diff --git a/assets/yq-final.txt b/assets/yq-final.txt
new file mode 100644
index 00000000..7d1948f6
--- /dev/null
+++ b/assets/yq-final.txt
@@ -0,0 +1,29 @@
+# remove the multivalued true annotation from these global slot definitions for the sake of linkml-convert
+#   esp to tsv? and dumping to SQLite?
+
+# follow the .string_serialization=="{text};{float} {unit}" and .multivalued == true pattern?
+
+'(.slots.[] | select(.range == "ControlledIdentifiedTermValue") | .range) = "string"'
+'(.slots.[] | select(.range == "ControlledTermValue") | .range) = "string"'
+'(.slots.[] | select(.range == "GeolocationValue") | .range) = "string"'
+'(.slots.[] | select(.range == "OntologyClass") | .range) = "string"'
+'(.slots.[] | select(.range == "QuantityValue") | .range) = "string"'
+'(.slots.[] | select(.range == "TextValue") | .range) = "string"'
+'(.slots.[] | select(.range == "TimestampValue") | .range) = "string"'
+
+#	yq -i '(.slots.[] | select(has("range") | not  ) | .range ) = "string"'
+#	yq -i '(.classes.[].slot_usage.[] | select(has("range") | not  ) | .range ) = "string"'
+
+'(.slots.[] | select(.name == "sample_link") | .range ) = "string"'
+'(.slots.[] | select(.range == "string") | .multivalued ) = false'
+'(.classes.[].slot_usage.[] | select(.range=="string") | .multivalued) = false'
+
+#	yq -i '(.slots.[] | select(.name == "dna_dnase") | .range) = "boolean"'
+#	yq -i '(.classes.[].slot_usage.[] | select(.name == "dna_dnase") | .range) = "boolean"'
+
+'(.slots.[] | select(.name == "oxy_stat_samp") | .range) = "OxyStatSampEnum"'
+'(.classes.[].slot_usage.[] | select(.name == "oxy_stat_samp") | .range) = "OxyStatSampEnum"'
+'(.slots.[] | select(.name == "dna_dnase") | .range) = "YesNoEnum"'
+'(.classes.[].slot_usage.[] | select(.name == "dna_dnase") | .range) = "YesNoEnum"'
+'(.slots.[] | select(.name == "dnase_rna") | .range) = "YesNoEnum"'
+'(.classes.[].slot_usage.[] | select(.name == "dnase_rna") | .range) = "YesNoEnum"'
\ No newline at end of file
diff --git a/assets/yq-for-shuttles.txt b/assets/yq-for-shuttles.txt
new file mode 100644
index 00000000..0cfa4b57
--- /dev/null
+++ b/assets/yq-for-shuttles.txt
@@ -0,0 +1,96 @@
+# using \x0A to represent a line feed
+# double $ gets reduced to one by make
+
+# .string_serialization=="{text};{float} {unit}": what about multivalueds? don't see any at this time
+# ControlledTermValue: experiential factor has string_serialization: '{termLabel} {[termID]}|{text}'
+# ControlledTermValue: what about multivalued CTVs? don't see any besides chem_administration above at this time
+# for water, can depth be a point, a range, or both?
+
+
+# globally replace structured ranges with strings.
+# undoes some of the range alterations that nmdc-schema makes when importing MIxS terms
+# future versions of the nmdc-schema might just use strings, too
+
+# there's still more to do. see schemasheets/populated_tsv/slot_usage.tsv
+# to some degree this should be handled globally by sheets_and_friends/tsv_in/validation_converter.tsv
+# and on a slot-by-slot basic by sheets_and_friends/tsv_in/modifications_long.tsv
+
+# we should be consistent about the following things in patterns
+# single or multiple whitespace?
+# [0-9] or \d?
+# include scientific notation? (eg quantity value)
+# what whitespace to exclude?
+
+# be careful about strings that look like numbers with quotes in YAML
+#   impact on other serializations?
+
+# escape pipes that are going to be used literally as future delimiters ?
+
+#	 should add a remove attribute option to sheets and friend's modify and validate
+#	  currently have nan string serializations
+
+# scrutinize the slots that currently accept xyz or 100 units. how could they be better constrained?
+
+# synchronize between guidance, examples and validation
