(grepl("//", x))) {
+                    x <- x[, -1]
+                }
+
+                cvcl_dt <- as.data.table(x)
+                names(cvcl_dt) <- as.character(cvcl_dt[1])
+                cvcl_dt[2]
+            }))
+            return(result)
+
+        } else {
+            stop("GETfxn must be either 'search/cell-line?' or 'cell-line/'")
+        }
+}
\ No newline at end of file
diff --git a/R/getDrugBank.R b/R/getDrugBank.R
index b42a273..d29b900 100644
--- a/R/getDrugBank.R
+++ b/R/getDrugBank.R
@@ -188,12 +188,12 @@ listColToDT <- function(col) {
 }
 
 # Function testing scripts, not run unless this file is called as a script
-if (sys.nframe() == 0) {
-    library(AnnotationGx)
-    library(xml2)
-    library(data.table)
-    library(BiocParallel)
+# if (sys.nframe() == 0) {
+#     library(AnnotationGx)
+#     library(xml2)
+#     library(data.table)
+#     library(BiocParallel)
 
-    drugTargetDT <- getDrugTargets('local_data/drugbank.xml')
+#     drugTargetDT <- getDrugTargets('local_data/drugbank.xml')
     
-}
\ No newline at end of file
+# }
\ No newline at end of file
diff --git a/R/getPubChem-helpers.R b/R/getPubChem-helpers.R
new file mode 100644
index 0000000..ac514c1
--- /dev/null
+++ b/R/getPubChem-helpers.R
@@ -0,0 +1,170 @@
+#' Checks to see if the PubChem query is exceeding the throttling limit
+#' @param response `httr::response`
+#' @param throttleMessage `logical` whether to print the throttling message
+#' @return `logical` whether the query is throttled
+.checkThrottlingStatus <- function(result, throttleMessage = FALSE){
+    message <- headers(result)$`x-throttling-control`
+
+    if (throttleMessage == TRUE){
+        message(message)
+    }
+    matches <- regmatches(message, gregexpr("\\((.*?)%\\)", message))  # Extracts text within parentheses
+    percentages <- gsub("\\(|%|\\)", "", unlist(matches[1:3]))
+    # print(percentages)
+    percentage <- max(as.numeric(percentages))
+    if(as.integer(percentage) > 15 && as.integer(percentage) < 30){
+        Sys.sleep(15)
+    }else if (as.integer(percentage) > 30 && as.integer(percentage) < 50){
+        Sys.sleep(20)
+    }else if (as.integer(percentage) > 50 && as.integer(percentage) < 75) {
+        print(paste0("Throttling at ", percentage, "%. Sleeping for 30 seconds."))
+        Sys.sleep(30)
+    }else if (as.integer(percentage) > 75) {
+        print(paste0("Throttling at ", percentage, "%. Sleeping for 60 seconds."))
+        Sys.sleep(60)
+    }else{
+        Sys.sleep(5)
+    }   
+
+    return(as.integer(percentage) > 15)
+}
+
+## TODO:: Retrieve PubChem server status to dynamically set query spacing
+##>based on server load
+## TODO:: Make the query away for server load status in response header
+#' @importFrom crayon strip_style
+.queryPubChemSleep <- function(x, ..., query_only=FALSE) {
+    proxy <- list(...)$proxy
+    t1 <- Sys.time()
+    queryRes <- tryCatch({
+        queryRequestPubChem(x, ..., query_only=query_only)
+    },
+        error=function(e) {
+            cat('\r')
+            print(e)
+        list(Error=list(
+            Code='.queryPubChemSleep.ERROR',
+            Message='See Details for error msg',
+            Details=paste0(strip_style(e), collapse=' ')
+        ))
+    })
+    t2 <- Sys.time()
+    queryTime <- t2 - t1
+    if (!isTRUE(proxy) && queryTime < 0.31) Sys.sleep(0.31 - queryTime)
+    return(queryRes)
+}
+
+# -----------------------------
+# getPubChemAnnotations Helpers
+
+#' @importFrom data.table data.table as.data.table merge.data.table last rbindlist
+.parseATCannotations <- function(DT) {
+    dataL <- DT$Data
+    names(dataL) <- DT$SourceID
+    dataDT <- rbindlist(dataL, fill=TRUE, use.names=TRUE, idcol='SourceID')
+    dataDT[, ATC_code := unlist(lapply(Value.StringWithMarkup,
+        function(x) last(x)[[1]]))]
+    annotationDT <- merge.data.table(
+        dataDT[, .(SourceID, ATC_code)],
+        DT[, .(SourceName, SourceID, LinkedRecords)],
+        by='SourceID',
+        allow.cartesian=TRUE
+    )
+    DT <- annotationDT[, .(CID=unlist(LinkedRecords)),
+        by=.(SourceName, SourceID, ATC_code)]
+    DT <- unique(DT)
+    return(DT)
+}
+
+#' @importFrom data.table data.table as.data.table merge.data.table last rbindlist
+.parseDILIannotations <- function(DT) {
+    dataL <- DT$Data
+    names(dataL) <- DT$SourceID
+    dataL <- lapply(dataL, FUN=`[`, i=Name %like% 'DILI')
+    dataDT <- rbindlist(dataL, fill=TRUE, use.names=TRUE, idcol='SourceID')
+    dataDT[, DILI := unlist(Value.StringWithMarkup)]
+    annotationDT <- merge.data.table(
+        dataDT[, .(SourceID, DILI)],
+        DT[, .(SourceID, SourceName, Name, LinkedRecords.CID,
+            LinkedRecords.SID)],
+        by='SourceID',
+        allow.cartesian=TRUE)
+    DT <- 
+    annotationDT[, 
+        .(CID=unlist(LinkedRecords.CID), SID=unlist(LinkedRecords.SID)),
+        by=.(SourceName, SourceID, Name, DILI)]
+    return(DT)
+}
+
+#' @importFrom data.table data.table as.data.table merge.data.table last rbindlist
+.parseNSCannotations <- function(DT) {
+    DT[, NSC := unlist(lapply(Data, `[[`, i=4))]
+    annotationDT <- DT[,
+        .(CID=unlist(LinkedRecords.CID), SID=unlist(LinkedRecords.SID)),
+        by=.(SourceName, SourceID, NSC)]
+    return(annotationDT)
+}
+
+#' @importFrom data.table data.table as.data.table merge.data.table last rbindlist
+.parseCTDannotations <- function(DT) {
+    annotationDT <- DT[, .(CID=unlist(LinkedRecords)),
+        by=.(SourceName, SourceID, URL)]
+    annotationDT[, CTD := gsub('::.*$', '', SourceID)]
+    return(annotationDT)
+}
+
+#' @importFrom data.table data.table as.data.table merge.data.table last rbindlist setnames
+.parseCASannotations <- function(list) {
+    # Make sure CIDs all go in the same column
+    CAS_list <- lapply(list, setnames, old='LinkedRecords.CID', new='LinkedRecords',
+        skip_absent=TRUE)
+    DT <- rbindlist(CAS_list, fill=TRUE, use.names=TRUE)
+    DT[, CAS := lapply(Data, function(x) unlist(x[[2]]))]
+    CAS_DT <- DT[, .(CAS=unlist(CAS)), by=.(SourceName, SourceID, Name)]
+    ID_DT <- DT[, 
+        .(CID=unlist(lapply(LinkedRecords, function(x) if(is.null(x)) NA_integer_ else x))),
+        by=.(SourceName, SourceID, Name, URL)]
+    annotationDT <- merge.data.table(
+        CAS_DT, ID_DT,
+        by=c('SourceName', 'SourceID', 'Name'), 
+        all.x=TRUE,
+        allow.cartesian=TRUE)
+    annotationDT <- unique(annotationDT)
+    return(annotationDT)
+}
+
+#' @importFrom data.table data.table as.data.table merge.data.table last rbindlist
+.parseSynonymsAndIdentifiers <- function(DT) {
+    dataList <- lapply(DT$Data, as.data.table)
+    names(dataList) <- DT$SourceID
+    dataDT <- rbindlist(dataList, fill=TRUE, use.names=TRUE,
+        idcol='SourceID')
+    DT[, Data := NULL]
+    dataDT[,
+        Synonyms := paste0(unlist(Value.StringWithMarkup[[1]]), collapse='|'),
+        by=SourceID]
+    dataDT[, Synonyms := paste(Synonyms, '|', Name), by=SourceID]
+    dataDT[, Value.StringWithMarkup := NULL]
+    annotationDT <- merge.data.table(dataDT, DT, by='SourceID', allow.cartesian=TRUE)
+    setnames(annotationDT,
+        old=c('TOCHeading.type', 'TOCHeading..TOCHeading', 'LinkedRecords'),
+        new=c('Type', 'Heading', 'ID')
+    )
+    annotationDT <- unique(annotationDT)
+    return(annotationDT)
+}
+
+#' @importFrom data.table data.table as.data.table merge.data.table last rbindlist
+.parseNamesAndSynonyms <- function(DT) {
+    DT[, Synonyms := lapply(Data, function(x) x[2, ]$Value[[1]][[1]])]
+    # Remove the weird annotation from the end of the synonym
+    DT[, Synonyms := lapply(Synonyms, FUN=gsub, pattern=' - .*$', replacement='')]
+    DT[, Synonyms := unlist(lapply(Synonyms, FUN=paste0, collapse='|'))]
+    # fix NULL list itemss
+    DT[, CID := lapply(LinkedRecords.CID, function(x) if(is.null(x)) NA_integer_ else x)]
+    DT[, SID := lapply(LinkedRecords.SID, function(x) if(is.null(x)) NA_integer_ else x)]
+    annotationDT <- DT[, .(CID=unlist(CID), SID=unlist(SID)),
+        by=.(SourceName, SourceID, Name, URL, Synonyms)]
+    annotationDT <- unique(annotationDT)
+    return(annotationDT)
+}
diff --git a/R/getPubChem.R b/R/getPubChem.R
index 218fbb2..1e71500 100644
--- a/R/getPubChem.R
+++ b/R/getPubChem.R
@@ -144,7 +144,7 @@
 #' @export
 getRequestPubChem <- function(id, domain='compound', namespace='cid', operation=NA,
         output='JSON', ..., url='https://pubchem.ncbi.nlm.nih.gov/rest/pug',
-        operation_options=NA, proxy=FALSE, raw=FALSE, query_only=FALSE) {
+        operation_options=NA, proxy=FALSE, raw=FALSE, query_only=FALSE, verbose = FALSE) {
     funContext <- .funContext('::getRequestPubChem')
 
