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Add energy domain value sets with SWEET ontology mappings
New value sets for DOE Genesis Mission energy domains: - Geothermal: system types, reservoir types, well types, applications, temperature classification - Hydrogen: color classification (green, blue, grey, etc.), production methods, storage, applications - Bioenergy: feedstock types, biofuel types, generation classification, bioconversion processes Enhanced existing schemas: - energy.yaml: Added SWEET mappings and CapabilityStatus enum for facility lifecycle - structural_biology.yaml: Added ontology mappings (CHMO, MOD, MI, FBbi, EDAM) Mapping predicates used intentionally: - exact_mappings: Exactly equivalent concepts - close_mappings: Nearly equivalent (e.g., ETHANOL→sweet:matrEnergy/Ethanol) - broad_mappings: Target is more general (e.g., HYDROGEN fuel→sweet:matrElement/Hydrogen) - narrow_mappings: Target is more specific - related_mappings: Conceptually related but different aspect Added enum-report script for generating CSV mapping statistics. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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‎docs/schema/valuesets.yaml‎

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‎justfile‎

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@@ -368,6 +368,12 @@ uniprot-stats:
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echo "Current YAML: [not found]"; \
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fi
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# Generate CSV report of all enums with mapping statistics
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[group('reports')]
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enum-report:
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uv run python scripts/generate_enum_report.py
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@echo "Report saved to enum_report.csv"
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# ============== Include project-specific recipes ==============
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import "python.justfile"

