nmdc-schema 11.12.1__py3-none-any.whl → 11.14.0__py3-none-any.whl

nmdc_schema/nmdc.py

@@ -1,5 +1,5 @@
 # Auto generated from nmdc.yaml by pythongen.py version: 0.0.1
-# Generation date: 2025-10-09T18:05:09
+# Generation date: 2025-12-08T16:54:05
 # Schema: NMDC
 #
 # id: https://w3id.org/nmdc/nmdc
@@ -60,7 +60,7 @@ from linkml_runtime.linkml_model.types import Boolean, Decimal, Double, Float, I
 from linkml_runtime.utils.metamodelcore import Bool, Decimal, URIorCURIE
 
 metamodel_version = "1.7.0"
-version = "11.12.1"
+version = "11.14.0"
 
 # Namespaces
 BFO = CurieNamespace('BFO', 'http://purl.obolibrary.org/obo/BFO_')
@@ -224,10 +224,6 @@ class EnvironmentalMaterialTermId(OntologyClassId):
     pass
 
 
-class ChemicalEntityId(OntologyClassId):
-    pass
-
-
 class MaterialEntityId(NamedThingId):
     pass
 
@@ -1506,39 +1502,6 @@ class EnvironmentalMaterialTerm(OntologyClass):
         self.type = str(self.class_class_curie)
 
 
-@dataclass(repr=False)
-class ChemicalEntity(OntologyClass):
-    """
-    An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products,
-    drugs. There may be different terms for distinct acid-base forms, protonation states. A chemical entity is a
-    physical entity that pertains to chemistry or biochemistry.
-    """
-    _inherited_slots: ClassVar[list[str]] = []
-
-    class_class_uri: ClassVar[URIRef] = NMDC["ChemicalEntity"]
-    class_class_curie: ClassVar[str] = "nmdc:ChemicalEntity"
-    class_name: ClassVar[str] = "ChemicalEntity"
-    class_model_uri: ClassVar[URIRef] = NMDC.ChemicalEntity
-
-    id: Union[str, ChemicalEntityId] = None
-    type: Union[str, URIorCURIE] = None
-    chemical_formula: Optional[str] = None
-
-    def __post_init__(self, *_: str, **kwargs: Any):
-        if self._is_empty(self.id):
-            self.MissingRequiredField("id")
-        if not isinstance(self.id, ChemicalEntityId):
-            self.id = ChemicalEntityId(self.id)
-
-        if self.chemical_formula is not None and not isinstance(self.chemical_formula, str):
-            self.chemical_formula = str(self.chemical_formula)
-
-        super().__post_init__(**kwargs)
-        if self._is_empty(self.type):
-            self.MissingRequiredField("type")
-        self.type = str(self.class_class_curie)
-
-
 @dataclass(repr=False)
 class OntologyRelation(YAMLRoot):
     """
@@ -1679,6 +1642,7 @@ class Biosample(Sample):
     img_identifiers: Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]] = empty_list()
     neon_biosample_identifiers: Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]] = empty_list()
     alternative_names: Optional[Union[str, list[str]]] = empty_list()
+    provenance_metadata: Optional[Union[dict, "ProvenanceMetadata"]] = None
     gold_biosample_identifiers: Optional[Union[Union[str, URIorCURIE], list[Union[str, URIorCURIE]]]] = empty_list()
     insdc_biosample_identifiers: Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]] = empty_list()
     emsl_biosample_identifiers: Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]] = empty_list()
@@ -2163,6 +2127,7 @@ class Biosample(Sample):
     ecosystem_type: Optional[str] = None
     ecosystem_subtype: Optional[str] = None
     specific_ecosystem: Optional[str] = None
+    ecosystem_path_id: Optional[int] = None
     add_date: Optional[str] = None
     community: Optional[str] = None
     habitat: Optional[str] = None
@@ -2198,10 +2163,10 @@ class Biosample(Sample):
     start_date_inc: Optional[str] = None
     start_time_inc: Optional[str] = None
     project_id: Optional[str] = None
-    replicate_number: Optional[str] = None
+    replicate_number: Optional[int] = None
     sample_shipped: Optional[str] = None
     sample_type: Optional[Union[str, "SampleTypeEnum"]] = None
-    technical_reps: Optional[str] = None
+    technical_reps: Optional[int] = None
     analysis_type: Optional[Union[Union[str, "AnalysisTypeEnum"], list[Union[str, "AnalysisTypeEnum"]]]] = empty_list()
     sample_link: Optional[Union[str, list[str]]] = empty_list()
     bulk_elect_conductivity: Optional[Union[dict, QuantityValue]] = None
@@ -2267,6 +2232,9 @@ class Biosample(Sample):
             self.alternative_names = [self.alternative_names] if self.alternative_names is not None else []
         self.alternative_names = [v if isinstance(v, str) else str(v) for v in self.alternative_names]
 
+        if self.provenance_metadata is not None and not isinstance(self.provenance_metadata, ProvenanceMetadata):
+            self.provenance_metadata = ProvenanceMetadata(**as_dict(self.provenance_metadata))
+
         if not isinstance(self.gold_biosample_identifiers, list):
             self.gold_biosample_identifiers = [self.gold_biosample_identifiers] if self.gold_biosample_identifiers is not None else []
         self.gold_biosample_identifiers = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.gold_biosample_identifiers]
@@ -3784,6 +3752,9 @@ class Biosample(Sample):
         if self.specific_ecosystem is not None and not isinstance(self.specific_ecosystem, str):
             self.specific_ecosystem = str(self.specific_ecosystem)
 
+        if self.ecosystem_path_id is not None and not isinstance(self.ecosystem_path_id, int):
+            self.ecosystem_path_id = int(self.ecosystem_path_id)
+
         if self.add_date is not None and not isinstance(self.add_date, str):
             self.add_date = str(self.add_date)
 
@@ -3889,8 +3860,8 @@ class Biosample(Sample):
         if self.project_id is not None and not isinstance(self.project_id, str):
             self.project_id = str(self.project_id)
 
-        if self.replicate_number is not None and not isinstance(self.replicate_number, str):
-            self.replicate_number = str(self.replicate_number)
+        if self.replicate_number is not None and not isinstance(self.replicate_number, int):
+            self.replicate_number = int(self.replicate_number)
 
         if self.sample_shipped is not None and not isinstance(self.sample_shipped, str):
             self.sample_shipped = str(self.sample_shipped)
@@ -3898,8 +3869,8 @@ class Biosample(Sample):
         if self.sample_type is not None and not isinstance(self.sample_type, SampleTypeEnum):
             self.sample_type = SampleTypeEnum(self.sample_type)
 
-        if self.technical_reps is not None and not isinstance(self.technical_reps, str):
-            self.technical_reps = str(self.technical_reps)
+        if self.technical_reps is not None and not isinstance(self.technical_reps, int):
+            self.technical_reps = int(self.technical_reps)
 
         if not isinstance(self.analysis_type, list):
             self.analysis_type = [self.analysis_type] if self.analysis_type is not None else []
@@ -5379,6 +5350,7 @@ class DataObject(InformationObject):
     url: Optional[str] = None
     was_generated_by: Optional[Union[str, DataEmitterProcessId]] = None
     in_manifest: Optional[Union[Union[str, ManifestId], list[Union[str, ManifestId]]]] = empty_list()
+    superseded_by: Optional[Union[str, WorkflowExecutionId]] = None
 
     def __post_init__(self, *_: str, **kwargs: Any):
         if self._is_empty(self.id):
@@ -5429,6 +5401,9 @@ class DataObject(InformationObject):
             self.in_manifest = [self.in_manifest] if self.in_manifest is not None else []
         self.in_manifest = [v if isinstance(v, ManifestId) else ManifestId(v) for v in self.in_manifest]
 
+        if self.superseded_by is not None and not isinstance(self.superseded_by, WorkflowExecutionId):
+            self.superseded_by = WorkflowExecutionId(self.superseded_by)
+
         super().__post_init__(**kwargs)
         if self._is_empty(self.type):
             self.MissingRequiredField("type")
@@ -5659,6 +5634,7 @@ class WorkflowExecution(DataEmitterProcess):
     execution_resource: Optional[Union[str, "ExecutionResourceEnum"]] = None
     version: Optional[str] = None
     processing_institution_workflow_metadata: Optional[str] = None
+    superseded_by: Optional[Union[str, WorkflowExecutionId]] = None
     has_output: Optional[Union[Union[str, DataObjectId], list[Union[str, DataObjectId]]]] = empty_list()
 
     def __post_init__(self, *_: str, **kwargs: Any):
@@ -5701,6 +5677,9 @@ class WorkflowExecution(DataEmitterProcess):
         if self.processing_institution_workflow_metadata is not None and not isinstance(self.processing_institution_workflow_metadata, str):
             self.processing_institution_workflow_metadata = str(self.processing_institution_workflow_metadata)
 
