remove schemasheets yaml and combine with the main cmdr yaml

src/cmdr/schema/cmdr.yaml

@@ -19,4 +19,255 @@ default_range: string
 
 imports:
   - linkml:types
-  - from_sheets
+
+classes:
+  Container:
+    from_schema: TEMP
+    slot_usage:
+      investigations:
+        inlined: true
+        inlined_as_list: true
+        multivalued: true
+        range: Investigation
+      material_processings:
+        inlined: true
+        inlined_as_list: true
+        multivalued: true
+        range: MaterialProcessing
+      materials:
+        inlined: true
+        inlined_as_list: true
+        multivalued: true
+        range: MaterialEntity
+      participations:
+        inlined: true
+        inlined_as_list: true
+        multivalued: true
+        range: Participation
+      specimen_collection_processes:
+        inlined: true
+        inlined_as_list: true
+        multivalued: true
+        range: SpecimenCollectionProcess
+      subjects:
+        inlined: true
+        inlined_as_list: true
+        multivalued: true
+        range: Subject
+    slots:
+    - materials
+    - participations
+    - material_processings
+    - specimen_collection_processes
+    - investigations
+    - subjects
+    tree_root: true
+  DataObject:
+    aliases:
+    - File
+    - Data
+    - DataFile
+    description: A DataFile Associated with a Subject or Investigation or MaterialEntity
+    from_schema: TEMP
+    see_also:
+    - include:DataFile
+  Investigation:
+    aliases:
+    - Study
+    - Proposal
+    description: General information about the Investigation
+    from_schema: TEMP
+    see_also:
+    - include:Study
+    slot_usage:
+      id:
+        identifier: true
+        range: uriorcurie
+      part_of:
+        range: Investigation
+    slots:
+    - id
+    - name
+    - part_of
+  MaterialEntity:
+    aliases:
+    - Substance
+    - Specimen
+    - Sample
+    - Biospecimen
+    - Biosample
+    description: Physical entity that is an input our output of a process from a Subject
+    from_schema: TEMP
+    see_also:
+    - include:Biospecimen
+    slot_usage:
+      concentration:
+        range: Quantity
+      id:
+        identifier: true
+        range: uriorcurie
+      source:
+        comments:
+        - this is a shortcut. to be expanded later.
+        range: Subject
+      used_in:
+        multivalued: true
+        range: Investigation
+      volume:
+        range: Quantity
+    slots:
+    - id
+    - name
+    - used_in
+    - source
+    - volume
+    - concentration
+  MaterialProcessing:
+    class_uri: OBI:0000094
+    description: A planned process which results in physical changes in a specified
+      input material
+    from_schema: TEMP
+    is_a: Process
+    slot_usage:
+      has_input:
+        multivalued: true
+        range: MaterialEntity
+      has_output:
+        multivalued: true
+        range: MaterialEntity
+    slots:
+    - has_input
+    - has_output
+  Participation:
+    description: Subject/Study participation information
+    from_schema: TEMP
+    see_also:
+    - include:Participant
+    slot_usage:
+      id:
+        identifier: true
+        range: uriorcurie
+      includes:
+        range: Subject
+      involved_in:
+        multivalued: true
+        range: Investigation
+    slots:
+    - id
+    - name
+    - involved_in
+    - includes
+  Process:
+    abstract: true
+    description: A planned process resulting in a material or data
+    from_schema: TEMP
+    slot_usage:
+      has_input:
+        multivalued: true
+      has_output:
+        multivalued: true
+      id:
+        identifier: true
+        range: uriorcurie
+    slots:
+    - id
+    - name
+    - has_input
+    - has_output
+  Quantity:
+    from_schema: TEMP
+    slot_usage:
+      comparator:
+        range: string
+      has_numeric_value:
+        range: float
+      has_raw_value:
+        range: string
+      has_unit:
+        range: string
+    slots:
+    - has_raw_value
+    - has_numeric_value
+    - has_unit
+    - comparator
+  SpecimenCollectionProcess:
+    aliases:
+    - MaterialCollectionProcess
+    class_uri: OBI:0000659
+    description: A planned process with the objective of collecting a specimen
+    from_schema: TEMP
+    is_a: Process
+    slot_usage:
+      has_input:
+        multivalued: true
+        range: Subject
+      has_output:
+        multivalued: true
+        range: MaterialEntity
+    slots:
+    - has_input
+    - has_output
+  Subject:
+    aliases:
+    - Site
+    - Participant
+    description: Demographic and clinical information about the subject
+    from_schema: TEMP
+    see_also:
+    - include:Participant
+    slot_usage:
+      id:
+        identifier: true
+        range: uriorcurie
+    slots:
+    - id
+    - name
+slots:
+  comparator:
+    from_schema: TEMP
+  concentration:
+    from_schema: TEMP
+  has_input:
+    from_schema: TEMP
+  has_numeric_value:
+    from_schema: TEMP
+  has_output:
+    from_schema: TEMP
+  has_raw_value:
+    from_schema: TEMP
+  has_unit:
+    from_schema: TEMP
+  id:
+    from_schema: TEMP
+  includes:
+    from_schema: TEMP
+  investigations:
+    from_schema: TEMP
+  involved_in:
+    from_schema: TEMP
+  material_processings:
+    from_schema: TEMP
+  materials:
+    from_schema: TEMP
+  name:
+    from_schema: TEMP
+  part_of:
+    from_schema: TEMP
+  participations:
+    from_schema: TEMP
+  source:
+    from_schema: TEMP
+  specimen_collection_processes:
+    from_schema: TEMP
+  subjects:
+    from_schema: TEMP
+  used_in:
+    from_schema: TEMP
+  volume:
+    from_schema: TEMP
+subsets:
+  potential_phi:
+    from_schema: TEMP
+  temporal_data:
+    from_schema: TEMP
+