BioTopLite
type: Ontology
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
rights: http://creativecommons.org/licenses/by/3.0
publisher: Institute fir Medical Informatics, Statistics and Documentation, Medical University of Graz, Austria
creator: Stefan Schulz, Martin Boeker, Elena Beisswanger, Holger Stenzhorn, Djamila Raufie, Daniel Schober, Udo Hahn
subject: Biology, Medicine
subject: An experimental top level ontology for biology and medicine. Lite Version
version info: Last modification November 6, 2012 by Stefan Schulz
format: application/rdf+xml
description: Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network (mapping files available)

is agent in
type: ObjectProperty
definition: agentIn (inverse: hasAgent) relates a participant with a process, with the condition that this participant is causally active in the relevant process. This is the reason why agentIn is subsumed by the relation causedBy. Example: A physician is the agent in a opeeration process; a solvent is the agent in a solving process.
range: process
sub property of: causes
sub property of: participates in
domain: Class
  union of: immaterial object
  union of: information object
  union of: material object

_deprecated
type: ObjectProperty

abstract part of
type: ObjectProperty
type: TransitiveProperty
definition: abstractPartOf (inverse: hasAbstractPart) Relates parts and wholes of abstract entities. Abstract entities are neither processes, material objects, regions or spaces. Typical abstract entities are pieces of information. For instance, a header is an abstract part of a jpg file.
range: information object
domain: information object
inverse of: has abstract part
sub property of: hasLocus

at some time
type: ObjectProperty
definition: this relation relates a continuant (objects, qualities, dispositions...) to some of its TQCs (snapshot continuant).
range: entity at some time
domain: Class
  complement of: Class
    union of: process
    union of: temporal region

caused by
type: ObjectProperty
definition: Causation of a process is here understood as the disjunction between agency (a continuant causes a process) and as the realization of a disposition or a function, i.e. a disposition is considered the cause of a process.
domain: process
property chain axiom: realization of
property chain axiom: inheres in

causes
type: ObjectProperty
definition: Causation of a process is here understood as the disjunction between agency (a continuant causes a process) and as the realization of a disposition or a function, i.e. a disposition is considered the cause of a process.
range: process
inverse of: caused by

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
range: material object
domain: material object
inverse of: derives from
sub property of: has origin

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
domain: material object
range: material object
sub property of: originates from

has abstract part
type: ObjectProperty
type: TransitiveProperty
definition: abstractPartOf (inverse: hasAbstractPart) Relates parts and wholes of abstract entities. Abstract entities are neither processes, material objects, regions or spaces. Typical abstract entities are pieces of information. For instance, a header is an abstract part of a jpg file.
range: information object
domain: information object
sub property of: locusOf

has agent
type: ObjectProperty
definition: agentIn (inverse: hasAgent) relates a participant with a process, with the condition that this participant is causally active in the relevant process. This is the reason why agentIn is subsumed by the relation causedBy. Example: A physician is the agent in a opeeration process; a solvent is the agent in a solving process.
inverse of: is agent in
domain: process
sub property of: caused by
sub property of: has participant
range: Class
  union of: immaterial object
  union of: information object
  union of: material object

has boundary
type: ObjectProperty
definition: physicallyBounds (inverse: physically boundedBy) relates a three-dimensional physical object with its two dimensional boundary. Example: the surface of my liver physically bounds my liver.
range: physical boundary
sub property of: has part
inverse of: is boundary of
domain: Class
  union of: immaterial object
  union of: material object

has component part
type: ObjectProperty
definition: The non-transitive relation hasComponentPart (inverse: componentPartOf) relates components with a compound. Components strictly partition the compound, and the compound is the mereological sum of its components. A loss of some component affects the integrity of the compound, and possibly the type it instantiates, e.g. a complete vs. a defective organism. The choice of what is a component of a compound is somewhat arbitrary, because there are several ways to divide a whole into parts. Strictly spoken, this relation should refer to some partition. Components should be - at least - partly bona fide parts. The use of this relation also requires the commitment to an underlying granularity level. So could we consider the codons (base triples) as the components of a DNA molecule but also the single nucleotides. Note that components of a compound may also be portions of matter. Examples: my liver is a component of my organism, a carboxy group is a component of some organic acid molecule.
sub property of: has part