+#   cross-reference MIxS' values for those aspects
+
+# use yq to add examples when the examples themselves include the packed value separator |
+#   good reason for using ! instead of |
+
+'(.classes.[].slot_usage.[] | select(.name=="chem_administration") | .examples) = [{"value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22"}, {"value": "agar [CHEBI:2509];2018-05"}]'
+
+# use yq to add patterns with a secondary condition like mutivalued
+'(.classes.[].slot_usage.[] | select(.range == "GeolocationValue")  | .pattern) = "^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$$"'
+'(.classes.[].slot_usage.[] | select(.range == "GeolocationValue")  | .range) = "string"'
+
+'(.classes.[].slot_usage.[] | select(.range == "QuantityValue") | .pattern) = "^[-+]?[0-9]*\.?[0-9]+ +\S.*$$"'
+'(.classes.[].slot_usage.[] | select(.range == "QuantityValue" and .multivalued == true)  | .pattern) = "^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$$"'
+
+# add a pattern for {termLabel} {[termID]} in teh validation configuration
+# need more invalid examples
+#yq -i '(.classes.[].slot_usage.[] | select(.string_serialization=="{termLabel} {[termID]}") | .range) = "string"' $@
+
+'(.classes.[].slot_usage.[] | select(.string_serialization=="{text};{float} {unit}") | .pattern) = "^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$$"'
+'(.classes.[].slot_usage.[] | select(.string_serialization=="{text};{float} {unit}" and .multivalued == true ) | .pattern) = "^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$$"'
+
+'(.slots.[] | select(.domain == "Activity") | .domain ) = "NamedThing"'
+'(.slots.[] | select(.domain == "Agent") | .domain ) = "NamedThing"'
+'(.slots.[] | select(.domain == "AttributeValue") | .domain ) = "NamedThing"'
+'(.slots.[] | select(.domain == "AttributeValue") | .domain ) = "NamedThing"'
+'(.slots.[] | select(.domain == "ControlledTermValue") | .domain ) = "NamedThing"'
+'(.slots.[] | select(.domain == "GeolocationValue") | .domain ) = "NamedThing"'
+
+'del(.classes.Activity)'
+'del(.classes.Agent)'
+'del(.classes.AttributeValue)'
+'del(.classes.ControlledIdentifiedTermValue)'
+'del(.classes.ControlledTermValue)'
+'del(.classes.GeolocationValue)'
+'del(.classes.OntologyClass)'
+'del(.classes.QuantityValue)'
+'del(.classes.TextValue)'
+'del(.classes.TimestampValue)'
+
+# use yq for global modifications
+# rel_to_oxygen / oxy_stat_samp
+'(.slots.[] | select(.name == "rel_to_oxygen") | .range) = "rel_to_oxygen_enum"'
+'(.slots.[] | select(.name == "oxy_stat_samp") | .range) = "rel_to_oxygen_enum"'
+
+# remove slots that are no longer necessary due to removal of classes above
+'del(.slots.[] | select(.name == "acted_on_behalf_of"))'
+'del(.slots.[] | select(.name == "ended_at_time"))'
+'del(.slots.[] | select(.name == "has_maximum_numeric_value"))'
+'del(.slots.[] | select(.name == "has_minimum_numeric_value"))'
+'del(.slots.[] | select(.name == "has_numeric_value"))'
+'del(.slots.[] | select(.name == "has_raw_value"))'
+'del(.slots.[] | select(.name == "has_unit"))'
+'del(.slots.[] | select(.name == "latitude"))'
+'del(.slots.[] | select(.name == "longitude"))'
+'del(.slots.[] | select(.name == "started_at_time"))'
+'del(.slots.[] | select(.name == "term"))'
+'del(.slots.[] | select(.name == "used"))'
+'del(.slots.[] | select(.name == "was_associated_with"))'
+'del(.slots.[] | select(.name == "was_generated_by"))'
+'del(.slots.[] | select(.name == "was_informed_by"))'
+
+'del(.slots.[] | select(.name == "was_informed_by"))'
\ No newline at end of file
diff --git a/project.Makefile b/project.Makefile
index 59fd278e..867df576 100644
--- a/project.Makefile
+++ b/project.Makefile
@@ -69,104 +69,9 @@ sheets_and_friends/tsv_in/import_slots_regardless.tsv
 			--format yaml $@.raw > $@
 		- $(RUN) linkml-lint $@ > local/with_shuttles.lint_report.txt
 
