gen-project for cmungall#14

turbomam · Jan 8, 2022 · ecf61fa · ecf61fa
1 parent 78d1fe9
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diff --git a/.gitignore b/.gitignore
@@ -1,7 +1,8 @@
+*.old
 .idea
-tests/outputs/*yaml
+/docs/    ## do not check  in - deploy directly
+__pycache__
+downloads/
 target/
-*.old
+tests/outputs/*yaml
 venv
-__pycache__
-/docs/    ## do not check  in - deploy directly
diff --git a/Makefile b/Makefile
@@ -22,7 +22,8 @@ GEN_OPTS =
 # ----------------------------------------
 # TOP LEVEL TARGETS
 # ----------------------------------------
-all: env.lock gen unlock
+# all: env.lock gen unlock
+all: clean env.lock generated unlock
 
 # ---------------------------------------
 # env.lock:  set up pipenv
@@ -35,6 +36,9 @@ unlock:
 #	pipenv --rm
 	rm env.lock
 
+generated: model/schema/mixs.yaml
+	$(RUN) gen-project --dir $@ $< 2> generated.log
+
 # ---------------------------------------
 # GEN: run generator for each target
 # ---------------------------------------
@@ -45,6 +49,7 @@ gen: $(patsubst %,gen-%,$(TGTS))
 # ---------------------------------------
 clean:
 	rm -rf target/
+	rm -rf generated/
 	rm -f env.lock
 #	pipenv --rm
 .PHONY: clean

diff --git a/generated.log b/generated.log
diff --git a/generated/docs/Air.md b/generated/docs/Air.md
diff --git a/generated/docs/AirMIGSBacteria.md b/generated/docs/AirMIGSBacteria.md
diff --git a/generated/docs/AirMIGSEukaryote.md b/generated/docs/AirMIGSEukaryote.md
diff --git a/generated/docs/AirMIGSOrg.md b/generated/docs/AirMIGSOrg.md
diff --git a/generated/docs/AirMIGSPlant.md b/generated/docs/AirMIGSPlant.md
diff --git a/generated/docs/AirMIGSVirus.md b/generated/docs/AirMIGSVirus.md
diff --git a/generated/docs/AirMIMAG.md b/generated/docs/AirMIMAG.md
diff --git a/generated/docs/AirMIMARKSSpecimen.md b/generated/docs/AirMIMARKSSpecimen.md
diff --git a/generated/docs/AirMIMARKSSurvey.md b/generated/docs/AirMIMARKSSurvey.md
diff --git a/generated/docs/AirMIMS.md b/generated/docs/AirMIMS.md
diff --git a/generated/docs/AirMISAG.md b/generated/docs/AirMISAG.md
diff --git a/generated/docs/AirMIUVIG.md b/generated/docs/AirMIUVIG.md
diff --git a/generated/docs/BuiltEnvironment.md b/generated/docs/BuiltEnvironment.md
diff --git a/generated/docs/BuiltEnvironmentMIGSBacteria.md b/generated/docs/BuiltEnvironmentMIGSBacteria.md
diff --git a/generated/docs/BuiltEnvironmentMIGSEukaryote.md b/generated/docs/BuiltEnvironmentMIGSEukaryote.md
diff --git a/generated/docs/BuiltEnvironmentMIGSOrg.md b/generated/docs/BuiltEnvironmentMIGSOrg.md
diff --git a/generated/docs/BuiltEnvironmentMIGSPlant.md b/generated/docs/BuiltEnvironmentMIGSPlant.md
diff --git a/generated/docs/BuiltEnvironmentMIGSVirus.md b/generated/docs/BuiltEnvironmentMIGSVirus.md
diff --git a/generated/docs/BuiltEnvironmentMIMAG.md b/generated/docs/BuiltEnvironmentMIMAG.md
diff --git a/generated/docs/BuiltEnvironmentMIMARKSSpecimen.md b/generated/docs/BuiltEnvironmentMIMARKSSpecimen.md
diff --git a/generated/docs/BuiltEnvironmentMIMARKSSurvey.md b/generated/docs/BuiltEnvironmentMIMARKSSurvey.md
diff --git a/generated/docs/BuiltEnvironmentMIMS.md b/generated/docs/BuiltEnvironmentMIMS.md
diff --git a/generated/docs/BuiltEnvironmentMISAG.md b/generated/docs/BuiltEnvironmentMISAG.md
diff --git a/generated/docs/BuiltEnvironmentMIUVIG.md b/generated/docs/BuiltEnvironmentMIUVIG.md
diff --git a/generated/docs/Checklist.md b/generated/docs/Checklist.md
@@ -0,0 +1,23 @@
+
+# Subset: checklist
+
+
+A MIxS checklist. These can be combined with packages
+
+URI: [mixs.vocab:checklist](https://w3id.org/mixs/vocab/checklist)
+
+
+### Classes
+
+
+### Mixins