+        if self.superseded_by is not None and not isinstance(self.superseded_by, WorkflowExecutionId):
+            self.superseded_by = WorkflowExecutionId(self.superseded_by)
+
         if not isinstance(self.has_output, list):
             self.has_output = [self.has_output] if self.has_output is not None else []
         self.has_output = [v if isinstance(v, DataObjectId) else DataObjectId(v) for v in self.has_output]
@@ -5756,8 +5735,9 @@ class MetagenomeAssembly(WorkflowExecution):
     gc_avg: Optional[float] = None
     num_input_reads: Optional[float] = None
     num_aligned_reads: Optional[float] = None
-    insdc_assembly_identifiers: Optional[str] = None
+    insdc_assembly_identifiers: Optional[Union[str, list[str]]] = empty_list()
     was_informed_by: Optional[Union[Union[str, NucleotideSequencingId], list[Union[str, NucleotideSequencingId]]]] = empty_list()
+    superseded_by: Optional[Union[str, MetagenomeAssemblyId]] = None
 
     def __post_init__(self, *_: str, **kwargs: Any):
         if self._is_empty(self.id):
@@ -5846,13 +5826,17 @@ class MetagenomeAssembly(WorkflowExecution):
         if self.num_aligned_reads is not None and not isinstance(self.num_aligned_reads, float):
             self.num_aligned_reads = float(self.num_aligned_reads)
 
-        if self.insdc_assembly_identifiers is not None and not isinstance(self.insdc_assembly_identifiers, str):
-            self.insdc_assembly_identifiers = str(self.insdc_assembly_identifiers)
+        if not isinstance(self.insdc_assembly_identifiers, list):
+            self.insdc_assembly_identifiers = [self.insdc_assembly_identifiers] if self.insdc_assembly_identifiers is not None else []
+        self.insdc_assembly_identifiers = [v if isinstance(v, str) else str(v) for v in self.insdc_assembly_identifiers]
 
         if not isinstance(self.was_informed_by, list):
             self.was_informed_by = [self.was_informed_by] if self.was_informed_by is not None else []
         self.was_informed_by = [v if isinstance(v, NucleotideSequencingId) else NucleotideSequencingId(v) for v in self.was_informed_by]
 
+        if self.superseded_by is not None and not isinstance(self.superseded_by, MetagenomeAssemblyId):
+            self.superseded_by = MetagenomeAssemblyId(self.superseded_by)
+
         super().__post_init__(**kwargs)
         if self._is_empty(self.type):
             self.MissingRequiredField("type")
@@ -5901,8 +5885,9 @@ class MetatranscriptomeAssembly(WorkflowExecution):
     gc_avg: Optional[float] = None
     num_input_reads: Optional[float] = None
     num_aligned_reads: Optional[float] = None
-    insdc_assembly_identifiers: Optional[str] = None
+    insdc_assembly_identifiers: Optional[Union[str, list[str]]] = empty_list()
     was_informed_by: Optional[Union[Union[str, NucleotideSequencingId], list[Union[str, NucleotideSequencingId]]]] = empty_list()
+    superseded_by: Optional[Union[str, MetatranscriptomeAssemblyId]] = None
 
     def __post_init__(self, *_: str, **kwargs: Any):
         if self._is_empty(self.id):
@@ -5991,13 +5976,17 @@ class MetatranscriptomeAssembly(WorkflowExecution):
         if self.num_aligned_reads is not None and not isinstance(self.num_aligned_reads, float):
             self.num_aligned_reads = float(self.num_aligned_reads)
 
-        if self.insdc_assembly_identifiers is not None and not isinstance(self.insdc_assembly_identifiers, str):
-            self.insdc_assembly_identifiers = str(self.insdc_assembly_identifiers)
+        if not isinstance(self.insdc_assembly_identifiers, list):
+            self.insdc_assembly_identifiers = [self.insdc_assembly_identifiers] if self.insdc_assembly_identifiers is not None else []
+        self.insdc_assembly_identifiers = [v if isinstance(v, str) else str(v) for v in self.insdc_assembly_identifiers]
 
         if not isinstance(self.was_informed_by, list):
             self.was_informed_by = [self.was_informed_by] if self.was_informed_by is not None else []
         self.was_informed_by = [v if isinstance(v, NucleotideSequencingId) else NucleotideSequencingId(v) for v in self.was_informed_by]
 
+        if self.superseded_by is not None and not isinstance(self.superseded_by, MetatranscriptomeAssemblyId):
+            self.superseded_by = MetatranscriptomeAssemblyId(self.superseded_by)
+
         super().__post_init__(**kwargs)
         if self._is_empty(self.type):
             self.MissingRequiredField("type")
@@ -6024,6 +6013,7 @@ class MetatranscriptomeExpressionAnalysis(WorkflowExecution):
     processing_institution: Union[str, "ProcessingInstitutionEnum"] = None
     img_identifiers: Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]] = empty_list()
     was_informed_by: Optional[Union[Union[str, NucleotideSequencingId], list[Union[str, NucleotideSequencingId]]]] = empty_list()
+    superseded_by: Optional[Union[str, MetatranscriptomeExpressionAnalysisId]] = None
 
     def __post_init__(self, *_: str, **kwargs: Any):
         if self._is_empty(self.id):
@@ -6039,6 +6029,9 @@ class MetatranscriptomeExpressionAnalysis(WorkflowExecution):
             self.was_informed_by = [self.was_informed_by] if self.was_informed_by is not None else []
         self.was_informed_by = [v if isinstance(v, NucleotideSequencingId) else NucleotideSequencingId(v) for v in self.was_informed_by]
 
+        if self.superseded_by is not None and not isinstance(self.superseded_by, MetatranscriptomeExpressionAnalysisId):
+            self.superseded_by = MetatranscriptomeExpressionAnalysisId(self.superseded_by)
+
         super().__post_init__(**kwargs)
         if self._is_empty(self.type):
             self.MissingRequiredField("type")
@@ -6071,6 +6064,7 @@ class MagsAnalysis(WorkflowExecution):
     unbinned_contig_num: Optional[int] = None
     img_identifiers: Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]] = empty_list()
     was_informed_by: Optional[Union[Union[str, NucleotideSequencingId], list[Union[str, NucleotideSequencingId]]]] = empty_list()
+    superseded_by: Optional[Union[str, MagsAnalysisId]] = None
 
     def __post_init__(self, *_: str, **kwargs: Any):
         if self._is_empty(self.id):
@@ -6105,6 +6099,9 @@ class MagsAnalysis(WorkflowExecution):
             self.was_informed_by = [self.was_informed_by] if self.was_informed_by is not None else []
         self.was_informed_by = [v if isinstance(v, NucleotideSequencingId) else NucleotideSequencingId(v) for v in self.was_informed_by]
 
+        if self.superseded_by is not None and not isinstance(self.superseded_by, MagsAnalysisId):
+            self.superseded_by = MagsAnalysisId(self.superseded_by)
+
         super().__post_init__(**kwargs)
         if self._is_empty(self.type):
             self.MissingRequiredField("type")
@@ -6138,6 +6135,7 @@ class ReadQcAnalysis(WorkflowExecution):
     output_read_bases: Optional[float] = None
     output_read_count: Optional[float] = None
     was_informed_by: Optional[Union[Union[str, NucleotideSequencingId], list[Union[str, NucleotideSequencingId]]]] = empty_list()
+    superseded_by: Optional[Union[str, ReadQcAnalysisId]] = None
 
     def __post_init__(self, *_: str, **kwargs: Any):
         if self._is_empty(self.id):
@@ -6167,6 +6165,9 @@ class ReadQcAnalysis(WorkflowExecution):
             self.was_informed_by = [self.was_informed_by] if self.was_informed_by is not None else []
         self.was_informed_by = [v if isinstance(v, NucleotideSequencingId) else NucleotideSequencingId(v) for v in self.was_informed_by]
 
+        if self.superseded_by is not None and not isinstance(self.superseded_by, ReadQcAnalysisId):
+            self.superseded_by = ReadQcAnalysisId(self.superseded_by)
+
         super().__post_init__(**kwargs)
         if self._is_empty(self.type):
             self.MissingRequiredField("type")
@@ -6192,6 +6193,7 @@ class ReadBasedTaxonomyAnalysis(WorkflowExecution):
     has_input: Union[Union[str, DataObjectId], list[Union[str, DataObjectId]]] = None
     processing_institution: Union[str, "ProcessingInstitutionEnum"] = None
     was_informed_by: Optional[Union[Union[str, NucleotideSequencingId], list[Union[str, NucleotideSequencingId]]]] = empty_list()
+    superseded_by: Optional[Union[str, ReadBasedTaxonomyAnalysisId]] = None
 
     def __post_init__(self, *_: str, **kwargs: Any):
         if self._is_empty(self.id):
@@ -6203,6 +6205,9 @@ class ReadBasedTaxonomyAnalysis(WorkflowExecution):
             self.was_informed_by = [self.was_informed_by] if self.was_informed_by is not None else []
         self.was_informed_by = [v if isinstance(v, NucleotideSequencingId) else NucleotideSequencingId(v) for v in self.was_informed_by]
 
+        if self.superseded_by is not None and not isinstance(self.superseded_by, ReadBasedTaxonomyAnalysisId):
+            self.superseded_by = ReadBasedTaxonomyAnalysisId(self.superseded_by)
+
         super().__post_init__(**kwargs)
         if self._is_empty(self.type):
             self.MissingRequiredField("type")
@@ -6228,6 +6233,7 @@ class MetabolomicsAnalysis(WorkflowExecution):
     has_metabolite_identifications: Optional[Union[Union[dict, MetaboliteIdentification], list[Union[dict, MetaboliteIdentification]]]] = empty_list()
     uses_calibration: Optional[Union[str, CalibrationInformationId]] = None
     was_informed_by: Optional[Union[Union[str, MassSpectrometryId], list[Union[str, MassSpectrometryId]]]] = empty_list()
+    superseded_by: Optional[Union[str, MetabolomicsAnalysisId]] = None
 
     def __post_init__(self, *_: str, **kwargs: Any):
         if self._is_empty(self.id):
@@ -6251,6 +6257,9 @@ class MetabolomicsAnalysis(WorkflowExecution):
             self.was_informed_by = [self.was_informed_by] if self.was_informed_by is not None else []
         self.was_informed_by = [v if isinstance(v, MassSpectrometryId) else MassSpectrometryId(v) for v in self.was_informed_by]
 