     # handle list or vector inputs for id
@@ -164,34 +164,13 @@ getRequestPubChem <- function(id, domain='compound', namespace='cid', operation=
 
     # get HTTP response, respecting the 30s max query time of PubChem API
     tryCatch({
-        if (isTRUE(proxy)) {
-            if (is.null(proxyManager$get_proxies())) {
-                tryCatch(proxyManager$connect(),
-                error=function(e)
-                    stop("proxyManager connection failed, set proxy=FALSE!\n\t", e)
-                )
-            }
-            result <- FALSE
-            count <- 1
-            while(isFALSE(result)) {
-                proxy <- unlist(proxyDT[sample(.N, 1), ])
-                result <- tryCatch({
-                    RETRY('GET', encodedQuery, timeout(29), times=3, quiet=TRUE,
-                        terminate_on=c(400, 404, 503),
-                        use_proxy(proxy[1], port=as.integer(proxy[2])))
-                }, error=function(e) FALSE)
-                count <- count + 1
-                if (count > 10) .error(funContext, 'Infinite retry loop
-                    due to failed proxy requests!')
-            }
-        } else {
-            result <- RETRY('GET', encodedQuery, timeout(29), times=3,
-                quiet=TRUE, terminate_on=c(400, 404, 503))
-        }
+        
+        result <- RETRY('GET', encodedQuery, timeout(29), times=3,
+            quiet=TRUE, terminate_on=c(400, 404, 503))
 
         if (isTRUE(raw)) return(result)
 
-        .checkThrottlingStatus(result)
+        .checkThrottlingStatus(result, throttleMessage = verbose)
 
         canParse <- tryCatch({ parseJSON(result, as='text'); TRUE },
             error=function(e) FALSE)
@@ -217,29 +196,6 @@ getRequestPubChem <- function(id, domain='compound', namespace='cid', operation=
         })
 }
 
-#' Checks to see if the PubChem query is exceeding the throttling limit
-#' @param response `httr::response`
-.checkThrottlingStatus <- function(response) {
-    throttling_control <- headers(response)$`x-throttling-control`
-    any_grepl <- function(...) any(grepl(...))
-    throttling_state <- max(which(vapply(
-        c('Green', 'Yellow', 'Red', 'Black', 'blacklisted'),
-        FUN=any_grepl, x=throttling_control, FUN.VALUE=logical(1))))
-    if (throttling_state == 2) {
-        .warning('PubChem Server returned Yellow status! Sleeping to compensate.')
-        Sys.sleep(5)
-    } else if (throttling_state == 3) {
-        .warning('PubChem Server returend Red status! Sleeping to compensate.')
-        Sys.sleep(10)
-    } else if (throttling_state == 4) {
-        .error('PubChem Server returned Black status! You could be ',
-            'black listed. The returned state message is: ',
-            throttling_control, '.')
-    } else if (throttling_state == 5) {
-        .error('PubChem server indicated: too many queries per second',
-            ' or you may be blacklisted.')
-    }
-}
 
 #' @title queryPubChem
 #'
@@ -259,7 +215,7 @@ getRequestPubChem <- function(id, domain='compound', namespace='cid', operation=
 queryPubChem <- function(id, domain='compound', namespace='cid', operation=NA,
         output='JSON', ..., url='https://pubchem.ncbi.nlm.nih.gov/rest/pug',
         operation_options=NA, batch=TRUE, raw=FALSE, proxy=FALSE,
-        query_only=FALSE) {
+        query_only=FALSE, verbose = FALSE) {
     if (!is.character(id)) id <- as.character(id)
     if (namespace %in% c('name', 'xref', 'smiles', 'inchi', 'sdf'))
         batch <- FALSE
@@ -290,12 +246,12 @@ queryPubChem <- function(id, domain='compound', namespace='cid', operation=NA,
         queryRes <- bplapply(queries, FUN=.queryPubChemSleep, domain=domain,
             namespace=namespace, operation=operation, output=output, url=url,
             operation_options=operation_options, BPPARAM=BPPARAM, proxy=proxy,
-            raw=raw, query_only=query_only)
+            raw=raw, query_only=query_only, verbose = verbose)
     } else {
         queryRes <- bplapply(id, FUN=.queryPubChemSleep, domain=domain,
             namespace=namespace, operation=operation, output=output, url=url,
             operation_options=operation_options, BPPARAM=BPPARAM, proxy=proxy,
-            raw=raw, query_only=query_only)
+            raw=raw, query_only=query_only, verbose = verbose)
         queries <- as.list(id)
     }
 
@@ -318,30 +274,6 @@ queryPubChem <- function(id, domain='compound', namespace='cid', operation=NA,
     return(queryRes)
 }
 
