BioTop
type: Ontology
creator: Stefan Schulz, Martin Boeker, Elena Beisswanger, Holger Stenzhorn, Djamila Raufie, Daniel Schober, Udo Hahn
rights: http://creativecommons.org/licenses/by/3.0
subject: An experimental top level ontology for biology and medicine.
format: application/rdf+xml
description: Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network (mapping files available)
subject: Biology, Medicine
publisher: Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Stefan-Meier-Strasse 26, 79104 Freiburg, Germany Institute of Medical Informatics, Statistics and Documentation, Medical University of Graz, Auenbruggerplatz 2/V , 8036 Graz (Austria)
description: BioTop Website: http://purl.org/biotop See related articles at: http://www.google.com/search?q=Schulz+BioTop+site:www.ncbi.nlm.nih.gov/pmc/articles+ontology+OR+ontologies
version info: Last modification Apr 24, 2012 by Stefan Schulz
imports: btl2.owl

attached to
type: ObjectProperty
type: SymmetricProperty
definition: Contiguous with a clear bona fide boundary between the connected parts. Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
sub property of: contiguous with
domain: Class
  union of: immaterial object
  union of: material object
range: Class
  union of: immaterial object
  union of: material object

branch of
type: ObjectProperty
definition: A is a branch of B if it is contiguous with B and if some flow of matter or energy of information flows form B to A. Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
sub property of: attached to
inverse of: has branch
domain: Class
  union of: immaterial object
  union of: material object
range: Class
  union of: immaterial object
  union of: material object

contiguous with
type: ObjectProperty
type: SymmetricProperty
definition: ContiguousWith describes the connection between two material objects that abut and can transmit forces.
sub property of: physically adjacent to
domain: Class
  union of: immaterial object
  union of: material object
range: Class
  union of: immaterial object
  union of: material object

continuous with
type: ObjectProperty
definition: Contiguous with a clear bona fide boundary between the connected parts. Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
sub property of: contiguous with
domain: Class
  union of: immaterial object
  union of: material object
range: Class
  union of: immaterial object
  union of: material object

derived into
type: ObjectProperty
type: TransitiveProperty
definition: DerivesFrom (inverse: derivedInto) holds between distinct material objects when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier object is included into the later. There is some instant of time t such that the first object exists only prior to and the second one only subsequent to t. These relations are borrowed from the OBO Relation Ontology Example: "Three simple kinds of instance-level derivation can then be distinguished (Figure 3): first, the succession of one single continuant by another single continuant across a temporal threshold (for example, this blastocyst derives from this zygote); second, the fusion of two or more continuants into one continuant (for example, this zygote derives from this sperm and from this ovum); and third, the fission of an earlier single continuant to create a plurality of later continuants (for example, these promyelocytes derive from this myeoloblast). " from http://genomebiology.com/2005/6/5/R46
inverse of: derives from
sub property of: has origin
domain: material object
range: material object

derives from
type: ObjectProperty
type: TransitiveProperty
definition: DerivesFrom (inverse: derivedInto) holds between distinct material objects when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier object is included into the later. There is some instant of time t such that the first object exists only prior to and the second one only subsequent to t. These relations are borrowed from the OBO Relation Ontology Example: "Three simple kinds of instance-level derivation can then be distinguished (Figure 3): first, the succession of one single continuant by another single continuant across a temporal threshold (for example, this blastocyst derives from this zygote); second, the fusion of two or more continuants into one continuant (for example, this zygote derives from this sperm and from this ovum); and third, the fission of an earlier single continuant to create a plurality of later continuants (for example, these promyelocytes derive from this myeoloblast). " from http://genomebiology.com/2005/6/5/R46
sub property of: originates from
range: material object
domain: material object

encodes
type: ObjectProperty
definition: EncodedBy (inverse: encodes) relates entities with symbols, which are information entities. In contrast to denotation, encoding entails that the makeup of the encoded entity is determined by the code. There is a dependence of the former on the latter. Note that the association of human-made codes with entities (e.g. for coding and classification systems like ICD-10) is nothing more than denotation and is therefore not in the scope of the encodedBy (encodes) relation. Example: A material gene sequence is related to a sequence of nucleotide symbols (like ACCGATTGA)

has branch
type: ObjectProperty
definition: B hasBranch A if it is contiguous with B and if some flow of matter or energy of information flows form B to A. Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
sub property of: attached to
domain: Class
  union of: immaterial object
  union of: material object
range: Class
  union of: immaterial object
  union of: material object

has duration
type: ObjectProperty
definition: hasDuration relates a process with the time interval it covers.
domain: process
range: time interval

has origin
type: ObjectProperty

has point in time
type: ObjectProperty
definition: hasPointInTome relates a processual entity with some point in the interval it occupies. If there is no temporal extension (process boundary) it relates it to the time it occurs.
range: point in time
domain: process

has proper physical part
type: ObjectProperty
type: TransitiveProperty
definition: hasProperPhysicalPart (inverse: properPhysicalPartOf) obtains between physical objects. The distinction between parthood and locatedness is complex and does not obey strict criteria. This relation is irreflexive, i.e. a physical object cannot have itself as a physical proper part. Note that for abstract entities like information artefacts there is a separate relation pair "abstractPartOf" and "hasAbstractPart" For processes there are the relations "hasProcessualPart" and "processualPartOf" Examples: my thumb is a proper physical part of my hand, this keyboard is a proper physical part of my computer.
inverse of: proper physical part of
sub property of: hasPart
domain: Class
  union of: immaterial object
  union of: material object
range: Class
  union of: immaterial object
  union of: material object

cooccurring with
type: ObjectProperty
type: SymmetricProperty
definition: The relation coocurring with relates two processes if their temporal extensions overlap.
range: process
domain: process

encodedBy
type: ObjectProperty
definition: EncodedBy (inverse: encodes) relates entities with symbols, which are information entities. In contrast to denotation, encoding entails that the makeup of the encoded entity is determined by the code. There is a dependence of the former on the latter. Note that the association of human-made codes with entities (e.g. for coding and classification systems like ICD-10) is nothing more than denotation and is therefore not in the scope of the encodedBy (encodes) relation. Example: A material gene sequence is related to a sequence of nucleotide symbols (like ACCGATTGA)
inverse of: encodes

physically connected to
type: ObjectProperty
type: SymmetricProperty
definition: physicallyConnectedTo (a symmetric relation) relates two spatially relevant entities (material entities or spaces) which overlap at least one point in space. Example: France is connected to Germany, my optic nerve is connected to my eyeball.
range: Class
  union of: immaterial object
  union of: material object
domain: Class
  union of: immaterial object
  union of: material object

physically contained in
type: ObjectProperty
definition: Containment is location without parthood. E.g. Food is contained in the stomach. Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
inverse of: physically contains
sub property of: isIncludedIn
range: Class
  union of: immaterial object
  union of: material object
domain: Class
  union of: immaterial object
  union of: material object

physically disconnected from
type: ObjectProperty
type: SymmetricProperty
definition: No sharing of parts and no sharing of boundaries. Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
range: Class
  union of: immaterial object
  union of: material object
domain: Class
  union of: immaterial object
  union of: material object

originates from
type: ObjectProperty
definition: originatesFrom relates two material objects one of which originates from the other in a very broad sense. It includes derivation (in the OBO RO sense), actual actual parts (provided they were always parts), as well as original (historical) parts. Examples: see Subrelations
range: material object
domain: material object

physically adjacent to
type: ObjectProperty
type: SymmetricProperty
definition: physicalAdjacentTo relates two physical objects that abut without physical overlap. Examples: see subrelations
sub property of: physically connected to
range: Class
  union of: immaterial object
  union of: material object
domain: Class
  union of: immaterial object
  union of: material object

physically contains
type: ObjectProperty
definition: Containment is location without parthood. E.g. Food is contained in the stomach. Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
sub property of: includes
domain: Class
  union of: immaterial object
  union of: material object
range: Class
  union of: immaterial object
  union of: material object

physically interconnects
type: ObjectProperty
sub property of: physically connected to
range: Class
  union of: immaterial object
  union of: material object
domain: Class
  union of: immaterial object
  union of: material object

physically surrounded by
type: ObjectProperty
definition: Partly or completely covering from outside (establishing boundaries, enclosing, confining, enclosing, circumscribing)
sub property of: physically connected to
inverse of: physically surrounds

physically surrounds
type: ObjectProperty
definition: Partly or completely covering from outside (establishing boundaries, enclosing, confining, enclosing, circumscribing)
sub property of: physically connected to
domain: Class
  union of: immaterial object
  union of: material object
range: Class
  union of: immaterial object
  union of: material object

physically traverses
type: ObjectProperty
definition: crossing over and crossing through
sub property of: physically connected to
domain: Class
  union of: immaterial object
  union of: material object
range: Class
  union of: immaterial object
  union of: material object

proper physical part of
type: ObjectProperty
type: TransitiveProperty
definition: hasProperPhysicalPart (inverse: properPhysicalPartOf) obtains between physical objects. The distinction between parthood and locatedness is complex and does not obey strict criteria. This relation is irreflexive, i.e. a physical object cannot have itself as a physical proper part. Note that for abstract entities like information artefacts there is a separate relation pair "abstractPartOf" and "hasAbstractPart" For processes there are the relations "hasProcessualPart" and "processualPartOf" Examples: my thumb is a proper physical part of my hand, this keyboard is a proper physical part of my computer.
sub property of: isPartOf
range: Class
  union of: immaterial object
  union of: material object
domain: Class
  union of: immaterial object
  union of: material object