+        if self.superseded_by is not None and not isinstance(self.superseded_by, MetabolomicsAnalysisId):
+            self.superseded_by = MetabolomicsAnalysisId(self.superseded_by)
+
         super().__post_init__(**kwargs)
         if self._is_empty(self.type):
             self.MissingRequiredField("type")
@@ -6274,6 +6283,7 @@ class NomAnalysis(WorkflowExecution):
     processing_institution: Union[str, "ProcessingInstitutionEnum"] = None
     uses_calibration: Optional[Union[str, CalibrationInformationId]] = None
     was_informed_by: Optional[Union[Union[str, MassSpectrometryId], list[Union[str, MassSpectrometryId]]]] = empty_list()
+    superseded_by: Optional[Union[str, NomAnalysisId]] = None
 
     def __post_init__(self, *_: str, **kwargs: Any):
         if self._is_empty(self.id):
@@ -6288,6 +6298,9 @@ class NomAnalysis(WorkflowExecution):
             self.was_informed_by = [self.was_informed_by] if self.was_informed_by is not None else []
         self.was_informed_by = [v if isinstance(v, MassSpectrometryId) else MassSpectrometryId(v) for v in self.was_informed_by]
 
+        if self.superseded_by is not None and not isinstance(self.superseded_by, NomAnalysisId):
+            self.superseded_by = NomAnalysisId(self.superseded_by)
+
         super().__post_init__(**kwargs)
         if self._is_empty(self.type):
             self.MissingRequiredField("type")
@@ -6341,6 +6354,7 @@ class MetatranscriptomeAnnotation(AnnotatingWorkflow):
     has_input: Optional[Union[Union[str, NamedThingId], list[Union[str, NamedThingId]]]] = empty_list()
     has_output: Optional[Union[Union[str, NamedThingId], list[Union[str, NamedThingId]]]] = empty_list()
     was_informed_by: Optional[Union[Union[str, NucleotideSequencingId], list[Union[str, NucleotideSequencingId]]]] = empty_list()
+    superseded_by: Optional[Union[str, MetatranscriptomeAnnotationId]] = None
 
     def __post_init__(self, *_: str, **kwargs: Any):
         if self._is_empty(self.id):
@@ -6368,6 +6382,9 @@ class MetatranscriptomeAnnotation(AnnotatingWorkflow):
             self.was_informed_by = [self.was_informed_by] if self.was_informed_by is not None else []
         self.was_informed_by = [v if isinstance(v, NucleotideSequencingId) else NucleotideSequencingId(v) for v in self.was_informed_by]
 
+        if self.superseded_by is not None and not isinstance(self.superseded_by, MetatranscriptomeAnnotationId):
+            self.superseded_by = MetatranscriptomeAnnotationId(self.superseded_by)
+
         super().__post_init__(**kwargs)
         if self._is_empty(self.type):
             self.MissingRequiredField("type")
@@ -6391,6 +6408,7 @@ class MetaproteomicsAnalysis(AnnotatingWorkflow):
     processing_institution: Union[str, "ProcessingInstitutionEnum"] = None
     metaproteomics_analysis_category: Union[str, "MetaproteomicsAnalysisCategoryEnum"] = None
     was_informed_by: Optional[Union[Union[str, MassSpectrometryId], list[Union[str, MassSpectrometryId]]]] = empty_list()
+    superseded_by: Optional[Union[str, MetaproteomicsAnalysisId]] = None
 
     def __post_init__(self, *_: str, **kwargs: Any):
         if self._is_empty(self.id):
@@ -6407,6 +6425,9 @@ class MetaproteomicsAnalysis(AnnotatingWorkflow):
             self.was_informed_by = [self.was_informed_by] if self.was_informed_by is not None else []
         self.was_informed_by = [v if isinstance(v, MassSpectrometryId) else MassSpectrometryId(v) for v in self.was_informed_by]
 
+        if self.superseded_by is not None and not isinstance(self.superseded_by, MetaproteomicsAnalysisId):
+            self.superseded_by = MetaproteomicsAnalysisId(self.superseded_by)
+
         super().__post_init__(**kwargs)
         if self._is_empty(self.type):
             self.MissingRequiredField("type")
@@ -6459,10 +6480,46 @@ class MetagenomeAnnotation(AnnotatingWorkflow):
         self.type = str(self.class_class_curie)
 
 
+@dataclass(repr=False)
+class ProvenanceMetadata(YAMLRoot):
+    """
+    Metadata pertaining to how a record was created.
+    """
+    _inherited_slots: ClassVar[list[str]] = []
+
+    class_class_uri: ClassVar[URIRef] = NMDC["ProvenanceMetadata"]
+    class_class_curie: ClassVar[str] = "nmdc:ProvenanceMetadata"
+    class_name: ClassVar[str] = "ProvenanceMetadata"
+    class_model_uri: ClassVar[URIRef] = NMDC.ProvenanceMetadata
+
+    type: Union[str, URIorCURIE] = None
+    git_url: Optional[str] = None
+    version: Optional[str] = None
+    source_system_of_record: Optional[Union[str, "SourceSystemEnum"]] = None
+
+    def __post_init__(self, *_: str, **kwargs: Any):
+        if self._is_empty(self.type):
+            self.MissingRequiredField("type")
+        self.type = str(self.class_class_curie)
+
+        if self.git_url is not None and not isinstance(self.git_url, str):
+            self.git_url = str(self.git_url)
+
+        if self.version is not None and not isinstance(self.version, str):
+            self.version = str(self.version)
+
+        if self.source_system_of_record is not None and not isinstance(self.source_system_of_record, SourceSystemEnum):
+            self.source_system_of_record = SourceSystemEnum(self.source_system_of_record)
+
+        super().__post_init__(**kwargs)
+
+
 # Enumerations
 class CalibrationTargetEnum(EnumDefinitionImpl):
 
-    mass_charge_ratio = PermissibleValue(text="mass_charge_ratio")
+    mass_charge_ratio = PermissibleValue(
+        text="mass_charge_ratio",
+        title="m/z")
     retention_time = PermissibleValue(text="retention_time")
     retention_index = PermissibleValue(text="retention_index")
 
@@ -6503,7 +6560,7 @@ class MassSpectrometryAcquisitionStrategyEnum(EnumDefinitionImpl):
 
     data_independent_acquisition = PermissibleValue(
         text="data_independent_acquisition",
-        description="""['Data independent mass spectrometer acquisition method wherein the full mass range is fragmented. Examples of such an approach include MS^E, AIF, and bbCID.']""")
+        description="""Data independent mass spectrometer acquisition method wherein the full mass range is fragmented. Examples of such an approach include MS^E, AIF, and bbCID.""")
     data_dependent_acquisition = PermissibleValue(
         text="data_dependent_acquisition",
         description="""Mass spectrometer data acquisition method wherein MSn spectra are triggered based on the m/z of precursor ions detected in the same run.""")
@@ -6585,15 +6642,19 @@ class EluentIntroductionCategoryEnum(EnumDefinitionImpl):
 
     liquid_chromatography = PermissibleValue(
         text="liquid_chromatography",
+        title="liquid chromatography",
         description="""The processed sample is introduced into the mass spectrometer through a liquid chromatography process.""")
     gas_chromatography = PermissibleValue(
         text="gas_chromatography",
+        title="gas chromatography",
         description="""The processed sample is introduced into the mass spectrometer through a gas chromatography process.""")
     direct_infusion_syringe = PermissibleValue(
         text="direct_infusion_syringe",
+        title="direct infusion syringe",
         description="""The processed sample is introduced into the mass spectrometer through a direct infusion process using a syringe.""")
     direct_infusion_autosampler = PermissibleValue(
         text="direct_infusion_autosampler",
+        title="direct infusion autosampler",
         description="""The processed sample is introduced into the mass spectrometer through a direct infusion process using an autosampler.""")
 
