text:
pattern_name: abnormallyIncreasedRateOfContinuousBiologicalProcess
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedRateOfContinuousBiologicalProcess.yaml
description: "Abnormally increased rate of a continuous biological process, e.g. rate of an enzyme reaction or growth rate. Does not include increases in rates of occurrence/frequency. Different to patterns using PATO:0002471 'increased velocity', which inheres in a physical object (continuant), rather than a process (occurrent)."

# examples:
#  - http://purl.obolibrary.org/obo/MP_0008965 # increased basal metabolism
#  - http://purl.obolibrary.org/obo/FBcv_0000792 # increased speed of aging
#  - http://purl.obolibrary.org/obo/ZP_0001532 # blood circulation increased rate, abnormal

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

classes:
  increased_rate_of_continuous_process: PATO:0055005
  abnormal: PATO:0000460
  biological_process: GO:0008150

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  biological_process: "'biological_process'"

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

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

annotations:
- annotationProperty: exact_synonym
  text: "increased speed of %s"
  vars:
  - biological_process
- annotationProperty: exact_synonym
  text: "increased %s velocity"
  vars:
  - biological_process

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


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

contributors:
  - https://orcid.org/0000-0001-9076-6015
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0002-1373-1705

classes:
  increased rate: PATO:0000912
  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 increased rate of %s"
  vars:
   - behavior_process

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

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

repo_name: obophenotype/upheno

repo_language: Makefile

mime_type: text/plain


text:
pattern_name: abnormallyDecreasedVolumeOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedVolumeOfAnatomicalEntity.yaml
description: "Decreased volume of an anatomical entity, e.g. HP:0012695 Decreased thalamic volume."

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-3528-5267
classes:
  decreased volume: PATO:0000596
  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 volume of the %s"
  vars:
  - anatomical_entity

def:
  text: "An abnormal reduction in the volume of the %s."
  vars:
  - anatomical_entity

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


text:
pattern_name: abnormallyDecreasedSizeOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedSizeOfAnatomicalEntityInLocation.yaml
description: "Abnormally small anatomical entity in a location, e.g. and abnormally small finger on the right hand."

contributors:
- https://orcid.org/0000-0002-7356-1779
- https://orcid.org/0000-0002-3528-5267
classes:
  decreased size: PATO:0000587
  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: "decreased size of the %s in the %s"
  vars:
  - anatomical_entity
  - location

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

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

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


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

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

classes:
  decreased occurrence: PATO:0002052
  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: "decreased occurrence of %s in %s"
  vars:
   - biological_process
   - location

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

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


text:
---
pattern_name: dislocatedAnatomicalEntity

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

description: "Use this phenotype pattern when an anatomical entity developed in
  its normal location, but later it is found outside of that original place or
  position. Consider the alternative 'mislocalised PATO:0000628' positional
  quality pattern when the anatomical entity is found outside of its usual or
  proper place, because it developed in the wrong (ectopic) location."

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0001373  # Joint dislocation
#    - http://purl.obolibrary.org/obo/HP_0002827  # Hip dislocation
#    - http://purl.obolibrary.org/obo/MP_0030795  # joint dislocation
#    - http://purl.obolibrary.org/obo/MP_0030796  # hip dislocation
#    - http://purl.obolibrary.org/obo/MP_0030843  # elbow dislocation

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

classes:
  dislocated: PATO:0001852
  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: "%s dislocation"
  vars:
    - anatomical_entity

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

def:
  text: "Dislocation or displacement of %s from the place or position where it
    developed."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormallyFusedAnatomicalEntitiesInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyFusedAnatomicalEntitiesInLocation.yaml
description: "An anatomical entity in a particular location that is abnormally fused with another anatomical entity in a particular location. Before using this pattern make sure abnormallyFusedAnatomicalEntities is not applicable."

classes:
  fused: PATO:0000642
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  independent continuant: BFO:0000004

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

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

name:
  text: "abnormally fused %s in %s with %s in %s"
  vars:
  - anatomical_entity
  - location
  - anatomical_entity_fused_with
  - location_fused_with

annotations:
- annotationProperty: exact_synonym
  text: "abnormal fusion of %s in %s and %s in %s"
  vars:
  - anatomical_entity
  - location
  - anatomical_entity_fused_with
  - location_fused_with

def:
  text: "Any abnormal fusion of the %s in the %s and the %s in the %s."
  vars:
  - anatomical_entity
  - location
  - anatomical_entity_fused_with
  - location_fused_with

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


text:
pattern_name: abnormallyIncreasedThicknessOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedThicknessOfAnatomicalEntityInLocation.yaml
description: "An abnormally thickened anatomical entity in a location, like an abnormally thick skin of the hand."

