Add AFSO ontology (for file system tokenization)

build/BasicTasks.fs

@@ -41,7 +41,7 @@ let buildOntologies =
             ontologySource
             |> File.read
             |> Seq.map (fun line -> line.Trim())
-            |> fun lines -> Seq.concat [seq{"!This file was auto generated. Do not edit it. All manual changes will be overwritten by the next generator run eventually."}; lines]
+            |> fun lines -> Seq.concat [seq{$"!This file was auto generated on {System.DateTime.Now.ToShortDateString()}. Do not edit it. All manual changes will be overwritten by the next generator run eventually."}; lines]
             |> File.write false (ontologySource.Replace(".yml", ".obo"))
         )
     }

build/ProjectInfo.fs

@@ -76,6 +76,7 @@ let structuralOntologySources = [
     "src/ARCTokenization/structural_ontologies/investigation_metadata_structural_ontology.yml"
     "src/ARCTokenization/structural_ontologies/study_metadata_structural_ontology.yml"
     "src/ARCTokenization/structural_ontologies/assay_metadata_structural_ontology.yml"
+    "src/ARCTokenization/structural_ontologies/arc_file_structure_ontology.yml"
 ]
 
 let solutionFile  = $"{project}.sln"

src/ARCTokenization/ARCTokenization.fsproj

@@ -14,12 +14,15 @@
 
   <ItemGroup>
     <None Include="RELEASE_NOTES.md" />
+    <Compile Include="structural_ontologies\AFSO.fs" />
     <Compile Include="structural_ontologies\INVMSO.fs" />
     <Compile Include="structural_ontologies\STDMSO.fs" />
     <Compile Include="structural_ontologies\ASSMSO.fs" />
+    <EmbeddedResource Include="structural_ontologies/arc_file_structure_ontology.obo" CopyToOutputDirectory="Always" Pack="true" PackagePath="structural_ontologies" />
     <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/arc_file_structure_ontology.yml" />
     <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/AFSO.fs

@@ -0,0 +1,26 @@
+
+// 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 collectAFSOn of terms needed for baseline WIP validatAFSOn
+
+namespace ARCTokenization.StructuralOntology
+
+open ControlledVocabulary
+
+module AFSO =
+
+    let ``File``      = CvTerm.create("AFSO:00000001","File","AFSO")
+    let ``Directory`` = CvTerm.create("AFSO:00000002","Directory","AFSO")
+    let ``File Type`` = CvTerm.create("AFSO:00000003","File Type","AFSO")
+    let ``Extension`` = CvTerm.create("AFSO:00000004","Extension","AFSO")
+
+    /// The name of the file.
+    let ``File Name``      = CvTerm.create("AFSO:00000005","File Name","AFSO")
+    let ``Directory Name`` = CvTerm.create("AFSO:00000006","Directory Name","AFSO")
+
+    /// The full path of the directory or file.
+    let ``Full Name``      = CvTerm.create("AFSO:00000007","Full Name","AFSO")
+
+    /// The full path, relative path or a Universal Naming ConventAFSOn (UNC) path
+    let ``Path``           = CvTerm.create("AFSO:00000008","Path","AFSO")
+    let ``File Path``      = CvTerm.create("AFSO:00000009","File Path","AFSO")
+    let ``Directory Path`` = CvTerm.create("AFSO:00000010","Directory Path","AFSO")

src/ARCTokenization/structural_ontologies/arc_file_structure_ontology.obo

@@ -0,0 +1,56 @@
+!This file was auto generated on 2023-10-26. 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
+default-namespace: afso
+ontology: AFSO
+
+[Term]
+id: AFSO:00000001
+name: File
+def: ""
+
+[Term]
+id: AFSO:00000002
+name: Directory
+def: ""
+
+[Term]
+id: AFSO:00000003
+name: File Type
+def: ""
+
+[Term]
+id: AFSO:00000004
+name: Extension
+def: ""
+
+[Term]
+id: AFSO:00000005
+name: File Name
+def: ""
+
+[Term]
+id: AFSO:00000006
+name: Directory Name
+def: ""
+
+[Term]
+id: AFSO:00000007
+name: Full Name
+def: ""
+
+[Term]
+id: AFSO:00000008
+name: Path
+def: ""
+
+[Term]
+id: AFSO:00000009
+name: File Path
+def: ""
+
+[Term]
+id: AFSO:00000010
+name: Directory Path
+def: ""

src/ARCTokenization/structural_ontologies/arc_file_structure_ontology.yml

@@ -0,0 +1,55 @@
+format-version: 1.2
+data-version: init/2023-10-26
+saved-by: Kevin Schneider
+default-namespace: afso
+ontology: AFSO
+
+[Term]
+id: AFSO:00000001
+name: File
+def: ""
+
+[Term]
+id: AFSO:00000002
+name: Directory
+def: ""
+
+[Term]
+id: AFSO:00000003
+name: File Type
+def: ""
+
+[Term]
+id: AFSO:00000004
+name: Extension
+def: ""
+
+[Term]
+id: AFSO:00000005
+name: File Name
+def: ""
+
+[Term]
+id: AFSO:00000006
+name: Directory Name
+def: ""
+
+[Term]
+id: AFSO:00000007
+name: Full Name
+def: ""
+
+[Term]
+id: AFSO:00000008
+name: Path
+def: ""
+
+[Term]
+id: AFSO:00000009
+name: File Path
+def: ""
+
+[Term]
+id: AFSO:00000010
+name: Directory Path
+def: ""

src/ARCTokenization/structural_ontologies/assay_metadata_structural_ontology.obo

@@ -1,4 +1,4 @@
-!This file was auto generated. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
+!This file was auto generated on 2023-10-26. 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

src/ARCTokenization/structural_ontologies/investigation_metadata_structural_ontology.obo

@@ -1,4 +1,4 @@
-!This file was auto generated. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
+!This file was auto generated on 2023-10-26. 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

src/ARCTokenization/structural_ontologies/study_metadata_structural_ontology.obo

@@ -1,4 +1,4 @@
-!This file was auto generated. Do not edit it. All manual changes will be overwritten by the next generator run eventually.
+!This file was auto generated on 2023-10-26. 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