     _defn = EnumDefinition(
@@ -6767,18 +6828,23 @@ class SamplePortionEnum(EnumDefinitionImpl):
     pellet = PermissibleValue(text="pellet")
     organic_layer = PermissibleValue(
         text="organic_layer",
+        title="Organic layer",
         description="The portion of a mixture containing dissolved organic material")
     aqueous_layer = PermissibleValue(
         text="aqueous_layer",
+        title="Aqueous layer",
         description="The portion of a mixture containing molecules dissolved in water")
     interlayer = PermissibleValue(
         text="interlayer",
+        title="Interlayer",
         description="The layer of material between liquid layers of a separated mixture")
     chloroform_layer = PermissibleValue(
         text="chloroform_layer",
+        title="Chloroform layer",
         description="The portion of a mixture containing molecules dissolved in chloroform")
     methanol_layer = PermissibleValue(
         text="methanol_layer",
+        title="Methanol layer",
         description="The portion of a mixture containing molecules dissolved in methanol")
 
     _defn = EnumDefinition(
@@ -6859,20 +6925,25 @@ class BiosampleCategoryEnum(EnumDefinitionImpl):
     """
     LTER = PermissibleValue(
         text="LTER",
+        title="National Science Foundation's Long Term Ecological Research Network",
         meaning=None)
     SIP = PermissibleValue(text="SIP")
     SFA = PermissibleValue(
         text="SFA",
+        title="Department of Energy Office of Science Biological and Environmental Research Program Laboratory Science Focus Areas",
         description="""Science Focus Area projects funded through the Department of Energy Office of Science Biological and Environmental Research Program""",
         meaning=None)
     FICUS = PermissibleValue(
         text="FICUS",
+        title="Facilities Integrating Collaborations for User Science",
         meaning=None)
     NEON = PermissibleValue(
         text="NEON",
+        title="National Science Foundation's National Ecological Observatory Network",
         meaning=None)
     BRC = PermissibleValue(
         text="BRC",
+        title="Bioenergy Research Centers",
         description="""Bioenergy Research Centers funded by the Biological Systems Science Division of the U.S. Department of Energy's Biological and Environmental Research Program.""",
         meaning=None)
 
@@ -7024,6 +7095,7 @@ class UnitEnum(EnumDefinitionImpl):
 
     Cel = PermissibleValue(
         text="Cel",
+        title="degrees Celsius",
         description="""The Unified Code for Units of Measure (UCUM) representation of degrees Celsius; a SI unit of temperature  equal to one unit Kelvin.""")
     cm = PermissibleValue(
         text="cm",
@@ -7057,6 +7129,7 @@ class UnitEnum(EnumDefinitionImpl):
         description="The Unified Code for Units of Measure (UCUM) representation of millimeter.")
     a = PermissibleValue(
         text="a",
+        title="years",
         description="The Unified Code for Units of Measure (UCUM) representation of year.")
     uL = PermissibleValue(
         text="uL",
@@ -7084,6 +7157,7 @@ class UnitEnum(EnumDefinitionImpl):
         description="The Unified Code for Units of Measure (UCUM) representation of kilogram.")
     lx = PermissibleValue(
         text="lx",
+        title="lux",
         description="The Unified Code for Units of Measure (UCUM) representation of lux.")
     deg = PermissibleValue(
         text="deg",
@@ -7195,6 +7269,7 @@ class UnitEnum(EnumDefinitionImpl):
         description="The Unified Code for Units of Measure (UCUM) representation of gray (absorbed dose).")
     RAD = PermissibleValue(
         text="RAD",
+        title="rad (radiation absorbed dose)",
         description="The Unified Code for Units of Measure (UCUM) representation of rad (radiation absorbed dose).")
     m3 = PermissibleValue(
         text="m3",
@@ -7219,6 +7294,7 @@ class UnitEnum(EnumDefinitionImpl):
         setattr(cls, "J/K",
             PermissibleValue(
                 text="J/K",
+                title="J/degree Celsius",
                 description="The Unified Code for Units of Measure (UCUM) representation of joule per kelvin."))
         setattr(cls, "m/s",
             PermissibleValue(
@@ -7287,6 +7363,7 @@ class UnitEnum(EnumDefinitionImpl):
         setattr(cls, "umol/m2/s",
             PermissibleValue(
                 text="umol/m2/s",
+                title="micromoles per square meter per second",
                 description="""The Unified Code for Units of Measure (UCUM) representation of micromoles per square meter per second."""))
         setattr(cls, "mg/m3",
             PermissibleValue(
@@ -7307,6 +7384,7 @@ class UnitEnum(EnumDefinitionImpl):
         setattr(cls, "1",
             PermissibleValue(
                 text="1",
+                title="ratio/unitless",
                 description="The Unified Code for Units of Measure (UCUM) representation of dimensionless quantity."))
         setattr(cls, "uL/kg",
             PermissibleValue(
@@ -7380,6 +7458,11 @@ class UnitEnum(EnumDefinitionImpl):
             PermissibleValue(
                 text="1/d",
                 description="The Unified Code for Units of Measure (UCUM) representation of per day (frequency)."))
+        setattr(cls, "1/[sft_i]",
+            PermissibleValue(
+                text="1/[sft_i]",
+                title="per square foot",
+                description="The Unified Code for Units of Measure (UCUM) representation of per square foot."))
         setattr(cls, "kW/m2",
             PermissibleValue(
                 text="kW/m2",
@@ -7407,10 +7490,12 @@ class UnitEnum(EnumDefinitionImpl):
         setattr(cls, "[NTU]",
             PermissibleValue(
                 text="[NTU]",
+                title="Nephelometric Turbidity Units",
                 description="""The Unified Code for Units of Measure (UCUM) representation of Nephelometric Turbidity Units."""))
         setattr(cls, "[FNU]",
             PermissibleValue(
                 text="[FNU]",
+                title="Formazin Nephelometric Units",
                 description="""The Unified Code for Units of Measure (UCUM) representation of Formazin Nephelometric Units."""))
         setattr(cls, "m3/min",
             PermissibleValue(
@@ -7423,6 +7508,7 @@ class UnitEnum(EnumDefinitionImpl):
         setattr(cls, "[lb_av]",
             PermissibleValue(
                 text="[lb_av]",
+                title="pounds (avoirdupois)",
                 description="The Unified Code for Units of Measure (UCUM) representation of pound (avoirdupois)."))
         setattr(cls, "kg/kg",
             PermissibleValue(
@@ -7455,6 +7541,7 @@ class UnitEnum(EnumDefinitionImpl):
         setattr(cls, "[g]",
             PermissibleValue(
                 text="[g]",
+                title="standard gravity",
                 description="The Unified Code for Units of Measure (UCUM) representation of standard gravity."))
         setattr(cls, "m/s2",
             PermissibleValue(
@@ -7471,14 +7558,17 @@ class UnitEnum(EnumDefinitionImpl):
         setattr(cls, "[sft_i]",
             PermissibleValue(
                 text="[sft_i]",
+                title="square feet",
                 description="The Unified Code for Units of Measure (UCUM) representation of square feet."))
         setattr(cls, "[cft_i]",
             PermissibleValue(
                 text="[cft_i]",
+                title="cubic feet",
                 description="The Unified Code for Units of Measure (UCUM) representation of cubic feet."))
         setattr(cls, "mm/a",
             PermissibleValue(
                 text="mm/a",
+                title="millimeters per year",
                 description="The Unified Code for Units of Measure (UCUM) representation of millimeters per year."))
         setattr(cls, "erg/cm2/s",
             PermissibleValue(
@@ -7499,6 +7589,7 @@ class UnitEnum(EnumDefinitionImpl):
         setattr(cls, "[kn_i]",
             PermissibleValue(
                 text="[kn_i]",
+                title="knots",
                 description="""The Unified Code for Units of Measure (UCUM) representation of knot (nautical miles per hour)."""))
         setattr(cls, "m3/s",
             PermissibleValue(
@@ -7507,6 +7598,7 @@ class UnitEnum(EnumDefinitionImpl):
         setattr(cls, "[in_i]",
             PermissibleValue(
                 text="[in_i]",
+                title="inches",
                 description="The Unified Code for Units of Measure (UCUM) representation of inch."))
 
 class ExecutionResourceEnum(EnumDefinitionImpl):
@@ -7714,6 +7806,18 @@ class FileTypeEnum(EnumDefinitionImpl):
             PermissibleValue(
                 text="Centrifuge Taxonomic Classification",
                 description="Centrifuge output read classification file"))
+        setattr(cls, "SingleM Taxonomic Classification",
+            PermissibleValue(
+                text="SingleM Taxonomic Classification",
+                description="SingleM taxonomic classification file"))
+        setattr(cls, "SingleM Krona Plot",
+            PermissibleValue(
+                text="SingleM Krona Plot",
+                description="SingleM krona plot HTML file"))
+        setattr(cls, "SingleM Clustered Report",
+            PermissibleValue(
+                text="SingleM Clustered Report",
+                description="SingleM taxonomic classification results, clustered by OTU"))
         setattr(cls, "Structural Annotation GFF",
             PermissibleValue(
                 text="Structural Annotation GFF",
@@ -7935,27 +8039,40 @@ class DoiProviderEnum(EnumDefinitionImpl):
 
     emsl = PermissibleValue(
         text="emsl",
+        title="EMSL",
         meaning=ROR["04rc0xn13"])
     jgi = PermissibleValue(
         text="jgi",
+        title="JGI",
         meaning=ROR["04xm1d337"])
     kbase = PermissibleValue(
         text="kbase",
+        title="KBase",
         meaning=ROR["01znn6x10"])
     osti = PermissibleValue(
         text="osti",
+        title="OSTI",
         meaning=ROR["031478740"])
     ess_dive = PermissibleValue(
         text="ess_dive",
+        title="ESS-DIVE",
         meaning=ROR["01t14bp54"])
-    massive = PermissibleValue(text="massive")
-    gsc = PermissibleValue(text="gsc")
-    zenodo = PermissibleValue(text="zenodo")
+    massive = PermissibleValue(
+        text="massive",
+        title="MassIVE")
+    gsc = PermissibleValue(
+        text="gsc",
+        title="GSC")
+    zenodo = PermissibleValue(
+        text="zenodo",
+        title="Zenodo")
     edi = PermissibleValue(
         text="edi",
+        title="EDI",
         meaning=ROR["0330j0z60"])
     figshare = PermissibleValue(
         text="figshare",
+        title="Figshare",
         meaning=ROR["041mxqs23"])
 