-local/with_shuttles_yq.yaml: local/with_shuttles.yaml
+local/with_shuttles_yq.yaml: local/with_shuttles.yaml assets/yq-for-shuttles.txt
 	cp $< $@
-	# using \x0A to represent a line feed
-	# double $ gets reduced to one by make
-
-	# .string_serialization=="{text};{float} {unit}": what about multivalueds? don't see any at this time
-	# ControlledTermValue: experiential factor has string_serialization: '{termLabel} {[termID]}|{text}'
-	# ControlledTermValue: what about multivalued CTVs? don't see any besides chem_administration above at this time
-	# for water, can depth be a point, a range, or both?
-
-
-# globally replace structured ranges with strings.
-# undoes some of the range alterations that nmdc-schema makes when importing MIxS terms
-# future versions of the nmdc-schema might just use strings, too
-
-# there's still more to do. see schemasheets/populated_tsv/slot_usage.tsv
-# to some degree this should be handled globally by sheets_and_friends/tsv_in/validation_converter.tsv
-# and on a slot-by-slot basic by sheets_and_friends/tsv_in/modifications_long.tsv
-
-# we should be consistent about the following things in patterns
-# single or multiple whitespace?
-# [0-9] or \d?
-# include scientific notation? (eg quantity value)
-# what whitespace to exclude?
-
-# be careful about strings that look like numbers with quotes in YAML
-#   impact on other serializations?
-
-# escape pipes that are going to be used literally as future delimiters ?
-
-#	 should add a remove attribute option to sheets and friend's modify and validate
-#	  currently have nan string serializations
-
-# scrutininze the slots that currerntly accept xyz or 100 units. how could they be better constrained?
-
-# synchronize between guidance, examples and validation
-#   cross reference MIxS' values for those aspects
-
-# use yq to add examples when the examples themselves include the packed value separator |
-#   good reason for using ! instead of |
-	yq -i '(.classes.[].slot_usage.[] | select(.name=="chem_administration") | .examples) = [{"value": "agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22"}, {"value": "agar [CHEBI:2509];2018-05"}]' $@
-
-# use yq to add patterns with a secondary condition like mutivalued
-	yq -i '(.classes.[].slot_usage.[] | select(.range == "GeolocationValue")  | .pattern) = "^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$$"' $@
-	yq -i '(.classes.[].slot_usage.[] | select(.range == "GeolocationValue")  | .range) = "string"' $@
-
-	yq -i '(.classes.[].slot_usage.[] | select(.range == "QuantityValue") | .pattern) = "^[-+]?[0-9]*\.?[0-9]+ +\S.*$$"' $@
-	yq -i '(.classes.[].slot_usage.[] | select(.range == "QuantityValue" and .multivalued == true)  | .pattern) = "^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$$"' $@
-
-# add a pattern for {termLabel} {[termID]} in teh validation configuration
-# need more invalid examples
-	#yq -i '(.classes.[].slot_usage.[] | select(.string_serialization=="{termLabel} {[termID]}") | .range) = "string"' $@
-
-	yq -i '(.classes.[].slot_usage.[] | select(.string_serialization=="{text};{float} {unit}") | .pattern) = "^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$$"' $@
-	yq -i '(.classes.[].slot_usage.[] | select(.string_serialization=="{text};{float} {unit}" and .multivalued == true ) | .pattern) = "^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$$"' $@
-
-	yq -i '(.slots.[] | select(.domain == "Activity") | .domain ) = "NamedThing"' $@
-	yq -i '(.slots.[] | select(.domain == "Agent") | .domain ) = "NamedThing"' $@
-	yq -i '(.slots.[] | select(.domain == "AttributeValue") | .domain ) = "NamedThing"' $@
-	yq -i '(.slots.[] | select(.domain == "AttributeValue") | .domain ) = "NamedThing"' $@
-	yq -i '(.slots.[] | select(.domain == "ControlledTermValue") | .domain ) = "NamedThing"' $@
-	yq -i '(.slots.[] | select(.domain == "GeolocationValue") | .domain ) = "NamedThing"' $@
-
-	yq -i 'del(.classes.Activity)'  $@
-	yq -i 'del(.classes.Agent)'  $@
-	yq -i 'del(.classes.AttributeValue)'  $@
-	yq -i 'del(.classes.ControlledIdentifiedTermValue)'  $@
-	yq -i 'del(.classes.ControlledTermValue)'  $@
-	yq -i 'del(.classes.GeolocationValue)'  $@
-	yq -i 'del(.classes.OntologyClass)'  $@
-	yq -i 'del(.classes.QuantityValue)'  $@
-	yq -i 'del(.classes.TextValue)'  $@
-	yq -i 'del(.classes.TimestampValue)'  $@
-
-# use yq for global modifications
-# rel_to_oxygen / oxy_stat_samp
-	yq -i '(.slots.[] | select(.name == "rel_to_oxygen") | .range) = "rel_to_oxygen_enum"' $@
-	yq -i '(.slots.[] | select(.name == "oxy_stat_samp") | .range) = "rel_to_oxygen_enum"' $@
-
-# remove slots that are no longer necessary due to removal of classes above
-	yq -i 'del(.slots.[] | select(.name == "acted_on_behalf_of"))' $@
-	yq -i 'del(.slots.[] | select(.name == "ended_at_time"))' $@
-	yq -i 'del(.slots.[] | select(.name == "has_maximum_numeric_value"))' $@
-	yq -i 'del(.slots.[] | select(.name == "has_minimum_numeric_value"))' $@
-	yq -i 'del(.slots.[] | select(.name == "has_numeric_value"))' $@
-	yq -i 'del(.slots.[] | select(.name == "has_raw_value"))' $@
-	yq -i 'del(.slots.[] | select(.name == "has_unit"))' $@
-	yq -i 'del(.slots.[] | select(.name == "latitude"))' $@
-	yq -i 'del(.slots.[] | select(.name == "longitude"))' $@
-	yq -i 'del(.slots.[] | select(.name == "started_at_time"))' $@
-	yq -i 'del(.slots.[] | select(.name == "term"))' $@
-	yq -i 'del(.slots.[] | select(.name == "used"))' $@
-	yq -i 'del(.slots.[] | select(.name == "was_associated_with"))' $@
-	yq -i 'del(.slots.[] | select(.name == "was_generated_by"))' $@
-	yq -i 'del(.slots.[] | select(.name == "was_informed_by"))' $@
-
-	yq -i 'del(.slots.[] | select(.name == "was_informed_by"))' $@
-
+	grep "^'" $(word 2, $^) | while IFS= read -r line ; do echo $$line ; eval yq -i $$line $@ ; done
 