has duration
type: ObjectProperty
definition: hasDuration relates a process with the time interval it covers.
domain: process
sub property of: _deprecated
range: Class
  union of: point in time
  union of: time interval

has granular part
type: ObjectProperty
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: has part

has object quality
type: ObjectProperty
range: object quality
sub property of: _deprecated
sub property of: has quality
inverse of: object quality of
domain: Class
  union of: immaterial object
  union of: material object

has origin
type: ObjectProperty
sub property of: _deprecated

has outcome
type: ObjectProperty
definition: outcomeOf (inverse: hasOutcome) relates a participant to a process. This participant either - a) comes into being during the process or - b) undergoes some change during the process, so that it instantiates a different class at the end of the process and it constitutes (one of) the main result(s) of the process Example: a Protein molecule is the outcome of a translation process.
domain: process
sub property of: has participant
range: Class
  union of: immaterial object
  union of: information object
  union of: material object
  union of: process

has part
type: ObjectProperty
type: TransitiveProperty
sub property of: includes

has participant
type: ObjectProperty
definition: HasParticipant (inverse: participatesIn) relates a process with a non processual entity which plays some role in the process. Process participants may exist during the whole process, remain unchanged or undergo changes; they may come into being or get out of being during the process. Process participation is distinguished from process location. Example: An urea molecule which is excreted in a renal filtration process is participant of this process. A person who undergoes an operation is participant of this process.
domain: process
inverse of: participates in
range: Class
  union of: immaterial object
  union of: information object
  union of: material object
  union of: process

has patient
type: ObjectProperty
definition: patientIn (inverse: hasPatient) relates a participant with a process, with the condition that that this participant is not causally active. Example: A prey is the patient in a hunting process; a solute is the patient in a solving process.
domain: process
sub property of: has participant
inverse of: is patient in
range: Class
  union of: immaterial object
  union of: information object
  union of: material object
  union of: process

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
sub property of: _deprecated

has process quality
type: ObjectProperty
definition: processQualityOf (abstract: hasProcessQuality) links a quality that further characterizes a process to this process. Process qualities are asserted where the process cannot sufficiently be described by the qualities of its participants only. Example: The process of heart beating has the process quality heart rate.
domain: process
range: quality
sub property of: has quality
inverse of: process quality of

has processual part
type: ObjectProperty
type: TransitiveProperty
definition: hasProcessualPart (inverse: processualPartOf) relates a process with a subprocess (process part). Example: G1 phase is a processual part of the process mitosis.
range: process
domain: process
sub property of: _deprecated
inverse of: processual part of

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.
sub property of: locusOf
range: Class
  union of: immaterial object
  union of: material object
domain: Class
  union of: immaterial object
  union of: material object

has quality
type: ObjectProperty
sub property of: _deprecated

has realization
type: ObjectProperty
definition: Realization occurs if a disposition, a function, or a role manifests itself as a process. Certain information entities can also have realizations, e.g. plans that are realized in processes. Example: the disposition of a bird to fly (which exists even when it does not fly) is realized by its process of flying.
range: process
sub property of: causes
inverse of: realization of
domain: Class
  union of: disposition
  union of: function
  union of: information object
  union of: role

includes
type: ObjectProperty
type: TransitiveProperty
definition: includedIn (inverse: includes) is a very broad relation which relates an entity with the place it occurs, inheres, or is part of. See property chains: a participant of a process at a given time is included in the region that includes the process. Example: A heart pumping process is included in a heart.

inheres in
type: ObjectProperty
definition: inheresIn (inverse: bearerOf) relates a quality, role, function, disposition, or information object with the physical entity it depends on. (Note that for processes there is a separate relation pair "hasProcessQuality" and "processQualityOf") Example: a color inheres in a paint, the ability to fly inheres in a bird, or a pdf file inheres in a USB stick.
sub property of: is included in
domain: Class
  union of: disposition
  union of: function
  union of: information object
  union of: quality
  union of: role
range: Class
  union of: immaterial object
  union of: material object
  union of: process

