valuesets 0.3.1__py3-none-any.whl

valuesets/schema/medical/neuroimaging.yaml

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+name: neuroimaging
+title: Neuroimaging Value Sets
+description: 'Value sets for neuroimaging including MRI modalities, fMRI paradigms, acquisition parameters, and image analysis methods.'
+id: https://w3id.org/valuesets/medical/neuroimaging
+imports:
+- linkml:types
+prefixes:
+  linkml: https://w3id.org/linkml/
+  NCIT: http://purl.obolibrary.org/obo/NCIT_
+  DICOM: http://dicom.nema.org/dcm/
+  MMO: http://purl.obolibrary.org/obo/MMO_
+  mesh: http://id.nlm.nih.gov/mesh/
+  EDAM: http://edamontology.org/
+  CHMO: http://purl.obolibrary.org/obo/CHMO_
+  STATO: http://purl.obolibrary.org/obo/STATO_
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+
+slots:
+  mri_modality:
+    description: MRI imaging modality type
+    range: MRIModalityEnum
+  mri_sequence_type:
+    description: MRI pulse sequence type
+    range: MRISequenceTypeEnum
+  mri_contrast_type:
+    description: MRI contrast mechanism
+    range: MRIContrastTypeEnum
+  fmri_paradigm_type:
+    description: fMRI experimental paradigm type
+    range: FMRIParadigmTypeEnum
+
+enums:
+  MRIModalityEnum:
+    description: MRI imaging modalities and techniques
+    permissible_values:
+      STRUCTURAL_T1:
+        title: T1-weighted structural MRI
+        description: High-resolution anatomical imaging with T1 contrast
+        meaning: NCIT:C116455
+        aliases:
+        - High Field Strength Magnetic Resonance Imaging
+        annotations:
+          contrast_mechanism: T1 relaxation
+          typical_use: anatomical reference, volumetric analysis
+          tissue_contrast: good gray/white matter contrast
+      STRUCTURAL_T2:
+        title: T2-weighted structural MRI
+        description: Structural imaging with T2 contrast
+        meaning: NCIT:C116456
+        aliases:
+        - Low Field Strength Magnetic Resonance Imaging
+        annotations:
+          contrast_mechanism: T2 relaxation
+          typical_use: pathology detection, CSF visualization
+          tissue_contrast: good fluid contrast
+      FLAIR:
+        title: Fluid-attenuated inversion recovery
+        description: T2-weighted sequence with CSF signal suppressed
+        meaning: NCIT:C82392
+        annotations:
+          contrast_mechanism: T2 with fluid suppression
+          typical_use: lesion detection, periventricular pathology
+          advantage: suppresses CSF signal
+      BOLD_FMRI:
+        title: Blood oxygen level dependent fMRI
+        description: Functional MRI based on blood oxygenation changes
+        meaning: NCIT:C17958
+        aliases:
+        - Functional Magnetic Resonance Imaging
+        annotations:
+          contrast_mechanism: BOLD signal
+          typical_use: brain activation mapping
+          temporal_resolution: seconds
+      ASL:
+        title: Arterial spin labeling
+        description: Perfusion imaging using magnetically labeled blood
+        meaning: NCIT:C116450
+        aliases:
+        - Arterial Spin Labeling Magnetic Resonance Imaging
+        annotations:
+          contrast_mechanism: arterial blood labeling
+          typical_use: cerebral blood flow measurement
+          advantage: no contrast agent required
+      DWI:
+        title: Diffusion-weighted imaging
+        description: Imaging sensitive to water molecule diffusion
+        meaning: mesh:D038524
+        annotations:
+          contrast_mechanism: water diffusion
+          typical_use: stroke detection, fiber tracking
+          parameter: apparent diffusion coefficient
+      DTI:
+        title: Diffusion tensor imaging
+        description: Advanced diffusion imaging with directional information
+        meaning: NCIT:C64862
+        annotations:
+          contrast_mechanism: directional diffusion
+          typical_use: white matter tractography
+          parameters: fractional anisotropy, mean diffusivity
+      PERFUSION_DSC:
+        title: Dynamic susceptibility contrast perfusion
+        description: Perfusion imaging using contrast agent bolus
+        meaning: NCIT:C116459
+        aliases:
+        - Secretin-Enhanced Magnetic Resonance Imaging
+        annotations:
+          contrast_mechanism: contrast agent dynamics
