Ontology
comment: HOZO:OWL Export(build-20120726)

Chromosome
type: Class
subclass of: Restriction
  all values from: polynucleotide
  on property: has polynucleotide
subclass of: Restriction
  on property: has polynucleotide
  cardinality: 1
subclass of: Restriction
  on property: has arm
  all values from: Chromosome_arm
subclass of: Restriction
  on property: has arm
  min cardinality: 1
subclass of: Restriction
  on property: has chromatid
  all values from: Chromatid
subclass of: Restriction
  on property: has chromatid
  min cardinality: 1
subclass of: Organelle_part

polynucleotide
type: Class
subclass of: Restriction
  on property: has part
  min cardinality: 1
subclass of: Molecule

Chromosome_arm
type: Class
subclass of: Chromosome_part

Chromatid
type: Class
subclass of: Chromosome_part
subclass of: Restriction
  on property: has molecular component
  all values from: polynucleotide
subclass of: Restriction
  on property: has molecular component
  cardinality: 1

Organelle_part
type: Class
subclass of: subcellular_component

Intrinsically_qualitative
type: Class
subclass of: Qualitative_property

Qualitative_property
type: Class
subclass of: YAMATO_property

RelationalConcept
type: Class

Mode_of_inheritance_value
type: Class
subclass of: Nominal_scale_value

Nominal_scale_value
type: Class
comment: This is a fully categorical quality value which do not represent any order or rank.
subclass of: Restriction
  all values from: YAMATO_Any
  on property: has depend on
subclass of: Restriction
  cardinality: 1
  on property: has depend on
subclass of: YAMATO_quality_value

Diversity
type: Class
subclass of: non-meta_generic_quality

non-meta_generic_quality
type: Class
subclass of: YAMATO_quantitative_generic_quality

Biological_replication
type: Class
subclass of: Restriction
  all values from: YAMATO_entity
  on property: has replica
subclass of: Restriction
  min cardinality: 1
  on property: has replica
subclass of: Restriction
  on property: has template
  all values from: YAMATO_entity
subclass of: Restriction
  min cardinality: 1
  on property: has template
subclass of: biological_process

YAMATO_entity
type: Class
subclass of: Restriction
  on property: has quality type
  min cardinality: 1
subclass of: Restriction
  on property: has quality value
  min cardinality: 1
subclass of: Restriction
  on property: has quality quantity
  min cardinality: 1
subclass of: Restriction
  on property: has quality quantity
  all values from: YAMATO_specifically_dependent
subclass of: Restriction
  cardinality: 1
  on property: has condition
subclass of: Restriction
  on property: has quality value
  all values from: YAMATO_quality_value
subclass of: Restriction
  on property: has quality type
  all values from: YAMATO_quality_1
subclass of: YAMATO_particular
comment: Something which exists independently of others. Entity requires time, space and substance to exist.

biological_process
type: Class
subclass of: Restriction
  all values from: YAMATO_specifically_dependent
  on property: has quality quantity
subclass of: Restriction
  min cardinality: 1
  on property: has quality quantity
subclass of: Restriction
  on property: has quality type
  all values from: YAMATO_quality_1
subclass of: Restriction
  on property: has quality type
  min cardinality: 1
subclass of: YAMATO_phenomenon

G_to_A_transition_process
type: Class
subclass of: Restriction
  on property: has terminal Event
  all values from: YAMATO_instantaneous_event
subclass of: Restriction
  on property: has terminal Event
  cardinality: 1
subclass of: purine_transition_event

YAMATO_instantaneous_event
type: Class
subclass of: YAMATO_instant_event

purine_transition_event
type: Class
subclass of: Restriction
  on property: has terminal Event
  all values from: YAMATO_instantaneous_event
subclass of: Restriction
  cardinality: 1
  on property: has terminal Event
subclass of: transition_process

Genetic_information_entity
type: Class
subclass of: Restriction
  on property: has content
  all values from: specification_of_gene_product
subclass of: Restriction
  on property: has form
  all values from: _5__to_3__Nucleotide_sequence
subclass of: Restriction
  on property: has form
  cardinality: 1
subclass of: Natural_representation-like

specification_of_gene_product
type: Class
subclass of: specification_of_biomolecule
subclass of: Restriction
  on property: has for what
  all values from: Molecule
subclass of: Restriction
  min cardinality: 1
  on property: has for what

_5__to_3__Nucleotide_sequence
type: Class
subclass of: nucleotide_sequence
subclass of: Restriction
  on property: has direction
  all values from: _5__to_3__direction
subclass of: Restriction
  on property: has direction
  cardinality: 1
subclass of: Restriction
  on property: has reverse sequence
  all values from: reverse_Nucleotide_sequence
subclass of: Restriction
  on property: has complementary sequence
  cardinality: 1
subclass of: Restriction
  on property: has sub-sequence
  all values from: _5__to_3__Nucleotide_sequence
subclass of: Restriction
  all values from: _5__to_3__Nucleotide_sequence
  on property: has complementary sequence
subclass of: Restriction
  on property: has symbol
  all values from: Symbol_designated_by_nucleotide
subclass of: Restriction
  min cardinality: 1
  on property: has symbol
subclass of: Restriction
  cardinality: 1
  on property: has reverse sequence

Natural_representation-like
type: Class
subclass of: Restriction
  all values from: YAMATO_proposition
  on property: has content
subclass of: Restriction
  on property: has content
  max cardinality: 1
subclass of: Restriction
  on property: has form
  all values from: YAMATO_epresentation_form
subclass of: Restriction
  cardinality: 1
  on property: has form
subclass of: YAMATO_representation
comment: Non-artificial content bearing thing, such as DNA sequence and single DNA as a molecular symbol. As the contrast to representation in artificial, this does'nt have agent as author.

Phenotypic_change_dependent_on_genetic_background
type: Class
subclass of: Transformation

Transformation
type: Class
subclass of: Mutation_of_organism

Negative_complementation
type: Class
subclass of: Complementation

Complementation
type: Class
subclass of: Phenotypic_change_dependent_on_genetic_background

Specification_of_polynucleotide
type: Class
subclass of: specification_of_biomolecule
subclass of: Restriction
  on property: has realizing representation
  all values from: Genetic_information_entity
subclass of: Restriction
  on property: has for what
  all values from: polynucleotide_group
subclass of: Restriction
  on property: has for what
  min cardinality: 1

specification_of_biomolecule
type: Class
subclass of: YAMATO_specification_plan

polynucleotide_group
type: Class
subclass of: Restriction
  on property: has realizing representation
  all values from: Genetic_information_entity
subclass of: Restriction
  on property: has realizing representation
  min cardinality: 1
subclass of: Restriction
  on property: has representation media
  all values from: polynucleotide
subclass of: Restriction
  cardinality: 1
  on property: has representation media
subclass of: Restriction
  on property: has sub fragment
  all values from: polynucleotide_group
subclass of: Restriction
  on property: has sub group
  all values from: radical_group
subclass of: radical_group

Poly-allelism_value
type: Class
subclass of: Restriction
  on property: has value of
  all values from: Poly-allelism
subclass of: Restriction
  on property: has value of
  cardinality: 1
subclass of: Attribute_dependent

Poly-allelism
type: Class
subclass of: meta-generic_quality

Attribute_dependent
type: Class
subclass of: Restriction
  on property: has value of
  all values from: YAMATO_quality_1
subclass of: Restriction
  cardinality: 1
  on property: has value of
subclass of: Ordinal_scale_value

Direct_repeat_sequence
type: Class
subclass of: Repetitive_sequence

Repetitive_sequence
type: Class
subclass of: repeat_sequence

quantity_per_time
type: Class
subclass of: attribute-specific

attribute-specific
type: Class
subclass of: Singleton_quantity

Polyatomic_stable_substance
type: Class
subclass of: chemical_entity

chemical_entity
type: Class
subclass of: Natural_object

repeat_sequence
type: Class
subclass of: Restriction
  on property: has repeat unit
  all values from: Molecular_sequence
subclass of: Structured_seqence

YAMATO_time_interval
type: Class
subclass of: Restriction
  on property: has dulation
  all values from: YAMATO_time_duration
subclass of: Restriction
  on property: has dulation
  cardinality: 1
subclass of: Restriction
  on property: has ending time
  all values from: YAMATO_time_point
subclass of: Restriction
  on property: has ending time
  cardinality: 1
subclass of: Restriction
  all values from: YAMATO_time_point
  on property: has starting time
subclass of: Restriction
  on property: has starting time
  cardinality: 1
subclass of: YAMATO_time

YAMATO_time_duration
type: Class
subclass of: YAMATO_time

YAMATO_time_point
type: Class
subclass of: YAMATO_time

YAMATO_time
type: Class
comment: The Time is indispensable for entities to exist in the world.
subclass of: YAMATO_substrate

Coding_of_gene_product
type: Class
subclass of: Genetic_information_entity
subclass of: Restriction
  on property: has content
  all values from: specification_of_gene_product
subclass of: Restriction
  cardinality: 1
  on property: has content
subclass of: Restriction
  all values from: _5__to_3__Nucleotide_sequence
  on property: has form
subclass of: Restriction
  cardinality: 1
  on property: has form

Combination_of_alleles_at_different_loci
type: Class
subclass of: Genetic_composition

Genetic_composition
type: Class
subclass of: Genuine_qualitative_generic_quality
subclass of: Restriction
  all values from: Organism_body
  on property: has on what
subclass of: Restriction
  on property: has on what
  cardinality: 1

biological_polulation
type: Class
subclass of: Restriction
  all values from: biological_polulation
  on property: has sub population
subclass of: YAMATO_group

YAMATO_group
type: Class
subclass of: Restriction
  all values from: YAMATO_group
  on property: has sub group
subclass of: Restriction
  on property: has member
  all values from: YAMATO_Any
subclass of: Restriction
  min cardinality: 1
  on property: has member
subclass of: YAMATO_group_like_thing

YAMATO_line_image
type: Class
subclass of: YAMATO_still_image

YAMATO_still_image
type: Class
subclass of: YAMATO_image_form

YAMATO_property
type: Class
comment: This is an abstration of the possession for things of a quality value. This is necessary to keep the interoperability with state which does NOT compatible with quality type or attribute. Consider "hungry" which is compatible with "being tall" rather than "length".
subclass of: YAMATO_quality_1
subclass of: Restriction
  on property: has value
  min cardinality: 1
subclass of: Restriction
  all values from: YAMATO_quality_value
  on property: has refer to
subclass of: Restriction
  cardinality: 1
  on property: has refer to

YAMATO_clock_time
type: Class
subclass of: YAMATO_time_point

gene_pool
type: Class
subclass of: Restriction
  all values from: variant_of_s-egment
  on property: has variant
subclass of: Restriction
  min cardinality: 1
  on property: has variant
subclass of: Restriction
  all values from: organism
  on property: has species
subclass of: Restriction
  cardinality: 1
  on property: has species
subclass of: Restriction
  all values from: spec_s-segment
  on property: has what for
subclass of: Restriction
  on property: has what for
  cardinality: 1
subclass of: YAMATO_group

variant_of_s-egment
type: Class
subclass of: UndefinedClass

organism
type: Class
subclass of: Restriction
  min cardinality: 1
  on property: has gamete
subclass of: Restriction
  min cardinality: 1
  on property: has body part
subclass of: Restriction
  on property: has genome
  cardinality: 1
subclass of: Restriction
  on property: has time for dead
  cardinality: 1
subclass of: Restriction
  max cardinality: 1
  on property: has female parent
subclass of: individual_related
subclass of: Restriction
  all values from: gamete
  on property: has gamete
subclass of: Restriction
  all values from: organism
  on property: has female parent
subclass of: Restriction
  on property: has time for born
  cardinality: 1
subclass of: Restriction
  all values from: Body_part_related
  on property: has body part
subclass of: Restriction
  all values from: genome
  on property: has genome
subclass of: Restriction
  on property: has male parent
  all values from: organism
subclass of: Restriction
  on property: has time for born
  all values from: YAMATO_time_point
subclass of: Restriction
  on property: has male parent
  max cardinality: 1
subclass of: Restriction
  on property: has time for dead
  all values from: YAMATO_time_point

spec_s-segment
type: Class
subclass of: UndefinedClass

Allelic
type: Class
subclass of: Restriction
  on property: has role
  all values from: YAMATO_Any
subclass of: Restriction
  on property: has role
  cardinality: 1
subclass of: Restriction
  on property: has role
  all values from: YAMATO_Any
subclass of: Restriction
  on property: has role
  cardinality: 1
subclass of: RelationalConcept

YAMATO_Any
type: Class
comment: The root class.