+
+
+### Slots
+
+
+### Types
+
+
+### Enums
+
diff --git a/generated/docs/ChecklistPackageCombination.md b/generated/docs/ChecklistPackageCombination.md
@@ -0,0 +1,23 @@
+
+# Subset: checklist_package_combination
+
+
+A combination of a checklist and a package
+
+URI: [mixs.vocab:checklist_package_combination](https://w3id.org/mixs/vocab/checklist_package_combination)
+
+
+### Classes
+
+
+### Mixins
+
+
+### Slots
+
+
+### Types
+
+
+### Enums
+
diff --git a/generated/docs/Core.md b/generated/docs/Core.md
diff --git a/generated/docs/Host-associated.md b/generated/docs/Host-associated.md
diff --git a/generated/docs/Host-associatedMIGSBacteria.md b/generated/docs/Host-associatedMIGSBacteria.md
diff --git a/generated/docs/Host-associatedMIGSEukaryote.md b/generated/docs/Host-associatedMIGSEukaryote.md
diff --git a/generated/docs/Host-associatedMIGSOrg.md b/generated/docs/Host-associatedMIGSOrg.md
diff --git a/generated/docs/Host-associatedMIGSPlant.md b/generated/docs/Host-associatedMIGSPlant.md
diff --git a/generated/docs/Host-associatedMIGSVirus.md b/generated/docs/Host-associatedMIGSVirus.md
diff --git a/generated/docs/Host-associatedMIMAG.md b/generated/docs/Host-associatedMIMAG.md
diff --git a/generated/docs/Host-associatedMIMARKSSpecimen.md b/generated/docs/Host-associatedMIMARKSSpecimen.md
diff --git a/generated/docs/Host-associatedMIMARKSSurvey.md b/generated/docs/Host-associatedMIMARKSSurvey.md
diff --git a/generated/docs/Host-associatedMIMS.md b/generated/docs/Host-associatedMIMS.md
diff --git a/generated/docs/Host-associatedMISAG.md b/generated/docs/Host-associatedMISAG.md
diff --git a/generated/docs/Host-associatedMIUVIG.md b/generated/docs/Host-associatedMIUVIG.md
diff --git a/generated/docs/Human-associated.md b/generated/docs/Human-associated.md
diff --git a/generated/docs/Human-associatedMIGSBacteria.md b/generated/docs/Human-associatedMIGSBacteria.md
diff --git a/generated/docs/Human-associatedMIGSEukaryote.md b/generated/docs/Human-associatedMIGSEukaryote.md
diff --git a/generated/docs/Human-associatedMIGSOrg.md b/generated/docs/Human-associatedMIGSOrg.md
diff --git a/generated/docs/Human-associatedMIGSPlant.md b/generated/docs/Human-associatedMIGSPlant.md
diff --git a/generated/docs/Human-associatedMIGSVirus.md b/generated/docs/Human-associatedMIGSVirus.md
diff --git a/generated/docs/Human-associatedMIMAG.md b/generated/docs/Human-associatedMIMAG.md
diff --git a/generated/docs/Human-associatedMIMARKSSpecimen.md b/generated/docs/Human-associatedMIMARKSSpecimen.md
diff --git a/generated/docs/Human-associatedMIMARKSSurvey.md b/generated/docs/Human-associatedMIMARKSSurvey.md
diff --git a/generated/docs/Human-associatedMIMS.md b/generated/docs/Human-associatedMIMS.md
diff --git a/generated/docs/Human-associatedMISAG.md b/generated/docs/Human-associatedMISAG.md
diff --git a/generated/docs/Human-associatedMIUVIG.md b/generated/docs/Human-associatedMIUVIG.md
diff --git a/generated/docs/Human-gut.md b/generated/docs/Human-gut.md
diff --git a/generated/docs/Human-gutMIGSBacteria.md b/generated/docs/Human-gutMIGSBacteria.md
diff --git a/generated/docs/Human-gutMIGSEukaryote.md b/generated/docs/Human-gutMIGSEukaryote.md
diff --git a/generated/docs/Human-gutMIGSOrg.md b/generated/docs/Human-gutMIGSOrg.md
diff --git a/generated/docs/Human-gutMIGSPlant.md b/generated/docs/Human-gutMIGSPlant.md
diff --git a/generated/docs/Human-gutMIGSVirus.md b/generated/docs/Human-gutMIGSVirus.md
diff --git a/generated/docs/Human-gutMIMAG.md b/generated/docs/Human-gutMIMAG.md
diff --git a/generated/docs/Human-gutMIMARKSSpecimen.md b/generated/docs/Human-gutMIMARKSSpecimen.md