touches
type: ObjectProperty
type: SymmetricProperty
definition: Abutting without mechanical connection. Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
sub property of: physically adjacent to
domain: Class
  union of: immaterial object
  union of: material object
range: Class
  union of: immaterial object
  union of: material object

acquired abnormal structure
type: Class
subclass of: pathological structure
disjoint with: congenital abnormal structure
definition: biological structure that deviates from what is considered normal and that evolved during lifetime

acquired pathological condition
type: Class
subclass of: pathological value region
disjoint with: congenital pathological condition
definition: Ill-formed state of a biological entity,acquired after birth [steschu 20071010]

acquired pathological static processual entity
type: Class
equivalent class: Class
  intersection of: pathological static processual entity
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: Canonicity
      intersection of: Restriction
        on property: projectsOnto
        some values from: acquired pathological condition
prior version: acquired pathological state
definition: pathological state acquired during lifetime

action on biological system
type: Class
subclass of: Action
subclass of: Restriction
  on property: hasPatient
  some values from: Class
    union of: living organism
    union of: Restriction
      on property: proper physical part of
      some values from: living organism
definition: an action which externally acts upon a biological system

adult organism
type: Class
equivalent class: Class
  intersection of: living organism
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: developmental quality
      intersection of: Restriction
        on property: projectsOnto
        some values from: adult value region
subclass of: OrganismByDevelopmentalStagePartition
disjoint with: embryonic organism
disjoint with: juvenile organism
definition: organism in reproductive phase

adult value region
type: Class
subclass of: developmental value region
comment: "adult" as the value of a developmental stage. E.g. a 4 year old dog has a quality which has its value located in "adult value region".

affecting
type: Class
subclass of: Action
definition: Producing a direct effect on

age quality
type: Class
subclass of: ObjectQuality
subclass of: Class
  intersection of: Restriction
    on property: inheresIn
    some values from: Class
      union of: immaterial object
      union of: material object
  intersection of: Restriction
    on property: inheresIn
    all values from: Class
      union of: immaterial object
      union of: material object
definition: the quality of having a livespan

alga
type: Class
subclass of: eukaryote

alpha particle
type: Class
subclass of: Atom
subclass of: Class
  intersection of: Class
    complement of: Restriction
      on property: has proper physical part
      some values from: electron
  intersection of: Restriction
    on property: has proper physical part
    some values from: neutron
definition: Positively charged particles composed of two protons and two neutrons, i.e. equivalent to Helium nuclei

amino acid molecule or residue
type: Class
subclass of: amino acid or peptide molecule or structure
subclass of: monomer
subclass of: Restriction
  on property: hasComponentPart
  some values from: submolecular group
disjoint with: peptide structure
comment: In chemistry, an amino acid is any molecule that contains both amine and carboxyl functional groups. However, in biochemistry, this more general term is frequently used to refer to alpha amino acids (amino acids in which the amino and carboxylate functionalities are attached to the same carbon, called ?–carbon). Amino Acids have at least one amino and one carboxy group. Those having two carboxy groups have only one amino group and vice versa.
definition: Amino Acids molecules or residues (residues as in peptide bonds)
comment: (QCR) ro:hasPart some CarbonHydrogenSubstructure and ((hasComponent myx 2 CarboxyGroup) and (hasComponent min 1 CarboxyGroup) and (hasComponent exactly 1 AminoGroup)) or ((hasComponent max 2 AminoGroup) and (hasComponent min 1 AminoGroup) and (hasComponent exactly 1 CarboxyGroup))

amino acid or peptide molecule or structure
type: Class
subclass of: OrganicMolecularEntityPartition
definition: amino acids as monomers and polymers

amino acid sequence
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: hasComponentPart
    some values from: amino acid molecule or residue
  intersection of: Restriction
    on property: hasComponentPart
    all values from: amino acid molecule or residue
subclass of: peptide structure
definition: Chain of amino acids, joined by peptide bonds. Folded or unfolded.

amino acid sequence information
type: Class
subclass of: SequenceInformation
definition: The information that describes the make-up of a (physical) amino acid sequence.

amount of body substance
type: Class
subclass of: CompoundOfCollectiveMaterialEntities
definition: collection with molecules or atoms as granular parts (but which may have also bigger granular parts) that is produced by a biological system (e.g. blood, urine, ivory)

amphibian
type: Class
subclass of: vertebrate

analyzing
type: Class
subclass of: human action

animal cell
type: Class
equivalent class: Class
  intersection of: Cell
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: taxon quality
      intersection of: Restriction
        on property: projectsOnto
        some values from: kingdom animalia value region
disjoint with: bacterial cell
disjoint with: plant cell

animal excluding human
type: Class
equivalent class: Class
  intersection of: animal including human
  intersection of: Class
    complement of: human

animal including human
type: Class
subclass of: eukaryote
subclass of: Restriction
  on property: isBearerOf
  some values from: Class
    intersection of: taxon quality
    intersection of: Restriction
      on property: projectsOnto
      some values from: kingdom animalia value region
    intersection of: Restriction
      on property: projectsOnto
      all values from: kingdom animalia value region
definition: Multicellular organisms of the kingdom Animalia

animal language
type: Class
subclass of: LanguagePartition
definition: language used in communication between animals

animal population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: animal including human
  intersection of: Restriction
    on property: hasGranularPart
    all values from: animal including human
comment: EXAMPLE OF POPULATION

antibiotic role
type: Class
subclass of: drug role
definition: the role a chemical plays if used to combat a bacterial infection

archaebacterial cell
type: Class
subclass of: prokaryote
subclass of: Restriction
  on property: isBearerOf
  some values from: Class
    intersection of: taxon quality
    intersection of: Restriction
      on property: projectsOnto
      all values from: kingdom archaea value region
synonym: Archaebacterium

artefact role
type: Class
subclass of: Role
definition: The role an entity plays when it has been artificially produced. [steschu 20071010]

arthropod
type: Class
subclass of: invertebrate
subclass of: Restriction
  on property: isBearerOf
  some values from: Class
    intersection of: taxon quality
    intersection of: Restriction
      on property: projectsOnto
      some values from: phylum arthropoda value region
comment: one arthropod

arthropod population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: arthropod
  intersection of: Restriction
    on property: hasGranularPart
    all values from: arthropod
comment: EXAMPLE OF POPULATION

bacteria population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: bacterial cell
  intersection of: Restriction
    on property: hasGranularPart
    all values from: bacterial cell
comment: EXAMPLE OF POPULATION

bacterial cell
type: Class
equivalent class: Class
  intersection of: Cell
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: taxon quality
      intersection of: Restriction
        on property: projectsOnto
        some values from: kingdom bacteria value region
subclass of: prokaryote
subclass of: Restriction
  on property: isBearerOf
  some values from: Class
    intersection of: taxon quality
    intersection of: Restriction
      on property: projectsOnto
      some values from: kingdom bacteria value region
disjoint with: plant cell
synonym: Bacterium

bacterial colony
type: Class
equivalent class: Class
  intersection of: biological colony
  intersection of: Restriction
    on property: hasGranularPart
    some values from: bacterial cell
  intersection of: Restriction
    on property: hasGranularPart
    all values from: bacterial cell
definition: Cluster of bacteria, usually cultured from a single cell.

bakers yeast cell
type: Class
subclass of: yeast cell
subclass of: Restriction
  on property: isBearerOf
  some values from: Class
    intersection of: taxon quality
    intersection of: Restriction
      on property: projectsOnto
      some values from: species saccharomyces cerevisiae value region
disjoint with: candida albicans cell
comment: one saccharomyces cerevisiae cell

bakers yeast population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: bakers yeast cell
  intersection of: Restriction
    on property: hasGranularPart
    all values from: bakers yeast cell
comment: EXAMPLE OF POPULATION

behavior
type: Class
subclass of: Action
definition: An (often habitual) action of an organism that is the realization of some disposition

bio molecular process
type: Class
subclass of: biological processual entity
definition: Process occuring on molecular level. It has exclusivly subclasses of MolecularEntity as participants.

bio molecular sequence information
type: Class
subclass of: SequenceInformation
definition: Sequence as an entity of information. The same sequence can inhere in different biopolymers. Sequence information can be theoretical, therefore a "real" sequence is not implied.

bio molecular sequence structure
type: Class
equivalent class: Class
  union of: amino acid sequence
  union of: chain of carbohydrate monomers
  union of: chain of nucleotide monomers
  union of: DNA chain
  union of: RNA chain
subclass of: organic molecular entity
definition: chain (segment) of similar monomers such as proteins or nucleotides

biological action
type: Class
equivalent class: Restriction
  on property: hasAgent
  some values from: Class
    union of: StructuredBiologicalEntity
    union of: Restriction
      on property: hasGranularPart
      some values from: StructuredBiologicalEntity
subclass of: Action
definition: Action that has some biological entity as agent

biological boundary
type: Class
equivalent class: Restriction
  on property: isBoundaryOf
  some values from: Class
    union of: biological space
    union of: StructuredBiologicalEntity
subclass of: OneDimensionalPhysicalEntity
definition: boundary in or of a biological entity

biological colony
type: Class
subclass of: PluralityOfOrganisms
definition: Plurality of several individual organisms living closely together, usually for mutual benefit

biological function
type: Class
equivalent class: Class
  intersection of: Function
  intersection of: Restriction
    on property: inheresIn
    some values from: StructuredBiologicalEntity
definition: a function that inheres in some structured biological entity.

biological life
type: Class
subclass of: organism process
definition: The whole process from origin to death of an organism

biological processual entity
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: hasParticipant
    some values from: StructuredBiologicalEntity
  intersection of: Restriction
    on property: isIncludedIn
    some values from: StructuredBiologicalEntity
disjoint with: physical processual entity
definition: Process specific for biological systems.