-## TODO:: Retrieve PubChem server status to dynamically set query spacing
-##>based on server load
-## TODO:: Make the query away for server load status in response header
-#' @importFrom crayon strip_style
-.queryPubChemSleep <- function(x, ..., query_only=FALSE) {
-    proxy <- list(...)$proxy
-    t1 <- Sys.time()
-    queryRes <- tryCatch({
-        queryRequestPubChem(x, ..., query_only=query_only)
-    },
-        error=function(e) {
-            cat('\r')
-            print(e)
-        list(Error=list(
-            Code='.queryPubChemSleep.ERROR',
-            Message='See Details for error msg',
-            Details=paste0(strip_style(e), collapse=' ')
-        ))
-    })
-    t2 <- Sys.time()
-    queryTime <- t2 - t1
-    if (!isTRUE(proxy) && queryTime < 0.31) Sys.sleep(0.31 - queryTime)
-    return(queryRes)
-}
 
 #' Parse a JSON into a list
 #'
@@ -539,8 +471,8 @@ getPubChemCompound <- function(ids, from='cid', to='property', ...,
         batch <- FALSE
     }
 
-    if (to == 'property')
-        to <- paste0(to, '/', paste0(properties, collapse=','))
+    if (to == 'property') to <- paste0(to, '/', paste0(properties, collapse=','))
+    
     queryRes <- queryPubChem(ids, domain='compound', namespace=from,
         operation=to, batch=batch, raw=raw, proxy=proxy,
         operation_options=options, query_only=query_only, ...)
@@ -644,6 +576,8 @@ getPubChemSubstance <- function(ids, from='cid', to='sids', ...,
     return(queryRes)
 }
 
+
+
 #' Get a selected annotation for all PubChem entries
 #'
 #' @description
@@ -684,15 +618,32 @@ getPubChemSubstance <- function(ids, from='cid', to='sids', ...,
 #' @importFrom data.table data.table as.data.table merge.data.table last rbindlist fwrite
 #' @importFrom BiocParallel bpparam bpworkers bpprogressbar bptry
 #' @export
-getPubChemAnnotations <- function(header='Available', type='Compound',
-        parseFUN=identity, ..., output='JSON', raw=FALSE,
+getAllPubChemAnnotations <- 
+    function(
+        header='Available', 
+        type='Compound',
+        parseFUN=identity, 
+        output='JSON', 
+        raw=FALSE, 
+        rawAnnotationDT=FALSE, 
+        verbose = FALSE,
         url='https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/annotations/heading',
-        BPPARAM=bpparam(), proxy=FALSE) {
+        BPPARAM=bpparam(),
+        proxy=FALSE,
+        retries=3,
+        maxPages=NA,
+        ...
+        ) {
     funContext <- .funContext('::getPubChemAnnotations')
     if (header == 'Available') {
         queryURL <-
             'https://pubchem.ncbi.nlm.nih.gov/rest/pug/annotations/headings/JSON'
-    } else {
+    } else if (header == 'data') {
+        url <- 'https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/'
+        queryURL <- paste0(.buildURL(url, header, output),
+            '?heading_type=', type)
+    } 
+    else {
         queryURL <- paste0(.buildURL(url, header, output),
             '?heading_type=', type)
     }
@@ -704,7 +655,7 @@ getPubChemAnnotations <- function(header='Available', type='Compound',
         count <- 1
         while(isFALSE(queryRes)) {
             proxy <- unlist(proxyDT[sample(.N, 1), ])
-            queryRes <- tryCatch({ RETRY('GET', encodedQueryURL, timeout(29), times=3,
+            queryRes <- tryCatch({ RETRY('GET', encodedQueryURL, timeout(29), times=retries,
                 quiet=TRUE, use_proxy(proxy[1], as.integer(proxy[2])))
             }, error=function(e) FALSE)
 
@@ -717,50 +668,42 @@ getPubChemAnnotations <- function(header='Available', type='Compound',
         }
         fwrite(proxyDT, file=file.path(tempdir(), 'proxy.csv'))
     } else {
-        queryRes <- RETRY('GET', encodedQueryURL, timeout(29), times=3,
+        queryRes <- RETRY('GET', encodedQueryURL, timeout(29), times=retries,
             quiet=TRUE)
     }
-
+    .checkThrottlingStatus(queryRes)
     if (isTRUE(raw)) return(queryRes)
 
     resultDT <- as.data.table(parseJSON(queryRes)[[1]][[1]])
 
     if (header == 'Available') return(resultDT)
 
-    numPages <- as.numeric(content(queryRes)[[1]]$TotalPages)
+    numPages <- content(queryRes)[[1]]$TotalPages
+    if (is.null(numPages)) {
+        numPages <- 1 
+    }else {
+        if (!is.na(maxPages)) numPages <- min(as.numeric(maxPages),as.numeric(numPages))
+        if (verbose) print(paste0("numPages: ", numPages))
+    }
+
+    
     if (numPages > 1) {
         tryCatch({
-            bpworkers(BPPARAM) <- 5
+            # bpworkers(BPPARAM) <- 5
             bpprogressbar(BPPARAM) <- TRUE
+            print(BPPARAM)
+            BiocParallel::register(BPPARAM)
         }, error=function(e) .warning(funContext, 'Failed to set parallelzation
             parameters! Please configure them yourself and pass in as the
             BPPARAM argument.'))
         pageList <- bplapply(seq(2, numPages), function(i, queryURL, numPages) {
             t1 <- Sys.time()
             encodedURL <- URLencode(paste0(queryURL, '&page=', i))
-            if (isTRUE(proxy)) {
-                proxyDT <- fread(file.path(tempdir(), 'proxy.csv'))
-                queryRes <- FALSE
-                count <- 1
-                while(isFALSE(queryRes)) {
-                    proxy <- unlist(proxyDT[sample(.N, 1), ])
-                    print(proxy)
-                    queryRes <- tryCatch({ RETRY('GET', encodedQueryURL, timeout(29), times=3,
-                        quiet=TRUE, use_proxy(proxy[1], as.integer(proxy[2])))
-                    }, error=function(e) FALSE)
-
-                    if (isFALSE(queryRes)) {
-                        proxyDT <- proxyDT[ip != proxy[1] & port != proxy[2], ]
-                    }
-                    count <- count + 1
-                    if (count > 10) .error(funContext, 'Infinite retry loop
-                        due to failed proxy requests!')
-                }
-                fwrite(proxyDT, file=file.path(tempdir(), 'proxy.csv'))
-            } else {
-                queryRes <- RETRY('GET', encodedQueryURL, timeout(29), times=3,
+            queryRes <- RETRY('GET', encodedQueryURL, timeout(1), times=10,
                     quiet=TRUE)
-            }
+            
+            .checkThrottlingStatus(queryRes)
+            
             page <- tryCatch({
                 as.data.table(parseJSON(queryRes)[[1]][[1]])
             }, error=function(e) {
@@ -770,9 +713,9 @@ getPubChemAnnotations <- function(header='Available', type='Compound',
             })
             t2 <- Sys.time()
             queryTime <- t2 - t1
-            if (queryTime < 0.31) Sys.sleep(0.31 - queryTime)
+            # if (queryTime < 0.31) Sys.sleep(0.31 - queryTime)
             return(page)
-        }, BPPARAM=BPPARAM, queryURL=queryURL, numPages=numPages)
+        },  queryURL=queryURL, numPages=numPages)
         pageList <- c(list(resultDT), pageList)
     } else {
         pageList <- list(resultDT)
@@ -780,9 +723,15 @@ getPubChemAnnotations <- function(header='Available', type='Compound',
 