+          typical_use: cerebral blood flow, blood volume
+          requires: gadolinium contrast
+      PERFUSION_DCE:
+        title: Dynamic contrast-enhanced perfusion
+        description: Perfusion imaging with pharmacokinetic modeling
+        meaning: NCIT:C116458
+        aliases:
+        - Multiparametric Magnetic Resonance Imaging
+        annotations:
+          contrast_mechanism: contrast enhancement kinetics
+          typical_use: blood-brain barrier permeability
+          analysis: pharmacokinetic modeling
+      SWI:
+        title: Susceptibility-weighted imaging
+        description: High-resolution venography and iron detection
+        meaning: NCIT:C121377
+        annotations:
+          contrast_mechanism: magnetic susceptibility
+          typical_use: venography, microbleeds, iron deposits
+          strength: high field preferred
+      TASK_FMRI:
+        title: Task-based functional MRI
+        description: fMRI during specific cognitive or motor tasks
+        meaning: NCIT:C178023
+        aliases:
+        - Task Functional Magnetic Resonance Imaging
+        annotations:
+          paradigm: stimulus-response
+          typical_use: localization of brain functions
+          analysis: statistical parametric mapping
+      RESTING_STATE_FMRI:
+        title: Resting-state functional MRI
+        description: fMRI acquired at rest without explicit tasks
+        meaning: NCIT:C178024
+        aliases:
+        - Resting Functional Magnetic Resonance Imaging
+        annotations:
+          paradigm: no task
+          typical_use: functional connectivity analysis
+          networks: default mode, attention, executive
+      FUNCTIONAL_CONNECTIVITY:
+        title: Functional connectivity MRI
+        description: Analysis of temporal correlations between brain regions
+        meaning: NCIT:C116454
+        aliases:
+        - Functional Connectivity Magnetic Resonance Imaging
+        annotations:
+          analysis_type: connectivity mapping
+          typical_use: network analysis
+          metric: correlation coefficients
+
+  MRISequenceTypeEnum:
+    description: MRI pulse sequence types
+    permissible_values:
+      GRADIENT_ECHO:
+        title: Gradient echo sequence
+        description: Fast imaging sequence using gradient reversal
+        meaning: NCIT:C154542
+        aliases:
+        - Gradient Echo MRI
+        annotations:
+          speed: fast
+          typical_use: T2*, functional imaging
+          artifact_sensitivity: susceptible to magnetic field inhomogeneity
+      SPIN_ECHO:
+        title: Spin echo sequence
+        description: Sequence using 180-degree refocusing pulse
+        meaning: CHMO:0001868
+        aliases:
+        - spin echo pulse sequence
+        annotations:
+          speed: slower
+          typical_use: T2 imaging, reduced artifacts
+          artifact_resistance: good
+      EPI:
+        title: Echo planar imaging
+        description: Ultrafast imaging sequence
+        meaning: NCIT:C17558
+        annotations:
+          speed: very fast
+          typical_use: functional MRI, diffusion imaging
+          temporal_resolution: subsecond
+      MPRAGE:
+        title: Magnetization prepared rapid gradient echo
+        description: T1-weighted 3D sequence with preparation pulse
+        meaning: NCIT:C118462
+        aliases:
+        - Magnetization-Prepared Rapid Gradient Echo MRI
+        annotations:
+          image_type: T1-weighted
+          typical_use: high-resolution anatomical imaging
+          dimension: 3D
+      SPACE:
+        title: Sampling perfection with application optimized contrasts
+        description: 3D turbo spin echo sequence
+        annotations:
+          image_type: T2-weighted
+          typical_use: high-resolution T2 imaging
+          dimension: 3D
+      TRUFI:
+        title: True fast imaging with steady-state precession
+        description: Balanced steady-state free precession sequence
+        meaning: NCIT:C200534
+        aliases:
+        - Constructive Interference In Steady State
+        annotations:
+          contrast: mixed T1/T2
+          typical_use: cardiac imaging, fast scanning
+          signal: high
+
+  MRIContrastTypeEnum:
+    description: MRI image contrast mechanisms
+    permissible_values:
+      T1_WEIGHTED:
