diff --git a/src/Spreadsheet/AnnotationTable/ArcTable.fs b/src/Spreadsheet/AnnotationTable/ArcTable.fs
index c1e5a26d..e7573d0a 100644
--- a/src/Spreadsheet/AnnotationTable/ArcTable.fs
+++ b/src/Spreadsheet/AnnotationTable/ArcTable.fs
@@ -1,6 +1,7 @@
-module ARCtrl.ISA.Spreadsheet.ArcTable
+module ARCtrl.Spreadsheet.ArcTable
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
 open FsSpreadsheet
 
 // I think we really should not add FSharpAux for exactly one function.
@@ -93,7 +94,7 @@ let tryFromFsWorksheet (sheet : FsWorksheet) =
                 |> Seq.map CompositeColumn.fixDeprecatedIOHeader
                 |> composeColumns
             ArcTable.init sheet.Name
-            |> ArcTable.addColumns(compositeColumns,SkipFillMissing = true)
+            |> ArcTable.addColumns(compositeColumns,skipFillMissing = true)
             |> Some
         | None ->
             None
diff --git a/src/Spreadsheet/AnnotationTable/CompositeCell.fs b/src/Spreadsheet/AnnotationTable/CompositeCell.fs
index ff0f2902..da43f5b3 100644
--- a/src/Spreadsheet/AnnotationTable/CompositeCell.fs
+++ b/src/Spreadsheet/AnnotationTable/CompositeCell.fs
@@ -1,6 +1,7 @@
-module ARCtrl.ISA.Spreadsheet.CompositeCell
+module ARCtrl.Spreadsheet.CompositeCell
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
 open FsSpreadsheet
 
 let fromFsCells (cells : list<FsCell>) : CompositeCell =
@@ -18,7 +19,7 @@ let toFsCells isTerm hasUnit (cell : CompositeCell) : list<FsCell> =
     | CompositeCell.FreeText v when isTerm -> [FsCell(v); FsCell(""); FsCell("")]
     | CompositeCell.FreeText v -> [FsCell(v)]
 
-    | CompositeCell.Term v when hasUnit -> [FsCell(v.NameText); FsCell(""); FsCell(v.TermSourceREFString); FsCell(v.TermAccessionOntobeeUrl)]
-    | CompositeCell.Term v -> [FsCell(v.NameText); FsCell(v.TermSourceREFString); FsCell(v.TermAccessionOntobeeUrl)]
+    | CompositeCell.Term v when hasUnit -> [FsCell(v.NameText); FsCell(""); FsCell(Option.defaultValue "" v.TermSourceREF); FsCell(v.TermAccessionOntobeeUrl)]
+    | CompositeCell.Term v -> [FsCell(v.NameText); FsCell(Option.defaultValue "" v.TermSourceREF); FsCell(v.TermAccessionOntobeeUrl)]
 
-    | CompositeCell.Unitized (v,unit) -> [FsCell(v); FsCell(unit.NameText); FsCell(unit.TermSourceREFString); FsCell(unit.TermAccessionOntobeeUrl)]
\ No newline at end of file
+    | CompositeCell.Unitized (v,unit) -> [FsCell(v); FsCell(unit.NameText); FsCell(Option.defaultValue "" unit.TermSourceREF); FsCell(unit.TermAccessionOntobeeUrl)]
\ No newline at end of file
diff --git a/src/Spreadsheet/AnnotationTable/CompositeColumn.fs b/src/Spreadsheet/AnnotationTable/CompositeColumn.fs
index 24f4a14e..4cc5e7d9 100644
--- a/src/Spreadsheet/AnnotationTable/CompositeColumn.fs
+++ b/src/Spreadsheet/AnnotationTable/CompositeColumn.fs
@@ -1,6 +1,7 @@
-module ARCtrl.ISA.Spreadsheet.CompositeColumn
+module ARCtrl.Spreadsheet.CompositeColumn
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
 open FsSpreadsheet
 
 /// Checks if the column header is a deprecated IO Header. If so, fixes it.
diff --git a/src/Spreadsheet/AnnotationTable/CompositeHeader.fs b/src/Spreadsheet/AnnotationTable/CompositeHeader.fs
index b8e9fe05..74e83ffa 100644
--- a/src/Spreadsheet/AnnotationTable/CompositeHeader.fs
+++ b/src/Spreadsheet/AnnotationTable/CompositeHeader.fs
@@ -1,11 +1,12 @@
-module ARCtrl.ISA.Spreadsheet.CompositeHeader
+module ARCtrl.Spreadsheet.CompositeHeader
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
 open FsSpreadsheet
 
 module ActivePattern = 
 
-    open ARCtrl.ISA.Regex.ActivePatterns
+    open Regex.ActivePatterns
 
     let mergeIDInfo idSpace1 localID1 idSpace2 localID2 =
         if idSpace1 <> idSpace2 then failwithf "TermSourceRef %s and %s do not match" idSpace1 idSpace2
@@ -18,7 +19,7 @@ module ActivePattern =
         let cellValues = cells |> List.map (fun c -> c.ValueAsString())
         match cellValues with
         | [AC name] -> 
-            let ont = OntologyAnnotation.fromString(name)
+            let ont = OntologyAnnotation.create(name)
             f ont
             |> Some
         | [AC name; TSRColumnHeader term1; TANColumnHeader term2] 
@@ -26,7 +27,7 @@ module ActivePattern =
         //| [AC name; Unit; TermAccessionNumber term1; TermSourceREF term2] 
         | [AC name; UnitColumnHeader _; TSRColumnHeader term1; TANColumnHeader term2] ->
             let term = mergeIDInfo term1.IDSpace term1.LocalID term2.IDSpace term2.LocalID
-            let ont = OntologyAnnotation.fromString(name, term.TermSourceRef, term.TermAccessionNumber)
+            let ont = OntologyAnnotation.create(name, term.TermSourceRef, term.TermAccessionNumber)
             f ont
             |> Some
         | _ -> None
diff --git a/src/Spreadsheet/ArcAssay.fs b/src/Spreadsheet/ArcAssay.fs
index e0677363..bdc08731 100644
--- a/src/Spreadsheet/ArcAssay.fs
+++ b/src/Spreadsheet/ArcAssay.fs
@@ -1,6 +1,7 @@
-module ARCtrl.ISA.Spreadsheet.ArcAssay
+module ARCtrl.Spreadsheet.ArcAssay
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
 open FsSpreadsheet
 
