nmdc-schema 11.13.0__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: 2025-10-29T21:55:59
+# 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 = "11.13.0"
+version = "11.14.0"
 
 # Namespaces
 BFO = CurieNamespace('BFO', 'http://purl.obolibrary.org/obo/BFO_')
@@ -1642,6 +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()
@@ -2126,6 +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
@@ -2230,6 +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]
@@ -3747,6 +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)
 
@@ -6472,10 +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")
 
@@ -6516,7 +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.""")
@@ -6598,15 +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(
@@ -6780,18 +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(
@@ -6872,20 +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)
 
@@ -7037,6 +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",
@@ -7070,6 +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",
@@ -7097,6 +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",
@@ -7208,6 +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",
@@ -7232,6 +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(
@@ -7300,6 +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(
@@ -7320,6 +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(
@@ -7393,6 +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",
@@ -7420,10 +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(
@@ -7436,6 +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(
@@ -7468,6 +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(
@@ -7484,14 +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(
@@ -7512,6 +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(
@@ -7520,6 +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):
@@ -7960,27 +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(
@@ -8021,10 +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(
@@ -8033,10 +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",
@@ -8063,27 +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(
@@ -8106,6 +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(
@@ -10443,9 +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")
@@ -10463,36 +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(
@@ -10573,9 +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])
 
@@ -11216,6 +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])
 
@@ -11294,6 +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]]])
 
@@ -11378,6 +11520,9 @@ slots.protocol_for = Slot(uri=NMDC['basic_classes/protocol_for'], name="protocol
 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.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.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])
 
@@ -13724,4 +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])