valuesets 0.3.1__py3-none-any.whl

valuesets/schema/slot_mixins.yaml

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+name: slot_mixins
+title: Slot Mixins for Value Sets
+description: 'Mixin classes and slot definitions that can be used with value set enums. This provides a pattern for creating
+  slots that reference the enums defined in other schema modules.
+
+  '
+id: https://w3id.org/valuesets/slot-mixins
+version: 1.0.0
+status: release
+imports:
+- linkml:types
+prefixes:
+  linkml: https://w3id.org/linkml/
+  # cval: https://w3id.org/linkml-common/
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+default_curi_maps:
+- semweb_context
+slots:
+  status:
+    description: The status or state of an entity
+    range: string
+  confidence_level:
+    description: The level of confidence in a measurement, observation or assertion
+    range: string
+  gender_identity:
+    description: The gender identity of a person
+    range: string
+  sex_at_birth:
+    description: The sex assigned at birth
+    range: string
+  race:
+    description: The race classification
+    range: string
+  ethnicity:
+    description: The ethnicity classification
+    range: string
+  diagnosis_type:
+    description: The type or classification of a diagnosis
+    range: string
+  procedure_type:
+    description: The type or classification of a medical procedure
+    range: string
+  medication_route:
+    description: The route of medication administration
+    range: string
+  study_design:
+    description: The design methodology of a study
+    range: string
+  statistical_test:
+    description: The statistical test applied
+    range: string
+  biotic_interaction_type:
+    description: The type of biotic interaction between organisms
+    range: string
+  mineralogy_feedstock_class:
+    description: The classification of mineral feedstock source
+    range: string
+  beneficiation_pathway:
+    description: The mineral separation and concentration method
+    range: string
+  in_situ_chemistry_regime:
+    description: The chemical leaching system for in-situ extraction
+    range: string
+  extractable_target_element:
+    description: The target element for extraction
+    multivalued: true
+    range: string
+  sensor_while_drilling_feature:
+    description: The MWD/LWD measurement feature
+    multivalued: true
+    range: string
+  process_performance_metric:
+    description: The key performance indicator for mining/processing
+    multivalued: true
+    range: string
+  bioleach_organism:
+    description: The microorganism used in bioleaching
+    range: string
+  bioleach_mode:
+    description: The mechanism of bioleaching
+    range: string
+  autonomy_level:
+    description: The level of autonomy for mining systems
+    range: string
+  regulatory_constraint:
+    description: The regulatory or community constraint
+    multivalued: true
+    range: string
+classes:
+  DemographicsMixin:
+    mixin: true
+    description: Mixin providing demographic-related slots
+    slots:
+    - gender_identity
+    - sex_at_birth
+    - race
+    - ethnicity
+  HealthcareMixin:
+    mixin: true
+    description: Mixin providing healthcare-related slots
+    slots:
+    - diagnosis_type
+    - procedure_type
+    - medication_route
+  StudyMixin:
+    mixin: true
+    description: Mixin providing study/investigation-related slots
+    slots:
+    - study_design
+    - statistical_test
+    - confidence_level
+  MiningProcessMixin:
+    mixin: true
+    description: Mixin providing mining and processing-related slots
+    slots:
+    - mineralogy_feedstock_class
+    - beneficiation_pathway
+    - extractable_target_element
+    - process_performance_metric
+  BioleachingMixin:
+    mixin: true
+    description: Mixin providing bioleaching-specific slots
+    slots:
+    - bioleach_organism
+    - bioleach_mode
+    - in_situ_chemistry_regime
+  MiningAutomationMixin:
+    mixin: true
+    description: Mixin providing mining automation-related slots
+    slots:
+    - autonomy_level
+    - sensor_while_drilling_feature
+  RegulatoryMixin:
+    mixin: true
+    description: Mixin providing regulatory and compliance slots
+    slots:
+    - regulatory_constraint
+  EcologicalInteractionMixin:
+    mixin: true
+    description: Mixin providing ecological interaction slots
+    slots:
+    - biotic_interaction_type