diff --git a/generated/docs/Human-gutMIMARKSSurvey.md b/generated/docs/Human-gutMIMARKSSurvey.md
diff --git a/generated/docs/Human-gutMIMS.md b/generated/docs/Human-gutMIMS.md
diff --git a/generated/docs/Human-gutMISAG.md b/generated/docs/Human-gutMISAG.md
diff --git a/generated/docs/Human-gutMIUVIG.md b/generated/docs/Human-gutMIUVIG.md
diff --git a/generated/docs/Human-oral.md b/generated/docs/Human-oral.md
diff --git a/generated/docs/Human-oralMIGSBacteria.md b/generated/docs/Human-oralMIGSBacteria.md
diff --git a/generated/docs/Human-oralMIGSEukaryote.md b/generated/docs/Human-oralMIGSEukaryote.md
diff --git a/generated/docs/Human-oralMIGSOrg.md b/generated/docs/Human-oralMIGSOrg.md
diff --git a/generated/docs/Human-oralMIGSPlant.md b/generated/docs/Human-oralMIGSPlant.md
diff --git a/generated/docs/Human-oralMIGSVirus.md b/generated/docs/Human-oralMIGSVirus.md
diff --git a/generated/docs/Human-oralMIMAG.md b/generated/docs/Human-oralMIMAG.md
diff --git a/generated/docs/Human-oralMIMARKSSpecimen.md b/generated/docs/Human-oralMIMARKSSpecimen.md
diff --git a/generated/docs/Human-oralMIMARKSSurvey.md b/generated/docs/Human-oralMIMARKSSurvey.md
diff --git a/generated/docs/Human-oralMIMS.md b/generated/docs/Human-oralMIMS.md
diff --git a/generated/docs/Human-oralMISAG.md b/generated/docs/Human-oralMISAG.md
diff --git a/generated/docs/Human-oralMIUVIG.md b/generated/docs/Human-oralMIUVIG.md
diff --git a/generated/docs/Human-skin.md b/generated/docs/Human-skin.md
diff --git a/generated/docs/Human-skinMIGSBacteria.md b/generated/docs/Human-skinMIGSBacteria.md
diff --git a/generated/docs/Human-skinMIGSEukaryote.md b/generated/docs/Human-skinMIGSEukaryote.md
diff --git a/generated/docs/Human-skinMIGSOrg.md b/generated/docs/Human-skinMIGSOrg.md
diff --git a/generated/docs/Human-skinMIGSPlant.md b/generated/docs/Human-skinMIGSPlant.md
diff --git a/generated/docs/Human-skinMIGSVirus.md b/generated/docs/Human-skinMIGSVirus.md
diff --git a/generated/docs/Human-skinMIMAG.md b/generated/docs/Human-skinMIMAG.md
diff --git a/generated/docs/Human-skinMIMARKSSpecimen.md b/generated/docs/Human-skinMIMARKSSpecimen.md
diff --git a/generated/docs/Human-skinMIMARKSSurvey.md b/generated/docs/Human-skinMIMARKSSurvey.md
diff --git a/generated/docs/Human-skinMIMS.md b/generated/docs/Human-skinMIMS.md
diff --git a/generated/docs/Human-skinMISAG.md b/generated/docs/Human-skinMISAG.md
diff --git a/generated/docs/Human-skinMIUVIG.md b/generated/docs/Human-skinMIUVIG.md
diff --git a/generated/docs/Human-vaginal.md b/generated/docs/Human-vaginal.md
diff --git a/generated/docs/Human-vaginalMIGSBacteria.md b/generated/docs/Human-vaginalMIGSBacteria.md
diff --git a/generated/docs/Human-vaginalMIGSEukaryote.md b/generated/docs/Human-vaginalMIGSEukaryote.md
diff --git a/generated/docs/Human-vaginalMIGSOrg.md b/generated/docs/Human-vaginalMIGSOrg.md
diff --git a/generated/docs/Human-vaginalMIGSPlant.md b/generated/docs/Human-vaginalMIGSPlant.md
diff --git a/generated/docs/Human-vaginalMIGSVirus.md b/generated/docs/Human-vaginalMIGSVirus.md
diff --git a/generated/docs/Human-vaginalMIMAG.md b/generated/docs/Human-vaginalMIMAG.md
diff --git a/generated/docs/Human-vaginalMIMARKSSpecimen.md b/generated/docs/Human-vaginalMIMARKSSpecimen.md
diff --git a/generated/docs/Human-vaginalMIMARKSSurvey.md b/generated/docs/Human-vaginalMIMARKSSurvey.md
diff --git a/generated/docs/Human-vaginalMIMS.md b/generated/docs/Human-vaginalMIMS.md
diff --git a/generated/docs/Human-vaginalMISAG.md b/generated/docs/Human-vaginalMISAG.md
diff --git a/generated/docs/Human-vaginalMIUVIG.md b/generated/docs/Human-vaginalMIUVIG.md