+        title: T1-weighted contrast
+        description: Image contrast based on T1 relaxation times
+        meaning: NCIT:C180727
+        aliases:
+        - T1-Weighted Magnetic Resonance Imaging
+        annotations:
+          tissue_contrast: gray matter darker than white matter
+          typical_use: anatomical structure
+      T2_WEIGHTED:
+        title: T2-weighted contrast
+        description: Image contrast based on T2 relaxation times
+        meaning: NCIT:C180729
+        aliases:
+        - T2-Weighted Magnetic Resonance Imaging
+        annotations:
+          tissue_contrast: CSF bright, gray matter brighter than white
+          typical_use: pathology detection
+      T2_STAR:
+        title: T2*-weighted contrast
+        description: Image contrast sensitive to magnetic susceptibility
+        meaning: NCIT:C156447
+        aliases:
+        - T2 (Observed)-Weighted Imaging
+        annotations:
+          sensitivity: blood, iron, air-tissue interfaces
+          typical_use: functional imaging, venography
+      PROTON_DENSITY:
+        title: Proton density weighted
+        description: Image contrast based on hydrogen density
+        meaning: NCIT:C170797
+        aliases:
+        - Proton Density MRI
+        annotations:
+          tissue_contrast: proportional to water content
+          typical_use: joint imaging, some brain pathology
+      DIFFUSION_WEIGHTED:
+        title: Diffusion-weighted contrast
+        description: Image contrast based on water diffusion
+        meaning: NCIT:C111116
+        aliases:
+        - Diffusion Weighted Imaging
+        annotations:
+          sensitivity: molecular motion
+          typical_use: stroke, tumor cellularity
+      PERFUSION_WEIGHTED:
+        title: Perfusion-weighted contrast
+        description: Image contrast based on blood flow dynamics
+        meaning: mesh:D000098642
+        annotations:
+          measurement: cerebral blood flow/volume
+          typical_use: stroke, tumor vascularity
+
+  FMRIParadigmTypeEnum:
+    description: fMRI experimental paradigm types
+    permissible_values:
+      BLOCK_DESIGN:
+        title: Block design paradigm
+        description: Alternating blocks of task and rest conditions
+        meaning: STATO:0000046
+        annotations:
+          duration: typically 15-30 seconds per block
+          advantage: high statistical power
+          typical_use: robust activation detection
+      EVENT_RELATED:
+        title: Event-related design
+        description: Brief stimuli presented at varying intervals
+        meaning: EDAM:topic_3678
+        aliases:
+        - Experimental design and studies
+        annotations:
+          duration: single events (seconds)
+          advantage: flexible timing, event separation
+          typical_use: studying cognitive processes
+      MIXED_DESIGN:
+        title: Mixed block and event-related design
+        description: Combination of block and event-related elements
+        meaning: EDAM:topic_3678
+        aliases:
+        - Experimental design and studies
+        annotations:
+          flexibility: high
+          advantage: sustained and transient responses
+          complexity: high
+      RESTING_STATE:
+        title: Resting state paradigm
+        description: No explicit task, spontaneous brain activity
+        meaning: NCIT:C178024
+        aliases:
+        - Resting Functional Magnetic Resonance Imaging
+        annotations:
+          instruction: rest, eyes open/closed
+          duration: typically 5-10 minutes
+          analysis: functional connectivity
+      NATURALISTIC:
+        title: Naturalistic paradigm
+        description: Ecologically valid stimuli (movies, stories)
+        meaning: EDAM:topic_3678
+        aliases:
+        - Experimental design and studies
+        annotations:
+          stimulus_type: complex, realistic
+          advantage: ecological validity
+          analysis: inter-subject correlation

valuesets/schema/mining_processing.yaml

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+name: mining_processing
+title: Mining and Mineral Processing Value Sets
+description: Value sets for mining operations, mineral processing, beneficiation, and in-situ extraction, including bioleaching
+  and autonomous mining systems.
