diff --git a/src/ARCTokenization/ARCMock.fs b/src/ARCTokenization/ARCMock.fs
index 644bbca..43bf16f 100644
--- a/src/ARCTokenization/ARCMock.fs
+++ b/src/ARCTokenization/ARCMock.fs
@@ -199,8 +199,7 @@ type ARCMock =
                 ["" ; yield! Study_Person_Roles_Term_Source_REF |> Option.defaultValue Seq.empty]
             ]
 
-        Terms.InvestigationMetadata.nonObsoleteCvTerms
-        |> List.skip 1 //(ignore root term)
+        Terms.InvestigationMetadata.nonObsoleteNonRootCvTerms
         |> List.filter (fun t -> (not (t.Name.StartsWith("Comment"))) || (t.Name.Equals("Comment[ORCID]"))) // ignore all comments except non-obsolete orcid
         |> List.zip valueRows
         |> List.map (fun (values,term) ->
@@ -343,8 +342,7 @@ type ARCMock =
             [""; yield! Study_Person_Roles_Term_Source_REF |> Option.defaultValue Seq.empty ]
         ]
 
-        Terms.StudyMetadata.nonObsoleteCvTerms
-        |> List.skip 1 //(ignore root term)
+        Terms.StudyMetadata.nonObsoleteNonRootCvTerms
         |> List.filter (fun t -> not (t.Name.StartsWith("Comment"))) // ignore all comments
         |> List.zip valueRows
         |> List.map (fun (values,term) ->
@@ -407,8 +405,7 @@ type ARCMock =
             [""; yield! Assay_Performer_Roles_Term_Source_REF |> Option.defaultValue Seq.empty ]
         ]
 
-        Terms.AssayMetadata.nonObsoleteCvTerms
-        |> List.skip 1 //(ignore root term)
+        Terms.AssayMetadata.nonObsoleteNonRootCvTerms
         |> List.filter (fun t -> not (t.Name.StartsWith("Comment"))) // ignore all comments
         |> List.zip valueRows
         |> List.map (fun (values,term) ->
diff --git a/src/ARCTokenization/MetadataSheet.fs b/src/ARCTokenization/MetadataSheet.fs
index e615c64..61108eb 100644
--- a/src/ARCTokenization/MetadataSheet.fs
+++ b/src/ARCTokenization/MetadataSheet.fs
@@ -34,8 +34,8 @@ module MetadataSheet =
         | UnMatchable name -> 
             fun (pv) -> UserParam(name, pv, attributes) 
 
-    let rec parseAssayKey = parseKeyWithTerms AssayMetadata.cvTerms
+    let rec parseAssayKey = parseKeyWithTerms AssayMetadata.nonRootCvTerms
 
-    let rec parseStudyKey = parseKeyWithTerms StudyMetadata.cvTerms
+    let rec parseStudyKey = parseKeyWithTerms StudyMetadata.nonRootCvTerms
 
-    let rec parseInvestigationKey = parseKeyWithTerms InvestigationMetadata.cvTerms
\ No newline at end of file
+    let rec parseInvestigationKey = parseKeyWithTerms InvestigationMetadata.nonRootCvTerms
\ No newline at end of file
diff --git a/src/ARCTokenization/Terms.fs b/src/ARCTokenization/Terms.fs
index 3397b0b..b0b8d2b 100644
--- a/src/ARCTokenization/Terms.fs
+++ b/src/ARCTokenization/Terms.fs
@@ -22,58 +22,123 @@ module InvestigationMetadata =
 
     let ontology = OboOntology.fromLines true obo
 
-    let nonObsoleteCvTerms = 
+    let nonRootOboTerms = 
         ontology.Terms
-        |> List.filter (fun t -> not t.IsObsolete)
-        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "INVMSO"))
+        |> List.skip 1
 
-    let obsoleteCvTerms = 
+    let nonObsoleteOboTerms = 
         ontology.Terms
+        |> List.filter (fun t -> not t.IsObsolete)
+
+    let nonObsoleteNonRootOboTerms = 
+        nonRootOboTerms
+        |> List.filter (fun t -> not t.IsObsolete)
+
+    let obsoleteOboTerms = 
+        nonRootOboTerms
         |> List.filter (fun t -> t.IsObsolete)
-        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "INVMSO"))
 
     let cvTerms = 
         ontology.Terms
         |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "INVMSO"))
 