YAMATO_symbol
type: Class
subclass of: Designed_proposition

Designed_proposition
type: Class
subclass of: YAMATO_representation-primary

molecular_form
type: Class
subclass of: YAMATO_epresentation_form

YAMATO_epresentation_form
type: Class
subclass of: YAMATO_semi-abstract
comment: This is identical to YATO's "representation form".This is what is left after extracting its meaning/content from "representation". The heart of this conceptualization is the separation between form and content.

YAMATO_intrinsic_generic_quality
type: Class
comment: This attribute is intrinsically essential to entity.
subclass of: YAMATO_generic_quality

YAMATO_generic_quality
type: Class
subclass of: YAMATO_quality_1
comment: This is a dependent entity such as the color of this tomato, or the length of tail of a specific mouse individual. Attribute cannot exist alone but always exists dependently on physical things which also need attribute to exist. This class is equivalent with "quality type" of DOLCE.

Chromosomal_polumorphism
type: Class
subclass of: Genetic_polymorphism

Genetic_polymorphism
type: Class
subclass of: Polymorphism

Execution_of_experiment
type: Class
subclass of: Restriction
  cardinality: 1
  on property: has experimental environment
subclass of: Restriction
  on property: has experimental procedure
  all values from: Experimental_procedure
subclass of: Restriction
  min cardinality: 1
  on property: has experimental object
subclass of: Restriction
  all values from: Experimental_action
  on property: has sub-experiment
subclass of: Restriction
  all values from: YAMATO_time_interval
  on property: has time
subclass of: Restriction
  on property: has participant
  all values from: YAMATO_entity
subclass of: Experimental_action
subclass of: Restriction
  on property: has time
  cardinality: 1
subclass of: Restriction
  on property: has experimental data
  min cardinality: 1
subclass of: Restriction
  all values from: YAMATO_entity
  on property: has experimental object
subclass of: Restriction
  min cardinality: 1
  on property: has doer
subclass of: Restriction
  on property: has doer
  all values from: YAMATO_agent

Experimental_procedure
type: Class
subclass of: Restriction
  on property: has purpose
  min cardinality: 1
subclass of: Restriction
  on property: has experimental material
  all values from: YAMATO_entity
subclass of: Restriction
  min cardinality: 1
  on property: has author
subclass of: Restriction
  on property: has used for
  all values from: Experimental_action
subclass of: Restriction
  on property: has documentation
  all values from: Scientific_paper_as_content
subclass of: Restriction
  on property: has parameter composition
  all values from: Parameter_composition
subclass of: Restriction
  all values from: Purpose
  on property: has purpose
subclass of: Restriction
  cardinality: 1
  on property: has experimental material
subclass of: protocol
subclass of: Restriction
  on property: has author
  all values from: YAMATO_agent
subclass of: Restriction
  on property: has used for
  min cardinality: 1

Experimental_action
type: Class
subclass of: YAMATO_action

YAMATO_agent
type: Class
subclass of: Restriction
  all values from: Scientific_paper_as_content
  on property: has paper as achievement
subclass of: YAMATO_object

Haplotype_generic_quality
type: Class
subclass of: Genuine_qualitative_generic_quality

Genuine_qualitative_generic_quality
type: Class
subclass of: YAMATO_qualitative_generic_quality

YAMATO_universal
type: Class
subclass of: YAMATO_Any
comment: This mean concepts which appear in our domain of discourse such as Concept, Instance, State, etc. This is not seriously elaborated yet.

Mouse_GDF5_protein
type: Class
subclass of: Polypeptide

Polypeptide
type: Class
subclass of: Restriction
  all values from: Polypeptide_sequence
  on property: has sequence
subclass of: Restriction
  cardinality: 1
  on property: has sequence
subclass of: Molecule

Guanine_based_nucleptide
type: Class
subclass of: Purine_nucleotide

Purine_nucleotide
type: Class
subclass of: nucleotide_group

Alphabet_figure_for_nucleotide_symbol
type: Class
subclass of: Restriction
  all values from: Symbol_designated_by_nucleotide
  on property: has content
subclass of: Restriction
  on property: has content
  cardinality: 1
subclass of: Restriction
  all values from: YAMATO_line_image
  on property: has form
subclass of: Restriction
  cardinality: 1
  on property: has form
subclass of: Symbol_figure

Symbol_designated_by_nucleotide
type: Class
subclass of: Molecular_symbol
subclass of: Restriction
  all values from: Symbol_designated_by_nucleotide
  on property: has antisense symbol
subclass of: Restriction
  on property: has antisense symbol
  cardinality: 1
comment: This is a element of genetic information. Natural symbol desiginated by nucleotide residues. This is identical to YAMATO's "AGCT symbol".

Symbol_figure
type: Class
subclass of: Restriction
  all values from: YAMATO_symbol
  on property: has content
subclass of: Restriction
  cardinality: 1
  on property: has content
subclass of: Restriction
  all values from: YAMATO_line_image
  on property: has form
subclass of: Restriction
  cardinality: 1
  on property: has form
subclass of: _2D_representation

_5__to_3__direction
type: Class
subclass of: Restriction
  all values from: _3__to_5__direction
  on property: has reverse direction
subclass of: Restriction
  cardinality: 1
  on property: has reverse direction
subclass of: Direction

_3__to_5__direction
type: Class
subclass of: Restriction
  on property: has reverse direction
  all values from: _5__to_3__direction
subclass of: Restriction
  cardinality: 1
  on property: has reverse direction
subclass of: Direction

Direction
type: Class
subclass of: Restriction
  all values from: Direction
  on property: has reverse direction
subclass of: Restriction
  cardinality: 1
  on property: has reverse direction
subclass of: YAMATO_abstract

RNA_group
type: Class
subclass of: single_stranded_polynucleotide_group
subclass of: Restriction
  all values from: RNA_group
  on property: has sub group

single_stranded_polynucleotide_group
type: Class
subclass of: polynucleotide_group

Composite_quantity
type: Class
subclass of: Rational_quantity

Rational_quantity
type: Class
comment: Most measurement in the physical sciences and engineering is done on ratio scales. Mass, length, time, plane angle, energy and electric charge are examples of physical measures that are ratio scales. The scale type takes its name from the fact that measurement is the estimation of the ratio between a magnitude of a continuous quantity and a unit magnitude of the same kind (Michell, 1997, 1999). Informally, the distinguishing feature of a ratio scale is the possession of a non-arbitrary zero value. For example, the Kelvin temperature scale has a non-arbitrary zero point of absolute zero, which is denoted 0K and is equal to -273.15 degrees Celsius. This zero point is non arbitrary as the particles which comprise matter at this temperature have zero kinetic energy. (wikipedia: http://en.wikipedia.org/wiki/Level_of_measurement)
subclass of: Restriction
  on property: has unit
  all values from: Unit
subclass of: Restriction
  on property: has unit
  cardinality: 1
subclass of: Restriction
  all values from: YAMATO_number
  on property: has value
subclass of: Restriction
  on property: has value
  cardinality: 1
subclass of: Continuous_quantity

YAMATO_proposition
type: Class
subclass of: YAMATO_content

YAMATO_content
type: Class
subclass of: YAMATO_semi-abstract

YAMATO_quantitative_generic_quality
type: Class
subclass of: YAMATO_basic_generic_quality
subclass of: Restriction
  on property: has referring to 2
  max cardinality: 1
subclass of: Restriction
  on property: has referring to 1
  all values from: Rational_quantity
subclass of: Restriction
  on property: has referring to 1
  cardinality: 1

YAMATO_basic_generic_quality
type: Class
subclass of: YAMATO_intrinsic_generic_quality

deletion_event
type: Class
subclass of: muation_event_of_unstructured_sequence
subclass of: Restriction
  all values from: YAMATO_instantaneous_event
  on property: has terminal Event
subclass of: Restriction
  on property: has terminal Event
  cardinality: 1
subclass of: Restriction
  all values from: YAMATO_instantaneous_event
  on property: has starting Event
subclass of: Restriction
  cardinality: 1
  on property: has starting Event

muation_event_of_unstructured_sequence
type: Class
subclass of: sequence_mutation_event

YAMATO_soft_symbol_sequence
type: Class
subclass of: YAMATO_symbol_sequence

YAMATO_symbol_sequence
type: Class
subclass of: YAMATO_ordinary_form
subclass of: Restriction
  on property: has sub-sequence
  all values from: YAMATO_symbol_sequence
subclass of: Restriction
  all values from: YAMATO_symbol
  on property: has symbol
subclass of: Restriction
  min cardinality: 1
  on property: has symbol

YAMATO_unit-related_form
type: Class
subclass of: YAMATO_epresentation_form

Supression
type: Class
subclass of: Phenotypic_change_dependent_on_genetic_background

Singleton_quantity
type: Class
subclass of: Rational_quantity
subclass of: Restriction
  on property: has unit
  all values from: Unit
subclass of: Restriction
  cardinality: 1
  on property: has unit
subclass of: Restriction
  all values from: YAMATO_number
  on property: has value
subclass of: Restriction
  cardinality: 1
  on property: has value

subcellular_component
type: Class
subclass of: Restriction
  all values from: chemical_entity
  on property: has molecular component
subclass of: Restriction
  cardinality: 1
  on property: has molecular component
subclass of: Biological_object

transition_process
type: Class
subclass of: Restriction
  on property: has terminal Event
  all values from: YAMATO_instantaneous_event
subclass of: Restriction
  cardinality: 1
  on property: has terminal Event
subclass of: base_substitution_event

base_substitution_event
type: Class
subclass of: muation_event_of_unstructured_sequence
subclass of: Restriction
  on property: has terminal Event
  all values from: YAMATO_instantaneous_event
subclass of: Restriction
  on property: has terminal Event
  cardinality: 1
subclass of: Restriction
  all values from: YAMATO_instantaneous_event
  on property: has starting Event
subclass of: Restriction
  on property: has starting Event
  cardinality: 1

meta-generic_quality
type: Class
subclass of: YAMATO_quantitative_generic_quality

YAMATO_abstract
type: Class
comment: It needs neither time nor sapce to exist.
subclass of: YAMATO_entity

single_strand_DNA_polymer
type: Class
subclass of: polynucleotide
subclass of: Restriction
  min cardinality: 1
  on property: has part

Wave_length_interval
type: Class
subclass of: Restriction
  on property: has upper end
  all values from: Wave_length_quantity
subclass of: Restriction
  on property: has upper end
  cardinality: 1
subclass of: Restriction
  on property: has lower end
  all values from: Wave_length_quantity
subclass of: Restriction
  cardinality: 1
  on property: has lower end
subclass of: interval_quantity

Wave_length_quantity
type: Class
subclass of: length_quantity

interval_quantity
type: Class
subclass of: Restriction
  all values from: Singleton_quantity
  on property: has upper end
subclass of: Restriction
  on property: has upper end
  cardinality: 1
subclass of: Restriction
  on property: has lower end
  all values from: Singleton_quantity
subclass of: Restriction
  on property: has lower end
  cardinality: 1
subclass of: Composite_quantity