 let [<Literal>] obsoleteAssaysLabel = "ASSAY METADATA"
@@ -20,7 +21,7 @@ let toMetadataSheet (assay : ArcAssay) : FsWorksheet =
             yield! Assays.toRows (Some assaysPrefix) [assay]
 
             yield SparseRow.fromValues [contactsLabel]
-            yield! Contacts.toRows (Some contactsPrefix) (List.ofArray assay.Performers)
+            yield! Contacts.toRows (Some contactsPrefix) (List.ofSeq assay.Performers)
         }
     let sheet = FsWorksheet(metaDataSheetName)
     assay
@@ -54,7 +55,7 @@ let fromMetadataSheet (sheet : FsWorksheet) : ArcAssay =
                         assays
                         |> Seq.tryHead 
                         |> Option.defaultValue (ArcAssay.create(Identifier.createMissingIdentifier()))
-                        |> ArcAssay.setPerformers (Array.ofList contacts)
+                        |> ArcAssay.setPerformers (ResizeArray contacts)
         
             if en.MoveNext () then
                 let currentLine = en.Current |> SparseRow.tryGetValueAt 0
diff --git a/src/Spreadsheet/ArcInvestigation.fs b/src/Spreadsheet/ArcInvestigation.fs
index c80fc3d4..f0208fee 100644
--- a/src/Spreadsheet/ArcInvestigation.fs
+++ b/src/Spreadsheet/ArcInvestigation.fs
@@ -1,6 +1,7 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
 open FsSpreadsheet
 open Comment
 open Remark
@@ -78,13 +79,12 @@ module ArcInvestigation =
             do matrix.Matrix.Add ((submissionDateLabel,i),      (Option.defaultValue "" investigation.SubmissionDate))
             do matrix.Matrix.Add ((publicReleaseDateLabel,i),   (Option.defaultValue "" investigation.PublicReleaseDate))
 
-            if Array.isEmpty investigation.Comments |> not then
-                investigation.Comments
-                |> Array.iter (fun comment -> 
-                    let n,v = comment |> Comment.toString
-                    commentKeys <- n :: commentKeys
-                    matrix.Matrix.Add((n,i),v)
-                )   
+            investigation.Comments
+            |> ResizeArray.iter (fun comment -> 
+                let n,v = comment |> Comment.toString
+                commentKeys <- n :: commentKeys
+                matrix.Matrix.Add((n,i),v)
+            )   
 
             {matrix with CommentKeys = commentKeys |> List.distinct |> List.rev}
 
@@ -106,14 +106,14 @@ module ArcInvestigation =
             (Option.fromValueWithDefault "" investigationInfo.Description) 
             (Option.fromValueWithDefault "" investigationInfo.SubmissionDate) 
             (Option.fromValueWithDefault "" investigationInfo.PublicReleaseDate)
-            (Array.ofList ontologySourceReference) 
-            (Array.ofList publications)  
-            (Array.ofList contacts)  
-            (ResizeArray(assays))
-            (ResizeArray(studies))  
-            (ResizeArray(studyIdentifiers))
-            (Array.ofList investigationInfo.Comments)  
-            (Array.ofList remarks)
+            (ResizeArray ontologySourceReference) 
+            (ResizeArray publications)  
+            (ResizeArray contacts)  
+            (ResizeArray assays)
+            (ResizeArray studies)
+            (ResizeArray studyIdentifiers)
+            (ResizeArray investigationInfo.Comments)  
+            (ResizeArray remarks)
 
 
     let fromRows (rows:seq<SparseRow>) =
@@ -183,16 +183,16 @@ module ArcInvestigation =
             with | _ -> rows |> Seq.toList
         seq {
             yield  SparseRow.fromValues [ontologySourceReferenceLabel]
-            yield! OntologySourceReference.toRows (List.ofArray investigation.OntologySourceReferences)
+            yield! OntologySourceReference.toRows (List.ofSeq investigation.OntologySourceReferences)
 
             yield  SparseRow.fromValues [investigationLabel]
             yield! InvestigationInfo.toRows investigation
 
             yield  SparseRow.fromValues [publicationsLabel]
-            yield! Publications.toRows (Some publicationsLabelPrefix) (List.ofArray investigation.Publications)
+            yield! Publications.toRows (Some publicationsLabelPrefix) (List.ofSeq investigation.Publications)
 
             yield  SparseRow.fromValues [contactsLabel]
-            yield! Contacts.toRows (Some contactsLabelPrefix) (List.ofArray investigation.Contacts)
+            yield! Contacts.toRows (Some contactsLabelPrefix) (List.ofSeq investigation.Contacts)
 
             if not isLight then
                 for studyIdentifier in investigation.RegisteredStudyIdentifiers do
@@ -200,7 +200,7 @@ module ArcInvestigation =
                     yield  SparseRow.fromValues [studyLabel]
                     yield! Studies.toRows study None
         }
-        |> insertRemarks (List.ofArray investigation.Remarks)
+        |> insertRemarks (List.ofSeq investigation.Remarks)
         |> seq
 
     let fromFsWorkbook (doc:FsWorkbook) =  
diff --git a/src/Spreadsheet/ArcStudy.fs b/src/Spreadsheet/ArcStudy.fs
index be2fcb70..bf6fb6ca 100644
--- a/src/Spreadsheet/ArcStudy.fs
+++ b/src/Spreadsheet/ArcStudy.fs
@@ -1,9 +1,9 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
+open ARCtrl
 open FsSpreadsheet
 