is bearer of
type: ObjectProperty
definition: inheresIn (inverse: bearerOf) relates a quality, role, function, disposition, or information object with the physical entity it depends on. (Note that for processes there is a separate relation pair "hasProcessQuality" and "processQualityOf") Example: a color inheres in a paint, the ability to fly inheres in a bird, or a pdf file inheres in a USB stick.
sub property of: includes
inverse of: inheres in
range: Class
  union of: disposition
  union of: function
  union of: information object
  union of: quality
  union of: role
domain: Class
  union of: immaterial object
  union of: material object
  union of: process

is boundary of
type: ObjectProperty
definition: physicallyBounds (inverse: physically boundedBy) relates a three-dimensional physical object with its two dimensional boundary. Example: the surface of my liver physically bounds my liver.
domain: physical boundary
sub property of: is part of
range: Class
  union of: immaterial object
  union of: material object

is component part of
type: ObjectProperty
definition: The non-transitive relation hasComponentPart (inverse: componentPartOf) relates components with a compound. Components strictly partition the compound, and the compound is the mereological sum of its components. A loss of some component affects the integrity of the compound, and possibly the type it instantiates, e.g. a complete vs. a defective organism. The choice of what is a component of a compound is somewhat arbitrary, because there are several ways to divide a whole into parts. Strictly spoken, this relation should refer to some partition. Components should be - at least - partly bona fide parts. The use of this relation also requires the commitment to an underlying granularity level. So could we consider the codons (base triples) as the components of a DNA molecule but also the single nucleotides. Note that components of a compound may also be portions of matter. Examples: my liver is a component of my organism, a carboxy group is a component of some organic acid molecule.
inverse of: has component part
sub property of: is part of

is granular part of
type: ObjectProperty
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: has granular part
sub property of: is part of

is included in
type: ObjectProperty
type: TransitiveProperty
definition: isIncludedIn is a very broad relation which relates an entity with the place it occurs, inheres, or is part of. See property chain: a participant of a process at a given time is located where the process is located.
definition: includedIn (inverse: includes) is a very broad relation which relates an entity with the place it occurs, inheres, or is part of. Example: A heart pumping process is included in a heart.
inverse of: includes
property chain axiom: participates in

is outcome of
type: ObjectProperty
definition: outcomeOf (inverse: hasOutcome) relates a participant to a process. This participant either - a) comes into being during the process or - b) undergoes some change during the process, so that it instantiates a different class at the end of the process and it constitutes (one of) the main result(s) of the process Example: a Protein molecule is the outcome of a translation process.
range: process
inverse of: has outcome
sub property of: participates in
domain: Class
  union of: immaterial object
  union of: information object
  union of: material object
  union of: process

is part of
type: ObjectProperty
type: TransitiveProperty
sub property of: is included in

is patient in
type: ObjectProperty
definition: patientIn (inverse: hasPatient) relates a participant with a process, with the condition that that this participant is not causally active. Example: A prey is the patient in a hunting process; a solute is the patient in a solving process.
range: process
sub property of: participates in
domain: Class
  union of: immaterial object
  union of: information object
  union of: material object
  union of: process

is preceded by
type: ObjectProperty
type: TransitiveProperty
definition: precedes (inverse: precededBy) relates two processes, one of which ends or totally happens before the second one begins. Example: fecundation preceeds embryonic development.
inverse of: precedes
domain: Class
  union of: process
  union of: temporal region
range: Class
  union of: process
  union of: temporal region

is projection of
type: ObjectProperty
definition: projectsOnto (inverse: isProjectionOf) relates a quality with an abstract value region. The underlying idea, borrowed from the DOLCE ontology, is that the attribute / value distinction - as ubiquitous in information systems - should at least be optionally expressible in ontologies. Value regions are abstract regions, in which qualitative just as quantitative "values" are located. Like in topographic regions, these entities can overlap or be disjoint. Example: "Color" as quality may be refined as "Red Color". It can be fully defined in by "projects onto some RedColorRegion"
sub property of: topObjectProperty
domain: Class
  union of: temporal region
  union of: value region
range: Class
  union of: process
  union of: Class
    intersection of: entity at some time
    intersection of: quality

