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Regenerate derived files #78

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4,054 changes: 4,051 additions & 3 deletions docs/schema/valuesets.yaml
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709 changes: 708 additions & 1 deletion project/jsonschema/valuesets.schema.json
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1,251 changes: 1,251 additions & 0 deletions src/valuesets/datamodel/valuesets.py
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1,251 changes: 1,251 additions & 0 deletions src/valuesets/datamodel/valuesets_pydantic.py
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46 changes: 45 additions & 1 deletion src/valuesets/enums/__init__.py
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Expand Up @@ -70,6 +70,7 @@
from .bioprocessing.scale_up import ProcessScaleEnum, BioreactorTypeEnum, FermentationModeEnum, OxygenationStrategyEnum, AgitationTypeEnum, DownstreamProcessEnum, FeedstockTypeEnum, ProductTypeEnum, SterilizationMethodEnum

# Business domain
from .business.currencies import CurrencyCode
from .business.human_resources import EmploymentTypeEnum, JobLevelEnum, HRFunctionEnum, CompensationTypeEnum, PerformanceRatingEnum, RecruitmentSourceEnum, TrainingTypeEnum, EmployeeStatusEnum, WorkArrangementEnum, BenefitsCategoryEnum
from .business.industry_classifications import NAICSSectorEnum, EconomicSectorEnum, BusinessActivityTypeEnum, IndustryMaturityEnum, MarketStructureEnum, IndustryRegulationLevelEnum
from .business.management_operations import ManagementMethodologyEnum, StrategicFrameworkEnum, OperationalModelEnum, PerformanceMeasurementEnum, DecisionMakingStyleEnum, LeadershipStyleEnum, BusinessProcessTypeEnum
Expand All @@ -79,6 +80,7 @@

# Chemistry domain
from .chemistry.chemical_entities import SubatomicParticleEnum, BondTypeEnum, PeriodicTableBlockEnum, ElementFamilyEnum, ElementMetallicClassificationEnum, HardOrSoftEnum, BronstedAcidBaseRoleEnum, LewisAcidBaseRoleEnum, OxidationStateEnum, ChiralityEnum, NanostructureMorphologyEnum
from .chemistry.identifiers import ChemicalIdentifierScheme
from .chemistry.reaction_directionality import RelativeTimeEnum, PresenceEnum, ReactionDirectionality
from .chemistry.reactions import ReactionTypeEnum, ReactionMechanismEnum, CatalystTypeEnum, ReactionConditionEnum, ReactionRateOrderEnum, EnzymeClassEnum, SolventClassEnum, ThermodynamicParameterEnum

Expand All @@ -99,6 +101,8 @@
from .computing.mime_types import MimeType, MimeTypeCategory, TextCharset, CompressionType
from .computing.ontologies import OWLProfileEnum
from .computing.quantum import QubitType, QuantumAlgorithmCategoryType
from .computing.systems_engineering import SystemLifeCycleProcess15288
from .computing.verification_validation_ieee_1012 import VerificationValidationProcessIEEE1012

# Core domain
from .confidence_levels import RelativeTimeEnum, PresenceEnum, ConfidenceLevel, CIOConfidenceLevel, OBCSCertaintyLevel, IPCCLikelihoodScale, IPCCConfidenceLevel, NCITFivePointConfidenceScale
Expand Down Expand Up @@ -221,6 +225,13 @@
from .preservation.events import PreservationEventType, PreservationEventOutcome
from .preservation.fixity import CryptographicHashFunction

# Process_Engineering domain
from .process_engineering.process_industries import ProcessIndustryCategory, ProcessOperationMode
from .process_engineering.process_modeling import DesignSimulationMethod, FlowsheetSolutionApproach, ProcessSimulator
from .process_engineering.process_streams import ProcessStreamRole, ProcessStreamPhase, UtilityType
from .process_engineering.thermodynamics import EquationOfStateModel, ActivityCoefficientModel, ThermodynamicPropertyPackage, MixingRuleModel, PoyntingCorrectionMethod
from .process_engineering.unit_operations import UnitOperationType, ProcessEquipmentType

# Publishing domain
from .publishing.arxiv_categories import ArxivCategory
from .publishing.osti_record import OstiWorkflowStatus, OstiAccessLimitation, OstiCollectionType, OstiSensitivityFlag, OstiOrganizationIdentifierType, OstiProductType, OstiOrganizationType, OstiPersonType, OstiContributorType, OstiRelatedIdentifierType, OstiRelationType, OstiIdentifierType, OstiGeolocationType, OstiMediaLocationType
Expand All @@ -234,12 +245,13 @@