+    let nonRootCvTerms = 
+        nonRootOboTerms
+        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "INVMSO"))
+
+    let nonObsoleteCvTerms =
+        nonObsoleteOboTerms
+        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "INVMSO"))
+
+    let nonObsoleteNonRootCvTerms =
+        nonObsoleteNonRootOboTerms
+        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "INVMSO"))
+
+    let obsoleteCvTerms =
+        obsoleteOboTerms
+        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "INVMSO"))
+
 module StudyMetadata =
     
     let internal obo = (EmbeddedResource.load "structural_ontologies.study_metadata_structural_ontology.obo").Replace("\r\n", "\n").Split('\n')
 
     let ontology = OboOntology.fromLines true obo
 
-    let nonObsoleteCvTerms = 
+    let nonRootOboTerms = 
         ontology.Terms
-        |> List.filter (fun t -> not t.IsObsolete)
-        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "INVMSO"))
+        |> List.skip 1
 
-    let obsoleteCvTerms = 
+    let nonObsoleteOboTerms = 
         ontology.Terms
+        |> List.filter (fun t -> not t.IsObsolete)
+
+    let nonObsoleteNonRootOboTerms = 
+        nonRootOboTerms
+        |> List.filter (fun t -> not t.IsObsolete)
+
+    let obsoleteOboTerms = 
+        nonRootOboTerms
         |> List.filter (fun t -> t.IsObsolete)
-        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "STDMSO"))
 
     let cvTerms = 
         ontology.Terms
-        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "STDMSO"))    
+        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "STDMSO"))
 
+    let nonRootCvTerms = 
+        nonRootOboTerms
+        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "STDMSO"))
+
+    let nonObsoleteCvTerms =
+        nonObsoleteOboTerms
+        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "STDMSO"))
+
+    let nonObsoleteNonRootCvTerms =
+        nonObsoleteNonRootOboTerms
+        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "STDMSO"))
+
+    let obsoleteCvTerms =
+        obsoleteOboTerms
+        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "STDMSO"))
 module AssayMetadata = 
     
     let internal obo = (EmbeddedResource.load "structural_ontologies.assay_metadata_structural_ontology.obo").Replace("\r\n", "\n").Split('\n')
 
     let ontology = OboOntology.fromLines true obo
 
-    let nonObsoleteCvTerms = 
+    let nonRootOboTerms = 
+        ontology.Terms
+        |> List.skip 1
+
+    let nonObsoleteOboTerms = 
         ontology.Terms
         |> List.filter (fun t -> not t.IsObsolete)
-        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "INVMSO"))
+
+    let nonObsoleteNonRootOboTerms = 
+        nonRootOboTerms
+        |> List.filter (fun t -> not t.IsObsolete)
+
+    let obsoleteOboTerms = 
+        nonRootOboTerms
+        |> List.filter (fun t -> t.IsObsolete)
 
     let cvTerms = 
         ontology.Terms
         |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "ASSMSO"))
 
-    let obsoleteCvTerms = 
-        ontology.Terms
-        |> List.filter (fun t -> t.IsObsolete)
+    let nonRootCvTerms = 
+        nonRootOboTerms
+        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "ASSMSO"))
+
+    let nonObsoleteCvTerms =
+        nonObsoleteOboTerms
+        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "ASSMSO"))
+
+    let nonObsoleteNonRootCvTerms =
+        nonObsoleteNonRootOboTerms
+        |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "ASSMSO"))
+
+    let obsoleteCvTerms =
+        obsoleteOboTerms
         |> List.map (fun t -> CvTerm.create(accession = t.Id, name = t.Name, ref = "ASSMSO"))
 