is represented by
type: ObjectProperty
definition: is represented by (inverse: represents) relates entities with information entities. In contrast to encoding, the represented entity is completely independent on the denoting one. Example: The inflammation of a sinus is representd by the word 'Sinusitis';, as well as by the ICD code "J10"
range: information object

object quality of
type: ObjectProperty
domain: object quality
sub property of: _deprecated
sub property of: quality of
range: 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
domain: material object
range: material object
sub property of: _deprecated

participates in
type: ObjectProperty
definition: HasParticipant (inverse: participatesIn) relates a process with a non processual entity which plays some role in the process. Process participants may exist during the whole process, remain unchanged or undergo changes; they may come into being or get out of being during the process. Process participation is distinguished from process location. Example: An urea molecule which is excreted in a renal filtration process is participant of this process. A person who undergoes an operation is participant of this process.
range: process
domain: Class
  union of: immaterial object
  union of: information object
  union of: material object
  union of: process

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 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.
sub property of: _deprecated
range: Class
  union of: immaterial object
  union of: material object
domain: Class
  union of: immaterial object
  union of: material object

precedes
type: ObjectProperty
type: TransitiveProperty
definition: precedes (inverse: precededBy) relates two processes, one of which ends or totally happens before the second one begins. Example: fecundation preceeds embryonic development.
domain: Class
  union of: process
  union of: temporal region
range: Class
  union of: process
  union of: temporal region

process quality of
type: ObjectProperty
definition: processQualityOf (abstract: hasProcessQuality) links a quality that further characterizes a process to this process. Process qualities are asserted where the process cannot sufficiently be described by the qualities of its participants only. Example: The process of heart beating has the process quality heart rate.
range: process
domain: quality
sub property of: quality of

processual part of
type: ObjectProperty
type: TransitiveProperty
definition: hasProcessualPart (inverse: processualPartOf) relates a process with a subprocess (process part). Example: G1 phase is a processual part of the process mitosis.
range: process
domain: process
sub property of: _deprecated

projects onto
type: ObjectProperty
definition: projectsOnto (inverse: projectionOf) relates a quality with an abstract value region. The underlying idea, borrowed from the DOLCE ontology, is that the attribute / value distinction - as ubiquitous in information systems - should at least be optionally expressible in ontologies. Value regions are abstract regions, in which qualitative just as quantitative "values" are located. Like in topographic regions, these entities can overlap or be disjoint. Example: "Color" as quality may be refined as "Red Color". It can be fully defined in by "projects onto some RedColorRegion"
inverse of: is projection of
sub property of: topObjectProperty
domain: Class
  union of: process
  union of: Class
    intersection of: entity at some time
    intersection of: quality
range: Class
  union of: temporal region
  union of: value region

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: _deprecated
sub property of: hasLocus
inverse of: has proper physical part
domain: Class
  union of: immaterial object
  union of: material object
range: Class
  union of: immaterial object
  union of: material object

quality of
type: ObjectProperty
sub property of: _deprecated
inverse of: has quality

realization of
type: ObjectProperty
definition: Realization occurs if a disposition, a function, or a role manifests itself as a process. Certain information entities can also have realizations, e.g. plans that are realized in processes. Example: the disposition of a bird to fly (which exists even when it does not fly) is realized by its process of flying.
domain: process
sub property of: caused by
range: Class
  union of: disposition
  union of: function
  union of: information object
  union of: role

represents
type: ObjectProperty
definition: is represented by (inverse: represents) relates entities with information entities. In contrast to encoding, the represented entity is completely independent on the denoting one. Example: The inflammation of a sinus is representd by the word 'Sinusitis';, as well as by the ICD code "J10"
domain: information object
inverse of: is represented by

action
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: has agent
    some values from: Thing
definition: An action is a processual entity that that is promoted by an agent, having a clear role distinction between agent and patient

amount of pure substance
type: Class
subclass of: collective material entity
subclass of: Restriction
  on property: has granular part
  all values from: Class
    union of: atom
    union of: mono molecular entity
disjoint with: plurality of organisms
definition: collection with molecules or atoms as granular parts of the same sort

atom
type: Class
subclass of: compound
definition: Basic building block of molecules. Particle of discrete types. Biologically important atoms are C, N, H, O, P, S, Na, Ca, K, Mg, Cl, J, Fe, Co, Zn ,... Atoms may be electrically neutral or ionic.