valuesets/schema/social/person_status.yaml

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+name: person_status
+id: https://w3id.org/linkml/valuesets/social/person_status
+prefixes:
+  PATO: http://purl.obolibrary.org/obo/PATO_
+  # linkml_common: https://w3id.org/linkml-common/
+  NCIT: http://purl.obolibrary.org/obo/NCIT_
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  person_status:
+    description: Vital status of a person (living or deceased)
+    range: PersonStatusEnum
+enums:
+  PersonStatusEnum:
+    description: Vital status of a person (living or deceased)
+    permissible_values:
+      ALIVE:
+        description: The person is living
+        meaning: PATO:0001421
+        title: Alive
+      DEAD:
+        description: The person is deceased
+        meaning: PATO:0001422
+        title: Dead
+      UNKNOWN:
+        description: The vital status is not known
+        meaning: NCIT:C17998
+        title: Unknown

valuesets/schema/spatial/spatial_qualifiers.yaml

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+name: spatial_qualifiers
+title: Spatial Qualifier Value Sets
+description: 'Value sets for spatial qualifiers, directions, and anatomical positions,
+
+  including both simple directional terms and biological spatial terminology'
+id: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers
+imports:
+- linkml:types
+prefixes:
+  valuesets: https://w3id.org/valuesets/
+  BSPO: http://purl.obolibrary.org/obo/BSPO_
+  PATO: http://purl.obolibrary.org/obo/PATO_
+  UBERON: http://purl.obolibrary.org/obo/UBERON_
+default_prefix: valuesets
+slots:
+  simple_spatial_direction:
+    description: Basic spatial directional terms for general use
+    range: SimpleSpatialDirection
+  anatomical_side:
+    description: Anatomical sides as defined in the Biological Spatial Ontology (BSPO)
+    range: AnatomicalSide
+  anatomical_region:
+    description: Anatomical regions based on spatial position
+    range: AnatomicalRegion
+  anatomical_axis:
+    description: Anatomical axes defining spatial organization
+    range: AnatomicalAxis
+  anatomical_plane:
+    description: Standard anatomical planes for sectioning
+    range: AnatomicalPlane
+  spatial_relationship:
+    description: Spatial relationships between anatomical structures
+    range: SpatialRelationship
+  cell_polarity:
+    description: Spatial polarity in cells and tissues
+    range: CellPolarity
+enums:
+  SimpleSpatialDirection:
+    description: Basic spatial directional terms for general use
+    permissible_values:
+      LEFT:
+        description: To the left side
+      RIGHT:
+        description: To the right side
+      FORWARD:
+        description: In the forward direction
+        annotations:
+          aliases: ahead, front
+      BACKWARD:
+        description: In the backward direction
+        annotations:
+          aliases: back, behind, rear
+      UP:
+        description: In the upward direction
+        annotations:
+          aliases: above, upward
+      DOWN:
+        description: In the downward direction
+        annotations:
+          aliases: below, downward
+      INWARD:
+        description: Toward the center or interior
+        annotations:
+          aliases: medial, toward center
+      OUTWARD:
+        description: Away from the center or exterior
+        annotations:
+          aliases: peripheral, away from center
+      TOP:
+        description: At or toward the top
+        annotations:
+          aliases: upper, uppermost
+      BOTTOM:
+        description: At or toward the bottom
+        annotations:
+          aliases: lower, lowermost
+      MIDDLE:
+        description: At or toward the middle
+        annotations:
+          aliases: center, central
+  AnatomicalSide:
+    description: 'Anatomical sides as defined in the Biological Spatial Ontology (BSPO).
+
+      An anatomical region bounded by a plane perpendicular to an axis through the middle.'
+    permissible_values:
+      LEFT:
+        title: Left side of a bilaterally symmetric organism
+        aliases:
+        - left side
+        meaning: BSPO:0000000
+      RIGHT:
+        title: Right side of a bilaterally symmetric organism
+        aliases:
+        - right side
+        meaning: BSPO:0000007
+      ANTERIOR:
+        title: Front/ventral side in most animals, toward the head
+        aliases:
+        - anterior side
+        meaning: BSPO:0000055
+        annotations:
+          aliases: front, rostral, cranial (in head region)
+      POSTERIOR:
+        title: Back/dorsal side in most animals, toward the tail
+        aliases:
+        - posterior side
+        meaning: BSPO:0000056
+        annotations:
+          aliases: back, caudal
+      DORSAL:
+        title: Back side of organism (top in humans when standing)
+        aliases:
+        - dorsal side
+        meaning: BSPO:0000063
+        annotations:
+          aliases: back (in vertebrates), upper (in humans)
+      VENTRAL:
+        title: Belly side of organism (front in humans when standing)
+        aliases:
+        - ventral side
+        meaning: BSPO:0000068
+        annotations:
+          aliases: belly, front (in vertebrates), lower (in humans)
