text:
pattern_name: aneurysmInAnatomicalStructure
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/aneurysmInAnatomicalStructure
description: "aneurysms only allowed at anatomical structures? why not any anatomical entity?"

classes:
  increased amount: PATO:0000470
  abnormal: PATO:0000460
  aneurysm: MPATH:90
  anatomical structure: UBERON:0000061

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  aneurysm: "aneurysm"
  anatomical_structure: "'anatomical structure'"

name:
  text: "%s %s"
  vars:
    - anatomical_structure
    - aneurysm

def:
  text: "An %s in the %s."
  vars:
    - aneurysm
    - anatomical_structure

equivalentTo:
  text: "'has_part' some ('increased amount' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some abnormal))"
  vars:
    - aneurysm
    - anatomical_structure

repo_name: obophenotype/upheno

repo_language: Makefile

mime_type: text/plain


text:
http://purl.obolibrary.org/obo/upheno/patterns-dev/aplasticGrowthOfAnatomicalEntity.yaml
http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyCurvedAnatomicalStructureByAnatomicalLocation.yaml
http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedProcessQualityInLocation.yaml
http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedSizeOfAnatomicalEntityInLocation.yaml
http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedWidthOfAnatomicalEntityInLocation.yaml
http://purl.obolibrary.org/obo/upheno/patterns-dev/duplicatedAnatomicalStructure.yaml
http://purl.obolibrary.org/obo/upheno/patterns-dev/duplicatedAnatomicalStructureInLocation.yaml
http://purl.obolibrary.org/obo/upheno/patterns-dev/incompleteClosureOfAnatomicalStructure.yaml
http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedCellProliferationInAnatomicalEntity.yaml

Check Nicole:

dysplasticAnatomicalEntity (check synonyms and labels and add def)
http://purl.obolibrary.org/obo/upheno/patterns-dev/arrestedBiologicalProcess.yaml
http://purl.obolibrary.org/obo/upheno/patterns-dev/arrestedBiologicalProcessInLocation.yaml
http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyBentAnatomicalStructure.yaml
http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedLengthOfAnatomicalEntityInLocation.yaml
http://purl.obolibrary.org/obo/upheno/patterns-dev/bifurcatedAnatomicalStructure.yaml
http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyClosedAnatomicalEntity.yaml
http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedProcessQuality.yaml


text:
pattern_name: abnormalPathology
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/abnormalPathology

classes:
  increased amount: PATO:0000470
  abnormal: PATO:0000460
  pathological entity: MPATH:0
  anatomical structure: UBERON:0000061

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  pathological_entity: "'pathological entity'"
  anatomical_structure: "'anatomical structure'"

name:
  text: "%s %s"
  vars:
    - anatomical_structure
    - pathological_entity

def:
  text: "An %s in the %s."
  vars:
    - pathological_entity
    - anatomical_structure

equivalentTo:
  text: "'has_part' some ('increased amount' and ('inheres_in' some %s) and ('part_of' some %s)) and ('has_modifier' some abnormal)"
  vars:
    - pathological_entity
    - anatomical_structure


text:
pattern_name: abnormallyAlteredNumberOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyAlteredNumberOfAnatomicalEntities.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:
  altered number of: PATO:0002083
  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 ('altered number of' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


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

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

classes:
  altered number of: PATO:0002083
  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 ('altered number of' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - cellular_component


text:
pattern_name: abnormallyAlteredNumberOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/dosdp-dev/abnormallyAlteredNumberOfAnatomicalEntityInLocation.yaml
description: "abnormal or altered number of anatomical entities in location. For example, has abnormal number of eyes in the head."

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

classes:
  altered number of: PATO:0002083
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  independent continuant: BFO:0000004

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

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

name:
  text: "abnormal number of anatomical entities of type %s in %s"
  vars:
   - anatomical_entity
   - location

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

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

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


text:
pattern_name: filenameWithoutFileExtension
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/filenameWithoutFileExtension.yaml
description: "A description that helps people chose this pattern for the appropriate scenario."

contributors:
  - https://orcid.org/0000-0002-9900-7880
  - https://orcid.org/0000-0001-9076-6015
  - https://orcid.org/0000-0003-4148-4606
  - https://orcid.org/0000-0002-3528-5267
  - https://orcid.org/0000-0002-7356-1779 (nico)
  - https://orcid.org/0000-0001-5208-3432 (nicole)
  - https://orcid.org/0000-0001-7941-2961 (leigh)

classes:
  quality: PATO:0000001
  process quality: PATO:0001236
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  biological process: GO:0008150
  chemical entity: CHEBI:24431
  molecular function: GO:0003674

relations:
  inheres_in: RO:0000052
  inheres_in_part_of: RO:0002314
  has_modifier: RO:0002573
  has_part: BFO:0000051
  occurs_in: BFO:0000066
  part_of: BFO:0000050
  towards: RO:0002503

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"
  chemical_entity: "'chemical entity'"
  biological_process: "'biological process'"
  molecular_function: "'molecular function'"
  location: "'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: vascularEctasia
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/vascularEctasia

classes:
  entity: BFO:0000001
  abnormal: PATO:0000460
  vessel: UBERON:0000055
  dilated: PATO:0001571

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

vars:
  entity: vessel
  location: "'entity'"

name:
  text: "%s lymphangiectasia"
  vars:
   - location

def:
  text: "A dilatation in the %s of the %s."
  vars:
    - entity
    - location

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


text:
pattern_name: abnormalNumberOfAnatomicalEntityByQuantityType
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/abnormalNumberOfAnatomyByType.yaml
description: "this pattern is used to describe phenotypes in which there is an abnormal number of anatomical enities. Examples of quantity terms that are appropriate are 'altered number of','has fewer parts of type', 'has extra parts of type', 'lacks all parts of type'. For example, has extra parts of type head."