     if (header != 'CAS') {
         annotationDT <- rbindlist(pageList, fill=TRUE, use.names=TRUE)
+        if (verbose) print("applying as.data.table to Data column of annotationDT")
         annotationDT[, Data := lapply(Data, as.data.table)]
+    } else {  
+        annotationDT <- pageList
+    }
+    if (isTRUE(rawAnnotationDT)) {
+        if(verbose) print(paste0("Not Parsing, ", header, " returning annotationDT"))
+        return(annotationDT)
     }
-
     # parse the results to a user friendly format
     switch(header,
         'ATC Code'=return(.parseATCannotations(annotationDT)),
@@ -791,7 +740,7 @@ getPubChemAnnotations <- function(header='Available', type='Compound',
         'CTD Chemical-Gene Interactions'=return(.parseCTDannotations(annotationDT)),
         'Names and Synonyms'=return(.parseNamesAndSynonyms(annotationDT)),
         'Synonyms and Identifiers'=return(.parseSynonymsAndIdentifiers(annotationDT)),
-        'CAS'=return(.parseCASannotations(pageList)),
+        'CAS'=return(.parseCASannotations(annotationDT)),
         tryCatch({
             parseFUN(annotationDT)
         },
@@ -803,107 +752,152 @@ getPubChemAnnotations <- function(header='Available', type='Compound',
         })
     )
 }
+#' @title getPubChemAnnotation
+#' @description queries the PubChem PUG-VIEW API to get a single annotation using a CID for a header
+#' 
+#' @param compound `character(1)` A valid CID to use for the query.
+#' @param header `character(1)` A valid header name for the PUG VIEW annotations
+#' @param url `character(1)` The URL to perform API queries on. default = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound'
+#' @param output `character(1)` The output format. Defaults to 'JSON'.
+#' @param timeout_s `numeric(1)` The number of seconds to wait before timing out. Default is 29.
+#' @param retries `numeric(1)` The number of times to retry a failed query. Default is 3.
+#' @param quiet `logical(1)` Should the function be quiet? Default is TRUE.
+#' @param throttleMessage `logical(1)` Should a message be printed when the query is throttled? Default is FALSE.
+#' @export
+getPubChemAnnotation <- function(
+    compound,
+    header = 'ChEMBL ID',
+    url = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound',
+    output = 'JSON', 
+    timeout_s = 29,
+    retries = 3,
+    quiet = TRUE,
+    throttleMessage = FALSE
+    ){
+        
+        # TODO:: add a check to see if the compound is a valid CID or SID
+        # TODO:: allow for variaitons of headers due to spelling errors
+        # Temporary:
+        if(header == "DILI") queryURL <- paste0(.buildURL(url, compound, output), '?heading=', "Drug Induced Liver Injury")
+        else queryURL <- paste0(.buildURL(url, compound, output), '?heading=', header)
 
-# -----------------------------
-# getPubChemAnnotations Helpers
-
-#' @importFrom data.table data.table as.data.table merge.data.table last rbindlist
-.parseATCannotations <- function(DT) {
-    dataL <- DT$Data
-    names(dataL) <- DT$SourceID
-    dataDT <- rbindlist(dataL, fill=TRUE, use.names=TRUE, idcol='SourceID')
-    dataDT[, ATC_code := unlist(lapply(Value.StringWithMarkup,
-        function(x) last(x)[[1]]))]
-    annotationDT <- merge.data.table(
-        dataDT[, .(SourceID, ATC_code)],
-        DT[, .(SourceName, SourceID, LinkedRecords)],
-        by='SourceID'
-    )
-    DT <- annotationDT[, .(CID=unlist(LinkedRecords)),
-        by=.(SourceName, SourceID, ATC_code)]
-    return(DT)
-}
+        tryCatch({
+            result <- RETRY('GET', URLencode(queryURL), times = retries, quiet = quiet)
+        }, error=function(e) {
+            print(paste0("Error: ", e$message))
+            return(NULL)
+        })
 
-#' @importFrom data.table data.table as.data.table merge.data.table last rbindlist
-.parseDILIannotations <- function(DT) {
-    dataL <- DT$Data
-    names(dataL) <- DT$SourceID
-    dataL <- lapply(dataL, FUN=`[`, i=Name %like% 'DILI')
-    dataDT <- rbindlist(dataL, fill=TRUE, use.names=TRUE, idcol='SourceID')
-    dataDT[, DILI := unlist(Value.StringWithMarkup)]
-    annotationDT <- merge.data.table(
-        dataDT[, .(SourceID, DILI)],
-        DT[, .(SourceID, SourceName, Name, LinkedRecords.CID,
-            LinkedRecords.SID)],
-        by='SourceID')
-    DT <- annotationDT[, .(CID=unlist(LinkedRecords.CID), SID=unlist(LinkedRecords.SID)),
-        by=.(SourceName, SourceID, Name, DILI)]
-    return(DT)
-}
+        .checkThrottlingStatus(result, throttleMessage = throttleMessage)
+        result <- parseJSON(result)
+        # switch(header,
+        #     'ATC Code'=return(.parseATCannotations(annotationDT)),
+        #     'Drug Induced Liver Injury'=return(.parseDILIannotations(annotationDT)),
+        #     'NSC Number'=return(.parseNSCannotations(annotationDT)),
+        #     'CTD Chemical-Gene Interactions'=return(.parseCTDannotations(annotationDT)),
+        #     'Names and Synonyms'=return(.parseNamesAndSynonyms(annotationDT)),
+        #     'Synonyms and Identifiers'=return(.parseSynonymsAndIdentifiers(annotationDT)),
+        #     'CAS'=return(.parseCASannotations(annotationDT)),
+        #     tryCatch({
+        #         parseFUN(annotationDT)
+        #     },
+        #     error=function(e) {
+        #         .warning(funContext, 'The parseFUN function failed: ', e,
+        #             '. Returning unparsed results instead. Please test the parseFUN
+        #             on the returned data.')
+        #         return(annotationDT)
+        #     })
+        # )
+
+
+        if (header == 'ChEMBL ID') {
+            result <- .parseCHEMBLresponse(result)
+        }else if (header == 'NSC Number'){
+            result <- .parseNSCresponse(result)
+        }else if (header == 'DILI' || header =='Drug Induced Liver Injury'){
+            result <- .parseDILIresponse(result)
+        }else if (header == 'CAS'){
+            result <- .parseCASresponse(result)
+        }else if (header == 'ATC Code'){
+            result <- .parseATCresponse(result)
+        }
+        
+        # Using switch instead of if statements
+        result <- switch(
+            header,
+            'ChEMBL ID'     = .parseCHEMBLresponse(result),
+            'NSC Number'    = .parseNSCresponse(result),
+            'DILI'          = .parseDILIresponse(result),
+            'CAS'           = .parseCASresponse(result),
+            'ATC Code'      = .parseATCresponse(result)
+        )
+
+        if (is.null(result)) result <- list(compound, "N/A")
+        else result <- list(compound,result)
+        names(result) <- c("cid", header)
+        return(result)
+    }
 
-#' @importFrom data.table data.table as.data.table merge.data.table last rbindlist
-.parseNSCannotations <- function(DT) {
-    DT[, NSC := unlist(lapply(Data, `[[`, i=4))]
-    annotationDT <- DT[,
-        .(CID=unlist(LinkedRecords.CID), SID=unlist(LinkedRecords.SID)),
-        by=.(SourceName, SourceID, NSC)]
-    return(annotationDT)
+#' Function that parses the results of the PubChem PUG-VIEW API for the CHEMBL ID header
+.parseCHEMBLresponse <- function(response){
+    result <- result$Record$Reference$SourceID
+    result <- gsub("::Compound", "", result)
+    return(result)
 }
 