+id: https://w3id.org/valuesets/mining-processing
+version: 1.0.0
+status: release
+imports:
+- linkml:types
+- ./core
+prefixes:
+  linkml: https://w3id.org/linkml/
+  ENVO: http://purl.obolibrary.org/obo/ENVO_
+  CHEBI: http://purl.obolibrary.org/obo/CHEBI_
+  NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_
+  OBI: http://purl.obolibrary.org/obo/OBI_
+  PATO: http://purl.obolibrary.org/obo/PATO_
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+default_curi_maps:
+- semweb_context
+slots:
+  mineralogy_feedstock:
+    description: Types of mineral feedstock sources for extraction and processing operations, including primary and secondary
+      sources
+    range: MineralogyFeedstockClass
+    required: true
+    comments:
+    - Required field for mining operation records
+    - Manual customization - do not modify
+  beneficiation_pathway:
+    description: Methods for mineral separation and concentration aligned with advanced ore processing initiatives (AOI-2)
+    range: BeneficiationPathway
+  in_situ_chemistry_regime:
+    description: Chemical leaching systems for in-situ extraction with associated parameters including pH, Eh, temperature,
+      and ionic strength
+    range: InSituChemistryRegime
+  extractable_target_element:
+    description: Target elements for extraction, particularly rare earth elements (REE) and critical minerals
+    range: ExtractableTargetElement
+    multivalued: true
+  sensor_while_drilling_feature:
+    description: Measurement while drilling (MWD) and logging while drilling (LWD) features for orebody ML and geosteering
+      applications
+    range: SensorWhileDrillingFeature
+    multivalued: true
+  process_performance_metric:
+    description: Key performance indicators for mining and processing operations tied to SMART milestones and sustainability
+      goals
+    range: ProcessPerformanceMetric
+    multivalued: true
+  bioleach_organism:
+    description: Microorganisms used in bioleaching and biomining operations, including engineered strains
+    range: BioleachOrganism
+  bioleach_mode:
+    description: Mechanisms of bioleaching including indirect and direct bacterial action
+    range: BioleachMode
+  autonomy_level:
+    description: Levels of autonomy for mining systems including drilling, hauling, and sorting robots (relevant for Topic
+      1 initiatives)
+    range: AutonomyLevel
+  regulatory_constraint:
+    description: Regulatory and community constraints affecting mining operations, particularly for in-situ extraction and
+      community engagement
+    range: RegulatoryConstraint
+    multivalued: true
+enums:
+  MineralogyFeedstockClass:
+    description: 'Types of mineral feedstock sources for extraction and processing operations, including primary and secondary
+      sources.
+
+      '
+    permissible_values:
+      HARDROCK_PRIMARY:
+        title: HARDROCK_PRIMARY
+        description: Primary ore from hardrock mining operations
+      TAILINGS_LEGACY:
+        title: TAILINGS_LEGACY
+        description: Historical mine tailings available for reprocessing
+      WASTE_PILES:
+        title: WASTE_PILES
+        description: Accumulated mining waste materials
+      COAL_BYPRODUCT:
+        title: COAL_BYPRODUCT
+        description: Byproducts from coal mining and processing
+      E_WASTE:
+        title: E_WASTE
+        description: Electronic waste containing recoverable metals
+      BRINES:
+        title: BRINES
+        description: Saline water sources containing dissolved minerals
+  BeneficiationPathway:
+    description: 'Methods for mineral separation and concentration aligned with advanced ore processing initiatives (AOI-2).
+
+      '
+    permissible_values:
+      ORE_SORTING:
+        description: Sensor-based sorting of ore particles
+      DENSE_MEDIUM_SEPARATION:
+        description: Gravity separation using dense media
+      MICROWAVE_PREWEAKENING:
+        description: Microwave treatment to weaken ore structure
+      ELECTRIC_PULSE_PREWEAKENING:
+        description: High-voltage electric pulse fragmentation
+      GRINDING_DYNAMIC:
+        description: Dynamic grinding optimization systems
+      ELECTROSTATIC_SEP:
+        description: Electrostatic separation of minerals
+      MAGNETIC_SEP:
+        description: Magnetic separation of ferromagnetic minerals
+      FLOTATION_LOW_H2O:
+        description: Low-water flotation processes
+      BIO_BENEFICIATION:
+        description: Biological methods for mineral beneficiation
+  InSituChemistryRegime:
+    description: 'Chemical leaching systems for in-situ extraction with associated parameters including pH, Eh, temperature,
+      and ionic strength.