biological size
type: Class
subclass of: ObjectQuality
subclass of: Restriction
  on property: projectsOnto
  all values from: biological size value region
subclass of: Restriction
  on property: projectsOnto
  some values from: biological size value region
definition: quality of being visible with or without microscope

biological size value region
type: Class
subclass of: ValueRegion
definition: values that describe the size of biological entities

biological space
type: Class
equivalent class: Class
  intersection of: ImmaterialThreeDimensionalPhysicalEntity
  intersection of: Restriction
    on property: physically contained in
    some values from: StructuredBiologicalEntity
definition: space that is located inside a biological entity

biological system role
type: Class
subclass of: Role
definition: A role specific to biological processes

biomedical material role
type: Class
subclass of: therapeutic role
disjoint with: drug role
definition: Role of Non-drug material used for therapeutic Purpose

biomolecule
type: Class
equivalent class: Class
  intersection of: MonoMolecularEntity
  intersection of: Restriction
    on property: originates from
    some values from: living organism
definition: Monomolecular entity that stems from some organism

bird
type: Class
subclass of: vertebrate

body
type: Class
subclass of: StructuredBiologicalEntity
definition: Entire biological structure that constitutes a (living) organism. A body can be living or dead. Whether a living organism coincides with its body or hasPart its body, is controversial. We use "hasPhysicalPart" for relating organism to body. Being reflexive, this would not be incompatible with a view in which a living organism is a body.
see also: FMAID:256135 Body

body liquid
type: Class
subclass of: portion of heterogenous liquid
subclass of: Restriction
  on property: hasComponentPart
  some values from: Restriction
    on property: hasGranularPart
    some values from: water molecule
subclass of: Restriction
  on property: originates from
  some values from: living organism
definition: Suspension and / or solution of biomolecules, ions, bigger particles in Water.

body system
type: Class
subclass of: OrganismPart
disjoint with: organ
definition: Mereological sum of heterogeneous body components that constitute a functional unity

candida albicans cell
type: Class
subclass of: yeast cell
subclass of: Restriction
  on property: isBearerOf
  some values from: Class
    intersection of: taxon quality
    intersection of: Restriction
      on property: projectsOnto
      some values from: species candida albicans value region
comment: One candida albicans cell

candida albicans population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: candida albicans cell
  intersection of: Restriction
    on property: hasGranularPart
    all values from: candida albicans cell
comment: EXAMPLE OF POPULATION

canonical processual entity
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: Canonicity
      intersection of: Restriction
        on property: projectsOnto
        some values from: canonical value region
disjoint with: noncanonical processual entity
definition: a process that is considered normal

canonical static processual entity
type: Class
equivalent class: Class
  intersection of: static processual entity
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: Canonicity
      intersection of: Restriction
        on property: projectsOnto
        some values from: canonical value region
disjoint with: noncanonical static processual entity
comment: a biological state that is considered "normal"
prior version: canonical state

carbohydrate molecule or residue
type: Class
subclass of: OrganicMolecularEntityPartition

carbohydrate monomer
type: Class
subclass of: carbohydrate molecule or residue
subclass of: monomer
subclass of: Restriction
  on property: hasComponentPart
  some values from: submolecular group
disjoint with: chain of carbohydrate monomers

carbohydrate sequence information
type: Class
subclass of: SequenceInformation
definition: The information that describes the make-up of a (physical) carbohydrate sequence.

catalytic role
type: Class
subclass of: chemical role
definition: The role a substance plays in accelerating a chemical reaction

categorization system
type: Class
subclass of: intellectual product
disjoint with: regulation or law
definition: A categorization system is a human artifact that aims at partinioning object classes, denotations, or concepts of a given domain.

causing
type: Class
subclass of: affecting
definition: action that causes an effect

cell in vivo
type: Class
subclass of: Cell
subclass of: Class
  union of: living organism
  union of: Restriction
    on property: proper physical part of
    some values from: living organism
disjoint with: modified cell
definition: Living cell that is not removed from a living system

cell membrane
type: Class
subclass of: cellular component
subclass of: Restriction
  on property: hasComponentPart
  some values from: Restriction
    on property: hasGranularPart
    some values from: peptide structure
subclass of: Restriction
  on property: hasComponentPart
  some values from: Restriction
    on property: hasGranularPart
    some values from: lipid molecule or residue
definition: Semipermeable lipid bilayer found in all cells.[1] It contains a wide variety of biological molecules, primarily proteins and lipids, which are involved in a vast array of cellular processes, and also serves as the attachment point for both the intracellular cytoskeleton and, if present, the cell wall.

cell nucleus
type: Class
subclass of: cellular component

central nervous system
type: Class
subclass of: organ system
definition: the central control unit of an organism. Constitutes the brain in higher organisms.

chain of carbohydrate monomers
type: Class
subclass of: carbohydrate molecule or residue
subclass of: Restriction
  on property: hasComponentPart
  some values from: carbohydrate monomer

chain of nucleotide monomers
type: Class
subclass of: nucleic acid structure

chemical role
type: Class
subclass of: Role
definition: Any role performed by a chemical substance.

child role
type: Class
subclass of: family role
definition: the role an organism plays in relation to its parent

chlamydia cell
type: Class
subclass of: prokaryote
disjoint with: rickettsia cell

chromosome
type: Class
subclass of: molecule complex
subclass of: Restriction
  on property: hasComponentPart
  some values from: entire nucleic acid molecule
definition: Organized form of DNA in cells, containing one very long, continuous piece of DNA, which contains many genes, regulatory elements and other intervening nucleotide sequences. Includes also the DNA-bound proteins which serve to package and manage the DNA.

class gamma proteobacteria value region
type: Class
subclass of: phylum proteobacteria value region
comment: EXAMPLE OF TAXON REGION

class insecta value region
type: Class
subclass of: phylum arthropoda value region
comment: EXAMPLE OF TAXON REGION

class mammalia value region
type: Class
subclass of: subphylum vertebrata value region
comment: EXAMPLE OF TAXON REGION

class saccharomycetes value region
type: Class
subclass of: subphylum saccharomycotina value region
comment: EXAMPLE OF TAXON REGION

complicating
type: Class
subclass of: affecting
definition: causes to become more severe

congenital abnormal structure
type: Class
subclass of: pathological structure
definition: biological structure that deviates from what is considered normal and that already existed at birth

congenital pathological condition
type: Class
subclass of: pathological value region
definition: Ill-formed state of a biological entity, present from birth [steschu 20071010]

congenital pathological static processual entity
type: Class
equivalent class: Class
  intersection of: pathological static processual entity
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: Canonicity
      intersection of: Restriction
        on property: projectsOnto
        some values from: congenital pathological condition
prior version: congenital pathological state
definition: pathological state present at birth

cytoplasm
type: Class
subclass of: cellular component
subclass of: Restriction
  on property: has proper physical part
  some values from: Restriction
    on property: hasGranularPart
    some values from: peptide structure
subclass of: Restriction
  on property: has proper physical part
  some values from: Restriction
    on property: hasGranularPart
    some values from: water molecule
definition: Gelatinous, semi-transparent fluid that fills most cells. E

DNA chain
type: Class
subclass of: chain of nucleotide monomers
disjoint with: RNA chain
definition: A DNA is a complex, high-molecular-weight biochemical macromolecule composed of deoxyribonumcleotide chains that convey genetic information. Any kind of NucleicAcid that is composed of Deoxyribonucleotides is here defined as DNA.

dead body
type: Class
subclass of: body
disjoint with: living body
definition: body that is the transformation of a living body after death

death
type: Class
subclass of: Class
  intersection of: biological processual entity
  intersection of: Class
    complement of: Restriction
      on property: has duration
      some values from: time interval
  intersection of: Restriction
    on property: has point in time
    some values from: point in time
definition: End of live of a biological system

developmental quality
type: Class
subclass of: ObjectQuality
subclass of: Restriction
  on property: projectsOnto
  some values from: developmental value region
subclass of: Restriction
  on property: projectsOnto
  all values from: developmental value region
definition: Ontogenetic stage

developmental value region
type: Class
subclass of: ValueRegion
definition: abstract region in which the values of developmental stages are located

digital entity
type: Class
subclass of: InformationObject
definition: any kind of information that is fully expressible by a sequence of binary values.
comment: (OBI 306)

disrupting
type: Class
subclass of: affecting
definition: Producing a negative effect on

drug role
type: Class
subclass of: therapeutic role
definition: The role of a chemical of biological entity of being deliberately used in virtue of its expected positive impact on a dysfunctional biological system

educator role
type: Class
subclass of: occupational role
definition: The role a person plays that is occupied by educational activities

eicosanoid
type: Class
subclass of: lipid molecule or residue
definition: An oxygenated metabolite from polyunsaturated 20 carbon fatty acids including lipoxygenase and cyclooxygenase products and their synthetic analogs. This includes the prostaglandins and thromboxanes. (UMLS SN)

electron
type: Class
subclass of: SubAtomicParticle
definition: Negatively Charged Particle

embryonic organism
type: Class
equivalent class: Class
  intersection of: living organism
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: developmental quality
      intersection of: Restriction
        on property: projectsOnto
        some values from: embryonic value region
subclass of: OrganismByDevelopmentalStagePartition
disjoint with: juvenile organism
definition: evolving organism before birth, with not yet fully formed organs

embryonic structure
type: Class
equivalent class: Class
  intersection of: StructuredBiologicalEntity
  intersection of: Class
    union of: embryonic organism
    union of: Restriction
      on property: originates from
      some values from: embryonic organism
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: developmental quality
      intersection of: Restriction
        on property: projectsOnto
        some values from: embryonic value region
definition: An embryo or any structure derived from it. There may be structures derived from an embryo that are no longer considered embryonic ones, hence no full definition.