-open Aux
+open ARCtrl.Helper
 
 module ArcStudy = 
 
diff --git a/src/Spreadsheet/CollectionAux.fs b/src/Spreadsheet/CollectionAux.fs
index 7d324f2d..fa4985e7 100644
--- a/src/Spreadsheet/CollectionAux.fs
+++ b/src/Spreadsheet/CollectionAux.fs
@@ -1,4 +1,4 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
         
 module Seq = 
diff --git a/src/Spreadsheet/Metadata/Assays.fs b/src/Spreadsheet/Metadata/Assays.fs
index 5b8ebd56..90466b17 100644
--- a/src/Spreadsheet/Metadata/Assays.fs
+++ b/src/Spreadsheet/Metadata/Assays.fs
@@ -1,9 +1,12 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
+open ARCtrl
 open Comment
 open Remark
 open System.Collections.Generic
+open ARCtrl.Helper
+open ARCtrl.Process.Conversion
+
 
 module Assays = 
 
@@ -24,15 +27,15 @@ module Assays =
 
     
     let fromString measurementType measurementTypeTermSourceREF measurementTypeTermAccessionNumber technologyType technologyTypeTermSourceREF technologyTypeTermAccessionNumber technologyPlatform fileName comments : ArcAssay = 
-        let measurementType = OntologyAnnotation.fromString(?termName = measurementType,?tan = measurementTypeTermAccessionNumber,?tsr = measurementTypeTermSourceREF)
-        let technologyType = OntologyAnnotation.fromString(?termName = technologyType,?tan = technologyTypeTermAccessionNumber,?tsr = technologyTypeTermSourceREF)
+        let measurementType = OntologyAnnotation.create(?name = measurementType,?tan = measurementTypeTermAccessionNumber,?tsr = measurementTypeTermSourceREF)
+        let technologyType = OntologyAnnotation.create(?name = technologyType,?tan = technologyTypeTermAccessionNumber,?tsr = technologyTypeTermSourceREF)
         ArcAssay.make 
             (fileName)
-            (Option.fromValueWithDefault OntologyAnnotation.empty measurementType)
-            (Option.fromValueWithDefault OntologyAnnotation.empty technologyType) 
-            (technologyPlatform |> Option.map ArcAssay.decomposeTechnologyPlatform)
+            (Option.fromValueWithDefault (OntologyAnnotation()) measurementType)
+            (Option.fromValueWithDefault (OntologyAnnotation()) technologyType) 
+            (technologyPlatform |> Option.map JsonTypes.decomposeTechnologyPlatform)
             (ResizeArray())             
-            [||] 
+            (ResizeArray())      
             (comments)
         
     let fromSparseTable (matrix : SparseTable) : ArcAssay list=
@@ -47,7 +50,7 @@ module Assays =
                     matrix.CommentKeys 
                     |> List.map (fun k -> 
                         Comment.fromString k (matrix.TryGetValueDefault("",(k,i))))
-                    |> Array.ofList
+                    |> ResizeArray
 
                 fromString
                     (matrix.TryGetValue(measurementTypeLabel,i))            
@@ -69,24 +72,23 @@ module Assays =
             let processedFileName =
                 if a.Identifier.StartsWith(Identifier.MISSING_IDENTIFIER) then Identifier.removeMissingIdentifier(a.Identifier) else Identifier.Assay.fileNameFromIdentifier(a.Identifier)
             let i = i + 1
-            let mt = Option.defaultValue OntologyAnnotation.empty a.MeasurementType |> fun mt -> OntologyAnnotation.toString(mt,true)
-            let tt = Option.defaultValue OntologyAnnotation.empty a.TechnologyType |> fun tt -> OntologyAnnotation.toString(tt,true)
+            let mt = Option.defaultValue (OntologyAnnotation()) a.MeasurementType |> fun mt -> OntologyAnnotation.toString(mt,true)
+            let tt = Option.defaultValue (OntologyAnnotation()) a.TechnologyType |> fun tt -> OntologyAnnotation.toString(tt,true)
             do matrix.Matrix.Add ((measurementTypeLabel,i),                       mt.TermName)
             do matrix.Matrix.Add ((measurementTypeTermAccessionNumberLabel,i),    mt.TermAccessionNumber)
             do matrix.Matrix.Add ((measurementTypeTermSourceREFLabel,i),          mt.TermSourceREF)
             do matrix.Matrix.Add ((technologyTypeLabel,i),                        tt.TermName)
             do matrix.Matrix.Add ((technologyTypeTermAccessionNumberLabel,i),     tt.TermAccessionNumber)
             do matrix.Matrix.Add ((technologyTypeTermSourceREFLabel,i),           tt.TermSourceREF)
-            do matrix.Matrix.Add ((technologyPlatformLabel,i),                    (Option.defaultValue "" (a.TechnologyPlatform |> Option.map ArcAssay.composeTechnologyPlatform)))
+            do matrix.Matrix.Add ((technologyPlatformLabel,i),                    (Option.defaultValue "" (a.TechnologyPlatform |> Option.map JsonTypes.composeTechnologyPlatform)))
             do matrix.Matrix.Add ((fileNameLabel,i),                              processedFileName)
 