+
+      '
+    permissible_values:
+      ACIDIC_SULFATE:
+        title: ACIDIC_SULFATE
+        description: Sulfuric acid-based leaching system
+      ACIDIC_CHLORIDE:
+        title: ACIDIC_CHLORIDE
+        description: Hydrochloric acid or chloride-based leaching
+      AMMONIA_BASED:
+        title: AMMONIA_BASED
+        description: Ammonia or ammonium-based leaching system
+      ORGANIC_ACID:
+        description: Organic acid leaching (citric, oxalic, etc.)
+      BIOLEACH_SULFUR_OXIDIZING:
+        description: Bioleaching using sulfur-oxidizing bacteria
+      BIOLEACH_IRON_OXIDIZING:
+        description: Bioleaching using iron-oxidizing bacteria
+  ExtractableTargetElement:
+    description: 'Target elements for extraction, particularly rare earth elements (REE) and critical minerals.
+
+      '
+    permissible_values:
+      REE_LA:
+        title: REE_LA
+        description: Lanthanum
+      REE_CE:
+        title: REE_CE
+        description: Cerium
+      REE_PR:
+        title: REE_PR
+        description: Praseodymium
+      REE_ND:
+        title: REE_ND
+        description: Neodymium
+      REE_PM:
+        title: REE_PM
+        description: Promethium
+      REE_SM:
+        title: REE_SM
+        description: Samarium
+      REE_EU:
+        title: REE_EU
+        description: Europium
+      REE_GD:
+        title: REE_GD
+        description: Gadolinium
+      REE_TB:
+        title: REE_TB
+        description: Terbium
+      REE_DY:
+        title: REE_DY
+        description: Dysprosium
+      REE_HO:
+        title: REE_HO
+        description: Holmium
+      REE_ER:
+        title: REE_ER
+        description: Erbium
+      REE_TM:
+        title: REE_TM
+        description: Thulium
+      REE_YB:
+        title: REE_YB
+        description: Ytterbium
+      REE_LU:
+        title: REE_LU
+        description: Lutetium
+      SC:
+        title: SC
+        description: Scandium
+      CO:
+        title: CO
+        description: Cobalt
+      NI:
+        title: NI
+        description: Nickel
+      LI:
+        title: LI
+        description: Lithium
+  SensorWhileDrillingFeature:
+    description: 'Measurement while drilling (MWD) and logging while drilling (LWD) features for orebody ML and geosteering
+      applications.
+
+      '
+    permissible_values:
+      WOB:
+        description: Weight on bit measurement
+      ROP:
+        description: Rate of penetration
+      TORQUE:
+        description: Rotational torque measurement
+      MWD_GAMMA:
+        description: Gamma ray logging while drilling
+      MWD_RESISTIVITY:
+        description: Resistivity logging while drilling
+      MUD_LOSS:
+        description: Drilling mud loss measurement
+      VIBRATION:
+        description: Drill string vibration monitoring
+      RSS_ANGLE:
+        description: Rotary steerable system angle
+  ProcessPerformanceMetric:
+    description: 'Key performance indicators for mining and processing operations tied to SMART milestones and sustainability
+      goals.
+
+      '
+    permissible_values:
+      RECOVERY_PCT:
+        description: Percentage recovery of target material
+      SELECTIVITY_INDEX:
+        description: Selectivity index for separation processes
+      SPECIFIC_ENERGY_KWH_T:
+        description: Specific energy consumption in kWh per tonne
+      WATER_INTENSITY_L_T:
+        description: Water usage intensity in liters per tonne
+      REAGENT_INTENSITY_KG_T:
+        description: Reagent consumption in kg per tonne
+      CO2E_KG_T:
+        description: CO2 equivalent emissions in kg per tonne
+      TAILINGS_MASS_REDUCTION_PCT:
+        description: Percentage reduction in tailings mass
+  BioleachOrganism:
+    description: 'Microorganisms used in bioleaching and biomining operations, including engineered strains.
