text:
pattern_name: abnormallyDecreasedThicknessOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedThicknessOfAnatomicalEntity.yaml
description: "An abnormally thinner anatomical entity, like HP:0100689 Decreased corneal thickness."

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-3528-5267
classes:
  decreased thickness: PATO:0000592
  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 thickness of the %s"
  vars:
  - anatomical_entity

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

def:
  text: "A decrease in the thickness of the %s."
  vars:
  - anatomical_entity

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


text:
pattern_name: abnormallyEvertedAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyEvertedAnatomicalEntity.yaml
description: "An abnormal configuration of an anatomical entity, such that it is turned outward in placement (ie the opposite of inverted). Such as HP_0000232 Everted lower lip vermilion"

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-3528-5267
classes:
  everted: PATO:0001597
  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: "everted %s"
  vars:
  - anatomical_entity

def:
  text: "An abnormal configuration of the %s such that it is turned outward i.e., everted,."
  vars:
  - anatomical_entity

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

repo_name: obophenotype/upheno

repo_language: Makefile

mime_type: text/plain


text:
pattern_name: abnormallyDetachedAnatomicalEntities
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDetachedAnatomicalEntities.yaml
description: "A partial or complete loss of connection between anatomical entities. For example, MP_0006023 detached Reissner membrane or MP_0003099 detached retina."

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

classes:
  detached: PATO:0001453
  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:
  anatomical_entity: "'anatomical entity'"
  anatomical_entity_detached_from: "'anatomical entity'"

name:
  text: "detached %s from %s"
  vars:
  - anatomical_entity
  - anatomical_entity_detached_from

def:
  text: "Detachment of the %s and from the %s."
  vars:
  - anatomical_entity
  - anatomical_entity_detached_from

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


text:
pattern_name: abnormallyDecreasedWidthOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedWidthOfAnatomicalEntity.yaml
description: "Decrease in the width of an anatomical entity. i.e., decreased width, skinny, 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
  decreased width: PATO:0000599

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 width of the %s"
  vars:
   - anatomical_entity

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

def:
  text: "skinny or decreased width of the %s."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormalEfficacyOfProteinLocalizationInCellularComponent
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalEfficacyOfProteinLocalizationInCellularComponent.yaml
description: "Abnormal efficacy or output of any process in which a protein is transported to, or maintained in, a specific sub-cellular location."

contributors:
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0001-8314-2140
  - https://orcid.org/0000-0002-4532-2703
  - https://orcid.org/0000-0003-4148-4606
  - https://orcid.org/0000-0002-7073-9172

classes:
  abnormal: PATO:0000460
  process efficacy: PATO:0015002
  protein localization: GO:0008104
  cellular component: GO:0005575

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  has_target_end_location: RO:0002339

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  location: "'cellular component'"

name:
  text: "abnormal protein localization in %s"
  vars:
   - location

def:
  text: "Abnormal protein localization %s."
  vars:
   - location

equivalentTo:
  text: "'has_part' some ('process efficacy' and ('inheres_in' some ('protein localization' and ('has_target_end_location' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
    - location


text:
pattern_name: abnormallyIncreasedSizeOfCellularComponent
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedSizeOfCellularComponent.yaml
description: "A enlarged cellular component, like increased phagolysosome size.'"

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

classes:
  increased size: PATO:0000586
  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: "increased size of the %s"
  vars:
  - entity

annotations:
- annotationProperty: exact_synonym
  text: "enlarged %s"
  vars:
  - entity

def:
  text: "An increase in the size of the %s."
  vars:
  - entity

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


text:
pattern_name: abnormallyIncreasedSizeOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedSizeOfAnatomicalEntityInLocation.yaml
description: "A enlarged entity, like an abnormally large anatomical structure in a location, such as an enlarged glomerulus in the kidney.'"

contributors:
- https://orcid.org/0000-0002-9900-7880
- https://orcid.org/0000-0002-9611-1279
- https://orcid.org/0000-0002-3528-5267
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0003-4148-4606
- https://orcid.org/0000-0001-9076-6015

classes:
  increased size: PATO:0000586
  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 size of the %s in %s"
  vars:
  - anatomical_entity
  - location

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

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

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


text:
pattern_name: abnormallyDecreasedLengthOfAnatomicalEntityAttachedToLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedLengthOfAnatomicalEntityAttachedToLocation.yaml
description: "Anatomical entity is observed to be of decreased length while attached to another anatomical entity. This pattern is primary used for HPO contracture terms, such as HP_0001239 'Wrist flexion contracture'."

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

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  decreased length: PATO:0000574
  independent continuant: BFO:0000004

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  attached_to: RO:0002371

annotationProperties:
  exact_synonym: oio:hasExactSynonym

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

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

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

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

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


text:
pattern_name: abnormalMobilityOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalMobilityOfAnatomicalEntity.yaml
description: "An abnormality of the ability to move (mobility) an anatomical entity, including cells. Examples include HP_0006256 'Abnormality of hand joint mobility' and MP_0008069 'abnormal joint mobility'."

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

classes:
  mobility: PATO:0000004
  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: "abnormal %s mobility"
  vars:
   - anatomical_entity

def:
  text: "anomaly in the ability to move %s."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormallyAsymmetricalAnatomicalEntity

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

description: 'Use this pattern for morphologically asymmetrical anatomical entity phenotypes. Here abnormal asymmetry includes the lack of radial, bilateral and other types of symmetry in size, shape, and relative position of anatomical entities, e.g. craniofacial asymmetry or foot asymmetry.'