-            if Array.isEmpty a.Comments |> not then
-                a.Comments
-                |> Array.iter (fun comment -> 
-                    let n,v = comment |> Comment.toString
-                    commentKeys <- n :: commentKeys
-                    matrix.Matrix.Add((n,i),v)
-                )   
+            a.Comments
+            |> ResizeArray.iter (fun comment -> 
+                let n,v = comment |> Comment.toString
+                commentKeys <- n :: commentKeys
+                matrix.Matrix.Add((n,i),v)
+            )   
         )
         {matrix with CommentKeys = commentKeys |> List.distinct |> List.rev}
 
diff --git a/src/Spreadsheet/Metadata/Comment.fs b/src/Spreadsheet/Metadata/Comment.fs
index d731e25a..454dc236 100644
--- a/src/Spreadsheet/Metadata/Comment.fs
+++ b/src/Spreadsheet/Metadata/Comment.fs
@@ -1,8 +1,8 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
+open ARCtrl
 open System.Text.RegularExpressions
-open ARCtrl.ISA.Regex.ActivePatterns
+open ARCtrl.Helper.Regex.ActivePatterns
 
 module Comment = 
 
@@ -29,7 +29,6 @@ module Comment =
 
     let fromString k v =
         Comment.make 
-            None 
             (Option.fromValueWithDefault "" k) 
             (Option.fromValueWithDefault "" v)
 
diff --git a/src/Spreadsheet/Metadata/Contacts.fs b/src/Spreadsheet/Metadata/Contacts.fs
index 1799dfbf..1c418c25 100644
--- a/src/Spreadsheet/Metadata/Contacts.fs
+++ b/src/Spreadsheet/Metadata/Contacts.fs
@@ -1,6 +1,8 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
+open ARCtrl.Process.Conversion
 open Comment
 open Remark
 open System.Collections.Generic
@@ -24,7 +26,6 @@ module Contacts =
     let fromString lastName firstName midInitials email phone fax address affiliation role rolesTermAccessionNumber rolesTermSourceREF comments =
         let roles = OntologyAnnotation.fromAggregatedStrings ';' role rolesTermSourceREF rolesTermAccessionNumber
         Person.make 
-            None 
             None
             (lastName   ) 
             (firstName  )
@@ -34,8 +35,8 @@ module Contacts =
             (fax        )
             (address    )
             (affiliation) 
-            (Option.fromValueWithDefault [||] roles    )
-            (Option.fromValueWithDefault [||] comments )
+            (roles    )
+            (comments )
         |> Person.setOrcidFromComments
 
     let fromSparseTable (matrix : SparseTable) =
@@ -49,7 +50,7 @@ module Contacts =
                     matrix.CommentKeys 
                     |> List.map (fun k -> 
                         Comment.fromString k (matrix.TryGetValueDefault("",(k,i))))
-                    |> Array.ofList
+                    |> ResizeArray
                 fromString
                     (matrix.TryGetValue(lastNameLabel,i))
                     (matrix.TryGetValue(firstNameLabel,i))
@@ -72,7 +73,7 @@ module Contacts =
         |> List.map Person.setCommentFromORCID
         |> List.iteri (fun i p ->
             let i = i + 1
-            let rAgg = Option.defaultValue [||] p.Roles |> OntologyAnnotation.toAggregatedStrings ';'
+            let rAgg = p.Roles |> Array.ofSeq |> OntologyAnnotation.toAggregatedStrings ';'
             do matrix.Matrix.Add ((lastNameLabel,i),                    (Option.defaultValue ""  p.LastName     ))
             do matrix.Matrix.Add ((firstNameLabel,i),                   (Option.defaultValue ""  p.FirstName    ))
             do matrix.Matrix.Add ((midInitialsLabel,i),                 (Option.defaultValue ""  p.MidInitials  ))
@@ -85,15 +86,12 @@ module Contacts =
             do matrix.Matrix.Add ((rolesTermAccessionNumberLabel,i),    rAgg.TermAccessionNumberAgg)
             do matrix.Matrix.Add ((rolesTermSourceREFLabel,i),          rAgg.TermSourceREFAgg)
 
-            match p.Comments with 
-            | None -> ()
-            | Some c ->
-                c
-                |> Array.iter (fun comment -> 
-                    let n,v = comment |> Comment.toString
-                    commentKeys <- n :: commentKeys
-                    matrix.Matrix.Add((n,i),v)
-                )
+            p.Comments
+            |> ResizeArray.iter (fun comment -> 
+                let n,v = comment |> Comment.toString
+                commentKeys <- n :: commentKeys
+                matrix.Matrix.Add((n,i),v)
+            )
         )
         {matrix with CommentKeys = commentKeys |> List.distinct |> List.rev} 
 
diff --git a/src/Spreadsheet/Metadata/Conversions.fs b/src/Spreadsheet/Metadata/Conversions.fs
index 0a912dd8..446adb66 100644
--- a/src/Spreadsheet/Metadata/Conversions.fs
+++ b/src/Spreadsheet/Metadata/Conversions.fs
@@ -1,7 +1,8 @@
-namespace ARCtrl.ISA.Spreadsheet
-
-open ARCtrl.ISA
+namespace ARCtrl.Spreadsheet
 
+open ARCtrl
+open ARCtrl.Helper
+open ARCtrl.Process
 
 module internal Option =
  
@@ -37,14 +38,15 @@ module OntologyAnnotation =
         ) 0
 
     /// Returns a list of ISAJson OntologyAnnotation objects from ISATab aggregated strings
-    let fromAggregatedStrings (separator:char) (terms:string) (source:string) (accessions:string) : OntologyAnnotation []=
+    let fromAggregatedStrings (separator:char) (terms:string) (source:string) (accessions:string) : ResizeArray<OntologyAnnotation> =
         let l = getLengthOfAggregatedStrings separator [|terms;source;accessions|]
-        if l = 0 then [||]
+        if l = 0 then ResizeArray()
         else 
             let terms : string [] = if terms = "" then Array.create l "" else terms.Split(separator)
             let sources : string [] = if source = "" then Array.create l "" else source.Split(separator)
             let accessions : string [] = if accessions = "" then Array.create l "" else accessions.Split(separator)
-            Array.map3 (fun a b c -> OntologyAnnotation.fromString(a,b,c)) terms sources accessions
+            Array.map3 (fun a b c -> OntologyAnnotation.create(a,b,c)) terms sources accessions
+            |> ResizeArray
 
