Add some temporary static modules representing structural ontologies

src/ARCTokenization/ARCTokenization.fsproj

@@ -14,9 +14,12 @@
 
   <ItemGroup>
     <None Include="RELEASE_NOTES.md" />
-    <EmbeddedResource Include="structural_ontologies/investigation_metadata_structural_ontology.obo" CopyToOutputDirectory="Always" Pack="true" PackagePath ="structural_ontologies" />
-    <EmbeddedResource Include="structural_ontologies/study_metadata_structural_ontology.obo" CopyToOutputDirectory="Always" Pack="true" PackagePath ="structural_ontologies" />
-    <EmbeddedResource Include="structural_ontologies/assay_metadata_structural_ontology.obo" CopyToOutputDirectory="Always" Pack="true" PackagePath ="structural_ontologies" />
+    <Compile Include="structural_ontologies\INVMSO.fs" />
+    <Compile Include="structural_ontologies\STDMSO.fs" />
+    <Compile Include="structural_ontologies\ASSMSO.fs" />
+    <EmbeddedResource Include="structural_ontologies/investigation_metadata_structural_ontology.obo" CopyToOutputDirectory="Always" Pack="true" PackagePath="structural_ontologies" />
+    <EmbeddedResource Include="structural_ontologies/study_metadata_structural_ontology.obo" CopyToOutputDirectory="Always" Pack="true" PackagePath="structural_ontologies" />
+    <EmbeddedResource Include="structural_ontologies/assay_metadata_structural_ontology.obo" CopyToOutputDirectory="Always" Pack="true" PackagePath="structural_ontologies" />
     <None Include="structural_ontologies/investigation_metadata_structural_ontology.yml" />
     <None Include="structural_ontologies/study_metadata_structural_ontology.yml" />
     <None Include="structural_ontologies/assay_metadata_structural_ontology.yml" />

src/ARCTokenization/structural_ontologies/ASSMSO.fs

@@ -0,0 +1,32 @@
+
+// This file should eventually be auto-generated from the respective obo files, to have a safe way of updating it from the same source.
+// For now, it is manually created and updated. It is not complete, just a collection of terms needed for baseline WIP validation
+
+namespace ARCTokenization.StructuralOntology
+
+open ControlledVocabulary
+
+module ASSMSO = 
+
+    module ``Assay Metadata`` =
+        let key =  CvTerm.create("ASSMSO:00000001","Assay Metadata","ASSMSO")
+
+        module ``ASSAY`` =
+            let key =  CvTerm.create("ASSMSO:00000002","ASSAY","ASSMSO")
+
+            let ``Assay File Name`` =  CvTerm.create("ASSMSO:00000019","Assay File Name","ASSMSO")
+
+        module ``ASSAY PERFORMERS`` =
+            let key =  CvTerm.create("ASSMSO:00000020","ASSAY PERFORMERS","ASSMSO")
+
+            let ``Assay Performer Last Name`` =  CvTerm.create("ASSMSO:00000021","Assay Performer Last Name","ASSMSO")
+            let ``Assay Performer First Name`` =  CvTerm.create("ASSMSO:00000023","Assay Performer First Name","ASSMSO")
+            let ``Assay Performer Mid Initials`` =  CvTerm.create("ASSMSO:00000025","Assay Performer Mid Initials","ASSMSO")
+            let ``Assay Performer Email`` =  CvTerm.create("ASSMSO:00000027","Assay Performer Email","ASSMSO")
+            let ``Assay Performer Phone`` =  CvTerm.create("ASSMSO:00000029","Assay Performer Phone","ASSMSO")
+            let ``Assay Performer Fax`` =  CvTerm.create("ASSMSO:00000031","Assay Performer Fax","ASSMSO")
+            let ``Assay Performer Address`` =  CvTerm.create("ASSMSO:00000033","Assay Performer Address","ASSMSO")
+            let ``Assay Performer Affiliation`` =  CvTerm.create("ASSMSO:00000035","Assay Performer Affiliation","ASSMSO")
+            let ``Assay Performer Roles`` =  CvTerm.create("ASSMSO:00000037","Assay Performer Roles","ASSMSO")
+            let ``Assay Performer Roles Term Accession Number`` =  CvTerm.create("ASSMSO:00000039","Assay Performer Roles Term Accession Number","ASSMSO")
+            let ``Assay Performer Roles Term Source REF`` =  CvTerm.create("ASSMSO:00000041","Assay Performer Roles Term Source REF","ASSMSO")