#  examples:
#    - http://purl.obolibrary.org/obo/MP_0008863  # craniofacial asymmetry
#    - http://purl.obolibrary.org/obo/HP_0002678  # Skull asymmetry
#    - http://purl.obolibrary.org/obo/HP_0010507  # Foot asymmetry
#    - http://purl.obolibrary.org/obo/ZP_0011548  # neural tube asymmetrical, abnormal

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

classes:
  asymmetrical: PATO:0000616
  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: "abnormal asymmetry of %s"
  vars:
    - anatomical_entity

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

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

  - annotationProperty: related_synonym
    text: "asymmetry of %s"
    vars:
      - anatomical_entity

def:
  text: "Abnormal morphological asymmetry of %s (or a set of thereof) across an axis of symmetry."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormallyProminentAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyProminentAnatomicalEntity.yaml
description: "An anatomical entity that stands out or projects beyond the surface or line, such as a HP_0000395 'Prominent antihelix'"

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-3528-5267
classes:
  prominent: PATO:0001482
  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: "prominent %s"
  vars:
  - anatomical_entity

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

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


text:
pattern_name: abnormalAbsenceOfChemicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfChemicalEntity.yaml
description: "A chemical (entity) or protein such as sodium or insulin that are normally present is absent."

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
- 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

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: "absent %s"
  vars:
  - chemical_entity

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

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


text:
---
pattern_name: foldedAnatomicalEntity

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

description: "Use this phenotype pattern when an anatomical entity has
  morphological abnormalities involving folding all or any part of it
  over another connected part. Consider the related 'PATO:0001810
  wrinkled' anatomical entity pattern where the abnormal anatomical
  entity is marked by one or more creases in a normally smooth surface."

#  examples:
#    - http://purl.obolibrary.org/obo/ZP_0011575  # caudal fin folded, abnormal
#    - http://purl.obolibrary.org/obo/MP_0003736  # folded helix
#    - http://purl.obolibrary.org/obo/HP_0008544  # Abnormally folded helix

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:
  folded: PATO:0001910
  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: "folded %s"
  vars:
    - anatomical_entity

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

def:
  text: "A morphological anomaly that involves folding all or any part
    of %s over another connected part."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormallySegmentedAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallySegmentedAnatomicalEntityInLocation.yaml
description: "Anatomical entity that is abnormally segmented in a particular location, e.g. abnormally segmented bone in a limb."

contributors:
- https://orcid.org/0000-0002-9611-1279

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  segmented: PATO:0002312
  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 segmentation of %s in %s"
  vars:
  - anatomical_entity
  - location

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

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

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


text:
pattern_name: abnormallyDecreasedTonicityOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedStrengthOfAnatomicalEntity.yaml
description: "A decrease in the normal presence of tone or tension (the resistance to passive stretch during resting state) in an anatomical entity, usually a a muscle or organ, such as HP_0001252 Muscular hypotonia or MP_0003089 'decreased skin tensile strength'."

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-3528-5267
classes:
  decreased tonicity: PATO:0001619
  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 tone"
  vars:
  - anatomical_entity

def:
  text: "Decreased tonicity of %s."
  vars:
  - anatomical_entity

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


text:
pattern_name: abnormalRateOfDevelopmentDuringStage
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalRateOfDevelopmentDuringStage.yaml
description: "An abnormally delayed or accelerated rate of a developmental process during a developmental stage in an organism."

contributors:
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0002-4532-2703
  - https://orcid.org/0000-0002-7073-9172

classes:
  abnormal: PATO:0000460
  rate: PATO:0000161
  developmental_process: GO:0032502
  life_cycle_stage: UBERON:0000105

relations:
  happens_during: RO:0002092
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  development: "'developmental_process'"
  stage: "'life_cycle_stage'"

name:
  text: "abnormal %s rate during %s"
  vars:
   - development
   - stage

def:
  text: "Abnormal rate of %s in the %s."
  vars:
   - development
   - stage

equivalentTo:
  text: "'has_part' some ('rate' and ('inheres_in' some (%s and ('happens_during' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
   - development
   - stage


text:
pattern_name: fibroticAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/fibroticAnatomicalEntity.yaml
description: "The presence of excessive fibrous connective tissue in an anatomical entity, e.g. Endocardial fibrosis (HP_0006685), Pulmonary fibrosis (HP_0002206)."

classes:
  fibrotic: PATO:0040019
  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 fibrosis"
  vars:
  - anatomical_entity

annotations:
- annotationProperty: exact_synonym
  text: "Fibrosis of the %s"
  vars:
  - anatomical_entity
def:
  text: "The presence of excessive fibrous connective tissue in the %s."
  vars:
  - anatomical_entity

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


text:
---
pattern_name: abnormalMassDensityOfAnatomicalEntityInLocation.yaml

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

description: 'Abnormal mass density (mass per unit volume) of an anatomical entity in a location. For example, this pattern can be used when a bone element at a location exhibits abnormal mass density. This pattern is not to be used for count per area (e.g. cell count) phenotypes.'

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:
  mass_density: PATO:0001019
  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: "abnormal %s of %s mass density"
  vars:
    - anatomical_entity
    - location

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

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

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


text:
---
pattern_name: abnormallyCurledAnatomicalEntity

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

description: 'Use this phenotype pattern when an anatomical entity is
  abnormally curled, waved, coiled or has  corkscrew-like or spiral
  shaped curl or curls.'