 
diff --git a/src/ARCTokenization/structural_ontologies/arc_file_structure_ontology.obo b/src/ARCTokenization/structural_ontologies/arc_file_structure_ontology.obo
index eaa86c1..f15987a 100644
--- a/src/ARCTokenization/structural_ontologies/arc_file_structure_ontology.obo
+++ b/src/ARCTokenization/structural_ontologies/arc_file_structure_ontology.obo
@@ -1,4 +1,4 @@
-!This file was auto generated on 2024-01-03. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
+!This file was auto generated on 2024-01-05. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
 format-version: 1.2
 data-version: init/2023-10-26
 saved-by: Kevin Schneider
diff --git a/src/ARCTokenization/structural_ontologies/assay_metadata_structural_ontology.obo b/src/ARCTokenization/structural_ontologies/assay_metadata_structural_ontology.obo
index b567d37..960f869 100644
--- a/src/ARCTokenization/structural_ontologies/assay_metadata_structural_ontology.obo
+++ b/src/ARCTokenization/structural_ontologies/assay_metadata_structural_ontology.obo
@@ -1,4 +1,4 @@
-!This file was auto generated on 2024-01-03. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
+!This file was auto generated on 2024-01-05. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
 format-version: 1.2
 data-version: init/2023-07-27
 saved-by: Kevin Schneider
diff --git a/src/ARCTokenization/structural_ontologies/investigation_metadata_structural_ontology.obo b/src/ARCTokenization/structural_ontologies/investigation_metadata_structural_ontology.obo
index 94052f6..8a37d85 100644
--- a/src/ARCTokenization/structural_ontologies/investigation_metadata_structural_ontology.obo
+++ b/src/ARCTokenization/structural_ontologies/investigation_metadata_structural_ontology.obo
@@ -1,4 +1,4 @@
-!This file was auto generated on 2024-01-03. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
+!This file was auto generated on 2024-01-05. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
 format-version: 1.2
 data-version: init/2023-07-20
 saved-by: Kevin Schneider
diff --git a/src/ARCTokenization/structural_ontologies/study_metadata_structural_ontology.obo b/src/ARCTokenization/structural_ontologies/study_metadata_structural_ontology.obo
index 78dda8b..dc4129e 100644
--- a/src/ARCTokenization/structural_ontologies/study_metadata_structural_ontology.obo
+++ b/src/ARCTokenization/structural_ontologies/study_metadata_structural_ontology.obo
@@ -1,4 +1,4 @@
-!This file was auto generated on 2024-01-03. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
+!This file was auto generated on 2024-01-05. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
 format-version: 1.2
 data-version: init/2023-07-27
 saved-by: Kevin Schneider
diff --git a/tests/ARCTokenization.Tests/ARCTokenization.Tests.fsproj b/tests/ARCTokenization.Tests/ARCTokenization.Tests.fsproj
index aa4ddec..5725122 100644
--- a/tests/ARCTokenization.Tests/ARCTokenization.Tests.fsproj
+++ b/tests/ARCTokenization.Tests/ARCTokenization.Tests.fsproj
@@ -11,7 +11,7 @@
     <Compile Include="TestUtils.fs" />
     <Compile Include="TestObjects.fs" />
     <Compile Include="ReferenceObjects.fs" />
-    <Compile Include="StructuralOntologytests.fs" />
+    <Compile Include="StructuralOntologyTests.fs" />
     <Compile Include="TokenizationTests\ParserFunctions.fs" />
     <Compile Include="MockAPITests\MockInvestigationMetadataTokens.fs" />
     <Compile Include="MockAPITests\MockStudyMetadataTokens.fs" />
diff --git a/tests/ARCTokenization.Tests/IntegrationTests/AssayMetadata.fs b/tests/ARCTokenization.Tests/IntegrationTests/AssayMetadata.fs
index 6569c36..f2482ad 100644
--- a/tests/ARCTokenization.Tests/IntegrationTests/AssayMetadata.fs
+++ b/tests/ARCTokenization.Tests/IntegrationTests/AssayMetadata.fs
@@ -11,6 +11,5 @@ module AssayMetadata =
     open TestUtils
 