classes:
  quantity: PATO:0001555
  abnormal: PATO:0000460
  entity: UBERON:0001062

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  entity: "'entity'"
  quantity: "'quantity'"

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

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

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

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


text:
pattern_name: increasedImmunoglobulinComplexAgainstEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/increasedImmunoglobulinComplexAgainstEntity

classes:
  immunoglobulin complex: GO:0019814
  entity: BFO:0000001

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  immunoglobulin_complex: "'immunoglobulin complex'"
  entity: "'entity'"

name:
  text: "increased anti-%s %s level"
  vars:
   - entity
   - immunoglobulin_complex

annotations:
  - annotationProperty: exact_synonym
    text: "increased level of anti-%s %s"
    vars:
     - entity
     - immunoglobulin_complex
  - annotationProperty: exact_synonym
    text: "increased %s %s antibody"
    vars:
     - entity
     - immunoglobulin_complex

def:
  text: "Increased level of %s against %s."
  vars:
   - immunoglobulin_complex
   - entity


text:
pattern_name: lesionInLocationByShape
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/lesionInLocationByShape
description: "this pattern describes a phenotype that results in lesions with a defined shape in an anatomical entity. i.e., a star shaped lesion in the head"

classes:
  shape: PATO:0000052
  abnormal: PATO:0000460
  entity: UBERON:0001062
  lesion: NCIT:C3824

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  entity: "'entity'"
  shape: "'shape'"

name:
  text: "abnormal %s with %s lesion"
  vars:
   - entity
   - shape

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

def:
  text: "An abnormal %s with a lesion that is %s."
  vars:
    - entity
    - shape

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


text:
{BFO: 'http://purl.obolibrary.org/obo/BFO_', CHEBI: 'http://purl.obolibrary.org/obo/CHEBI_',
  GO: 'http://purl.obolibrary.org/obo/GO_', MPATH: 'http://purl.obolibrary.org/obo/MPATH_',
  NBO: 'http://purl.obolibrary.org/obo/NBO_', PATO: 'http://purl.obolibrary.org/obo/PATO_',
  RO: 'http://purl.obolibrary.org/obo/RO_', UBERON: 'http://purl.obolibrary.org/obo/UBERON_',
  oio: 'http://www.geneontology.org/formats/oboInOwl#'}


text:
# adapted from https://github.com/dosumis/dead_simple_owl_design_patterns/blob/master/spec/test_schema.py by cjm
import yaml
from jsonschema import Draft4Validator
import warnings
import argparse
import logging
import sys

def main():
    """
    Wrapper for schema testing
    """
    logging.basicConfig(level=logging.INFO)
    logging.info("Welcome!")
    parser = argparse.ArgumentParser(description='Tests yaml DP syntax and structure'
                                                 """
                                                 foo
                                                 """,
                                     formatter_class=argparse.RawTextHelpFormatter)

    parser.add_argument('files',nargs='*')
    args = parser.parse_args()

    dosdp_full_file = open("./util/DOSDP_schema_full.yaml", "r")
    dosdp = yaml.load(dosdp_full_file.read())
    V = Draft4Validator(dosdp)
    stat = True
    for file in args.files:
        print('PARSING: '+file)
        if not test_jschema(V, file):
            print("FAILED to validate: "+file)
            stat = False
        else:
            print("SUCCESS ON: "+file)
    if not stat:
        print("FAILURES ENCOUNTERED")
        sys.exit(1)
    else:
        print("ALL PASS")
        sys.exit(0)

def test_jschema(validator, file_path):
    test_file = open(file_path, "r")
    test_pattern = yaml.load(test_file.read())

    if not validator.is_valid(test_pattern):
        es = validator.iter_errors(test_pattern)
        for e in es:
            warnings.warn(str(e))
            return False
    else:
        return True

if __name__ == "__main__":
    main()


text: Documentation of the Default DOSDP Pipeline


text:
pattern_name: abnormalQuantityOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalQuantityOfAnatomicalEntity.yaml
description: "Abnormal number/quantity of anatomical enities. Example, PLANP_0000526, altered number of heads."

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

classes:
  altered number of: PATO:0002083
  abnormal: PATO:0000460
  anatomical_entity: UBERON:0001062

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical_entity'"

name:
  text: "abnormal number of %ss"
  vars:
   - anatomical_entity

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

def:
  text: "An abnormal number of %ss."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('altered number of' and ('inheres_in' some %s) and ('qualifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormallyLackingAllPartsOfTypeAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/abnormallyLackingAllPartsOfTypeAnatomicalEntityInLocation.yaml
description: "lacks all parts of an anatomical entity in location. For example, lacks all parts of type head."

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

classes:
  lacks all parts of type: PATO:0002000
  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: "lacks all parts of type %s in %s"
  vars:
   - anatomical_entity
   - location

annotations:
  -
    annotationProperty: exact_synonym
    text: "missing all parts of type %s in %s"
    vars:
     - anatomical_entity
     - location

def:
  text: "Any structural anomaly that causes there to no parts of type %s in %s."
  vars:
    - anatomical_entity
    - location

equivalentTo:
  text: "'has_part' some ('lacks all parts of type' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity
    - location


text:
# Other obsoleted patterns

- abnormallyAlteredNumberOfAnatomicalEntities
- abnormallyAlteredNumberOfAnatomicalEntityInLocation
- abnormallyAlteredNumberOfCellularComponent


text:
pattern_name: abnormallyLackingAllPartsOfTypeAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyLackingAllPartsOfTypeAnatomicalEntity.yaml
description: "lacks all parts of an anatomical entity. For example, lacks all parts of type head."