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

classes:
  increased thickness: PATO:0000591
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  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 thickness of the %s in %s"
  vars:
   - anatomical_entity
   - location

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

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

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


text:
---
pattern_name: obstructedAnatomicalEntity

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

description: 'Use this phenotype pattern when an anatomical space of an
  anatomical entity is blocked or filled with filled with one or more
  obstacles. Typically, this results in some impediment, blockage, or reversal
  of the normal flow of the contents of the entity or space. The use of an
  anatomical space class would be preferred to material anatomical entities for
  this phenotype pattern, but the logical pattern definition is kept permissive
  for now.'

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0005214  # Intestinal obstruction
#    - http://purl.obolibrary.org/obo/MP_0003270  # intestinal obstruction
#    - http://purl.obolibrary.org/obo/MP_0006134  # artery occlusion
#    - http://purl.obolibrary.org/obo/HP_0006000  # Ureteral obstruction
#    - http://purl.obolibrary.org/obo/MP_0031101  # nasal obstruction
#    - http://purl.obolibrary.org/obo/ZP_0021087  # bile canaliculus obstructed, abnormal

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

classes:
  obstructed: PATO:0000648
  abnormal: PATO:0000460
  anatomical_entity: UBERON:0001062  # anatomical_space: UBERON:0000464

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym
  related_synonym: oio:hasRelatedSynonym
  xref: oio:hasDbXref

vars:
  anatomical_space: "'anatomical_entity'"

name:
  text: "%s obstruction"
  vars:
    - anatomical_space

annotations:
  - annotationProperty: exact_synonym
    text: "obstruction of %s"
    vars:
      - anatomical_space

  - annotationProperty: exact_synonym
    text: "obstructed %s"
    vars:
      - anatomical_space

def:
  text: "Obstructed %s due to it being blocked or filled with one or more
    obstacles."
  vars:
    - anatomical_space

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


text:
pattern_name: abnormalMolecularFunction
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalMolecularFunction.yaml
description: "An abnormality in a molecular function, like abnormal DNA ligase activity, or abnormal catalase activity."

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/0000-0003-4148-4606
- https://orcid.org/0000-0001-7941-2961
classes:
  process quality: PATO:0001236
  abnormal: PATO:0000460
  molecular function: GO:0003674

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

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

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

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


text:
pattern_name: abnormallyFusedAnatomicalEntities
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyFusedAnatomicalEntities.yaml
description: "An anatomical entity that is abnormally fused with another anatomical entity."

classes:
  fused: PATO:0000642
  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_fused_with: "'anatomical entity'"

name:
  text: "abnormally fused %s and %s"
  vars:
  - anatomical_entity
  - anatomical_entity_fused_with

annotations:
- annotationProperty: exact_synonym
  text: "abnormal fusion of %s and %s"
  vars:
  - anatomical_entity
  - anatomical_entity_fused_with

def:
  text: "Any abnormal fusion of the %s and the %s."
  vars:
  - anatomical_entity
  - anatomical_entity_fused_with

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


text:
pattern_name: irregularMassDensityOfAnatomicalEntity

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

description: "Use it in cases of irregular mass density of anatomical entity. Please, note that 'density' in 'irregular density' implies mass density in PATO right now. This is going to change. Area and volume density will be split out and made siblings of mass density. It means that there will be new patterns to be used for phenotypes where irregular mass density is inappropriate, i.e counts of entities per unit area/volume."

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0003948  # Irregular epiphyses of the elbow
#    - http://purl.obolibrary.org/obo/HP_0003301  # Irregular vertebral endplates
#    - http://purl.obolibrary.org/obo/HP_0004019  # Radial metaphyseal irregularity
#    - http://purl.obolibrary.org/obo/ZP_0015028  # iridophore mass density, 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:
  irregular_density: PATO:0002141
  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: "irregular mass density of %s"
  vars:
    - anatomical_entity

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

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

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


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

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

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  decreased speed: PATO:0000304

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 speed of the %s"
  vars:
   - anatomical_entity

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

def:
  text: "slower, decreased speed of %s"
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormallyIncreasedHeightOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedHeightOfAnatomicalEntity.yaml
description: "An abnormally tall anatomical structure, such as HP_0000348 High forehead.'"