     let allExpectedMetadataTermsEmpty = 
-        Terms.AssayMetadata.cvTerms
-        |> List.skip 1 //(ignore root term)
+        Terms.AssayMetadata.nonObsoleteNonRootCvTerms
         |> List.map (fun p -> CvParam(p, ParamValue.CvValue (CvTerm.create(accession = "AGMO:00000001", name = "Metadata Section Key", ref = "AGMO")), []))
\ No newline at end of file
diff --git a/tests/ARCTokenization.Tests/IntegrationTests/InvestigationMetadata.fs b/tests/ARCTokenization.Tests/IntegrationTests/InvestigationMetadata.fs
index b77a78a..6fb8120 100644
--- a/tests/ARCTokenization.Tests/IntegrationTests/InvestigationMetadata.fs
+++ b/tests/ARCTokenization.Tests/IntegrationTests/InvestigationMetadata.fs
@@ -14,10 +14,8 @@ module InvestigationMetadata =
     let parsedInvestigationMetadataSimple = Investigation.parseMetadataSheetFromFile "Fixtures/correct/investigation_simple.xlsx"
 
     let allExpectedMetadataTermsEmpty = 
-        Terms.InvestigationMetadata.cvTerms
-        |> List.skip 1 //(ignore root term)
+        Terms.InvestigationMetadata.nonObsoleteNonRootCvTerms
         |> List.filter (fun t -> not (t.Name.StartsWith("Comment"))) // ignore orcids
-        |> List.filter (fun t -> not (List.contains t Terms.InvestigationMetadata.obsoleteCvTerms)) // ignore obsolete terms
         |> List.map (fun p -> CvParam(p, ParamValue.CvValue (CvTerm.create(accession = "AGMO:00000001", name = "Metadata Section Key", ref = "AGMO")), []))
 
     [<Fact>]
diff --git a/tests/ARCTokenization.Tests/IntegrationTests/StudyMetadata.fs b/tests/ARCTokenization.Tests/IntegrationTests/StudyMetadata.fs
index 7f7958b..287cbf7 100644
--- a/tests/ARCTokenization.Tests/IntegrationTests/StudyMetadata.fs
+++ b/tests/ARCTokenization.Tests/IntegrationTests/StudyMetadata.fs
@@ -11,6 +11,5 @@ module StudyMetadata =
     open TestUtils
 
     let allExpectedMetadataTermsEmpty = 
-        Terms.StudyMetadata.cvTerms
-        |> List.skip 1 //(ignore root term)
+        Terms.StudyMetadata.nonObsoleteNonRootCvTerms
         |> List.map (fun p -> CvParam(p, ParamValue.CvValue (CvTerm.create(accession = "AGMO:00000001", name = "Metadata Section Key", ref = "AGMO")), []))
\ No newline at end of file
diff --git a/tests/ARCTokenization.Tests/ReferenceObjects.fs b/tests/ARCTokenization.Tests/ReferenceObjects.fs
index 7852c03..d6e9942 100644
--- a/tests/ARCTokenization.Tests/ReferenceObjects.fs
+++ b/tests/ARCTokenization.Tests/ReferenceObjects.fs
@@ -4,6 +4,16 @@ open ControlledVocabulary
 open ARCTokenization
 open FsSpreadsheet
 
+module Terms =
+
+    let referenceInvestigationMetadataOntologyName = "INVMSO"
+    let referenceStudyMetadataOntologyName = "INVMSO"
+    let referenceAssayMetadataOntologyName = "INVMSO"
+
+    let referenceInvestigationMetadataOntologyRootTerm = CvTerm.create(accession = "INVMSO:00000001", name = "Investigation Metadata", ref = "INVMSO")
+    let referenceStudyMetadataOntologyRootTerm = CvTerm.create(accession = "STDMSO:00000001", name = "Study Metadata", ref = "STDMSO")
+    let referenceAssayMetadataOntologyRootTerm = CvTerm.create(accession = "ASSMSO:00000001", name = "Assay Metadata", ref = "ASSMSO")
+
 module Tokenization =
     
     module KeyParser = 
@@ -224,8 +234,7 @@ module MockAPI =
 
         // equivalent to a metadatasheet with only the first column that contains metadata section keys
         let empty =
-            Terms.InvestigationMetadata.nonObsoleteCvTerms
-            |> List.skip 1 //(ignore root term)
+            Terms.InvestigationMetadata.nonObsoleteNonRootCvTerms
             |> List.filter (fun t -> (not (t.Name.StartsWith("Comment"))) || (t.Name.Equals("Comment[ORCID]"))) // ignore all comments except non-obsolete orcid
             |> List.map (fun cvTerm -> CvParam(cvTerm, ParamValue.CvValue Terms.StructuralTerms.metadataSectionKey, []))
 