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

classes:
  lacks all parts of type: PATO:0002000
  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: "lacks all parts of type %s"
  vars:
   - anatomical_entity

annotations:
  -
    annotationProperty: exact_synonym
    text: "missing all parts of type %s"
    vars:
     - anatomical_entity

def:
  text: "Any structural anomaly that causes there to no parts of type %s."
  vars:
    - anatomical_entity

equivalentTo:
  text: "'has_part' some ('lacks all parts of type' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abscessInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abscessInLocation.yaml
description: "The presence of an abscess in an anatomical entity. HP_0025044 'Lung abscess'."

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

classes:
  increased amount: PATO:0000470
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  abscess: MPATH:608

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

vars:
  anatomical_entity: "'anatomical entity'"
  abscess: "'abscess'"

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

def:
  text: "The presence of an abscess of the %s."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormalMorphologyOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalMorphologyOfAnatomicalEntity.yaml
description: "An morphologically abnormal anatomical entity. Morphological encompasses shape and colour, but more specific patterns exist."

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

classes:
  morphology: PATO:0000051
  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 morphology"
  vars:
   - anatomical_entity

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

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

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


text:
pattern_name: abnormalShapeOfAnatomicalEntityByShapeTypeInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalShapeOfAnatomicalEntityByShapeTypeInLocation.yaml
description: "Anatomical entity with an abnormal shape of a specified shape in a particular location, e.g. Y-shaped bone in the leg."

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

classes:
  shape: PATO:0000052
  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'"
  shape: "'shape'"
  location: "'independent continuant'"

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

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

def:
  text: "Any structural anomaly that causes %s in the %s to be %s shaped."
  vars:
  - anatomical_entity
  - location
  - shape

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


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

contributors:
- https://orcid.org/0000-0001-7487-610X
- https://orcid.org/0000-0002-3528-5267
classes:
  premature: PATO:0000694
  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: "premature %s"
  vars:
  - biological_process

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

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


text:
---
pattern_name: abnormalThicknessOfAnatomicalEntity

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

description: 'Use this phenotype pattern when an anatomical entity displays
  abnormal thickness.'

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0011486  # Abnormality of corneal thickness
#    - http://purl.obolibrary.org/obo/MP_0011961  # abnormal cornea thickness
#    - http://purl.obolibrary.org/obo/MP_0020135  # abnormal heart ventricle wall thickness

contributors:
  - https://orcid.org/0000-0001-8314-2140  # Ray Stefancsik
  - https://orcid.org/0000-0001-5208-3432  # Nicole Vasilevsky
  - https://orcid.org/0000-0002-3528-5267  # Sofia Robb
  - https://orcid.org/0000-0002-6490-7723  # Anna V. Anagnostopoulos
  - https://orcid.org/0000-0002-7356-1779  # Nicolas Matentzoglu
  - https://orcid.org/0000-0003-4606-0597  # Susan Bello

classes:
  thickness: PATO:0000915
  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 thickness"
  vars:
    - anatomical_entity

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

def:
  text: "Abnormal thickness of %s in a dimension that is perpendicular to its
    length or width."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormallyDecreasedSizeOfCellularComponent
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedSizeOfCellularComponent.yaml
description: "Abnormally small cellular component, e.g. decreased contractile vacuole size'"

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

classes:
  decreased size: PATO:0000587
  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: "decreased size of the %s"
  vars:
  - entity

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

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

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


text:
pattern_name: abnormallyIncreasedDistanceBetweenAnatomicalEntities
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedDistanceBetweenAnatomicalEntities.yaml
description: "The distance between two anatomical entites has increased. For example the distance between eyes."

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
  entity1: UBERON:0001062
  entity2: UBERON:0001062
  increased distance: PATO:0000374

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  entity1: "'entity1'"
  entity2: "'entity2'"

name:
  text: "increased distance between %s and %s"
  vars:
   - entity1
   - entity2

annotations:
  - annotationProperty: exact_synonym
    text: "distance increased between %s and %s"
    vars:
     - entity1
     - entity2

def:
  text: "Increased distance between %s and %s."
  vars:
    - entity1
    - entity2

equivalentTo:
  text: "'has_part' some ('increased distance' and ('inheres_in' some %s) and ('towards' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - entity1
    - entity2


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

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

classes:
  abnormal: PATO:0000460
  cell population proliferation: GO:0008283
  cell: CL:0000003
  process quality: PATO:0001236

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  cell: "'cell'"

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

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

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


text:
pattern_name: abnormalMorphologyOfCellularComponent
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalMorphologyOfCellularComponent.yaml
description: "An abnormality in the morphology of a cellular component, like an abnormal morphology of mitochondria."

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

classes:
  morphology: PATO:0000051
  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 morphology of %s"
  vars:
   - cellular_component

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

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

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


text:
pattern_name: abnormalNumberOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/dosdp-dev/abnormalNumberOfAnatomicalEntityInLocation.yaml
description: "abnormal or altered number of anatomical entities in location. For example, has abnormal number of eyes in the head."