#  examples:
#    - http://purl.obolibrary.org/obo/MP_0001274  # curly vibrissae
#    - http://purl.obolibrary.org/obo/MP_0003051  # curly tail
#    - http://purl.obolibrary.org/obo/HP_0007665  # Curly eyelashes
#    - http://purl.obolibrary.org/obo/HP_0002212  # Curly hair
#    - http://purl.obolibrary.org/obo/ZP_0010670  # trunk curled, abnormal
#    - http://purl.obolibrary.org/obo/ZP_0141717  # barbel curled, abnormal

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

classes:
  curled: PATO:0000405
  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: "abnormally curled %s"
  vars:
    - anatomical_entity

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

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

def:
  text: "A curled %s that shows abnormal waves, coils or undulations."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormallyIncreasedQualityOfBiologicalProcessInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedQualityOfBiologicalProcessInLocation.yaml
description: "Process in a location that appears in some (unspecified) way strengthened or increased (more frequent, more strong)."

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

classes:
  increased process quality: PATO:0002304
  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: "increased qualitatively %s in %s"
  vars:
   - biological_process
   - location

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

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


text:
pattern_name: abnormallyDelayedBiologicalProcessInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDelayedBiologicalProcessInLocation.yaml
description: "Occurrence of a biological process in some location that is abnormally delayed."

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

classes:
  delayed: PATO:0000502
  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: "delayed %s in %s"
  vars:
   - biological_process
   - location

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

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


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

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

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: "absent %s"
  vars:
   - biological_process

def:
  text: "Lack of %s."
  vars:
    - biological_process

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


text:
pattern_name: abnormallyIncreasedNumberOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedNumberOfAnatomicalEntityInLocation.yaml
description: "An increased number of an anatomical entity in a location, such a increased number of teeth in the mouth."

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

classes:
  increased amount: PATO:0000470
  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: "abnormally increased number of %s in the %s"
  vars:
   - anatomical_entity
   - location

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

def:
  text: "The presence of an increased number of %s in the %s."
  vars:
    - anatomical_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:
    - anatomical_entity
    - location


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

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

classes:
  process quality: PATO:0001236
  abnormal: PATO:0000460
  cellular developmental process: GO:0048869
  cell type: CL:0000003

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  results_in_acquisition_of_features_of: RO:0002315

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  celltype: "'cell type'"

name:
  text: "abnormal %s cell differentiation"
  vars:
  - celltype

def:
  text: "An abnormality in the cell differentiation of the %s."
  vars:
  - celltype

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


text:
pattern_name: abnormallyDecreasedResistanceOfWholeOrganismToEntity.yaml
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedResistanceOfWholeOrganismToEntity.yaml
description: "A phenotype in which an organism shows decreased resistance to a something, like radiation."

contributors:
- https://orcid.org/0000-0002-7356-1779
- https://orcid.org/0000-0002-3528-5267
classes:
  decreased resistance to: PATO:0001651
  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: "decreased resistance of organism to %s"
  vars:
  - entity

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

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

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


text:
pattern_name: abnormalWeightOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalWeightOfAnatomicalEntity.yaml
description: "An abnormality of the mass of an anatomical entity, e.g. increased or decreased mass of the whole organism. NOTE: We are using mass (PATO:0000125), not weight, to model this phenotype, see also https://github.com/obophenotype/bio-attribute-ontology/issues/39"

contributors:
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0002-9611-1279

classes:
  mass: PATO:0000125
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

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

annotationProperties:
  narrow_synonym: oio:hasNarrowSynonym

vars:
  anatomical_entity: "'anatomical entity'"

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

def:
  text: "An abnormality of mass in the %s."
  vars:
    - anatomical_entity

annotations:
  - annotationProperty: narrow_synonym
    text: "abnormality of %s weight"
    vars:
    - anatomical_entity

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


text:
pattern_name: bifurcatedAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/bifurcatedAnatomicalEntity.yaml
description: "Branching of an anatomical entity into two branches. Example: HP_0010309 'Bifid sternum'."

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

classes:
  bifurcated: PATO:0001784
  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: "bifurcated %s"
  vars:
   - anatomical_entity

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

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

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


text:
pattern_name: abnormallyDecreasedQualityOfBiologicalProcess
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedQualityOfBiologicalProcess.yaml
description: "Process that appears in some (unspecified) way impaired or decreased (less frequent, less strong)."

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

classes:
  decreased process quality: PATO:0002302
  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: "decreased qualitatively %s"
  vars:
   - biological_process

def:
  text: "Decreased qualitatively %s."
  vars:
    - biological_process

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


text:
pattern_name: increasedProportionOfCellTypeTowardsCellTypeInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/increasedProportionOfCellTypeTowardsCellTypeInLocation.yaml
description: "An increased proportion of a cell type relative to another cell type, in a location, like the blood. For example: 'increased CD4+CD25+ regulatory T cell proportion relative to T cells in the blood'."

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

classes:
  increased proportionality to: PATO:0040043
  abnormal: PATO:0000460
  cell: CL:0000000
  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:
  cell: "'cell'"
  compared_cell: "'cell'"
  location: "'independent continuant'"

name:
  text: "increased proportion of %s relative to %s in %s"
  vars:
  - cell
  - compared_cell
  - location

def:
  text: "An increased proportion of %s relative to %s in the %s."
  vars:
  - cell
  - compared_cell
  - location

equivalentTo:
  text: "'has_part' some ('increased proportionality to' and ('inheres_in' some (%s and ('part_of' some %s))) and ('towards' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
  - cell
  - location
  - compared_cell


text:
pattern_name: abnormalBiologicalProcess
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalBiologicalProcess.yaml
description: "Any unspecified abnormality of a biological process, a specific objective that the organism is genetically programmed to achieve, such as apoptosis or cell proliferation. i.e. HP_0012647 'Abnormal inflammatory response'"

contributors:
- 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/0000-0002-1373-1705
- https://orcid.org/0000-0003-4148-4606
- https://orcid.org/0000-0001-7941-2961
classes:
  process quality: PATO:0001236
  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: "abnormal %s"
  vars:
  - biological_process