embryonic value region
type: Class
subclass of: developmental value region
comment: "embryonic" as the value of a developmental stage. E.g. a 3 days old mouse embryo has a quality which has its value located in "embryonic value region".

entire carbohydrate monomer
type: Class
subclass of: carbohydrate monomer

entire molecular entity
type: Class
subclass of: MonoMolecularEntity
disjoint with: molecular residue
definition: Separately distinguishable molecular structure, neither part of nor attached to any other molecular structure. Atoms are not considered molecular structures. The hierarchy of entire entities mirrors the hierarchy of structures.

entire nucleic acid molecule
type: Class
subclass of: entire molecular entity
subclass of: Restriction
  on property: hasComponentPart
  some values from: monomer
comment: not (properPartOf some MonoMolecularEntity) REMOVED

entire protein molecule
type: Class
subclass of: peptide structure
definition: Amino Acid Polymer longer than 100 monomers.
comment: (QCR) Peptide and hasComponent min 101 AminoAcidMonomer and not (ro:properPartOf some MolecularEntity)

enzyme role
type: Class
equivalent class: Class
  intersection of: catalytic role
  intersection of: Restriction
    on property: inheresIn
    some values from: Class
      union of: peptide structure
      union of: RNA chain
comment: The role a peptide plays in accelerating a biochemical reaction

epithelial cell
type: Class
subclass of: Cell

escherichia coli cell
type: Class
subclass of: bacterial cell
subclass of: Restriction
  on property: isBearerOf
  some values from: Class
    intersection of: taxon quality
    intersection of: Restriction
      on property: projectsOnto
      some values from: species escherichia coli value region

escherichia coli population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: escherichia coli cell
  intersection of: Restriction
    on property: hasGranularPart
    all values from: escherichia coli cell
comment: EXAMPLE OF POPULATION

eukaryote
type: Class
subclass of: OrganismByTaxonPartition
definition: An eukaryote is an organism with a complex cell or cells, in which the genetic material is organized into a membrane-bound nucleus or nuclei. Most Eukaryots are multicellular, haowever, there are some which are always unicellular (protists, some fungi) but there are also unicellular developmental stages (zygotes) of plants and animals.

eukaryote population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: eukaryote
  intersection of: Restriction
    on property: hasGranularPart
    all values from: eukaryote
comment: EXAMPLE OF POPULATION

examination result role
type: Class
subclass of: finding role
disjoint with: sign or symptom role
definition: The role a measurement plays if it has been produced in the context of the quantitative assessment of a biological system

family drosophilidae value region
type: Class
subclass of: order diptera value region
comment: EXAMPLE OF TAXON REGION

family enterobacteriaceaea value region
type: Class
subclass of: order enterobacteriales value region
comment: EXAMPLE OF TAXON REGION

family hominidae value region
type: Class
subclass of: order primates value region
comment: EXAMPLE OF TAXON REGION

family role
type: Class
subclass of: Role
subclass of: Restriction
  on property: inheresIn
  all values from: Class
    union of: animal including human
    union of: animal population

family saccharomycetaceae value region
type: Class
subclass of: order saccharomycetales value region
comment: EXAMPLE OF TAXON REGION

fatty acid molecule or residue
type: Class
subclass of: OrganicMolecularEntityPartition
subclass of: Restriction
  on property: hasComponentPart
  some values from: submolecular group
definition: Carboxylic acid often with a long unbranched aliphatic tail.

finding role
type: Class
subclass of: health related role
definition: The role that may inhere in any biological structure, state, or process that is of reportable interest in a diagnostic process.

fish
type: Class
subclass of: vertebrate

food role
type: Class
subclass of: health related role
definition: The role of an entity components of which are used for supplying energy and vital substrates to a biological system

fruit fly
type: Class
subclass of: insect
subclass of: Restriction
  on property: isBearerOf
  some values from: Class
    intersection of: taxon quality
    intersection of: Restriction
      on property: projectsOnto
      some values from: species drosophila melanogaster value region
comment: one drosophila melanogaster

fruit fly population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: fruit fly
  intersection of: Restriction
    on property: hasGranularPart
    all values from: fruit fly
comment: EXAMPLE OF POPULATION

fungus
type: Class
subclass of: eukaryote
subclass of: Restriction
  on property: isBearerOf
  some values from: Class
    intersection of: taxon quality
    intersection of: Restriction
      on property: projectsOnto
      some values from: kingdom fungi value region
    intersection of: Restriction
      on property: projectsOnto
      all values from: kingdom fungi value region
comment: On fungus organisms
definition: Heterotrophic organisms characterized by a chitinous cell wall.

fungus population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: fungus
  intersection of: Restriction
    on property: hasGranularPart
    all values from: fungus
comment: EXAMPLE OF POPULATION

gaseous value region
type: Class
subclass of: state of matter value region
comment: "gaseous" as the value of a states of matter. E.g. a portion of air has a quality which has its value located in "gaseous value region"

gene
type: Class
subclass of: nucleic acid structure
subclass of: Restriction
  on property: isBearerOf
  some values from: genetic information
version info: TODO: Discuss whether all genes are DNA !
definition: region of nucleic acid macromolecule that carry information

gene information
type: Class
subclass of: InformationObject
definition: Information that resides on a gene.

genetic information
type: Class
subclass of: Class
  intersection of: InformationObject
  intersection of: Restriction
    on property: inheresIn
    some values from: Class
      union of: chain of nucleotide monomers
      union of: gene
      union of: genome
definition: information that can be interpreted by a genetic code

genome
type: Class
subclass of: cellular component
subclass of: Restriction
  on property: isBearerOf
  some values from: genetic information
comment: sum of genetic material in a cell

genome information
type: Class
subclass of: InformationObject
definition: The totality of hereditary information of an organism

genus candida value region
type: Class
subclass of: family saccharomycetaceae value region
disjoint with: genus saccharomyces value region
comment: EXAMPLE OF TAXON REGION

genus drosophila value region
type: Class
subclass of: subfamily drosophilinae value region
comment: EXAMPLE OF TAXON REGION

genus escherichia value region
type: Class
subclass of: family enterobacteriaceaea value region
comment: EXAMPLE OF TAXON REGION

genus homo value region
type: Class
subclass of: family hominidae value region
comment: EXAMPLE OF TAXON REGION

genus saccharomyces value region
type: Class
subclass of: family saccharomycetaceae value region
comment: EXAMPLE OF TAXON REGION

geographic surface
type: Class
subclass of: TwoDimensionalPhysicalEntity
comment: previous name "geographic entity"
definition: delineated surface of a large solid body in space (earth, moon, sun,...)

government
type: Class
subclass of: organization
definition: entity governing a defined group of people

great ape
type: Class
subclass of: mammal
subclass of: Restriction
  on property: isBearerOf
  some values from: Class
    intersection of: taxon quality
    intersection of: Restriction
      on property: projectsOnto
      some values from: family hominidae value region
comment: one great ape

great ape population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: great ape
  intersection of: Restriction
    on property: hasGranularPart
    all values from: great ape
comment: EXAMPLE OF POPULATION

group interaction
type: Class
subclass of: interacting
subclass of: Restriction
  on property: hasParticipant
  all values from: Class
    union of: legal entity
    union of: Restriction
      on property: hasGranularPart
      some values from: living organism
definition: action in which physical or legal groups interact

growing process
type: Class
subclass of: tissue process

health professional role
type: Class
subclass of: occupational role
definition: the role a human plays as active part in a health system

health related role
type: Class
subclass of: Role
definition: A role an entity plays as an actor or participant in processes that assess or influence the health status of an organism.

heterocyclic base molecule or residue
type: Class
subclass of: OrganicMolecularEntityPartition
subclass of: Restriction
  on property: hasComponentPart
  some values from: submolecular group
definition: Organic compounds that contain a ring structure containing N as proton receptor. Important parts of DNA and RNA molecules.

hormone role
type: Class
subclass of: signalling role
definition: The role a biologically active substance plays when it participates in the transmission of messages across a certain distance in an organism.

human
type: Class
subclass of: primate
subclass of: Restriction
  on property: isBearerOf
  some values from: Class
    intersection of: taxon quality
    intersection of: Restriction
      on property: projectsOnto
      some values from: species homo sapiens value region
    intersection of: Restriction
      on property: projectsOnto
      all values from: species homo sapiens value region

human action
type: Class
subclass of: organism action
subclass of: Restriction
  on property: hasAgent
  some values from: Class
    union of: human
    union of: Restriction
      on property: hasGranularPart
      some values from: human
definition: Action that has some human as agent

human epithelial cell
type: Class
equivalent class: Class
  intersection of: epithelial cell
  intersection of: Restriction
    on property: originates from
    some values from: Restriction
      on property: isBearerOf
      some values from: Class
        intersection of: taxon quality
        intersection of: Restriction

human language
type: Class
subclass of: LanguagePartition
definition: language used in communication between non-human animals

human population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: human
  intersection of: Restriction
    on property: hasGranularPart
    all values from: human
comment: EXAMPLE OF POPULATION

human reasoning
type: Class
equivalent class: Class
  intersection of: human action
  intersection of: Restriction
    on property: hasAgent
    some values from: human
  intersection of: Restriction
    on property: hasOutcome
    some values from: intellectual product
subclass of: human action
definition: Process in which a human creates an intellectual product

hurting
type: Class
subclass of: action on biological system
subclass of: Restriction
  on property: isBearerOf
  some values from: PhysicalForce
comment: negatively affecting a biological system by using physical force

immaterial processual entity
type: Class
subclass of: process
definition: A process with non-material participants, e.g. legal or organizational entities or information objects

immunologic role
type: Class
subclass of: biological system role
definition: A role that is played by any biological entity in virtue of the defense of an organism against infective agents

indicating
type: Class
subclass of: affecting
definition: action that indicates something

indicator role
type: Class
subclass of: chemical role
definition: A role a chemical plays for measuring or analyzing other chemical processes

individual behavior
type: Class
equivalent class: Class
  intersection of: behavior
  intersection of: Restriction
    on property: hasAgent
    some values from: living organism
  intersection of: Restriction
    on property: hasAgent
    all values from: living organism
disjoint with: social behavior
definition: Behavior of an individual organism

inorganic molecular entity
type: Class
subclass of: MonoMolecularEntity
disjoint with: organic molecular entity
definition: Substances which do not include carbon and its derivatives as their principal elements. However, carbides, carbonates, cyanides, cyanates and carbon disulfide are included in this class.

