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Add earth science module with SESAR vocabularies
This commit adds comprehensive earth science vocabularies based on the SESAR (System for Earth Sample Registration) standard from geosamples.org. New Schema Files: - src/valuesets/schema/earth_science/material_types.yaml * 15 material types (ROCK, SEDIMENT, SOIL, MINERAL, ICE, etc.) * Ontology mappings to ENVO, CHEBI, and PO - src/valuesets/schema/earth_science/sample_types.yaml * 23 sample object types (CORE, DREDGE, GRAB, CTD, etc.) * Describes physical form and collection context - src/valuesets/schema/earth_science/collection_methods.yaml * 32+ collection methods with hierarchical organization * Main methods: BLASTING, CORING, DREDGING, GRAB, MANUAL, PROBE * Subtypes for specialized techniques (17 coring variants, ROV/HOV grab, etc.) - src/valuesets/schema/earth_science/physiographic_features.yaml * 67 physiographic features (geological/geographical contexts) * Features: VOLCANO, HYDROTHERMAL_VENT, SEAMOUNT, CANYON, REEF, etc. * 11 features mapped to ENVO ontology terms Generated Code: - Python enums in src/valuesets/enums/earth_science/ - Updated documentation in docs/schema/valuesets.yaml All schemas validated successfully with proper ontology mappings. References: - https://www.geosamples.org/vocabularies - SESAR material types, sample types, collection methods, and physiographic features 🤖 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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source_file: valuesets.yaml
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source_file_date: '2025-10-30T12:09:22'
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source_file_size: 2816
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generation_date: '2025-10-31T16:49:01'
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generation_date: '2025-11-03T17:34:51'
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‎src/valuesets/enums/__init__.py‎

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from .data_science.sentiment_analysis import SentimentClassificationEnum, FineSentimentClassificationEnum
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from .data_science.text_classification import NewsTopicCategoryEnum, ToxicityClassificationEnum, IntentClassificationEnum
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# Earth_Science domain
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from .earth_science.collection_methods import SESARCollectionMethod
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from .earth_science.material_types import SESARMaterialType
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from .earth_science.physiographic_features import SESARPhysiographicFeature
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from .earth_science.sample_types import SESARSampleType
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# Energy domain
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from .energy.energy import EnergySource, EnergyUnit, PowerUnit, EnergyEfficiencyRating, BuildingEnergyStandard, GridType, EnergyStorageType, EmissionScope, CarbonIntensity, ElectricityMarket
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from .energy.fossil_fuels import FossilFuelTypeEnum
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"ResearchReactorTypeEnum",
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"ResearchRole",
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"RoboticArmTypeEnum",
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"SESARCollectionMethod",
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"SESARMaterialType",
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"SESARPhysiographicFeature",
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"SESARSampleType",
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"SafetyColorEnum",
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"SafetySystemClassEnum",
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"SampleProcessingOperationEnum",

‎src/valuesets/enums/earth_science/__init__.py‎

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"""Auto-generated package."""