     _defn = EnumDefinition(
@@ -7996,10 +8113,15 @@ class StatusEnum(EnumDefinitionImpl):
 
 class NucleotideSequencingEnum(EnumDefinitionImpl):
 
-    metagenome = PermissibleValue(text="metagenome")
-    metatranscriptome = PermissibleValue(text="metatranscriptome")
+    metagenome = PermissibleValue(
+        text="metagenome",
+        title="Metagenome")
+    metatranscriptome = PermissibleValue(
+        text="metatranscriptome",
+        title="Metatranscriptome")
     amplicon_sequencing_assay = PermissibleValue(
         text="amplicon_sequencing_assay",
+        title="Amplicon",
         meaning=OBI["0002767"])
 
     _defn = EnumDefinition(
@@ -8008,10 +8130,18 @@ class NucleotideSequencingEnum(EnumDefinitionImpl):
 
 class MassSpectrometryEnum(EnumDefinitionImpl):
 
-    metaproteome = PermissibleValue(text="metaproteome")
-    metabolome = PermissibleValue(text="metabolome")
-    lipidome = PermissibleValue(text="lipidome")
-    nom = PermissibleValue(text="nom")
+    metaproteome = PermissibleValue(
+        text="metaproteome",
+        title="Metaproteome")
+    metabolome = PermissibleValue(
+        text="metabolome",
+        title="Metabolome")
+    lipidome = PermissibleValue(
+        text="lipidome",
+        title="Lipidome")
+    nom = PermissibleValue(
+        text="nom",
+        title="Natural Organic Matter")
 
     _defn = EnumDefinition(
         name="MassSpectrometryEnum",
@@ -8038,27 +8168,35 @@ class ProcessingInstitutionEnum(EnumDefinitionImpl):
 
     NMDC = PermissibleValue(
         text="NMDC",
+        title="National Microbiome Data Collaborative",
         meaning=ROR["05cwx3318"])
     UCSD = PermissibleValue(
         text="UCSD",
+        title="University of California, San Diego",
         meaning=ROR["0168r3w48"])
     JGI = PermissibleValue(
         text="JGI",
+        title="Joint Genome Institute",
         meaning=ROR["04xm1d337"])
     EMSL = PermissibleValue(
         text="EMSL",
+        title="Environmental Molecular Sciences Laboratory",
         meaning=ROR["04rc0xn13"])
     Battelle = PermissibleValue(
         text="Battelle",
+        title="Battelle Memorial Institute",
         meaning=ROR["01h5tnr73"])
     ANL = PermissibleValue(
         text="ANL",
+        title="Argonne National Laboratory",
         meaning=ROR["05gvnxz63"])
     UCD_Genome_Center = PermissibleValue(
         text="UCD_Genome_Center",
+        title="University of California, Davis Genome Center",
         meaning=None)
     Azenta = PermissibleValue(
         text="Azenta",
+        title="Azenta Life Sciences",
         meaning=None)
 
     _defn = EnumDefinition(
@@ -8081,6 +8219,28 @@ class DataCategoryEnum(EnumDefinitionImpl):
         name="DataCategoryEnum",
     )
 
+class SourceSystemEnum(EnumDefinitionImpl):
+
+    NMDC_Submission_Portal = PermissibleValue(
+        text="NMDC_Submission_Portal",
+        description="The National Microbiome Data Collaborative's Submission Portal")
+    GOLD = PermissibleValue(
+        text="GOLD",
+        description="JGI's GOLD system")
+    NEON_Data_Portal = PermissibleValue(
+        text="NEON_Data_Portal",
+        description="National Science Foundation National Ecologial Observatory Network's Data Portal")
+    NCBI = PermissibleValue(
+        text="NCBI",
+        description="National Center for Biotechnology Information database")
+    custom = PermissibleValue(
+        text="custom",
+        description="""Metadata was generated by custom methods such as an offline spreadsheet provided by a user or staff member.""")
+
+    _defn = EnumDefinition(
+        name="SourceSystemEnum",
+    )
+
 class CreditEnum(EnumDefinitionImpl):
 
     Conceptualization = PermissibleValue(
@@ -8190,6 +8350,7 @@ class InstrumentModelEnum(EnumDefinitionImpl):
     orbitrap_eclipse_tribid = PermissibleValue(text="orbitrap_eclipse_tribid")
     orbitrap_q_exactive = PermissibleValue(text="orbitrap_q_exactive")
     orbitrap_iqx_tribrid = PermissibleValue(text="orbitrap_iqx_tribrid")
+    orbitrap_exploris_120 = PermissibleValue(text="orbitrap_exploris_120")
     solarix_7T = PermissibleValue(text="solarix_7T")
     solarix_12T = PermissibleValue(text="solarix_12T")
     solarix_15T = PermissibleValue(text="solarix_15T")
@@ -10417,9 +10578,11 @@ class AnalysisTypeEnum(EnumDefinitionImpl):
     lipidomics = PermissibleValue(text="lipidomics")
     metagenomics = PermissibleValue(
         text="metagenomics",
+        title="Metagenomics",
         description="Standard short-read metagenomic sequencing")
     metagenomics_long_read = PermissibleValue(
         text="metagenomics_long_read",
+        title="Metagenomics (long read)",
         description="Long-read metagenomic sequencing")
     metaproteomics = PermissibleValue(text="metaproteomics")
     metatranscriptomics = PermissibleValue(text="metatranscriptomics")
@@ -10437,36 +10600,38 @@ class AnalysisTypeEnum(EnumDefinitionImpl):
         setattr(cls, "amplicon sequencing assay",
             PermissibleValue(
                 text="amplicon sequencing assay",
+                title="Amplicon sequencing assay",
                 meaning=OBI["0002767"]))
 
 class SubmissionStatusEnum(EnumDefinitionImpl):
 
     InProgress = PermissibleValue(
         text="InProgress",
+        title="In Progress",
         description="The submitter is currently working on the submission.")
     SubmittedPendingReview = PermissibleValue(
         text="SubmittedPendingReview",
+        title="Submitted - Pending Review",
         description="Submission is ready for NMDC review, the submitter cannot edit.")
-    ResubmittedPendingReview = PermissibleValue(
-        text="ResubmittedPendingReview",
-        description="""Submission has been resubmitted after updates. It is now ready for NMDC review. The submitter cannot edit.""")
     ApprovedHeld = PermissibleValue(
         text="ApprovedHeld",
+        title="Approved - Held",
         description="""Submission has been reviewed and approved. Information is complete, but not yet shared on the data portal. The submitter cannot edit.""")
-    PendingUserFacility = PermissibleValue(
-        text="PendingUserFacility",
-        description="""Submission has been reviewed and approved. Information is complete, but not yet shared on the data portal. Sample information shared with designated user facility and pending approvals. The submitter cannot edit.""")
+    ApprovedPendingUserFacility = PermissibleValue(
+        text="ApprovedPendingUserFacility",
+        title="Approved - Sent to User Facility",
+        description="""Submission has been reviewed and approved by NMDC. Sample information has been shared with designated user facility and is ready for their review. The submitter cannot edit.""")
     UpdatesRequired = PermissibleValue(
         text="UpdatesRequired",
-        description="""Submission has been reviewed and submitter edits are required for approval. The submitter can reopen and edit the submission.""")
-    InProgressUpdate = PermissibleValue(
-        text="InProgressUpdate",
-        description="""NMDC reviewer has reopened submission on behalf of submitter. The submitter is currently editing the submission.""")
+        title="Updates Required",
+        description="""Submission has been reviewed and submitter edits are required for approval. The submitter can edit the submission.""")
     Denied = PermissibleValue(
         text="Denied",
+        title="Denied",
         description="Submission has been reviewed and denied. The submitter cannot edit.")
     Released = PermissibleValue(
         text="Released",
+        title="Released",
         description="""Submission has been reviewed and approved and data is released on the data portal. The submitter cannot edit.""")
 
     _defn = EnumDefinition(
@@ -10547,9 +10712,6 @@ slots.count = Slot(uri=NMDC.count, name="count", curie=NMDC.curie('count'),
 slots.functional_annotation_agg = Slot(uri=NMDC.functional_annotation_agg, name="functional_annotation_agg", curie=NMDC.curie('functional_annotation_agg'),
                    model_uri=NMDC.functional_annotation_agg, domain=None, range=Optional[Union[Union[dict, FunctionalAnnotationAggMember], list[Union[dict, FunctionalAnnotationAggMember]]]])
 
-slots.ecosystem_path_id = Slot(uri=NMDC.ecosystem_path_id, name="ecosystem_path_id", curie=NMDC.curie('ecosystem_path_id'),
-                   model_uri=NMDC.ecosystem_path_id, domain=None, range=Optional[str])
-
 slots.sample_collection_year = Slot(uri=NMDC.sample_collection_year, name="sample_collection_year", curie=NMDC.curie('sample_collection_year'),
                    model_uri=NMDC.sample_collection_year, domain=None, range=Optional[int])
 
@@ -11190,6 +11352,9 @@ slots.notes = Slot(uri=NMDC.notes, name="notes", curie=NMDC.curie('notes'),
 slots.funding_sources = Slot(uri=NMDC.funding_sources, name="funding_sources", curie=NMDC.curie('funding_sources'),
                    model_uri=NMDC.funding_sources, domain=None, range=Optional[Union[str, list[str]]])
 