diff --git a/generated/docs/HydrocarbonResources-cores.md b/generated/docs/HydrocarbonResources-cores.md
diff --git a/generated/docs/HydrocarbonResources-coresMIGSBacteria.md b/generated/docs/HydrocarbonResources-coresMIGSBacteria.md
diff --git a/generated/docs/HydrocarbonResources-coresMIGSEukaryote.md b/generated/docs/HydrocarbonResources-coresMIGSEukaryote.md
diff --git a/generated/docs/HydrocarbonResources-coresMIGSOrg.md b/generated/docs/HydrocarbonResources-coresMIGSOrg.md
diff --git a/generated/docs/HydrocarbonResources-coresMIGSPlant.md b/generated/docs/HydrocarbonResources-coresMIGSPlant.md
diff --git a/generated/docs/HydrocarbonResources-coresMIGSVirus.md b/generated/docs/HydrocarbonResources-coresMIGSVirus.md
diff --git a/generated/docs/HydrocarbonResources-coresMIMAG.md b/generated/docs/HydrocarbonResources-coresMIMAG.md
diff --git a/generated/docs/HydrocarbonResources-coresMIMARKSSpecimen.md b/generated/docs/HydrocarbonResources-coresMIMARKSSpecimen.md
diff --git a/generated/docs/HydrocarbonResources-coresMIMARKSSurvey.md b/generated/docs/HydrocarbonResources-coresMIMARKSSurvey.md
diff --git a/generated/docs/HydrocarbonResources-coresMIMS.md b/generated/docs/HydrocarbonResources-coresMIMS.md
diff --git a/generated/docs/HydrocarbonResources-coresMISAG.md b/generated/docs/HydrocarbonResources-coresMISAG.md
diff --git a/generated/docs/HydrocarbonResources-coresMIUVIG.md b/generated/docs/HydrocarbonResources-coresMIUVIG.md
diff --git a/generated/docs/HydrocarbonResources-fluidsSwabs.md b/generated/docs/HydrocarbonResources-fluidsSwabs.md
diff --git a/generated/docs/HydrocarbonResources-fluidsSwabsMIGSBacteria.md b/generated/docs/HydrocarbonResources-fluidsSwabsMIGSBacteria.md
diff --git a/generated/docs/HydrocarbonResources-fluidsSwabsMIGSEukaryote.md b/generated/docs/HydrocarbonResources-fluidsSwabsMIGSEukaryote.md
diff --git a/generated/docs/HydrocarbonResources-fluidsSwabsMIGSOrg.md b/generated/docs/HydrocarbonResources-fluidsSwabsMIGSOrg.md
diff --git a/generated/docs/HydrocarbonResources-fluidsSwabsMIGSPlant.md b/generated/docs/HydrocarbonResources-fluidsSwabsMIGSPlant.md
diff --git a/generated/docs/HydrocarbonResources-fluidsSwabsMIGSVirus.md b/generated/docs/HydrocarbonResources-fluidsSwabsMIGSVirus.md
diff --git a/generated/docs/HydrocarbonResources-fluidsSwabsMIMAG.md b/generated/docs/HydrocarbonResources-fluidsSwabsMIMAG.md
diff --git a/generated/docs/HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md b/generated/docs/HydrocarbonResources-fluidsSwabsMIMARKSSpecimen.md
diff --git a/generated/docs/HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md b/generated/docs/HydrocarbonResources-fluidsSwabsMIMARKSSurvey.md
diff --git a/generated/docs/HydrocarbonResources-fluidsSwabsMIMS.md b/generated/docs/HydrocarbonResources-fluidsSwabsMIMS.md
diff --git a/generated/docs/HydrocarbonResources-fluidsSwabsMISAG.md b/generated/docs/HydrocarbonResources-fluidsSwabsMISAG.md
diff --git a/generated/docs/HydrocarbonResources-fluidsSwabsMIUVIG.md b/generated/docs/HydrocarbonResources-fluidsSwabsMIUVIG.md
diff --git a/generated/docs/MIGSBacteria.md b/generated/docs/MIGSBacteria.md
diff --git a/generated/docs/MIGSEukaryote.md b/generated/docs/MIGSEukaryote.md
diff --git a/generated/docs/MIGSOrg.md b/generated/docs/MIGSOrg.md
diff --git a/generated/docs/MIGSPlant.md b/generated/docs/MIGSPlant.md
diff --git a/generated/docs/MIGSVirus.md b/generated/docs/MIGSVirus.md
diff --git a/generated/docs/MIGS_bacteria_adapters.md b/generated/docs/MIGS_bacteria_adapters.md
@@ -0,0 +1,50 @@
+
+# Slot: adapters
+
+
+Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters
+
+URI: [mixs.vocab:MIGS_bacteria_adapters](https://w3id.org/mixs/vocab/MIGS_bacteria_adapters)
+
+
+## Domain and Range
+
+[MIGSBacteria](MIGSBacteria.md) &#8594;  <sub>0..1</sub> [String](types/String.md)
+
+## Parents
+
+ *  is_a: [adapters](adapters.md)
+
+## Children
+
+
+## Used by
+
+ * [MIGSBacteria](MIGSBacteria.md)
+ * [AirMIGSBacteria](AirMIGSBacteria.md)
+ * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md)
+ * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md)
+ * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md)
+ * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md)
+ * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md)
+ * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md)
+ * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md)
+ * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md)
+ * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md)
+ * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md)
+ * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md)
+ * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md)
+ * [SedimentMIGSBacteria](SedimentMIGSBacteria.md)
+ * [SoilMIGSBacteria](SoilMIGSBacteria.md)
+ * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md)
+ * [WaterMIGSBacteria](WaterMIGSBacteria.md)
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Aliases:** | | adapters |
+| **Mappings:** | | MIXS:0000048 |
+| **Comments:** | | Expected value: adapter A and B sequence |
+| **Examples:** | | Example(value='AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT', description=None) |
+
diff --git a/generated/docs/MIGS_bacteria_annot.md b/generated/docs/MIGS_bacteria_annot.md
@@ -0,0 +1,50 @@
+
+# Slot: annot
+
+
+Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter
+
+URI: [mixs.vocab:MIGS_bacteria_annot](https://w3id.org/mixs/vocab/MIGS_bacteria_annot)
+
+
+## Domain and Range
+
+[MIGSBacteria](MIGSBacteria.md) &#8594;  <sub>0..1</sub> [String](types/String.md)
+
+## Parents
+
+ *  is_a: [annot](annot.md)
+
+## Children
+
+
+## Used by
+
+ * [MIGSBacteria](MIGSBacteria.md)
+ * [AirMIGSBacteria](AirMIGSBacteria.md)
+ * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md)
+ * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md)
+ * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md)
+ * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md)
+ * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md)
+ * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md)
+ * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md)
+ * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md)
+ * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md)
+ * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md)
+ * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md)
+ * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md)
+ * [SedimentMIGSBacteria](SedimentMIGSBacteria.md)
+ * [SoilMIGSBacteria](SoilMIGSBacteria.md)
+ * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md)
+ * [WaterMIGSBacteria](WaterMIGSBacteria.md)
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Aliases:** | | annotation |
+| **Mappings:** | | MIXS:0000059 |
+| **Comments:** | | Expected value: name of tool or pipeline used, or annotation source description |
+| **Examples:** | | Example(value='prokka', description=None) |
+
diff --git a/generated/docs/MIGS_bacteria_assembly_name.md b/generated/docs/MIGS_bacteria_assembly_name.md
@@ -0,0 +1,50 @@
+
+# Slot: assembly_name
+
+
+Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community
+
+URI: [mixs.vocab:MIGS_bacteria_assembly_name](https://w3id.org/mixs/vocab/MIGS_bacteria_assembly_name)