     /// Returns the aggregated ISATab OntologyAnnotation Name, ontology source and Accession number from a list of ISAJson OntologyAnnotation objects
     let toAggregatedStrings (separator:char) (oas : OntologyAnnotation []) =
@@ -52,15 +54,15 @@ module OntologyAnnotation =
         if oas = [||] then {|TermNameAgg = ""; TermAccessionNumberAgg = ""; TermSourceREFAgg = ""|}       
         else
             oas
-            |> Array.map OntologyAnnotation.toString
             |> Array.fold (fun (nameAgg,tsrAgg,tanAgg) term -> 
+                let name,tsr,tan = Option.defaultValue "" term.Name, Option.defaultValue "" term.TermSourceREF, Option.defaultValue "" term.TermAccessionNumber
                 if first then 
                     first <- false
-                    term.TermName,term.TermSourceREF,term.TermAccessionNumber
+                    name,tsr,tan
                 else 
-                    sprintf "%s%c%s" nameAgg    separator term.TermName,
-                    sprintf "%s%c%s" tsrAgg     separator term.TermSourceREF,
-                    sprintf "%s%c%s" tanAgg     separator term.TermAccessionNumber
+                    sprintf "%s%c%s" nameAgg    separator name,
+                    sprintf "%s%c%s" tsrAgg     separator tsr,
+                    sprintf "%s%c%s" tanAgg     separator tan
             ) ("","","")
             |> fun (nameAgg,tsrAgg,tanAgg) -> {|TermNameAgg = nameAgg; TermAccessionNumberAgg = tanAgg; TermSourceREFAgg = tsrAgg|}
 
@@ -76,7 +78,7 @@ module Component =
             let sources : string [] = if source = "" then Array.create l "" else source.Split(separator)
             let accessions : string [] = if accessions = "" then Array.create l "" else accessions.Split(separator)
             Array.map4 (fun a b c d -> Component.fromString(a,b,c,d)) names terms sources accessions
-            |> Array.toList
+            |> List.ofArray
 
     /// Returns the aggregated ISATAb Component Name, Ontology Annotation value, Accession number and ontology source from a list of ISAJson Component objects
     let toAggregatedStrings (separator:char) (cs : Component list) =
@@ -102,7 +104,7 @@ module ProtocolParameter =
     /// Returns a list of ISAJson ProtocolParameter objects from ISATab aggregated strings
     let fromAggregatedStrings (separator:char) (terms:string) (source:string) (accessions:string) =
         OntologyAnnotation.fromAggregatedStrings separator terms source accessions
-        |> Array.map (Some >> (ProtocolParameter.make None))
+        |> ResizeArray.map (Some >> (ProtocolParameter.make None))
 
     /// Returns the aggregated ISATAb Ontology Annotation value, Accession number and ontology source from a list of ISAJson ProtocolParameter objects
     let toAggregatedStrings (separator:char) (oas : ProtocolParameter list) =
diff --git a/src/Spreadsheet/Metadata/DesignDescriptors.fs b/src/Spreadsheet/Metadata/DesignDescriptors.fs
index f694379c..3a7ba089 100644
--- a/src/Spreadsheet/Metadata/DesignDescriptors.fs
+++ b/src/Spreadsheet/Metadata/DesignDescriptors.fs
@@ -1,6 +1,6 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
+open ARCtrl
 open Comment
 open Remark
 open System.Collections.Generic
diff --git a/src/Spreadsheet/Metadata/Factors.fs b/src/Spreadsheet/Metadata/Factors.fs
index 5ea7d090..92f41b97 100644
--- a/src/Spreadsheet/Metadata/Factors.fs
+++ b/src/Spreadsheet/Metadata/Factors.fs
@@ -1,6 +1,8 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
+open ARCtrl.Process
 open Comment
 open Remark
 open System.Collections.Generic
@@ -15,12 +17,11 @@ module Factors =
     let labels = [nameLabel;factorTypeLabel;typeTermAccessionNumberLabel;typeTermSourceREFLabel]
     
     let fromString name designType typeTermSourceREF typeTermAccessionNumber comments =
-        let factorType = OntologyAnnotation.fromString(?termName = designType,?tan = typeTermAccessionNumber, ?tsr = typeTermSourceREF)
+        let factorType = OntologyAnnotation.create(?name = designType,?tan = typeTermAccessionNumber, ?tsr = typeTermSourceREF)
         Factor.make 
-            None 
             (name) 
-            (Option.fromValueWithDefault OntologyAnnotation.empty factorType) 
-            (Option.fromValueWithDefault [||] comments)
+            (Option.fromValueWithDefault (OntologyAnnotation()) factorType) 
+            (Option.fromValueWithDefault (ResizeArray()) comments)
 
     let fromSparseTable (matrix : SparseTable) =
         if matrix.ColumnCount = 0 && matrix.CommentKeys.Length <> 0 then
@@ -34,7 +35,7 @@ module Factors =
                     matrix.CommentKeys 
                     |> List.map (fun k -> 
                         Comment.fromString k (matrix.TryGetValueDefault("",(k,i))))
-                    |> Array.ofList
+                    |> ResizeArray
 