# Statistics domain
from .statistics.prediction_outcomes import OutcomeTypeEnum
from .statistics.statistical_tests import StatisticalTestEnum, TTestTypeEnum, NormalityTestEnum, HomoscedasticityTestEnum, PostHocTestEnum, MultipleTestingCorrectionEnum, CorrelationCoefficientEnum, TestTailednessEnum, DistributionalAssumptionEnum, ComparisonObjectiveEnum

# Time domain
from .time.temporal import DayOfWeek, Month, Quarter, Season, TimePeriod, TimeOfDay, BusinessTimeFrame, GeologicalEra, HistoricalPeriod

# Units domain
from .units.measurements import LengthUnitEnum, MassUnitEnum, VolumeUnitEnum, TemperatureUnitEnum, TimeUnitEnum, PressureUnitEnum, ConcentrationUnitEnum, FrequencyUnitEnum, AngleUnitEnum, DataSizeUnitEnum
from .units.measurements import LengthUnitEnum, MassUnitEnum, VolumeUnitEnum, TemperatureUnitEnum, TimeUnitEnum, PressureUnitEnum, ConcentrationUnitEnum, FrequencyUnitEnum, AngleUnitEnum, DataSizeUnitEnum, MassFlowRateUnitEnum, MolarFlowRateUnitEnum, VolumetricFlowRateUnitEnum
from .units.quantity_kinds import QuantityKindEnum