-#' @importFrom data.table data.table as.data.table merge.data.table last rbindlist
-.parseCTDannotations <- function(DT) {
-    annotationDT <- DT[, .(CID=unlist(LinkedRecords)),
-        by=.(SourceName, SourceID, URL)]
-    annotationDT[, CTD := gsub('::.*$', '', SourceID)]
-    return(annotationDT)
+#' Function that parses the results of the PubChem PUG-VIEW API for the NSC Number header
+.parseNSCresponse <- function(response){
+    result <- result$Record$Reference$SourceID[1]
+    result <- gsub(" ", "", result)
+    return(result)
 }
 
-#' @importFrom data.table data.table as.data.table merge.data.table last rbindlist setnames
-.parseCASannotations <- function(list) {
-    # Make sure CIDs all go in the same column
-    CAS_list <- lapply(list, setnames, old='LinkedRecords.CID', new='LinkedRecords',
-        skip_absent=TRUE)
-    DT <- rbindlist(CAS_list, fill=TRUE, use.names=TRUE)
-    DT[, CAS := lapply(Data, function(x) unlist(x[[2]]))]
-    CAS_DT <- DT[, .(CAS=unlist(CAS)), by=.(SourceName, SourceID, Name)]
-    ID_DT <- DT[, .(
-        CID=unlist(lapply(LinkedRecords, function(x) if(is.null(x)) NA_integer_ else x)),
-        SID=unlist(lapply(LinkedRecords.SID, function(x) if(is.null(x)) NA_integer_ else x)))
-        , by=.(SourceName, SourceID, Name, URL)]
-    annotationDT <- merge.data.table(CAS_DT, ID_DT,
-        by=c('SourceName', 'SourceID', 'Name'), all.x=TRUE)
-    return(annotationDT)
+#' Function that parses the results of the PubChem PUG-VIEW API for the DILI header
+.parseDILIresponse <- function(response){
+    if(length(result$Record$Section) == 0){
+                result <- "NA"
+    }else{
+        dt_ <- as.data.table(result$Record$Section)
+        dt_ <- as.data.table(dt_)$Section[[1]]
+        dt_ <- as.data.table(dt_)$Section
+        dt_ <- as.data.table(dt_)
+        dt_ <- as.data.table(dt_)$Information
+        # print(as.data.table(dt_)[1:3,  .(Name,unlist(Value))])
+        section <- as.data.table(dt_)[1:3, "DILI" := paste0(unlist(Name), ":", unlist(Value))]
+
+        # if any of the first 4 rows are NA, remove it 
+        section <- section[!is.na(section$DILI)]
+
+
+        section <- paste0(section[1:3, DILI], collapse= "; ")
+
+        # create a list for each row as Name:Value string with no spaces and no new lines
+        reference <- paste0("LTKBID:", result$Record$Reference$SourceID)
+        result <- c(section, reference)
+        result <- paste0(result, collapse = "; ")
+    }
 }
 
-#' @importFrom data.table data.table as.data.table merge.data.table last rbindlist
-.parseSynonymsAndIdentifiers <- function(DT) {
-    dataList <- lapply(DT$Data, as.data.table)
-    names(dataList) <- DT$SourceID
-    dataDT <- rbindlist(dataList, fill=TRUE, use.names=TRUE,
-        idcol='SourceID')
-    DT[, Data := NULL]
-    dataDT[,
-        Synonyms := paste0(unlist(Value.StringWithMarkup[[1]]), collapse='|'),
-        by=SourceID]
-    dataDT[, Synonyms := paste(Synonyms, '|', Name), by=SourceID]
-    dataDT[, Value.StringWithMarkup := NULL]
-    annotationDT <- merge.data.table(dataDT, DT, by='SourceID')
-    setnames(annotationDT,
-        old=c('TOCHeading.type', 'TOCHeading..TOCHeading', 'LinkedRecords'),
-        new=c('Type', 'Heading', 'ID')
-    )
-    return(annotationDT)
+#' Function that parses the results of the PubChem PUG-VIEW API for the CAS header
+.parseCASresponse <- function(response){
+    result <- result$Record$Reference$SourceID[1]
+    return(result)
 }
 
-#' @importFrom data.table data.table as.data.table merge.data.table last rbindlist
-.parseNamesAndSynonyms <- function(DT) {
-    DT[, Synonyms := lapply(Data, function(x) x[2, ]$Value[[1]][[1]])]
-    # Remove the weird annotation from the end of the synonym
-    DT[, Synonyms := lapply(Synonyms, FUN=gsub, pattern=' - .*$', replacement='')]
-    DT[, Synonyms := unlist(lapply(Synonyms, FUN=paste0, collapse='|'))]
-    # fix NULL list itemss
-    DT[, CID := lapply(LinkedRecords, function(x) if(is.null(x)) NA_integer_ else x)]
-    annotationDT <- DT[, .(CID=unlist(CID)),
-        by=.(SourceName, SourceID, Name, URL, Synonyms)]
-    return(annotationDT)
-}
+#' Function that parses the results of the PubChem PUG-VIEW API for the ATC Code header
+.parseATCresponse <- function(response){
+    if(length(result$Record$Section) == 0){
+                result <- "NA"
+                
+    }else{dt_ <- as.data.table(result$Record$Section)
+    dt_ <- as.data.table(dt_)$Section[[1]]
+    dt_ <- as.data.table(dt_)$Information
+    dt_ <- as.data.table(dt_)$Value
+    dt_ <- as.data.table(dt_[[1]])
+    result <- paste0("ATC:", dt_$String)
+    if(length(result) > 1){
+        result <- paste0(result, collapse = "; ")
+    }}
+
+    return(result)
+}
\ No newline at end of file
diff --git a/R/getUniProt.R b/R/getUniProt.R
index 1dee2a6..ab05110 100644
--- a/R/getUniProt.R
+++ b/R/getUniProt.R
@@ -30,25 +30,24 @@ getUniProt <- function(url='') {
 #' @return A httr::response object containing the query results as `format`.
 #'
 #' @import httr
-#' @importFrom CoreGx .errorMsg .warnMsg
 # #' @export
-queryUniProt <- function(query, columns='', limit='', offset='', format='xml',
-        include=TRUE, compress=TRUE, ...,
-        url='https://www.uniprot.org/uniprot') {
-    stop("Not implemented yet!")
-    if (missing(query)) stop(.errorMsg(.context(), 'The query parameter is
-        missing! This parameter is mandatory.'))
+# queryUniProt <- function(query, columns='', limit='', offset='', format='xml',
+#         include=TRUE, compress=TRUE, ...,
+#         url='https://www.uniprot.org/uniprot') {
+#     stop("Not implemented yet!")
+#     if (missing(query)) stop(.errorMsg(.context(), 'The query parameter is
+#         missing! This parameter is mandatory.'))
 
-    ##TODO:: handle more errors
+#     ##TODO:: handle more errors
 
-    # parse parameters
-    include <- if (include) 'yes' else 'no'
-    compress <- if (compress) 'yes' else 'no'
+#     # parse parameters
+#     include <- if (include) 'yes' else 'no'
+#     compress <- if (compress) 'yes' else 'no'
 
-    response <- GET()
-}
+#     response <- GET()
+# }
 
-#'
+# #'
 #'
 #'
 #'
diff --git a/R/queryCellosaurus.R b/R/queryCellosaurus.R
index 222cd27..4eba2e6 100644
--- a/R/queryCellosaurus.R
+++ b/R/queryCellosaurus.R
@@ -92,125 +92,3 @@ queryCellosaurus <- function(url = "https://ftp.expasy.org/databases/cellosaurus
 