+
+
+## Domain and Range
+
+[MIGSBacteria](MIGSBacteria.md) &#8594;  <sub>0..1</sub> [String](types/String.md)
+
+## Parents
+
+ *  is_a: [assembly_name](assembly_name.md)
+
+## Children
+
+
+## Used by
+
+ * [MIGSBacteria](MIGSBacteria.md)
+ * [AirMIGSBacteria](AirMIGSBacteria.md)
+ * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md)
+ * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md)
+ * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md)
+ * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md)
+ * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md)
+ * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md)
+ * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md)
+ * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md)
+ * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md)
+ * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md)
+ * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md)
+ * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md)
+ * [SedimentMIGSBacteria](SedimentMIGSBacteria.md)
+ * [SoilMIGSBacteria](SoilMIGSBacteria.md)
+ * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md)
+ * [WaterMIGSBacteria](WaterMIGSBacteria.md)
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Aliases:** | | assembly name |
+| **Mappings:** | | MIXS:0000057 |
+| **Comments:** | | Expected value: name and version of assembly |
+| **Examples:** | | Example(value='HuRef, JCVI_ISG_i3_1.0', description=None) |
+
diff --git a/generated/docs/MIGS_bacteria_assembly_qual.md b/generated/docs/MIGS_bacteria_assembly_qual.md
@@ -0,0 +1,50 @@
+
+# Slot: assembly_qual
+
+
+The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated
+
+URI: [mixs.vocab:MIGS_bacteria_assembly_qual](https://w3id.org/mixs/vocab/MIGS_bacteria_assembly_qual)
+
+
+## Domain and Range
+
+[MIGSBacteria](MIGSBacteria.md) &#8594;  <sub>1..1</sub> [assembly_qual_enum](assembly_qual_enum.md)
+
+## Parents
+
+ *  is_a: [assembly_qual](assembly_qual.md)
+
+## Children
+
+
+## Used by
+
+ * [MIGSBacteria](MIGSBacteria.md)
+ * [AirMIGSBacteria](AirMIGSBacteria.md)
+ * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md)
+ * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md)
+ * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md)
+ * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md)
+ * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md)
+ * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md)
+ * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md)
+ * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md)
+ * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md)
+ * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md)
+ * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md)
+ * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md)
+ * [SedimentMIGSBacteria](SedimentMIGSBacteria.md)
+ * [SoilMIGSBacteria](SoilMIGSBacteria.md)
+ * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md)
+ * [WaterMIGSBacteria](WaterMIGSBacteria.md)
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Aliases:** | | assembly quality |
+| **Mappings:** | | MIXS:0000056 |
+| **Comments:** | | Expected value: enumeration |
+| **Examples:** | | Example(value='High-quality draft genome', description=None) |
+
diff --git a/generated/docs/MIGS_bacteria_assembly_software.md b/generated/docs/MIGS_bacteria_assembly_software.md
@@ -0,0 +1,50 @@
+
+# Slot: assembly_software
+
+
+Tool(s) used for assembly, including version number and parameters
+
+URI: [mixs.vocab:MIGS_bacteria_assembly_software](https://w3id.org/mixs/vocab/MIGS_bacteria_assembly_software)