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

classes:
  amount: PATO:0000070
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  independent continuant: BFO:0000004

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

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

name:
  text: "abnormal number of anatomical entities of type %s in %s"
  vars:
   - anatomical_entity
   - location

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

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

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


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

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/0000-0001-7941-2961
- https://orcid.org/0000-0001-9076-6015
classes:
  process quality: PATO:0001236
  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: "abnormal %s in %s"
  vars:
  - biological_process
  - location

def:
  text: "An abnormality of the %s in %s."
  vars:
  - biological_process
  - location

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


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

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

classes:
  closed: PATO:0000608
  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 closing of the %s"
  vars:
   - anatomical_entity

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

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

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


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

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

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

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

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


text:
pattern_name: abnormallyIncreasedLevelOfChemicalEntityWithRole
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedLevelOfChemicalEntityWithRole.yaml
description: "An abnormally increased level of a chemical with a specific role, e.g. metabolite. For example, increased biopterin level"

classes:
  increased amount: PATO:0000470
  abnormal: PATO:0000460
  chemical entity: CHEBI:24431
  role: CHEBI:50906

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  role: "role"

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

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

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


text:
pattern_name: cystInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/cystInLocation.yaml
description: "The presence of a cyst in an anatomical entity. For example,
  HP_0010604 'Cyst of the eyelid'."

contributors:
  - https://orcid.org/0000-0001-5208-3432  # Nicole Vasilevsky
  - https://orcid.org/0000-0002-3528-5267  # Sofia Robb
  - https://orcid.org/0000-0001-8314-2140  # Ray Stefancsik
  - https://orcid.org/0000-0003-4606-0597  # Susan Bello
  - https://orcid.org/0000-0002-6490-7723  # Anna V. Anagnostopoulos
  - https://orcid.org/0000-0002-4142-7153  # Sabrina Toro
  - https://orcid.org/0000-0001-7941-2961  # Leigh Carmody
  - https://orcid.org/0000-0002-0736-9199  # Peter N Robinson

classes:
  cystic: PATO:0001673
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

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

vars:
  anatomical_entity: "'anatomical entity'"

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

def:
  text: "The presence of a cyst in the %s."
  vars:
    - anatomical_entity

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


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

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

classes:
  increased occurrence: PATO:0002051
  abnormal: PATO:0000460
  biological process: GO:0008150
  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: "increased occurrence of %s in %s"
  vars:
   - biological_process
   - location

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

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


text:
pattern_name: abnormallyIncreasedResistanceOfWholeOrganismToEntity.yaml
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedResistanceOfWholeOrganismToEntity.yaml
description: "A phenotype in which an organism shows increased resistance to something, for example radition."

contributors:
- https://orcid.org/0000-0002-7356-1779
- https://orcid.org/0000-0002-3528-5267
classes:
  increased resistance to: PATO:0001650
  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: "increased resistance of organism to %s"
  vars:
  - entity

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

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

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


text:
pattern_name: metaplasticAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/metaplasticAnatomicalEntity.yaml
description: "The abnormal change from one fully differentiated cellular state into another in an anatomical entity."

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

classes:
  metaplastic: PATO:0002101
  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: "metaplastic %s"
  vars:
  - anatomical_entity

def:
  text: "Abnormal change from one fully differentiated cellular state into another in %s."
  vars:
  - anatomical_entity

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


text:
pattern_name: abnormallyDecreasedLevelOfChemicalEntityWithRoleInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedLevelOfChemicalEntityWithRoleInLocation.yaml
description: "An abnormally decreased 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_0030349 'Decreased circulating androgen level'."

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

classes:
  decreased amount: PATO:0001997
  abnormal: PATO:0000460
  chemical entity: CHEBI:24431
  role: CHEBI:50906
  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: "decreased %s %s level"
  vars:
  - role
  - location

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

equivalentTo:
  text: "'has_part' some ('decreased 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: abnormallyInvertedAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyInvertedAnatomicalEntityInLocation.yaml
description: "An abnormal configuration of an anatomical entity such that it is reversed in position, order, or condition in a particular location, e.g. an inverted joint in a limb."

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

classes:
  inverted: PATO:0000625
  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: "inverted %s in %s"
  vars:
  - anatomical_entity
  - location

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

def:
  text: "An abnormal configuration of the %s such that it is reversed in position, order, or condition in in %s."
  vars:
  - anatomical_entity
  - location

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


text:
pattern_name: bifurcatedAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/bifurcatedAnatomicalEntityInLocation.yaml
description: "Abnormal branching of an anatomical entity into two branches in a particular location, e.g. bifurcated blood vessel in a limb."

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

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

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

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

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


text:
---
pattern_name: herniatedAnatomicalEntity

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

description: 'Use this phenotype pattern when an anatomical entity pushes
  through a layer which surrounds or encloses it.'

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0001539  # Omphalocele
#    - http://purl.obolibrary.org/obo/HP_0004299  # Hernia of the abdominal wall
#    - http://purl.obolibrary.org/obo/MP_0000757  # herniated abdominal wall
#    - http://purl.obolibrary.org/obo/MP_0010146  # umbilical hernia

contributors:
  - https://orcid.org/0000-0001-8314-2140  # Ray Stefancsik
  - https://orcid.org/0000-0003-4606-0597  # Susan Bello
  - https://orcid.org/0000-0002-6490-7723  # Anna V. Anagnostopoulos
  - https://orcid.org/0000-0002-9900-7880  # Yvonne M. Bradford
  - https://orcid.org/0000-0002-1373-1705  # Clare Pilgrim

classes:
  herniated: PATO:0000643
  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: "herniated %s"
  vars:
    - anatomical_entity

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

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

def:
  text: "A herniated %s which protrudes through an abnormal opening in the wall
    or tissue layer that contains it."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormallyDuplicatedAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDuplicatedAnatomicalEntity.yaml
description: "An anatomical entity that was abnormally duplicated, such as a duplicated digit 1."

classes:
  duplicated: PATO:0001473
  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 duplication of %s"
  vars:
  - anatomical_entity

annotations:
- annotationProperty: exact_synonym
  text: "abnormal duplication of %s"
  vars:
  - anatomical_entity
- annotationProperty: exact_synonym
  text: "abnormally duplicated %s"
  vars:
  - anatomical_entity

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

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


text:
---
pattern_name: abnormallyGlisteningAnatomicalEntity

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

description: 'Use this phenotype pattern when an anatomical entity reflects
  more light than it does normally.'

#  examples:
#    - http://purl.obolibrary.org/obo/MP_0000411  # shiny fur
#    - http://purl.obolibrary.org/obo/MP_0001196  # shiny skin

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

classes:
  glistening: PATO:0001373
  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: "glistening %s"
  vars:
    - anatomical_entity

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

def:
  text: "Abnormally shiny, glossy or glistening appearance of %s."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormallyDecreasedCoilingOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedCoilingOfAnatomicalEntity.yaml
description: "An anatomical entity (or whole organism) that exhibits abnormally decreased coiling, or wound into a spiral or sequence of rings, like an abnormally decreased coiling of tail."

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

classes:
  decreased coiling: PATO:0001796
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

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

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

def:
  text: "Abnormally decreased coiling of the %s."
  vars:
  - anatomical_entity

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


text:
pattern_name: abnormallyOpenAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyOpenAnatomicalEntity.yaml
description: "Example: abnormal open anterior neural tube"

contributors:
- https://orcid.org/0000-0002-7356-1779
- https://orcid.org/0000-0002-3528-5267
classes:
  open: PATO:0000610
  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 opening of the %s"
  vars:
  - anatomical_entity

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

def:
  text: "Abnormally open %s."
  vars:
  - anatomical_entity

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


text:
pattern_name: abnormallyIncreasedWeightOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedWeightOfAnatomicalEntity.yaml
description: "Increased mass of an anatomical entity, e.g. increased mass of the whole organism. NOTE: We are using increased mass (PATO:0001563), 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:
  increased mass: PATO:0001563
  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: "increased %s mass"
  vars:
   - anatomical_entity

annotations:
  - annotationProperty: exact_synonym
    text: "large %s mass"
    vars:
    - anatomical_entity
  - annotationProperty: exact_synonym
    text: "high %s mass"
    vars:
    - anatomical_entity
  - annotationProperty: narrow_synonym
    text: "increased %s weight"
    vars:
    - anatomical_entity

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

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


text:
pattern_name: abnormallyIncreasedVolumeOfAnatomicalEntity

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

description: 'Abnormally increased volume of anatomical entity, e.g. overexpanded pulmonary alveoli.'

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0000414  # Bulbous nose
#    - http://purl.obolibrary.org/obo/XPO_0115308  # abnormally increased volume of brain
#    - http://purl.obolibrary.org/obo/MP_0001183  # overexpanded pulmonary alveoli
#    - http://purl.obolibrary.org/obo/ZP_0003908  # head increased volume, abnormal
#    - http://purl.obolibrary.org/obo/ZP_0142585  #  macrophage increased volume, abnormal

contributors:
  - https://orcid.org/0000-0002-7073-9172  # David Osumi-Sutherland
  - 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

classes:
  increased_volume: PATO:0000595
  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 increased volume of %s"
  vars:
    - anatomical_entity

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

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

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


text:
pattern_name: abnormallyDecreasedEfficacyOfProteinLocalizationInCellularComponent
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedEfficacyOfProteinLocalizationInCellularComponent.yaml
description: "Abnormally decreased 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
  decreased efficacy: PATO:0015003
  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: "decreased protein localization in %s"
  vars:
   - location

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

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


text:
pattern_name: abnormallyIncreasedRateOfBiologicalProcessInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedRateOfBiologicalProcessInLocation.yaml
description: "Abnormally increased frequency of a biological process occuring (per some unit of time) in some location, such as increased apoptosis in a tissue."

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

classes:
  increased rate: PATO:0000912
  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: "increased %s in %s"
  vars:
   - biological_process
   - location

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

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


text:
pattern_name: abnormallyDecreasedMotilityOfCellularComponentInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedMotilityOfCellularComponentInLocation.yaml
description: "Decreased 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:
  decreased rate: PATO:0000911
  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: "decreased %s motility in %s"
  vars:
   - cellular_component
   - location

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

equivalentTo:
  text: "'has_part' some ('decreased 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: abnormallyIncreasedNumberOfCellularComponent
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedNumberOfCellularComponent.yaml
description: "An increased number of a cellular component."

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

classes:
  increased amount: PATO:0000470
  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: "Increased number of %s"
  vars:
   - cellular_component

annotations:
  - annotationProperty: exact_synonym
    text: "Extra %s"
    vars:
     - cellular_component

def:
  text: "The presence of an increased number of %s."
  vars:
    - cellular_component

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


text:
pattern_name: atreticAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/atreticAnatomicalEntity.yaml
description: "Failure of an anatomcial entity to properly form. HP_0011984 'Atretic gallbladder'."

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

classes:
  atretic: PATO:0001819
  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 atresia"
  vars:
   - anatomical_entity

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

def:
  text: "A developmental defect resulting in complete obliteration of the lumen of the %s."
  vars:
    - anatomical_entity

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


text:
---
pattern_name: abnormallyIncreasedMassDensityOfAnatomicalEntity.yaml

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

description: 'Abnormally increased mass density (mass per unit volume) of an anatomical entity, for example "Dense calvaria". This pattern is not to be used for count per area (e.g. cell count) phenotypes.'

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0000250  # Dense calvaria
#    - http://purl.obolibrary.org/obo/HP_0011001  # Increased bone mineral density
#    - http://purl.obolibrary.org/obo/MP_0000062  # increased bone mineral density
#    - http://purl.obolibrary.org/obo/ZP_0008359  # vertebra increased 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:
  increased_mass_density: PATO:0001788
  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 increased %s mass density"
  vars:
    - anatomical_entity

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

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

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


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

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

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 %s"
  vars:
  - biological_process

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

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


text:
---
pattern_name: exsertedAnatomicalEntity

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

description: 'Use this phenotype pattern when an anatomical entity is
  abnormally protruding or projecting from the body. These anatomical
  entities may be described as being prolapsed, protuberant or sticking out.'

#  examples:
#    - http://purl.obolibrary.org/obo/ZP_0016742  # pectoral fin exserted, abnormal
#    - http://purl.obolibrary.org/obo/HP_0002035  # Rectal prolapse
#    - http://purl.obolibrary.org/obo/MP_0000493  # rectal prolapse

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:
  exserted: PATO:0000623
  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
  narrow_synonym: oio:hasNarrowSynonym

vars:
  anatomical_entity: "'anatomical_entity'"

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

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

  - annotationProperty: narrow_synonym
    text: "%s prolapse"
    vars:
      - anatomical_entity

  - annotationProperty: narrow_synonym
    text: "prolapsed %s"
    vars:
      - anatomical_entity

def:
  text: "An exserted %s is protruding or projecting from the body abnormally."
  vars:
    - anatomical_entity

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


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

contributors:
- https://orcid.org/0000-0002-7356-1779
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-3528-5267
classes:
  decreased amount: PATO:0001997
  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 decreased number of %s in the %s"
  vars:
  - anatomical_entity
  - location

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

def:
  text: "The presence of a reduced number of %s in the %s."
  vars:
  - anatomical_entity
  - location

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


text:
pattern_name: abnormallyPunctateAnatomicalEntity

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

description: 'Use this pattern for punctate morphological phenotypes where the surface of the anatomical entity exhibits dots, punctures, points or pits. Also use this pattern in cases of dotted or stippled anatomical entity surface phenotypes, e.g. epiphyseal stippling.'

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0010158  # Stippling of the epiphysis of the 1st metatarsal
#    - http://purl.obolibrary.org/obo/HP_0010237  # Epiphyseal stippling of finger phalanges
#    - http://purl.obolibrary.org/obo/HP_0010655  # Epiphyseal stippling
#    - http://purl.obolibrary.org/obo/ZP_0002299  # melanocyte punctate, abnormal
#    - http://purl.obolibrary.org/obo/ZP_0015120  # melanophore stripe punctate, 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:
  punctate: PATO:0001512
  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: "abnormally punctate %s"
  vars:
    - anatomical_entity

annotations:
  - annotationProperty: related_synonym
    text: "abnormally stippled %s"
    vars:
      - anatomical_entity

def:
  text: "The presence of abnormal dots, punctures, points or pits in %s."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormallyPunctateAnatomicalEntityInLocation

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

description: 'Use this pattern for punctate morphological phenotypes where the surface of the anatomical entity in location exhibits dots, punctures, points or pits. Also use this pattern in cases of dotted or stippled anatomical entity surface in location phenotypes, e.g. stippling of the epiphyses of the 3rd toe.'

#  examples:
#    - http://purl.obolibrary.org/obo/HP_0100064  # Stippling of the epiphyses of the 3rd toe
#    - http://purl.obolibrary.org/obo/HP_0009165  # Stippling of the epiphysis of the distal phalanx of the 5th finger
#    - http://purl.obolibrary.org/obo/HP_0009344  # Stippling of the epiphysis of the distal phalanx of the 3rd finger
#    - http://purl.obolibrary.org/obo/ZP_0004687  # basement membrane median fin fold punctate, 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
  - https://orcid.org/0000-0002-6490-7723  # Anna V. Anagnostopoulos

classes:
  punctate: PATO:0001512
  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

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

name:
  text: "abnormally punctate %s of %s"
  vars:
    - anatomical_entity
    - location

annotations:
  - annotationProperty: related_synonym
    text: "abnormally stippled %s of %s"
    vars:
      - anatomical_entity
      - location

def:
  text: "The presence of abnormal dots, punctures, points or pits in %s of %s."
  vars:
    - anatomical_entity
    - location

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


text:
pattern_name: malformedAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/malformedAnatomicalEntityInLocation.yaml
description : "Congenital malformation of an anatomical entity in a location, such as 'malformed anterior chamber in the eye'."

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
  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 formed %s in %s"
  vars:
   - anatomical_entity
   - location

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

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

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


text:
pattern_name: abnormallyDecreasedSizeOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedSizeOfAnatomicalEntity.yaml
description: "Abnormally small anatomical entity, e.g. MP:0020533 'decreased pons size'"
contributors:
- https://orcid.org/0000-0001-9076-6015
- https://orcid.org/0000-0002-9611-1279
- https://orcid.org/0000-0002-3528-5267
- https://orcid.org/0000-0002-7356-1779
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0003-4148-4606
- https://orcid.org/0000-0001-7941-2961
- https://orcid.org/0000-0002-9900-7880
classes:
  decreased size: PATO:0000587
  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 size of the %s"
  vars:
  - anatomical_entity

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

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

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


text:
pattern_name: abnormallyIncreasedRateOfMolecularFunction
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedRateOfMolecularFunction.yaml
description: "Increased functionality of a molecular process, like 'growth hormone secretion' or 'ketone body biosynthetic process'. For example: HP_0000845 'Growth hormone excess' and HP_0001946 Ketosis."

classes:
  increased rate: PATO:0000912
  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: "increased %s"
  vars:
  - molecular_function

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

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


text:
pattern_name: fracturedAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/fracturedAnatomicalEntity.yaml
description: "An abnormal fracture in an anatomical entity. A normal fracture is when you fall off your bike and break your arm. A pathological or abnormal fracture means that for instance you have cancer and a metastasis has weakened a bone that then fractures without an adequate trauma."

contributors:
  - https://orcid.org/0000-0001-5208-3432
  - https://orcid.org/0000-0002-8169-9049

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

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

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

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

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

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


text:
pattern_name: abnormalHasExtraPartsOfTypeAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns/abnormalHasExtraPartsOfTypeAnatomicalEntityInLocation.yaml
description: "extra parts of an anatomical entity in a location. For example, has extra parts of type eye in the head."

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

classes:

  has extra parts of type: PATO:0002002
  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: "has extra parts of type %s in %s"
  vars:
   - anatomical_entity
   - location

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

def:
  text: "Any structural anomaly that causes there to be extra parts of type %s in %s."
  vars:
    - anatomical_entity
    - location

equivalentTo:
  text: "'has_part' some ('has extra parts of type' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity
    - location


text:
pattern_name: abnormalHasExtraPartsOfTypeAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalHasExtraPartsOfTypeAnatomicalEntity.yaml
description: "extra parts of an anatomical entity. For example, has extra parts of type eye."

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

classes:

  has extra parts of type: PATO:0002002
  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: "has extra parts of type %s"
  vars:
   - anatomical_entity

annotations:
  -
    annotationProperty: exact_synonym
    text: "extra %ss"
    vars:
     - anatomical_entity

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

equivalentTo:
  text: "'has_part' some ('has extra parts of type' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
    - anatomical_entity


text:
pattern_name: abnormallyDecreasedRateOfContinuousBiologicalProcess
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedRateOfContinuousBiologicalProcess.yaml
description: "Abnormally decreased rate of a continuous biological process, e.g. rate of an enzyme reaction or growth rate. Does not include decreases in rates of occurrence/frequency. Different to patterns using PATO:0002472 'decreased velocity', which inheres in a physical object (continuant), rather than a process (occurrent)."

# examples:
#  - http://purl.obolibrary.org/obo/MP_0020234 # decreased basal metabolism
#  - http://purl.obolibrary.org/obo/FBcv_0000791 # decreased speed of aging
#  - http://purl.obolibrary.org/obo/ZP_0001531 # blood circulation decreased rate, abnormal
#  - http://purl.obolibrary.org/obo/ZP_0102933 # digestion decreased 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:
  decreased_rate_of_continuous_process: PATO:0055006
  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: "decreased continuous rate of %s"
  vars:
  - biological_process

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

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

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


text:
pattern_name: abnormalCellProliferationInAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalCellProliferationInAnatomicalEntity.yaml
description: "Any abnormality in cell proliferation in anatomical entity, such as 'abnormal B cell proliferation in peripheral blood'."

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

classes:
  process quality: PATO:0001236
  abnormal: PATO:0000460
  cell_population_proliferation: GO:0008283
  anatomical_entity: UBERON:0001062

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical_entity'"

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

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

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


text:
pattern_name: abnormalCellularComponentProcess
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalCellularComponentProcess.yaml
description: "An abnormal biological process involving the participation of a cellular component."

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

classes:
  process quality: PATO:0001236
  abnormal: PATO:0000460
  biological process: GO:0008150
  cellular component: GO:0005575

relations:
  inheres_in: RO:0000052
  has_modifier: RO:0002573
  has_part: BFO:0000051
  has_participant: RO:0002218

vars:
 cellular_component: "'cellular component'"
 biological_process: "'biological process'"

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

def:
  text: "Abnormal %s involving the active participant %s."
  vars:
    - biological_process
    - cellular_component

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


text:
pattern_name: abnormallyDecreasedMobilityOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedMobilityOfAnatomicalEntity.yaml
description: "An abnormally decreased or reduced ability to move an anatomical entity. Example: MP:0030863 decreased joint mobility."

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

classes:
  decreased mobility: PATO:0002283
  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 mobility"
  vars:
   - anatomical_entity

def:
  text: "Decreased or reduced ability to move %s."
  vars:
    - anatomical_entity

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


text:
pattern_name: disorganizedAnatomicalEntity

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

description: "Use this pattern when an anatomical entity is structurally disorganized, e.g. in case of a disorganized corneal epithelium. Do not use this pattern for fragmented or otherwise broken anatomical entities, even though you might argue that in some sense there is disorganisation in those cases as well. However, those cases belong to different phenotype patterns that are covered by structural phenotype terms in PATO that are different from the 'disorganized' quality."

#  examples:
#    - http://purl.obolibrary.org/obo/MP_0031131  # myocardial fiber disarray
#    - http://purl.obolibrary.org/obo/MP_0020859  # disorganized corneal epithelium
#    - http://purl.obolibrary.org/obo/XPO_0115471  # abnormally disorganized myotome
#    - http://purl.obolibrary.org/obo/ZP_0000138  # chondrocyte disorganized, 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:
  disorganized: PATO:0000937
  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: "disorganized %s"
  vars:
    - anatomical_entity

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

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

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


text:
pattern_name: abnormallyDecreasedLengthOfAnatomicalEntityInLocation
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedLengthOfAnatomicalEntityInLocation.yaml
description: "Anatomical entity is observed to be of decreased length, such as decreased length of finger on the hand."

contributors:
- https://orcid.org/0000-0002-7356-1779
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-3528-5267
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
  part_of: BFO:0000050

annotationProperties:
  exact_synonym: oio:hasExactSynonym

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

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

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

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

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


text:
pattern_name: abnormallyIncreasedCoilingOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedCoilingOfAnatomicalEntity.yaml
description: "An anatomical entity (or whole organism) that exhibits abnormally increased coiling, or wound into a spiral or sequence of rings, like an abnormally increased coiling of tail."

contributors:
- https://orcid.org/0000-0002-7356-1779
- https://orcid.org/0000-0002-3528-5267
classes:
  increased coiling: PATO:0001795
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "abnormally increased coiling of %s"
  vars:
  - anatomical_entity

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

def:
  text: "Abnormally increased coiling of the %s."
  vars:
  - anatomical_entity

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


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

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

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

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

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


text:
---
pattern_name: abnormallyArchedAnatomicalEntity

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

description: 'Use this phenotype pattern when an anatomical entity shows an
  abnormal shape or structure with a curve forming or resembling an arch.'

#  examples:
#    - http://purl.obolibrary.org/obo/MP_0003761  # arched palate
#    - http://purl.obolibrary.org/obo/ZP_0102340  # trunk arched, abnormal
#    - http://purl.obolibrary.org/obo/HP_0002553  # Highly arched eyebrow

contributors:
  - https://orcid.org/0000-0001-8314-2140  # Ray Stefancsik
  - https://orcid.org/0000-0003-4606-0597  # Susan Bello
  - https://orcid.org/0000-0002-7073-9172  # David Osumi-Sutherland
  - https://orcid.org/0000-0002-6490-7723  # Anna V. Anagnostopoulos
  - https://orcid.org/0000-0001-7941-2961  # Leigh Carmody
  - https://orcid.org/0000-0002-9900-7880  # Yvonne M. Bradford
  - https://orcid.org/0000-0002-1373-1705  # Clare Pilgrim

classes:
  arched: PATO:0001594
  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: "arched %s"
  vars:
    - anatomical_entity

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

def:
  text: "An abnormally concave %s which forms or resembles an arch."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormalAgenesisOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalAgenesisOfAnatomicalEntity.yaml
description: "Abnormal absence of a tissue or organ due to failure to develop. Agenesis is a specific process to describe the failure of a tissue to develop, such as HP_0001341 Olfactory lobe agenesis. It is more specific than an absent anatomical entity."

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

classes:
  agenesis: PATO:0002291
  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: "agenesis of %s"
  vars:
   - anatomical_entity

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

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


text:
pattern_name: abnormallyDecreasedNumberOfAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedNumberOfAnatomicalEntity.yaml
description: "A decreased number of an anatomical entity, such a decreased number of teeth."

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

classes:
  decreased amount: PATO:0001997
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

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

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

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

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


text:
pattern_name: lysedAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/lysedAnatomicalEntity.yaml
description: "expansive cellular membrane destruction in anatomical entity."

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

classes:
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062
  lysed: PATO:0065001

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

vars:
  anatomical_entity: "'anatomical entity'"

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

def:
  text: "%s with extensive cellular membrane destruction."
  vars:
  - anatomical_entity

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


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

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/0000-0001-7941-2961
  - https://orcid.org/0000-0003-4148-4606

classes:
  absent: PATO:0000462
  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: "absent %s"
  vars:
   - anatomical_entity

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

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

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


text:
pattern_name: abnormallyBentAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyBentAnatomicalEntity.yaml
description: "An anatomical entity that has one or more angles in its length, such as a bent/crooked nose."

classes:
  bent: PATO:0000617
  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 bending of %s"
  vars:
  - anatomical_entity

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

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

equivalentTo:
  text: "'has_part' some ('bent' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
  vars:
  - anatomical_entity
contributors:
- https://orcid.org/0000-0001-9076-6015


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

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0001-9076-6015
- https://orcid.org/0000-0002-3528-5267
- https://orcid.org/0000-0002-7356-1779
classes:
  increased amount: PATO:0000470
  abnormal: PATO:0000460
  anatomical entity: UBERON:0001062

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

annotationProperties:
  exact_synonym: oio:hasExactSynonym

vars:
  anatomical_entity: "'anatomical entity'"

name:
  text: "abnormally increased number of %s"
  vars:
  - anatomical_entity

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

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

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


text:
---
pattern_name: abnormallyProtrudingAnatomicalEntity

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

description: 'Use this phenotype pattern template, when an anatomical entity is
  protruding or projecting out or beyond a surface or boundary. When an
  anatomical entity is abnormally protruding or projecting from the body, use
  the more specific pattern of "exsertedAnatomicalEntity" instead of the
  pattern defined below.'

#  examples:
#    - http://purl.obolibrary.org/obo/ZP_0002287  # forebrain protruding, abnormal
#    - http://purl.obolibrary.org/obo/HP_0010808  # Protruding tongue
#    - http://purl.obolibrary.org/obo/MP_0009908  # protruding tongue
#    - http://purl.obolibrary.org/obo/XPO_0115495  # abnormally protruding proctodeum

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:
  protruding: PATO:0001598
  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 protruding %s"
  vars:
    - anatomical_entity

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

def:
  text: "An abnormally protruding %s that extends out above or beyond an
    anatomical surface or boundary."
  vars:
    - anatomical_entity

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


text:
pattern_name: abnormallyRotatedAnatomicalEntity
pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyRotatedAnatomicalEntity.yaml
description: "An anatomical entity that is abnormally rotated or malrotated, such as HP_0004785 'Malrotation of colon'."

contributors:
- https://orcid.org/0000-0001-5208-3432
- https://orcid.org/0000-0002-3528-5267
classes:
  rotated: PATO:0001599
  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: "rotated %s"
  vars:
  - anatomical_entity

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

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