insect
type: Class
subclass of: arthropod
subclass of: Restriction
  on property: isBearerOf
  some values from: Class
    intersection of: taxon quality
    intersection of: Restriction
      on property: projectsOnto
      some values from: class insecta value region
definition: one insect

insect population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: insect
  intersection of: Restriction
    on property: hasGranularPart
    all values from: insect
comment: EXAMPLE OF POPULATION

intellectual product
type: Class
subclass of: InformationObject
subclass of: Restriction
  on property: isPatientIn
  some values from: Class
    intersection of: process
    intersection of: Restriction
      on property: hasAgent
      some values from: human
definition: An intellectual product is a piece of information that is the outcome of a human reasoning process

interacting
type: Class
equivalent class: Class
  union of: group interaction
  union of: organism interaction
  union of: substance interaction
subclass of: affecting
definition: two or more interaction partners exerce a mutual effect that may lead to structural transformation.

intra cellular process
type: Class
equivalent class: Class
  intersection of: biological processual entity
  intersection of: Restriction
    on property: isIncludedIn
    some values from: Cell
definition: Process occuring in a cell.

invertebrate
type: Class
subclass of: animal including human
disjoint with: vertebrate

juvenile organism
type: Class
equivalent class: Class
  intersection of: living organism
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: developmental quality
      intersection of: Restriction
        on property: projectsOnto
        some values from: juvenile value region
subclass of: OrganismByDevelopmentalStagePartition
definition: born organism, not yet in reproductive age

juvenile value region
type: Class
subclass of: developmental value region

kingdom animalia value region
type: Class
subclass of: TaxonValueRegion
comment: EXAMPLE OF TAXON REGION

kingdom archaea value region
type: Class
subclass of: TaxonValueRegion
comment: EXAMPLE OF TAXON REGION

kingdom bacteria value region
type: Class
subclass of: TaxonValueRegion
comment: EXAMPLE OF TAXON REGION

kingdom chromista value region
type: Class
subclass of: TaxonValueRegion
comment: EXAMPLE OF TAXON REGION

kingdom fungi value region
type: Class
subclass of: TaxonValueRegion
comment: EXAMPLE OF TAXON REGION

kingdom plantae value region
type: Class
subclass of: TaxonValueRegion
comment: EXAMPLE OF TAXON REGION

kingdom protozoa value region
type: Class
subclass of: TaxonValueRegion
comment: EXAMPLE OF TAXON REGION

kingdom viruses value region
type: Class
subclass of: TaxonValueRegion
comment: EXAMPLE OF TAXON REGION

language
type: Class
subclass of: InformationObject
definition: system of signs used for communication between biological and / or machine agents

LanguagePartition
type: Class
equivalent class: Class
  intersection of: language
  intersection of: Class
    union of: animal language
    union of: human language
    union of: machine language
definition: Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint.

legal entity
type: Class
subclass of: InformationObject
definition: nonmaterial entity that as an existence in a legal system

lipid molecule or residue
type: Class
subclass of: OrganicMolecularEntityPartition
subclass of: Restriction
  on property: hasComponentPart
  some values from: submolecular group
definition: Fat-soluble (lipophilic), naturally-occurring molecule.

liquid value region
type: Class
subclass of: state of matter value region
comment: "liquid" as the value of a states of matter. E.g. a portion of water has a quality which has its value located in "liquid value region"

living body
type: Class
subclass of: body
subclass of: Restriction
  on property: isParticipantIn
  some values from: biological life
subclass of: Class
  union of: living organism
  union of: Restriction
    on property: proper physical part of
    some values from: living organism
definition: Entirety of the biological structure that constitutes a living organism

living organism
type: Class
subclass of: Organism
subclass of: Restriction
  on property: isParticipantIn
  some values from: biological life
prior version: organism
definition: Living complex biological system which functions as a stable whole. In contrast to colonial organisms their components generally cannot survive on their own. We conceive organisms in a material sense. Therefore we do not assume any ontological difference between a unicellular organism and the cell it is made of. "Colonial Organism" are not considered Organisms. We here include viruses into the category of organisms. Organism in an inactive form which are not dead are considered living organisms. Whether a living organism coincides with its body or hasPart its body, is controversial. We use "hasPhysicalPart" for relating organism to body. Being reflexive, this would not be incompatible with a view in which a living organism is a body.

machine action
type: Class
equivalent class: Class
  intersection of: Action
  intersection of: Restriction
    on property: hasAgent
    some values from: Class
      intersection of: material object
      intersection of: Restriction
        on property: isBearerOf
        some values from: artefact role
definition: An action performed by a machine. A machine is here seen as a non-biological artifact.

machine language
type: Class
subclass of: LanguagePartition
definition: language used for processing by machines

macroscopic value region
type: Class
subclass of: biological size value region
disjoint with: microscopic value region
definition: size values of objects that are visible to the naked eye

mammal
type: Class
subclass of: vertebrate
subclass of: Restriction
  on property: isBearerOf
  some values from: Class
    intersection of: taxon quality
    intersection of: Restriction
      on property: projectsOnto
      some values from: class mammalia value region
comment: one mammal

mammal population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: mammal
  intersection of: Restriction
    on property: hasGranularPart
    all values from: mammal
comment: EXAMPLE OF POPULATION

managing care
type: Class
subclass of: affecting
subclass of: Restriction
  on property: hasParticipant
  all values from: Class
    union of: human
    union of: legal entity
    union of: Restriction
      on property: hasGranularPart
      some values from: human
definition: action in which a subject cares for the well-being of some biological entity

measure
type: Class
subclass of: InformationObject
definition: Numeric quantity or cardinality, reference for measurement processes. Example kilogram, hour, ampere.

measurement method
type: Class
equivalent class: Class
  intersection of: Plan
  intersection of: Restriction
    on property: hasRealization
    all values from: measuring action
subclass of: Plan
definition: Plan that is realized by a measurement process.

measuring action
type: Class
subclass of: Action
definition: an action that aims at producing a measurement

membership
type: Class
subclass of: immaterial processual entity
subclass of: Restriction
  on property: hasPatient
  some values from: legal entity
subclass of: Restriction
  on property: hasAgent
  some values from: Class
    union of: human
    union of: legal entity
definition: Process that endures while something or some person is part of a legal entity

mental function
type: Class
subclass of: Class
  intersection of: biological function
  intersection of: Restriction
    on property: inheresIn
    some values from: central nervous system
definition: biological function ascribed to the behavioral manisfestations of the brain

mental process
type: Class
subclass of: organism process
comment: process in an organism as a realization of a mental function

microorganism
type: Class
equivalent class: Class
  intersection of: living organism
  intersection of: Restriction
    on property: isBearerOf
    some values from: Restriction
      on property: projectsOnto
      some values from: microscopic value region
subclass of: living organism
definition: organism that can be seen only through a microscope

microscopic value region
type: Class
subclass of: biological size value region
definition: size values of objects that are too small to be seen without a microscope

mind
type: Class
subclass of: InformationObject
comment: Difficult concept. Better to be expressed by the primitive "mental function"

modified cell
type: Class
subclass of: Cell
subclass of: Class
  complement of: Restriction
    on property: proper physical part of
    some values from: living organism
subclass of: Restriction
  on property: derives from
  some values from: cell in vivo
definition: Cells that grow and replicate continuously outside the living organism.

molecular function
type: Class
subclass of: Function
definition: Inherent function of a single molecule.

molecular residue
type: Class
subclass of: MonoMolecularEntity
definition: not self-standing aggregation of atoms which are part of a bigger molecule

molecule complex
type: Class
subclass of: PolyMolecularCompositeEntity
subclass of: Restriction
  on property: hasComponentPart
  some values from: entire molecular entity
definition: Particle that consists of entire molecules.

monomer
type: Class
subclass of: MonoMolecularEntity
disjoint with: oligo or polymer
disjoint with: submolecular group
definition: Monomers can be described as constituted by molecularl groups. They are not repetitive and can constitute the building blocks of Polymers.

multicellular organism
type: Class
equivalent class: Class
  intersection of: living organism
  intersection of: Restriction
    on property: has proper physical part
    some values from: Cell
  intersection of: Restriction
    on property: isBearerOf
    some values from: developmental quality
definition: Organisms that are composed by more than one cell.