src/ARCTokenization/structural_ontologies/INVMSO.fs

@@ -0,0 +1,75 @@
+
+// This file should eventually be auto-generated from the respective obo files, to have a safe way of updating it from the same source.
+// For now, it is manually created and updated. It is not complete, just a collection of terms needed for baseline WIP validation
+
+namespace ARCTokenization.StructuralOntology
+
+open ControlledVocabulary
+
+module INVMSO =
+
+    module ``Investigation Metadata`` =
+        let key =  CvTerm.create("INVMSO:00000001","Investigation Metadata","INVMSO")
+
+        module ``ONTOLOGY SOURCE REFERENCE`` =
+            let key =  CvTerm.create("INVMSO:00000002","ONTOLOGY SOURCE REFERENCE","INVMSO")
+
+        module ``INVESTIGATION`` =
+            let key =  CvTerm.create("INVMSO:00000007","INVESTIGATION","INVMSO")
+
+            let ``Investigation Identifier`` = CvTerm.create("INVMSO:00000008","Investigation Identifier","INVMSO")
+            let ``Investigation Title`` = CvTerm.create("INVMSO:00000009","Investigation Title","INVMSO")
+            let ``Investigation Description`` = CvTerm.create("INVMSO:00000010","Investigation Description","INVMSO")
+            let ``Investigation Submission Date`` = CvTerm.create("INVMSO:00000011","Investigation Submission Date","INVMSO")
+            let ``Investigation Public Release Date`` = CvTerm.create("INVMSO:00000012","Investigation Public Release Date","INVMSO")
+
+        module ``INVESTIGATION PUBLICATIONS`` =
+            let key =  CvTerm.create("INVMSO:00000013","INVESTIGATION PUBLICATIONS","INVMSO")
+
+        module ``INVESTIGATION CONTACTS`` =
+            let key =  CvTerm.create("INVMSO:00000021","INVESTIGATION CONTACTS","INVMSO")
+
+            let ``Investigation Person Last Name`` = CvTerm.create("INVMSO:00000022","Investigation Person Last Name","INVMSO")
+            let ``Investigation Person First Name`` = CvTerm.create("INVMSO:00000023","Investigation Person First Name","INVMSO")
+            let ``Investigation Person Mid Initials`` = CvTerm.create("INVMSO:00000024","Investigation Person Mid Initials","INVMSO")
+            let ``Investigation Person Email`` = CvTerm.create("INVMSO:00000025","Investigation Person Email","INVMSO")
+            let ``Investigation Person Phone`` = CvTerm.create("INVMSO:00000026","Investigation Person Phone","INVMSO")
+            let ``Investigation Person Fax`` = CvTerm.create("INVMSO:00000027","Investigation Person Fax","INVMSO")
+            let ``Investigation Person Address`` = CvTerm.create("INVMSO:00000028","Investigation Person Address","INVMSO")
+            let ``Investigation Person Affiliation`` = CvTerm.create("INVMSO:00000029","Investigation Person Affiliation","INVMSO")
+            let ``Investigation Person Roles`` = CvTerm.create("INVMSO:00000030","Investigation Person Roles","INVMSO")
+            let ``Investigation Person Roles Term Accession Number`` = CvTerm.create("INVMSO:00000031","Investigation Person Roles Term Accession Number","INVMSO")
+            let ``Investigation Person Roles Term Source REF`` = CvTerm.create("INVMSO:000000","Investigation Person Roles Term Source REF","INVMSO")
+            let ``Comment[<Investigation Person ORCID>]`` = CvTerm.create("INVMSO:00000093","Comment[<Investigation Person ORCID>]","INVMSO")
+            let ``Comment[Investigation Person ORCID]`` = CvTerm.create("INVMSO:00000094","Comment[Investigation Person ORCID]","INVMSO")
+            let ``Comment[ORCID]`` = CvTerm.create("INVMSO:00000095","Comment[ORCID]","INVMSO")
+
+        module ``STUDY`` =
+            let key = CvTerm.create("INVMSO:00000033","STUDY","INVMSO")
+
+            let ``Study Identifier`` = CvTerm.create("INVMSO:00000034","Study Identifier","INVMSO")
+            let ``Study Title`` = CvTerm.create("INVMSO:00000035","Study Title","INVMSO")
+            let ``Study Description`` = CvTerm.create("INVMSO:00000036","Study Description","INVMSO")
+            let ``Study Submission Date`` = CvTerm.create("INVMSO:00000037","Study Submission Date","INVMSO")
+            let ``Study Public Release Date`` = CvTerm.create("INVMSO:00000038","Study Public Release Date","INVMSO")
+            let ``Study File Name`` = CvTerm.create("INVMSO:00000039","Study File Name","INVMSO")
+
+        module ``STUDY DESIGN DESCRIPTORS`` =
+            let key = CvTerm.create("INVMSO:00000040","STUDY DESIGN DESCRIPTORS","INVMSO")
+
+        module ``STUDY PUBLICATIONS`` =
+            let key = CvTerm.create("INVMSO:00000044","STUDY PUBLICATIONS","INVMSO")
+
+        module ``STUDY FACTORS`` =
+            let key = CvTerm.create("INVMSO:00000052","STUDY FACTORS","INVMSO")
+
+        module ``STUDY ASSAYS`` =
+            let key = CvTerm.create("INVMSO:00000057","STUDY ASSAYS","INVMSO")
+
+            let ``Study Assay File Name`` = CvTerm.create("INVMSO:00000065","Study Assay File Namee","INVMSO")
+
+        module ``STUDY PROTOCOLS`` =
+            let key = CvTerm.create("INVMSO:00000066","STUDY PROTOCOLS","INVMSO")
+
+        module ``STUDY CONTACTS`` =
+            let key = CvTerm.create("INVMSO:00000081","STUDY CONTACTS","INVMSO")