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

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


text:
pattern_name: neoplasticAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/neoplasticAnatomicalEntity.yaml
description: "The presence of abnormally proliferating masses of cells in an anatomical entity."

contributors:
- https://orcid.org/0000-0002-9611-1279

classes:
  neoplastic: PATO:0002011
  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: "neoplastic %s"
  vars:
  - anatomical_entity

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

def:
  text: "The presence of abnormally proliferating masses of cells in %s."
  vars:
  - anatomical_entity

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


text:
pattern_name: abnormalStabilityOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalStabilityOfAnatomicalEntity.yaml
description: "An abnormality in the 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:
  stability: PATO:0015026
  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: "abnormal stability of %s"
  vars:
   - anatomical_entity

def:
  text: "Any abnormality in the stability of the %s."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormalMorphologyOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalMorphologyOfAnatomicalEntityInLocation.yaml
description: "An abnormally shaped anatomical entity, in a specific location, like an abnormally shaped tip of the finger, or bone of the lower limb."

contributors:
- https://orcid.org/0000-0002-3528-5267
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0003-4148-4606
- https://orcid.org/0000-0002-7356-1779
- https://orcid.org/0000-0001-9076-6015
classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  morphology: PATO:0000051
  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 morphology in the %s"
  vars:
  - anatomical_entity
  - location

annotations:
- annotationProperty: exact_synonym
  text: "Abnormal morphology of the %s in the %s"
  vars:
  - anatomical_entity
  - location

def:
  text: "A morphological abnormality of the %s in the %s."
  vars:
  - anatomical_entity
  - location

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


text:
pattern_name: abnormalProportionOfCellTypeInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalProportionOfCellTypeInLocation.yaml
description: "An abnormal proportion of a cell, in a location, like the blood. For example: HP_0020111 'Abnormal CD4+CD25+ regulatory T cell proportion'."

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

classes:
  proportionality to: PATO:0001470
  abnormal: PATO:0000460
  cell: CL:0000000
  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:
  cell: "'cell'"
  location: "'independent continuant'"

name:
  text: "abnormal proportion of %s in %s"
  vars:
  - cell
  - location

def:
  text: "A deviation from the normal proportion of %s in the %s."
  vars:
  - cell
  - location

equivalentTo:
  text: "'has_part' some ('proportionality to' and ('inheres_in' some (%s and ('part_of' some %s))) and ('towards' some 'cell') and ('has_modifier' some 'abnormal'))"
  vars:
  - cell
  - location


text:
pattern_name: abnormallyDecreasedRateOfBehavior
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedRateOfBehavior.yaml
description: "Behavior occurs with a lower frequency (less often) or more slowly than usual (less behavior per unit of time)."

contributors:
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0002-1373-1705
  - https://orcid.org/0000-0001-5208-3432

classes:
  decreased rate: PATO:0000911
  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: "abnormally decreased rate of %s"
  vars:
   - behavior_process

def:
  text: "Decrease in rate (amount or occurrence per unit of time) of %s."
  vars:
    - behavior_process

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


text:
pattern_name: prematureClosureOfAnatomicalEntity

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

description: 'Use this phenotype pattern in cases of premature closure of anatomical entity, e.g. premature cranial suture closure. Please, note that there may be more specific patterns for cranial suture closure phenotypes if a suitable GO biological process term becomes available.'

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0004440  # Coronal craniosynostosis
#    - http://purl.obolibrary.org/obo/MP_0030350  # premature coronal suture closure
#    - http://purl.obolibrary.org/obo/MP_0000081  # premature cranial suture closure

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

classes:
  premature_closure: PATO:0002166
  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: "premature %s closure"
  vars:
    - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "premature closure of %s"
    vars:
      - anatomical_entity

def:
  text: "Premature closure of %s."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormallyIncreasedQualityOfBiologicalProcess
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedQualityOfBiologicalProcess.yaml
description: "Process that appears in some (unspecified) way strengthened or increased (more frequent, more strong)."

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

classes:
  increased process quality: PATO:0002304
  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: "increased qualitatively %s"
  vars:
   - biological_process

def:
  text: "Increased qualitatively %s."
  vars:
    - biological_process

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


text:
pattern_name: abnormalDegenerationOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalDegenerationOfAnatomicalEntity.yaml
description: "deterioration or loss of function of a tissue that was once present, such as HP_0000546 retinal degeneration."

contributors:
- https://orcid.org/0000-0002-3528-5267
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0001-9076-6015
classes:
  degenerate: PATO:0000639
  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 degeneration"
  vars:
  - anatomical_entity

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

def:
  text: "Partial or complete degeneration of %s tissue that was once present."
  vars:
  - anatomical_entity

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


text:
pattern_name: abnormallyDecreasedStrengthOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedStrengthOfAnatomicalEntity.yaml
description: "Weakness or decreased ability to exert power of an anatomical entity, such as HP_0001324 Muscle weakness."

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-3528-5267
classes:
  decreased strength: PATO:0001779
  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 strength"
  vars:
  - anatomical_entity

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

def:
  text: "Weakness or decreased strength of %s."
  vars:
  - anatomical_entity

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


text:
pattern_name: atrophiedAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/atrophiedAnatomicalEntity.yaml
description: "Atrophy (wasting) of an anatomical structure, such as HP_0410279 'Atrophic pituitary gland'."

contributors:
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0002-3528-5267

classes:
  atrophied: PATO:0001623
  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 atrophy"
  vars:
   - anatomical_entity

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

def:
  text: "Partial or complete wasting (loss) of %s tissue that was once present."
  vars:
    - anatomical_entity

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


text:
---
pattern_name: abnormalLengthOfAnatomicalEntity

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

description: "Use this phenotype pattern when the length of an anatomical
  entity is abnormal. If the anatomical entity is specifically longer or
  shorter than normal, then use the more specific increased length or decreased
  length phenotype patterns, respectively."