‎src/valuesets/enums/earth_science/collection_methods.py‎

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"""
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Earth Science Sample Collection Methods
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Methods for collecting earth samples, based on SESAR (System for Earth Sample Registration) vocabulary
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Generated from: earth_science/collection_methods.yaml
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"""
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from __future__ import annotations
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from typing import Dict, Any, Optional
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from valuesets.generators.rich_enum import RichEnum
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class SESARCollectionMethod(RichEnum):
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"""
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Sample collection methods as defined by SESAR (System for Earth Sample Registration). These describe the method by which a sample was collected.
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"""
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# Enum members
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BLASTING = "BLASTING"
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CAMERA_SLED = "CAMERA_SLED"
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CORING = "CORING"
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CORING_BOX_CORER = "CORING_BOX_CORER"
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CORING_CAMERA_MOUNTED = "CORING_CAMERA_MOUNTED"
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CORING_DRILL_CORER = "CORING_DRILL_CORER"
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CORING_FREE_FALL_CORER = "CORING_FREE_FALL_CORER"
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CORING_GRAVITY = "CORING_GRAVITY"
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CORING_HAND_HELD = "CORING_HAND_HELD"
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CORING_KASTENLOT = "CORING_KASTENLOT"
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CORING_MULTI = "CORING_MULTI"
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CORING_PISTON = "CORING_PISTON"
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CORING_ROCK = "CORING_ROCK"
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CORING_SIDE_SADDLE = "CORING_SIDE_SADDLE"
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CORING_SUBMERSIBLE_MOUNTED = "CORING_SUBMERSIBLE_MOUNTED"
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CORING_TRIGGER_WEIGHT = "CORING_TRIGGER_WEIGHT"
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CORING_VIBRATING = "CORING_VIBRATING"
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DREDGING = "DREDGING"
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DREDGING_CHAIN_BAG = "DREDGING_CHAIN_BAG"
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DREDGING_CHAIN_BAG_DREDGE = "DREDGING_CHAIN_BAG_DREDGE"
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EXPERIMENTAL_APPARATUS = "EXPERIMENTAL_APPARATUS"
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GRAB = "GRAB"
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GRAB_HOV = "GRAB_HOV"
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GRAB_ROV = "GRAB_ROV"
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MANUAL = "MANUAL"
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MANUAL_HAMMER = "MANUAL_HAMMER"
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PROBE = "PROBE"
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SEDIMENT_TRAP = "SEDIMENT_TRAP"
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SUSPENDED_SEDIMENT = "SUSPENDED_SEDIMENT"
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UNKNOWN = "UNKNOWN"
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# Set metadata after class creation
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SESARCollectionMethod._metadata = {
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"BLASTING": {'description': 'Sample collected using blasting techniques'},
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"CAMERA_SLED": {'description': 'Sample collected via camera sled or camera tow', 'annotations': {'aliases': 'Camera tow'}},
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"CORING": {'description': 'Sample collected using coring techniques'},
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"CORING_BOX_CORER": {'description': 'Sample collected using a box corer', 'annotations': {'parent_method': 'Coring'}},
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"CORING_CAMERA_MOUNTED": {'description': 'Sample collected using camera-mounted corer', 'annotations': {'parent_method': 'Coring'}},
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"CORING_DRILL_CORER": {'description': 'Sample collected using a drill corer', 'annotations': {'parent_method': 'Coring'}},
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"CORING_FREE_FALL_CORER": {'description': 'Sample collected using a free-fall corer', 'annotations': {'parent_method': 'Coring'}},
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"CORING_GRAVITY": {'description': 'Sample collected using a gravity corer', 'annotations': {'parent_method': 'Coring'}},
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"CORING_HAND_HELD": {'description': 'Sample collected using a hand-held corer', 'annotations': {'parent_method': 'Coring'}},
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"CORING_KASTENLOT": {'description': 'Sample collected using a kastenlot corer', 'annotations': {'parent_method': 'Coring'}},
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"CORING_MULTI": {'description': 'Sample collected using a multi-corer', 'annotations': {'parent_method': 'Coring'}},
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"CORING_PISTON": {'description': 'Sample collected using a piston corer', 'annotations': {'parent_method': 'Coring'}},
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"CORING_ROCK": {'description': 'Sample collected using a rock corer', 'annotations': {'parent_method': 'Coring'}},
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"CORING_SIDE_SADDLE": {'description': 'Sample collected using a side saddle corer', 'annotations': {'parent_method': 'Coring'}},
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"CORING_SUBMERSIBLE_MOUNTED": {'description': 'Sample collected using a submersible-mounted corer', 'annotations': {'parent_method': 'Coring'}},
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"CORING_TRIGGER_WEIGHT": {'description': 'Sample collected using a trigger weight corer', 'annotations': {'parent_method': 'Coring'}},
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"CORING_VIBRATING": {'description': 'Sample collected using a vibrating corer', 'annotations': {'parent_method': 'Coring'}},
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"DREDGING": {'description': 'Sample collected by dredging'},
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"DREDGING_CHAIN_BAG": {'description': 'Sample collected using a chain bag dredge', 'annotations': {'parent_method': 'Dredging'}},
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"DREDGING_CHAIN_BAG_DREDGE": {'description': 'Sample collected using a chain bag dredge', 'annotations': {'parent_method': 'Dredging'}},
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"EXPERIMENTAL_APPARATUS": {'description': 'Sample collected using experimental apparatus'},
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"GRAB": {'description': 'Sample collected using a grab sampler'},
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"GRAB_HOV": {'description': 'Sample collected using Human-Occupied Vehicle grab', 'annotations': {'parent_method': 'Grab', 'full_name': 'Human-Occupied Vehicle'}},
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"GRAB_ROV": {'description': 'Sample collected using Remotely Operated Vehicle grab', 'annotations': {'parent_method': 'Grab', 'full_name': 'Remotely Operated Vehicle'}},
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"MANUAL": {'description': 'Sample collected manually'},
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"MANUAL_HAMMER": {'description': 'Sample collected manually using a hammer', 'annotations': {'parent_method': 'Manual'}},
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"PROBE": {'description': 'Sample collected using a probe'},
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"SEDIMENT_TRAP": {'description': 'Sample collected using a sediment trap'},
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"SUSPENDED_SEDIMENT": {'description': 'Suspended sediment sample'},
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"UNKNOWN": {'description': 'Collection method unknown'},
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}
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__all__ = [
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"SESARCollectionMethod",
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]

