text:
pattern_name: abnormallyIncreasedResistanceOfWholeOrganismToChemicalEntity.yaml
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedResistanceOfWholeOrganismToChemicalEntity.yaml
description: "A phenotype in which an organism shows increased resistance to a chemical, for example 4-aminosalicylic acid. NOTE: There is a more general pattern (abnormallyIncreasedResistanceOfWholeOrganismToEntity), so this one should probably be obsoleted."

contributors:
  - https://orcid.org/0000-0001-9076-6015
  - https://orcid.org/0000-0001-7487-610X

classes:
  increased resistance to: PATO:0001650
  abnormal: PATO:0000460
  cellular organism: CARO:0010004
  chemical entity: CHEBI:24431

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  towards: RO:0002503

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  chemical_entity: "'chemical entity'"

name:
  text: "increased resistance of organism to %s"
  vars:
    - chemical_entity

annotations:
- annotationProperty: exact_synonym
  text: "decreased sensitivity of organism to %s"
  vars:
    - chemical_entity

def:
  text: "Increased resistance of organism to %s."
  vars:
    - chemical_entity

equivalentTo:
  text: "'has_part' some ('increased resistance to' and ('inheres_in' some 'cellular organism') and ('towards' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - chemical_entity


text:
pattern_name: abnormalLevelOfChemicalEntityWithRoleInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalLevelOfChemicalEntityWithRoleInLocation.yaml
description: "An abnormal level of a chemical with a specific role, such as a metabolite or hormone like androgen, in a location, such as blood. For example, HP_0030347 'Abnormal circulating androgen level'."

contributors:
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0002-3528-5267

classes:
  amount: PATO:0000070
  abnormal: PATO:0000460
  chemical entity: CHEBI:24431
  role: CHEBI:50906
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  has_role: RO:0000087
  part_of: BFO:0000050

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  role: "role"
  location: "'independent continuant'"

name:
  text: "abnormal %s %s level"
  vars:
  - role
  - location

def:
  text: "An abnormal amount of %s in the %s."
  vars:
  - role
  - location

equivalentTo:
  text: "'has_part' some ('amount' and ('inheres_in' some ('chemical entity' and ('has_role' some %s) and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
  - role
  - location

repo_name: obophenotype/upheno

repo_language: Makefile

mime_type: text/plain


text:
pattern_name: abnormallyDilatedAnatomicalEntity

pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDilatedAnatomicalEntity.yaml

description: 'An abnormally dilated anatomical entity, for example, an abnormally dilated cardiac ventricle.'

# examples:
#  - http://purl.obolibrary.org/obo/HP_0010955
#  - http://purl.obolibrary.org/obo/XPO_0115624
#  - http://purl.obolibrary.org/obo/MP_0001123

contributors:
  - https://orcid.org/0000-0001-8314-2140
  - https://orcid.org/0000-0003-4606-0597
  - https://orcid.org/0000-0002-9900-7880

classes:
  abnormal: PATO:0000460
  anatomical_entity: UBERON:0001062
  dilated: PATO:0001571

relations:
  characteristic_of: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical_entity'"

name:
  text: "abnormally dilated %s"
  vars:
    - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "abnormal %s dilation"
    vars:
      - anatomical_entity

  - annotationProperty: exact_synonym
    text: "dilated %s"
    vars:
      - anatomical_entity

def:
  text: "Abnormal dilation of %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('dilated' and ('characteristic_of' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormalSizeOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalSizeOfAnatomicalEntity.yaml
description: "An abnormal size (the relative extent of something) of an anatomical entity, such as HP_0012504 'Abnormal size of pituitary gland'."

contributors:
- https://orcid.org/0000-0002-9900-7880
- https://orcid.org/0000-0001-9076-6015
- https://orcid.org/0000-0002-9611-1279
- https://orcid.org/0000-0002-3528-5267
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-1373-1705
- https://orcid.org/0000-0003-4148-4606
- https://orcid.org/0000-0002-7356-1779
- https://orcid.org/0000-0001-7941-2961
classes:
  size: PATO:0000117
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  entity: "'anatomical entity'"

name:
  text: "abnormal size of %s"
  vars:
  - entity

annotations:
- annotationProperty: exact_synonym
  text: "abnormal size of the %s"
  vars:
  - entity

def:
  text: "A deviation from the normal size of the %s."
  vars:
  - entity

equivalentTo:
  text: "'has_part' some ('size' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
  - entity


text:
---
pattern_name: ivoryAnatomicalEntity

pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/ivoryAnatomicalEntity.yaml

description: 'The term "ivory" in the context of this phenotype pattern refers to the increased density of an anatomical entity (e.g. epiphysis) observable by radiography (X-rays).'

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0010583  # Ivory epiphyses
#    - http://purl.obolibrary.org/obo/HP_0009191  # Ivory epiphyses of the metacarpals
#    - http://purl.obolibrary.org/obo/HP_0010234  # Ivory epiphyses of the phalanges of the hand

contributors:
  - https://orcid.org/0000-0001-8314-2140  # Ray Stefancsik
  - https://orcid.org/0000-0002-7356-1779  # Nicolas Matentzoglu
  - https://orcid.org/0000-0002-7073-9172  # David Osumi-Sutherland
  - https://orcid.org/0000-0003-4606-0597  # Susan Bello
  - https://orcid.org/0000-0002-6490-7723  # Anna V. Anagnostopoulos
  - https://orcid.org/0000-0001-7941-2961  # Leigh Carmody

classes:
  ivory: PATO:0002149
  abnormal: PATO:0000460
  anatomical_entity: UBERON:0001062

relations:
  characteristic_of: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical_entity'"

name:
  text: "ivory %s"
  vars:
    - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "abnormal radiographic density of %s"
    vars:
      - anatomical_entity

def:
  text: "An abnormal increase in the density of %s resulting in increased degree of radiopacity (in X-rays)."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some (
            'ivory' and
            ('characteristic_of' some %s) and
            ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormalRateOfContinuousBiologicalProcess
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalRateOfContinuousBiologicalProcess.yaml
description: "Abnormal rate of a continuous biological process, e.g. rate of an enzyme reaction or growth rate. Does not include changes in rates of occurrence/frequency. Different to patterns using PATO:0002242 'velocity', which inheres in a physical object (continuant), rather than a process (occurrent)."

# examples:
#  - http://purl.obolibrary.org/obo/MP_0008961 # abnormal basal metabolism
#  - http://purl.obolibrary.org/obo/ZP_0017453 # blood circulation rate, abnormal

contributors:
  - https://orcid.org/0000-0002-1373-1705
  - https://orcid.org/0000-0003-4606-0597
  - https://orcid.org/0000-0002-9900-7880
  - https://orcid.org/0000-0001-8314-2140

classes:
  rate_of_continuous_process: PATO:0050001
  abnormal: PATO:0000460
  biological_process: GO:0008150

relations:
  characteristic_of: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  biological_process: "'biological_process'"

name:
  text: "abnormal continuous rate of %s"
  vars:
  - biological_process

def:
  text: "Abnormal continuous rate of %s, i.e. %s has a different amount of output per unit time while it is occurring."
  vars:
  - biological_process
  - biological_process

annotations:
- annotationProperty: exact_synonym
  text: "changed speed of %s"
  vars:
  - biological_process
- annotationProperty: exact_synonym
  text: "abnormal speed of %s"
  vars:
  - biological_process
- annotationProperty: exact_synonym
  text: "changed continuous rate of %s"
  vars:
  - biological_process
- annotationProperty: exact_synonym
  text: "abnormal %s velocity"
  vars:
  - biological_process

equivalentTo:
  text: "'has_part' some ('rate_of_continuous_process' and ('characteristic_of' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
  - biological_process


text:
---
pattern_name: deviationTowardsLateralSideOfAnatomicalEntity

pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/deviationTowardsLateralSideOfAnatomicalEntity.yaml

description: 'Use this pattern for phenotypes involving changed
  direction of position towards the side of an anatomical entity that is
  abnormal in space or time (e.g. permanent).'