neoplastic process
type: Class
equivalent class: Class
  intersection of: growing process
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: Canonicity
      intersection of: Restriction
        on property: projectsOnto
        some values from: noncanonical value region

neuroreactive role
type: Class
subclass of: signalling role
definition: A role a molecule plays if it acts as a neurotransmitter

neutron
type: Class
subclass of: SubAtomicParticle
synonym: Neutral Particle

non steroid lipid
type: Class
subclass of: lipid molecule or residue
definition: Lipids that have aliphatic chains and no steroid rings

noncanonical processual entity
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: Canonicity
      intersection of: Restriction
        on property: projectsOnto
        some values from: noncanonical value region
definition: a process that is considered abnormal

noncanonical static processual entity
type: Class
equivalent class: Class
  intersection of: static processual entity
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: Canonicity
      intersection of: Restriction
        on property: projectsOnto
        some values from: noncanonical value region
definition: a biological state that is considered "abnormal"
prior version: noncanonical state

nucleic acid nucleotide or nucleoside molecule or residue
type: Class
subclass of: OrganicMolecularEntityPartition

nucleic acid structure
type: Class
subclass of: nucleic acid nucleotide or nucleoside molecule or residue
subclass of: Restriction
  on property: hasComponentPart
  some values from: nucleotide molecule
subclass of: Restriction
  on property: hasComponentPart
  all values from: nucleotide molecule
definition: A nucleic acid is a complex, high-molecular-weight biochemical macromolecule composed of nucleotide chains that convey genetic information.

nucleoside molecule
type: Class
subclass of: nucleic acid nucleotide or nucleoside molecule or residue
subclass of: Restriction
  on property: hasComponentPart
  some values from: submolecular group

nucleotide molecule
type: Class
subclass of: nucleic acid nucleotide or nucleoside molecule or residue
subclass of: Restriction
  on property: hasComponentPart
  some values from: submolecular group
definition: Comment: (QCR) hasComponent exactly 1 HeterocyclicBase and hasComponent exactly 1 Phosphate and hasComponent only (Phosphate or Ribose or HeterocyclicBase) and hasComponent exactly 1 Pentose

nucleotide sequence information
type: Class
subclass of: SequenceInformation
definition: The information that describes the make-up of a (physical) nucleotide sequence.

nurse role
type: Class
subclass of: health professional role
disjoint with: physician role
definition: The role a nurse plays

occupational role
type: Class
subclass of: Role
definition: The role that determines the occupation that characterizes the daily life of a human being or animal.

oligo or polymer
type: Class
subclass of: MonoMolecularEntity
subclass of: Restriction
  on property: hasComponentPart
  some values from: monomer
subclass of: Restriction
  on property: hasComponentPart
  all values from: monomer
disjoint with: submolecular group
definition: An oligo or polymer macromolecular structure is a molecule of moderate to high relative molecular mass, the structure of which essentially comprises the multiple repetition (n >= 2) of units derived from molecules of low relative molecular mass.

one dimensional boundary
type: Class
subclass of: OneDimensionalPhysicalEntity
definition: line bounding a two-dimensional biological entity

order diptera value region
type: Class
subclass of: class insecta value region
comment: EXAMPLE OF TAXON REGION

order enterobacteriales value region
type: Class
subclass of: class gamma proteobacteria value region
comment: EXAMPLE OF TAXON REGION

order primates value region
type: Class
subclass of: class mammalia value region
comment: EXAMPLE OF TAXON REGION

order saccharomycetales value region
type: Class
subclass of: class saccharomycetes value region
comment: EXAMPLE OF TAXON REGION

organ
type: Class
subclass of: OrganismPart
definition: Macroscopic, well delimited, functionally and structurally characterized part of an organism. Exact criteria of what an organ is do not exist.

organ part
type: Class
subclass of: OrganismPart
see also: FMAID:82472 Cardinal organ part

organ system
type: Class
subclass of: body system
see also: FMAID:7149 Organ system

organ system part
type: Class
subclass of: body system
see also: FMAID:67509 Organ system subdivistion

organic molecular entity
type: Class
subclass of: MonoMolecularEntity
definition: Substances containing carbon and its derivatives as their prinicipal elements, usually combined with itself and with atoms of one or more other element such as hydrogen, oxygen, nitrogen, sulfur, phosphorus, chlorine or fluorine. They exist in either carbon chain or carbon ring form. Excludes carbides, carbonates and carbon oxides.

OrganicMolecularEntityPartition
type: Class
equivalent class: Class
  intersection of: organic molecular entity
  intersection of: Class
    union of: amino acid or peptide molecule or structure
    union of: carbohydrate molecule or residue
    union of: fatty acid molecule or residue
    union of: heterocyclic base molecule or residue
    union of: lipid molecule or residue
    union of: nucleic acid nucleotide or nucleoside molecule or residue
comment: Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint.

organism action
type: Class
equivalent class: Restriction
  on property: hasAgent
  some values from: Class
    union of: living organism
    union of: Restriction
      on property: hasGranularPart
      some values from: living organism
subclass of: biological action
definition: Action that has some organism as agent

OrganismByDevelopmentalStagePartition
type: Class
equivalent class: Class
  intersection of: living organism
  intersection of: Class
    union of: adult organism
    union of: embryonic organism
    union of: juvenile organism
subclass of: Class
  union of: adult organism
  union of: embryonic organism
  union of: juvenile organism
definition: Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint.

OrganismByTaxonPartition
type: Class
equivalent class: Class
  intersection of: living organism
  intersection of: Class
    union of: eukaryote
    union of: prokaryote
    union of: virus
comment: Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint.

organism interaction
type: Class
subclass of: interacting
subclass of: Restriction
  on property: hasParticipant
  all values from: living organism
definition: action in which single biological organisms interact

organism part
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has proper physical part
    some values from: tissue
  intersection of: Restriction
    on property: originates from
    some values from: multicellular organism
subclass of: StructuredBiologicalEntity
disjoint with: syncytium
disjoint with: cellular component
definition: A well defined and circumscribed subdivision of an organism, not any arbitrary part. Macroscopic organism parts may be delimited mainly by natural boundaries but always exhibit at least small regions of fiat boundaries. An organism part may derive from an organism, i.e. it may continue to exist even when the organism does not exist any longer.

organism process
type: Class
equivalent class: Class
  intersection of: biological processual entity
  intersection of: Restriction
    on property: hasParticipant
    some values from: living organism
definition: any biological process that involves a whole organism

organization
type: Class
subclass of: legal entity
definition: collection of human or legal entities

parent role
type: Class
subclass of: family role
definition: the role an organism plays in relation to its children

pathological condition
type: Class
equivalent class: Class
  union of: pathological disposition
  union of: pathological process
  union of: pathological structure
subclass of: Condition
definition: pathological structure, disposition, or process. This disjoint category helps properly represent diseases becauses it is often left open whether they are meant as pathological structure, disposition, or process. In case this is to be left open, the relation has_locus should be used to connect them to anatomical entities

pathological disposition
type: Class
equivalent class: Class
  intersection of: Disposition
  intersection of: Restriction
    on property: inheresIn
    some values from: Restriction
      on property: isBearerOf
      some values from: Class
        intersection of: Canonicity
        intersection of: Restriction
definition: any kind of disposition considered non-canonical. The criteria of canonicity are not further specified. The classification of certain dispositions as dysfunctional or pathological is dependent on a historic and cultural context. Dysfunction or disease therefore hasn't the status of a universal.
prior version: prior label "dysfunction"

pathological process
type: Class
equivalent class: Class
  intersection of: biological processual entity
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: Canonicity
      intersection of: Restriction
        on property: projectsOnto
        some values from: noncanonical value region
definition: a biological process which is non-canonic

pathological static processual entity
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: hasParticipant
    some values from: Class
      union of: structured biological entity
      union of: Restriction
        on property: hasGranularPart
        some values from: structured biological entity
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: Canonicity
      intersection of: Restriction
        on property: projectsOnto
        some values from: pathological value region
subclass of: noncanonical static processual entity
prior version: pathological state
comment: Condition of an organism that deviates from what is considered normal. Often referred to by the terms "disorder", "disease", "syndrome", "sign", or "symptom". None of these denote clearly delineated ontological categories. See disease role etc.

pathological structure
type: Class
equivalent class: Class
  intersection of: StructuredBiologicalEntity
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: Canonicity
      intersection of: Restriction
        on property: projectsOnto
        some values from: noncanonical value region
disjoint with: well formed biological structure
prior version: former name: "ill formed biological structure"
definition: biological structure that is non-canonic

pathological value region
type: Class
subclass of: Class
  intersection of: noncanonical value region
  intersection of: Class
    union of: Class
      intersection of: Canonicity
      intersection of: Restriction
        on property: inheresIn
        some values from: Class
    union of: Restriction
      on property: isProjectionOf
      some values from: Class
        intersection of: Canonicity
        intersection of: Restriction
definition: state of an organism or an organism part requiring therapeutic or palliative intervention

peptide function
type: Class
equivalent class: Class
  intersection of: molecular function
  intersection of: Restriction
    on property: inheresIn
    some values from: peptide structure
definition: Inherent Function of a protein or a part of it.

peptide structure
type: Class
subclass of: amino acid or peptide molecule or structure
subclass of: Restriction
  on property: hasComponentPart
  some values from: amino acid molecule or residue
comment: Comment: We here use the term peptide in the most general sense, viz. a oligo or polymer made out of amino acids.

phosphate
type: Class
subclass of: inorganic molecular entity
definition: Phosphate is a salt of phosphoric acid or a functional group on organic compounds.