Electronic_file_with_genetic_information
type: Class
subclass of: electronic_version
subclass of: Restriction
  on property: has media
  all values from: Electronic_file
subclass of: Restriction
  min cardinality: 1
  on property: has media
subclass of: Restriction
  on property: has representaion
  all values from: Coding_of_polypeptide
subclass of: Restriction
  min cardinality: 1
  on property: has representaion

electronic_version
type: Class
subclass of: symbol_sequence_stuff

Electronic_file
type: Class
subclass of: Non-represented_thing

Coding_of_polypeptide
type: Class
subclass of: Coding_of_gene_product
subclass of: Restriction
  all values from: specification_of_polypeptide
  on property: has content
subclass of: Restriction
  on property: has content
  cardinality: 1
subclass of: Restriction
  on property: has form
  all values from: _5__to_3__Nucleotide_sequence
subclass of: Restriction
  cardinality: 1
  on property: has form

deviation_2
type: Class
subclass of: meta_attribute_value

meta_attribute_value
type: Class
subclass of: attribute_independent

Physical_distance
type: Class
subclass of: Restriction
  all values from: Physical_location_on_chromosome
  on property: has value of
subclass of: Restriction
  on property: has value of
  cardinality: 1
subclass of: Restriction
  on property: has unit
  all values from: bp
subclass of: Restriction
  on property: has unit
  cardinality: 1
subclass of: Base_pair_count_value

Physical_location_on_chromosome
type: Class
subclass of: Restriction
  all values from: nucleotide_group
  on property: has of what
subclass of: Restriction
  cardinality: 1
  on property: has of what
subclass of: Restriction
  all values from: Chromosome
  on property: has depend on
subclass of: Restriction
  cardinality: 1
  on property: has depend on
subclass of: Restriction
  all values from: Chromosomal_interval
  on property: has referring to 1
subclass of: Restriction
  cardinality: 1
  on property: has referring to 1
subclass of: number_of_basepair

bp
type: Class
subclass of: UndefinedClass

Base_pair_count_value
type: Class
subclass of: numbers_quantity
subclass of: Restriction
  all values from: number_of_basepair
  on property: has value of
subclass of: Restriction
  cardinality: 1
  on property: has value of
subclass of: Restriction
  on property: has unit
  all values from: bp
subclass of: Restriction
  cardinality: 1
  on property: has unit

Thimine_based_nucleotide
type: Class
subclass of: Thimine_Uracil_based_nucleotide

Thimine_Uracil_based_nucleotide
type: Class
subclass of: Pyrimidine_nucleotide

cell_division
type: Class
subclass of: biological_process

Non-represented_thing
type: Class
subclass of: YAMATO_artifact

YAMATO_representation
type: Class
comment: Artificial content bearing non-physical thing. This has a content and form as a substance to bear the content. Representation is represented by a agent.
subclass of: YAMATO_semi-abstract

YAMATO_semi-abstract
type: Class
comment: It needs only time to exist.
subclass of: YAMATO_entity

Electronic_file_with_natural_language_representation
type: Class
subclass of: electronic_version
subclass of: Restriction
  on property: has media
  all values from: Electronic_file
subclass of: Restriction
  min cardinality: 1
  on property: has media
subclass of: Restriction
  all values from: Text
  on property: has representaion
subclass of: Restriction
  min cardinality: 1
  on property: has representaion

Text
type: Class
subclass of: Restriction
  all values from: Sentence
  on property: has component
subclass of: Restriction
  on property: has component
  cardinality: 1
subclass of: Composite_representation

set_of_RNA
type: Class
subclass of: Restriction
  all values from: polynucleotide
  on property: has part
subclass of: Restriction
  on property: has part
  min cardinality: 1
subclass of: set_of_polynucleotide_molecules

set_of_polynucleotide_molecules
type: Class
subclass of: Restriction
  all values from: polynucleotide
  on property: has part
subclass of: Restriction
  on property: has part
  min cardinality: 1
subclass of: Set_of_molecule

Attribute_neutral
type: Class
subclass of: Extrinsically_qualitative

Extrinsically_qualitative
type: Class
subclass of: Qualitative_property

Haplotype
type: Class
subclass of: Genetic_composition_value
subclass of: Restriction
  on property: has value of
  all values from: Combination_of_alleles_at_different_loci
subclass of: Restriction
  cardinality: 1
  on property: has value of

Genetic_composition_value
type: Class
subclass of: Restriction
  all values from: Genetic_composition
  on property: has value of
subclass of: Restriction
  on property: has value of
  cardinality: 1
subclass of: Nominal_scale_value

Adenin_based_nucleotide
type: Class
subclass of: Purine_nucleotide

Composite_representation
type: Class
subclass of: Artificial_representation
subclass of: Restriction
  all values from: YAMATO_representation
  on property: has component
subclass of: Restriction
  min cardinality: 1
  on property: has component

Artificial_representation
type: Class
subclass of: Restriction
  on property: has content
  all values from: YAMATO_proposition
subclass of: Restriction
  cardinality: 1
  on property: has content
subclass of: Restriction
  all values from: YAMATO_epresentation_form
  on property: has form
subclass of: Restriction
  on property: has form
  cardinality: 1
subclass of: YAMATO_representation

Pyrimidine_nucleotide
type: Class
subclass of: nucleotide_group

nucleotide_group
type: Class
subclass of: Restriction
  on property: has monosymbolic sequence
  all values from: _5__to_3__Nucleotide_sequence
subclass of: Restriction
  cardinality: 1
  on property: has monosymbolic sequence
subclass of: radical_group

Inverted_repeat_sequence
type: Class
subclass of: Structured_seqence

Structured_seqence
type: Class
subclass of: Restriction
  all values from: Unstructured_sequence
  on property: has structure symbol
subclass of: Restriction
  min cardinality: 1
  on property: has structure symbol
subclass of: Sequence_with_pattern

Tripret_repeat
type: Class
subclass of: Repetitive_sequence
subclass of: Restriction
  on property: has repeat unit
  all values from: Triplet

Triplet
type: Class
subclass of: Unstructured_sequence

insersion_event
type: Class
subclass of: Restriction
  on property: has terminal Event
  all values from: YAMATO_instantaneous_event
subclass of: Restriction
  cardinality: 1
  on property: has terminal Event
subclass of: Restriction
  on property: has starting Event
  all values from: YAMATO_instantaneous_event
subclass of: Restriction
  cardinality: 1
  on property: has starting Event
subclass of: muation_event_of_unstructured_sequence

Anatomical_part
type: Class
subclass of: Body_part_related
subclass of: Restriction
  all values from: cell
  on property: has cell
subclass of: Restriction
  on property: has cell
  min cardinality: 1
subclass of: Restriction
  on property: has sub part
  all values from: Anatomical_part

Body_part_related
type: Class
subclass of: Organism_body

cell
type: Class
subclass of: Body_part_related
subclass of: Restriction
  all values from: multiploid_genome
  on property: has genome
subclass of: Restriction
  cardinality: 1
  on property: has genome
subclass of: Restriction
  on property: has organelle
  all values from: Organelle
subclass of: Restriction
  on property: has organelle
  min cardinality: 1

multiploid_genome
type: Class
subclass of: genome
subclass of: Restriction
  on property: has haploid
  all values from: Haploid_genome
subclass of: Restriction
  on property: has haploid
  min cardinality: 1

genome
type: Class
subclass of: Restriction
  on property: has genomic polynucleotide
  all values from: set_of_polynucleotide_molecules
subclass of: Restriction
  on property: has genomic polynucleotide
  cardinality: 1
subclass of: Organelle_part
comment: In this ontology "genome" is not the entirety of an organism's hereditary information, but the entirety of a bearer of an organism's hereditary information.

Haploid_genome
type: Class
subclass of: genome
subclass of: Restriction
  all values from: allele
  on property: has component
subclass of: Restriction
  on property: has component
  min cardinality: 1

Chromosome_part
type: Class
subclass of: Organelle_part

Chromosome_disjunction
type: Class
subclass of: Disjunction

Disjunction
type: Class
subclass of: biological_process

diploid_genome
type: Class
subclass of: multiploid_genome

Conservation
type: Class
subclass of: biological_process

YAMATO_artifact
type: Class
subclass of: YAMATO_functional

Monovalent_chromosome
type: Class
subclass of: Chromosome

YAMATO_physical
type: Class
subclass of: YAMATO_entity
comment: It needs both 3D space and time to exist.

Locus
type: Class
subclass of: Restriction
  all values from: Physical_location_on_chromosome
  on property: has value of
subclass of: Restriction
  on property: has value of
  cardinality: 1
subclass of: Nominal_scale_value
comment: Locus is a nominal scale value for chromosomal location. Usually, it is represented by the name of a genetic marker. Locus itself does not represent ordinal feature of chromosomal location such as genetic or phisical distance.

A_to_G_transition_process
type: Class
subclass of: Restriction
  on property: has terminal Event
  all values from: YAMATO_instantaneous_event
subclass of: Restriction
  on property: has terminal Event
  cardinality: 1
subclass of: purine_transition_event

specification_of_polypeptide
type: Class
subclass of: specification_of_gene_product
subclass of: Restriction
  on property: has for what
  all values from: Polypeptide
subclass of: Restriction
  min cardinality: 1
  on property: has for what

Chromosomal_interval
type: Class
subclass of: Restriction
  all values from: Physical_location_on_chromosome
  on property: has value of
subclass of: Restriction
  on property: has value of
  cardinality: 1
subclass of: Restriction
  on property: has chromosomal interval
  all values from: Basepair_interval
subclass of: Restriction
  cardinality: 1
  on property: has chromosomal interval
subclass of: Restriction
  on property: has chromosome ID
  all values from: integer
subclass of: Restriction
  on property: has chromosome ID
  cardinality: 1
subclass of: Composite_quantity

number_of_basepair
type: Class
subclass of: number_of_objects
subclass of: Restriction
  on property: has of what
  all values from: nucleotide_group
subclass of: Restriction
  on property: has of what
  cardinality: 1
subclass of: Restriction
  on property: has referring to 1
  all values from: Base_pair_count_value
subclass of: Restriction
  cardinality: 1
  on property: has referring to 1

YAMATO_1D-space
type: Class
subclass of: YAMATO_space

YAMATO_space
type: Class
comment: Space is indispensable for things to exist in the world.
subclass of: YAMATO_substrate

YAMATO_role
type: Class
comment: Roles are not adequately reflected in YATO, since it is already reflected/imbedded in Hozo tool. While ordinary types such as human, table, etc. are defined independently, roles are defined within a context which they necessarily depends on in our role theory [Mizoguchi 07]. In fact, roles are used in defining all the types in YATO. These are the reasons why YATO does not have to incorporate roles in it. When one uses Hozo with YATO, he/she can enjoy maximally the benefits presented by both. See [Mizoguchi 2007] Mizoguchi R., Sunagawa E., Kozaki K. and Kitamura Y.: A Model of Roles within an Ontology Development Tool: Hozo, J. of Applied Ontology, Vol.2, No.2, pp.159-179. Sep. 2007.
subclass of: YAMATO_specifically_dependent

YAMATO_specifically_dependent
type: Class
subclass of: YAMATO_dependent_entity

Molecular_symbol
type: Class
comment: This is not artificial symbol such as alphabets. This is natural symbol to compose information such as genetic information.
subclass of: YAMATO_symbol

Partial_dominance
type: Class
subclass of: Dominance_value

Dominance_value
type: Class
subclass of: Restriction
  all values from: Dominance
  on property: has value of
subclass of: Restriction
  on property: has value of
  cardinality: 1
subclass of: Attribute_dependent

YAMATO_I_O_relational
type: Class
subclass of: YAMATO_intrinsic_generic_quality

design_of_functional_RNA
type: Class
subclass of: specification_of_RNA
subclass of: Restriction
  all values from: Single_strand_RNA_polymer
  on property: has for what
subclass of: Restriction
  min cardinality: 1
  on property: has for what

specification_of_RNA
type: Class
subclass of: Restriction
  on property: has for what
  all values from: Single_strand_RNA_polymer
subclass of: Restriction
  min cardinality: 1
  on property: has for what
subclass of: specification_of_gene_product

