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microbiomedata · Jan 23, 2025 · 5446500 · 5446500
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diff --git a/nmdc_schema/nmdc.py b/nmdc_schema/nmdc.py
@@ -1,5 +1,5 @@
 # Auto generated from nmdc.yaml by pythongen.py version: 0.0.1
-# Generation date: 2025-01-23T12:18:34
+# Generation date: 2025-01-23T12:47:12
 # Schema: NMDC
 #
 # id: https://w3id.org/nmdc/nmdc

diff --git a/src/data/valid/ChemicalConversionProcess-digest.yaml b/src/data/valid/ChemicalConversionProcess-digest.yaml
@@ -5,18 +5,18 @@ has_input:
 has_output:
   - nmdc:procsm-99-39
 substances_used:
-  - known_as: nmdc:chem-99-000005 # see src/data/valid/Database-chemical_entity_set-1.yaml
+  - known_as: acetonitrile # see src/data/valid/Database-chemical_entity_set-1.yaml
     type: nmdc:PortionOfSubstance
     sample_state_information: liquid
     substance_role: solvent
-  - known_as: nmdc:chem-99-000002
+  - known_as: isopropyl_alcohol
     type: nmdc:PortionOfSubstance
     substance_role: buffer
     source_concentration:
       type: nmdc:QuantityValue
       has_unit: mM
       has_numeric_value: 50
-  - known_as: nmdc:chem-99-000014
+  - known_as: glucose
     type: nmdc:PortionOfSubstance
     substance_role: ms_proteolytic_enzyme
     final_concentration:

diff --git a/src/data/valid/ChemicalConversionProcess-minimal.yaml b/src/data/valid/ChemicalConversionProcess-minimal.yaml
@@ -6,7 +6,7 @@ has_output:
   - nmdc:procsm-99-555555
 chemical_conversion_category: acid_base
 substances_used:
-  - known_as: nmdc:chem-99-000003 # see src/data/valid/Database-chemical_entity_set-1.yaml
+  - known_as: isopropyl_alcohol
     type: nmdc:PortionOfSubstance
     sample_state_information: liquid
     volume:

diff --git a/src/data/valid/ChemicalEntity-1.yaml b/src/data/valid/ChemicalEntity-1.yaml
diff --git a/src/data/valid/ChromatographicSeparationProcess-SPE.yaml b/src/data/valid/ChromatographicSeparationProcess-SPE.yaml
@@ -10,7 +10,7 @@ chromatographic_category: solid_phase_extraction
 ordered_mobile_phases:
   - type: nmdc:MobilePhaseSegment
     substances_used:
-      - known_as: nmdc:chem-99-000003 # see src/data/valid/Database-chemical_entity_set-1.yaml
+      - known_as: water
         type: nmdc:PortionOfSubstance
         final_concentration:
           type: nmdc:QuantityValue
@@ -22,7 +22,7 @@ ordered_mobile_phases:
       has_unit: mL
   - type: nmdc:MobilePhaseSegment
     substances_used:
-      - known_as: nmdc:chem-99-000015 # see src/data/valid/Database-chemical_entity_set-1.yaml
+      - known_as: acetonitrile
         type: nmdc:PortionOfSubstance
         final_concentration:
           type: nmdc:QuantityValue

diff --git a/src/data/valid/ChromatographyConfiguration-LC.yaml b/src/data/valid/ChromatographyConfiguration-LC.yaml
@@ -15,15 +15,15 @@ ordered_mobile_phases:
       has_unit: min
       has_numeric_value: 60
     substances_used:
-      - known_as: nmdc:chem-99-000003 # see src/data/valid/Database-chemical_entity_set-1.yaml
+      - known_as: glucose
         type: nmdc:PortionOfSubstance
         final_concentration:
           type: nmdc:QuantityValue
           has_unit: '%'
           has_numeric_value: 10
   - type: nmdc:MobilePhaseSegment
     substances_used:
-      - known_as: nmdc:chem-99-000015 # see src/data/valid/Database-chemical_entity_set-1.yaml
+      - known_as: acetonitrile
         type: nmdc:PortionOfSubstance
         final_concentration:
           type: nmdc:QuantityValue

diff --git a/src/data/valid/Database-NOM-material-processing.yaml b/src/data/valid/Database-NOM-material-processing.yaml
@@ -7,7 +7,7 @@ material_processing_set:
       - nmdc:procsm-00-1
     substances_used:
       - type: nmdc:PortionOfSubstance
-        known_as: nmdc:chem-99-000005 # see src/data/valid/Database-chemical_entity_set-1.yaml
+        known_as: glucose
         final_concentration:
           type: nmdc:QuantityValue
           has_unit: 'g.mL-1'
@@ -20,7 +20,7 @@ material_processing_set:
     has_output:
       - nmdc:procsm-00-2
     substances_used:
-      - known_as: nmdc:chem-99-000016 # see src/data/valid/Database-chemical_entity_set-1.yaml
+      - known_as: water
         type: nmdc:PortionOfSubstance
         substance_role: acid
         final_concentration:
@@ -55,17 +55,17 @@ material_processing_set:
     ordered_mobile_phases:
       - type: nmdc:MobilePhaseSegment
         substances_used:
-          - known_as: nmdc:chem-99-000003 # see src/data/valid/Database-chemical_entity_set-1.yaml
+          - known_as: water
             type: nmdc:PortionOfSubstance
         volume:
           type: nmdc:QuantityValue
           has_unit: 'mL'
           has_numeric_value: 700
       - type: nmdc:MobilePhaseSegment
         substances_used:
-          - known_as: nmdc:chem-99-000004 # see src/data/valid/Database-chemical_entity_set-1.yaml
+          - known_as: acetonitrile
             type: nmdc:PortionOfSubstance
-          - known_as: nmdc:chem-99-000015 # see src/data/valid/Database-chemical_entity_set-1.yaml
+          - known_as: glucose
             type: nmdc:PortionOfSubstance
             substance_role: acid
             final_concentration:
@@ -78,7 +78,7 @@ material_processing_set:
           has_numeric_value: 700
       - type: nmdc:MobilePhaseSegment
         substances_used:
-          - known_as: nmdc:chem-99-000003 # see src/data/valid/Database-chemical_entity_set-1.yaml
+          - known_as: alphaLP
             type: nmdc:PortionOfSubstance
         volume:
           type: nmdc:QuantityValue
@@ -92,7 +92,7 @@ material_processing_set:
       - nmdc:procsm-00-5
     substances_used:
       - type: nmdc:PortionOfSubstance
-        known_as: nmdc:chem-99-000005 # see src/data/valid/Database-chemical_entity_set-1.yaml
+        known_as: Asp-N
         volume:
           type: nmdc:QuantityValue
           has_unit: 'mL'
@@ -105,7 +105,7 @@ material_processing_set:
     has_output:
       - nmdc:procsm-00-6
     substances_used:
-      - known_as: nmdc:chem-99-000015 # see src/data/valid/Database-chemical_entity_set-1.yaml
+      - known_as: formic_acid
         type: nmdc:PortionOfSubstance
         substance_role: acid
         final_concentration:

diff --git a/src/data/valid/Database-chemical_entity_set-1.yaml b/src/data/valid/Database-chemical_entity_set-1.yaml