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-3528-5267
classes:
  increased height: PATO:0000570
  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 height of the %s"
  vars:
  - anatomical_entity

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

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

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


text:
pattern_name: abnormallyDecreasedDistanceBetweenAnatomicalEntities
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedDistanceBetweenAnatomicalEntities.yaml
description: "The distance between two anatomical entities is decreased. For example the distance between eyes."

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

classes:
  abnormal: PATO:0000460
  anatomical entity1: UBERON:0001062
  anatomical entity2: UBERON:0001062
  decreased distance: PATO:0000375

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity1: "'anatomical entity1'"
  anatomical_entity2: "'anatomical entity2'"

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

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

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

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


text:
---
pattern_name: abnormalConstrictionOfAnatomicalEntity

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

description: "An anatomical entity that is being drawn together, compressed or squeezed physically."

# examples
# http://purl.obolibrary.org/obo/HP_0001650      # Aortic valve stenosis
# http://purl.obolibrary.org/obo/HP_0002043      # Esophageal stricture
# http://purl.obolibrary.org/obo/MP_0003389      # constriction of pericardium

contributors:
  - https://orcid.org/0000-0001-5208-3432  # Nicole Vasilevsky
  - https://orcid.org/0000-0001-6757-4744  # Arwa Ibrahim
  - 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/0000-0002-4142-7153  # Sabrina Toro
  - https://orcid.org/0000-0002-8361-2795  # James McLaughlin

classes:
  constricted: PATO:0001847
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

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

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

def:
  text: "An %s that is being drawn together, compressed or squeezed physically."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormalHasFewerPartsOfTypeAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/abnormalHasFewerPartsOfTypeAnatomicalEntityInLocation.yaml
description: "An anatomical entity (which is located somewhere) has fewer instances of a part. For example, the hand (which is part of the right arm) has fewer digits. Consider using decreased number of anatomical entity in location instead."

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

classes:
  has fewer parts of type: PATO:0002001
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  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:
  whole_anatomical_entity: "'anatomical entity'"
  part_anatomical_entity: "'anatomical entity'"
  location: "'independent continuant'"

name:
  text: "has fewer parts of type %s in %s, which is located in %s"
  vars:
   - part_anatomical_entity
   - whole_anatomical_entity
   - location

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

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

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


text:
pattern_name: abnormallyDecreasedWeightOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedWeightOfAnatomicalEntity.yaml
description: "Decreased mass of an anatomical entity, e.g. decreased mass of the whole organism. NOTE: We are using decreased mass (PATO:0001562), 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:
  decreased mass: PATO:0001562
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym
  narrow_synonym: oio:hasNarrowSynonym

vars:
  anatomical_entity: "'anatomical entity'"

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

annotations:
  - annotationProperty: exact_synonym
    text: "small %s mass"
    vars:
    - anatomical_entity
  - annotationProperty: exact_synonym
    text: "low %s mass"
    vars:
    - anatomical_entity
  - annotationProperty: narrow_synonym
    text: "decreased %s weight"
    vars:
    - anatomical_entity

def:
  text: "An abnormal decrease in mass in the %s."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormallyIncreasedLevelOfChemicalEntityWithRoleInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedLevelOfChemicalEntityWithRoleInLocation.yaml
description: "An abnormally increased level of a chemical with a specific role, such as a metabolite or hormone like androgen, in a location, such as blood. For example, HP_0030348 'Increased circulating androgen level'."

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

classes:
  increased amount: PATO:0000470
  abnormal: PATO:0000460
  chemical entity: CHEBI:24431
  role: CHEBI:50906
  independent continuant: BFO:0000004

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

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

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

def:
  text: "An abnormally increased level of %s in the %s."
  vars:
  - role
  - location

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


text:
pattern_name: abnormalColorOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalColorOfAnatomicalEntity.yaml
description: "Any unspecified abnormality of the color of an anatomical entity, such as HP_0012086 'Abnormal urinary color'. Abnormal pigmentation does not necessarily mean a change in color, nor does a change in color require that the root cause be due to a change in the pigment cells/granules. Pigment cells are specialized cell type and can contain different colored pigment granules. There are also differences in the process of pigmentation (such as pattern of cells or pattern of granules in those cells) as well as the dependent continuant that is the color."