# Visual domain
Expand All @@ -250,6 +262,7 @@
"AcademicDegree",
"AccessRights",
"AcousticRadiationTypeEnum",
"ActivityCoefficientModel",
"AdditiveManufacturingEnum",
"AgeGroupEnum",
"AgitationTypeEnum",
Expand Down Expand Up @@ -334,6 +347,7 @@
"CellPolarity",
"CellProliferationState",
"CellularityEnum",
"ChemicalIdentifierScheme",
"ChipFabricationNodeType",
"ChiralityEnum",
"ChromatographyType",
Expand All @@ -347,6 +361,7 @@
"CommonMineral",
"CommonOrganismTaxaEnum",
"CommunicationProtocolEnum",
"ComparisonObjectiveEnum",
"CompassDirection",
"CompensationTypeEnum",
"ComplianceStandardEnum",
Expand All @@ -365,6 +380,7 @@
"CoordinationGeometry",
"CopyrightStatus",
"CorporateGovernanceRoleEnum",
"CorrelationCoefficientEnum",
"CountryCodeISO2Enum",
"CountryCodeISO3Enum",
"CriticalMineral",
Expand All @@ -375,6 +391,7 @@
"CrystalSystemEnum",
"CrystallizationMethod",
"CurrencyChemical",
"CurrencyCode",
"CurrencyCodeISO4217Enum",
"DNABaseEnum",
"DNABaseExtendedEnum",
Expand Down Expand Up @@ -402,11 +419,13 @@
"DefectClassificationEnum",
"DefenseInDepthLevelEnum",
"DerivatizationMethod",
"DesignSimulationMethod",
"DetectionModeEnum",
"Detector",
"DetectorType",
"DiagnosticTestTypeEnum",
"DigitalObjectCategory",
"DistributionalAssumptionEnum",
"DocumentFormatEnum",
"DownstreamProcessEnum",
"DrugExposureProvenanceEnum",
Expand Down Expand Up @@ -438,6 +457,7 @@
"EnvironmentalImpact",
"EnzymeClassEnum",
"EnzymologyAssayEnum",
"EquationOfStateModel",
"EthnicityOMB1997Enum",
"ExecutionModeEnum",
"ExperimentalDesignMethodType",
Expand Down Expand Up @@ -469,6 +489,7 @@
"FireSafetyColorEnum",
"FissileIsotopeEnum",
"FlowerColorEnum",
"FlowsheetSolutionApproach",
"FoodColoringEnum",
"FossilFuelTypeEnum",
"FraudDetectionEnum",
Expand Down Expand Up @@ -518,6 +539,7 @@
"HeavyMetalEnum",
"HistoricalPeriod",
"HistoricalStatusEnum",
"HomoscedasticityTestEnum",
"HousingStatus",
"HumanAgeGroupEnum",
"HumanDevelopmentalStage",
Expand Down Expand Up @@ -597,6 +619,7 @@
"MaritimeSignalColorEnum",
"MarketStructureEnum",
"MassErrorUnit",
"MassFlowRateUnitEnum",
"MassSpectrometerFileFormat",
"MassSpectrometerVendor",
"MassSpectrometryAssayEnum",
Expand Down Expand Up @@ -625,11 +648,14 @@
"MiningPhase",
"MiningType",
"MitoticPhase",
"MixingRuleModel",
"ModeOfInheritance",
"ModelSystemTypeEnum",
"MolarFlowRateUnitEnum",
"Month",
"MouseDevelopmentalStage",
"MousePostnatalAgeGroupEnum",
"MultipleTestingCorrectionEnum",
"NAICSSectorEnum",
"NCITFivePointConfidenceScale",
"NIHInstituteCenterEnum",
Expand All @@ -640,6 +666,7 @@
"NetworkProtocolEnum",
"NeuroblastomaRiskGroup",
"NewsTopicCategoryEnum",
"NormalityTestEnum",
"NuclearFacilityTypeEnum",
"NuclearForensicsMethodType",
"NuclearFuelCycleStageEnum",
Expand Down Expand Up @@ -708,8 +735,10 @@
"PlateCoatingEnum",
"PlateMaterialEnum",
"PolymerTypeEnum",
"PostHocTestEnum",
"PowerPlantStatusEnum",
"PowerUnit",
"PoyntingCorrectionMethod",
"PredictionOutcomeType",
"PresenceEnum",
"PreservationEventOutcome",
Expand All @@ -718,9 +747,15 @@
"PreservationLevelValue",
"PressureUnitEnum",
"PriorityLevelEnum",
"ProcessEquipmentType",
"ProcessImprovementApproachEnum",
"ProcessIndustryCategory",
"ProcessOperationMode",
"ProcessPerformanceMetric",
"ProcessScaleEnum",
"ProcessSimulator",
"ProcessStreamPhase",
"ProcessStreamRole",
"ProcessingStatus",
"ProcurementTypeEnum",
"ProductTypeEnum",
Expand Down Expand Up @@ -836,6 +871,7 @@
"StandardsMaturityLevel",
"StandardsOrganizationEnum",
"StateOfMatterEnum",
"StatisticalTestEnum",
"StatusEnum",
"SterilizationMethodEnum",
"StrandType",
Expand All @@ -852,11 +888,14 @@
"SupplyChainStrategyEnum",
"SymptomSeverityEnum",
"SynthesisMethodEnum",
"SystemLifeCycleProcess15288",
"TTestTypeEnum",
"TailingCharacterizationType",
"TaxonomicRank",
"TechnologyReadinessLevel",
"TemperatureUnitEnum",
"TemporalAggregationEnum",
"TestTailednessEnum",
"TextCharset",
"TextureEnum",
"TherapeuticActionabilityEnum",
Expand All @@ -865,6 +904,7 @@
"ThermalCyclerTypeEnum",
"ThermalCyclingStepEnum",
"ThermodynamicParameterEnum",
"ThermodynamicPropertyPackage",
"TimeOfDay",
"TimePeriod",
"TimeUnitEnum",
Expand All @@ -889,15 +929,18 @@
"USStateCodeEnum",
"UnconventionalMineralResourceType",
"UniProtSpeciesCode",
"UnitOperationType",
"UpdateFrequency",
"UraniumEnrichmentLevelEnum",
"UtilityType",
"VaccinationPeriodicityEnum",
"VaccinationStatusEnum",
"VaccineCategoryEnum",
"VaccineTypeEnum",
"ValueSetStewardEnum",
"VectorTypeEnum",
"VendorCategoryEnum",
"VerificationValidationProcessIEEE1012",
"ViabilityEnum",
"VideoFormatEnum",
"ViralGenomeTypeEnum",
Expand All @@ -906,6 +949,7 @@
"VitalStatusEnum",
"VitrificationMethod",
"VolumeUnitEnum",
"VolumetricFlowRateUnitEnum",
"WasteDisposalMethodEnum",
"WasteFacilityTypeEnum",
"WasteHalfLifeCategoryEnum",
Expand Down
4 changes: 2 additions & 2 deletions src/valuesets/enums/bio/expression_units.py
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Expand Up @@ -34,8 +34,8 @@ class ExpressionUnitEnum(RichEnum):
"NORMALIZED_COUNTS": {'description': 'Counts normalized by a method such as DESeq2 or edgeR', 'annotations': {'normalization': 'library size', 'use': 'differential expression'}, 'aliases': ['Normalized Counts']},
"COUNTS": {'description': 'General read counts category', 'aliases': ['Counts']},
"TPM": {'description': 'Transcripts per million - normalized for gene length and sequencing depth', 'meaning': 'NCIT:C181327', 'annotations': {'normalization': 'length and depth', 'use': 'within and between sample comparisons', 'formula': '(reads/gene_length_kb) / sum(reads/gene_length_kb) * 1e6'}, 'aliases': ['Transcript per million']},
"FPKM": {'description': 'Fragments per kilobase of transcript per million reads mapped', 'meaning': 'STATO:0000172', 'annotations': {'normalization': 'length and depth', 'use': 'within-sample comparisons', 'library_type': 'paired-end'}, 'aliases': ['Fragments per kilobase of transcript per million reads mapped']},
"RPKM": {'description': 'Reads per kilobase of transcript per million reads mapped', 'meaning': 'STATO:0000206', 'annotations': {'normalization': 'length and depth', 'use': 'within-sample comparisons', 'library_type': 'single-end'}, 'aliases': ['Reads per kilobase of transcript per million reads mapped']},
"FPKM": {'description': 'Fragments per kilobase of transcript per million reads mapped', 'meaning': 'STATO:0000172', 'annotations': {'normalization': 'length and depth', 'use': 'within-sample comparisons', 'library_type': 'paired-end'}, 'aliases': ['Fragments per kilobase of transcript per million reads mapped', 'FPKM-fragments per kilobase of transcript per million fragments mapped']},
"RPKM": {'description': 'Reads per kilobase of transcript per million reads mapped', 'meaning': 'STATO:0000206', 'annotations': {'normalization': 'length and depth', 'use': 'within-sample comparisons', 'library_type': 'single-end'}, 'aliases': ['Reads per kilobase of transcript per million reads mapped', 'RPKM-reads per kilobase of transcript per million fragments mapped']},
"CPM": {'description': 'Counts per million reads', 'annotations': {'normalization': 'depth only'}, 'aliases': ['Counts per million']},
"RPKM_UQ": {'description': 'RPKM with upper quartile normalization', 'annotations': {'normalization': 'length, depth, and upper quartile'}},
"VST": {'description': 'Variance stabilizing transformation values', 'annotations': {'method': 'DESeq2', 'use': 'visualization, clustering'}},
Expand Down
20 changes: 20 additions & 0 deletions src/valuesets/enums/bioprocessing/scale_up.py
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Expand Up @@ -139,6 +139,16 @@ class DownstreamProcessEnum(RichEnum):
DISTILLATION = "DISTILLATION"
DRYING = "DRYING"
HOMOGENIZATION = "HOMOGENIZATION"
CLARIFICATION = "CLARIFICATION"
FLOCCULATION = "FLOCCULATION"
ULTRAFILTRATION = "ULTRAFILTRATION"
DIAFILTRATION = "DIAFILTRATION"
TANGENTIAL_FLOW_FILTRATION = "TANGENTIAL_FLOW_FILTRATION"
BUFFER_EXCHANGE = "BUFFER_EXCHANGE"
ADSORPTION = "ADSORPTION"
VIRAL_INACTIVATION = "VIRAL_INACTIVATION"
POLISHING = "POLISHING"
LYOPHILIZATION = "LYOPHILIZATION"