+slots.ecosystem_path_id = Slot(uri=NMDC.ecosystem_path_id, name="ecosystem_path_id", curie=NMDC.curie('ecosystem_path_id'),
+                   model_uri=NMDC.ecosystem_path_id, domain=None, range=Optional[int])
+
 slots.gold_path_field = Slot(uri=NMDC.gold_path_field, name="gold_path_field", curie=NMDC.curie('gold_path_field'),
                    model_uri=NMDC.gold_path_field, domain=None, range=Optional[str])
 
@@ -11268,6 +11433,9 @@ slots.start_date = Slot(uri=NMDC.start_date, name="start_date", curie=NMDC.curie
 slots.end_date = Slot(uri=NMDC.end_date, name="end_date", curie=NMDC.curie('end_date'),
                    model_uri=NMDC.end_date, domain=None, range=Optional[str])
 
+slots.source_system_of_record = Slot(uri=NMDC['basic_classes/source_system_of_record'], name="source_system_of_record", curie=NMDC.curie('basic_classes/source_system_of_record'),
+                   model_uri=NMDC.source_system_of_record, domain=None, range=Optional[Union[str, "SourceSystemEnum"]])
+
 slots.associated_studies = Slot(uri=NMDC['basic_classes/associated_studies'], name="associated_studies", curie=NMDC.curie('basic_classes/associated_studies'),
                    model_uri=NMDC.associated_studies, domain=None, range=Union[Union[str, StudyId], list[Union[str, StudyId]]])
 
@@ -11349,23 +11517,23 @@ slots.qc_failure_what = Slot(uri=NMDC['basic_classes/qc_failure_what'], name="qc
 slots.protocol_for = Slot(uri=NMDC['basic_classes/protocol_for'], name="protocol_for", curie=NMDC.curie('basic_classes/protocol_for'),
                    model_uri=NMDC.protocol_for, domain=None, range=Optional[Union[str, "ProtocolForEnum"]])
 
-slots.emsl_store_temp = Slot(uri=NMDC.emsl_store_temp, name="emsl_store_temp", curie=NMDC.curie('emsl_store_temp'),
-                   model_uri=NMDC.emsl_store_temp, domain=None, range=Optional[str])
+slots.superseded_by = Slot(uri=NMDC['basic_classes/superseded_by'], name="superseded_by", curie=NMDC.curie('basic_classes/superseded_by'),
+                   model_uri=NMDC.superseded_by, domain=None, range=Optional[Union[str, WorkflowExecutionId]])
 
-slots.project_id = Slot(uri=NMDC.project_id, name="project_id", curie=NMDC.curie('project_id'),
-                   model_uri=NMDC.project_id, domain=None, range=Optional[str])
+slots.provenance_metadata = Slot(uri=NMDC['basic_classes/provenance_metadata'], name="provenance_metadata", curie=NMDC.curie('basic_classes/provenance_metadata'),
+                   model_uri=NMDC.provenance_metadata, domain=None, range=Optional[Union[dict, ProvenanceMetadata]])
 
-slots.replicate_number = Slot(uri=NMDC.replicate_number, name="replicate_number", curie=NMDC.curie('replicate_number'),
-                   model_uri=NMDC.replicate_number, domain=None, range=Optional[str])
+slots.rna_collect_site = Slot(uri=NMDC.rna_collect_site, name="rna_collect_site", curie=NMDC.curie('rna_collect_site'),
+                   model_uri=NMDC.rna_collect_site, domain=None, range=Optional[str])
 
-slots.sample_shipped = Slot(uri=NMDC.sample_shipped, name="sample_shipped", curie=NMDC.curie('sample_shipped'),
-                   model_uri=NMDC.sample_shipped, domain=None, range=Optional[str])
+slots.rna_isolate_meth = Slot(uri=NMDC.rna_isolate_meth, name="rna_isolate_meth", curie=NMDC.curie('rna_isolate_meth'),
+                   model_uri=NMDC.rna_isolate_meth, domain=None, range=Optional[str])
 
-slots.sample_type = Slot(uri=NMDC.sample_type, name="sample_type", curie=NMDC.curie('sample_type'),
-                   model_uri=NMDC.sample_type, domain=None, range=Optional[Union[str, "SampleTypeEnum"]])
+slots.rna_organisms = Slot(uri=NMDC.rna_organisms, name="rna_organisms", curie=NMDC.curie('rna_organisms'),
+                   model_uri=NMDC.rna_organisms, domain=None, range=Optional[str])
 
-slots.technical_reps = Slot(uri=NMDC.technical_reps, name="technical_reps", curie=NMDC.curie('technical_reps'),
-                   model_uri=NMDC.technical_reps, domain=None, range=Optional[str])
+slots.dna_lr_isolate_meth = Slot(uri=NMDC.dna_lr_isolate_meth, name="dna_lr_isolate_meth", curie=NMDC.curie('dna_lr_isolate_meth'),
+                   model_uri=NMDC.dna_lr_isolate_meth, domain=None, range=Optional[str])
 
 slots.dna_collect_site = Slot(uri=NMDC.dna_collect_site, name="dna_collect_site", curie=NMDC.curie('dna_collect_site'),
                    model_uri=NMDC.dna_collect_site, domain=None, range=Optional[str])
@@ -11376,14 +11544,23 @@ slots.dna_isolate_meth = Slot(uri=NMDC.dna_isolate_meth, name="dna_isolate_meth"
 slots.dna_organisms = Slot(uri=NMDC.dna_organisms, name="dna_organisms", curie=NMDC.curie('dna_organisms'),
                    model_uri=NMDC.dna_organisms, domain=None, range=Optional[str])
 
-slots.rna_collect_site = Slot(uri=NMDC.rna_collect_site, name="rna_collect_site", curie=NMDC.curie('rna_collect_site'),
-                   model_uri=NMDC.rna_collect_site, domain=None, range=Optional[str])
+slots.emsl_store_temp = Slot(uri=NMDC.emsl_store_temp, name="emsl_store_temp", curie=NMDC.curie('emsl_store_temp'),
+                   model_uri=NMDC.emsl_store_temp, domain=None, range=Optional[float])
 
-slots.rna_isolate_meth = Slot(uri=NMDC.rna_isolate_meth, name="rna_isolate_meth", curie=NMDC.curie('rna_isolate_meth'),
-                   model_uri=NMDC.rna_isolate_meth, domain=None, range=Optional[str])
+slots.project_id = Slot(uri=NMDC.project_id, name="project_id", curie=NMDC.curie('project_id'),
+                   model_uri=NMDC.project_id, domain=None, range=Optional[str])
 
-slots.rna_organisms = Slot(uri=NMDC.rna_organisms, name="rna_organisms", curie=NMDC.curie('rna_organisms'),
-                   model_uri=NMDC.rna_organisms, domain=None, range=Optional[str])
+slots.sample_shipped = Slot(uri=NMDC.sample_shipped, name="sample_shipped", curie=NMDC.curie('sample_shipped'),
+                   model_uri=NMDC.sample_shipped, domain=None, range=Optional[str])
+
+slots.sample_type = Slot(uri=NMDC.sample_type, name="sample_type", curie=NMDC.curie('sample_type'),
+                   model_uri=NMDC.sample_type, domain=None, range=Optional[Union[str, "SampleTypeEnum"]])
+
+slots.replicate_number = Slot(uri=NMDC.replicate_number, name="replicate_number", curie=NMDC.curie('replicate_number'),
+                   model_uri=NMDC.replicate_number, domain=None, range=Optional[int])
+
+slots.technical_reps = Slot(uri=NMDC.technical_reps, name="technical_reps", curie=NMDC.curie('technical_reps'),
+                   model_uri=NMDC.technical_reps, domain=None, range=Optional[int])
 
 slots.collection_date_inc = Slot(uri=NMDC.collection_date_inc, name="collection_date_inc", curie=NMDC.curie('collection_date_inc'),
                    model_uri=NMDC.collection_date_inc, domain=None, range=Optional[str])
@@ -11444,28 +11621,36 @@ slots.img_identifiers = Slot(uri=NMDC.img_identifiers, name="img_identifiers", c
                    pattern=re.compile(r'^img\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\/\.]*$'))
 
 slots.igsn_identifiers = Slot(uri=NMDC.igsn_identifiers, name="igsn_identifiers", curie=NMDC.curie('igsn_identifiers'),
-                   model_uri=NMDC.igsn_identifiers, domain=None, range=Optional[str])
+                   model_uri=NMDC.igsn_identifiers, domain=None, range=Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]],
+                   pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
 
 slots.gold_identifiers = Slot(uri=NMDC.gold_identifiers, name="gold_identifiers", curie=NMDC.curie('gold_identifiers'),
-                   model_uri=NMDC.gold_identifiers, domain=None, range=Optional[str])
+                   model_uri=NMDC.gold_identifiers, domain=None, range=Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]],
+                   pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
 
 slots.emsl_identifiers = Slot(uri=NMDC.emsl_identifiers, name="emsl_identifiers", curie=NMDC.curie('emsl_identifiers'),
-                   model_uri=NMDC.emsl_identifiers, domain=None, range=Optional[str])
+                   model_uri=NMDC.emsl_identifiers, domain=None, range=Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]],
+                   pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
 
 slots.mgnify_identifiers = Slot(uri=NMDC.mgnify_identifiers, name="mgnify_identifiers", curie=NMDC.curie('mgnify_identifiers'),
-                   model_uri=NMDC.mgnify_identifiers, domain=None, range=Optional[str])
+                   model_uri=NMDC.mgnify_identifiers, domain=None, range=Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]],
+                   pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
 