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0001822  # Hallux valgus
#    - http://purl.obolibrary.org/obo/HP_0003049  # Ulnar deviation of the wrist
#    - http://purl.obolibrary.org/obo/HP_0100500  # Fibular deviation of toes

contributors:
  - https://orcid.org/0000-0001-8314-2140  # Ray Stefancsik
  - https://orcid.org/0000-0003-4606-0597  # Susan Bello
  - https://orcid.org/0000-0002-9900-7880  # Yvonne M. Bradford
  - https://orcid.org/0000-0002-6490-7723  # Anna V. Anagnostopoulos

classes:
  deviation_towards_the_lateral_side: PATO:0002176
  abnormal: PATO:0000460
  anatomical_entity: UBERON:0001062

relations:
  characteristic_of: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical_entity'"

name:
  text: "lateral deviation of %s"
  vars:
    - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "%s lateral deviation"
    vars:
      - anatomical_entity

def:
  text: "A changed direction of position or shift towards the side of %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some (
    'deviation_towards_the_lateral_side' and
    ('characteristic_of' some %s) and
    ('has_modifier' some 'abnormal')
    )"
  vars:
    - anatomical_entity
...


text:
pattern_name: calcifiedAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/calcifiedAnatomicalEntity.yaml
description: "A hardening of an anatomical entity, caused by deposition of or conversion into calcium carbonate or some other insoluble calcium compounds. Example: HP_0011415 'Calcified placenta."

contributors:
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432

classes:
  calcified: PATO:0001447
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "%s calcification"
  vars:
   - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "calcified %s"
    vars:
     - anatomical_entity

def:
  text: "Calcification of the %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('calcified' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormallyDecreasedLevelOfChemicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedLevelOfChemicalEntityInLocation.yaml
description: ""

contributors:
  - https://orcid.org/0000-0003-4606-0597
  - https://orcid.org/0000-0002-9900-7880
  - https://orcid.org/0000-0001-9076-6015
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0001-7941-2961
  - https://orcid.org/0000-0003-4148-4606

classes:
  decreased amount: PATO:0001997
  abnormal: PATO:0000460
  chemical entity: CHEBI:24431
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  part_of: BFO:0000050

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  chemical_entity: "'chemical entity'"
  location: "'independent continuant'"

name:
  text: "decreased level of %s in %s"
  vars:
   - chemical_entity
   - location

def:
  text: "A decrease in the level of %s in %s."
  vars:
    - chemical_entity
    - location

equivalentTo:
  text: "'has_part' some ('decreased amount' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
    - chemical_entity
    - location


text:
pattern_name: abnormallyIncreasedHeightOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedHeightOfAnatomicalEntityInLocation.yaml
description: "An abnormally tall anatomical structure in a location.'"

contributors:
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0001-5208-3432

classes:
  increased height: PATO:0000570
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  part_of: BFO:0000050

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"
  location: "'independent continuant'"

name:
  text: "increased height of %s in %s"
  vars:
   - anatomical_entity
   - location

annotations:
  - annotationProperty: exact_synonym
    text: "higher %s in %s"
    vars:
     - anatomical_entity
     - location

def:
  text: "An increase in the height of the %s in the %s."
  vars:
    - anatomical_entity
    - location

equivalentTo:
  text: "'has_part' some ('increased height' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity
    - location


text:
pattern_name: abnormallyIncreasedLevelOfChemicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedLevelOfChemicalEntityInLocation.yaml
description: "An abnormal increase of a chemical entity in a lcoation. Example 'Increased CSF lactate', i.e. increased lactate in cerebrospinal fluid (HP_0002490)."

classes:
  increased amount: PATO:0000470
  abnormal: PATO:0000460
  chemical entity: CHEBI:24431
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  part_of: BFO:0000050

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  chemical_entity: "'chemical entity'"
  location: "'independent continuant'"
name:
  text: "increased level of %s in %s"
  vars:
  - chemical_entity
  - location

def:
  text: "An increase in the level of %s in %s."
  vars:
  - chemical_entity
  - location

annotations:
- annotationProperty: exact_synonym
  text: "increased level of %s in %s"
  vars:
  - chemical_entity
  - location

equivalentTo:
  text: "'has_part' some ('increased amount' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
  - chemical_entity
  - location
contributors:
- https://orcid.org/0000-0002-3528-5267


text:
pattern_name: abnormallyDecreasedNumberOfCellularComponent
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedNumberOfCellularComponent.yaml
description: "A decreased number of a cellular component, such as HP:0040013 'Decreased mitochondrial number'."

contributors:
  - https://orcid.org/0000-0001-5208-3432

classes:
  decreased amount: PATO:0001997
  abnormal: PATO:0000460
  cellular component: GO:0005575

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  cellular_component: "'cellular component'"

name:
  text: "abnormally decreased number of %s"
  vars:
   - cellular_component

annotations:
  - annotationProperty: exact_synonym
    text: "Reduced number of %s"
    vars:
     - cellular_component

def:
  text: "The presence of a reduced number of %s."
  vars:
    - cellular_component

equivalentTo:
  text: "'has_part' some ('decreased amount' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - cellular_component


text:
pattern_name: abnormallyIncreasedLevelOfChemicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedLevelOfChemicalEntity.yaml
description: ""

contributors:
  - https://orcid.org/0000-0003-4606-0597
  - https://orcid.org/0000-0002-9900-7880
  - https://orcid.org/0000-0001-9076-6015
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0001-7941-2961
  - https://orcid.org/0000-0003-4148-4606

classes:
  increased amount: PATO:0000470
  abnormal: PATO:0000460
  chemical entity: CHEBI:24431

relations:
  inheres in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  chemical_entity: "'chemical entity'"

name:
  text: "increased level of %s"
  vars:
   - chemical_entity

def:
  text: "An increased amount in the level of %s."
  vars:
    - chemical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "increased %s level"
    vars:
     - chemical_entity

equivalentTo:
  text: "'has_part' some ('increased amount' and ('inheres in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - chemical_entity


text:
pattern_name: abnormalDegenerationOfCellularComponentInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalDegenerationOfCellularComponentInLocation.yaml
description: "Deterioration or loss of function of a cellular component that was once present in a location, such as HP_0007305 CNS demyelination."

classes:
  degenerate: PATO:0000639
  abnormal: PATO:0000460
  cellular component: GO:0005575
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  part_of: BFO:0000050

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  cellular_component: "'cellular component'"
  location: "'independent continuant'"

name:
  text: "%s degeneration in %s"
  vars:
  - cellular_component
  - location

annotations:
- annotationProperty: exact_synonym
  text: "degeneration of the %s in %s"
  vars:
  - cellular_component
  - location

def:
  text: "Partial or complete degeneration of %s tissue in the %s that was once present."
  vars:
  - cellular_component
  - location

equivalentTo:
  text: "'has_part' some ('degenerate' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
  - cellular_component
  - location
contributors:
- https://orcid.org/0000-0002-3528-5267


text:
pattern_name: abnormalDevelopmentOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalDevelopmentOfAnatomicalEntity.yaml
description: "A phenotype in which an organism exhibits an abnormal development of some anatomical entity. For example, abnormal development of the heart."

contributors:
- https://orcid.org/0000-0001-9076-6015

classes:
  process quality: PATO:0001236
  abnormal: PATO:0000460
  developmental process: GO:0032502
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  results_in_developmental_progression_of: RO:0002295

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "abnormal development of %s"
  vars:
  - anatomical_entity

def:
  text: "An abnormal development of the %s."
  vars:
  - anatomical_entity

equivalentTo:
  text: "'has_part' some ('process quality' and ('inheres_in' some ('developmental process' and ('results_in_developmental_progression_of' some %s))) and  ('has_modifier' some 'abnormal'))"
  vars:
  - anatomical_entity


text:
---
pattern_name: abnormallyIncreasedMassDensityOfAnatomicalEntityInLocation

pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedMassDensityOfAnatomicalEntityInLocation.yaml

description: 'Abnormally increased mass density (mass per unit volume) of an anatomical entity in a location. For example, it can be a bone element at a location, such as the "Increased density of long bone diaphyses". This pattern is not to be used for count per area (e.g. cell count) phenotypes.'