+
+      '
+    permissible_values:
+      ACIDITHIOBACILLUS_FERROOXIDANS:
+        description: Iron and sulfur oxidizing bacterium
+        meaning: NCBITaxon:920
+      LEPTOSPIRILLUM_FERROOXIDANS:
+        description: Iron oxidizing bacterium
+        meaning: NCBITaxon:180
+      ASPERGILLUS_NIGER:
+        description: Organic acid producing fungus
+        meaning: NCBITaxon:5061
+      ENGINEERED_STRAIN:
+        description: Genetically modified organism for enhanced bioleaching
+  BioleachMode:
+    description: 'Mechanisms of bioleaching including indirect and direct bacterial action.
+
+      '
+    permissible_values:
+      INDIRECT_BIOLEACH_ORGANIC_ACIDS:
+        description: Indirect bioleaching through organic acid production
+      SULFUR_OXIDATION:
+        description: Direct bacterial oxidation of sulfur compounds
+      IRON_OXIDATION:
+        description: Direct bacterial oxidation of iron compounds
+  AutonomyLevel:
+    description: 'Levels of autonomy for mining systems including drilling, hauling, and sorting robots (relevant for Topic
+      1 initiatives).
+
+      '
+    permissible_values:
+      ASSISTIVE:
+        description: Human operator with assistive technologies
+      SUPERVISED_AUTONOMY:
+        description: Autonomous operation with human supervision
+      SEMI_AUTONOMOUS:
+        description: Partial autonomy with human intervention capability
+      FULLY_AUTONOMOUS:
+        description: Complete autonomous operation without human intervention
+  RegulatoryConstraint:
+    description: 'Regulatory and community constraints affecting mining operations, particularly for in-situ extraction and
+      community engagement.
+
+      '
+    permissible_values:
+      AQUIFER_PROTECTION:
+        title: AQUIFER_PROTECTION
+        description: Requirements for groundwater and aquifer protection
+      EMISSIONS_CAP:
+        description: Limits on atmospheric emissions
+      CULTURAL_HERITAGE_ZONE:
+        description: Protection of cultural heritage sites
+      WATER_RIGHTS_LIMIT:
+        description: Restrictions based on water usage rights

valuesets/schema/physics/states_of_matter.yaml

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+name: valuesets-physics-states-of-matter
+title: valuesets-physics-states-of-matter
+description: Physics-related value sets for states of matter
+id: https://w3id.org/valuesets/physics/states-of-matter
+prefixes:
+  # linkml_common: https://w3id.org/valuesets/
+  linkml: https://w3id.org/linkml/
+  AFO: http://purl.allotrope.org/ontologies/quality#
+  SNOMED: http://snomed.info/id/
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  state_of_matter:
+    description: The physical state or phase of matter
+    range: StateOfMatterEnum
+enums:
+  StateOfMatterEnum:
+    description: The physical state or phase of matter
+    permissible_values:
+      SOLID:
+        description: A state of matter where particles are closely packed together with fixed positions
+        meaning: AFO:AFQ_0000112
+      LIQUID:
+        description: A nearly incompressible fluid that conforms to the shape of its container
+        meaning: AFO:AFQ_0000113
+      GAS:
+        description: A compressible fluid that expands to fill its container
+        meaning: AFO:AFQ_0000114
+      PLASMA:
+        description: An ionized gas with freely moving charged particles
+        meaning: AFO:AFQ_0000115
+      BOSE_EINSTEIN_CONDENSATE:
+        description: A state of matter formed at extremely low temperatures where particles occupy the same quantum state
+      FERMIONIC_CONDENSATE:
+        description: A superfluid phase formed by fermionic particles at extremely low temperatures
+      SUPERCRITICAL_FLUID:
+        description: A state where distinct liquid and gas phases do not exist
+      SUPERFLUID:
+        description: A phase of matter with zero viscosity
+      SUPERSOLID:
+        description: A spatially ordered material with superfluid properties
+      QUARK_GLUON_PLASMA:
+        description: An extremely hot phase where quarks and gluons are not confined
+license: MIT
+see_also:
+- https://linkml.github.io/valuesets