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0040157  # Abnormal intermamillary distance
#    - http://purl.obolibrary.org/obo/HP_0200011  # Abnormal length of corpus callosum
#    - http://purl.obolibrary.org/obo/MP_0011999  # abnormal tail length
#    - http://purl.obolibrary.org/obo/MP_0020999  # abnormal small intestine length
#    - http://purl.obolibrary.org/obo/ZP_0022039  # head length, abnormal

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

classes:
  length: PATO:0000122
  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: "abnormal %s length"
  vars:
    - anatomical_entity

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

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

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


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

classes:
  concentration of: PATO:0000033
  abnormal: PATO:0000460
  chemical: CHEBI:24431

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  chemical: "chemical"

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

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

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

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


text:
pattern_name: abnormalFunctionalityOfPartOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalFunctionalityOfPartOfAnatomicalEntity.yaml
description: "Dysfunction of a part of an anatomical entity, such as HP_0007905 'Abnormal iris vasculature'."

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

classes:
  functionality: PATO:0001509
  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: "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_part_of' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormalRateOfBiologicalProcessBeforeStage
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalRateOfBiologicalProcessBeforeStage.yaml
description: "An abnormal rate of a biological process that must occur before progresssing to the next developmental stage in an organism. For example FBcv:0000450 'abnormal developmental rate', that must occur during development (before mature adult stage)."

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

classes:
  abnormal: PATO:0000460
  rate: PATO:0000161
  biological_process: GO:0008150
  life_cycle_stage: UBERON:0000105

relations:
  before: RO:0002083
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  biological_process: "'biological_process'"
  stage: "'life_cycle_stage'"

name:
  text: "abnormal %s rate before %s"
  vars:
   - biological_process
   - stage

def:
  text: "Abnormal rate of %s before the %s."
  vars:
   - biological_process
   - stage

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


text:
---
pattern_name: non-functionalAnatomicalEntity

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

description: 'Use this phenotype pattern when an anatomical entity is unable or
  completely fails to perform its regular function or functions. In cases of
  decreased functionality of the anatomical entity, consider the phenotype
  pattern "abnormallyDecreasedFunctionalityOfAnatomicalEntity.yaml".'

#  examples:
#    - http://purl.obolibrary.org/obo/ZP_0003641  # heart non-functional, abnormal
#    - http://purl.obolibrary.org/obo/HP_0000083  # Renal insufficiency
#    - http://purl.obolibrary.org/obo/MP_0003606  # kidney failure
#    - http://purl.obolibrary.org/obo/HP_0001399  # Hepatic failure
#    - http://purl.obolibrary.org/obo/MP_0003326  # liver failure

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

classes:
  non-functional: PATO:0001511
  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: "non-functional %s"
  vars:
    - anatomical_entity

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

def:
  text: "Inability or failure of %s to perform its regular function or
    functions."
  vars:
    - anatomical_entity

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


text:
---
pattern_name: abnormallyOpaqueAnatomicalEntity

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

description: 'Use this phenotype pattern in case of reduced clarity of an
  anatomical entity, for example, when it is cloudy or shows decreased
  transparency.'

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0000518  # Cataract
#    - http://purl.obolibrary.org/obo/HP_0007787  # Posterior subcapsular cataract
#    - http://purl.obolibrary.org/obo/MP_0001304  # cataract
#    - http://purl.obolibrary.org/obo/MP_0002700  # opacity of vitreous body
#    - http://purl.obolibrary.org/obo/ZP_0002198  # yolk opaque, abnormal

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

classes:
  opaque: PATO:0000963
  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: "opaque %s"
  vars:
    - anatomical_entity

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

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

def:
  text: "Impaired ability or inability of light to pass through %s."
  vars:
    - anatomical_entity

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


text:
---
pattern_name: spatialDeviationOfAnatomicalEntity

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

description: "Use this phenotype pattern in case an anatomical entity
  displays abnormal deviation in a spatial sense. The anatomical entity
  shows altered direction or position, but the deviation is smaller than
  in the case of a 'PATO:0000628 mislocalised' anatomical entity, where
  there is a large change in the position of the entire object.
  Moreover, if the shape of anatomical entity is characterised by an
  abnormal curvature (of an entity being inherently curved), then use
  the alternative 'PATO:0000406 curved' phenotype pattern."

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0004097  # Deviation of finger
#    - http://purl.obolibrary.org/obo/HP_0100498  # Deviation of toes
#    - http://purl.obolibrary.org/obo/MP_0030199  # deviated nasal septum
#    - http://purl.obolibrary.org/obo/ZP_0010713  # vertebral column deviation, abnormal

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

classes:
  deviation: PATO:0002175
  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: "deviation of %s"
  vars:
    - anatomical_entity

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

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

def:
  text: "Spatial deviation of %s from its normal direction or position."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormalNumberOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalNumberOfAnatomicalEntity.yaml
description: "abnormal or altered number of anatomical enities. For example, has abnormal number of heads."