                 fromString
                     (matrix.TryGetValue(nameLabel,i))
@@ -50,7 +51,7 @@ module Factors =
         factors
         |> List.iteri (fun i f ->
             let i = i + 1
-            let ft = f.FactorType |> Option.defaultValue OntologyAnnotation.empty |> fun f -> OntologyAnnotation.toString(f,true)
+            let ft = f.FactorType |> Option.defaultValue (OntologyAnnotation()) |> fun f -> OntologyAnnotation.toString(f,true)
             do matrix.Matrix.Add ((nameLabel,i),                    (Option.defaultValue "" f.Name))
             do matrix.Matrix.Add ((factorTypeLabel,i),              ft.TermName)
             do matrix.Matrix.Add ((typeTermAccessionNumberLabel,i), ft.TermAccessionNumber)
@@ -60,7 +61,7 @@ module Factors =
             | None -> ()
             | Some c ->
                 c
-                |> Array.iter (fun comment -> 
+                |> ResizeArray.iter (fun comment -> 
                     let n,v = comment |> Comment.toString
                     commentKeys <- n :: commentKeys
                     matrix.Matrix.Add((n,i),v)
diff --git a/src/Spreadsheet/Metadata/OntologyAnnotation.fs b/src/Spreadsheet/Metadata/OntologyAnnotation.fs
index 678645ea..b0a64c06 100644
--- a/src/Spreadsheet/Metadata/OntologyAnnotation.fs
+++ b/src/Spreadsheet/Metadata/OntologyAnnotation.fs
@@ -1,6 +1,7 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
 open Comment
 open Remark
 open System.Collections.Generic
@@ -20,14 +21,13 @@ module OntologyAnnotationSection =
                     matrix.CommentKeys 
                     |> List.map (fun k -> 
                         Comment.fromString k (matrix.TryGetValueDefault("",(k,i))))
-                    |> Array.ofList
-                    |> Option.fromValueWithDefault [||]
+                    |> ResizeArray
 
-                OntologyAnnotation.fromString(
-                    ?termName = matrix.TryGetValue(label,i),
+                OntologyAnnotation(
+                    ?name = matrix.TryGetValue(label,i),
                     ?tsr = matrix.TryGetValue(labelTSR,i),
                     ?tan = matrix.TryGetValue(labelTAN,i),
-                    ?comments = comments
+                    comments = comments
                 )
             )
 
@@ -42,15 +42,12 @@ module OntologyAnnotationSection =
             do matrix.Matrix.Add ((labelTAN,i),   oa.TermAccessionNumber)
             do matrix.Matrix.Add ((labelTSR,i),         oa.TermSourceREF)
 
-            match d.Comments with 
-            | None -> ()
-            | Some c ->
-                c
-                |> Array.iter (fun comment -> 
-                    let n,v = comment |> Comment.toString
-                    commentKeys <- n :: commentKeys
-                    matrix.Matrix.Add((n,i),v)
-                )
+            d.Comments
+            |> ResizeArray.iter (fun comment -> 
+                let n,v = comment |> Comment.toString
+                commentKeys <- n :: commentKeys
+                matrix.Matrix.Add((n,i),v)
+            )
         )
         {matrix with CommentKeys = commentKeys |> List.distinct |> List.rev} 
 
diff --git a/src/Spreadsheet/Metadata/OntologySourceReference.fs b/src/Spreadsheet/Metadata/OntologySourceReference.fs
index 63df6929..a41022d3 100644
--- a/src/Spreadsheet/Metadata/OntologySourceReference.fs
+++ b/src/Spreadsheet/Metadata/OntologySourceReference.fs
@@ -1,7 +1,8 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
 open FsSpreadsheet
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
 
 open System.Collections.Generic
 
@@ -21,7 +22,7 @@ module OntologySourceReference =
             (file)
             (name)
             (version)
-            (Option.fromValueWithDefault [||] comments)
+            comments
 
     let fromSparseTable (matrix : SparseTable) =
         if matrix.ColumnCount = 0 && matrix.CommentKeys.Length <> 0 then
@@ -35,7 +36,7 @@ module OntologySourceReference =
                     matrix.CommentKeys 
                     |> List.map (fun k -> 
                         Comment.fromString k (matrix.TryGetValueDefault("",(k,i))))
-                    |> Array.ofList
+                    |> ResizeArray
 
                 fromString
                     (matrix.TryGetValue(descriptionLabel,i))
@@ -56,15 +57,13 @@ module OntologySourceReference =
             do matrix.Matrix.Add ((versionLabel,i),     (Option.defaultValue "" o.Version))
             do matrix.Matrix.Add ((descriptionLabel,i), (Option.defaultValue "" o.Description))
 
-            match o.Comments with 
-            | None -> ()
-            | Some c ->
-                c
-                |> Array.iter (fun comment -> 
-                    let n,v = comment |> Comment.toString
-                    commentKeys <- n :: commentKeys
-                    matrix.Matrix.Add((n,i),v)
-                )     
+
+            o.Comments
+            |> ResizeArray.iter (fun comment -> 
+                let n,v = comment |> Comment.toString
+                commentKeys <- n :: commentKeys
+                matrix.Matrix.Add((n,i),v)
+            )     
         )
         {matrix with CommentKeys = commentKeys |> List.distinct |> List.rev}
 
diff --git a/src/Spreadsheet/Metadata/Protocols.fs b/src/Spreadsheet/Metadata/Protocols.fs
index 4132198b..0c6180c2 100644
--- a/src/Spreadsheet/Metadata/Protocols.fs
+++ b/src/Spreadsheet/Metadata/Protocols.fs
@@ -1,6 +1,7 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Process
 open Comment
 open Remark
 open System.Collections.Generic
@@ -30,14 +31,14 @@ module Protocols =
         ]
 
     let fromString name protocolType typeTermAccessionNumber typeTermSourceREF description uri version parametersName parametersTermAccessionNumber parametersTermSourceREF componentsName componentsType componentsTypeTermAccessionNumber componentsTypeTermSourceREF comments =
-        let protocolType = OntologyAnnotation.fromString(?termName = protocolType,?tan =  typeTermAccessionNumber,?tsr = typeTermSourceREF)
-        let parameters = ProtocolParameter.fromAggregatedStrings ';' parametersName parametersTermSourceREF parametersTermAccessionNumber |> List.ofArray
+        let protocolType = OntologyAnnotation.create(?name = protocolType,?tan =  typeTermAccessionNumber,?tsr = typeTermSourceREF)
+        let parameters = ProtocolParameter.fromAggregatedStrings ';' parametersName parametersTermSourceREF parametersTermAccessionNumber |> List.ofSeq
         let components = Component.fromAggregatedStrings ';' componentsName componentsType componentsTypeTermSourceREF componentsTypeTermAccessionNumber
         