‎src/valuesets/enums/earth_science/material_types.py‎

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"""
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Earth Science Material Types
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Material types for earth samples, based on SESAR (System for Earth Sample Registration) vocabulary
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Generated from: earth_science/material_types.yaml
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"""
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from __future__ import annotations
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from typing import Dict, Any, Optional
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from valuesets.generators.rich_enum import RichEnum
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class SESARMaterialType(RichEnum):
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"""
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Material types as defined by SESAR (System for Earth Sample Registration). These describe what a sample consists of (e.g., rock, mineral, liquid).
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"""
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# Enum members
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BIOLOGY = "BIOLOGY"
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GAS = "GAS"
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ICE = "ICE"
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LIQUID_AQUEOUS = "LIQUID_AQUEOUS"
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LIQUID_ORGANIC = "LIQUID_ORGANIC"
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MINERAL = "MINERAL"
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NOT_APPLICABLE = "NOT_APPLICABLE"
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ORGANIC_MATERIAL = "ORGANIC_MATERIAL"
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OTHER = "OTHER"
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PARTICULATE = "PARTICULATE"
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PLANT_STRUCTURE = "PLANT_STRUCTURE"
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ROCK = "ROCK"
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SEDIMENT = "SEDIMENT"
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SOIL = "SOIL"
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SYNTHETIC = "SYNTHETIC"
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# Set metadata after class creation
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SESARMaterialType._metadata = {
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"BIOLOGY": {'description': 'Biological material or specimens'},
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"GAS": {'description': 'Gaseous material'},
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"ICE": {'description': 'Frozen water or ice samples', 'meaning': 'ENVO:01001125'},
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"LIQUID_AQUEOUS": {'description': 'Aqueous (water-based) liquid', 'annotations': {'sesar_label': 'Liquid>aqueous'}},
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"LIQUID_ORGANIC": {'description': 'Organic liquid', 'annotations': {'sesar_label': 'Liquid>organic'}},
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"MINERAL": {'description': 'Mineral specimen', 'meaning': 'CHEBI:46662'},
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"NOT_APPLICABLE": {'description': 'Material type not applicable', 'annotations': {'sesar_label': 'NotApplicable'}},
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"ORGANIC_MATERIAL": {'description': 'Organic material (non-living)', 'meaning': 'ENVO:01000155'},
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"OTHER": {'description': 'Other material type not listed'},
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"PARTICULATE": {'description': 'Particulate matter'},
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"PLANT_STRUCTURE": {'description': 'Plant structure or tissue', 'meaning': 'PO:0009011'},
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"ROCK": {'description': 'Rock specimen', 'meaning': 'ENVO:00001995'},
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"SEDIMENT": {'description': 'Sediment sample', 'meaning': 'ENVO:00002007'},
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"SOIL": {'description': 'Soil sample', 'meaning': 'ENVO:00001998'},
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"SYNTHETIC": {'description': 'Synthetic or artificial material'},
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}
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__all__ = [
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"SESARMaterialType",
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]