 ## ============================= CELLOSAURUS WORK ==============================
 # these functions will be put into annotationGx for ease:
-
-#' Create a list of query URLS for Cellosaurus API
-#'
-#' @description
-#' This function creates a queryURL for the cellosaurus API using a list of cell line names
-#'
-#' @details 
-#' Function to create a URL query for Cellosaurus to search for a cell-line using its name 
-#' An example call:   finalURLs <- createQueryURLs(api = CLurl, cl_names = cl_names, fields = c("id", "ac"))
-#' @return A list of URLS
-#' @param api is the link to the API to build the URL. i.e "https://api.cellosaurus.org/"
-#' @param cl_names is a list of the cell line names
-#' @param format is the type of format to return from the API. Can be "txt" or "json" 
-#' @param clnum is the number of of cell lines to return, DEFAULT=1
-#' @param GETfxn is the function to use on the cellosaurus website. Currently only supports "search/cell-line?"
-#' @param fields is a list of desired fields to include in the response 
-#' 
-#' @md
-#' 
-createQueryURLs <- 
-    function(api,
-             cl_names,
-             format = "txt",
-             clnum = 1,
-             GETfxn = "search/cell-line?",
-             fields) {
-        # create urls 
-        finalURLs <- paste0(api,
-                            GETfxn,
-                            "q=",
-                            "idsy:",
-                            gsub(" ", "%20",cl_names),
-                            "&",
-                            "rows=",
-                            clnum,
-                            "&",
-                            "format=",format,
-                            "&",
-                            "fields=", paste(fields, collapse=",")
-                            )
-        return(finalURLs)
-}
-
-#' Query Cellosaurus
-#'
-#' @description
-#' This function takes a list of cell line names and gets responses from the Cellosaurus API 
-#'
-#' @details 
-#' Function to get responses from Cellosaurus API
-#' 
-#' @return A list of responses
-#' @param cl_names is a list of the cell line names
-#' 
-#' @md
-#' @export
-#' 
-getCellApi <-
-    function(cl_names){
-        CLurl <- "https://api.cellosaurus.org/"
-
-        fields <- c("id",           # Recommended name. Most frequently the name of the cell line as provided in the original publication.
-                    "ac",           # Primary accession. It is the unique identifier of the cell line. It is normally stable across Cellosaurus versions ...
-                    "sy",           # List of synonyms.
-                    "misspelling",  # Identified misspelling(s) of the cell line name
-                    "din",           # Disease(s) suffered by the individual from which the cell line originated with its NCI Thesaurus or ORDO identifier.
-                    "ca",           # Category to which a cell line belongs, one of 14 defined terms. Example: cancer cell line, hybridoma, transformed cell line.
-                    "sx",           # Sex
-                    "ag",           # Age at sampling time of the individual from which the cell line was established.
-                    "sampling-site", # Body part, organ, cell-type the cell line is derived from
-                    "metastatic-site" # Body part, organ the cell line is derived from in the case of a cell line originating from a cancer metastasis.
-                    # "cc"            # comments
-        )
-        
-        finalURLs <- createQueryURLs(api = CLurl, cl_names = cl_names, fields = fields)
-        responseList <- bplapply(finalURLs, function(x) GET(x)) 
-        names(responseList) <- cl_names
-        return(responseList)
-}
-
-#' Clean cellosaurus responses
-#'
-#' @description
-#' This function takes a list of Cellosaurus Responses and cleans them for use 
-#'
-#' @details This function takes a list of Cellosaurus Responses and cleans them for use 
-#' @return A list of responses
-#' @param responseList is a list of responses
-#' 
-#' @md
-#' @export
-#' 
-cleanCellosaurusResponse <- 
-    function(responseList){
-        # Get content of each response, then separate content on newline character
-        responseContent <- lapply(lapply(responseList, httr::content),
-                                    function(x) strsplit(x=x, split="\n"))
-        
-        #Remove first 15 rows of content
-        responseContent_sub <- lapply(responseContent, function(x) x[[1]][-(1:15)]) 
-
-        # Split on first "  " appearance
-        responseContent_sub_split <- lapply(responseContent_sub, function(x) strsplit(x, split = "  ."))
-        
-        # rbind responses (do.call returns as one large matrix instead of dataframe)
-        df_ <- lapply(responseContent_sub_split, function(x) do.call(rbind, x))
-
-        # convert each response from matrix to data.table
-        df_2 <- lapply(df_, function(x) data.table(x))
-
-        # rbinds all responses (creates new column so all of cell line x will have its name in col cellLine)
-        df_3<- rbindlist(df_2, idcol = "cellLine")
-        df_3 <- df_3[V1!="//"]
-
-        # Collapse all rows with the same cellLine & V1 (most often rows for cc) and separate by "; "
-        df_4 <- df_3[, list(data = paste0(unique(na.omit(V2)), collapse ="; ")), by = c("cellLine", "V1")]
-
-        # transpose 
-        df_5 <- dcast(df_4, cellLine ~ ...)
-
-        return(df_5) 
-}
\ No newline at end of file
diff --git a/build/README.md b/build/README.md
new file mode 100644
index 0000000..1fbcec0
--- /dev/null
+++ b/build/README.md
@@ -0,0 +1,19 @@
+Set env variables for dockerfile:
+
+``` bash
+export DOCKER_REPO="jjjermiah"
+export DOCKER_IMAGE_NAME="annotationgx-r"
+export DOCKER_TAG="0.1"
+```
+
+Commands to build the docker container:
+
+``` bash
+docker build -t $DOCKER_REPO/$DOCKER_IMAGE_NAME:$DOCKER_TAG -f build/annotationGx.Dockerfile .
+```
+Command to push to dockerhub:
+
+``` bash
+docker push $DOCKER_REPO/$DOCKER_IMAGE_NAME:$DOCKER_TAG
+
+```
diff --git a/build/annotationGx.Dockerfile b/build/annotationGx.Dockerfile
new file mode 100644
index 0000000..8d2e1a6
--- /dev/null
+++ b/build/annotationGx.Dockerfile
@@ -0,0 +1,37 @@
+# This file is for building the annotationGx image for linux
+
+FROM bioconductor/bioconductor_docker:3.17-R-4.3.0
+
+# Install required libraries -- using prebuild binaries where available
+# RUN apt-get update && apt-get install -y \
+#     git \
+#     r-cran-data.table \
+#     r-cran-doparallel \
+#     r-cran-dygraphs \
+#     r-cran-foreach \
+#     r-cran-fs \
+#     r-cran-future.apply \
+#     r-cran-gh \
+#     r-cran-git2r \
+#     r-cran-igraph \
+#     r-cran-memoise \
+#     r-cran-png \
+#     r-cran-rcpparmadillo \
+#     r-cran-rex \
+#     r-cran-runit \
+#     r-cran-stringdist \
+#     r-cran-testthat \
+#     r-cran-tidyverse \
+#     r-cran-tinytest \
+#     r-cran-xts \
+#     sqlite3 \
+#     sudo
+
+# Install R packages
+# RUN install2.r --error --deps TRUE BiocManager
+
+
+
+RUN rm -rf /tmp/*
+
+CMD ["R"]
\ No newline at end of file
diff --git a/build/buildimage.sh b/build/buildimage.sh
new file mode 100755
index 0000000..f02d1b0
--- /dev/null
+++ b/build/buildimage.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+export DOCKER_REPO="jjjermiah"
+export DOCKER_IMAGE_NAME="annotationgx-r"
+export DOCKER_TAG="0.1"
+
+docker build -t $DOCKER_REPO/$DOCKER_IMAGE_NAME:$DOCKER_TAG -f build/annotationGx.Dockerfile .
+
diff --git a/man/cleanCellnames.Rd b/man/cleanCellnames.Rd
new file mode 100644
index 0000000..9329132
--- /dev/null
+++ b/man/cleanCellnames.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/getCellosaurus.R
+\name{cleanCellnames}
+\alias{cleanCellnames}
+\title{Clean Cell Names}
+\usage{
+cleanCellnames(main_xml, verbose = TRUE)
+}
+\description{
+TODO::
+}
diff --git a/man/cleanCellosaurusResponse.Rd b/man/cleanCellosaurusResponse.Rd
index d9344a4..7797d54 100644
--- a/man/cleanCellosaurusResponse.Rd
+++ b/man/cleanCellosaurusResponse.Rd
@@ -1,10 +1,13 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/queryCellosaurus.R
+% Please edit documentation in R/getCellosaurusAPI.R
 \name{cleanCellosaurusResponse}
 \alias{cleanCellosaurusResponse}
 \title{Clean cellosaurus responses}
 \usage{
-cleanCellosaurusResponse(responseList)
+cleanCellosaurusResponse(
+  responseList,
+  GETfxn = c("search/cell-line?", "cell-line/")
+)
 }
 \arguments{
 \item{responseList}{is a list of responses}
diff --git a/man/dot-checkThrottlingStatus.Rd b/man/dot-checkThrottlingStatus.Rd
index f3eafde..cd83fca 100644
--- a/man/dot-checkThrottlingStatus.Rd
+++ b/man/dot-checkThrottlingStatus.Rd
@@ -1,14 +1,19 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/getPubChem.R
+% Please edit documentation in R/getPubChem-helpers.R
 \name{.checkThrottlingStatus}
 \alias{.checkThrottlingStatus}
 \title{Checks to see if the PubChem query is exceeding the throttling limit}
 \usage{
-.checkThrottlingStatus(response)
+.checkThrottlingStatus(result, throttleMessage = FALSE)
 }
 \arguments{
+\item{throttleMessage}{\code{logical} whether to print the throttling message}
+
 \item{response}{\code{httr::response}}
 }
+\value{
+\code{logical} whether the query is throttled
+}
 \description{
 Checks to see if the PubChem query is exceeding the throttling limit
 }
diff --git a/man/createQueryURLs.Rd b/man/dot-createQueryURLs.Rd
similarity index 63%
rename from man/createQueryURLs.Rd
rename to man/dot-createQueryURLs.Rd
index 78169f9..abc16c5 100644
--- a/man/createQueryURLs.Rd
+++ b/man/dot-createQueryURLs.Rd
@@ -1,16 +1,17 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/queryCellosaurus.R
-\name{createQueryURLs}
-\alias{createQueryURLs}
+% Please edit documentation in R/getCellosaurusAPI.R
+\name{.createQueryURLs}
+\alias{.createQueryURLs}
 \title{Create a list of query URLS for Cellosaurus API}
 \usage{
-createQueryURLs(
-  api,
+.createQueryURLs(
+  api = "https://api.cellosaurus.org/",
   cl_names,
   format = "txt",
-  clnum = 1,
-  GETfxn = "search/cell-line?",
-  fields
+  num_results = 1,
+  GETfxn = c("search/cell-line?", "cell-line/"),
+  fields,
+  q = "idsy:"
 )
 }
 \arguments{
@@ -20,7 +21,7 @@ createQueryURLs(
 