src/ARCTokenization/structural_ontologies/STDMSO.fs

@@ -0,0 +1,54 @@
+
+// This file should eventually be auto-generated from the respective obo files, to have a safe way of updating it from the same source.
+// For now, it is manually created and updated. It is not complete, just a collection of terms needed for baseline WIP validation
+
+namespace ARCTokenization.StructuralOntology
+
+open ControlledVocabulary
+
+module STDMSO = 
+
+    module ``Study Metadata`` =
+        let key =  CvTerm.create("STDMSO:00000001","Study Metadata","STDMSO")
+
+        module ``STUDY`` =
+            let key =  CvTerm.create("STDMSO:00000002","STUDY","STDMSO")
+
+            let ``Study Identifier`` = CvTerm.create("STDMSO:00000003","STUDY","STDMSO")
+            let ``Study Title`` = CvTerm.create("STDMSO:00000004","Study Title","STDMSO")
+            let ``Study Description`` = CvTerm.create("STDMSO:00000005","Study Description","STDMSO")
+            let ``Study Submission Date`` = CvTerm.create("STDMSO:00000006","Study Submission Date","STDMSO")
+            let ``Study Public Release Date`` = CvTerm.create("STDMSO:00000007","Study Public Release Date","STDMSO")
+            let ``Study File Name`` = CvTerm.create("STDMSO:00000008","Study File Name","STDMSO")
+
+        module ``STUDY DESIGN DESCRIPTORS`` =
+            let key =  CvTerm.create("STDMSO:00000009","STUDY DESIGN DESCRIPTORS","STDMSO")
+
+        module ``STUDY PUBLICATIONS`` =
+            let key =  CvTerm.create("STDMSO:00000013","STUDY PUBLICATIONS","STDMSO")
+
+        module ``STUDY FACTORS`` =
+            let key =  CvTerm.create("STDMSO:00000021","STUDY FACTORS","STDMSO")
+
+        module ``STUDY ASSAYS`` =
+            let key =  CvTerm.create("STDMSO:00000026","STUDY ASSAYS","STDMSO")
+
+            let ``Study Assay File Name`` = CvTerm.create("STDMSO:00000034","Study Assay File Name","STDMSO")
+
+        module ``STUDY PROTOCOLS`` =
+            let key =  CvTerm.create("STDMSO:00000035","STUDY PROTOCOLS","STDMSO")
+
+        module ``STUDY CONTACTS`` =
+            let key =  CvTerm.create("STDMSO:00000050","STUDY CONTACTS","STDMSO")
+
+            let ``Study Person Last Name`` = CvTerm.create("STDMSO:000000051","Study Person Last Name","STDMSO")
+            let ``Study Person First Name`` = CvTerm.create("STDMSO:000000052","Study Person First Name","STDMSO")
+            let ``Study Person Mid Initials`` = CvTerm.create("STDMSO:000000053","Study Person Mid Initials","STDMSO")
+            let ``Study Person Email`` = CvTerm.create("STDMSO:000000054","Study Person Email","STDMSO")
+            let ``Study Person Phone`` = CvTerm.create("STDMSO:000000055","Study Person Phone","STDMSO")
+            let ``Study Person Fax`` = CvTerm.create("STDMSO:000000056","Study Person Fax","STDMSO")
+            let ``Study Person Address`` = CvTerm.create("STDMSO:000000057","Study Person Address","STDMSO")
+            let ``Study Person Affiliation`` = CvTerm.create("STDMSO:000000058","Study Person Affiliation","STDMSO")
+            let ``Study Person Roles`` = CvTerm.create("STDMSO:000000059","Study Person Roles","STDMSO")
+            let ``Study Person Roles Term Accession Number`` = CvTerm.create("STDMSO:000000060","Study Person Roles Term Accession Number","STDMSO")
+            let ``Study Person Roles Term Source REF`` = CvTerm.create("STDMSO:000000061","Study Person Roles Term Source REF","STDMSO")