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0006440  # Increased density of long bone diaphyses

contributors:
  - https://orcid.org/0000-0001-8314-2140  # Ray Stefancsik
  - https://orcid.org/0000-0002-7073-9172  # David Osumi-Sutherland
  - https://orcid.org/0000-0002-7356-1779  # Nicolas Matentzoglu
  - https://orcid.org/0000-0002-9900-7880  # Yvonne M. Bradford
  - https://orcid.org/0000-0003-4606-0597  # Susan Bello
  - https://orcid.org/0000-0002-6490-7723  # Anna V. Anagnostopoulos

classes:
  increased_mass_density: PATO:0001788
  abnormal: PATO:0000460
  anatomical_entity: UBERON:0001062
  independent_continuant: BFO:0000004

relations:
  characteristic_of: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  part_of: BFO:0000050

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical_entity'"
  location: "'independent_continuant'"

name:
  text: "abnormally increased %s of %s mass density"
  vars:
    - anatomical_entity
    - location

annotations:
  - annotationProperty: exact_synonym
    text: "abnormally increased mass density of %s of %s"
    vars:
      - anatomical_entity
      - location

def:
  text: "Abnormally increased mass density (mass per unit volume) of %s of %s."
  vars:
    - anatomical_entity
    - location

equivalentTo:
  text: "'has_part' some (
            'increased_mass_density' and
            ('characteristic_of' some (
                %s and
                ('part_of' some %s)) and
            ('has_modifier' some 'abnormal')))"
  vars:
    - anatomical_entity
    - location


text:
pattern_name: abnormalRateOfBiologicalProcessInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalRateOfBiologicalProcessInLocation.yaml
description: "Changed rate of a biological process, i.e. changed number of events per unit time of a biological process, or changed output of a continuous biological process) in a location."

contributors:
  - https://orcid.org/0000-0001-9076-6015
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0002-6490-7723
  - https://orcid.org/0000-0002-7356-1779
classes:
  rate: PATO:0000161
  abnormal: PATO:0000460
  biological_process: GO:0008150
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  qualifier: RO:0002573
  has_part: BFO:0000051
  occurs_in: BFO:0000066

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  biological_process: "'biological_process'"
  location: "'independent continuant'"
name:
  text: "changed %s rate in %s"
  vars:
  - biological_process
  - location

def:
  text: "Changed rate of %s in %s."
  vars:
  - biological_process
  - location

equivalentTo:
  text: "'has_part' some ('rate' and ('inheres_in' some (%s and ('occurs_in' some %s))) and ('qualifier' some 'abnormal'))"
  vars:
  - biological_process
  - location


text:
pattern_name: abnormallyIncreasedLengthOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedLengthOfAnatomicalEntityInLocation.yaml
description: "Increased length/abnormally long in a particular anatomical entity. Example: HP_0012743 'Abdominal obesity'"

contributors:
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432

# Declaration of entities used in pattern: classes, relations, annotation props.
# This is used to relate labels to their term IDs. The labels are NOT related to
# the rdfs:label used in the ontology.
classes:
  increased length: PATO:0000573
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  part_of: BFO:0000050

annotationProperties:
  exact_synonym: oio:hasExactSynonym

# These are the variables used in string variable substitution.
# These vars are only ever classes, not relations.
vars:
  anatomical_entity: "'anatomical entity'"
  location: "'independent continuant'"

# Corresponds to rdfs:label
name:
  text: "increased %s length in %s"
  vars:
   - anatomical_entity
   - location

def:
  text: "An abnormal increase in length in %s in location %s."
  vars:
    - anatomical_entity
    - location

equivalentTo:
  text: "'has_part' some ('increased length' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity
    - location


text:
pattern_name: abnormallyPatchyPigmentationOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyPatchyPigmentationOfAnatomicalEntity.yaml
description: "Patchy pigmentation of an anatomical entity, such as patchy skin pigmentation."

contributors:
- https://orcid.org/0000-0002-3528-5267

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  patchy pigmentation: PATO:0065002

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "patchy pigmentation in the %s"
  vars:
  - anatomical_entity

annotations:
- annotationProperty: exact_synonym
  text: "irregular pigment in the %s"
  vars:
  - anatomical_entity

def:
  text: "%s with a degree of pigmentation quality that is diversified with patches, or irregularity."
  vars:
  - anatomical_entity

equivalentTo:
  text: "'has_part' some ('patchy pigmentation' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
  - anatomical_entity


text:
pattern_name: abnormallyDecreasedPositionOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedPositionOfAnatomicalEntity.yaml
description: "The postion or placement of an anatomical entity is lowered or decreased, such as MP_0000024 'lowered ear position' or HP_0000369 Low-set ears."

contributors:
  - https://orcid.org/0000-0001-5208-3432

classes:
  decreased position: PATO:0001476
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "Decreased %s position"
  vars:
   - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "Lowered %s position"
    vars:
     - anatomical_entity

def:
  text: "Lowered position or placement of %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('decreased position' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormalPositionOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalPositionOfAnatomicalEntity.yaml
description: "An abnormal placement or position of an anatomical entity, such as HP_0004307 'Abnormal anatomic location of the heart'."

contributors:
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0003-4148-4606

classes:
  position: PATO:0000140
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  entity: "'anatomical entity'"

name:
  text: "abnormal location of %s"
  vars:
   - entity

def:
  text: "An abnormal location of %s."
  vars:
    - entity

equivalentTo:
  text: "'has_part' some ('position' and ('inheres_in' some %s) and ('has_modifier' some abnormal))"
  vars:
    - entity


text:
pattern_name: abnormalMorphologyOfPartOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalMorphologyOfPartOfAnatomicalEntity.yaml
description: "An morphological abnormality in a part of an anatomical entity. Morphology encompasses shape and colour, but more specific patterns exist. Example: HP:0012718 Morphological abnormality of the gastrointestinal tract. Note that pattern is very powerful, because it captures all parts of an anatomical entity, down to the cells! If in doubt, consider using abnormalMorphologyOfAnatomicalEntity instead, which captures only the abnormal morphology of the referenced anatomical entity as a whole."

contributors:
  - https://orcid.org/0000-0001-5208-3432

classes:
  morphology: PATO:0000051
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in_part_of: RO:0002314
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "abnormal %s morphology"
  vars:
   - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "abnormal morphology of %s"
    vars:
     - anatomical_entity

def:
  text: "Any unspecified morphological anomaly of part of the %s, such as, for example, abnormal shape or colour."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('morphology' and ('inheres_in_part_of' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
---
pattern_name: perforateAnatomicalEntity

pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/perforateAnatomicalEntity.yaml

description: "Use this pattern for phenotypes when an anatomical entity has an
  abnormal hole or a series of holes. Consider the alternative 'PATO:0000609
  closure incomplete' pattern for anatomical entities where a hole is present
  normally at one developmental period but it remains open."

#  examples:
#    - http://purl.obolibrary.org/obo/ZP_0002341  # retina perforate, abnormal
#    - http://purl.obolibrary.org/obo/HP_0100583  # Corneal perforation
#    - http://purl.obolibrary.org/obo/MP_0030414  # tympanic membrane perforation

contributors:
  - https://orcid.org/0000-0001-8314-2140  # Ray Stefancsik
  - https://orcid.org/0000-0003-4606-0597  # Susan Bello
  - https://orcid.org/0000-0002-6490-7723  # Anna V. Anagnostopoulos
  - https://orcid.org/0000-0002-7356-1779  # Nicolas Matentzoglu

classes:
  perforate: PATO:0002112
  abnormal: PATO:0000460
  anatomical_entity: UBERON:0001062

relations:
  characteristic_of: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym
  related_synonym: oio:hasRelatedSynonym

vars:
  anatomical_entity: "'anatomical_entity'"

name:
  text: "%s perforation"
  vars:
    - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "perforated %s"
    vars:
      - anatomical_entity

def:
  text: "The presence of one or more abnormal holes in %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some (
    'perforate' and
    ('characteristic_of' some %s) and
    ('has_modifier' some 'abnormal')
    )"
  vars:
    - anatomical_entity
...


text:
pattern_name: abnormallyDecreasedLevelOfChemicalEntityWithRole
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedLevelOfChemicalEntityWithRole.yaml
description: "An abnormally decreased level of a chemical with a specific role, such as a metabolite or hormone like androgen, for example, 'decreased androgen level'."

contributors:
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0002-3528-5267

classes:
  decreased amount: PATO:0001997
  abnormal: PATO:0000460
  chemical entity: CHEBI:24431
  role: CHEBI:50906

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  has_role: RO:0000087

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  role: "role"

name:
  text: "decreased %s level"
  vars:
  - role

def:
  text: "An abnormally decreased level of %s."
  vars:
  - role

equivalentTo:
  text: "'has_part' some ('decreased amount' and ('inheres_in' some ('chemical entity' and ('has_role' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
  - role


text:
pattern_name: fracturedAnatomicalEntityByFractureType
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/fracturedAnatomicalEntityByFractureType.yaml
description: "This pattern is for generating fractured bone terms, such as Linear fracture in tibia or Spiral fracture in humerus."

contributors:
  - https://orcid.org/0000-0001-5208-3432

classes:
  fractured: PATO:0040034
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  fractured: "fractured"
  anatomical_entity: "'anatomical entity'"

name:
  text: "%s %s"
  vars:
   - fractured
   - anatomical_entity

def:
  text: "A %s that is %s."
  vars:
    - anatomical_entity
    - fractured

equivalentTo:
  text: "'has_part' some (%s and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - fractured
    - anatomical_entity


text:
pattern_name: brokenAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/brokenAnatomicalEntity.yaml
description: "A broken anatomical entity. Consider fracturedAnatomicalEntity pattern instead."

contributors:
  - https://orcid.org/0000-0001-5208-3432

classes:
  broken: PATO:0001444
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "broken %s"
  vars:
   - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "bone %s"
    vars:
     - anatomical_entity

def:
  text: "A partial or complete breakage of the %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('broken' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
---
pattern_name: collapsedAnatomicalEntity

pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/collapsedAnatomicalEntity.yaml

description: 'Use this phenotype pattern when an anatomical entity has
  collapsed and loses its normal structure by becoming flat or caved in.'