 \item{format}{is the type of format to return from the API. Can be "txt" or "json"}
 
-\item{clnum}{is the number of of cell lines to return, DEFAULT=1}
+\item{num_results}{is the number of of items to return, DEFAULT=1}
 
 \item{GETfxn}{is the function to use on the cellosaurus website. Currently only supports "search/cell-line?"}
 
@@ -34,5 +35,5 @@ This function creates a queryURL for the cellosaurus API using a list of cell li
 }
 \details{
 Function to create a URL query for Cellosaurus to search for a cell-line using its name
-An example call:   finalURLs <- createQueryURLs(api = CLurl, cl_names = cl_names, fields = c("id", "ac"))
+An example call:   computedURLs <- .createQueryURLs(api = "https://api.cellosaurus.org/", cl_names = c("22rv1", "Hela"), fields = c("id", "ac"))
 }
diff --git a/man/dot-parseATCresponse.Rd b/man/dot-parseATCresponse.Rd
new file mode 100644
index 0000000..a6d6a4f
--- /dev/null
+++ b/man/dot-parseATCresponse.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/getPubChem.R
+\name{.parseATCresponse}
+\alias{.parseATCresponse}
+\title{Function that parses the results of the PubChem PUG-VIEW API for the ATC Code header}
+\usage{
+.parseATCresponse(response)
+}
+\description{
+Function that parses the results of the PubChem PUG-VIEW API for the ATC Code header
+}
diff --git a/man/dot-parseCASresponse.Rd b/man/dot-parseCASresponse.Rd
new file mode 100644
index 0000000..2bc0510
--- /dev/null
+++ b/man/dot-parseCASresponse.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/getPubChem.R
+\name{.parseCASresponse}
+\alias{.parseCASresponse}
+\title{Function that parses the results of the PubChem PUG-VIEW API for the CAS header}
+\usage{
+.parseCASresponse(response)
+}
+\description{
+Function that parses the results of the PubChem PUG-VIEW API for the CAS header
+}
diff --git a/man/dot-parseCHEMBLresponse.Rd b/man/dot-parseCHEMBLresponse.Rd
new file mode 100644
index 0000000..7404b71
--- /dev/null
+++ b/man/dot-parseCHEMBLresponse.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/getPubChem.R
+\name{.parseCHEMBLresponse}
+\alias{.parseCHEMBLresponse}
+\title{Function that parses the results of the PubChem PUG-VIEW API for the CHEMBL ID header}
+\usage{
+.parseCHEMBLresponse(response)
+}
+\description{
+Function that parses the results of the PubChem PUG-VIEW API for the CHEMBL ID header
+}
diff --git a/man/dot-parseDILIresponse.Rd b/man/dot-parseDILIresponse.Rd
new file mode 100644
index 0000000..d1a2edd
--- /dev/null
+++ b/man/dot-parseDILIresponse.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/getPubChem.R
+\name{.parseDILIresponse}
+\alias{.parseDILIresponse}
+\title{Function that parses the results of the PubChem PUG-VIEW API for the DILI header}
+\usage{
+.parseDILIresponse(response)
+}
+\description{
+Function that parses the results of the PubChem PUG-VIEW API for the DILI header
+}
diff --git a/man/dot-parseNSCresponse.Rd b/man/dot-parseNSCresponse.Rd
new file mode 100644
index 0000000..4bc5180
--- /dev/null
+++ b/man/dot-parseNSCresponse.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/getPubChem.R
+\name{.parseNSCresponse}
+\alias{.parseNSCresponse}
+\title{Function that parses the results of the PubChem PUG-VIEW API for the NSC Number header}
+\usage{
+.parseNSCresponse(response)
+}
+\description{
+Function that parses the results of the PubChem PUG-VIEW API for the NSC Number header
+}
diff --git a/man/downloadAndExtract.Rd b/man/downloadAndExtract.Rd
index 7d0735d..66fa13f 100644
--- a/man/downloadAndExtract.Rd
+++ b/man/downloadAndExtract.Rd
@@ -24,5 +24,5 @@ the specified \code{extract_fun} for more details.}
 Download a compressed file from a remote URL and extract it.
 }
 \seealso{
-\link[utils:unzip]{utils::unzip}, \link[utils:untar]{utils::untar}, \link[R.utils:compressFile]{R.utils::gunzip}, \link[R.utils:compressFile]{R.utils::bunzip2}
+\link[utils:unzip]{utils::unzip}, \link[utils:untar]{utils::untar}, \link[R.utils:gunzip]{R.utils::gunzip}, \link[R.utils:bunzip2]{R.utils::bunzip2}
 }
diff --git a/man/getPubChemAnnotations.Rd b/man/getAllPubChemAnnotations.Rd
similarity index 91%
rename from man/getPubChemAnnotations.Rd
rename to man/getAllPubChemAnnotations.Rd
index b7c86c7..d0dca8a 100644
--- a/man/getPubChemAnnotations.Rd
+++ b/man/getAllPubChemAnnotations.Rd
@@ -1,19 +1,23 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/getPubChem.R
-\name{getPubChemAnnotations}
-\alias{getPubChemAnnotations}
+\name{getAllPubChemAnnotations}
+\alias{getAllPubChemAnnotations}
 \title{Get a selected annotation for all PubChem entries}
 \usage{
-getPubChemAnnotations(
+getAllPubChemAnnotations(
   header = "Available",
   type = "Compound",
   parseFUN = identity,
-  ...,
   output = "JSON",
   raw = FALSE,
+  rawAnnotationDT = FALSE,
+  verbose = FALSE,
   url = "https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/annotations/heading",
   BPPARAM = bpparam(),
-  proxy = FALSE
+  proxy = FALSE,
+  retries = 3,
+  maxPages = NA,
+  ...
 )
 }
 \arguments{
@@ -30,8 +34,6 @@ Defaults to identity, i.e., it returned the results unparsed. Some
 default parsing is implemented inside the function for 'ATC Code' and
 'Drug Induced Liver Injury' headers.}
 