phylum arthropoda value region
type: Class
subclass of: kingdom animalia value region
disjoint with: phylum chordata value region
comment: EXAMPLE OF TAXON REGION

phylum ascomycota value region
type: Class
subclass of: kingdom fungi value region
comment: EXAMPLE OF TAXON REGION

phylum chordata value region
type: Class
subclass of: kingdom animalia value region
comment: EXAMPLE OF TAXON REGION

phylum proteobacteria value region
type: Class
subclass of: kingdom bacteria value region
comment: EXAMPLE OF TAXON REGION

physical processual entity
type: Class
subclass of: process
subclass of: Class
  complement of: biological processual entity
definition: process that only involves non-biological participants

physical state
type: Class
subclass of: ObjectQuality
subclass of: Restriction
  on property: inheresIn
  some values from: material object
subclass of: Restriction
  on property: inheresIn
  all values from: material object
definition: Quality of being solid, liquid, gaseous, ... [steschu20080127]
comment: former name: StateOfAggregation

physician role
type: Class
subclass of: health professional role
definition: The role a physician plays

plant
type: Class
subclass of: eukaryote
subclass of: Restriction
  on property: isBearerOf
  some values from: Class
    intersection of: taxon quality
    intersection of: Restriction
      on property: projectsOnto
      some values from: kingdom plantae value region
definition: Organism of the kingdom Plantae.

plant cell
type: Class
equivalent class: Class
  intersection of: Cell
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: taxon quality
      intersection of: Restriction
        on property: projectsOnto
        some values from: kingdom plantae value region

plant population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: plant
  intersection of: Restriction
    on property: hasGranularPart
    all values from: plant
comment: EXAMPLE OF POPULATION

poison role
type: Class
subclass of: health related role
definition: The role of a substance of mixture of substance of a defined amount thereof to be toxic to (parts of) biological organisms

poisoning
type: Class
subclass of: action on biological system
comment: negatively affecting the integrity of a biologival system caused by one or more chemical substances

population
type: Class
subclass of: PluralityOfOrganisms
comment: all child classes of population are only meant as examples demonstrating how population classes can be postcoordinated
definition: Collection of Organisms of a defined taxon living in a given geographic area. In contrast to the "official" definition ("same species") this definition is broader and corresponds better to the use of the term in some contexts (e.g. "mixed population of 2 species")

portion of heterogenous liquid
type: Class
equivalent class: Class
  intersection of: CompoundOfCollectiveMaterialEntities
  intersection of: Restriction
    on property: isBearerOf
    some values from: Restriction
      on property: projectsOnto
      some values from: liquid value region
definition: Liquid constituted by different kinds of collectives, e.g. aqueous NaCl solution

portion of heterogenous solid
type: Class
equivalent class: Class
  intersection of: CompoundOfCollectiveMaterialEntities
  intersection of: Restriction
    on property: isBearerOf
    some values from: Restriction
      on property: projectsOnto
      some values from: solid value region
definition: Solid constituted by different kinds of collectives, e.g. a NaCl crystal, granite

prevention action
type: Class
subclass of: Action
subclass of: Class
  intersection of: Restriction
    on property: hasAgent
    all values from: material object
  intersection of: Restriction
    on property: hasPatient
    all values from: process
definition: Hinders a process or the realization of a function. As the second argument represents sth non-existent, it cannot be expressed in FOL. Hence the special status of this class. (Cf. Condovardi et al. "Preventing Existence, FOIS 2001)

preventive role
type: Class
subclass of: health related role
definition: The role an action plays if it is intended to protect an organism against negative external influences.

primate
type: Class
subclass of: great ape
subclass of: Restriction
  on property: isBearerOf
  some values from: Class
    intersection of: taxon quality
    intersection of: Restriction
      on property: projectsOnto
      some values from: order primates value region
    intersection of: Restriction
      on property: projectsOnto
      all values from: order primates value region
comment: one primate

primate population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: primate
  intersection of: Restriction
    on property: hasGranularPart
    all values from: primate
comment: EXAMPLE OF POPULATION

producing
type: Class
subclass of: affecting
definition: action in which a new physical or informational entity comes into being

prokaryote
type: Class
subclass of: OrganismByTaxonPartition
subclass of: Restriction
  on property: isBearerOf
  some values from: Restriction
    on property: projectsOnto
    some values from: microscopic value region
definition: Cell lacking membrane enclosed organells

protein complex
type: Class
subclass of: molecule complex
definition: Mostly only proteins but composition with other molecules possible (e.g. Fe -> Hemoglobin) or also lipoproteins

protein domain
type: Class
subclass of: peptide structure
subclass of: Restriction
  on property: proper physical part of
  some values from: entire protein molecule
definition: Structural domain is the smallest element of protein tertiary structure that is self-stabilizing and often folds independently of the rest of the amino acid chain. It may contain one or more structural motives (ProteinSubstructure). A protein domain typically has its own function, the overall function of the protein results from the composition of the functions of all of its structural domains.

protein substructure
type: Class
subclass of: peptide structure
subclass of: Restriction
  on property: proper physical part of
  some values from: entire protein molecule
definition: A secondary substructure of a protein (protein Motif)

protein subunit
type: Class
subclass of: entire protein molecule
definition: A protein molecule that assembles with other protein molecules to form a protein complex. May have its own function. However, most proteinsubunits do not gain functionality until associated with the other subunits.

protist
type: Class
subclass of: eukaryote
subclass of: Restriction
  on property: isBearerOf
  some values from: Restriction
    on property: projectsOnto
    some values from: microscopic value region
definition: Organisms of the kingdom Protista

protist population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: protist
  intersection of: Restriction
    on property: hasGranularPart
    all values from: protist
comment: EXAMPLE OF POPULATION

proton
type: Class
subclass of: SubAtomicParticle
definition: Positively Charged Particle

RNA chain
type: Class
subclass of: chain of nucleotide monomers
definition: any kind of NucleicAcid that is composed of Ribonucleotides which are not Deoxyribonucleotides

radiation
type: Class
subclass of: material object
definition: process in which energy-rich particles or electromagnetic waves participate

reagent role
type: Class
subclass of: chemical role
definition: A role a chemical plays as participant in a chemical reation

receptor role
type: Class
subclass of: signalling role
definition: The role a (membrane) protein or protein complex plays in acting as a receptor.

regulation or law
type: Class
subclass of: intellectual product
definition: set of rules governing a particular kind of activity (WordNet)

regulatory body
type: Class
subclass of: organization
definition: organization that has the function of issuing regulations or laws

reptile
type: Class
subclass of: vertebrate

researcher role
type: Class
subclass of: occupational role
definition: the role a human plays if he / she is involved in research activities

rickettsia cell
type: Class
subclass of: prokaryote

sibling role
type: Class
subclass of: family role
definition: the role an organism plays in relation to another organism that has the same parents

sign or symptom role
type: Class
subclass of: finding role
definition: A role that can inhere in states, processes, or even in certain independent continuants (e.g. in a deformity). This a role is ascribed to an entity in a diagnostic process where the symptom is suspected to indicate a second state or process)

signalling role
type: Class
subclass of: biological system role
definition: The role of a biological entity that participates in a biological signalling process.

social action
type: Class
subclass of: Action
subclass of: Restriction
  on property: hasAgent
  all values from: Class
    union of: human population
    union of: organization
definition: action that targets a population

social behavior
type: Class
equivalent class: Class
  intersection of: behavior
  intersection of: Restriction
    on property: hasAgent
    some values from: population
definition: Behaviour of a group of organisms

solid value region
type: Class
subclass of: state of matter value region
comment: "solid" as the value of a states of matter. E.g. a stone has a quality which has its value located in "solid value region"

spatial reference role
type: Class
subclass of: Role
definition: The role attributed to a - mainly fiat - part of an object that is the site of some process or the location of some object of interest.

spatial region
type: Class
subclass of: ImmaterialThreeDimensionalPhysicalEntity
definition: An independent continuant entity that is neither a bearer of qualities nor inheres in any other entity (snap:SpatialRegion)

species candida albicans value region
type: Class
subclass of: genus candida value region
comment: EXAMPLE OF TAXON REGION

species drosophila melanogaster value region
type: Class
subclass of: genus drosophila value region
comment: EXAMPLE OF TAXON REGION

species escherichia coli value region
type: Class
subclass of: genus escherichia value region
comment: EXAMPLE OF TAXON REGION

species homo sapiens value region
type: Class
subclass of: genus homo value region
comment: EXAMPLE OF TAXON REGION

species saccharomyces cerevisiae value region
type: Class
subclass of: genus saccharomyces value region
comment: EXAMPLE OF TAXON REGION

state of matter
type: Class
subclass of: ObjectQuality
subclass of: Restriction
  on property: projectsOnto
  all values from: state of matter value region
subclass of: Restriction
  on property: projectsOnto
  some values from: state of matter value region
definition: States of matter are the distinct forms that different phases of matter take on.

state of matter value region
type: Class
subclass of: ValueRegion
subclass of: Restriction
  on property: isProjectionOf
  some values from: state of matter
definition: Values that a states of matter can have, e.g. liquid, solid.

static processual entity
type: Class
subclass of: process
subclass of: Restriction
  on property: hasParticipant
  some values from: Class
    union of: immaterial object
    union of: InformationObject
    union of: material object
    union of: TwoDimensionalPhysicalEntity
prior version: State
comment: Static condition as a special case of process in which temporal parts are neglected.