#  examples:
#    - http://purl.obolibrary.org/obo/MP_0006024  # collapsed Reissner membrane
#    - http://purl.obolibrary.org/obo/MP_0012681  # collapsed brain ventricles
#    - http://purl.obolibrary.org/obo/ZP_0000118  # forebrain ventricle collapsed, abnormal
#    - http://purl.obolibrary.org/obo/ZP_0131104  # atrioventricular canal collapsed, abnormal

contributors:
  - https://orcid.org/0000-0001-8314-2140  # Ray Stefancsik
  - https://orcid.org/0000-0002-9900-7880  # Yvonne M. Bradford [ybradford]
  - https://orcid.org/0000-0002-6490-7723  # Anna V. Anagnostopoulos

classes:
  collapsed: PATO:0001478
  abnormal: PATO:0000460
  anatomical_entity: UBERON:0001062

relations:
  characteristic_of: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical_entity'"

name:
  text: "collapsed %s"
  vars:
    - anatomical_entity

def:
  text: "A structural failure that affects %s so that it becomes flat or caved
    in."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some (
    'collapsed' and
    ('characteristic_of' some %s) and
    ('has_modifier' some 'abnormal')
    )"
  vars:
    - anatomical_entity
...


text:
pattern_name: abnormalPigmentationOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalPigmentationOfAnatomicalEntity.yaml
description: "Any change in the amount of pigmentation in an anatomical Entity. i.e. Abnormal pigmentation of the epidermis"

contributors:
  - https://orcid.org/0000-0001-9076-6015
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  degree of pigmentation: PATO:0002247

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "abnormal degree of pigmentation of the %s"
  vars:
   - anatomical_entity

annotations:
  -
    annotationProperty: exact_synonym
    text: "abnormal pigmentation of the %s"
    vars:
     - anatomical_entity

def:
  text: "abnormal degree of pigmentation of the %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('degree of pigmentation' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormallyApoptoticAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyApoptoticAnatomicalEntityInLocation.yaml
description : "The presence of abnormal programmed cell death (apoptosis), consisting of blebbing of the nucleus and DNA fragmentation, in an anatomical entity in some location."

contributors:
- https://orcid.org/0000-0002-7356-1779
- https://orcid.org/0000-0002-9900-7880
- https://orcid.org/0000-0002-9611-1279

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  apoptotic: PATO:0000638
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  part_of: BFO:0000050

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"
  location: "'independent continuant'"

name:
  text: "abnormally apoptotic %s in %s"
  vars:
   - anatomical_entity
   - location

def:
  text: "An abnormally apoptotic %s in %s."
  vars:
    - anatomical_entity
    - location

annotations:
  - annotationProperty: exact_synonym
    text: "%s %s with apoptosis"
    vars:
     - location
     - anatomical_entity

equivalentTo:
  text: "'has_part' some ('apoptotic' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity
    - location


text:
pattern_name: abnormalCellularComponent
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/abnormalCellularComponent.yaml
description: "Any unspecified abnormality of a cellular component, such as an abnormal mitochondria."

contributors:
  - https://orcid.org/0000-0001-5208-3432

classes:
  quality: PATO:0000001
  abnormal: PATO:0000460
  cellular component: GO:0005575

relations:
  inheres_in_part_of: RO:0002314
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  cellular_component: "'cellular component'"

name:
  text: "abnormal %s"
  vars:
   - cellular_component

annotations:
  - annotationProperty: exact_synonym
    text: "abnormality of %s"
    vars:
     - cellular_component

def:
  text: "Abnormality of %s."
  vars:
    - cellular_component

equivalentTo:
  text: "'has_part' some ('quality' and ('inheres_in_part_of' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - cellular_component


text:
pattern_name: abnormalAbsenceOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfAnatomicalEntityInLocation.yaml
description: "Absence of an anatomical entity in a location, such as absent aortic valve in the heart."

contributors:
  - https://orcid.org/0000-0001-5208-3432

classes:
  absent: PATO:0000462
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  part_of: BFO:0000050

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"
  location: "'independent continuant'"

name:
  text: "absent %s in the %s"
  vars:
   - anatomical_entity
   - location

annotations:
  - annotationProperty: exact_synonym
    text: "Missing %s in the %s"
    vars:
     - anatomical_entity
     - location

def:
  text: "Absence of the %s in the %s."
  vars:
    - anatomical_entity
    - location

equivalentTo:
  text: "'has_part' some ('absent' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity
    - location


text:
pattern_name: abnormalRateOfBiologicalProcess
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalRateOfBiologicalProcess.yaml
description: "Changed rate of a biological process, i.e. changed number of events per unit time of a biological process, or changed output of a continuous biological process)."

contributors:
  - https://orcid.org/0000-0001-9076-6015
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0002-6490-7723
  - https://orcid.org/0000-0002-7356-1779
classes:
  rate: PATO:0000161
  abnormal: PATO:0000460
  biological_process: GO:0008150

relations:
  inheres_in: RO:0000052
  qualifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  biological_process: "'biological_process'"
name:
  text: "changed %s rate"
  vars:
  - biological_process

def:
  text: "Changed rate of %s."
  vars:
  - biological_process

equivalentTo:
  text: "'has_part' some ('rate' and ('inheres_in' some %s) and ('qualifier' some 'abnormal'))"
  vars:
  - biological_process


text:
pattern_name: abnormalConcentrationOfChemicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalConcentrationOfChemicalEntityInLocation.yaml
description: "An abnormal concentration of a chemical, like sodium, in a location, like the blood."

classes:
  concentration of: PATO:0000033
  abnormal: PATO:0000460
  chemical: CHEBI:24431
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  part_of: BFO:0000050

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  chemical: "chemical"
  location: "'independent continuant'"

name:
  text: "abnormal %s concentration in %s"
  vars:
  - chemical
  - location

def:
  text: "An abnormal concentration of %s in %s."
  vars:
  - chemical
  - location

equivalentTo:
  text: "'has_part' some ('concentration of' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
  - chemical
  - location

contributors:
- https://orcid.org/0000-0002-3528-5267


text:
---
pattern_name: abnormallyGreasyAnatomicalEntity

pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyGreasyAnatomicalEntity.yaml

description: 'Use this phenotype pattern when an anatomical entity has an
  abnormal coating which is oily and slippery.'

#  examples:
#    - http://purl.obolibrary.org/obo/MP_0001197  # oily skin
#    - http://purl.obolibrary.org/obo/MP_0003849  # greasy coat
#    - http://purl.obolibrary.org/obo/ZP_0016607  # liver greasy, abnormal

contributors:
  - https://orcid.org/0000-0001-8314-2140  # Ray Stefancsik
  - https://orcid.org/0000-0003-4606-0597  # Susan Bello
  - https://orcid.org/0000-0002-1373-1705  # Clare Pilgrim
  - https://orcid.org/0000-0002-6490-7723  # Anna V. Anagnostopoulos
  - https://orcid.org/0000-0002-7073-9172  # David Osumi-Sutherland
  - https://orcid.org/0000-0002-9900-7880  # Yvonne M. Bradford
  - https://orcid.org/0000-0003-2699-3066  # Meghan A. Balk

classes:
  greasy: PATO:0001606
  abnormal: PATO:0000460
  anatomical_entity: UBERON:0001062

relations:
  characteristic_of: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical_entity'"

name:
  text: "greasy %s"
  vars:
    - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "oily %s"
    vars:
      - anatomical_entity

def:
  text: "An abnormal coating of %s which is oily and slippery."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some (
    'greasy' and
    ('characteristic_of' some %s) and
    ('has_modifier' some 'abnormal')
    )"
  vars:
    - anatomical_entity
...


text:
pattern_name: abnormallyIncreasedOccurrenceOfBiologicalProcess
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedOccurrenceOfBiologicalProcess.yaml
description: "Occurrence of a biological process that is abnormally high."

contributors:
- https://orcid.org/0000-0002-7356-1779
- https://orcid.org/0000-0002-9900-7880
- https://orcid.org/0000-0002-9611-1279

classes:
  increased occurrence: PATO:0002051
  abnormal: PATO:0000460
  biological_process: GO:0008150

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  biological_process: "'biological_process'"

name:
  text: "increased occurrence of %s"
  vars:
  - biological_process

def:
  text: "An increased occurrence of %s."
  vars:
  - biological_process

equivalentTo:
  text: "'has_part' some ('increased occurrence' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
  - biological_process


text:
pattern_name: mislocalisedAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/mislocalisedAnatomicalEntity.yaml
description : "Abnormal anatomic location of an anatomicaly entity, such as HP_0012731 'Ectopic anterior pituitary gland'."