 slots.insdc_identifiers = Slot(uri=NMDC.insdc_identifiers, name="insdc_identifiers", curie=NMDC.curie('insdc_identifiers'),
-                   model_uri=NMDC.insdc_identifiers, domain=None, range=Optional[str])
+                   model_uri=NMDC.insdc_identifiers, domain=None, range=Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]],
+                   pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
 
 slots.neon_identifiers = Slot(uri=NMDC.neon_identifiers, name="neon_identifiers", curie=NMDC.curie('neon_identifiers'),
-                   model_uri=NMDC.neon_identifiers, domain=None, range=Optional[str])
+                   model_uri=NMDC.neon_identifiers, domain=None, range=Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]],
+                   pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
 
 slots.jgi_portal_identifiers = Slot(uri=NMDC.jgi_portal_identifiers, name="jgi_portal_identifiers", curie=NMDC.curie('jgi_portal_identifiers'),
-                   model_uri=NMDC.jgi_portal_identifiers, domain=None, range=Optional[str])
+                   model_uri=NMDC.jgi_portal_identifiers, domain=None, range=Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]],
+                   pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
 
 slots.gnps_identifiers = Slot(uri=NMDC.gnps_identifiers, name="gnps_identifiers", curie=NMDC.curie('gnps_identifiers'),
-                   model_uri=NMDC.gnps_identifiers, domain=None, range=Optional[str])
+                   model_uri=NMDC.gnps_identifiers, domain=None, range=Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]],
+                   pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
 
 slots.study_identifiers = Slot(uri=NMDC.study_identifiers, name="study_identifiers", curie=NMDC.curie('study_identifiers'),
                    model_uri=NMDC.study_identifiers, domain=None, range=Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]],
@@ -11529,7 +11714,7 @@ slots.emsl_biosample_identifiers = Slot(uri=NMDC.emsl_biosample_identifiers, nam
 
 slots.igsn_biosample_identifiers = Slot(uri=NMDC.igsn_biosample_identifiers, name="igsn_biosample_identifiers", curie=NMDC.curie('igsn_biosample_identifiers'),
                    model_uri=NMDC.igsn_biosample_identifiers, domain=None, range=Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]],
-                   pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
+                   pattern=re.compile(r'^igsn:[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$'))
 
 slots.omics_processing_identifiers = Slot(uri=NMDC.omics_processing_identifiers, name="omics_processing_identifiers", curie=NMDC.curie('omics_processing_identifiers'),
                    model_uri=NMDC.omics_processing_identifiers, domain=None, range=Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]],
@@ -11567,7 +11752,7 @@ slots.assembly_identifiers = Slot(uri=NMDC.assembly_identifiers, name="assembly_
                    model_uri=NMDC.assembly_identifiers, domain=None, range=Optional[str])
 
 slots.insdc_assembly_identifiers = Slot(uri=NMDC.insdc_assembly_identifiers, name="insdc_assembly_identifiers", curie=NMDC.curie('insdc_assembly_identifiers'),
-                   model_uri=NMDC.insdc_assembly_identifiers, domain=None, range=Optional[str],
+                   model_uri=NMDC.insdc_assembly_identifiers, domain=None, range=Optional[Union[str, list[str]]],
                    pattern=re.compile(r'^insdc.sra:[A-Z]+[0-9]+(\.[0-9]+)?$'))
 
 slots.abs_air_humidity = Slot(uri=MIXS['0000122'], name="abs_air_humidity", curie=MIXS.curie('0000122'),
@@ -13291,6 +13476,9 @@ slots.MetagenomeAssembly_id = Slot(uri=NMDC.id, name="MetagenomeAssembly_id", cu
 slots.MetagenomeAssembly_was_informed_by = Slot(uri=NMDC['basic_classes/was_informed_by'], name="MetagenomeAssembly_was_informed_by", curie=NMDC.curie('basic_classes/was_informed_by'),
                    model_uri=NMDC.MetagenomeAssembly_was_informed_by, domain=MetagenomeAssembly, range=Optional[Union[Union[str, NucleotideSequencingId], list[Union[str, NucleotideSequencingId]]]])
 
+slots.MetagenomeAssembly_superseded_by = Slot(uri=NMDC['basic_classes/superseded_by'], name="MetagenomeAssembly_superseded_by", curie=NMDC.curie('basic_classes/superseded_by'),
+                   model_uri=NMDC.MetagenomeAssembly_superseded_by, domain=MetagenomeAssembly, range=Optional[Union[str, MetagenomeAssemblyId]])
+
 slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAssembly_id", curie=NMDC.curie('id'),
                    model_uri=NMDC.MetatranscriptomeAssembly_id, domain=MetatranscriptomeAssembly, range=Union[str, MetatranscriptomeAssemblyId],
                    pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
@@ -13298,6 +13486,9 @@ slots.MetatranscriptomeAssembly_id = Slot(uri=NMDC.id, name="MetatranscriptomeAs
 slots.MetatranscriptomeAssembly_was_informed_by = Slot(uri=NMDC['basic_classes/was_informed_by'], name="MetatranscriptomeAssembly_was_informed_by", curie=NMDC.curie('basic_classes/was_informed_by'),
                    model_uri=NMDC.MetatranscriptomeAssembly_was_informed_by, domain=MetatranscriptomeAssembly, range=Optional[Union[Union[str, NucleotideSequencingId], list[Union[str, NucleotideSequencingId]]]])
 
+slots.MetatranscriptomeAssembly_superseded_by = Slot(uri=NMDC['basic_classes/superseded_by'], name="MetatranscriptomeAssembly_superseded_by", curie=NMDC.curie('basic_classes/superseded_by'),
+                   model_uri=NMDC.MetatranscriptomeAssembly_superseded_by, domain=MetatranscriptomeAssembly, range=Optional[Union[str, MetatranscriptomeAssemblyId]])
+
 slots.MetatranscriptomeAnnotation_id = Slot(uri=NMDC.id, name="MetatranscriptomeAnnotation_id", curie=NMDC.curie('id'),
                    model_uri=NMDC.MetatranscriptomeAnnotation_id, domain=MetatranscriptomeAnnotation, range=Union[str, MetatranscriptomeAnnotationId],
                    pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
@@ -13319,6 +13510,9 @@ slots.MetatranscriptomeAnnotation_gold_analysis_project_identifiers = Slot(uri=N
                    model_uri=NMDC.MetatranscriptomeAnnotation_gold_analysis_project_identifiers, domain=MetatranscriptomeAnnotation, range=Optional[Union[Union[str, ExternalIdentifier], list[Union[str, ExternalIdentifier]]]],
                    pattern=re.compile(r'^gold:Ga[0-9]+$'))
 
+slots.MetatranscriptomeAnnotation_superseded_by = Slot(uri=NMDC['basic_classes/superseded_by'], name="MetatranscriptomeAnnotation_superseded_by", curie=NMDC.curie('basic_classes/superseded_by'),
+                   model_uri=NMDC.MetatranscriptomeAnnotation_superseded_by, domain=MetatranscriptomeAnnotation, range=Optional[Union[str, MetatranscriptomeAnnotationId]])
+
 slots.MetatranscriptomeExpressionAnalysis_id = Slot(uri=NMDC.id, name="MetatranscriptomeExpressionAnalysis_id", curie=NMDC.curie('id'),
                    model_uri=NMDC.MetatranscriptomeExpressionAnalysis_id, domain=MetatranscriptomeExpressionAnalysis, range=Union[str, MetatranscriptomeExpressionAnalysisId],
                    pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
@@ -13330,6 +13524,9 @@ slots.MetatranscriptomeExpressionAnalysis_img_identifiers = Slot(uri=NMDC.img_id
 slots.MetatranscriptomeExpressionAnalysis_was_informed_by = Slot(uri=NMDC['basic_classes/was_informed_by'], name="MetatranscriptomeExpressionAnalysis_was_informed_by", curie=NMDC.curie('basic_classes/was_informed_by'),
                    model_uri=NMDC.MetatranscriptomeExpressionAnalysis_was_informed_by, domain=MetatranscriptomeExpressionAnalysis, range=Optional[Union[Union[str, NucleotideSequencingId], list[Union[str, NucleotideSequencingId]]]])
 
+slots.MetatranscriptomeExpressionAnalysis_superseded_by = Slot(uri=NMDC['basic_classes/superseded_by'], name="MetatranscriptomeExpressionAnalysis_superseded_by", curie=NMDC.curie('basic_classes/superseded_by'),
+                   model_uri=NMDC.MetatranscriptomeExpressionAnalysis_superseded_by, domain=MetatranscriptomeExpressionAnalysis, range=Optional[Union[str, MetatranscriptomeExpressionAnalysisId]])
+
 slots.MagsAnalysis_id = Slot(uri=NMDC.id, name="MagsAnalysis_id", curie=NMDC.curie('id'),
                    model_uri=NMDC.MagsAnalysis_id, domain=MagsAnalysis, range=Union[str, MagsAnalysisId],
                    pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
@@ -13341,6 +13538,9 @@ slots.MagsAnalysis_img_identifiers = Slot(uri=NMDC.img_identifiers, name="MagsAn
 slots.MagsAnalysis_was_informed_by = Slot(uri=NMDC['basic_classes/was_informed_by'], name="MagsAnalysis_was_informed_by", curie=NMDC.curie('basic_classes/was_informed_by'),
                    model_uri=NMDC.MagsAnalysis_was_informed_by, domain=MagsAnalysis, range=Optional[Union[Union[str, NucleotideSequencingId], list[Union[str, NucleotideSequencingId]]]])
 