steroid
type: Class
subclass of: lipid molecule or residue
definition: One of a group of polycyclic, 17-carbon-atom, fused-ring compounds occurring both in natural and synthetic forms. Included here are naturally occurring and synthetic steroids, bufanolides, cardanolides, homosteroids, norsteroids, and secosteroids. (UMLS SN)

structured biological entity
type: Class
subclass of: PolyMolecularCompositeEntity
subclass of: Restriction
  on property: isBearerOf
  some values from: taxon quality
definition: Corresponds to FMA anatomical structure but extends to any kind of orgnaism: Material anatomical entity which is generated by coordinated expression of the organism's own genes that guide its morphogenesis; has inherent 3D shape; its parts are connected and spatially related to one another in patterns determined by coordinated gene expression. Examples: heart, right ventricle, mitral valve, myocardium, endothelium, lymphocyte, fibroblast, thorax, cardiovascular system, hemoglobin, T cell receptor. Old name: anatomical structure

structured nonbiological compound
type: Class
subclass of: PolyMolecularCompositeEntity
subclass of: Restriction
  on property: isBearerOf
  all values from: Class
    complement of: taxon quality
definition: All those things that are not identified by belonging to any biological species Borderline cases are artifacts that use biological substance (a table, a cloth, a house, a meal ...) A criterion to draw the boundary is whether or not the species affiliation has some structural or functional implication.

subfamily drosophilinae value region
type: Class
subclass of: family drosophilidae value region
comment: EXAMPLE OF TAXON REGION

subject of care role
type: Class
subclass of: health related role
definition: the role an animal or human plays as receiver of health care

submolecular group
type: Class
subclass of: MonoMolecularEntity
subclass of: Class
  complement of: entire molecular entity
subclass of: Restriction
  on property: isComponentPartOf
  some values from: Class
    complement of: oligo or polymer
comment: A submolecular group or moiety is a group of covalently bound atoms that occurs only as part of a molecule

subphylum saccharomycotina value region
type: Class
subclass of: phylum ascomycota value region
comment: EXAMPLE OF TAXON REGION

subphylum vertebrata value region
type: Class
subclass of: phylum chordata value region
comment: EXAMPLE OF TAXON REGION

substance interaction
type: Class
subclass of: interacting
definition: action in which molecular entities interact

syncytium
type: Class
subclass of: StructuredBiologicalEntity
subclass of: Class
  intersection of: Restriction
    on property: has proper physical part
    some values from: cytoplasm
  intersection of: Restriction
    on property: hasComponentPart
    some values from: cell membrane
  intersection of: Restriction
    on property: hasComponentPart
    some values from: cellular component
disjoint with: cellular component
definition: Fusion of cells

therapeutic role
type: Class
subclass of: health related role
definition: 1. The role of a continuant participating in a process with an expected positive impact on a dysfunctional biological system. 2. The role of a process with an expected positive impact on a dysfunctional biological system.

tissue
type: Class
subclass of: portion of heterogenous solid
subclass of: Restriction
  on property: hasComponentPart
  some values from: Restriction
    on property: hasGranularPart
    some values from: Cell
subclass of: Restriction
  on property: hasComponentPart
  some values from: Restriction
    on property: hasGranularPart
    some values from: entire molecular entity
subclass of: Restriction
  on property: originates from
  some values from: multicellular organism
definition: Aggregate of an arbitrary number of congeneric cells (cells with identical specialized characteristics), embedded into an amount of matter (matrix) that work together to perform a specific function.

tissue process
type: Class
equivalent class: Class
  intersection of: biological processual entity
  intersection of: Restriction
    on property: hasParticipant
    some values from: tissue
definition: process occurring in a tissue

treating
type: Class
equivalent class: Class
  union of: treating condition
  union of: treating organism
subclass of: affecting
definition: action with the intention to produce a positive effect on a biological organism or in which a malfunctioning is relieved or disrupted.

treating condition
type: Class
subclass of: affecting
subclass of: Restriction
  on property: hasAgent
  all values from: Restriction
    on property: isBearerOf
    some values from: therapeutic role
subclass of: Restriction
  on property: hasPatient
  all values from: Restriction
    on property: isParticipantIn
    some values from: noncanonical static processual entity
definition: action with the intention to relieve or disrupt a malfunctioning of a biological entity

treating organism
type: Class
subclass of: affecting
subclass of: Restriction
  on property: hasAgent
  all values from: Restriction
    on property: isBearerOf
    some values from: occupational role
subclass of: Restriction
  on property: hasPatient
  all values from: Class
    union of: living organism
    union of: Restriction
      on property: hasGranularPart
      some values from: living organism
definition: action with the intention to produce a positive effect on a biological organism

two dimensional biological entity
type: Class
equivalent class: Class
  intersection of: TwoDimensionalPhysicalEntity
  intersection of: Class
    union of: Restriction
      on property: proper physical part of
      some values from: structured biological entity
    union of: Restriction
      on property: isBoundaryOf
      some values from: biological space
    union of: Restriction
      on property: isBoundaryOf
      some values from: structured biological entity
  intersection of: Class
    complement of: Class
      union of: biological space
      union of: structured biological entity
  intersection of: Restriction
    on property: isBoundaryOf
    all values from: Class
      union of: biological space
      union of: structured biological entity
definition: surface or plane in a biological entity

unicellular organism
type: Class
equivalent class: Class
  intersection of: living organism
  intersection of: Class
    complement of: syncytium
  intersection of: Restriction
    on property: has proper physical part
    some values from: cytoplasm
  intersection of: Restriction
    on property: hasComponentPart
    some values from: cell membrane
  intersection of: Restriction
    on property: hasComponentPart
    some values from: cellular component
definition: Organisms that (always or in certain initial stages) consist of a single cell. We conceive organisms in a material sense. Therefore we do not assume any ontological difference between a monocellular organism and the cell it is made of.

using action
type: Class
subclass of: Action
definition: action that relates a user with an object he/she uses

vertebrate
type: Class
subclass of: animal including human
subclass of: Class
  complement of: Restriction
    on property: isBearerOf
    some values from: Restriction
      on property: projectsOnto
      some values from: microscopic value region
subclass of: Restriction
  on property: isBearerOf
  some values from: Class
    intersection of: taxon quality
    intersection of: Restriction
      on property: projectsOnto
      some values from: subphylum vertebrata value region
    intersection of: Restriction
      on property: projectsOnto
      all values from: subphylum vertebrata value region
comment: one vertebrate

vertebrate population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: vertebrate
  intersection of: Restriction
    on property: hasGranularPart
    all values from: vertebrate
comment: EXAMPLE OF POPULATION

virus
type: Class
subclass of: OrganismByTaxonPartition
subclass of: Class
  complement of: Restriction
    on property: has proper physical part
    some values from: Cell
subclass of: Class
  complement of: Cell
subclass of: Restriction
  on property: isBearerOf
  some values from: Restriction
    on property: projectsOnto
    some values from: microscopic value region
definition: Sub-microscopic agent that requires a host cell to grow and reproduce. Viruses resemble other organisms in that they possess genes, and can evolve in infected cells by natural selection. We therefore classify viruses as organisms, although there is an open debate.

virus population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: virus
  intersection of: Restriction
    on property: hasGranularPart
    all values from: virus
comment: EXAMPLE OF POPULATION

vitamin role
type: Class
subclass of: biological system role
definition: The role a certain substance can play in an organism. Vitamins are organic compounds that are essential to an organism for metabolic reactions. They are not food. Vitamin does not include essential fatty acids or essential amino acids

water molecule
type: Class
subclass of: inorganic molecular entity
definition: A water molecule is composed by one oxygen molecule and two hydrogen molecules

well formed biological structure
type: Class
equivalent class: Class
  intersection of: StructuredBiologicalEntity
  intersection of: Restriction
    on property: isBearerOf
    some values from: Class
      intersection of: Canonicity
      intersection of: Restriction
        on property: projectsOnto
        some values from: canonical value region

yeast cell
type: Class
subclass of: fungus
subclass of: Restriction
  on property: isBearerOf
  some values from: Restriction
    on property: projectsOnto
    some values from: microscopic value region
subclass of: Restriction
  on property: has proper physical part
  some values from: cytoplasm
subclass of: Class
  intersection of: Restriction
    on property: hasComponentPart
    some values from: cell membrane
  intersection of: Restriction
    on property: hasComponentPart
    some values from: cellular component
subclass of: Restriction
  on property: has proper physical part
  all values from: Class
    complement of: Cell
comment: Unicellular Fungi.

yeast population
type: Class
equivalent class: Class
  intersection of: population
  intersection of: Restriction
    on property: hasGranularPart
    some values from: yeast cell
  intersection of: Restriction
    on property: hasGranularPart
    all values from: yeast cell
comment: EXAMPLE OF POPULATION

canonical value region
type: Class
disjoint with: noncanonical value region
comment: abstract region in which the value "canonical" of canonicity is located

cellular component
type: Class
subclass of: Restriction
  on property: originates from
  some values from: Cell
definition: Components which only can be formed inside living cells but which may survive their host cell.

immaterial object
type: Class
prior version: immaterial physical entity
definition: Physical spaces that have a threedimensional spatial dimension but no mass. Old name: immaterial anatomical entity

material object
type: Class
definition: A material object that has exactly one mass and one volume at a time. Material objects may have Immaterial nonphysical entities as parts (e.g. Heart and Heart Ventricle).
prior version: material entity

noncanonical value region
type: Class
comment: abstract region in which the value "noncanonical" of canonicity is located

point in time
type: Class
disjoint with: time interval
definition: typically the boundary of a time interval

process
type: Class
definition: Process is in BioTop the generic subsumer of anything that "occurs". Processes can span across time and have temporal parts (i.e. there is no time in which all parts of a process are simultaneously present). A special kind of process is the event, which has no temporal extension. It can be regarded as Process Boundary (BFO). Processes have physical or informational entities as participants.
prior version: processual entity

process quality
type: Class
subclass of: Restriction
  on property: inheresIn
  some values from: process
definition: A quality that inheres in some process

taxon quality
type: Class
definition: The quality of one or more biological organisms, as well as of parts of organism of partaining to a biological taxon. [steschu20080127]

time interval
type: Class
definition: the interval between two time points