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

classes:
  amount: PATO:0000070
  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 number of anatomical enitites of type %s"
  vars:
   - anatomical_entity

annotations:
  -
    annotationProperty: exact_synonym
    text: "altered number of %ss"
    vars:
     - anatomical_entity
  -
    annotationProperty: exact_synonym
    text: "abnormal number of %ss"
    vars:
     - anatomical_entity

def:
  text: "Any structural anomaly that causes there to be an abnormal number %s."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormalArrestedDevelopmentDuringStage
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalArrestedDevelopmentDuringStage.yaml
description: "Arrest or prematurely terminated development at a specific development stage in an organism."

contributors:
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0002-4532-2703
  - https://orcid.org/0000-0002-7073-9172

classes:
  arrested: PATO:0000297
  abnormal: PATO:0000460
  developmental_process: GO:0032502
  life_cycle_stage: UBERON:0000105

relations:
  happens_during: RO:0002092
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  development: "'developmental_process'"
  stage: "'life_cycle_stage'"

name:
  text: "arrested %s during %s"
  vars:
   - development
   - stage

def:
  text: "Abnormal(ly) arrested (of) %s in the %s."
  vars:
   - development
   - stage

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


text:
pattern_name: abnormallyIncreasedFunctionalityOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedFunctionalityOfAnatomicalEntityInLocation.yaml
description: "Overactivity or hyperfunctionality of an organ or anatomical entity in a specific location."

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

classes:
  increased functionality: PATO:0001625
  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'"
  location: "'independent continuant'"

name:
  text: "%s hyperactivity in %s"
  vars:
   - anatomical_entity
   - location

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

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


text:
pattern_name: abnormalNumberOfCellularComponent
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalNumberOfCellularComponent.yaml
description: "abnormal or altered number of cellular components. For example, HP_0012102 Abnormal mitochondrial number."

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

classes:
  amount: PATO:0000070
  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: "abnormal number of %s"
  vars:
   - cellular_component

annotations:
  -
    annotationProperty: exact_synonym
    text: "altered number of %ss"
    vars:
     - cellular_component
  -
    annotationProperty: exact_synonym
    text: "abnormal number of %ss"
    vars:
     - cellular_component

def:
  text: "Any anomaly that causes there to be an abnormal number %s."
  vars:
    - cellular_component

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


text:
pattern_name: edematousAnatomicalEntity

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

description: 'Use this pattern when the phenotype is abnormal accumulation of fluid in an anatomical entity, e.g. edema in lung.'

#  examples:
#    - http://purl.obolibrary.org/obo/XPO_0141324  # edema in brain
#    - http://purl.obolibrary.org/obo/XPO_0141593  # edema in lung
#    - http://purl.obolibrary.org/obo/XPO_0115698  # abnormally edematous pericardium
#    - http://purl.obolibrary.org/obo/MP_0012270  # cardiac edema
#    - http://purl.obolibrary.org/obo/ZP_0000038  # pericardium edematous, abnormal
#    - http://purl.obolibrary.org/obo/ZP_0001451  # head edematous, abnormal

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/0000-0003-4606-0597  # Susan Bello
  - https://orcid.org/0000-0002-9900-7880  # Yvonne M. Bradford
  - https://orcid.org/0000-0002-3528-5267  # Sofia Robb

classes:
  edematous: PATO:0001450
  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: "edematous %s"
  vars:
    - anatomical_entity

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

  - annotationProperty: exact_synonym
    text: "oedema in %s"
    vars:
      - anatomical_entity

def:
  text: "Abnormal accumulation of fluid in %s."
  vars:
    - anatomical_entity

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


text:
pattern_name: blisteredAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/blisteredAnatomicalEntityInLocation.yaml
description: "Blistering of an an anatomical entity, like blistered skin or feet."

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  blistered: PATO:0001928
  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 blistered %s in %s"
  vars:
  - anatomical_entity
  - location

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

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

equivalentTo:
  text: "'has_part' some ('blistered' 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: abnormallyIncreasedSizeOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedSizeOfAnatomicalEntity.yaml
description: "A enlarged entity, like an abnormally large anatomical structure.\ti.e. HP_0012081 'Enlarged cerebellum'"

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/0000-0003-4148-4606
- https://orcid.org/0000-0001-7941-2961
classes:
  increased size: PATO:0000586
  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 size of the %s"
  vars:
  - anatomical_entity

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

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

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


text:
pattern_name: abnormallyIncreasedEfficacyOfBehavior
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedEfficacyOfBehavior.yaml
description: "Behavior occurs with a higher efficacy, i.e. an increased ability to produce its output. For example, male courtship behavior that is more attractive to females, or memory that results in a stronger aversive response to a stimulus associated with punishment."

contributors:
  - http://orcid.org/0000-0002-1373-1705

classes:
  increased efficacy: PATO:0015004
  abnormal: PATO:0000460
  behavior process: NBO:0000313

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

vars:
  behavior_process: "'behavior process'"

name:
  text: "abnormally increased efficacy of %s"
  vars:
   - behavior_process

def:
  text: "Increased ability of %s to produce its output."
  vars:
    - behavior_process

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


text:
pattern_name: abnormallyDecreasedLevelOfChemicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedLevelOfChemicalEntity.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

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: "decreased level of %s"
  vars:
   - chemical_entity

def:
  text: "A decreased amount in the level of %s."
  vars:
    - chemical_entity

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


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

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
  increased pigmentation: PATO:0002250

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 pigmentation in the %s"
  vars:
   - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "increasing of pigment in the %s"
    vars:
     - anatomical_entity
  - annotationProperty: exact_synonym
    text: "%s hyperpigmentation"
    vars:
     - anatomical_entity

def:
  text: "Increased or increasing of pigmentation of %s."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormallyDecreasedQualityOfBiologicalProcessInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedQualityOfBiologicalProcessInLocation.yaml
description: "Process in a location that appears in some (unspecified) way impaired or decreased (less frequent, less strong)."