@@ -233,8 +242,7 @@ module MockAPI =
 
         // equivalent to a metadatasheet with only the first column that contains metadata section keys
         let empty =
-            Terms.StudyMetadata.nonObsoleteCvTerms
-            |> List.skip 1 //(ignore root term)
+            Terms.StudyMetadata.nonObsoleteNonRootCvTerms
             |> List.filter (fun t -> not (t.Name.StartsWith("Comment")) ) // ignore all comments
             |> List.map (fun cvTerm -> CvParam(cvTerm, ParamValue.CvValue Terms.StructuralTerms.metadataSectionKey, []))
 
@@ -242,7 +250,6 @@ module MockAPI =
         
         // equivalent to a metadatasheet with only the first column that contains metadata section keys
         let empty =
-            Terms.AssayMetadata.nonObsoleteCvTerms
-            |> List.skip 1 //(ignore root term)
+            Terms.AssayMetadata.nonObsoleteNonRootCvTerms
             |> List.filter (fun t -> not (t.Name.StartsWith("Comment")) ) // ignore all comments
             |> List.map (fun cvTerm -> CvParam(cvTerm, ParamValue.CvValue Terms.StructuralTerms.metadataSectionKey, []))
\ No newline at end of file
diff --git a/tests/ARCTokenization.Tests/StructuralOntologytests.fs b/tests/ARCTokenization.Tests/StructuralOntologytests.fs
index 7b00433..df66808 100644
--- a/tests/ARCTokenization.Tests/StructuralOntologytests.fs
+++ b/tests/ARCTokenization.Tests/StructuralOntologytests.fs
@@ -5,6 +5,8 @@ open ARCTokenization
 open ARCTokenization.Terms
 open Xunit
 
+open TestUtils
+
 module InvestigationMetadata =
     
     [<Fact>]
@@ -21,6 +23,18 @@ module InvestigationMetadata =
             (fun (e,a) -> Assert.Equal(e,a))
         )
 
+    [<Fact>] 
+    let ``no root term in non root terms`` () =
+        Assert.All(
+            InvestigationMetadata.nonRootCvTerms,
+            (fun t -> 
+                Assert.True(
+                    t.Name <> ReferenceObjects.Terms.referenceInvestigationMetadataOntologyRootTerm.Name
+                    && t.Accession <> ReferenceObjects.Terms.referenceInvestigationMetadataOntologyRootTerm.Accession
+                )
+            )
+        )
+
 module StudyMetadata =
     
     [<Fact>]
@@ -37,6 +51,18 @@ module StudyMetadata =
             (fun (e,a) -> Assert.Equal(e,a))
         )
 
+    [<Fact>] 
+    let ``no root term in non root terms`` () =
+        Assert.All(
+            StudyMetadata.nonRootCvTerms,
+            (fun t -> 
+                Assert.True(
+                    t.Name <> ReferenceObjects.Terms.referenceStudyMetadataOntologyRootTerm.Name
+                    && t.Accession <> ReferenceObjects.Terms.referenceStudyMetadataOntologyRootTerm.Accession
+                )
+            )
+        )
+
     [<Fact>]
     let ``"STUDY METADATA" has correct ID`` () =
         let smTerm = 
@@ -100,4 +126,16 @@ module AssayMetadata =
         Assert.All(
             List.zip expected actual,
             (fun (e,a) -> Assert.Equal(e,a))
+        )
+
+    [<Fact>] 
+    let ``no root term in non root terms`` () =
+        Assert.All(
+            AssayMetadata.nonRootCvTerms,
+            (fun t -> 
+                Assert.True(
+                    t.Name <> ReferenceObjects.Terms.referenceAssayMetadataOntologyRootTerm.Name
+                    && t.Accession <> ReferenceObjects.Terms.referenceAssayMetadataOntologyRootTerm.Accession
+                )
+            )
         )
\ No newline at end of file