+slots.MagsAnalysis_superseded_by = Slot(uri=NMDC['basic_classes/superseded_by'], name="MagsAnalysis_superseded_by", curie=NMDC.curie('basic_classes/superseded_by'),
+                   model_uri=NMDC.MagsAnalysis_superseded_by, domain=MagsAnalysis, range=Optional[Union[str, MagsAnalysisId]])
+
 slots.ReadQcAnalysis_id = Slot(uri=NMDC.id, name="ReadQcAnalysis_id", curie=NMDC.curie('id'),
                    model_uri=NMDC.ReadQcAnalysis_id, domain=ReadQcAnalysis, range=Union[str, ReadQcAnalysisId],
                    pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
@@ -13348,6 +13548,9 @@ slots.ReadQcAnalysis_id = Slot(uri=NMDC.id, name="ReadQcAnalysis_id", curie=NMDC
 slots.ReadQcAnalysis_was_informed_by = Slot(uri=NMDC['basic_classes/was_informed_by'], name="ReadQcAnalysis_was_informed_by", curie=NMDC.curie('basic_classes/was_informed_by'),
                    model_uri=NMDC.ReadQcAnalysis_was_informed_by, domain=ReadQcAnalysis, range=Optional[Union[Union[str, NucleotideSequencingId], list[Union[str, NucleotideSequencingId]]]])
 
+slots.ReadQcAnalysis_superseded_by = Slot(uri=NMDC['basic_classes/superseded_by'], name="ReadQcAnalysis_superseded_by", curie=NMDC.curie('basic_classes/superseded_by'),
+                   model_uri=NMDC.ReadQcAnalysis_superseded_by, domain=ReadQcAnalysis, range=Optional[Union[str, ReadQcAnalysisId]])
+
 slots.ReadBasedTaxonomyAnalysis_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAnalysis_id", curie=NMDC.curie('id'),
                    model_uri=NMDC.ReadBasedTaxonomyAnalysis_id, domain=ReadBasedTaxonomyAnalysis, range=Union[str, ReadBasedTaxonomyAnalysisId],
                    pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
@@ -13355,6 +13558,9 @@ slots.ReadBasedTaxonomyAnalysis_id = Slot(uri=NMDC.id, name="ReadBasedTaxonomyAn
 slots.ReadBasedTaxonomyAnalysis_was_informed_by = Slot(uri=NMDC['basic_classes/was_informed_by'], name="ReadBasedTaxonomyAnalysis_was_informed_by", curie=NMDC.curie('basic_classes/was_informed_by'),
                    model_uri=NMDC.ReadBasedTaxonomyAnalysis_was_informed_by, domain=ReadBasedTaxonomyAnalysis, range=Optional[Union[Union[str, NucleotideSequencingId], list[Union[str, NucleotideSequencingId]]]])
 
+slots.ReadBasedTaxonomyAnalysis_superseded_by = Slot(uri=NMDC['basic_classes/superseded_by'], name="ReadBasedTaxonomyAnalysis_superseded_by", curie=NMDC.curie('basic_classes/superseded_by'),
+                   model_uri=NMDC.ReadBasedTaxonomyAnalysis_superseded_by, domain=ReadBasedTaxonomyAnalysis, range=Optional[Union[str, ReadBasedTaxonomyAnalysisId]])
+
 slots.MetabolomicsAnalysis_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysis_id", curie=NMDC.curie('id'),
                    model_uri=NMDC.MetabolomicsAnalysis_id, domain=MetabolomicsAnalysis, range=Union[str, MetabolomicsAnalysisId],
                    pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
@@ -13362,6 +13568,9 @@ slots.MetabolomicsAnalysis_id = Slot(uri=NMDC.id, name="MetabolomicsAnalysis_id"
 slots.MetabolomicsAnalysis_was_informed_by = Slot(uri=NMDC['basic_classes/was_informed_by'], name="MetabolomicsAnalysis_was_informed_by", curie=NMDC.curie('basic_classes/was_informed_by'),
                    model_uri=NMDC.MetabolomicsAnalysis_was_informed_by, domain=MetabolomicsAnalysis, range=Optional[Union[Union[str, MassSpectrometryId], list[Union[str, MassSpectrometryId]]]])
 
+slots.MetabolomicsAnalysis_superseded_by = Slot(uri=NMDC['basic_classes/superseded_by'], name="MetabolomicsAnalysis_superseded_by", curie=NMDC.curie('basic_classes/superseded_by'),
+                   model_uri=NMDC.MetabolomicsAnalysis_superseded_by, domain=MetabolomicsAnalysis, range=Optional[Union[str, MetabolomicsAnalysisId]])
+
 slots.MetaproteomicsAnalysis_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysis_id", curie=NMDC.curie('id'),
                    model_uri=NMDC.MetaproteomicsAnalysis_id, domain=MetaproteomicsAnalysis, range=Union[str, MetaproteomicsAnalysisId],
                    pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
@@ -13369,6 +13578,9 @@ slots.MetaproteomicsAnalysis_id = Slot(uri=NMDC.id, name="MetaproteomicsAnalysis
 slots.MetaproteomicsAnalysis_was_informed_by = Slot(uri=NMDC['basic_classes/was_informed_by'], name="MetaproteomicsAnalysis_was_informed_by", curie=NMDC.curie('basic_classes/was_informed_by'),
                    model_uri=NMDC.MetaproteomicsAnalysis_was_informed_by, domain=MetaproteomicsAnalysis, range=Optional[Union[Union[str, MassSpectrometryId], list[Union[str, MassSpectrometryId]]]])
 
+slots.MetaproteomicsAnalysis_superseded_by = Slot(uri=NMDC['basic_classes/superseded_by'], name="MetaproteomicsAnalysis_superseded_by", curie=NMDC.curie('basic_classes/superseded_by'),
+                   model_uri=NMDC.MetaproteomicsAnalysis_superseded_by, domain=MetaproteomicsAnalysis, range=Optional[Union[str, MetaproteomicsAnalysisId]])
+
 slots.NomAnalysis_id = Slot(uri=NMDC.id, name="NomAnalysis_id", curie=NMDC.curie('id'),
                    model_uri=NMDC.NomAnalysis_id, domain=NomAnalysis, range=Union[str, NomAnalysisId],
                    pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
@@ -13376,6 +13588,9 @@ slots.NomAnalysis_id = Slot(uri=NMDC.id, name="NomAnalysis_id", curie=NMDC.curie
 slots.NomAnalysis_was_informed_by = Slot(uri=NMDC['basic_classes/was_informed_by'], name="NomAnalysis_was_informed_by", curie=NMDC.curie('basic_classes/was_informed_by'),
                    model_uri=NMDC.NomAnalysis_was_informed_by, domain=NomAnalysis, range=Optional[Union[Union[str, MassSpectrometryId], list[Union[str, MassSpectrometryId]]]])
 
+slots.NomAnalysis_superseded_by = Slot(uri=NMDC['basic_classes/superseded_by'], name="NomAnalysis_superseded_by", curie=NMDC.curie('basic_classes/superseded_by'),
+                   model_uri=NMDC.NomAnalysis_superseded_by, domain=NomAnalysis, range=Optional[Union[str, NomAnalysisId]])
+
 slots.ChemicalConversionProcess_id = Slot(uri=NMDC.id, name="ChemicalConversionProcess_id", curie=NMDC.curie('id'),
                    model_uri=NMDC.ChemicalConversionProcess_id, domain=ChemicalConversionProcess, range=Union[str, ChemicalConversionProcessId],
                    pattern=re.compile(r'^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$'))
@@ -13654,4 +13869,13 @@ slots.WorkflowExecution_processing_institution = Slot(uri=NMDC.processing_instit
                    model_uri=NMDC.WorkflowExecution_processing_institution, domain=WorkflowExecution, range=Union[str, "ProcessingInstitutionEnum"])
 
 slots.WorkflowExecution_was_informed_by = Slot(uri=NMDC['basic_classes/was_informed_by'], name="WorkflowExecution_was_informed_by", curie=NMDC.curie('basic_classes/was_informed_by'),
-                   model_uri=NMDC.WorkflowExecution_was_informed_by, domain=WorkflowExecution, range=Union[Union[str, DataGenerationId], list[Union[str, DataGenerationId]]])
+                   model_uri=NMDC.WorkflowExecution_was_informed_by, domain=WorkflowExecution, range=Union[Union[str, DataGenerationId], list[Union[str, DataGenerationId]]])
+
+slots.WorkflowExecution_version = Slot(uri=NMDC.version, name="WorkflowExecution_version", curie=NMDC.curie('version'),
+                   model_uri=NMDC.WorkflowExecution_version, domain=WorkflowExecution, range=Optional[str])
+
+slots.ProvenanceMetadata_version = Slot(uri=NMDC.version, name="ProvenanceMetadata_version", curie=NMDC.curie('version'),
+                   model_uri=NMDC.ProvenanceMetadata_version, domain=ProvenanceMetadata, range=Optional[str])
+
+slots.ProvenanceMetadata_git_url = Slot(uri=NMDC.git_url, name="ProvenanceMetadata_git_url", curie=NMDC.curie('git_url'),
+                   model_uri=NMDC.ProvenanceMetadata_git_url, domain=ProvenanceMetadata, range=Optional[str])