 modifications-clean:
 	rm -rf sheets_and_friends/yaml_out/with_modifications.yaml
@@ -174,7 +79,6 @@ modifications-clean:
 local/nmdc.yaml:
 	wget -O $@ https://raw.githubusercontent.com/microbiomedata/nmdc-schema/v10.3.0/nmdc_schema/nmdc_materialized_patterns.yaml
 
-# sheets-for-nmdc-submission-schema_validation_converter_empty.tsv
 local/with_modifications.yaml: local/with_shuttles_yq.yaml \
 sheets_and_friends/tsv_in/modifications_long.tsv \
 sheets_and_friends/tsv_in/validation_converter.tsv \
@@ -185,61 +89,28 @@ local/nmdc.yaml
 		--validation_config_tsv $(word 3,$^) \
 		--yaml_output $@.raw
 
-	# # having trouble selectively injecting rules based on title pattern
-#	yq eval-all \
-#		'select(fileIndex==1).classes.JgiMtInterface.rules = (select(fileIndex==0).classes.Biosample.rules.[] | select(.title == "rna*")) | select(fileIndex==1)' \
-#		local/nmdc.yaml src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml | cat > ruleswap.yaml
-	# # so just inject all rules...
-	# # using | cat > because yq fails to write to STDOUT (permissions error?!)
+	# apply all rules from Biosample to JgiMgInterface and JgiMtInterface
 	yq eval-all \
 		'select(fileIndex==1).classes.JgiMgInterface.rules = select(fileIndex==0).classes.Biosample.rules | select(fileIndex==1)' \
 		local/nmdc.yaml $@.raw | cat > $@.raw2
 	yq eval-all \
 		'select(fileIndex==1).classes.JgiMtInterface.rules = select(fileIndex==0).classes.Biosample.rules | select(fileIndex==1)' \
 		local/nmdc.yaml $@.raw2 | cat > $@.raw
-	# # ...then removing rules that aren't relevant to a class
-	# # requires some prior knowledge
+
+	# remove some rules
 	yq -i 'del(.classes.JgiMgInterface.rules.[] | select(.title == "rna*"))' $@.raw
 	yq -i 'del(.classes.JgiMtInterface.rules.[] | select(.title == "dna*"))' $@.raw
 