+      LATERAL:
+        title: Away from the midline
+        aliases:
+        - lateral side
+        meaning: BSPO:0000066
+        annotations:
+          aliases: side, outer
+      MEDIAL:
+        title: Toward the midline
+        aliases:
+        - medial side
+        meaning: BSPO:0000067
+        annotations:
+          aliases: inner, middle
+      PROXIMAL:
+        title: Closer to the point of attachment or origin
+        aliases:
+        - proximal side
+        meaning: BSPO:0000061
+        annotations:
+          context: commonly used for limbs
+      DISTAL:
+        title: Further from the point of attachment or origin
+        aliases:
+        - distal side
+        meaning: BSPO:0000062
+        annotations:
+          context: commonly used for limbs
+      APICAL:
+        title: At or toward the apex or tip
+        aliases:
+        - apical side
+        meaning: BSPO:0000057
+        annotations:
+          context: cells, organs, organisms
+      BASAL:
+        title: At or toward the base
+        aliases:
+        - basal side
+        meaning: BSPO:0000058
+        annotations:
+          context: cells, organs, organisms
+      SUPERFICIAL:
+        title: Near the surface
+        aliases:
+        - superficial side
+        meaning: BSPO:0000004
+        annotations:
+          aliases: external, outer
+      DEEP:
+        title: Away from the surface
+        aliases:
+        - deep side
+        meaning: BSPO:0000003
+        annotations:
+          aliases: internal, inner
+      SUPERIOR:
+        title: Above or upper (in standard anatomical position)
+        aliases:
+        - superior side
+        meaning: BSPO:0000022
+        annotations:
+          aliases: cranial (toward head), upper
+      INFERIOR:
+        title: Below or lower (in standard anatomical position)
+        aliases:
+        - inferior side
+        meaning: BSPO:0000025
+        annotations:
+          aliases: caudal (toward tail), lower
+      IPSILATERAL:
+        title: On the same side
+        aliases:
+        - ipsilateral side
+        meaning: BSPO:0000065
+        annotations:
+          context: relative to a reference point
+      CONTRALATERAL:
+        title: On the opposite side
+        aliases:
+        - contralateral side
+        meaning: BSPO:0000060
+        annotations:
+          context: relative to a reference point
+      CENTRAL:
+        title: At or near the center
+        aliases:
+        - central side
+        meaning: BSPO:0000059
+        annotations:
+          aliases: middle
+  AnatomicalRegion:
+    description: Anatomical regions based on spatial position
+    permissible_values:
+      ANTERIOR_REGION:
+        title: Region in the anterior portion
+        aliases:
+        - anterior region
+        meaning: BSPO:0000071
+      POSTERIOR_REGION:
+        title: Region in the posterior portion
+        aliases:
+        - posterior region
+        meaning: BSPO:0000072
+      DORSAL_REGION:
+        title: Region in the dorsal portion
+        aliases:
+        - dorsal region
+        meaning: BSPO:0000079
+      VENTRAL_REGION:
+        title: Region in the ventral portion
+        aliases:
+        - ventral region
+        meaning: BSPO:0000084
+      LATERAL_REGION:
+        title: Region in the lateral portion
+        aliases:
+        - lateral region
+        meaning: BSPO:0000082
+      MEDIAL_REGION:
+        title: Region in the medial portion
+        aliases:
+        - medial region
+        meaning: BSPO:0000083
+      PROXIMAL_REGION:
+        title: Region in the proximal portion
+        aliases:
+        - proximal region
+        meaning: BSPO:0000077
+      DISTAL_REGION:
+        title: Region in the distal portion
+        aliases:
+        - distal region
+        meaning: BSPO:0000078
+      APICAL_REGION:
+        title: Region in the apical portion
+        aliases:
+        - apical region
+        meaning: BSPO:0000073
+      BASAL_REGION:
+        title: Region in the basal portion
+        aliases:
+        - basal region
+        meaning: BSPO:0000074
+      CENTRAL_REGION:
+        title: Region in the central portion
+        aliases:
+        - central region
+        meaning: BSPO:0000075
+      PERIPHERAL_REGION:
+        title: Region in the peripheral portion
+        aliases:
+        - peripheral region
+        meaning: BSPO:0000127
+  AnatomicalAxis:
+    description: Anatomical axes defining spatial organization
+    permissible_values:
+      ANTERIOR_POSTERIOR:
+        title: Anterior-posterior axis (head-tail axis)
+        aliases:
+        - anterior-posterior axis
+        meaning: BSPO:0000013
+        annotations:
+          aliases: AP axis, rostrocaudal axis
+      DORSAL_VENTRAL:
+        title: Dorsal-ventral axis (back-belly axis)
+        aliases:
+        - dorsal-ventral axis
+        meaning: BSPO:0000016
+        annotations:
+          aliases: DV axis
+      LEFT_RIGHT:
+        title: Left-right axis (lateral axis)
+        aliases:
+        - left-right axis
+        meaning: BSPO:0000017
+        annotations:
+          aliases: LR axis, mediolateral axis
+      PROXIMAL_DISTAL:
+        title: Proximal-distal axis
+        aliases:
+        - transverse plane
+        meaning: BSPO:0000018
+        annotations:
+          context: commonly used for appendages
+      APICAL_BASAL:
+        title: Apical-basal axis
+        aliases:
+        - apical-basal gradient
+        meaning: BSPO:0000023
+        annotations:
+          context: epithelial cells, plant structures
+  AnatomicalPlane:
+    description: Standard anatomical planes for sectioning
+    permissible_values:
+      SAGITTAL:
+        title: Vertical plane dividing body into left and right
+        aliases:
+        - sagittal plane
+        meaning: BSPO:0000417
+        annotations:
+          orientation: parallel to the median plane
+      MIDSAGITTAL:
+        title: Sagittal plane through the midline
+        aliases:
+        - midsagittal plane
+        meaning: BSPO:0000009
+        annotations:
+          aliases: median plane
+          note: divides body into equal left and right halves
+      PARASAGITTAL:
+        title: Sagittal plane parallel to midline
+        aliases:
+        - parasagittal plane
+        meaning: BSPO:0000008
+        annotations:
+          note: any sagittal plane not at midline
+      CORONAL:
+        title: Vertical plane dividing body into anterior and posterior
+        aliases:
+        - horizontal plane
+        meaning: BSPO:0000019
+        annotations:
+          aliases: frontal plane
+          orientation: perpendicular to sagittal plane
+      TRANSVERSE:
+        title: Horizontal plane dividing body into superior and inferior
+        aliases:
+        - transverse plane
+        meaning: BSPO:0000018
+        annotations:
+          aliases: horizontal plane, axial plane
+          orientation: perpendicular to longitudinal axis
+      OBLIQUE:
+        description: Any plane not parallel to sagittal, coronal, or transverse planes
+        annotations:
+          note: angled section
+  SpatialRelationship:
+    description: Spatial relationships between anatomical structures
+    permissible_values:
+      ADJACENT_TO:
+        title: Next to or adjoining
+        aliases:
+        - adjacent to
+        meaning: RO:0002220
+      ANTERIOR_TO:
+        title: In front of
+        aliases:
+        - anterior to
+        meaning: BSPO:0000096
+      POSTERIOR_TO:
+        title: Behind
+        aliases:
+        - posterior to
+        meaning: BSPO:0000099
+      DORSAL_TO:
+        title: Above/on the back side of
+        aliases:
+        - dorsal to
+        meaning: BSPO:0000098
+      VENTRAL_TO:
+        title: Below/on the belly side of
+        aliases:
+        - ventral to
+        meaning: BSPO:0000102
+      LATERAL_TO:
+        title: To the side of
+        aliases:
+        - lateral to
+        meaning: BSPO:0000114
+      MEDIAL_TO:
+        title: Toward the midline from
+        aliases:
+        - X medial to y if x is closer to the midsagittal plane than y.
+        meaning: BSPO:0000115
+      PROXIMAL_TO:
+        title: Closer to the origin than
+        aliases:
+        - proximal to
+        meaning: BSPO:0000100
+      DISTAL_TO:
+        title: Further from the origin than
+        aliases:
+        - distal to
+        meaning: BSPO:0000097
+      SUPERFICIAL_TO:
+        title: Closer to the surface than
+        aliases:
+        - superficial to
+        meaning: BSPO:0000108
+      DEEP_TO:
+        title: Further from the surface than
+        aliases:
+        - deep to
+        meaning: BSPO:0000107
+      SURROUNDS:
+        title: Encircles or encompasses
+        aliases:
+        - surrounds
+        meaning: RO:0002221
+      WITHIN:
+        description: Inside or contained by
+        annotations:
+          inverse_of: contains
+      BETWEEN:
+        description: In the space separating two structures
+        annotations:
+          note: requires two reference points
+  CellPolarity:
+    description: Spatial polarity in cells and tissues
+    permissible_values:
+      APICAL:
+        description: The free surface of an epithelial cell
+        annotations:
+          location: typically faces lumen or external environment
+      BASAL:
+        description: The attached surface of an epithelial cell
+        annotations:
+          location: typically attached to basement membrane
+      LATERAL:
+        description: The sides of an epithelial cell
+        annotations:
+          location: faces neighboring cells
+      APICAL_LATERAL:
+        description: Junction between apical and lateral surfaces
+      BASAL_LATERAL:
+        description: Junction between basal and lateral surfaces
+      LEADING_EDGE:
+        description: Front of a migrating cell
+        annotations:
+          context: cell migration
+      TRAILING_EDGE:
+        description: Rear of a migrating cell
+        annotations:
+          context: cell migration
+      PROXIMAL_POLE:
+        description: Pole closer to the cell body
+        annotations:
+          context: neurons, polarized cells
+      DISTAL_POLE:
+        description: Pole further from the cell body
+        annotations:
+          context: neurons, polarized cells