contributors:
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0001-9076-6015

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  mislocalised: PATO:0000628

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "abnormally localised %s"
  vars:
   - anatomical_entity

def:
  text: "An abnormally localised %s."
  vars:
    - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "abnormal position of %s"
    vars:
     - anatomical_entity

equivalentTo:
  text: "'has_part' some ('mislocalised' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormalFunctionalityOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalFunctionalityOfAnatomicalEntity.yaml
description: "Dysfunction of an entity, such as an anatomical entity, like an organ, for example HP_0030964 'Abnormal aortic physiology'"

contributors:
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0001-7941-2961

classes:
  functionality: PATO:0001509
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "abnormality of %s physiology"
  vars:
   - anatomical_entity

def:
  text: "Any functional anomaly of the %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('functionality' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormallyDecreasedFunctionalityOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedFunctionalityOfAnatomicalEntityInLocation.yaml
description: "An impaired function of an anatomical entity or part, in a specific anatomical location, such as Beta-cell dysfunction in the pancreas."

contributors:
- https://orcid.org/0000-0001-5208-3432
classes:
  decreased functionality: PATO:0001624
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  part_of: BFO:0000050

vars:
  anatomical_entity: "'anatomical entity'"
  entity: "'independent continuant'"

name:
  text: "%s dysfunction in %s"
  vars:
  - anatomical_entity
  - entity

def:
  text: "A functional abnormality of the %s in %s."
  vars:
  - anatomical_entity
  - entity

equivalentTo:
  text: "'has_part' some ('decreased functionality' and ('inheres_in' some (%s and ('part_of' some %s))) and  ('has_modifier' some 'abnormal'))"
  vars:
  - anatomical_entity
  - entity


text:
pattern_name: abnormalFunctionalityOfCellularComponent
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalFunctionalityOfCellularComponent.yaml
description: "Dysfunction of a cellular component, such as an organelle, for example HP:0003398 Abnormal synaptic transmission at the neuromuscular junction'"

contributors:
  - https://orcid.org/0000-0001-5208-3432

classes:
  functionality: PATO:0001509
  abnormal: PATO:0000460
  cellular component: GO:0005575

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  cellular_component: "'cellular component'"

name:
  text: "abnormality of %s function"
  vars:
   - cellular_component

def:
  text: "Any functional anomaly of the %s."
  vars:
    - cellular_component

equivalentTo:
  text: "'has_part' some ('functionality' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - cellular_component


text:
pattern_name: abnormalPersistenceOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalPersistenceOfAnatomicalEntity.yaml
description: "The unexpected persistent presence of an anatomical entity that is not expected to be there, that should have been removed, ejected, replaced, etc, but continues to be present. For example, HP_0006335	Persistence of primary teeth, where the teeth should have fallen out during the normal developmental process, but continue to persist."

contributors:
  - https://orcid.org/0000-0001-5208-3432

classes:
  persistence: PATO:0000082
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "abnormally persistent %s"
  vars:
   - anatomical_entity

def:
  text: "The abnormal persistence of %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('persistence' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormallyProtrudingAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyProtrudingAnatomicalEntityInLocation.yaml
description: ""

contributors:
  - https://orcid.org/0000-0001-9076-6015
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  protruding out of: PATO:0001646
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  part_of: BFO:0000050
  towards: RO:0002503

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"
  location: "'independent continuant'"

name:
  text: "abnormal protrusion of %s through %s"
  vars:
   - anatomical_entity
   - location

annotations:
  - annotationProperty: exact_synonym
    text: "protruding %s in %s"
    vars:
     - anatomical_entity
     - location

def:
  text: "hernial protrusion of the %s through an opening or defect in the %s."
  vars:
    - anatomical_entity
    - location

equivalentTo:
  text: "'has_part' some ('protruding out of' and ('inheres_in' some %s) and ('towards' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity
    - location


text:
pattern_name: abnormalSpatialPatternOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalSpatialPatternOfAnatomicalEntity.yaml
description: "Any unspecified abnormality of the spatial pattern (ie the repetition of the placement of its parts) of an anatomical entity, such as HP_0010720 Abnormal hair pattern."

contributors:
  - https://orcid.org/0000-0001-5208-3432

classes:
  spatial pattern: PATO:0000060
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "abnormal spatial pattern of %s"
  vars:
   - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "abnormality of %s spatial pattern"
    vars:
     - anatomical_entity

def:
  text: "Abnormal spatial pattern of %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('spatial pattern' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormalAbsenceOfMolecularFunction
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfMolecularFunction.yaml
description: "An abnormal absence of a molecular function i.e., absent or undetectable level of chromatin binding."

classes:
  absent: PATO:0000462
  abnormal: PATO:0000460
  molecular function: GO:0003674

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  molecular_function: "'molecular function'"
name:
  text: "absent %s"
  vars:
  - molecular_function

def:
  text: "Absent or undetectable level of %s."
  vars:
  - molecular_function

equivalentTo:
  text: "'has_part' some ('absent' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
  - molecular_function
contributors:
- https://orcid.org/0000-0002-3528-5267


text:
pattern_name: abnormalHasFewerPartsOfTypeAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalHasFewerPartsOfTypeAnatomicalEntity.yaml
description: "An anatomical entity has fewer instances of a part. For example, has the hand has fewer digits. Consider using decreased number of anatomical entity in location instead."

contributors:
  - https://orcid.org/0000-0002-3528-5267

classes:
  has fewer parts of type: PATO:0002001
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  towards: RO:0002503

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  whole_anatomical_entity: "'anatomical entity'"
  part_anatomical_entity: "'anatomical entity'"

name:
  text: "%s that has fewer parts of type %s"
  vars:
   - whole_anatomical_entity
   - part_anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "fewer %ss in %s"
    vars:
     - part_anatomical_entity
     - whole_anatomical_entity

def:
  text: "Any structural anomaly of %s that causes there to be fewer parts of type %s."
  vars:
    - whole_anatomical_entity
    - part_anatomical_entity

equivalentTo:
  text: "'has_part' some ('has fewer parts of type' and ('inheres_in' some %s) and ('towards' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - whole_anatomical_entity
    - part_anatomical_entity


text:
pattern_name: abnormalCoilingOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalCoilingOfAnatomicalEntity.yaml
description: "An anatomical entity that is abnormally coiled, or wound into a spiral or sequence of rings, like an abnormally coiled tail. This pattern captures both more coiled AND less coiled anatomical entities."

contributors:
- https://orcid.org/0000-0002-7356-1779

classes:
  coiled: PATO:0000404
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "abnormally coiled %s"
  vars:
  - anatomical_entity

annotations:
- annotationProperty: exact_synonym
  text: "abnormal coiling of %s"
  vars:
  - anatomical_entity

def:
  text: "Any abnormal coiling of the %s."
  vars:
  - anatomical_entity

equivalentTo:
  text: "'has_part' some ('coiled' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
  - anatomical_entity


text:
pattern_name: abnormallyIncompleteClosureOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/abnormallyIncompleteClosureOfAnatomicalEntity.yaml
description: ""

contributors:
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0001-5208-3432

classes:
  closure incomplete: PATO:0000609
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
 anatomical_entity: "'anatomical entity'"

name:
  text: "abnormal incomplete closing of the %s"
  vars:
   - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "abnormally incompletely closed %s"
    vars:
     - anatomical_entity

def:
  text: "Abnormally incompletely closed %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('closure incomplete' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormalPositionOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalPositionOfAnatomicalEntityInLocation.yaml
description: "An abnormally placed anatomical entity, in a position it is not normally in, such as an abnormally placed/position of a valve in the heart."

contributors:
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0003-4148-4606

classes:
  position: PATO:0000140
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  part_of: BFO:0000050

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"
  location: "'independent continuant'"

name:
  text: "abnormal %s topology in %s"
  vars:
   - anatomical_entity
   - location

def:
  text: "An abnormal position of the %s in the %s."
  vars:
    - anatomical_entity
    - location

equivalentTo:
  text: "'has_part' some (position and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some abnormal))"
  vars:
    - anatomical_entity
    - location


text:
pattern_name: abnormallyIncreasedThicknessOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedThicknessOfAnatomicalEntity.yaml
description: "An abnormally thickened anatomical entity, like HP_0001072 Thickened skin."

