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Replace SizeEnum with RelativeChangeEnum and IntensityEnum
SizeEnum (increased/decreased/normal size) was really just the general PATO deviation-from-normal pattern applied to size. Replace with: - RelativeChangeEnum: general direction of change (normal, abnormal, increased, decreased, increased/decreased magnitude) from PATO's qualitative > deviation hierarchy (PATO:0000069) - IntensityEnum: severity scale (borderline, mild, moderate, severe, profound, remittent) from PATO intensity (PATO:0000049) These crosscut all PATO quality attributes and are more broadly useful than size-specific terms. https://claude.ai/code/session_01MiTizpCfAcDRMFmSzpSMdi
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src/valuesets/schema/bio/pato.yaml

Lines changed: 84 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -21,9 +21,12 @@ slots:
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pato_shape:
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description: Shape quality of an entity
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range: ShapeEnum
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pato_size:
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description: Relative size quality of an entity
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range: SizeEnum
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pato_relative_change:
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description: Direction of change of a quality relative to normal or baseline
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range: RelativeChangeEnum
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pato_intensity:
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description: Intensity or severity of a quality
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range: IntensityEnum
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pato_texture:
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description: Surface texture quality of an entity
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range: TextureEnum
@@ -252,36 +255,95 @@ enums:
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- coiled
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- helical
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SizeEnum:
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title: Size
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RelativeChangeEnum:
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title: Relative Change
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description: >-
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A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
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Derived from PATO size (PATO:0000117) child values.
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Direction of change of any quality relative to normal or baseline.
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This is PATO's general-purpose deviation-from-normal axis (PATO:0000069)
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that crosscuts all specific quality attributes (size, rate, amount, etc.).
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status: DRAFT
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contributors:
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- orcid:0000-0002-6601-2165
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- https://github.com/anthropics/claude-code
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instantiates:
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- valuesets_meta:ValueSetEnumDefinition
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permissible_values:
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NORMAL_SIZE:
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description: A size quality which is relatively normal or average
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meaning: PATO:0045050
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title: normal size
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INCREASED_SIZE:
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description: A size quality which is relatively high
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meaning: PATO:0000586
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title: increased size
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NORMAL:
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description: Exhibiting no deviation from normal or average
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meaning: PATO:0000461
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title: normal
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ABNORMAL:
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description: Deviating from normal or average
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meaning: PATO:0000460
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title: abnormal
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INCREASED:
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description: A value that is increased compared to normal or average
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meaning: PATO:0002300
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title: increased quality
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aliases:
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- enlarged
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- large
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DECREASED_SIZE:
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description: A size quality which is relatively low
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meaning: PATO:0000587
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title: decreased size
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- elevated
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- high
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DECREASED:
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description: A value that is decreased compared to normal or average
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meaning: PATO:0002301
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title: decreased quality
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aliases:
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- reduced
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- small
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- low
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INCREASED_MAGNITUDE:
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description: An increased magnitude of a quality
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meaning: PATO:0002017
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title: increased magnitude
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DECREASED_MAGNITUDE:
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description: A decreased magnitude of a quality
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meaning: PATO:0002018
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title: decreased magnitude
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IntensityEnum:
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title: Intensity
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description: >-
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A quality inhering in a bearer by virtue of the bearer's possessing or displaying
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a distinctive feature in type or degree or effect or force. Derived from PATO
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intensity (PATO:0000049) child values.
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status: DRAFT
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contributors:
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- orcid:0000-0002-6601-2165
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- https://github.com/anthropics/claude-code
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instantiates:
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- valuesets_meta:ValueSetEnumDefinition
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permissible_values:
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BORDERLINE:
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description: Borderline in effect or force compared to baseline or normal
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meaning: PATO:0002628
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title: borderline intensity
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MILD:
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description: Less than moderate in type or degree or effect or force
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meaning: PATO:0000394
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title: mild intensity
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MODERATE:
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description: Less than extreme in type or degree or effect or force
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meaning: PATO:0000395
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title: moderate intensity
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SEVERE:
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description: Extremely bad or unpleasant in type or degree or effect or force
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meaning: PATO:0000396
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title: severe intensity
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PROFOUND:
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description: Very severe in intensity
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meaning: PATO:0002629
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title: profound intensity
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INCREASED_INTENSITY:
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description: Intensity which is relatively high
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meaning: PATO:0001782
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title: increased intensity
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DECREASED_INTENSITY:
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description: Intensity which is relatively low
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meaning: PATO:0001783
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title: decreased intensity
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REMITTENT:
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description: Characterised by temporary abatement in severity
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meaning: PATO:0001841
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title: remittent intensity
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TextureEnum:
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title: Texture

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