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

classes:
  color: PATO:0000014
  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 %s color"
  vars:
   - anatomical_entity

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

  - annotationProperty: exact_synonym
    text: "abnormal %s colour"
    vars:
     - anatomical_entity

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

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


text:
pattern_name: abnormallyDecreasedWidthOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedWidthOfAnatomicalEntityInLocation.yaml
description: "Abnormal decrease in the width of an anatomical entity, e.g. decreased width of the tail"

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  decreased width: PATO:0000599
  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: "decreased width of the %s in %s"
  vars:
  - anatomical_entity
  - location

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

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

equivalentTo:
  text: "'has_part' some ('decreased width' 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: increasedProportionOfCellTypeInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/increasedProportionOfCellTypeInLocation.yaml
description: "An increased proportion of a cell, in a location, like the blood. For example: HP_0032184 Increased proportion of memory T cells."

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'"
  location: "'independent continuant'"

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

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

equivalentTo:
  text: "'has_part' some ('increased 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: abnormallyIncreasedMotilityOfCellularComponentInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedMotilityOfCellularComponentInLocation.yaml
description: "Increased ability to move a cellular component in an anatomical entity/location."

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

classes:
  increased rate: PATO:0000912
  abnormal: PATO:0000460
  cellular component: GO:0005575
  independent continuant: BFO:0000004
  movement of cell or subcellular component: GO:0006928

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  occurs_in: BFO:0000066
  results_in_movement_of: RO:0002565

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

name:
  text: "increased %s motility in %s"
  vars:
   - cellular_component
   - location

def:
  text: "Increased ability to move %s in %s."
  vars:
    - cellular_component
    - location

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


text:
pattern_name: mislocalisedAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/mislocalisedAnatomicalEntityInLocation.yaml
description : "Abnormal anatomic location of an anatomicaly entity, such as XAO:0005038 'mislocalised nucleus in the myoblast'."

contributors:
  - https://orcid.org/0000-0002-7356-1779
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0001-9076-6015
  - https://orcid.org/0000-0003-1074-8103

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  mislocalised: PATO:0000628
  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 localised %s in %s"
  vars:
   - anatomical_entity
   - location

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

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

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


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

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'"
  compared_cell: "'cell'"
  location: "'independent continuant'"

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

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

equivalentTo:
  text: "'has_part' some ('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: abnormalMassDensityOfAnatomicalEntity

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

description: 'Abnormal mass density (mass per unit volume) of an anatomical entity,  for example abnormal bone mineral density. This pattern is not to be used for count per area (e.g. cell count) phenotypes.'

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0004348  # Abnormality of bone mineral density
#    - http://purl.obolibrary.org/obo/HP_0009132  # Abnormal tarsal bone mineral density
#    - http://purl.obolibrary.org/obo/MP_0010119  # abnormal bone mineral density
#    - http://purl.obolibrary.org/obo/ZP_0015028  # iridophore mass density, 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/0000-0002-9900-7880  # 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

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 mass density"
  vars:
    - anatomical_entity

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

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

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


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

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

classes:
  decreased proportionality to: PATO:0040042
  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: "decreased proportion of %s relative to %s in %s"
  vars:
  - cell
  - compared_cell
  - location

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

equivalentTo:
  text: "'has_part' some ('decreased 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: decreasedProportionOfCellTypeInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/decreasedProportionOfCellTypeInLocation.yaml
description: "An decreased proportion of a cell, in a location, like the blood. For example: HP_0032183 Decreased proportion of memory T cells."

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

classes:
  decreased proportionality to: PATO:0040042
  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: "decreased proportion of %s in %s"
  vars:
  - cell
  - location

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

equivalentTo:
  text: "'has_part' some ('decreased 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: aplasticHypoplasticAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/aplasticHypoplasticAnatomicalEntity.yaml
description: "An underdeveloped or absent anatomical entity. This pattern should be used in cases where the anatomical entity is small or missing, but the clinician or researcher is unable to definitively say if it is a case of aplasia or hypoplasia. Using the moree specific term is preferred.For example, HP_0006265 'Aplasia/Hypoplasia of fingers'"

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-3528-5267
classes:
  aplastic or hypoplastic: PATO:0002290
  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: "aplasia or hypoplasia of %s"
  vars:
  - anatomical_entity

annotations:
- annotationProperty: exact_synonym
  text: "aplasia or hypoplasia affecting the %s"
  vars:
  - anatomical_entity

def:
  text: "Absence or underdevelopment of the %s."
  vars:
  - anatomical_entity

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


text:
pattern_name: abnormallyArrestedBiologicalProcessInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyArrestedBiologicalProcessInLocation.yaml
description: "A process that started but failed to occur, such as cell migration in the neural crest."