contributors:
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0001-5208-3432

classes:
  increased thickness: PATO:0000591
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "increased thickness of the %s"
  vars:
   - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "thickened %s"
    vars:
     - anatomical_entity

def:
  text: "An increase in the thickness of the %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('increased thickness' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormallyIncreasedSpeedOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedSpeedOfAnatomicalEntity.yaml
description: "Increased speed of an antomical entity. i.e., increased speed of whole organism"

contributors:
  - https://orcid.org/0000-0002-3528-5267

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  increased speed: PATO:0000303

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "increased speed of the %s"
  vars:
   - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "fast moving %s"
    vars:
     - anatomical_entity

def:
  text: "faster, increased speed of %s"
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('increased speed' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormallyDecreasedLengthOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedLengthOfAnatomicalEntity.yaml
description: "Anatomical entity is observed to be of decreased length. i.e., decreased length of tail"

contributors:
  - https://orcid.org/0000-0001-9076-6015
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0003-4148-4606

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  decreased length: PATO:0000574

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "decreased length of %s"
  vars:
   - anatomical_entity

annotations:
  -
    annotationProperty: exact_synonym
    text: "short %s"
    vars:
     - anatomical_entity

def:
  text: "Decreased length or shortening of the %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('decreased length' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormalResistanceOfWholeOrganismToEntity.yaml
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalResistanceOfWholeOrganismToEntity.yaml
description: "A phenotype in which an organism shows a changed resistance to a something, for example a chemical or a process, and it is unknown unspecified whether the resistance appears increased or decreased."

contributors:
  - https://orcid.org/0000-0002-7356-1779

classes:
  resistance to: PATO:0001178
  abnormal: PATO:0000460
  cellular organism: CARO:0010004
  entity: BFO:0000001

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  towards: RO:0002503

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  entity: "'entity'"

name:
  text: "abnormally changed resistance of organism to %s"
  vars:
    - entity

annotations:
- annotationProperty: exact_synonym
  text: "abnormally changed  sensitivity of organism to %s"
  vars:
    - entity

def:
  text: "abnormally changed resistance of organism to %s."
  vars:
    - entity

equivalentTo:
  text: "'has_part' some ('resistance to' and ('inheres_in' some 'cellular organism') and ('towards' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - entity


text:
pattern_name: abnormallyDecreasedMassDensityOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedMassDensityOfAnatomicalEntity
description: "The mass density (its mass per unit volume) of anatomical entity is lower than normal, such as HP_0004349 Reduced bone mineral density."

contributors:
  - https://orcid.org/0000-0001-5208-3432

classes:
  decreased mass density: PATO:0001790
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "Decreased %s mass density"
  vars:
   - anatomical_entity

def:
  text: "Reduced or decreased mass density of %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('decreased mass density' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormallyDecreasedMassOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedMassOfAnatomicalEntity.yaml
description: "The mass (the amount of matter or substance that makes up an object) of anatomical entity is lower than normal, such as HP_0003199 Decreased muscle mass. Note, mass density (mass per unit volume) is different than overall mass."

contributors:
  - https://orcid.org/0000-0001-5208-3432

classes:
  decreased mass: PATO:0001562
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "Decreased %s mass"
  vars:
   - anatomical_entity

def:
  text: "Reduced or decreased mass of %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('decreased mass' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormalAbsenceOfBiologicalProcessInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfBiologicalProcessInLocation.yaml
description: "A biological process that normally occurs does not occur in an anatomical entity/location."

contributors:
  - https://orcid.org/0000-0001-9076-6015
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0003-4148-4606

classes:
  absent: PATO:0000462
  abnormal: PATO:0000460
  biological process: GO:0008150
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  occurs_in: BFO:0000066

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  biological_process: "'biological process'"
  location: "'independent continuant'"

name:
  text: "absent %s in %s"
  vars:
   - biological_process
   - location

def:
  text: "Absent or undetectable %s in %s."
  vars:
   - biological_process
   - location

equivalentTo:
  text: "'has_part' some ('absent' and ('inheres_in' some (%s and ('occurs_in' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
    - biological_process
    - location


text:
pattern_name: hypertrophicAnatomicalEntity

pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/hypertrophicAnatomicalEntity.yaml

description: 'Use this pattern for overgrowth of multicellular structures due to overgrowth and enlargement of their cells. When the mechanism is unknown or for enlargement of any other type of structure, including enlargement of single cells, please use abnormallyIncreasedSizeOfAnatomicalEntity.'

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0003712  # Skeletal muscle hypertrophy
#    - http://purl.obolibrary.org/obo/MP_0009461  # skeletal muscle hypertrophy
#    - http://purl.obolibrary.org/obo/MP_0000053  # excessive ear growth
#    - http://purl.obolibrary.org/obo/MP_0005603  # neuron hypertrophy
#    - http://purl.obolibrary.org/obo/ZP_0016896  # kidney hypertrophic, abnormal
#    - http://purl.obolibrary.org/obo/ZP_0007444  # ciliary zone hypertrophic, abnormal

contributors:
  - https://orcid.org/0000-0001-8314-2140  # Ray Stefancsik
  - https://orcid.org/0000-0001-5208-3432  # Nicole Vasilevsky
  - https://orcid.org/0000-0002-9900-7880  # Yvonne M. Bradford
  - https://orcid.org/0000-0002-7073-9172  # David Osumi-Sutherland
  - https://orcid.org/0000-0003-4606-0597  # Susan Bello

classes:
  hypertrophic: PATO:0000584
  abnormal: PATO:0000460
  multicellular_anatomical_structure: UBERON:0010000

relations:
  characteristic_of: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'multicellular_anatomical_structure'"

name:
  text: "hypertrophic %s"
  vars:
    - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "%s hypertrophy"
    vars:
      - anatomical_entity

def:
  text: "Increased size of %s due to overgrowth and enlargement of its constituent cells."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some (
        'hypertrophic' and
        'characteristic_of' some %s and
        'has_modifier' some 'abnormal')"

  vars:
    - anatomical_entity


text:
pattern_name: abnormallyDecreasedPigmentationOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedPigmentationOfAnatomicalEntity.yaml
description: "Decreased pigmentation of an anatomical entity, such as decreased skin pigmentation."

contributors:
- https://orcid.org/0000-0002-3528-5267
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0001-9076-6015
classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  decreased pigmentation: PATO:0002251

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "decreased pigmentation in the %s"
  vars:
  - anatomical_entity

annotations:
- annotationProperty: exact_synonym
  text: "loss of pigment in the %s"
  vars:
  - anatomical_entity
- annotationProperty: exact_synonym
  text: "%s hypopigmentation"
  vars:
  - anatomical_entity

def:
  text: "Decreased or loss of pigmentation of %s."
  vars:
  - anatomical_entity

equivalentTo:
  text: "'has_part' some ('decreased pigmentation' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
  - anatomical_entity


text:
pattern_name: blisteredAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/blisteredAnatomicalEntity.yaml
description: "The presence of blisters on an anatomical entity, such as blisters on the skin."

contributors:
- https://orcid.org/0000-0002-7356-1779
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0001-9076-6015
- https://orcid.org/0000-0002-3528-5267
classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  blistered: PATO:0001928

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "abnormally blistered %s"
  vars:
  - anatomical_entity

def:
  text: "Abnormal local accumulation of fluid underneath the surface causing a blistered %s."
  vars:
  - anatomical_entity

annotations:
- annotationProperty: exact_synonym
  text: "%s with blister"
  vars:
  - anatomical_entity

equivalentTo:
  text: "'has_part' some ('blistered' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
  - anatomical_entity


text:
pattern_name: abnormallyDuplicatedAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDuplicatedAnatomicalEntityInLocation.yaml
description: "An anatomical entity that was abnormally duplicated in a location, such as a duplicated digit 1 on the right hand, or HP:0006176 Two carpal ossification centers present at birth.."

classes:
  duplicated: PATO:0001473
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  part_of: BFO:0000050

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"
  location: "'independent continuant'"

name:
  text: "abnormal duplication of %s in %s"
  vars:
  - anatomical_entity
  - location

annotations:
- annotationProperty: exact_synonym
  text: "abnormally duplicated %s in %s"
  vars:
  - anatomical_entity
  - location

def:
  text: "Any abnormal duplication of the %s in %s."
  vars:
  - anatomical_entity
  - location

equivalentTo:
  text: "'has_part' some ('duplicated' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
  - anatomical_entity
  - location
contributors:
- https://orcid.org/0000-0002-3528-5267


text:
pattern_name: malformedAnatomicalEntityByType
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/malformedAnatomicalEntityByType.yaml
description: A malformed subtype of an anatomical entity, such as a wholly dorsalized embryo. This pattern can use any subclass of PATO malformed.