valuesets/schema/statistics/prediction_outcomes.yaml

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+name: prediction_outcomes
+id: https://w3id.org/linkml/valuesets/statistics/prediction_outcomes
+prefixes:
+  # linkml_common: https://w3id.org/linkml-common/
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  outcome_type:
+    description: Types of prediction outcomes for classification tasks
+    range: OutcomeTypeEnum
+enums:
+  OutcomeTypeEnum:
+    description: Types of prediction outcomes for classification tasks
+    permissible_values:
+      TP:
+        description: True Positive
+        title: True Positive
+      FP:
+        description: False Positive
+        title: False Positive
+      TN:
+        description: True Negative
+        title: True Negative
+      FN:
+        description: False Negative
+        title: False Negative

valuesets/schema/statistics.yaml

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+name: valuesets-statistics
+title: valuesets-statistics
+description: 'Common Data Model Elements: Human and statistics activities'
+id: https://w3id.org/valuesets/statistics
+prefixes:
+  # linkml_common: https://w3id.org/valuesets/
+  linkml: https://w3id.org/linkml/
+  biolink: https://w3id.org/biolink/
+  schema: http://schema.org/
+  PATO: http://purl.obolibrary.org/obo/PATO_
+  fhir: http://hl7.org/fhir/
+  prov: http://www.w3.org/ns/prov#
+  dcterms: http://purl.org/dc/terms/
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  prediction_outcome:
+    description: The prediction outcome classification
+    range: PredictionOutcomeType
+enums:
+  PredictionOutcomeType:
+    permissible_values:
+      TP:
+        description: True Positive
+      FP:
+        description: False Positive
+      TN:
+        description: True Negative
+      FN:
+        description: False Negative
+license: MIT
+see_also:
+- https://linkml.github.io/valuesets
+default_range: string