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

classes:
  arrested: PATO:0000297
  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: "arrested %s in %s"
  vars:
   - biological_process
   - location

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

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

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


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

classes:
  degenerate: PATO:0000639
  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: "%s degeneration"
  vars:
  - cellular_component

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

def:
  text: "Partial or complete degeneration of %s."
  vars:
  - cellular_component

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


text:
pattern_name: malformedAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/malformedAnatomicalEntity.yaml
description : "Congenital malformation of an anatomical entity, such as HP_0007993 'Malformed lacrimal duct'."

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

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  malformed: PATO:0000646

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 formed %s"
  vars:
   - anatomical_entity

def:
  text: "An abnormally formed/malformed %s."
  vars:
    - anatomical_entity

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

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


text:
pattern_name: abnormallyIncreasedMobilityOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedMobilityOfAnatomicalEntity.yaml
description: "An increased or enhanced ability to move an anatomical entity, including cells. Example: HP_0003318 'Cervical spine hypermobility' ."

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-3528-5267
classes:
  increased mobility: PATO:0002282
  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 %s mobility"
  vars:
  - anatomical_entity

def:
  text: "Increased or enhanced ability to move %s."
  vars:
  - anatomical_entity

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


text:
pattern_name: abnormalBehavior
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalBehavior.yaml
description: "Any unspecified abnormality of a behavior, such as HP_0012433 abnormal social behavior."

contributors:
  - https://orcid.org/0000-0001-9076-6015
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0002-1373-1705
  - https://orcid.org/0000-0001-7941-2961

classes:
  process quality: PATO:0001236
  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: "abnormal %s"
  vars:
   - behavior_process

def:
  text: "An anomaly in %s."
  vars:
    - behavior_process

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


text:
pattern_name: damagedAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/damagedAnatomicalEntityInLocation.yaml
description: "A damaged or injured anatomical entity in a location, such as HP_0003390 'Sensory axonal neuropathy'. The damage or injury may lead to loss of functionality or cell death."

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-3528-5267
classes:
  damaged: PATO:0001167
  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: "damaged %s in the %s"
  vars:
  - anatomical_entity
  - location

def:
  text: "A damaged or injured %s in the %s, that may lead to impaired function."
  vars:
  - anatomical_entity
  - location

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


text:
# Pattern directory
Moved here:
https://github.com/obophenotype/upheno/blob/master/src/patterns/dosdp-patterns/README.md


text:
pattern_name: hypoplasticAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/hypoplasticAnatomicalEntityInLocation.yaml
description: "An underdeveloped or small anatomical entity in a location. For example, PLANP:0000832 underdeveloped eyes in tail fragment"

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
  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 hypoplasia in %s"
  vars:
  - anatomical_entity
  - location

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

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

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


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

contributors:
- https://orcid.org/0000-0002-7356-1779
- https://orcid.org/0000-0001-7487-610X
- https://orcid.org/0000-0001-9076-6015
classes:
  decreased resistance to: PATO:0001651
  abnormal: PATO:0000460
  cellular organism: CARO:0010004
  chemical entity: CHEBI:24431

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  chemical_entity: "'chemical entity'"

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

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

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


text:
pattern_name: lesionedAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/lesionedAnatomicalEntity.yaml
description : "an antomical strucuture with one or more lesions. i.e., one or more lesions in the head"

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

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  lesioned: PATO:0040025

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'"

name:
  text: "lesion in %s"
  vars:
   - anatomical_entity

def:
  text: "An abnormal %s with one or more lesions."
  vars:
    - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "%s with lesion(s)"
    vars:
     - anatomical_entity

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


text:
pattern_name: abnormalColorOfAnatomicalEntityByColor

pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalColorOfAnatomicalEntityByColor.yaml
description: "Anatomical entity with an abnormal specified color."