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-3528-5267
classes:
  malformed: PATO:0000646
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

vars:
  malformed: "'malformed'"
  anatomical_entity: "'anatomical entity'"

name:
  text: "%s %s"
  vars:
  - malformed
  - anatomical_entity

def:
  text: "A %s %s."
  vars:
  - malformed
  - anatomical_entity

equivalentTo:
  text: "'has_part' some (%s and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
  - malformed
  - anatomical_entity


text:
pattern_name: abnormallyIncreasedWidthOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedWidthOfAnatomicalEntity.yaml
description: "Increased width of an antomical entity. i.e., wider tail."

contributors:
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0003-4148-4606

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  increased width: PATO:0000600

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "increased width of %s"
  vars:
   - anatomical_entity

annotations:
  -
    annotationProperty: exact_synonym
    text: "wider %s"
    vars:
     - anatomical_entity

def:
  text: "Increased width of %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('increased width' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormalAbsenceOfPigmentationOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfPigmentationOfAnatomicalEntity.yaml
description: "Complete loss of pigmentation in an antomical entity. i.e., unpigmented eye."

contributors:
- https://orcid.org/0000-0002-3528-5267
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0001-9076-6015
classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  unpigmented: PATO:0002249

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "unpigmented %s"
  vars:
  - anatomical_entity

annotations:
- annotationProperty: exact_synonym
  text: "complete loss of pigmentation in the %s"
  vars:
  - anatomical_entity
- annotationProperty: exact_synonym
  text: "absence of pigment in the %s"
  vars:
  - anatomical_entity

def:
  text: "complete loss of pigmenation of the %s."
  vars:
  - anatomical_entity

equivalentTo:
  text: "'has_part' some ('unpigmented' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
  - anatomical_entity


text:
pattern_name: abnormalLevelOfChemicalEntityWithRole
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalLevelOfChemicalEntityWithRole.yaml
description: "An abnormal level of a chemical with a specific role, such as a metabolite or hormone like androgen, for example, 'abnormal androgen level'."

contributors:
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0002-3528-5267

classes:
  amount: PATO:0000070
  abnormal: PATO:0000460
  chemical entity: CHEBI:24431
  role: CHEBI:50906

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  has_role: RO:0000087

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  role: "role"

name:
  text: "abnormal %s level"
  vars:
  - role

def:
  text: "An abnormal amount of %s."
  vars:
  - role

equivalentTo:
  text: "'has_part' some ('amount' and ('inheres_in' some ('chemical entity' and ('has_role' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
  - role


text:
pattern_name: abnormallyDecreasedRateOfMolecularFunction
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedRateOfMolecularFunction.yaml
description: "Decreased or reduced functionality of a molecular function, which is a process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities, such as binding, catalysis, enzyme activities (like hydrolases, ligases), etc. Example: HP_0002932 'Aldehyde oxidase deficiency'"

contributors:
  - https://orcid.org/0000-0002-9900-7880
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0003-4148-4606

classes:
  decreased rate: PATO:0000911
  abnormal: PATO:0000460
  molecular function: GO:0003674

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  molecular_function: "'molecular function'"

name:
  text: "decreased %s"
  vars:
   - molecular_function

def:
  text: "Abnormally reduced functionality of %s."
  vars:
    - molecular_function

equivalentTo:
  text: "'has_part' some ('decreased rate' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - molecular_function


text:
pattern_name: abnormallyArrestedBiologicalProcess
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyArrestedBiologicalProcess.yaml
description: "A partial failure or arrested development of a biological process, such as arrested cell migration."

contributors:
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0001-9076-6015
  - https://orcid.org/0000-0002-9611-1279

classes:
  arrested: PATO:0000297
  abnormal: PATO:0000460
  biological_process: GO:0008150

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  biological_process: "'biological_process'"

name:
  text: "arrested %s"
  vars:
   - biological_process

annotations:
  - annotationProperty: exact_synonym
    text: "incomplete %s"
    vars:
     - biological_process
  - annotationProperty: exact_synonym
    text: "failure to complete %s"
    vars:
     - biological_process
  - annotationProperty: exact_synonym
    text: "failed %s"
    vars:
     - biological_process
  - annotationProperty: exact_synonym
    text: "%s arrest"
    vars:
     - biological_process

def:
  text: "Arrested %s."
  vars:
    - biological_process

equivalentTo:
  text: "'has_part' some ('arrested' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - biological_process


text:
pattern_name: dysplasticAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/dysplasticAnatomicalEntity.yaml
description: "A congenital malformation of an anatomical entity, such as HP_0005176 'Dysplastic aortic valve'."

contributors:
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0001-5208-3432

classes:
  dysplastic: PATO:0000640
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
 anatomical_entity: "'anatomical entity'"

name:
  text: "dysgenesis of the %s"
  vars:
   - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "%s dysgenesis"
    vars:
     - anatomical_entity

def:
  text: "Defective development of the %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('dysplastic' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
---
pattern_name: deviationTowardsTheMedialSideOfAnatomicalEntity

pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/deviationTowardsTheMedialSideOfAnatomicalEntity.yaml

description: 'Use this pattern for phenotypes involving angulation,
  directional change or bending towards the middle of an anatomical
  entity that is abnormal in space or time (e.g. permanent).'

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0030084  # Clinodactyly
#    - http://purl.obolibrary.org/obo/HP_0001863  # Toe clinodactyly
#    - http://purl.obolibrary.org/obo/HP_0009486  # Radial deviation of the hand
#    - http://purl.obolibrary.org/obo/MP_0006253  # clinodactyly

contributors:
  - https://orcid.org/0000-0001-8314-2140  # Ray Stefancsik
  - https://orcid.org/0000-0003-4606-0597  # Susan Bello
  - https://orcid.org/0000-0002-9900-7880  # Yvonne M. Bradford

classes:
  deviation_towards_the_medial_side: PATO:0002177
  abnormal: PATO:0000460
  anatomical_entity: UBERON:0001062

relations:
  characteristic_of: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  broad_synonym: oio:hasBroadSynonym

vars:
  anatomical_entity: "'anatomical_entity'"

name:
  text: "deviation of %s towards the middle"
  vars:
    - anatomical_entity

annotations:
  - annotationProperty: broad_synonym
    text: "shift of %s towards the middle"
    vars:
      - anatomical_entity

  - annotationProperty: broad_synonym
    text: "permanent bending of %s"
    vars:
      - anatomical_entity

def:
  text: "A changed direction of position or shift towards the middle of %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some (
    'deviation_towards_the_medial_side'
    and ('characteristic_of' some %s)
    and ('has_modifier' some 'abnormal')
    )"
  vars:
    - anatomical_entity
...


text:
pattern_name: abnormalAbsenceOfChemicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfChemicalEntityInLocation.yaml
description: "A chemical (entity) such as sodium is missing from an anatomical location, such as blood."

contributors:
- https://orcid.org/0000-0003-4606-0597
- https://orcid.org/0000-0002-3528-5267
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0003-4148-4606
- https://orcid.org/0000-0001-7941-2961
- https://orcid.org/0000-0001-9076-6015
classes:
  absent: PATO:0000462
  abnormal: PATO:0000460
  chemical entity: CHEBI:24431
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  part_of: BFO:0000050

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  chemical_entity: "'chemical entity'"
  location: "'independent continuant'"
name:
  text: "absent %s in %s"
  vars:
  - chemical_entity
  - location

def:
  text: "Absent or undetectable level of %s in %s."
  vars:
  - chemical_entity
  - location

equivalentTo:
  text: "'has_part' some ('absent' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
  - chemical_entity
  - location


text:
pattern_name: abnormallyIncreasedStabilityOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedStabilityOfAnatomicalEntity.yaml
description: "An abnormally increased or impaired ability of an anatomical entity to to retain a particular structure or homeostatic set of structures. For example, abnormal spore stability."

contributors:
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0002-4532-2703

classes:
  increased stability: PATO:0015027
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "abnormally increased %s stability"
  vars:
   - anatomical_entity

def:
  text: "An abnormally increased stability of the %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('increased stability' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
---
pattern_name: abnormallyDecreasedWetnessOfAnatomicalEntity

pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedWetnessOfAnatomicalEntity.yaml

description: "Use this phenotype pattern when an anatomical entity exhibits
  decreased liquid coverage, for example, when the aqueous or oily layer on its
  surface is reduced. Consider the alternative 'PATO:0001801 decreased water
  composition' phenotype pattern when the water contained in an entity is
  reduced as opposed to a reduced amount of liquid on its surface."