 	$(RUN) gen-linkml \
 		--no-materialize-attributes \
 		--format yaml $@.raw > $@
+
 	- $(RUN) linkml-lint $@ > local/with_modifications.lint_report.txt
 
-src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml: local/with_modifications.yaml project/thirdparty/GoldEcosystemTree.json
+src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml: local/with_modifications.yaml \
+project/thirdparty/GoldEcosystemTree.json assets/yq-final.txt
 	$(RUN) inject-gold-pathway-terms -g $(word 2,$^) -i $< -o $@
-# remove the multivalued true annotation from these gloabl slot definitions for the sake of linkml-convert
-#   esp to tsv? and dumping to SQLite?
-# follow the .string_serialization=="{text};{float} {unit}" and .multivalued == true pattern?
-
-	yq -i '(.slots.[] | select(.range == "ControlledIdentifiedTermValue") | .range) = "string"' $@
-	yq -i '(.slots.[] | select(.range == "ControlledTermValue") | .range) = "string"' $@
-	yq -i '(.slots.[] | select(.range == "GeolocationValue") | .range) = "string"' $@
-	yq -i '(.slots.[] | select(.range == "OntologyClass") | .range) = "string"' $@
-	yq -i '(.slots.[] | select(.range == "QuantityValue") | .range) = "string"' $@
-	yq -i '(.slots.[] | select(.range == "TextValue") | .range) = "string"' $@
-	yq -i '(.slots.[] | select(.range == "TimestampValue") | .range) = "string"' $@
-
-#	yq -i '(.slots.[] | select(has("range") | not  ) | .range ) = "string"' $@
-#	yq -i '(.classes.[].slot_usage.[] | select(has("range") | not  ) | .range ) = "string"' $@
-
-	yq -i '(.slots.[] | select(.name == "sample_link") | .range ) = "string"' $@
-
-	yq -i '(.slots.[] | select(.range == "string") | .multivalued ) = false' $@
-	yq -i '(.classes.[].slot_usage.[] | select(.range=="string") | .multivalued) = false' $@
-
-#	yq -i '(.slots.[] | select(.name == "dna_dnase") | .range) = "boolean"' $@
-#	yq -i '(.classes.[].slot_usage.[] | select(.name == "dna_dnase") | .range) = "boolean"' $@
-
-	yq -i '(.slots.[] | select(.name == "oxy_stat_samp") | .range) = "OxyStatSampEnum"' $@
-	yq -i '(.classes.[].slot_usage.[] | select(.name == "oxy_stat_samp") | .range) = "OxyStatSampEnum"' $@
-
-	yq -i '(.slots.[] | select(.name == "dna_dnase") | .range) = "YesNoEnum"' $@
-	yq -i '(.classes.[].slot_usage.[] | select(.name == "dna_dnase") | .range) = "YesNoEnum"' $@
-
-	yq -i '(.slots.[] | select(.name == "dnase_rna") | .range) = "YesNoEnum"' $@
-	yq -i '(.classes.[].slot_usage.[] | select(.name == "dnase_rna") | .range) = "YesNoEnum"' $@
+	grep "^'" $(word 3, $^) | while IFS= read -r line ; do echo $$line ; eval yq -i $$line $@ ; done
 
 run-examples: examples-clean examples/output/README.md
 
@@ -273,6 +144,7 @@ src/data/invalid src/data/valid
 
 local/SampleData-water-data-exhaustive.tsv: src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml \
 src/data/valid/SampleData-water-data-exhaustive.yaml
+	mkdir -p local
 	$(RUN) linkml-convert \
 		--output $@ \
 		--target-class SampleData \
@@ -281,6 +153,7 @@ src/data/valid/SampleData-water-data-exhaustive.yaml
 
 examples/output/SampleData-water-data-exhaustive.regen.yaml: src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml \
 local/SampleData-water-data-exhaustive.tsv
+	mkdir -p examples/output
 	$(RUN) linkml-convert \
 		--output $@ \
 		--target-class SampleData \