         Protocol.make 
             None 
             (name |> Option.map URI.fromString) 
-            (Option.fromValueWithDefault OntologyAnnotation.empty protocolType)
+            (Option.fromValueWithDefault (OntologyAnnotation()) protocolType)
             (description)
             (uri |> Option.map URI.fromString) 
             (version)
@@ -49,7 +50,7 @@ module Protocols =
     let fromSparseTable (matrix : SparseTable) =
         if matrix.ColumnCount = 0 && matrix.CommentKeys.Length <> 0 then
             let comments = SparseTable.GetEmptyComments matrix
-            Protocol.create(Comments = List.ofArray comments)
+            Protocol.create(Comments = List.ofSeq comments)
             |> List.singleton
         else
             List.init matrix.ColumnCount (fun i -> 
@@ -83,7 +84,7 @@ module Protocols =
         protocols
         |> List.iteri (fun i p ->
             let i = i + 1
-            let pt = p.ProtocolType |> Option.defaultValue OntologyAnnotation.empty |> fun pt -> OntologyAnnotation.toString(pt,true)
+            let pt = p.ProtocolType |> Option.defaultValue (OntologyAnnotation()) |> fun pt -> OntologyAnnotation.toString(pt,true)
             let pAgg = p.Parameters |> Option.defaultValue [] |> ProtocolParameter.toAggregatedStrings ';' 
             let cAgg = p.Components |> Option.defaultValue [] |> Component.toAggregatedStrings ';' 
 
diff --git a/src/Spreadsheet/Metadata/Publication.fs b/src/Spreadsheet/Metadata/Publication.fs
index fb1a1b64..22bd73e6 100644
--- a/src/Spreadsheet/Metadata/Publication.fs
+++ b/src/Spreadsheet/Metadata/Publication.fs
@@ -1,6 +1,7 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
+open ARCtrl
+open ARCtrl.Helper
 open Comment
 open Remark
 open System.Collections.Generic
@@ -18,14 +19,14 @@ module Publications =
     let labels = [pubMedIDLabel;doiLabel;authorListLabel;titleLabel;statusLabel;statusTermAccessionNumberLabel;statusTermSourceREFLabel]
 
     let fromString pubMedID doi author title status statusTermSourceREF statusTermAccessionNumber comments =
-        let status = OntologyAnnotation.fromString(?termName = status,?tan = statusTermAccessionNumber,?tsr = statusTermSourceREF)
+        let status = OntologyAnnotation(?name = status,?tan = statusTermAccessionNumber,?tsr = statusTermSourceREF)
         Publication.make 
             (pubMedID |> Option.map URI.fromString)
             (doi)
             (author)
             (title) 
-            (Option.fromValueWithDefault OntologyAnnotation.empty status) 
-            (Option.fromValueWithDefault [||] comments)
+            (Option.fromValueWithDefault (OntologyAnnotation()) status) 
+            comments
 
     let fromSparseTable (matrix : SparseTable) =
         if matrix.ColumnCount = 0 && matrix.CommentKeys.Length <> 0 then
@@ -39,7 +40,7 @@ module Publications =
                     matrix.CommentKeys 
                     |> List.map (fun k -> 
                         Comment.fromString k (matrix.TryGetValueDefault("",(k,i))))
-                    |> Array.ofList
+                    |> ResizeArray
 
                 fromString
                     (matrix.TryGetValue(pubMedIDLabel,i))            
@@ -58,7 +59,7 @@ module Publications =
         publications
         |> List.iteri (fun i p ->
             let i = i + 1
-            let s = Option.defaultValue OntologyAnnotation.empty p.Status |> fun s -> OntologyAnnotation.toString (s,true)
+            let s = Option.defaultValue (OntologyAnnotation()) p.Status |> fun s -> OntologyAnnotation.toString (s,true)
             do matrix.Matrix.Add ((pubMedIDLabel,i),                    (Option.defaultValue "" p.PubMedID))
             do matrix.Matrix.Add ((doiLabel,i),                         (Option.defaultValue "" p.DOI))
             do matrix.Matrix.Add ((authorListLabel,i),                  (Option.defaultValue "" p.Authors))
@@ -67,15 +68,12 @@ module Publications =
             do matrix.Matrix.Add ((statusTermAccessionNumberLabel,i),   s.TermAccessionNumber)
             do matrix.Matrix.Add ((statusTermSourceREFLabel,i),         s.TermSourceREF)
 
-            match p.Comments with 
-            | None -> ()
-            | Some c ->
-                c
-                |> Array.iter (fun comment -> 
-                    let n,v = comment |> Comment.toString
-                    commentKeys <- n :: commentKeys
-                    matrix.Matrix.Add((n,i),v)
-                )
+            p.Comments
+            |> ResizeArray.iter (fun comment -> 
+                let n,v = comment |> Comment.toString
+                commentKeys <- n :: commentKeys
+                matrix.Matrix.Add((n,i),v)
+            )
         )
         {matrix with CommentKeys = commentKeys |> List.distinct |> List.rev} 
 
diff --git a/src/Spreadsheet/Metadata/SparseTable.fs b/src/Spreadsheet/Metadata/SparseTable.fs
index 1c68dd93..a8679a36 100644
--- a/src/Spreadsheet/Metadata/SparseTable.fs
+++ b/src/Spreadsheet/Metadata/SparseTable.fs
@@ -1,7 +1,6 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
-open ARCtrl.ISA.Aux
+open ARCtrl
 open System.Collections.Generic
 open FsSpreadsheet.DSL
 open FsSpreadsheet
@@ -158,7 +157,7 @@ type SparseTable =
                 (SparseRow.fromValues (Comment.wrapCommentKey key :: List.init (matrix.ColumnCount - 1) (fun i -> matrix.TryGetValueDefault("",(key,i + 1)))))
         }
 
-    static member GetEmptyComments(matrix) : Comment [] = 
+    static member GetEmptyComments(matrix) : ResizeArray<Comment> = 
         matrix.CommentKeys
-        |> List.map (fun key -> Comment.create(Name = key))
-        |> Array.ofList
\ No newline at end of file
+        |> List.map (fun key -> Comment.create(name = key))
+        |> ResizeArray
\ No newline at end of file
diff --git a/src/Spreadsheet/Metadata/Study.fs b/src/Spreadsheet/Metadata/Study.fs
index 4fa8af2c..23c51e1e 100644
--- a/src/Spreadsheet/Metadata/Study.fs
+++ b/src/Spreadsheet/Metadata/Study.fs
@@ -1,9 +1,12 @@
-namespace ARCtrl.ISA.Spreadsheet
+namespace ARCtrl.Spreadsheet
 
-open ARCtrl.ISA
+open ARCtrl
 open Comment
 open Remark
 open System.Collections.Generic
+open ARCtrl.Helper
+open ARCtrl.Process
+open ARCtrl.Process.Conversion
 
 module Studies = 
 
@@ -86,13 +89,12 @@ module Studies =
             do matrix.Matrix.Add ((publicReleaseDateLabel,i),   (Option.defaultValue "" study.PublicReleaseDate))
             do matrix.Matrix.Add ((fileNameLabel,i),            processedFileName)
 
-            if Array.isEmpty study.Comments |> not then
-                study.Comments
-                |> Array.iter (fun comment -> 
-                    let n,v = comment |> Comment.toString
-                    commentKeys <- n :: commentKeys
-                    matrix.Matrix.Add((n,i),v)
-                )    
+            study.Comments
+            |> ResizeArray.iter (fun comment -> 
+                let n,v = comment |> Comment.toString
+                commentKeys <- n :: commentKeys
+                matrix.Matrix.Add((n,i),v)
+            )    
 
             {matrix with CommentKeys = commentKeys |> List.distinct |> List.rev}
 
@@ -105,6 +107,8 @@ module Studies =
             |> StudyInfo.ToSparseTable
             |> SparseTable.ToRows
     
+    /// FACTORS AND PROTOCOLS ARE NOT USED ANYMORE, Lukas, 21.03.24
+    // We made these changes as merging duplicated top level metadata with the underlying Table sequence is time consuming, complex and error prone
     let fromParts (studyInfo:StudyInfo) (designDescriptors:OntologyAnnotation list) (publications: Publication list) (factors: Factor list) (assays: ArcAssay list) (protocols : Protocol list) (contacts: Person list) =
         let assayIdentifiers = assays |> List.map (fun assay -> assay.Identifier)
         ArcStudy.make 
@@ -113,13 +117,12 @@ module Studies =
             (Option.fromValueWithDefault "" studyInfo.Description) 
             (Option.fromValueWithDefault "" studyInfo.SubmissionDate)
             (Option.fromValueWithDefault "" studyInfo.PublicReleaseDate)
-            (Array.ofList publications)
-            (Array.ofList contacts)
-            (Array.ofList designDescriptors)  
-            (protocols |> List.map ArcTable.fromProtocol |> ResizeArray)
+            (ResizeArray publications)
+            (ResizeArray contacts)
+            (ResizeArray designDescriptors)  
+            (ResizeArray())
             (ResizeArray(assayIdentifiers))
-            (Array.ofList factors) 
-            (Array.ofList studyInfo.Comments)
+            (ResizeArray studyInfo.Comments)
         |> fun arcstudy -> 
             if arcstudy.isEmpty && arcstudy.Identifier = "" 
             then None else Some (arcstudy,assays)
@@ -163,18 +166,19 @@ module Studies =
     
     let toRows (study : ArcStudy) (assays : ArcAssay list option) =
         let protocols = study.Tables |> Seq.collect (fun p -> p.GetProtocols()) |> List.ofSeq
+        let factors = study.Tables |> Seq.collect (fun f -> f.GetProcesses() |> ProcessSequence.getFactors) |> List.ofSeq
         let assays = assays |> Option.defaultValue (study.GetRegisteredAssaysOrIdentifier() |> List.ofSeq)
         seq {          
             yield! StudyInfo.toRows study
 
             yield  SparseRow.fromValues [designDescriptorsLabel]
-            yield! DesignDescriptors.toRows (Some designDescriptorsLabelPrefix) (List.ofArray study.StudyDesignDescriptors)
+            yield! DesignDescriptors.toRows (Some designDescriptorsLabelPrefix) (List.ofSeq study.StudyDesignDescriptors)
 
             yield  SparseRow.fromValues [publicationsLabel]
-            yield! Publications.toRows (Some publicationsLabelPrefix) (List.ofArray study.Publications)
+            yield! Publications.toRows (Some publicationsLabelPrefix) (List.ofSeq study.Publications)
 
             yield  SparseRow.fromValues [factorsLabel]
-            yield! Factors.toRows (Some factorsLabelPrefix) (List.ofArray study.Factors)
+            yield! Factors.toRows (Some factorsLabelPrefix) factors
 
             yield  SparseRow.fromValues [assaysLabel]
             yield! Assays.toRows (Some assaysLabelPrefix) assays
@@ -183,5 +187,5 @@ module Studies =
             yield! Protocols.toRows (Some protocolsLabelPrefix) protocols
 
             yield  SparseRow.fromValues [contactsLabel]
-            yield! Contacts.toRows (Some contactsLabelPrefix) (List.ofArray study.Contacts)
+            yield! Contacts.toRows (Some contactsLabelPrefix) (List.ofSeq study.Contacts)
         }
\ No newline at end of file