‎src/valuesets/enums/earth_science/physiographic_features.py‎

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"""
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Earth Science Physiographic Features
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Physiographic features for earth sample collection sites, based on SESAR (System for Earth Sample Registration) vocabulary
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Generated from: earth_science/physiographic_features.yaml
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"""
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from __future__ import annotations
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from typing import Dict, Any, Optional
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from valuesets.generators.rich_enum import RichEnum
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class SESARPhysiographicFeature(RichEnum):
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"""
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Physiographic feature types as defined by SESAR (System for Earth Sample Registration). These describe the type of physical feature from which a sample was collected.
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"""
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# Enum members
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ABYSSAL_FEATURE = "ABYSSAL_FEATURE"
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ALLUVIAL_FAN = "ALLUVIAL_FAN"
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ANTICLINE = "ANTICLINE"
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AQUIFER = "AQUIFER"
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ARCH = "ARCH"
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ARROYO = "ARROYO"
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BADLANDS = "BADLANDS"
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BANK = "BANK"
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BAR = "BAR"
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BASIN = "BASIN"
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BAY = "BAY"
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BEACH = "BEACH"
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BIGHT = "BIGHT"
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CANYON = "CANYON"
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CAPE = "CAPE"
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CAVE = "CAVE"
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CHANNEL = "CHANNEL"
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CIRQUE = "CIRQUE"
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CLIFF = "CLIFF"
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CONTINENTAL_DIVIDE = "CONTINENTAL_DIVIDE"
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CONTINENTAL_MARGIN = "CONTINENTAL_MARGIN"
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CRATER = "CRATER"
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DELTA = "DELTA"
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DRAINAGE_BASIN = "DRAINAGE_BASIN"
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DRUMLIN = "DRUMLIN"
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DUNE = "DUNE"
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EARTHQUAKE_FEATURE = "EARTHQUAKE_FEATURE"
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ESTUARY = "ESTUARY"
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FAULT = "FAULT"
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FAULT_ZONE = "FAULT_ZONE"
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FLAT = "FLAT"
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FLOODPLAIN = "FLOODPLAIN"
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FOLD = "FOLD"
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FRACTURE_ZONE = "FRACTURE_ZONE"
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GAP = "GAP"
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GULF = "GULF"
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GUT = "GUT"
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HYDROTHERMAL_VENT = "HYDROTHERMAL_VENT"
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ICE_MASS = "ICE_MASS"
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ISTHMUS = "ISTHMUS"
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KARST_AREA = "KARST_AREA"
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LAKE = "LAKE"
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LAVA_FIELD = "LAVA_FIELD"
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LEDGE = "LEDGE"
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MASSIF = "MASSIF"
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MESA = "MESA"
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MINERAL_DEPOSIT_AREA = "MINERAL_DEPOSIT_AREA"
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MORAINE = "MORAINE"
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MOUNTAIN = "MOUNTAIN"
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MOUNTAIN_RANGE = "MOUNTAIN_RANGE"
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MOUNTAIN_SUMMIT = "MOUNTAIN_SUMMIT"
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OCEAN_TRENCH = "OCEAN_TRENCH"
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OUTCROP = "OUTCROP"
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PLAIN = "PLAIN"
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PLATEAU = "PLATEAU"
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PLAYA = "PLAYA"
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REEF = "REEF"
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RIDGE = "RIDGE"
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RIFT_ZONE = "RIFT_ZONE"
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ROADCUT = "ROADCUT"
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SEAMOUNT = "SEAMOUNT"
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SEA = "SEA"
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STREAM = "STREAM"
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SUBMARINE_CANYON = "SUBMARINE_CANYON"
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SYNCLINE = "SYNCLINE"
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THERMAL_FEATURE = "THERMAL_FEATURE"
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VALLEY = "VALLEY"
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VOLCANO = "VOLCANO"
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# Set metadata after class creation
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SESARPhysiographicFeature._metadata = {
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"ABYSSAL_FEATURE": {'description': 'Deep ocean floor feature'},
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"ALLUVIAL_FAN": {'description': 'Fan-shaped deposit formed by flowing water'},
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"ANTICLINE": {'description': 'Upward-folded rock formation'},
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"AQUIFER": {'description': 'Underground layer of water-bearing rock'},
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"ARCH": {'description': 'Natural arch formation', 'annotations': {'note': 'natural formation'}},
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"ARROYO": {'description': 'Steep-sided gully cut by running water'},
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"BADLANDS": {'description': 'Dry terrain with eroded sedimentary rocks'},
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"BANK": {'description': 'Raised area of seabed or riverbed', 'annotations': {'note': 'hydrographic'}},