#  examples:
#    - http://purl.obolibrary.org/obo/MP_0003136
#    - http://purl.obolibrary.org/obo/MP_0011414

contributors:
  - https://orcid.org/0000-0001-8314-2140
  - https://orcid.org/0000-0002-7073-9172
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0003-4606-0597
  - https://orcid.org/0000-0002-9900-7880

classes:
  abnormal: PATO:0000460
  anatomical_entity: UBERON:0001062
  color: PATO:0000014

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  entity: "'anatomical_entity'"
  color: "'color'"

name:
  text: "abnormally %s %s color"
  vars:
    - color
    - entity

annotations:
  - annotationProperty: exact_synonym
    text: "%s type abnormality of %s color"
    vars:
      - color
      - entity

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

def:
  text: "An abnormally %s %s."
  vars:
    - color
    - entity

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


text:
pattern_name: abnormallyIncreasedEfficacyOfProteinLocalizationInCellularComponent
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedEfficacyOfProteinLocalizationInCellularComponent.yaml
description: "Abnormally increased 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
  increased efficacy: PATO:0015004
  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: "increased protein localization in %s"
  vars:
   - location

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

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


text:
pattern_name: abnormallyPrematureBiologicalProcessInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyPrematureBiologicalProcessInLocation.yaml
description: "A biological process in a location that starts earlier than the natural start time or the reference process."

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

classes:
  premature: PATO:0000694
  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: "premature %s in %s"
  vars:
  - biological_process
  - location

def:
  text: "An abnormally early start time of %s in %s."
  vars:
  - biological_process
  - location

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


text:
pattern_name: abnormalAnatomicalEntityNotParts
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAnatomicalEntityNotParts.yaml
description: "Any unspecified abnormality of an anatomical entity, but excluding its parts. For example, abnormal cardiovascular system if it is not supposed to subsume abnormal heart."

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

classes:
  quality: PATO:0000001
  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 %s"
  vars:
   - anatomical_entity

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

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

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


text:
pattern_name: abnormalAbsenceOfMotilityOfCellularComponentInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAbsenceOfMotilityOfCellularComponentInLocation.yaml
description: "Absence of the ability to move (immotility) a cellular component in an anatomical entity/location."

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

classes:
  absent: PATO:0000462
  abnormal: PATO:0000460
  cellular component: GO:0005575
  independent continuant: BFO:0000004
  movement of cell or subcellular component: GO:0006928

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  occurs_in: BFO:0000066
  results_in_movement_of: RO:0002565

annotationProperties:
  exact_synonym: oio:hasExactSynonym

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

name:
  text: "absent %s motility in %s"
  vars:
   - cellular_component
   - location

annotations:
- annotationProperty: exact_synonym
  text: "immotile %s in %s"
  vars:
  - cellular_component
  - location

def:
  text: "Inability to move %s in %s."
  vars:
    - cellular_component
    - location

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


text:
pattern_name: abnormallyDecreasedHeightOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedHeightOfAnatomicalEntity.yaml
description: "An abnormally short anatomical structure, such as HP:0004322 Short stature."

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

classes:
  decreased height: PATO:0000569
  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 height of the %s"
  vars:
   - anatomical_entity

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

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

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


text:
#!/usr/bin/perl
while(<>) {
    if (m@^\*(.*)@) {
        my @vals = split(/\t/,$1);
        print join("\t",@vals)."\n" if $vals[4] > 0.4;
    }
}


text:
#!/usr/bin/perl
my $efile = shift @ARGV;

my %excludeh = ();
while(<>) {
    chomp;
    my ($id,$n) = split(/\t/);
    $excludeh{$id}=1;
}
print "entity\tentity label\n";
open(F,$efile) || die $efile;
while(<F>) {
    chomp;
    my ($id,$n) = split(/\t/);
    $id =~ m@/obo/(\w+)_@;
    my $s = $1;
    next unless $s eq 'UBERON' || $s eq 'GO' || $s eq 'CL' || $s eq 'WBbt' || $s eq 'FBbt' || $s eq 'MPATH' || $s eq 'NBO';
    if ($excludeh{$id}) {
        print STDERR "EXCLUDING: $_\n";
        next;
    }
    $id =~ s@^http://purl.obolibrary.org/obo/@@;
    print "$id\t$n\n";

}
close(F);