-\item{...}{Force subsequent parameters to be named. Not used.}
-
 \item{output}{\code{character(1)} The output format. Defaults to 'JSON'. For
 options other than 'JSON', you must set \code{raw=TRUE} or the fuction will
 fail.}
@@ -41,6 +43,8 @@ developer use only and should not be changed.}
 
 \item{BPPARAM}{\code{BiocParallelParam} A BiocParallel back-end to parallelize
 with. Defaults to \code{bpparam()}. To run in serial, set to \code{SerialParam()}.}
+
+\item{...}{Force subsequent parameters to be named. Not used.}
 }
 \value{
 A \code{data.table} of resulting annotations. If the header is not
diff --git a/man/getCellApi.Rd b/man/getCellApi.Rd
deleted file mode 100644
index 7f37f22..0000000
--- a/man/getCellApi.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/queryCellosaurus.R
-\name{getCellApi}
-\alias{getCellApi}
-\title{Query Cellosaurus}
-\usage{
-getCellApi(cl_names)
-}
-\arguments{
-\item{cl_names}{is a list of the cell line names}
-}
-\value{
-A list of responses
-}
-\description{
-This function takes a list of cell line names and gets responses from the Cellosaurus API
-}
-\details{
-Function to get responses from Cellosaurus API
-}
diff --git a/man/getCellosaurusAPI.Rd b/man/getCellosaurusAPI.Rd
new file mode 100644
index 0000000..54c3394
--- /dev/null
+++ b/man/getCellosaurusAPI.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/getCellosaurusAPI.R
+\name{getCellosaurusAPI}
+\alias{getCellosaurusAPI}
+\title{Query Cellosaurus}
+\usage{
+getCellosaurusAPI(
+  cl_names,
+  fields = c("id", "ac", "sy", "misspelling", "din", "ca", "sx", "ag", "sampling-site",
+    "metastatic-site"),
+  GETfxn = c("search/cell-line?", "cell-line/"),
+  querydomain = "ac:"
+)
+}
+\arguments{
+\item{cl_names}{is a list of the cell line names}
+
+\item{fields}{is a list of desired fields to obtain for each cell line in the API query, i.e if only trying to get synonynms and primary accesssion then fields=c("sy", "ac"). see https://api.cellosaurus.org/static/fields_help.html for all fields.}
+}
+\value{
+A list of responses
+}
+\description{
+This function takes a list of cell line names and interested fields and gets responses from the Cellosaurus API
+}
+\details{
+Function to get responses from Cellosaurus API
+}
diff --git a/man/getPubChemAnnotation.Rd b/man/getPubChemAnnotation.Rd
new file mode 100644
index 0000000..80a751e
--- /dev/null
+++ b/man/getPubChemAnnotation.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/getPubChem.R
+\name{getPubChemAnnotation}
+\alias{getPubChemAnnotation}
+\title{getPubChemAnnotation}
+\usage{
+getPubChemAnnotation(
+  compound,
+  header = "ChEMBL ID",
+  url = "https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound",
+  output = "JSON",
+  timeout_s = 29,
+  retries = 3,
+  quiet = TRUE,
+  throttleMessage = FALSE
+)
+}
+\arguments{
+\item{compound}{\code{character(1)} A valid CID to use for the query.}
+
+\item{header}{\code{character(1)} A valid header name for the PUG VIEW annotations}
+
+\item{url}{\code{character(1)} The URL to perform API queries on. default = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound'}
+
+\item{output}{\code{character(1)} The output format. Defaults to 'JSON'.}
+
+\item{timeout_s}{\code{numeric(1)} The number of seconds to wait before timing out. Default is 29.}
+
+\item{retries}{\code{numeric(1)} The number of times to retry a failed query. Default is 3.}
+
+\item{quiet}{\code{logical(1)} Should the function be quiet? Default is TRUE.}
+
+\item{throttleMessage}{\code{logical(1)} Should a message be printed when the query is throttled? Default is FALSE.}
+}
+\description{
+queries the PubChem PUG-VIEW API to get a single annotation using a CID for a header
+}
diff --git a/man/getRequestPubChem.Rd b/man/getRequestPubChem.Rd
index 00e7c6b..90187c9 100644
--- a/man/getRequestPubChem.Rd
+++ b/man/getRequestPubChem.Rd
@@ -15,7 +15,8 @@ getRequestPubChem(
   operation_options = NA,
   proxy = FALSE,
   raw = FALSE,
-  query_only = FALSE
+  query_only = FALSE,
+  verbose = FALSE
 )
 }
 \arguments{
diff --git a/man/queryPubChem.Rd b/man/queryPubChem.Rd
index 2979e2a..cd486da 100644
--- a/man/queryPubChem.Rd
+++ b/man/queryPubChem.Rd
@@ -16,7 +16,8 @@ queryPubChem(
   batch = TRUE,
   raw = FALSE,
   proxy = FALSE,
-  query_only = FALSE
+  query_only = FALSE,
+  verbose = FALSE
 )
 }
 \arguments{
diff --git a/man/queryUniProt.Rd b/man/queryUniProt.Rd
deleted file mode 100644
index 2143b1c..0000000
--- a/man/queryUniProt.Rd
+++ /dev/null
@@ -1,46 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/getUniProt.R
-\name{queryUniProt}
-\alias{queryUniProt}
-\title{Query the UniProt website REST API}
-\usage{
-queryUniProt(
-  query,
-  columns = "",
-  limit = "",
-  offset = "",
-  format = "xml",
-  include = TRUE,
-  compress = TRUE,
-  ...,
-  url = "https://www.uniprot.org/uniprot"
-)
-}
-\arguments{
-\item{query}{A \code{character} vector of the API query to return. See
-https://www.uniprot.org/help/text-search for information on query
-structure.}
-
-\item{format}{A \code{character} vector specifying the return format. Options
-are 'html', 'tab', 'xls', 'fasta', 'gff', 'txt', 'xml', 'rdf', 'list' or
-'rss'. Default is 'xml'. See https://www.uniprot.org/help/api\%5Fqueries
-for more information.}
-
-\item{include}{A \code{boolean} indicating if isoforms or description of
-referenced data should be included.}
-
-\item{compress}{TODO::}
-
-\item{...}{Catch all unnamed arguments. All parameters after ... must be
-specified with as name=value or they will be ignored.}
-
-\item{url}{A \code{character} vector of the URL for the REST API. Should not
-include trailing '/', this will be added inside the function. This
-parameter must be passed named or it will not work.}
-}
-\value{
-A httr::response object containing the query results as \code{format}.
-}
-\description{
-Query the UniProt website REST API
-}