Merge pull request #7 from microbiomedata/1525-add-slots-to-MaterialP…

…rocessing-classes-that-were-on-OmicsProcessing 1525 add slots to material processing classes that were on omics processing
microbiomedata · Dec 13, 2023 · df30da1 · df30da1
2 parents e75c8e3 + 971eb2e
commit df30da1
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Showing 5 changed files with 13 additions and 7 deletions.
diff --git a/src/data/invalid/Database-Extraction-invalid-sample_mass.yaml b/src/data/invalid/Database-Extraction-invalid-sample_mass.yaml
@@ -17,6 +17,6 @@ extraction_set:
       has_unit: gram 
     quality_control_report:
       status: pass
-    extraction_method: phenol/chloroform extraction
+    # extraction_method: phenol/chloroform extraction # instantiate in ProtocolExtraction class
     extraction_target: DNA
 
diff --git a/src/data/valid/Database-extraction_set-exhaustive.yaml b/src/data/valid/Database-extraction_set-exhaustive.yaml
@@ -30,7 +30,7 @@ extraction_set:
       #status range should be new status_enum with possible values of 'Pass' or Failed'
       status: pass
     #leaving as extraction_method to make the model generic, other option considered was 'Nucleic Acid Extraction Method' http://purl.obolibrary.org/obo/NCIT_C177560
-    extraction_method: phenol/chloroform extraction
+    # extraction_method: phenol/chloroform extraction # instantiate in ProtocolExtraction class
     #extraction_type should have range of dna_extraction_enum with possible values of 'DNA extraction', 'RNA extraction', 'protein extraction'
     #http://purl.obolibrary.org/obo/OBI_0000257
     extraction_target: DNA

diff --git a/src/data/valid/Database-nucleic-extraction.yaml b/src/data/valid/Database-nucleic-extraction.yaml
@@ -42,7 +42,7 @@ extraction_set:
     #      status: Pass
 
     #leaving as extraction_method to make the model generic, other option considered was 'Nucleic Acid Extraction Method' http://purl.obolibrary.org/obo/NCIT_C177560
-    extraction_method: phenol/chloroform extraction
+    # extraction_method: phenol/chloroform extraction #instantiate in ProtocolExtraction class
 
     #extraction_type should have range of dna_extraction_enum with possible values of 'DNA extraction', 'RNA extraction', 'protein extraction'
     #http://purl.obolibrary.org/obo/OBI_0000257

diff --git a/src/schema/basic_slots.yaml b/src/schema/basic_slots.yaml
@@ -106,11 +106,19 @@ slots:
     recommended: true
     minimum_value: 0
     maximum_value: 2000
+
   extraction_target:
+    description: Provides the target biomolecule that has been separated from a sample during an extraction process.
     rank: 1000
     domain_of:
       - Extraction
     range: ExtractionTargetEnum
+    notes:
+      - todos, remove nucl_acid_ext from OmicsProcessing (DataGeneration)
+    narrow_mappings:
+      - NCIT:C177560
+      - MIXS:0000037
+
   id:
     required: true
     identifier: true

diff --git a/src/schema/nmdc.yaml b/src/schema/nmdc.yaml
@@ -245,7 +245,6 @@ classes:
       - OBI:0302884
     slots:
       - extractant
-      - extraction_method
       - extraction_target
       - input_mass
       - quality_control_report
@@ -2460,6 +2459,8 @@ slots:
 
   library_preparation_kit:
     range: string
+
+ ## WHY ARE THESE COMMENTED OUT?
   #    exact_mappings:
   #      - GENEPIO:0001450
   #  processed_date: # can we move this or infer this from the date of some other process?
@@ -2468,9 +2469,6 @@ slots:
   #  extraction_date: # replacing with start_ and end_date
   #    #    range: date
   #    range: string
-  extraction_method:
-    domain: Extraction
-    range: ExtractionTargetEnum
 
   quality_control_report:
     domain: PlannedProcess