# Set metadata after class creation
DownstreamProcessEnum._metadata = {
Expand All @@ -151,6 +161,16 @@ class DownstreamProcessEnum(RichEnum):
"DISTILLATION": {'description': 'Distillation', 'meaning': 'CHMO:0001534', 'annotations': {'principle': 'Boiling point difference'}},
"DRYING": {'description': 'Drying operations', 'meaning': 'CHMO:0001551', 'annotations': {'types': 'Spray, freeze, vacuum'}},
"HOMOGENIZATION": {'description': 'Cell disruption/homogenization', 'annotations': {'methods': 'High pressure, bead mill'}},
"CLARIFICATION": {'description': 'Removal of cells and debris to produce a clarified harvest', 'annotations': {'methods': 'Centrifugation, depth filtration'}},
"FLOCCULATION": {'description': 'Aggregation of cells and debris into flocs to aid clarification'},
"ULTRAFILTRATION": {'description': 'Membrane concentration retaining macromolecules such as proteins', 'meaning': 'CHMO:0001645', 'annotations': {'mwco': 'Typically 1-1000 kDa'}},
"DIAFILTRATION": {'description': 'Buffer exchange and desalting by ultrafiltration with continuous makeup'},
"TANGENTIAL_FLOW_FILTRATION": {'description': 'Crossflow membrane filtration used for concentration and diafiltration', 'annotations': {'aliases': 'TFF, crossflow filtration'}},
"BUFFER_EXCHANGE": {'description': 'Replacement of the buffer matrix of a product stream'},
"ADSORPTION": {'description': 'Capture of product or impurities onto a solid sorbent'},
"VIRAL_INACTIVATION": {'description': 'Treatment step that inactivates potential viral contaminants', 'annotations': {'methods': 'Low pH, solvent/detergent, heat'}},
"POLISHING": {'description': 'Final chromatographic or filtration steps to remove trace impurities'},
"LYOPHILIZATION": {'description': 'Freeze-drying to produce a stable solid product', 'meaning': 'CHMO:0001553', 'annotations': {'aliases': 'freeze drying'}},
}

class FeedstockTypeEnum(RichEnum):
Expand Down
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