Single_strand_RNA_polymer
type: Class
subclass of: polynucleotide
subclass of: Restriction
  min cardinality: 1
  on property: has part

UndefinedClass
type: Class

counting_value
type: Class
subclass of: meta_attribute_value

Acceleration_of_function
type: Class
subclass of: Alteration_of_gene_function

Alteration_of_gene_function
type: Class
subclass of: Transformation

Trans-splicing
type: Class
subclass of: RNA_splicing

RNA_splicing
type: Class
subclass of: Restriction
  on property: has output entity
  all values from: Single_strand_RNA_polymer
subclass of: Restriction
  on property: has output entity
  min cardinality: 1
subclass of: Restriction
  all values from: Single_strand_RNA_polymer
  on property: has input entity
subclass of: Restriction
  min cardinality: 1
  on property: has input entity
subclass of: biological_process

Alu_sequence
type: Class
subclass of: Unstructured_sequence

Unstructured_sequence
type: Class
subclass of: Sequence_with_pattern

Parameter_composition
type: Class
subclass of: Restriction
  all values from: Experimental_data
  on property: has content
subclass of: Restriction
  on property: has content
  cardinality: 1
subclass of: protocol

Experimental_data
type: Class
subclass of: Restriction
  all values from: Scientific_paper_as_content
  on property: has outcome paper
subclass of: Restriction
  all values from: YAMATO_quality_1
  on property: has mesured parameter
subclass of: Restriction
  on property: has mesured parameter
  min cardinality: 1
subclass of: Restriction
  min cardinality: 1
  on property: has content
subclass of: Restriction
  all values from: YAMATO_entity
  on property: has mesured for
subclass of: Restriction
  on property: has mesured for
  min cardinality: 1
subclass of: YAMATO_representation_secondary

protocol
type: Class
subclass of: YAMATO_plan-related
subclass of: Restriction
  on property: has mesured parameter
  all values from: YAMATO_quality_1
subclass of: Restriction
  cardinality: 1
  on property: has mesured parameter
subclass of: Restriction
  all values from: protocol
  on property: has sub procedure
subclass of: Restriction
  all values from: YAMATO_agent
  on property: has author
subclass of: Restriction
  on property: has author
  min cardinality: 1

virtual_locaiton
type: Class
subclass of: YAMATO_accidental_attribute

YAMATO_accidental_attribute
type: Class
comment: This is a non-essential attribute. There is no clear boundary between intrinsic and accidental attributes in theory.
subclass of: YAMATO_generic_quality

Genetic_background
type: Class
subclass of: Restriction
  all values from: Genotype_at_a_locus
  on property: has component
subclass of: Restriction
  on property: has component
  min cardinality: 1
subclass of: Restriction
  all values from: Genetic_composition
  on property: has value of
subclass of: Restriction
  cardinality: 1
  on property: has value of
subclass of: genotype
comment: Genetic background is a nominal scale value of the gentetic attribute of a biological entity. This is composed of genotypes.

Genotype_at_a_locus
type: Class
subclass of: Restriction
  all values from: Locus
  on property: has locus
subclass of: Restriction
  cardinality: 1
  on property: has locus
subclass of: Restriction
  on property: has depend on
  all values from: allele
subclass of: Restriction
  min cardinality: 1
  on property: has depend on
subclass of: Restriction
  all values from: Genetic_composition
  on property: has value of
subclass of: Restriction
  cardinality: 1
  on property: has value of
subclass of: genotype

genotype
type: Class
subclass of: Genetic_composition_value
subclass of: Restriction
  on property: has value
  all values from: specification_of_phenotype
subclass of: Restriction
  cardinality: 1
  on property: has value
subclass of: Restriction
  on property: has value of
  all values from: Zygousis_composition
subclass of: Restriction
  on property: has value of
  cardinality: 1
comment: Genotype is a nominal scale value represents genomic feature of the biological entity focused on specific genetic marker (or possibly locus), It depends on the composition of alleles of the genetic marker. Genotype is a part of genetic background.

YAMATO_process
type: Class
subclass of: Restriction
  on property: has participant
  all values from: YAMATO_entity
subclass of: Restriction
  on property: has participant
  min cardinality: 1
subclass of: YAMATO_stative

YAMATO_stative
type: Class
subclass of: YAMATO_occurent

TATA_box
type: Class
subclass of: Functional_sequence

Functional_sequence
type: Class
subclass of: Unstructured_sequence

YAMATO_date
type: Class
subclass of: YAMATO_time_point

attribute_independent
type: Class
subclass of: Ordinal_scale_value

Ordinal_scale_value
type: Class
subclass of: Quantity
comment: This is a non-categorical quality value represents only the rank order (1st, 2nd, 3rd etc.).

sequence_mutation_event
type: Class
subclass of: Restriction
  on property: has terminal Event
  all values from: YAMATO_instantaneous_event
subclass of: Restriction
  on property: has terminal Event
  cardinality: 1
subclass of: Restriction
  on property: has constituted by
  all values from: sequence_mutation_process
subclass of: Restriction
  cardinality: 1
  on property: has constituted by
subclass of: Restriction
  all values from: YAMATO_instantaneous_event
  on property: has starting Event
subclass of: Restriction
  cardinality: 1
  on property: has starting Event
subclass of: biological_event

YAMATO_complex_agent
type: Class
subclass of: YAMATO_agent

Transient_polymorphism
type: Class
subclass of: Genetic_polymorphism

Sense_codon
type: Class
subclass of: codon

codon
type: Class
subclass of: Restriction
  on property: has complementary sequence
  all values from: Nucleotide_triplet
subclass of: Restriction
  on property: has complementary sequence
  cardinality: 1
subclass of: Nucleotide_triplet

Chromosome_pairing
type: Class
subclass of: Restriction
  on property: has pair
  all values from: Chromosome
subclass of: Restriction
  on property: has pair
  min cardinality: 1
subclass of: Pairing

Pairing
type: Class
subclass of: Restriction
  on property: has pair
  all values from: YAMATO_entity
subclass of: Restriction
  min cardinality: 1
  on property: has pair
subclass of: biological_process

Dominance
type: Class
subclass of: Dominace_related

Dominace_related
type: Class
subclass of: meta-generic_quality

Alphabet
type: Class
subclass of: YAMATO_symbol

counting_generic_quality
type: Class
subclass of: Restriction
  on property: has on what
  all values from: YAMATO_entity
subclass of: Restriction
  on property: has on what
  cardinality: 1
subclass of: meta-generic_quality

radical_group
type: Class
subclass of: Restriction
  on property: has sub group
  all values from: radical_group
subclass of: chemical_entity

YAMATO_stative_2
type: Class
subclass of: YAMATO_stative

DNA_group
type: Class
subclass of: double_stranded_polynucleotide_group

double_stranded_polynucleotide_group
type: Class
subclass of: polynucleotide_group
subclass of: Restriction
  on property: has sequence
  all values from: _5__to_3__Nucleotide_sequence
subclass of: Restriction
  cardinality: 1
  on property: has sequence

Primitive_representation
type: Class
subclass of: Artificial_representation
subclass of: Restriction
  all values from: YAMATO_proposition
  on property: has content
subclass of: Restriction
  cardinality: 1
  on property: has content
subclass of: Restriction
  on property: has form
  all values from: YAMATO_epresentation_form
subclass of: Restriction
  on property: has form
  cardinality: 1

reproduction
type: Class
subclass of: reproduction-related
subclass of: Restriction
  all values from: organism
  on property: has offspring
subclass of: Restriction
  on property: has offspring
  min cardinality: 1
subclass of: Restriction
  all values from: organism
  on property: has parent
subclass of: Restriction
  on property: has parent
  min cardinality: 1

reproduction-related
type: Class
subclass of: biological_process

Context_dependent_phenotypic_change
type: Class
subclass of: Mutation_of_organism

Mutation_of_organism
type: Class
subclass of: Restriction
  on property: has output entity
  all values from: organism
subclass of: Restriction
  min cardinality: 1
  on property: has output entity
subclass of: changing_process

YAMATO_quality_value
type: Class
comment: This is a dependent entity such as long, 10cm, red. Quality value reprents equivalence and difference of quality types belonging a same class, which is an important basic reality for the scientific reseach. This may be regarded as quantity in broad sense. It is just a quantity independent of what quantity it is of. That is, 10cm and 11cm exist just as it is in the quantity space and are just different. On the other hand, when a thing's length is 10cm long at time t1 and 11cm long at t2, we say the length of the thing CHANGED. The 10cm long of a thing has its identity which persists having possibly different values.
subclass of: YAMATO_generically_dependent
subclass of: Restriction
  on property: has value of
  all values from: YAMATO_quality_1
subclass of: Restriction
  on property: has value of
  cardinality: 1

YAMATO_quality_1
type: Class
comment: This is a dependent entity such as the color of this tomato, or the length of tail of a specific mouse individual. Quality type cannot exist alone but always exists dependently on physical things which also need quality types to exist.
subclass of: Restriction
  all values from: YAMATO_entity
  on property: has on what
subclass of: Restriction
  on property: has on what
  cardinality: 1
subclass of: Restriction
  on property: has referring to
  all values from: YAMATO_Any
subclass of: Restriction
  max cardinality: 2
  on property: has referring to
subclass of: YAMATO_specifically_dependent

YAMATO_particular
type: Class
comment: Ordinary top-most type.
subclass of: YAMATO_Any

Form
type: Class
subclass of: YAMATO_Structure

YAMATO_Structure
type: Class
subclass of: Restriction
  all values from: YAMATO_space
  on property: has dimension
subclass of: Restriction
  cardinality: 1
  on property: has dimension
subclass of: YAMATO_abstract

Experimental_cohort
type: Class
subclass of: YAMATO_group
subclass of: Restriction
  all values from: Body_part_related
  on property: has body part
subclass of: Restriction
  on property: has body part
  min cardinality: 1
subclass of: Restriction
  on property: has sub class
  all values from: Experimental_cohort
subclass of: Restriction
  all values from: Biological_object
  on property: has organism
subclass of: Restriction
  on property: has organism
  cardinality: 1

Biological_object
type: Class
subclass of: Natural_object
subclass of: Restriction
  on property: has phenotype
  cardinality: 1
subclass of: Restriction
  all values from: YAMATO_generic_quality
  on property: has trait
subclass of: Restriction
  on property: has trait
  min cardinality: 1

nucleoside_group
type: Class
subclass of: radical_group

measured_for_2
type: Class
subclass of: Restriction
  cardinality: 1
  on property: has value
subclass of: Restriction
  all values from: YAMATO_quality_1
  on property: has objected attribute
subclass of: Restriction
  cardinality: 1
  on property: has objected attribute
subclass of: RelationalConcept

YAMATO_specification_plan
type: Class
subclass of: Restriction
  on property: has for what
  all values from: YAMATO_Any
subclass of: Restriction
  on property: has for what
  min cardinality: 1
subclass of: Designed_proposition

Natural_object
type: Class
subclass of: YAMATO_functional

cM
type: Class
subclass of: UndefinedClass

number_of_objects
type: Class
subclass of: Restriction
  all values from: YAMATO_object
  on property: has of what
subclass of: Restriction
  on property: has of what
  cardinality: 1
subclass of: Restriction
  all values from: numbers_quality_value
  on property: has referring to 2
subclass of: Restriction
  cardinality: 1
  on property: has referring to 2
subclass of: Restriction
  on property: has referring to 1
  all values from: numbers_quantity
subclass of: Restriction
  on property: has referring to 1
  cardinality: 1
subclass of: counting_generic_quality

Taxonomic_rank
type: Class
subclass of: Metaclass
comment: Taxonomic rank indicates the level of biological classification such as domain, kingdom, phylum, class, order, family genus and species.We cannot represent these ranks as the classes in the "Particular" world.

Metaclass
type: Class
comment: This shows some aggregation of classes which can not be represented by the classification system in Particular world.
subclass of: YAMATO_universal

Chromosome_replication
type: Class
subclass of: Biological_replication

integer
type: Class
subclass of: UndefinedClass

Deviation_value
type: Class
subclass of: Restriction
  all values from: deviation_from_normal__PATO_0000069
  on property: has value of
subclass of: Restriction
  on property: has value of
  cardinality: 1
subclass of: Attribute_dependent

deviation_from_normal__PATO_0000069
type: Class
subclass of: meta-generic_quality

purine_to_pyrimidine_transversion_event
type: Class
subclass of: Restriction
  on property: has terminal Event
  all values from: YAMATO_instantaneous_event
subclass of: Restriction
  on property: has terminal Event
  cardinality: 1
subclass of: transversion_event

transversion_event
type: Class
subclass of: Restriction
  on property: has terminal Event
  all values from: YAMATO_instantaneous_event
subclass of: Restriction
  on property: has terminal Event
  cardinality: 1
subclass of: base_substitution_event

Stop_codon
type: Class
subclass of: Nonsense_codon

Nonsense_codon
type: Class
subclass of: codon

Mus_musculus
type: Class
subclass of: mammal
subclass of: Restriction
  on property: has genome
  all values from: genome
subclass of: Restriction
  on property: has genome
  cardinality: 1

mammal
type: Class
subclass of: animal
subclass of: Restriction
  on property: has genome
  all values from: genome
subclass of: Restriction
  cardinality: 1
  on property: has genome

Length_value
type: Class
subclass of: Restriction
  all values from: length
  on property: has value of
subclass of: Restriction
  on property: has value of
  cardinality: 1
subclass of: Attribute_dependent

length
type: Class
subclass of: Restriction
  on property: has referring to 1
  all values from: length_quantity
subclass of: Restriction
  cardinality: 1
  on property: has referring to 1
subclass of: non-meta_generic_quality

Mitochondrion
type: Class
subclass of: Organelle

Organelle
type: Class
subclass of: subcellular_component
subclass of: Restriction
  on property: has part
  all values from: Organelle_part
subclass of: Restriction
  min cardinality: 1
  on property: has part

YAMATO_instant_event
type: Class
subclass of: YAMATO_event

YAMATO_event
type: Class
subclass of: Restriction
  on property: has subevent
  all values from: YAMATO_event
subclass of: YAMATO_occurent

YAMATO_action
type: Class
subclass of: Restriction
  all values from: YAMATO_action
  on property: has sub-action
subclass of: Restriction
  all values from: YAMATO_entity
  on property: has participant
subclass of: Restriction
  on property: has participant
  min cardinality: 1
subclass of: Restriction
  all values from: YAMATO_agent
  on property: has agent
subclass of: Restriction
  min cardinality: 1
  on property: has agent
subclass of: YAMATO_process

Amplified_fragment_length_polymorphism
type: Class
subclass of: Genetic_polymorphism

T_U_to_C_transition_event
type: Class
subclass of: Restriction
  all values from: YAMATO_instantaneous_event
  on property: has terminal Event
subclass of: Restriction
  cardinality: 1
  on property: has terminal Event
subclass of: pyrimidine_transition_event

pyrimidine_transition_event
type: Class
subclass of: Restriction
  all values from: YAMATO_instantaneous_event
  on property: has terminal Event
subclass of: Restriction
  cardinality: 1
  on property: has terminal Event
subclass of: transition_process

nucleotide_sequence
type: Class
subclass of: Molecular_sequence

reverse_Nucleotide_sequence
type: Class
subclass of: nucleotide_sequence

YAMATO_state
type: Class
subclass of: YAMATO_stative_2

YAMATO_2D-space
type: Class
subclass of: YAMATO_space

YAMATO_phenomenon
type: Class
subclass of: YAMATO_process

Transcription
type: Class
subclass of: Restriction
  on property: has participant
  all values from: polynucleotide_group
subclass of: Restriction
  on property: has transcript
  min cardinality: 1
subclass of: Restriction
  all values from: chemical_interaction
  on property: has sub occurent
subclass of: Restriction
  on property: has sub occurent
  cardinality: 1
subclass of: Restriction
  min cardinality: 1
  on property: has participant
subclass of: Restriction
  on property: has sub occurent
  min cardinality: 1
subclass of: Restriction
  on property: has sub occurent
  all values from: chemical_interaction
subclass of: biological_process
subclass of: Restriction
  on property: has transcript
  all values from: Single_strand_RNA_polymer
subclass of: Restriction
  on property: has sub occurent
  all values from: chemical_interaction
subclass of: Restriction
  on property: has sub occurent
  cardinality: 1

chemical_interaction
type: Class
subclass of: Restriction
  all values from: YAMATO_entity
  on property: has output entity
subclass of: Restriction
  min cardinality: 1
  on property: has output entity
subclass of: Restriction
  on property: has input entity
  all values from: YAMATO_entity
subclass of: Restriction
  on property: has input entity
  min cardinality: 1
subclass of: YAMATO_phenomenon

Change_of_mendelian_population
type: Class
subclass of: Restriction
  on property: has sexual reproduction
  min cardinality: 1
subclass of: Restriction
  all values from: mutation_event_of_s-segment
  on property: has mutation event of gene
subclass of: Restriction
  all values from: sequence_mutation_event
  on property: has mutation event
subclass of: Restriction
  on property: has mutation event
  min cardinality: 1
subclass of: Restriction
  all values from: Mendelian_population
  on property: has participant
subclass of: Restriction
  cardinality: 1
  on property: has participant
subclass of: changing_process

mutation_event_of_s-segment
type: Class
subclass of: UndefinedClass

Mendelian_population
type: Class
subclass of: Restriction
  on property: has member
  min cardinality: 1
subclass of: Restriction
  all values from: organism
  on property: has member
subclass of: Restriction
  all values from: Mendelian_population
  on property: has sub population
subclass of: Restriction
  on property: has species
  cardinality: 1
subclass of: biological_polulation
subclass of: Restriction
  on property: has gene pool
  min cardinality: 1
subclass of: Restriction
  on property: has gene pool
  all values from: gene_pool
subclass of: Restriction
  all values from: organism
  on property: has species

changing_process
type: Class
subclass of: biological_process

complimentary
type: Class
subclass of: Restriction
  on property: has role
  all values from: YAMATO_Any
subclass of: Restriction
  on property: has role
  cardinality: 1
subclass of: Restriction
  all values from: YAMATO_Any
  on property: has role
subclass of: Restriction
  cardinality: 1
  on property: has role
subclass of: RelationalConcept

YAMATO_ordinary_event
type: Class
subclass of: Restriction
  all values from: YAMATO_instantaneous_event
  on property: has terminal Event
subclass of: Restriction
  on property: has terminal Event
  cardinality: 1
subclass of: Restriction
  all values from: YAMATO_process
  on property: has constituted by
subclass of: Restriction
  on property: has constituted by
  cardinality: 1
subclass of: Restriction
  all values from: YAMATO_instantaneous_event
  on property: has starting Event
subclass of: Restriction
  cardinality: 1
  on property: has starting Event
subclass of: YAMATO_event

Molecular_complex
type: Class
subclass of: Restriction
  all values from: Molecule
  on property: has component
subclass of: Restriction
  min cardinality: 2
  on property: has component
subclass of: Polyatomic_stable_substance

Molecule
type: Class
subclass of: Restriction
  on property: has part
  all values from: radical_group
subclass of: Polyatomic_stable_substance

YAMATO_substrate
type: Class
subclass of: YAMATO_particular
comment: This needs further elaboration. Anyway, this is what entities need to exist in the real world.

abstract_document
type: Class
subclass of: Restriction
  all values from: YAMATO_natural_language
  on property: has form
subclass of: Restriction
  cardinality: 1
  on property: has form
subclass of: Restriction
  all values from: Text
  on property: has component
subclass of: Restriction
  min cardinality: 1
  on property: has component
subclass of: Composite_representation

YAMATO_natural_language
type: Class
subclass of: Restriction
  all values from: Alphabet
  on property: has symbol
subclass of: Restriction
  min cardinality: 1
  on property: has symbol
subclass of: YAMATO_language_related

YAMATO_number
type: Class
subclass of: YAMATO_abstract

length_quantity
type: Class
subclass of: ordinaly_quantity
subclass of: Restriction
  on property: has value of
  all values from: length
subclass of: Restriction
  on property: has value of
  cardinality: 1

ordinaly_quantity
type: Class
subclass of: attribute-specific

decrease_of_gene_function
type: Class
subclass of: Alteration_of_gene_function

Organism_body
type: Class
subclass of: Restriction
  all values from: genome
  on property: has genome
subclass of: Restriction
  on property: has genome
  cardinality: 1
subclass of: Restriction
  on property: has genotype
  all values from: genotype
subclass of: Restriction
  min cardinality: 1
  on property: has genotype
subclass of: Biological_object

animal
type: Class
subclass of: organism

Visible_mutation
type: Class
subclass of: Mutation_of_organism

death
type: Class
subclass of: biological_process

Atom
type: Class
subclass of: chemical_entity

Shape
type: Class
subclass of: Genuine_qualitative_generic_quality

Inversion_polymorphism
type: Class
subclass of: Chromosomal_polumorphism

YAMATO_group_like_thing
type: Class
subclass of: YAMATO_non-unitary

YAMATO_non-unitary
type: Class
subclass of: YAMATO_continuant

transcription_plus_splicing
type: Class
subclass of: biological_process

Basepair_interval
type: Class
subclass of: Restriction
  all values from: Base_pair_count_value
  on property: has upper end
subclass of: Restriction
  on property: has upper end
  cardinality: 1
subclass of: Restriction
  all values from: Base_pair_count_value
  on property: has lower end
subclass of: Restriction
  cardinality: 1
  on property: has lower end
subclass of: interval_quantity

Restriction_fragment_length_polymorphism
type: Class
subclass of: Genetic_polymorphism

YAMATO_occurent
type: Class
subclass of: Restriction
  on property: has environmental factor
  cardinality: 1
subclass of: Restriction
  all values from: YAMATO_entity
  on property: has participant
subclass of: Restriction
  min cardinality: 1
  on property: has participant
subclass of: Restriction
  on property: has sub occurent
  all values from: YAMATO_occurent
subclass of: Restriction
  all values from: YAMATO_time_interval
  on property: has time
subclass of: Restriction
  on property: has time
  cardinality: 1
subclass of: YAMATO_physical

Coding_sequence
type: Class
subclass of: Sequence_only_by_codon

Sequence_only_by_codon
type: Class
subclass of: Restriction
  all values from: codon
  on property: has structure symbol
subclass of: Restriction
  on property: has structure symbol
  min cardinality: 1
subclass of: Restriction
  on property: has symbol
  all values from: Symbol_designated_by_nucleotide
subclass of: Restriction
  cardinality: 1
  on property: has symbol
subclass of: _5__to_3__Nucleotide_sequence

representation_of_genetic_symbol
type: Class
subclass of: Natural_representation-like

C57BL_6
type: Class
subclass of: Mouse_Strain

Mouse_Strain
type: Class
subclass of: Mus_musculus

Irregular_structure
type: Class
subclass of: YAMATO_Structure

YAMATO_plan-related
type: Class
subclass of: Designed_proposition

C_to_T_U_transition_event
type: Class
subclass of: Restriction
  all values from: YAMATO_instantaneous_event
  on property: has terminal Event
subclass of: Restriction
  on property: has terminal Event
  cardinality: 1
subclass of: pyrimidine_transition_event

Cis-dominance
type: Class
subclass of: Dominace_related

Picture
type: Class
subclass of: _2D_representation

_2D_representation
type: Class
subclass of: Primitive_representation

Represented_thing
type: Class
subclass of: Restriction
  all values from: YAMATO_physical
  on property: has media
subclass of: Restriction
  on property: has media
  min cardinality: 1
subclass of: Restriction
  on property: has representaion
  all values from: YAMATO_representation
subclass of: Restriction
  min cardinality: 1
  on property: has representaion
subclass of: Representation_related

Representation_related
type: Class
subclass of: YAMATO_artifact

Start_codon
type: Class
subclass of: Sense_codon

Quantitative_property
type: Class
subclass of: YAMATO_property

Organization
type: Class
subclass of: Restriction
  all values from: Person
  on property: has member
subclass of: Restriction
  min cardinality: 1
  on property: has member
subclass of: YAMATO_complex_agent

Person
type: Class
subclass of: YAMATO_singleton_agent

_3D_irregular_structure
type: Class
subclass of: Restriction
  all values from: YAMATO_3D-space
  on property: has dimension
subclass of: Restriction
  cardinality: 1
  on property: has dimension
subclass of: Irregular_structure

YAMATO_3D-space
type: Class
subclass of: YAMATO_space

sequence_mutation_process
type: Class
subclass of: changing_process
subclass of: Restriction
  on property: has participant
  all values from: polynucleotide_group
subclass of: Restriction
  on property: has participant
  cardinality: 1

individual_related
type: Class
subclass of: Restriction
  on property: has part
  all values from: Body_part_related
subclass of: Restriction
  min cardinality: 1
  on property: has part
subclass of: Organism_body

gamete
type: Class
subclass of: cell

Genetic_instability
type: Class
subclass of: Transformation

style_of_text
type: Class
subclass of: Designed_proposition

incomplete_dominance
type: Class
subclass of: Dominance_value

spec_genomic_segment
type: Class
subclass of: UndefinedClass

allele
type: Class
subclass of: UndefinedClass

Polypeptide_sequence
type: Class
subclass of: Molecular_sequence

Polymorphism
type: Class
subclass of: meta-generic_quality

Product_proposition
type: Class
subclass of: YAMATO_representation-primary

YAMATO_representation-primary
type: Class
subclass of: Restriction
  all values from: YAMATO_process
  on property: has used for
subclass of: Restriction
  on property: has used for
  min cardinality: 1
subclass of: YAMATO_proposition

YAMATO_image_form
type: Class
subclass of: YAMATO_ordinary_form

YAMATO_ordinary_form
type: Class
subclass of: YAMATO_epresentation_form

Allelic_frequency
type: Class
subclass of: Frequency_quantity

Frequency_quantity
type: Class
subclass of: attribute-specific
subclass of: Restriction
  on property: has value of
  all values from: YAMATO_quality_1
subclass of: Restriction
  on property: has value of
  cardinality: 1

YAMATO_language_related
type: Class
subclass of: YAMATO_soft_symbol_sequence

Phisical_distance_in_genome_assembly
type: Class
subclass of: Restriction
  on property: has value of
  cardinality: 1
subclass of: Restriction
  all values from: bp
  on property: has unit
subclass of: Restriction
  cardinality: 1
  on property: has unit
subclass of: Base_pair_count_value

population_of_a_species
type: Class
subclass of: Restriction
  on property: has species
  cardinality: 1
subclass of: Restriction
  all values from: organism
  on property: has species
subclass of: Restriction
  on property: has sub population
  all values from: partial_population_in_species
subclass of: Restriction
  all values from: organism
  on property: has member
subclass of: Restriction
  all values from: spec_genomic_segment
  on property: has species specific specification of genomic segment
subclass of: Mendelian_population
subclass of: Restriction
  on property: has gene pool
  all values from: gene_pool
subclass of: Restriction
  min cardinality: 1
  on property: has member
subclass of: Restriction
  on property: has species specific specification of genomic segment
  cardinality: 1
subclass of: Restriction
  min cardinality: 1
  on property: has gene pool
subclass of: Restriction
  all values from: spec_gene_type
  on property: has species specific specification of genomic segment
subclass of: Restriction
  on property: has species specific specification of genomic segment
  cardinality: 1

partial_population_in_species
type: Class
subclass of: Mendelian_population

spec_gene_type
type: Class
subclass of: UndefinedClass

Eukaryotic_cell
type: Class
subclass of: Restriction
  all values from: Nucleus
  on property: has organelle
subclass of: Restriction
  cardinality: 1
  on property: has organelle
subclass of: cell

Nucleus
type: Class
subclass of: Restriction
  on property: has part
  all values from: Chromosome
subclass of: Restriction
  min cardinality: 1
  on property: has part
subclass of: Organelle

document
type: Class
subclass of: Restriction
  all values from: YAMATO_physical
  on property: has media
subclass of: Restriction
  min cardinality: 1
  on property: has media
subclass of: Restriction
  on property: has representaion
  all values from: abstract_document
subclass of: Restriction
  on property: has representaion
  min cardinality: 1
subclass of: symbol_sequence_stuff

symbol_sequence_stuff
type: Class
subclass of: Represented_thing

Quantity
type: Class
subclass of: Non-categorical
comment: This is a quality value represents order or rank intrinsically exept for unit.

Doublet_repeat
type: Class
subclass of: Restriction
  on property: has repeat unit
  all values from: Dublet
subclass of: Repetitive_sequence

Dublet
type: Class
subclass of: Unstructured_sequence

Polymorphism_value
type: Class
subclass of: Restriction
  on property: has value of
  all values from: Polymorphism
subclass of: Restriction
  cardinality: 1
  on property: has value of
subclass of: Attribute_dependent

Intervening_sequence
type: Class
subclass of: Functional_sequence

PPML_throuput_description
type: Class
subclass of: Restriction
  on property: has throuput
  all values from: Continuous_quantity
subclass of: Restriction
  on property: has throuput
  cardinality: 1
subclass of: PPML_component

Continuous_quantity
type: Class
comment: This is a quantitavive quality value represents the rank order and intervals between a rank and next rank are equal.
subclass of: Quantity

PPML_component
type: Class
subclass of: protocol

Underdominance
type: Class
subclass of: Dominance_value

Alternative_RNA_splicing
type: Class
subclass of: RNA_splicing

Sequence_of_Gdf5
type: Class
subclass of: _5__to_3__Nucleotide_sequence

Coding_of_mammal_Gdf5
type: Class
subclass of: Coding_of_Gdf5_type_protein

Coding_of_Gdf5_type_protein
type: Class
subclass of: Coding_of_polypeptide

Single-strand_conformation_polymorphism
type: Class
subclass of: Genetic_polymorphism

YAMATO_continuant
type: Class
subclass of: Restriction
  on property: has material
  all values from: YAMATO_substance
subclass of: Restriction
  cardinality: 1
  on property: has material
subclass of: YAMATO_physical

YAMATO_substance
type: Class
comment: This is Identical to YATO's "Substance".
subclass of: Restriction
  all values from: chemical_entity
  on property: has made of
subclass of: Restriction
  cardinality: 1
  on property: has made of
subclass of: YAMATO_substrate

discrete_locus
type: Class
subclass of: Locus

tRNA
type: Class
subclass of: Restriction
  all values from: double_stranded_polynucleotide_group
  on property: has anticodon site
subclass of: Restriction
  cardinality: 1
  on property: has anticodon site
subclass of: Single_strand_RNA_polymer

alphabet_1
type: Class
subclass of: Restriction
  all values from: Alphabet
  on property: has content
subclass of: Restriction
  cardinality: 1
  on property: has content
subclass of: Restriction
  on property: has form
  all values from: YAMATO_line_image
subclass of: Restriction
  cardinality: 1
  on property: has form
subclass of: Symbol_figure

Genetic_distance_value
type: Class
subclass of: attribute-specific
subclass of: Restriction
  all values from: cM
  on property: has unit
subclass of: Restriction
  on property: has unit
  cardinality: 1

Nucleotide_triplet
type: Class
subclass of: Restriction
  on property: has complementary sequence
  all values from: Nucleotide_triplet
subclass of: Restriction
  cardinality: 1
  on property: has complementary sequence
subclass of: Triplet

Complex_locus
type: Class
subclass of: discrete_locus

Stem_and_loop
type: Class
subclass of: Form

Canonical_sequence
type: Class
subclass of: Functional_sequence

Chromosomal_location_value
type: Class
subclass of: Restriction
  all values from: Base_pair_count_value
  on property: has chromosomal location
subclass of: Restriction
  on property: has chromosomal location
  cardinality: 1
subclass of: Restriction
  all values from: integer
  on property: has chromosome ID
subclass of: Restriction
  on property: has chromosome ID
  cardinality: 1
subclass of: Composite_quantity

numbers_quantity
type: Class
subclass of: ordinaly_quantity

biological_event
type: Class
subclass of: YAMATO_ordinary_event

Production_of_mouse_GDF5
type: Class
subclass of: Restriction
  on property: has third process
  all values from: Translation
subclass of: Restriction
  on property: has second process
  all values from: RNA_splicing
subclass of: Restriction
  on property: has first process
  all values from: Transcription
subclass of: Production_of_polypeptide_in_eukaryote

Translation
type: Class
subclass of: Restriction
  all values from: Polypeptide
  on property: has participant
subclass of: Restriction
  on property: has participant
  min cardinality: 1
subclass of: Restriction
  on property: has participant
  all values from: Single_strand_RNA_polymer
subclass of: Restriction
  on property: has participant
  min cardinality: 1
subclass of: Restriction
  all values from: tRNA
  on property: has participant
subclass of: Restriction
  min cardinality: 1
  on property: has participant
subclass of: biological_process

Production_of_polypeptide_in_eukaryote
type: Class
subclass of: Restriction
  all values from: Translation
  on property: has third process
subclass of: Restriction
  on property: has second process
  all values from: RNA_splicing
subclass of: Restriction
  all values from: Transcription
  on property: has first process
subclass of: biological_process

Meta_property
type: Class
subclass of: Attribute_neutral

Pseudodominance
type: Class
subclass of: Dominace_related

Molecular_sequence
type: Class
subclass of: YAMATO_hard_symbol_sequence
subclass of: Restriction
  on property: has symbol
  all values from: Molecular_symbol
subclass of: Restriction
  min cardinality: 1
  on property: has symbol
subclass of: Restriction
  on property: has structure
  all values from: _1D_discrete_structure
subclass of: Restriction
  on property: has sub-sequence
  all values from: Molecular_sequence
subclass of: Restriction
  cardinality: 1
  on property: has structure
subclass of: Restriction
  all values from: radical_group
  on property: has radical group
subclass of: Restriction
  min cardinality: 1
  on property: has radical group

YAMATO_hard_symbol_sequence
type: Class
subclass of: YAMATO_symbol_sequence

_1D_discrete_structure
type: Class
subclass of: Restriction
  all values from: YAMATO_1D-space
  on property: has dimension
subclass of: Restriction
  on property: has dimension
  cardinality: 1
subclass of: Discrete_Structure

Pseudo-qualitative_generic_quality
type: Class
subclass of: YAMATO_qualitative_generic_quality

YAMATO_qualitative_generic_quality
type: Class
subclass of: YAMATO_basic_generic_quality

Partial_loss_of_gene_function
type: Class
subclass of: decrease_of_gene_function

Uracil_based_nucleotide
type: Class
subclass of: Thimine_Uracil_based_nucleotide

Monogenic
type: Class
subclass of: Multigenisity_value

Multigenisity_value
type: Class
subclass of: Restriction
  on property: has value of
  all values from: Multigenisity
subclass of: Restriction
  cardinality: 1
  on property: has value of
subclass of: Attribute_dependent

Consensus_sequence
type: Class
subclass of: Recognition_sequence

Recognition_sequence
type: Class
subclass of: Functional_sequence

YAMATO_functional
type: Class
subclass of: YAMATO_object

Location
type: Class
subclass of: YAMATO_accidental_attribute

specification_of_phenotype
type: Class
subclass of: Restriction
  all values from: Phenotype
  on property: has for what
subclass of: Restriction
  min cardinality: 1
  on property: has for what
subclass of: YAMATO_specification_plan

Zygousis_composition
type: Class
subclass of: Genetic_composition

YAMATO_dependent_entity
type: Class
comment: It cannot exist alone but always exists dependently on physical things.
subclass of: Restriction
  on property: has on what
  all values from: YAMATO_entity
subclass of: Restriction
  cardinality: 1
  on property: has on what
subclass of: YAMATO_particular

Purpose
type: Class
subclass of: YAMATO_representation_secondary

YAMATO_representation_secondary
type: Class
subclass of: YAMATO_proposition

Inter_group_comprex
type: Class
subclass of: chemical_entity

Developmental_process
type: Class
subclass of: biological_process
subclass of: Restriction
  on property: has partcipant
  min cardinality: 1

Bivalent_chromosome
type: Class
subclass of: Restriction
  all values from: Monovalent_chromosome
  on property: has part
subclass of: Restriction
  on property: has part
  cardinality: 2
subclass of: Multivalent_chromosome

Multivalent_chromosome
type: Class
subclass of: Restriction
  all values from: Monovalent_chromosome
  on property: has part
subclass of: Restriction
  min cardinality: 2
  on property: has part
subclass of: Chromosome

Interval_quantity
type: Class
comment: This is a continuous quantity. However, ratios between them are not meaningful. A highly familiar example of interval scale measurement is temperature with the Celsius scale.
subclass of: Restriction
  on property: has lower end
  all values from: Singleton_quantity
subclass of: Restriction
  on property: has lower end
  cardinality: 1
subclass of: Restriction
  on property: has upper end
  all values from: Singleton_quantity
subclass of: Restriction
  cardinality: 1
  on property: has upper end
subclass of: Continuous_quantity

Balanced_polymorphism
type: Class
subclass of: Genetic_polymorphism

Mode_of_inheritance
type: Class
subclass of: Genuine_qualitative_generic_quality

dinucleotide_repeat
type: Class
subclass of: Doublet_repeat

Coding_of_transcript
type: Class
subclass of: Coding_of_gene_product
subclass of: Restriction
  all values from: design_of_functional_RNA
  on property: has content
subclass of: Restriction
  cardinality: 1
  on property: has content
subclass of: Restriction
  all values from: _5__to_3__Nucleotide_sequence
  on property: has form
subclass of: Restriction
  on property: has form
  cardinality: 1

Shape_value
type: Class
subclass of: Restriction
  all values from: Form
  on property: has value
subclass of: Restriction
  cardinality: 1
  on property: has value
subclass of: Nominal_scale_value
comment: Square, triangle, and so on.

physical_phenomenon
type: Class
subclass of: YAMATO_phenomenon

Allelic_complementation
type: Class
subclass of: Complementation

Unit
type: Class
subclass of: Restriction
  on property: has value of
  all values from: YAMATO_generic_quality
subclass of: Restriction
  on property: has value of
  cardinality: 1
subclass of: YAMATO_abstract
comment: This is a simplified version and should be elaborated more. The size is one in any case. It is not a kind of dimension but a quantity of the size 1. This is why cm, m, etc. don't need "#" operator.

Double_strand_DNA
type: Class
subclass of: Restriction
  on property: has part
  min cardinality: 1
subclass of: Restriction
  all values from: single_strand_DNA_polymer
  on property: has single strand DNA
subclass of: Restriction
  cardinality: 1
  on property: has single strand DNA
subclass of: Restriction
  all values from: single_strand_DNA_polymer
  on property: has single strand DNA
subclass of: Restriction
  cardinality: 1
  on property: has single strand DNA
subclass of: polynucleotide

YAMATO_morphological_whole
type: Class
subclass of: YAMATO_object

YAMATO_object
type: Class
subclass of: YAMATO_continuant

Sequence_with_pattern
type: Class
subclass of: Molecular_sequence

initiation_tRNA
type: Class
subclass of: Restriction
  on property: has anticodon site
  all values from: double_stranded_polynucleotide_group
subclass of: Restriction
  cardinality: 1
  on property: has anticodon site
subclass of: tRNA

Ion
type: Class
subclass of: chemical_entity

Simple_locus
type: Class
subclass of: discrete_locus

Attribute_inclusive
type: Class
subclass of: Extrinsically_qualitative

Condensation
type: Class
subclass of: biological_process

Base_pair
type: Class
subclass of: Inter_group_comprex

Overdominance
type: Class
subclass of: Dominance_value

Discrete_Structure
type: Class
subclass of: YAMATO_Structure

Cytosine_based_nucleptide
type: Class
subclass of: Pyrimidine_nucleotide

Non-categorical
type: Class
subclass of: YAMATO_quality_value
comment: This is a quality value represents order or rank intrinsically.

gamete_lineage
type: Class
subclass of: Restriction
  all values from: gamete
  on property: has participant
subclass of: Restriction
  on property: has participant
  min cardinality: 1
subclass of: Restriction
  all values from: sequence_mutation_process
  on property: has mutation
subclass of: Developmental_process

Coding_of_functional_RNA
type: Class
subclass of: Coding_of_transcript

amino_acid_group
type: Class
subclass of: radical_group

pyrimidine_to_purine_transversion_event
type: Class
subclass of: Restriction
  on property: has terminal Event
  all values from: YAMATO_instantaneous_event
subclass of: Restriction
  on property: has terminal Event
  cardinality: 1
subclass of: transversion_event

Multigenisity
type: Class
subclass of: non-meta_generic_quality

Tripret_nucleotide_repeat
type: Class
subclass of: Tripret_repeat

Heterozygousity
type: Class
subclass of: Attribute_inclusive

YAMATO_singleton_agent
type: Class
subclass of: YAMATO_agent

Mouse_Gdf5_design
type: Class
subclass of: Restriction
  on property: has for what
  all values from: Mouse_GDF5_protein
subclass of: Restriction
  min cardinality: 1
  on property: has for what
subclass of: specification_of_polypeptide

Chromosome_condensation
type: Class
subclass of: Condensation

document_of_genetic_information
type: Class
subclass of: Restriction
  on property: has media
  all values from: YAMATO_physical
subclass of: Restriction
  on property: has media
  min cardinality: 1
subclass of: Restriction
  on property: has representaion
  all values from: YAMATO_representation
subclass of: Restriction
  on property: has representaion
  min cardinality: 1
subclass of: symbol_sequence_stuff

zygosis
type: Class
subclass of: Restriction
  on property: has zygote
  all values from: organism
subclass of: Restriction
  on property: has zygote
  cardinality: 1
subclass of: Restriction
  on property: has gamete
  all values from: gamete
subclass of: Restriction
  on property: has gamete
  cardinality: 2
subclass of: Restriction
  all values from: organism
  on property: has parent
subclass of: Restriction
  min cardinality: 1
  on property: has parent
subclass of: reproduction-related

Sentence
type: Class
subclass of: Restriction
  on property: has form
  all values from: YAMATO_natural_language
subclass of: Restriction
  on property: has form
  cardinality: 1
subclass of: Representation_by_symbol

Emagency_procedure
type: Class
subclass of: protocol

Karyotype
type: Class
subclass of: Genetic_composition_value
subclass of: Restriction
  on property: has value of
  all values from: Composition_of_chromosome
subclass of: Restriction
  on property: has value of
  cardinality: 1

Composition_of_chromosome
type: Class
subclass of: Genetic_composition

Leader_sequence
type: Class
subclass of: Functional_sequence

numbers_quality_value
type: Class
subclass of: counting_value

Symbol_of_aminoacid
type: Class
subclass of: Molecular_symbol

Representation_of_nucleotide_symbol
type: Class
subclass of: Restriction
  on property: has content
  all values from: Symbol_designated_by_nucleotide
subclass of: Restriction
  on property: has content
  cardinality: 1
subclass of: Restriction
  all values from: nucleotide_group
  on property: has form
subclass of: Restriction
  on property: has form
  cardinality: 1
subclass of: representation_of_genetic_symbol
comment: This is identical to "DNA alphabet" in YATO. This is similar to a "symbol figure" compsed of the 2D image and symbol. A form of this is molecular entity. The content is a symbol.

Hemizygosity
type: Class
subclass of: Attribute_inclusive

Intracistronic_complementation
type: Class
subclass of: Complementation

Suppressor_mutation
type: Class
subclass of: Context_dependent_phenotypic_change

Allelism
type: Class
subclass of: Genuine_qualitative_generic_quality

YAMATO_programing_language
type: Class
subclass of: YAMATO_language_related

YAMATO_generically_dependent
type: Class
subclass of: YAMATO_dependent_entity

Conservation_of_sequence
type: Class
subclass of: Restriction
  all values from: Molecular_sequence
  on property: has output entity
subclass of: Restriction
  on property: has output entity
  min cardinality: 1
subclass of: Restriction
  on property: has input entity
  all values from: Molecular_sequence
subclass of: Restriction
  min cardinality: 1
  on property: has input entity
subclass of: Conservation

Set_of_molecule
type: Class
subclass of: Restriction
  on property: has subset
  all values from: Set_of_molecule
subclass of: Restriction
  on property: has part
  all values from: Polyatomic_stable_substance
subclass of: Restriction
  on property: has part
  min cardinality: 1
subclass of: chemical_entity

color_c
type: Class
subclass of: Restriction
  all values from: color
  on property: has value of
subclass of: Restriction
  on property: has value of
  cardinality: 1
subclass of: Nominal_scale_value

color
type: Class
subclass of: non-meta_generic_quality

Developmental_event
type: Class
subclass of: Restriction
  all values from: Developmental_process
  on property: has made of
subclass of: Restriction
  on property: has made of
  cardinality: 1
subclass of: biological_event

in_xxxx_quality_for_experiment
type: Class
subclass of: Genuine_qualitative_generic_quality

Reversion_of_phenotype
type: Class
subclass of: Phenotypic_change_dependent_on_genetic_background

YAMATO_topological_whole
type: Class
subclass of: YAMATO_non-unitary
comment: This is Identical to YATO's "Topological whole". Its identity is tightly dependent on the topolocial relations between constituents.

Representation_by_symbol
type: Class
subclass of: Restriction
  all values from: YAMATO_proposition
  on property: has content
subclass of: Restriction
  on property: has content
  cardinality: 1
subclass of: Restriction
  all values from: YAMATO_symbol_sequence
  on property: has form
subclass of: Restriction
  on property: has form
  cardinality: 1
subclass of: Primitive_representation

Scientific_paper_as_content
type: Class
subclass of: Product_proposition

replication_of_polynucleotide
type: Class
subclass of: Restriction
  on property: has replica
  all values from: polynucleotide_group
subclass of: Restriction
  min cardinality: 1
  on property: has replica
subclass of: Restriction
  on property: has template
  all values from: polynucleotide_group
subclass of: Restriction
  min cardinality: 1
  on property: has template
subclass of: Biological_replication

Process_of_central_dogma
type: Class
subclass of: Restriction
  on property: has sub occurent
  all values from: Translation
subclass of: Restriction
  all values from: Transcription
  on property: has sub occurent
subclass of: biological_process

Dominant_negative_effect
type: Class
subclass of: Phenotypic_change_dependent_on_genetic_background

termination_tRNA
type: Class
subclass of: Restriction
  all values from: double_stranded_polynucleotide_group
  on property: has anticodon site
subclass of: Restriction
  cardinality: 1
  on property: has anticodon site
subclass of: tRNA

Phenotype
type: Class
subclass of: UndefinedClass

Autosome
type: Class
subclass of: Monovalent_chromosome

Loss-of-function
type: Class
subclass of: decrease_of_gene_function

Paper
type: Class
subclass of: Non-represented_thing

Gain-of-function
type: Class
subclass of: Alteration_of_gene_function

Homo_sapiens
type: Class
subclass of: mammal

set_of_DNA
type: Class
subclass of: set_of_polynucleotide_molecules

Co-dominance
type: Class
subclass of: Dominace_related

Quantitative_trait_locus
type: Class
subclass of: Locus

Virtural_physical_distance_system
type: Class
subclass of: Restriction
  all values from: Physical_location_on_chromosome
  on property: has what for
subclass of: Restriction
  cardinality: 1
  on property: has what for
subclass of: virtual_locaiton

Single_nucleotide_polymorphism
type: Class
subclass of: Genetic_polymorphism

Basic_action
type: Class
subclass of: YAMATO_action

PPML_pipleine_description
type: Class
subclass of: PPML_component

YAMATO_word
type: Class
subclass of: YAMATO_language_related

Non-meta_property
type: Class
subclass of: Attribute_neutral

Homeotic_transformation
type: Class
subclass of: Transformation

Open_reading_frame
type: Class
subclass of: Coding_sequence
subclass of: Restriction
  on property: has structure symbol
  all values from: codon
subclass of: Restriction
  cardinality: 1
  on property: has translated to
subclass of: Restriction
  min cardinality: 1
  on property: has structure symbol
subclass of: Restriction
  cardinality: 1
  on property: has structure symbol
subclass of: Restriction
  on property: has structure symbol
  all values from: Start_codon
subclass of: Restriction
  all values from: Polypeptide_sequence
  on property: has translated to
subclass of: Restriction
  all values from: Stop_codon
  on property: has structure symbol
subclass of: Restriction
  on property: has structure symbol
  cardinality: 1

Coding_of_Gdf5
type: Class
subclass of: Coding_of_mammal_Gdf5
subclass of: Restriction
  all values from: Mouse_Gdf5_design
  on property: has content
subclass of: Restriction
  on property: has content
  cardinality: 1
subclass of: Restriction
  all values from: _5__to_3__Nucleotide_sequence
  on property: has form
subclass of: Restriction
  on property: has form
  cardinality: 1

Multigenic
type: Class
subclass of: Multigenisity_value

Subatomic_particle
type: Class
subclass of: chemical_entity

Chromosomal_rearrangement_process
type: Class
subclass of: changing_process

Silent_mutation
type: Class
subclass of: Mutation_of_organism

Helix
type: Class
subclass of: Form

Proximo-distal_value
type: Class
subclass of: attribute_independent

hasPart
type: ObjectProperty

hasAttribute
type: ObjectProperty

depends_on
type: ObjectProperty

"Thr"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate threonine.

"Cys"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate cysteine.

AUG
type: Genetics Ontology GXO 2.owlStart codon

"Asp"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate aspartic acid.

length of group 1
type: Genetics Ontology GXO 2.owllength

Mouse 2
type: Genetics Ontology GXO 2.owlC57BL 6

Mouse 1
type: Genetics Ontology GXO 2.owlC57BL 6

"Val"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate valine.

proximal
type: Genetics Ontology GXO 2.owlProximo-distal value

the population of Homo Sapiense
type: Genetics Ontology GXO 2.owlpopulation of a species
genetics ontology GXO 2.owlhas specification of gene: spec_human BMP4 (ins)
genetics ontology GXO 2.owlhas specification of gene: spec_human GDF5 (ins)
genetics ontology GXO 2.owlhas gene pool: gene pool of human BMP4 (ins)
genetics ontology GXO 2.owlhas gene pool: gene pool of human GDF5 (ins)

spec_human BMP4 (ins)
type: Genetics Ontology GXO 2.owlspec BMP4 type

spec_human GDF5 (ins)
type: Genetics Ontology GXO 2.owlspec GDF5 type

gene pool of human BMP4 (ins)
type: Genetics Ontology GXO 2.owlgene pool

gene pool of human GDF5 (ins)
type: Genetics Ontology GXO 2.owlgene pool

UUU
type: Genetics Ontology GXO 2.owlSense codon

"U"
type: Genetics Ontology GXO 2.owlSymbol designated by nucleotide
genetics ontology GXO 2.owlhas antisense symbol: A

dominant
type: Genetics Ontology GXO 2.owlMode of inheritance value

"Arg"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: The Simbol designate arginine.

UAA Ochre
type: Genetics Ontology GXO 2.owlStop codon

the change of mouse population
type: Genetics Ontology GXO 2.owlChange of mendelian population
genetics ontology GXO 2.owlhas participant: the population of Mus musclus
genetics ontology GXO 2.owlhas mutation event of gene: mutation event of mouse BMP4
genetics ontology GXO 2.owlhas mutation event of gene: mutation event of mouse Gdf5

mutation event of mouse BMP4
type: Genetics Ontology GXO 2.owlmutation event of s-segment
genetics ontology GXO 2.owlhas terminal event: mutation ending event of s-segment

mutation event of mouse Gdf5
type: Genetics Ontology GXO 2.owlmutation event of s-segment
genetics ontology GXO 2.owlhas terminal event: mutation ending event of s-segment

recessive
type: Genetics Ontology GXO 2.owlMode of inheritance value

Bi-allelic
type: Genetics Ontology GXO 2.owlPoly-allelism value

UUC
type: Genetics Ontology GXO 2.owlSense codon

Polymorphic
type: Genetics Ontology GXO 2.owlPolymorphism value

"A"
type: Genetics Ontology GXO 2.owlSymbol designated by nucleotide
genetics ontology GXO 2.owlhas antisense symbol: T

cM
type: Genetics Ontology GXO 2.owlUnit

"Gln"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate glutamine.

co-dominant
type: Genetics Ontology GXO 2.owlMode of inheritance value

"Asn"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate asparagine.

bp
type: Genetics Ontology GXO 2.owlUnit

decreased length!PATO:0000574
type: Genetics Ontology GXO 2.owlLength value

"T"
type: Genetics Ontology GXO 2.owlSymbol designated by nucleotide
genetics ontology GXO 2.owlhas antisense symbol: A

"Lys"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate lysine.

semidominant
type: Genetics Ontology GXO 2.owlMode of inheritance value

"Gly"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate glycine.

distal
type: Genetics Ontology GXO 2.owlProximo-distal value

UGA Opal
type: Genetics Ontology GXO 2.owlStop codon

"Pro"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate proline.

UAG Amber
type: Genetics Ontology GXO 2.owlStop codon

"Tyr"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate tyrosine.

mono-morphic
type: Genetics Ontology GXO 2.owlPolymorphism value

"Leu"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate leucine.

increased length!PATO:0000573
type: Genetics Ontology GXO 2.owlLength value

length of hair of wild
type: Genetics Ontology GXO 2.owllength

"Phe"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate phenylalanine.

Coding of wildtype Gdf5
type: Genetics Ontology GXO 2.owlCoding of Gdf5
genetics ontology GXO 2.owlhas form: information for mouse Gdf5 wildtype itself
genetics ontology GXO 2.owlhas content: Design of wildtype Gdf5

information for mouse Gdf5 wildtype itself
type: Genetics Ontology GXO 2.owlSequence of wildtype Gdf5
genetics ontology GXO 2.owlhas style of form: spec_Gdf5<wild> (ins)

spec_Gdf5<wild> (ins)
type: Genetics Ontology GXO 2.owlspec mouse Gdf5 ins

"Glu"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate glutamic acid.

normal!PATO:0000461
type: Genetics Ontology GXO 2.owlDeviation value

abnormal!PATO:0000460
type: Genetics Ontology GXO 2.owlDeviation value

"G"
type: Genetics Ontology GXO 2.owlSymbol designated by nucleotide
genetics ontology GXO 2.owlhas antisense symbol: C

Sequence of Gdf5_Rgsc451
type: Genetics Ontology GXO 2.owlSequence of Gdf5
genetics ontology GXO 2.owlhas symbol: A

Design of wildtype Gdf5
type: Genetics Ontology GXO 2.owlMouse Gdf5 design

"Ala"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: The Simbol designate alanine.

"Met"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate methionine.

"Ile"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate isoleucine.

"C"
type: Genetics Ontology GXO 2.owlSymbol designated by nucleotide
genetics ontology GXO 2.owlhas antisense symbol: G

the population of Mus musclus
type: Genetics Ontology GXO 2.owlpopulation of a species
genetics ontology GXO 2.owlhas gene pool: gene pool of mouse Bmp4 (ins)
genetics ontology GXO 2.owlhas gene pool: gene pool of mouse for Gdf5 (ins)
genetics ontology GXO 2.owlhas specification of gene: spec mouse BMP4 (ins)
genetics ontology GXO 2.owlhas specification of gene: spec_mouse Gdf5 (ins)

gene pool of mouse Bmp4 (ins)
type: Genetics Ontology GXO 2.owlgene pool

gene pool of mouse for Gdf5 (ins)
type: Genetics Ontology GXO 2.owlgene pool
genetics ontology GXO 2.owlhas major allele: Gdf5<wild>
genetics ontology GXO 2.owlhas variantion: spec_Gdf5<wild> (ins)
genetics ontology GXO 2.owlhas variant: Gdf5<rgsc451>
genetics ontology GXO 2.owlhas variant: spec_Gdf5<Rgsc451> (ins)
genetics ontology GXO 2.owlhas variant: Gdf5<bp>
genetics ontology GXO 2.owlhas variant: spec_Gdf5<bp> (ins)
genetics ontology GXO 2.owlhas variant: Gdf5<wild>

Gdf5<wild>
type: Genetics Ontology GXO 2.owlvariant of mouse Gdf5

Gdf5<rgsc451>
type: Genetics Ontology GXO 2.owlvariant of mouse Gdf5

spec_Gdf5<Rgsc451> (ins)
type: Genetics Ontology GXO 2.owlspec mouse Gdf5 ins

Gdf5<bp>
type: Genetics Ontology GXO 2.owlvariant of mouse Gdf5

spec_Gdf5<bp> (ins)
type: Genetics Ontology GXO 2.owlspec mouse Gdf5 ins

spec mouse BMP4 (ins)
type: Genetics Ontology GXO 2.owlspec BMP4 type

spec_mouse Gdf5 (ins)
type: Genetics Ontology GXO 2.owlspec GDF5 type

Monoallelic
type: Genetics Ontology GXO 2.owlPoly-allelism value

"Ser"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate serine.

Coding of Gdf5_Rgsc451
type: Genetics Ontology GXO 2.owlCoding of Gdf5
genetics ontology GXO 2.owlhas form: information for mouse Gdf5<Rgsc451> itself
genetics ontology GXO 2.owlhas content: design of Gdf5 Rgsc451

information for mouse Gdf5<Rgsc451> itself
type: Genetics Ontology GXO 2.owlSequence of Gdf5 Rgsc451
genetics ontology GXO 2.owlhas style of form: spec_Gdf5<Rgsc451> (ins)

"His"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate histidine.

design of Gdf5_Rgsc451
type: Genetics Ontology GXO 2.owlMouse Gdf5 design

Sequence of wildtype Gdf5
type: Genetics Ontology GXO 2.owlSequence of Gdf5
genetics ontology GXO 2.owlhas symbol: T

"Trp"
type: Genetics Ontology GXO 2.owlSymbol of aminoacid
comment: Symbol designate tryptophan.

length of hair of homo
type: Genetics Ontology GXO 2.owllength

DNA fragment B
type: Genetics Ontology GXO 2.owlDNA group
genetics ontology GXO 2.owlhas representaion: Coding of Gdf5 Rgsc451
genetics ontology GXO 2.owlhas media: DNA fragment B

DNA fragment A
type: Genetics Ontology GXO 2.owlDNA group
genetics ontology GXO 2.owlhas media: DNA fragment A
genetics ontology GXO 2.owlhas representaion: Coding of wildtype Gdf5