‎project/jsonschema/valuesets.schema.json‎

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"title": "AnatomicalAxis",
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"type": "string"
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},
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"AnatomicalOrientation": {
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"description": "Directional orientation between anatomical positions based on OME NGFF specification",
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"enum": [
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"LEFT_TO_RIGHT",
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"RIGHT_TO_LEFT",
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"ANTERIOR_TO_POSTERIOR",
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"POSTERIOR_TO_ANTERIOR",
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"INFERIOR_TO_SUPERIOR",
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"SUPERIOR_TO_INFERIOR",
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"DORSAL_TO_VENTRAL",
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"VENTRAL_TO_DORSAL",
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"DORSAL_TO_PALMAR",
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"PALMAR_TO_DORSAL",
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"DORSAL_TO_PLANTAR",
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"PLANTAR_TO_DORSAL",
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"ROSTRAL_TO_CAUDAL",
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"CAUDAL_TO_ROSTRAL",
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"CRANIAL_TO_CAUDAL",
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"CAUDAL_TO_CRANIAL",
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"PROXIMAL_TO_DISTAL",
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"DISTAL_TO_PROXIMAL"
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],
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"title": "AnatomicalOrientation",
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"type": "string"
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},
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"AnatomicalPlane": {
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"description": "Standard anatomical planes for sectioning",
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"enum": [
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"title": "BinaryClassificationEnum",
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"type": "string"
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},
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"BioconversionProcess": {
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"description": "Processes for converting biomass feedstocks into biofuels and bioproducts.",
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"enum": [
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"FERMENTATION",
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"ANAEROBIC_DIGESTION",
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"TRANSESTERIFICATION",
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"HYDROTREATING",
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"PYROLYSIS",
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"GASIFICATION",
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"HYDROTHERMAL_LIQUEFACTION",
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"ENZYMATIC_HYDROLYSIS",
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"ACID_HYDROLYSIS",
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"FISCHER_TROPSCH",
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"ALCOHOL_TO_JET"
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],
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"title": "BioconversionProcess",
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"type": "string"
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},
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"BiofuelGeneration": {
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"description": "Classification of biofuels by feedstock source and technology generation.",
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"enum": [
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"FIRST_GENERATION",
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"SECOND_GENERATION",
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"THIRD_GENERATION",
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"FOURTH_GENERATION"
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],
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"title": "BiofuelGeneration",
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"type": "string"
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},
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"BiofuelType": {
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"description": "Types of fuels produced from biomass feedstocks.",
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"enum": [
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"ETHANOL",
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"BIODIESEL",
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"RENEWABLE_DIESEL",
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"SUSTAINABLE_AVIATION_FUEL",
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"BIOGAS",
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"BIOMETHANE",
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"BIO_OIL",
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"SYNGAS",
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"BUTANOL",
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"METHANOL",
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"DIMETHYL_ETHER"
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],
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"title": "BiofuelType",
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"type": "string"
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},
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"BioleachMode": {
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"description": "Mechanisms of bioleaching including indirect and direct bacterial action.",
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"enum": [
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"title": "BiologicalSexEnum",
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"type": "string"
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},
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"BiomassFeedstockType": {
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"description": "Types of biomass materials used as feedstocks for bioenergy production. Includes dedicated energy crops, agricultural residues, forest residues, and waste streams.",
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"enum": [
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"CORN_STOVER",
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"WHEAT_STRAW",
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"RICE_STRAW",
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"SWITCHGRASS",
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"MISCANTHUS",
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"ENERGY_CANE",
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"SWEET_SORGHUM",
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"POPLAR",
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"WILLOW",
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"FOREST_RESIDUE",
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"WOOD_PROCESSING_RESIDUE",
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"MUNICIPAL_SOLID_WASTE",
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"FOOD_WASTE",
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"ANIMAL_MANURE",
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"ALGAE",
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"USED_COOKING_OIL",
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"SOYBEAN_OIL",
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"CORN_GRAIN",
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"SUGARCANE"
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],
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"title": "BiomassFeedstockType",
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"type": "string"
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},
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"BioreactorTypeEnum": {
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"description": "Types of bioreactors used in fermentation and cell culture",
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"enum": [
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"title": "CapabilityMaturityLevel",
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"type": "string"
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},
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"CapabilityStatus": {
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"description": "Operational status of a capability, facility, or infrastructure. Applicable to energy facilities, research capabilities, and other infrastructure throughout their lifecycle.",
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"enum": [
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"OPERATIONAL",
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"COMING_ONLINE",
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"PILOT",
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"UNDER_DEVELOPMENT",
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"DECOMMISSIONED"
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],
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"title": "CapabilityStatus",
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"type": "string"
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},
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"CarbonIntensity": {
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"description": "Carbon intensity levels for energy sources",
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"enum": [
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"title": "GeologicalEra",
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"type": "string"
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},
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"GeothermalApplication": {
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"description": "Applications and uses of geothermal energy.",
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"enum": [
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"ELECTRICITY_GENERATION",
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"DIRECT_USE_HEATING",
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"GREENHOUSE_HEATING",
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"AQUACULTURE",
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"INDUSTRIAL_PROCESS_HEAT",
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"FOOD_PROCESSING",
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"BATHING_RECREATION",
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"LITHIUM_EXTRACTION"
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],
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"title": "GeothermalApplication",
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"type": "string"
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},
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"GeothermalReservoirType": {
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"description": "Classification of geothermal reservoirs by geological setting and characteristics.",
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"enum": [
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"VOLCANIC",
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"SEDIMENTARY",
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"FRACTURED_BASEMENT",
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"FAULT_CONTROLLED",
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"MAGMATIC",
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"CONDUCTION_DOMINATED"
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],
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"title": "GeothermalReservoirType",
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"type": "string"
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},
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"GeothermalResourceTemperature": {
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"description": "Classification of geothermal resources by temperature range.",
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"enum": [
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"LOW_TEMPERATURE",
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"MODERATE_TEMPERATURE",
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"HIGH_TEMPERATURE",
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"SUPERCRITICAL"
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],
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"title": "GeothermalResourceTemperature",
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"type": "string"
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},
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"GeothermalSystemType": {
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"description": "Types of geothermal energy systems, including conventional hydrothermal and enhanced/engineered geothermal systems.",
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"enum": [
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"HYDROTHERMAL",
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"ENHANCED_GEOTHERMAL_SYSTEM",
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"ADVANCED_GEOTHERMAL_SYSTEM",
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"HOT_DRY_ROCK",
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"GEOPRESSURED",
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"SUPERCRITICAL",
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"GROUND_SOURCE_HEAT_PUMP"
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],
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"title": "GeothermalSystemType",
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"type": "string"
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},
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"GeothermalWellType": {
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"description": "Types of wells used in geothermal energy development and production.",
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"enum": [
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"PRODUCTION_WELL",
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"INJECTION_WELL",
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"EXPLORATION_WELL",
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"OBSERVATION_WELL",
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"SLIM_HOLE",
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"DIRECTIONAL_WELL"
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],
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"title": "GeothermalWellType",
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"type": "string"
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},
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"GridType": {
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"description": "Types of electrical grid systems",
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"enum": [
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"title": "HumanDevelopmentalStage",
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"type": "string"
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},
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"HydrogenApplication": {
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"description": "End-use applications for hydrogen.",
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"enum": [
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"FUEL_CELL_VEHICLE",
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"FUEL_CELL_STATIONARY",
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"INDUSTRIAL_FEEDSTOCK",
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"STEEL_PRODUCTION",
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"AMMONIA_SYNTHESIS",
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"METHANOL_SYNTHESIS",
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"POWER_TO_GAS",
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"BLENDING_NATURAL_GAS",
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"SYNTHETIC_FUELS"
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],
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"title": "HydrogenApplication",
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"type": "string"
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},
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"HydrogenProductionMethod": {
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"description": "Methods and processes for producing hydrogen.",
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"enum": [
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"STEAM_METHANE_REFORMING",
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"AUTOTHERMAL_REFORMING",
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"PARTIAL_OXIDATION",
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"COAL_GASIFICATION",
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"WATER_ELECTROLYSIS",
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"ALKALINE_ELECTROLYSIS",
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"PEM_ELECTROLYSIS",
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"SOLID_OXIDE_ELECTROLYSIS",
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"METHANE_PYROLYSIS",
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"BIOMASS_GASIFICATION",
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"BIOLOGICAL_PRODUCTION",
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"THERMOCHEMICAL_WATER_SPLITTING",
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"PHOTOELECTROCHEMICAL"
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],
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"title": "HydrogenProductionMethod",
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"type": "string"
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},
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"HydrogenStorageMethod": {
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"description": "Methods for storing hydrogen for later use or transport.",
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"enum": [
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"COMPRESSED_GAS",
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"LIQUID_HYDROGEN",
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"METAL_HYDRIDE",
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"CHEMICAL_HYDRIDE",
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"UNDERGROUND_STORAGE",
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"CRYO_COMPRESSED"
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],
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"title": "HydrogenStorageMethod",
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"type": "string"
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},
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"HydrogenType": {
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"description": "Color-coded classification of hydrogen based on production method and carbon intensity. This informal industry taxonomy differentiates hydrogen by its carbon footprint and energy source.",
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"enum": [
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"GREEN_HYDROGEN",
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"BLUE_HYDROGEN",
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"GREY_HYDROGEN",
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"BROWN_HYDROGEN",
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"BLACK_HYDROGEN",
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"PINK_HYDROGEN",
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"TURQUOISE_HYDROGEN",
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"WHITE_HYDROGEN",
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"YELLOW_HYDROGEN",
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"ORANGE_HYDROGEN"
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],
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"title": "HydrogenType",
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"type": "string"
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},
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"IAEAWasteClassificationEnum": {
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"description": "IAEA General Safety Requirements radioactive waste classification scheme",
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"enum": [

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