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

classes:
  decreased process quality: PATO:0002302
  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 qualitatively %s in %s"
  vars:
   - biological_process
   - location

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

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


text:
---
pattern_name: wrinkledAnatomicalEntity

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

description: "Use this phenotype pattern when anatomical entity is
  marked by one or more creases in a normally smooth surface. Consider
  the 'foldedAnatomicalEntity.yaml' phenotype pattern when the
  anatomical when an anatomical entity has morphological abnormalities
  involving folding all or any part of it over another connected part."

#  examples:
#    - http://purl.obolibrary.org/obo/MP_0021107  # retina fold
#    - http://purl.obolibrary.org/obo/MP_0011205  # excessive folding of visceral yolk sac
#    - http://purl.obolibrary.org/obo/HP_0008052  # Retinal fold
#    - http://purl.obolibrary.org/obo/MP_0001211  # wrinkled skin
#    - http://purl.obolibrary.org/obo/ZP_0015987  # nuclear envelope cell wrinkled, abnormal

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

classes:
  wrinkled: PATO:0001810
  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: "wrinkled %s"
  vars:
    - anatomical_entity

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

def:
  text: "Wrinkled %s displaying one or more creases in a normally smooth
    surface."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormalAbsenceOfProteinLocalizationInCellularComponent
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfProteinLocalizationInCellularComponent.yaml
description: "Any process in which a protein is transported to, or maintained in, a specific sub-cellular location that normally occurs does not occur."

contributors:
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0001-8314-2140
  - https://orcid.org/0000-0002-4532-2703
  - https://orcid.org/0000-0003-4148-4606
  - https://orcid.org/0000-0002-7073-9172

classes:
  abnormal: PATO:0000460
  absent: PATO:0000462
  protein localization: GO:0008104
  cellular component: GO:0005575

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  has_target_end_location: RO:0002339

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  location: "'cellular component'"

name:
  text: "absent protein localization in %s"
  vars:
   - location

def:
  text: "Absent or undetectable protein localization %s."
  vars:
   - location

equivalentTo:
  text: "'has_part' some ('absent' and ('inheres_in' some ('protein localization' and ('has_target_end_location' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
    - location


text:
pattern_name: abnormalMotilityOfCellularComponent
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalMotilityOfCellularComponent.yaml
description: "An abnormality of the ability to move (motility) a cellular component/cells. Examples include 'Abnormal cilium motility'."

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

classes:
  process quality: PATO:0001236
  abnormal: PATO:0000460
  cellular component: GO:0005575
  movement of cell or subcellular component: GO:0006928

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  results_in_movement_of: RO:0002565

vars:
 cellular_component: "'cellular component'"

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

def:
  text: "Abnormal ability to move %s."
  vars:
    - cellular_component

equivalentTo:
  text: "'has_part' some ('process quality' and ('inheres_in' some ('movement of cell or subcellular component' and ('results_in_movement_of' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
    - cellular_component


text:
pattern_name: paralysedAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/paralysedAnatomicalEntity.yaml
description: "The complete loss of the ability to move a body part, e.g. a paralysed tail."

contributors:
  - https://orcid.org/0000-0002-9611-1279

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  paralysed: PATO:0000763

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: "paralysed %s"
  vars:
  - anatomical_entity

def:
  text: "Complete loss of the ability to move %s."
  vars:
  - anatomical_entity

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

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


text:
---
pattern_name: delaminatedAnatomicalEntity

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

description: 'Use this pattern where sheets that constitute or are part of an
  anatomical entity show separation into constituent layers.'

#  examples:
#    - http://purl.obolibrary.org/obo/ZP_0009315  # ectoderm delaminated, abnormal
#    - http://purl.obolibrary.org/obo/MP_0000791  # delaminated cerebral cortex
#    - http://purl.obolibrary.org/obo/MP_0000884  # delaminated Purkinje cell layer
#    - http://purl.obolibrary.org/obo/MP_0000887  # delaminated cerebellar granule layer
#    - http://purl.obolibrary.org/obo/MP_0002648  # delaminated enamel

contributors:
  - https://orcid.org/0000-0001-8314-2140  # Ray Stefancsik
  - https://orcid.org/0000-0002-7356-1779  # Nicolas Matentzoglu
  - 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:
  delaminated: PATO:0001514
  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: "delaminated %s"
  vars:
    - anatomical_entity

def:
  text: "Separation of %s, or its layers or sheets into constituent layers."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormalDegenerationOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalDegenerationOfAnatomicalEntityInLocation.yaml
description: "Deterioration or loss of function of a tissue that was once present in a location."

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

classes:
  degenerate: PATO:0000639
  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: "%s degeneration in %s"
  vars:
  - anatomical_entity
  - location

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

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

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


text:
---
pattern_name: abnormallyIvoryAnatomicalEntityInLocation

pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIvoryAnatomicalEntityInLocation.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). Use this pattern for anatomical locations for which the anatomical class is composed of two anatomical terms (e.g. "Ivory epiphyses of the toes").'

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0010119  # Ivory epiphyses of the hallux
#    - http://purl.obolibrary.org/obo/HP_0010168  # Ivory epiphyses of the toes
#    - http://purl.obolibrary.org/obo/HP_0009388  # Ivory epiphyses of the 5th finger

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
  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
  related_synonym: oio:hasRelatedSynonym
  xref: oio:hasDbXref

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

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

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

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

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


text:
pattern_name: abnormalShapeOfAnatomicalEntityByShapeType
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalShapeOfAnatomicalEntityByShapeType.yaml
description: "Anatomical enity with an abnormal shape of a specified shape, e.g. columnar shaped head."