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"BAR": {'description': 'Elongated landform feature', 'annotations': {'note': 'physiographic'}},
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"BASIN": {'description': "Depression in the Earth's surface"},
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"BAY": {'description': 'Body of water partly enclosed by land'},
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"BEACH": {'description': 'Landform along a body of water'},
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"BIGHT": {'description': 'Shallow bay or bend in a coastline'},
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"CANYON": {'description': 'Deep gorge with steep sides', 'meaning': 'ENVO:00000169'},
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"CAPE": {'description': 'Pointed land projection into water'},
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"CAVE": {'description': 'Natural underground chamber', 'meaning': 'ENVO:00000067'},
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"CHANNEL": {'description': 'Watercourse or strait'},
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"CIRQUE": {'description': 'Amphitheater-like valley carved by glacial erosion'},
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"CLIFF": {'description': 'Steep rock face'},
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"CONTINENTAL_DIVIDE": {'description': 'Drainage divide on a continent'},
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"CONTINENTAL_MARGIN": {'description': 'Zone between continental shelf and deep ocean'},
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"CRATER": {'description': 'Bowl-shaped depression'},
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"DELTA": {'description': 'Landform at river mouth', 'meaning': 'ENVO:00000101'},
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"DRAINAGE_BASIN": {'description': 'Area drained by a river system'},
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"DRUMLIN": {'description': 'Elongated hill formed by glacial action'},
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"DUNE": {'description': 'Hill of sand formed by wind or water'},
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"EARTHQUAKE_FEATURE": {'description': 'Landform created by seismic activity'},
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"ESTUARY": {'description': 'Partially enclosed coastal body of water', 'meaning': 'ENVO:00000045'},
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"FAULT": {'description': 'Fracture in rock with displacement'},
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"FAULT_ZONE": {'description': 'Area containing multiple faults'},
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"FLAT": {'description': 'Level land area'},
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"FLOODPLAIN": {'description': 'Flat area adjacent to a river'},
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"FOLD": {'description': 'Bend in rock layers', 'annotations': {'note': 'geologic'}},
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"FRACTURE_ZONE": {'description': 'Area of crustal fractures'},
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"GAP": {'description': 'Mountain pass or opening'},
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"GULF": {'description': 'Large bay'},
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"GUT": {'description': 'Narrow water passage'},
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"HYDROTHERMAL_VENT": {'description': 'Fissure releasing geothermally heated water', 'meaning': 'ENVO:00000215'},
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"ICE_MASS": {'description': 'Large accumulation of ice'},
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"ISTHMUS": {'description': 'Narrow strip of land connecting two larger areas'},
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"KARST_AREA": {'description': 'Landscape formed by limestone dissolution'},
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"LAKE": {'description': 'Body of standing water', 'meaning': 'ENVO:00000020'},
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"LAVA_FIELD": {'description': 'Area covered by lava flows'},
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"LEDGE": {'description': 'Narrow horizontal surface projecting from rock'},
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"MASSIF": {'description': 'Compact group of mountains'},
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"MESA": {'description': 'Isolated flat-topped hill'},
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"MINERAL_DEPOSIT_AREA": {'description': 'Area with concentrated mineral deposits'},
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"MORAINE": {'description': 'Glacially formed accumulation of debris'},
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"MOUNTAIN": {'description': 'Large natural elevation', 'meaning': 'ENVO:00000081'},
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"MOUNTAIN_RANGE": {'description': 'Series of connected mountains', 'meaning': 'ENVO:00000080'},
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"MOUNTAIN_SUMMIT": {'description': 'Highest point of a mountain'},
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"OCEAN_TRENCH": {'description': 'Deep oceanic depression'},
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"OUTCROP": {'description': 'Exposed rock formation'},
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"PLAIN": {'description': 'Flat or gently rolling land'},
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"PLATEAU": {'description': 'Elevated flat area'},
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"PLAYA": {'description': 'Dried lake bed'},
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"REEF": {'description': 'Ridge of rock or coral near water surface', 'meaning': 'ENVO:01001899'},
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"RIDGE": {'description': 'Long narrow elevation'},
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"RIFT_ZONE": {'description': "Area where Earth's crust is pulling apart"},
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"ROADCUT": {'description': 'Artificial rock exposure along roadway'},
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"SEAMOUNT": {'description': 'Underwater mountain', 'meaning': 'ENVO:00000264'},
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"SEA": {'description': 'Large body of salt water'},
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"STREAM": {'description': 'Flowing body of water'},
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"SUBMARINE_CANYON": {'description': 'Steep-sided valley on seafloor', 'meaning': 'ENVO:00000267'},
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"SYNCLINE": {'description': 'Downward-folded rock formation'},
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"THERMAL_FEATURE": {'description': 'Geothermal feature'},
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"VALLEY": {'description': 'Low area between hills or mountains'},
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"VOLCANO": {'description': "Vent in Earth's crust through which lava erupts", 'meaning': 'ENVO:00000247'},
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}
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__all__ = [
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"SESARPhysiographicFeature",
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]

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