#  examples:
#    - http://purl.obolibrary.org/obo/PATO_0001824  # http://purl.obolibrary.org/obo/HP_0000217	Xerostomia
#    - http://purl.obolibrary.org/obo/PATO_0001824  # http://purl.obolibrary.org/obo/HP_0011359	Dry hair
#    - http://purl.obolibrary.org/obo/PATO_0001824  # http://purl.obolibrary.org/obo/MP_0000624	xerostomia
#    - http://purl.obolibrary.org/obo/PATO_0001824  # http://purl.obolibrary.org/obo/MP_0001337	dry eyes
#    - http://purl.obolibrary.org/obo/MP_0003536  # vagina dryness

contributors:
  - https://orcid.org/0000-0001-8314-2140  # Ray Stefancsik
  - https://orcid.org/0000-0003-4606-0597  # Susan Bello
  - https://orcid.org/0000-0002-6490-7723  # Anna V. Anagnostopoulos
  - https://orcid.org/0000-0002-4142-7153  # Sabrina Toro
  - https://orcid.org/0000-0001-7941-2961  # Leigh Carmody

classes:
  decreased_surface_wetness: PATO:0001826
  abnormal: PATO:0000460
  anatomical_entity: UBERON:0001062

relations:
  characteristic_of: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym
  related_synonym: oio:hasRelatedSynonym

vars:
  anatomical_entity: "'anatomical_entity'"

name:
  text: "decreased surface wetness of %s"
  vars:
    - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "decreased wetness of %s"
    vars:
      - anatomical_entity

  - annotationProperty: exact_synonym
    text: "decreased %s surface wetness"
    vars:
      - anatomical_entity

  - annotationProperty: exact_synonym
    text: "decreased %s wetness"
    vars:
      - anatomical_entity

  - annotationProperty: related_synonym
    text: "%s dryness"
    vars:
      - anatomical_entity

  - annotationProperty: related_synonym
    text: "dry %s"
    vars:
      - anatomical_entity

def:
  text: "A relatively low wetness on the surface of %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some (
    'decreased_surface_wetness' and
    ('characteristic_of' some %s) and
    ('has_modifier' some 'abnormal')
    )"
  vars:
    - anatomical_entity
...


text:
pattern_name: abnormallyDecreasedFunctionalityOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedFunctionalityOfAnatomicalEntity.yaml
description: "Decreased functionality of an anatomical entity or part, such as decreased functionality of the gall bladder."

contributors:
- https://orcid.org/0000-0001-9076-6015

classes:
  decreased functionality: PATO:0001624
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "abnormally decreased functionality of the %s"
  vars:
  - anatomical_entity

def:
  text: "An abnormally decreased functionality of the %s."
  vars:
  - anatomical_entity

equivalentTo:
  text: "'has_part' some ('decreased functionality' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
  - anatomical_entity


text:
pattern_name: abnormalAbsenceOfBehavior
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfBehavior.yaml
description: "A behavior that normally would occur does not occur."

contributors:
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0002-1373-1705

classes:
  absent: PATO:0000462
  abnormal: PATO:0000460
  behavior process: NBO:0000313

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  behavior_process: "'behavior process'"

name:
  text: "absent %s"
  vars:
   - behavior_process

def:
  text: "Absence of %s."
  vars:
    - behavior_process

equivalentTo:
  text: "'has_part' some ('absent' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - behavior_process


text:
pattern_name: abnormallyDecreasedRateOfBiologicalProcessInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedRateOfBiologicalProcessInLocation.yaml
description: "Decreased frequency of a biological process occuring (per some unit of time) in a location, such as HP_0003469 Peripheral dysmyelination."

contributors:
- https://orcid.org/0000-0001-9076-6015
- https://orcid.org/0000-0002-3528-5267
classes:
  decreased rate: PATO:0000911
  abnormal: PATO:0000460
  biological_process: GO:0008150
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  qualifier: RO:0002573
  has_part: BFO:0000051
  occurs_in: BFO:0000066

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  biological_process: "'biological_process'"
  location: "'independent continuant'"
name:
  text: "decreased %s in %s"
  vars:
  - biological_process
  - location

def:
  text: "decreased %s in %s."
  vars:
  - biological_process
  - location

equivalentTo:
  text: "'has_part' some ('decreased rate' and ('inheres_in' some (%s and ('occurs_in' some %s))) and ('qualifier' some 'abnormal'))"
  vars:
  - biological_process
  - location


text:
pattern_name: abnormalDistanceBetweenAnatomicalEntities
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalDistanceBetweenAnatomicalEntities.yaml
description: "Distance between two anatomical entites has deviated from normal. For example, PLANP_0000512 'abnormal distance between eye and eye'"

contributors:
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0003-4148-4606

classes:
  abnormal: PATO:0000460
  anatomical_entity1: UBERON:0001062
  anatomical_entity2: UBERON:0001062
  distance: PATO:0000040

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  towards: RO:0002503

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity1: "'anatomical_entity1'"
  anatomical_entity2: "'anatomical_entity2'"

name:
  text: "abnormal distance between %s and %s"
  vars:
   - anatomical_entity1
   - anatomical_entity2

annotations:
  -
    annotationProperty: exact_synonym
    text: "abnormal distance between %s and %s"
    vars:
     - anatomical_entity1
     - anatomical_entity2
  -
    annotationProperty: exact_synonym
    text: "distance abnormal between %s and %s"
    vars:
     - anatomical_entity1
     - anatomical_entity2

def:
  text: "abnormal distance between %s and %s."
  vars:
    - anatomical_entity1
    - anatomical_entity2

equivalentTo:
  text: "'has_part' some ('distance' and ('inheres_in' some %s) and ('towards' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity1
    - anatomical_entity2


text:
pattern_name: abnormallyIncreasedLengthOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedLengthOfAnatomicalEntity.yaml
description: "Increased length of an antomical entity. i.e., increased length of tail"

contributors:
  - https://orcid.org/0000-0001-9076-6015
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0003-4148-4606

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  increased length: PATO:0000573

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "increased length of the %s"
  vars:
   - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "longer %s"
    vars:
     - anatomical_entity

def:
  text: "longer, increased length of, %s"
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('increased length' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormalCellProliferationActingOnCellsOfTypeInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalCellProliferationActingOnCellsOfTypeInLocation.yaml
description: "Any abnormal cell proliferation in a specific cell type in a location, such as abnormal retinal vascular proliferation in the eye."

contributors:
  - https://orcid.org/0000-0001-5208-3432

classes:
  abnormal: PATO:0000460
  cell population proliferation: GO:0008283
  cell: CL:0000003
  process quality: PATO:0001236
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  acts_on_population_of: obo:GOREL_0001006
  occurs_in: BFO:0000066

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  cell: "'cell'"
  anatomical_entity: "'anatomical entity'"

name:
  text: "abnormal %s proliferation in %s"
  vars:
   - cell
   - anatomical_entity

def:
  text: "Abnormal proliferation of %s in %s."
  vars:
   - cell
   - anatomical_entity

equivalentTo:
  text: "'has_part' some ('process quality' and ('inheres_in' some ('cell population proliferation' and ('acts_on_population_of' some %s) and ('occurs_in' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
    - cell
    - anatomical_entity


text:
pattern_name: abnormalSizeOfCellularComponent
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalSizeOfCellularComponent.yaml
description: "An abnormal size (the relative extent of something) of a cellular component, such as abnormal vacuole size."

contributors:
- https://orcid.org/0000-0001-5208-3432

classes:
  size: PATO:0000117
  abnormal: PATO:0000460
  cellular component: GO:0005575

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  entity: "'cellular component'"

name:
  text: "abnormal size of %s"
  vars:
  - entity

annotations:
- annotationProperty: exact_synonym
  text: "abnormal size of the %s"
  vars:
  - entity

def:
  text: "A deviation from the normal size of the %s."
  vars:
  - entity

equivalentTo:
  text: "'has_part' some ('size' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
  - entity


text:
pattern_name: abnormallyDecreasedStabilityOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedStabilityOfAnatomicalEntity.yaml
description: "An abnormally decreased or impaired ability of an anatomical entity to to retain a particular structure or homeostatic set of structures. For example, abnormal spore stability."

contributors:
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0002-4532-2703

classes:
  decreased stability: PATO:0015028
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "abnormally decreased %s stability"
  vars:
   - anatomical_entity

def:
  text: "An abnormally decreased stability of the %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('decreased stability' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormallyCurvedAnatomicalEntityByOrientation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyCurvedAnatomicalEntityByOrientation.yaml
description: ""

contributors:
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0001-5208-3432

classes:
  curved: PATO:0000406
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"
  orientation: "'curved'"

name:
  text: "abnormal %s, %s"
  vars:
   - anatomical_entity
   - orientation

annotations:
  - annotationProperty: exact_synonym
    text: "%s %s"
    vars:
     - orientation
     - anatomical_entity

def:
  text: "Any abnormal %s that is %sly."
  vars:
    - anatomical_entity
    - orientation

equivalentTo:
  text: "'has_part' some (%s and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - orientation
    - anatomical_entity