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

classes:
  shape: PATO:0000052
  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'"
  shape: "'shape'"

name:
  text: "%s %s"
  vars:
   - shape
   - entity

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

def:
  text: "Any structural anomaly that causes %s to be %s shaped."
  vars:
    - entity
    - shape

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


text:
pattern_name: abnormallyIncreasedWidthOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedWidthOfAnatomicalEntityInLocation.yaml
description: "An abnormal increase in the width of an anatomical entity in a location, e.g. an abnormally wide bone in the hand."

contributors:
- https://orcid.org/0000-0002-9611-1279

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  increased width: PATO:0000600
  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 width of the %s in %s"
  vars:
  - anatomical_entity
  - location

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

def:
  text: "Wide or increased width of the %s in %s."
  vars:
  - anatomical_entity
  - location

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


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

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

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 apoptotic %s"
  vars:
  - anatomical_entity

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

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

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


text:
pattern_name: hypoplasticAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/hypoplasticAnatomicalEntity.yaml
description: "An underdeveloped or small anatomical entity. For example, HP_0008417 'Vertebral hypoplasia'"

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-3528-5267
classes:
  hypoplastic: PATO:0000645
  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 hypoplasia"
  vars:
  - anatomical_entity

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

def:
  text: "Small, underdeveloped %s."
  vars:
  - anatomical_entity

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


text:
pattern_name: necroticAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/necroticAnatomicalEntity.yaml
description: "The presence of unprogrammed cell death in an anatomical entity."

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

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  necrotic: PATO:0000647

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

vars:
  anatomical_entity: "'anatomical entity'"

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

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

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


text:
pattern_name: hyperplasticAnatomicalEntity.yaml

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

description: 'Hyperplastic anatomical entity, for example, thyroid gland hyperplasia, characterised by an increase in cell number.'

# examples:
#   - http://purl.obolibrary.org/obo/HP_0008249
#   - http://purl.obolibrary.org/obo/MP_0000630
#   - http://purl.obolibrary.org/obo/MP_0013765

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
  hyperplastic: PATO:0000644

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: "%s hyperplasia"
  vars:
    - anatomical_entity

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

def:
  text: "%s shows abnormally increased number of cells in a tissue (hyperplasia) typically resulting in increased size."
  vars:
    - anatomical_entity

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


text:
pattern_name: aplasticAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/aplasticAnatomicalEntity.yaml
description: "A congenital absence of an anatomical entity. For example, HP_0009238 'Aplasia of the 5th finger'."

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-3528-5267
classes:
  aplastic: PATO:0001483
  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: "aplastic %s"
  vars:
  - anatomical_entity

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

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

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


text:
pattern_name: abnormalShapeOfPhysicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalShapeOfPhysicalEntity.yaml
description: "abnormal shape of an anatomical entity or a measurement of a process, such as an ECG wave"

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

classes:
  shape: PATO:0000052
  abnormal: PATO:0000460
  entity: BFO:0000002

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  entity: "'entity'"

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

annotations:
  -
    annotationProperty: exact_synonym
    text: "abnormally shaped %s"
    vars:
     - entity

def:
  text: "Any structural anomaly in the shape of the %s."
  vars:
    - entity

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


text:
pattern_name: abnormallyImmobileAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyImmobileAnatomicalEntity.yaml
description: "An abnormality of the complete lack of the ability to move (immobility) an anatomical entity, including cells."

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

classes:
  immobile: PATO:0000300
  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 immobile %s"
  vars:
   - anatomical_entity

def:
  text: "complete lack of mobility of the %s."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormallyDecreasedEfficacyOfBehavior
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedEfficacyOfBehavior.yaml
description: "Behavior occurs with a reduced efficacy, i.e. a decreased ability to produce its output. For example, male courtship behavior that is less attractive to females, or memory that results in a weaker aversive response to a stimulus associated with punishment."

contributors:
  - http://orcid.org/0000-0002-1373-1705

classes:
  decreased efficacy: PATO:0015003
  abnormal: PATO:0000460
  behavior process: NBO:0000313

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

vars:
  behavior_process: "'behavior process'"

name:
  text: "abnormally decreased efficacy of %s"
  vars:
   - behavior_process

def:
  text: "Decreased ability of %s to produce its output."
  vars:
    - behavior_process

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


text:
pattern_name: abnormallyIncreasedRateOfBiologicalProcess
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedRateOfBiologicalProcess.yaml
description: "Abnormally increased frequency of a biological process occuring (per some unit of time)."

contributors:
- https://orcid.org/0000-0001-9076-6015
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0003-4148-4606
- https://orcid.org/0000-0002-7356-1779
- https://orcid.org/0000-0002-3528-5267
classes:
  increased rate: PATO:0000912
  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 %s"
  vars:
  - biological_process

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

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


text:
pattern_name: abnormalHeightOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalHeightOfAnatomicalEntity.yaml
description: "An abnormally tall or short anatomical structure, such as HP:0000002 Abnormality of body height.'"

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

classes:
  height: PATO:0000119
  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 height"
  vars:
   - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "Abnormal %s height"
    vars:
     - anatomical_entity

def:
  text: "Deviation from the norm of %s height with respect to that which is expected according to age and gender norms."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormalAbsenceOfAnatomicalEntityDueToDegeneration
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfAnatomicalEntityDueToDegeneration.yaml
description: "The complete loss of an antomical entity due to degeneration."

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

classes:
  absence due to degeneration: PATO:0015001
  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: "missing %s due to degeneration"
  vars:
   - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "loss of %s due to degeneration"
    vars:
     - anatomical_entity

def:
  text: "Complete wasting (loss) of %s tissue that was once present."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('absence due to degeneration' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity