Chemical entity deprecation, adding enumeration for limited set of chemicals needed (at the moment) in submissions

Makefile

@@ -191,7 +191,7 @@ gendoc: $(DOCDIR) prefixmaps
 	$(RUN) cp $(SRC)/scripts/*.js $(DOCDIR)/javascripts/
 	# Use `refgraph` to generate an interactive diagram within the compiled documentation website file tree.
 	mkdir -p $(DOCDIR)/visualizations
-	$(RUN) refgraph --schema nmdc_schema/nmdc_materialized_patterns.yaml --subject collection --graph $(DOCDIR)/visualizations/collection-graph.html
+	$(RUN) refscan graph --schema nmdc_schema/nmdc_materialized_patterns.yaml --subject collection --graph $(DOCDIR)/visualizations/collection-graph.html
 testdoc: gendoc serve
 
 MKDOCS = $(RUN) mkdocs

pyproject.toml

@@ -59,7 +59,7 @@ python-dotenv = "^0.21.0"
 rdflib = "^6.2.0" # some LinkML components are not compatible with rdflib 7+ yet
 # We use `refscan` to generate diagrams of inter-collection relationships.
 # Reference: https://github.com/microbiomedata/refscan
-refscan = "==0.1.21"
+refscan = "^0.2.0"
 ruff = "^0.4.7"
 schemasheets = "^0.1.24" # was in main dependencies but brings in so much like pandas
 sheets_and_friends = "^0.5.0" # for do_shuttle (and possibly more)

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:

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:

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

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

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: