Organism
type: Ontology
creator: Hans Cools, MD, Agfa Healthcare/Belgium
contributor: Until 2010: Pieterjan De Potter, Pedro Debevere, Ghent University - IBBT/ELIS - Multimedia Lab/Belgium
publisher: Agfa Healthcare/Belgium
description: Formal general description of organism.
format: OWL Full

organism
type: Class
definition: Something that lives.
note: Superclass can be organism in a more general way: any complex thing having properties and functions determined not only by the properties of its individual parts, but by the character of the whole that they compose and by the relations of the parts to the whole.
subclass of: Agent
subclass of: Resource
subclass of: Restriction
  on property: hasState
  some values from: alive

Concept
in scheme: sct20080731
notation: 410607006

life
type: Class
definition: The action of being alive.
subclass of: Action
subclass of: Existence

individual life
type: Class
definition: Life of an organism after birth.
subclass of: life

alive
type: Class
definition: State of being capable of response to stimuli, reproduction, growth and development, and maintenance of homeostasis as a stable whole.
note: Up till now no satisfying definition.

mortal
type: Class
definition: State of having a limited lifetime.

death
type: Class
definition: Finding of the remains of an organism.
subclass of: Finding

Concept
in scheme: sct20080731
notation: 419620001

dead
type: Class
definition: State of being not alive anymore.

Concept
in scheme: sct20080731
notation: 419099009

Concept
in scheme: icpc2
notation: A96

Concept
in scheme: icd10
notation: R99

cause of death
type: Class
definition: Action causing death.
subclass of: Restriction
  on property: causes
  some values from: death

development state
type: Class
definition: Any state of development.

immature
type: Class
type: development state
definition: State of being biologically not full-grown.

mature
type: Class
type: development state
definition: State of being biologically full-grown.
comment: A criterium can be: capable of reproduction.

mature organism
type: Class
definition: Organism being mature.
subclass of: organism
subclass of: Restriction
  on property: hasDevelopmentState
  some values from: mature

immature organism
type: Class
definition: Organism being immature.
subclass of: organism
subclass of: Restriction
  on property: hasDevelopmentState
  some values from: immature

gravidity
type: Class
definition: Any state of gravidity.
one of: pregnant
one of: nonpregnant

pregnant
type: Class
type: gravidity
definition: State of an organism of having offspring developing in its body.

nonpregnant
type: Class
type: gravidity
definition: State of an organism of not having offspring developing in its body.

pregnant organism
type: Class
definition: Organism being pregnant.
subclass of: organism
subclass of: Restriction
  on property: hasGravidity
  some values from: pregnant

biological ascendant
type: Class
definition: Living ascendant of any kind.
subclass of: Ascendant
subclass of: organism
comment: Organism that is an earlier form of another organism.

biological parent
type: Class
definition: First grade ascendant of an organism.
comment: Organism that produces another.
subclass of: Parent
subclass of: mature organism
subclass of: biological ascendant
subclass of: Restriction
  on property: hasChild
  min cardinality: 1

Parents
type: Class
subclass of: Ancestry
subclass of: Restriction
  on property: member
  some values from: biological parent
subclass of: Restriction
  on property: member
  cardinality: 2

biological mother
type: Class
definition: Female biological parent.
subclass of: biological parent
disjoint with: biological father

biological father
type: Class
definition: Male biological parent.
subclass of: biological parent

biological descendant
type: Class
definition: Living descendant of any kind.
comment: Organism deriving from an earlier form.
subclass of: Descendant
subclass of: organism

biological child
type: Class
definition: First grade living descendant of any kind.
subclass of: Child
subclass of: biological descendant
comment: Organism that is produced by another.
subclass of: Restriction
  on property: hasParent
  min cardinality: 1

Concept
in scheme: sct20080731
notation: 75226009

biological offspring
type: Class
subclass of: Offspring
subclass of: Restriction
  on property: member
  all values from: biological descendant

Children
type: Class
definition: Children of the same biological parent(s).
subclass of: biological offspring
subclass of: Restriction
  on property: member
  all values from: biological child

eukaryote
type: Class
definition: Organism with a cellular nucleus.
subclass of: organism

unbranched bioPolymer
type: Class
definition: Polymer of an organism without branch.

genome
type: Class
definition: All hereditary information of an organism coded in nucleotide chains.

deoxyribonucleic acid
type: Class
definition: Nucleic acid containing genetic instructions for development and functioning of organisms, except RNA viruses.

karyotyping
type: Class
definition: Classifying chromosomes from a nucleus of a eukaryotic cell according to number, size, shape, banding pattern, placement of centromere or other characteristics.
subclass of: Examining
subclass of: Restriction
  on property: hasOutput
  some values from: karyotype

karyotype
type: Class
definition: Classification of chromosomes from a nucleus of a eukaryotic cell according to the number, size, shape, banding pattern, placement of centromere or other characteristics.
subclass of: Examination
subclass of: Restriction
  on property: outputOf
  some values from: karyotyping

sequencing
type: Class
definition: Determining a primary structure or sequence of an unbranched biopolymer of an organism.
subclass of: Examining
subclass of: Restriction
  on property: hasOutput
  some values from: sequence

sequence
type: Class
definition: Determination of a primary structure or sequence of an unbranched biopolymer of an organism.
subclass of: Examination
subclass of: Restriction
  on property: outputOf
  some values from: sequencing

DNA sequencing
type: Class
definition: Determining a nucleotide order of DNA of an organism.
subclass of: sequencing
subclass of: Restriction
  on property: hasOutput
  some values from: DNA sequence

DNA sequence
type: Class
definition: Determination of a nucleotide order of DNA of an organism.
subclass of: sequence
subclass of: Restriction
  on property: outputOf
  some values from: DNA sequencing
subclass of: Restriction
  on property: sequence of
  some values from: deoxyribonucleic acid

lives
type: ObjectProperty
definition: Specifying a life process of an organism.
sub property of: exists
domain: organism
range: life

hasDevelopmentState
type: ObjectProperty
definition: Specifying the state of development of an individual organism.
domain: organism
range: development state

hasGravidity
type: ObjectProperty
definition: Specifying the gravidity of an organism.
domain: organism
range: gravidity

begins
type: DatatypeProperty
type: FunctionalProperty
definition: Specifying the beginning of a life of an organism as individual.
note: End of a delivery.
sub property of: begins
domain: individual life
range: dateTime

beginDate
type: DatatypeProperty
type: FunctionalProperty
definition: Specifying the beginning of a life of an organism as individual.
note: End of a delivery.
sub property of: beginDate
domain: individual life
range: date

has birth date time
type: DatatypeProperty
type: FunctionalProperty
definition: Specifying a snapshot event's date and time an organism is born on.
property chain axiom: lives
property chain axiom: begins
sub property of: hasOriginationDateTime
domain: organism
range: dateTime

has birth date
type: DatatypeProperty
type: FunctionalProperty
definition: Specifying a date an organism is born on.
property chain axiom: lives
property chain axiom: beginDate
sub property of: hasOriginationDate
domain: organism
range: date

has birth time
type: DatatypeProperty
type: FunctionalProperty
definition: Specifying a snapshot event's time of a day an organism is born on.
domain: organism
range: time

ends
type: DatatypeProperty
type: FunctionalProperty
definition: Specifying the endpoint in time of a life of an organism.
sub property of: expires
domain: life
range: dateTime

Concept
in scheme: sct20080731
notation: 399753006

endDate
type: DatatypeProperty
type: FunctionalProperty
definition: Specifying the endpoint in time of a life of an organism.
domain: life
range: date

has death date time
type: DatatypeProperty
type: FunctionalProperty
definition: Specifying a snapshot event's date and time an organism died on.
property chain axiom: lives
property chain axiom: ends
sub property of: hasVanishingDateTime
domain: organism
range: dateTime

has death date
type: DatatypeProperty
type: FunctionalProperty
definition: Specifying a snapshot event's date an organism died on.
property chain axiom: lives
property chain axiom: endDate
domain: organism
range: date

has death time
type: DatatypeProperty
type: FunctionalProperty
definition: Specifying the time of a day an organism died.
domain: organism
range: time

hasCauseOfDeath
type: ObjectProperty
definition: Specifying a cause of death of an organism.
domain: organism
range: cause of death

hasParent
type: ObjectProperty
definition: Specifying the first grade ascendent of an organism or group of organisms.
sub property of: hasParent
domain:
  union of: biological child
  union of: Children
range: biological parent

hasMother
type: ObjectProperty
type: FunctionalProperty
definition: Specifying the first grade female ascendent of an organism.
sub property of: hasParent
domain: biological child
range: biological mother

hasFather
type: ObjectProperty
type: FunctionalProperty
definition: Specifying the first grade male ascendent of an organism.
sub property of: hasParent
domain: biological child
range: biological father

hasChild
type: ObjectProperty
definition: Specifying the first grade descendant of an organism or group of organisms.
sub property of: hasChild
domain:
  union of: biological parent
  union of: Parents
range: biological child

hasTaxon
type: ObjectProperty
definition: Specifying the taxonomic identity of an organism as defined in uniprot taxonomy.
domain: organism
range: Taxon

has sequence
type: ObjectProperty
definition: Specifying a sequence of an organism.
domain: organism
range: sequence

sequence of
type: ObjectProperty
definition: Specifying an organism's specimen having a sequence.
sub property of: examinationOf
property chain axiom: containedBy
domain: sequence
range: unbranched bioPolymer

has karyotype
type: ObjectProperty
definition: Specifying a karyotype of a eukaryote.
domain: eukaryote
range: karyotype

has DNA Sequence
type: ObjectProperty
definition: Specifying a DNA sequence of an organism.
domain: organism
range: DNA sequence