+
+
+## Domain and Range
+
+[MIGSBacteria](MIGSBacteria.md) &#8594;  <sub>1..1</sub> [String](types/String.md)
+
+## Parents
+
+ *  is_a: [assembly_software](assembly_software.md)
+
+## Children
+
+
+## Used by
+
+ * [MIGSBacteria](MIGSBacteria.md)
+ * [AirMIGSBacteria](AirMIGSBacteria.md)
+ * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md)
+ * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md)
+ * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md)
+ * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md)
+ * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md)
+ * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md)
+ * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md)
+ * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md)
+ * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md)
+ * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md)
+ * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md)
+ * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md)
+ * [SedimentMIGSBacteria](SedimentMIGSBacteria.md)
+ * [SoilMIGSBacteria](SoilMIGSBacteria.md)
+ * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md)
+ * [WaterMIGSBacteria](WaterMIGSBacteria.md)
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Aliases:** | | assembly software |
+| **Mappings:** | | MIXS:0000058 |
+| **Comments:** | | Expected value: name and version of software, parameters used |
+| **Examples:** | | Example(value='metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise', description=None) |
+
diff --git a/generated/docs/MIGS_bacteria_associated_resource.md b/generated/docs/MIGS_bacteria_associated_resource.md
@@ -0,0 +1,50 @@
+
+# Slot: associated resource
+
+
+A related resource that is referenced, cited, or otherwise associated to the sequence.
+
+URI: [mixs.vocab:MIGS_bacteria_associated_resource](https://w3id.org/mixs/vocab/MIGS_bacteria_associated_resource)
+
+
+## Domain and Range
+
+[MIGSBacteria](MIGSBacteria.md) &#8594;  <sub>0..1</sub> [String](types/String.md)
+
+## Parents
+
+ *  is_a: [associated resource](associated_resource.md)
+
+## Children
+
+
+## Used by
+
+ * [MIGSBacteria](MIGSBacteria.md)
+ * [AirMIGSBacteria](AirMIGSBacteria.md)
+ * [BuiltEnvironmentMIGSBacteria](BuiltEnvironmentMIGSBacteria.md)
+ * [Host-associatedMIGSBacteria](Host-associatedMIGSBacteria.md)
+ * [Human-associatedMIGSBacteria](Human-associatedMIGSBacteria.md)
+ * [Human-gutMIGSBacteria](Human-gutMIGSBacteria.md)
+ * [Human-oralMIGSBacteria](Human-oralMIGSBacteria.md)
+ * [Human-skinMIGSBacteria](Human-skinMIGSBacteria.md)
+ * [Human-vaginalMIGSBacteria](Human-vaginalMIGSBacteria.md)
+ * [HydrocarbonResources-coresMIGSBacteria](HydrocarbonResources-coresMIGSBacteria.md)
+ * [HydrocarbonResources-fluidsSwabsMIGSBacteria](HydrocarbonResources-fluidsSwabsMIGSBacteria.md)
+ * [MicrobialMatBiofilmMIGSBacteria](MicrobialMatBiofilmMIGSBacteria.md)
+ * [MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria](MiscellaneousNaturalOrArtificialEnvironmentMIGSBacteria.md)
+ * [Plant-associatedMIGSBacteria](Plant-associatedMIGSBacteria.md)
+ * [SedimentMIGSBacteria](SedimentMIGSBacteria.md)
+ * [SoilMIGSBacteria](SoilMIGSBacteria.md)
+ * [WastewaterSludgeMIGSBacteria](WastewaterSludgeMIGSBacteria.md)
+ * [WaterMIGSBacteria](WaterMIGSBacteria.md)
+
+## Other properties
+
+|  |  |  |
+| --- | --- | --- |
+| **Aliases:** | | relevant electronic resources |
+| **Mappings:** | | MIXS:0000091 |
+| **Comments:** | | Expected value: reference to resource |
+| **Examples:** | | Example(value='http://www.earthmicrobiome.org/', description=None) |
+