Create Class ProtocolExecution

src/data/invalid/ProtocolExecution-inlined_not_valid.yaml

@@ -0,0 +1,31 @@
+id: nmdc:pex-99-18sD2
+has_input: 
+  - nmdc:bsm-6
+has_process_parts:
+  - id: "nmdc:extrp-71-r2pk"
+    has_input:
+      - "nmdc:ome-6"
+    has_output:
+      - "nmdc:ome-8"
+    extractant: # range: Solution... multivalued? (no) -> has_solution_component
+      has_solution_components:
+        - compound: deionized water
+        - compound: methanol
+          concentration:
+            has_numeric_value: 5
+            has_unit: "%"
+  #- id: nmdc:filtpr-22-32G2BS
+  #  has_input:
+  #    - nmdc:processed-sample-3
+  #  has_output:
+  #    - nmdc:7
+  #  conditionings:
+  #    - Methanol
+  #    - Sterile water #Milli-Q
+  #  filtration_category: pressure
+  #  instrument_name: CEREX System 96 processor
+  #  is_pressurized: true
+protocol_execution_category: Organic Matter Extraction
+protocol_link: 
+  url: https://www.protocols.io/view/water-extractable-organic-matter-weom-ewov1o4oylr2/v1
+  name: Water Extractable Organic Matter (WEOM)

src/data/valid/Database-extraction_set-exhaustive.yaml

@@ -14,9 +14,9 @@ extraction_set:
     #range for processing_institution should be processing_institution_enum
     #processing_institution: Battelle
     #updating protocol info to be nested
-    protocol_link:
-      name: BMI_dnaExtractionSOP_v7
-      url: https://data.neonscience.org/documents/10179/2431540/BMI_dnaExtractionSOP_v7/61204962-bb01-a0b9-3354-ccdaab5132c3
+    #protocol_link:
+    #  name: BMI_dnaExtractionSOP_v7
+    #  url: https://data.neonscience.org/documents/10179/2431540/BMI_dnaExtractionSOP_v7/61204962-bb01-a0b9-3354-ccdaab5132c3
     #extraction_date http://purl.obolibrary.org/obo/OBI_0003081
     # extraction_date: "2019-11-08"
     start_date: "2019-11-08"

src/data/valid/Extraction-metabolomics.yaml

@@ -1,8 +1,8 @@
 id: "nmdc:extrp-71-r2pk"
 has_input:
-  - "nmdc:ome-6"
+  - "nmdc:bsm-6"
 has_output:
-  - "nmdc:ome-8"
+  - "nmdc:psm-8"
 extractant: # range: Solution... multivalued? (no) -> has_solution_component
   has_solution_components:
     - compound: deionized water

src/data/valid/ProtocolExecution-minimal.yaml

@@ -0,0 +1,10 @@
+id: nmdc:pex-99-18sD2
+has_input: 
+  - nmdc:bsm-6
+has_process_parts:
+  - nmdc:extrp-71-r2pk
+  - nmdc:filtpr-22-32G2BS
+protocol_execution_category: organic_matter_extraction
+protocol_link: 
+  url: https://www.protocols.io/view/water-extractable-organic-matter-weom-ewov1o4oylr2/v1
+  name: Water Extractable Organic Matter (WEOM)

src/data/valid/ProtocolExecution-single_step.yaml

@@ -0,0 +1,9 @@
+id: nmdc:pex-99-18sD2
+has_input: 
+  - nmdc:bsm-6
+has_process_parts:
+  - nmdc:extrp-71-r2pk
+protocol_execution_category: organic_matter_extraction
+protocol_link: 
+  url: https://www.protocols.io/view/water-extractable-organic-matter-weom-ewov1o4oylr2/v1
+  name: Water Extractable Organic Matter (WEOM)

src/schema/nmdc.yaml

@@ -1544,6 +1544,20 @@ classes:
       - "sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757"
       - "GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers, but no longer for the Study.id"
 
+  ProtocolExecution:
+    is_a: PlannedProcess
+    description: A PlannedProces that has PlannedProcess parts. Can be used to represent the case of someone following a Protocol.
+    slots:
+      - has_process_parts
+      - protocol_execution_category
+    slot_usage:
+      id:
+        required: true
+        structured_pattern:
+          syntax: "{id_nmdc_prefix}:pex-{id_shoulder}-{id_blade}{id_version}{id_locus}"
+          interpolated: true
+
+
   MaterialProcessing:
     is_a: PlannedProcess
     description:
@@ -2377,6 +2391,21 @@ enums:
       ZIC-pHILIC:
       ZIC-cHILIC:
 
+  ProtocolCategoryEnum:
+    description: The possible protocols that may be followed for an assay.
+    permissible_values:
+      mplex:
+      derivatization:
+      filter_clean_up:
+      organic_matter_extraction:
+      solid_phase_extraction:
+      phosphorus_extraction:
+      ph_measurement:
+      respiration_measurement:
+      texture_measurement:
+      dna_extraction:
+      phenol_chloroform_extraction: { }
+
 slots:
 
   analyte_category:
@@ -3117,6 +3146,18 @@ slots:
       description: The conductivity measurement was 0.017 millisiemens per centimeter.
     range: QuantityValue
 
+  protocol_execution_category:
+    domain: ProtocolExecution
+    range: ProtocolCategoryEnum
+    required: true
+
+  has_process_parts:
+    domain: ProtocolExecution
+    range: PlannedProcess
+    description: A list of process parts that make up a protocol.
+    required: true
+    multivalued: true
+    list_elements_ordered: true
 
   filter_material:
     description: "A porous material on which solid particles present in air or other fluid which flows through it are largely caught and retained."