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

canonicity
type: Class
subclass of: quality
subclass of: Restriction
  on property: is included in
  all values from: Class
    union of: immaterial object
    union of: material object
    union of: process
subclass of: Restriction
  on property: projects onto
  all values from: canonicity value region
definition: The condition of an entity (state, process, function, object) in terms of being well or ill-formed or behaving

canonicity value region
type: Class
subclass of: value region
subclass of: Restriction
  on property: is projection of
  all values from: canonicity
disjoint with: taxon value region
definition: abstract region in which values of canonicity are located

cell
type: Class
subclass of: structured biological entity
disjoint with: cellular component
disjoint with: organism part
definition: Constituting unit of an organism. The boundary between cell, syncytium and subcellular fragments such as platelets is problematic. Hence no full definition possible.

cellular component
type: Class
subclass of: structured biological entity
subclass of: Restriction
  on property: at some time
  some values from: Restriction
    on property: is part of
    some values from: cell
disjoint with: organism part
definition: Components which only can be formed inside living cells but which may survive their host cell.

collective material entity
type: Class
subclass of: material object
comment: The fuzzyness of this class is due to the "same sort" criterion.
definition: Mereological Sum of multiple grains of the same sort without clear identity and unity criteria. Whether or not the grains are considered of the same sort depends on the view. Therefore this class does not really make a clear categorial distinction, because all matter can be described as a collection of atoms. As a consequence, these classes are not fully defined.

compound
type: Class
subclass of: material object

compound of collective material entities
type: Class
equivalent class: Class
  intersection of: compound
  intersection of: Restriction
    on property: has component part
    all values from: collective material entity
subclass of: compound
disjoint with: plurality of organisms
definition: Composition of different kinds of collections without clear unity and identity criteria. Old name: compound of collections. Practically all naturally occurring substances are of this sort. The different compounds are also called fractions

condition
type: Class
equivalent class: Class
  union of: disposition
  union of: function
  union of: material object
  union of: process
subclass of: Thing
definition: Union of material entity, process, or disposition. The rationale of this class is to represent the ambiguous nature of what is commonly referred to by health-related condition (not necessarily pathologic)

disposition
type: Class
subclass of: particular
subclass of: Restriction
  on property: has realization
  all values from: process
subclass of: Restriction
  on property: is part of
  all values from: disposition
subclass of: Restriction
  on property: has part
  all values from: disposition
definition: A disposition is a realizable entity. Its manifestation is a process its bearer is involved in virtue of the bearer's physical make-up.

entity at some time
type: Class
subclass of: Thing
subclass of: Class
  complement of: temporal region
subclass of: Class
  complement of: process
definition: A temporally qualified continuant is the temporal snapshot of a temporally extended object

function
type: Class
subclass of: particular
subclass of: Restriction
  on property: has part
  all values from: function
subclass of: Restriction
  on property: is part of
  all values from: function
definition: A classical definition of function according to Wright is that the function F of X is Z means that X is there because it Zs, and Z is a consequence of X being there. For artefacts, functions are distinguished from dispositions by the purpose they have been built. For example, a hammer has the function to drive in nails, but not to be used as a weapon. However, it has the disposition to be used as a weapon under certain circumstances. For biological objects, which developed by evolution, the definition of function is still subject to controversy (e.g. Barry Smith's view of function as pertaining to a canonical life plan, cf. http://www.slideserve.com/presentation/103450/The-Canonical-Life). In BFO "Disposition" and "Function" are siblings, in BioTop Function is more specific.

immaterial object
type: Class
subclass of: particular
subclass of: Restriction
  on property: is part of
  all values from: Class
    intersection of: entity at some time
    intersection of: Class
      union of: immaterial object
      union of: material object
subclass of: Restriction
  on property: includes
  all values from: entity at some time
subclass of: Class
  complement of: Restriction
    on property: is bearer of
    some values from: physical mass
subclass of: Restriction
  on property: has part
  all values from: Class
    intersection of: entity at some time
    intersection of: immaterial object
prior version: immaterial physical entity
definition: Physical spaces that have a threedimensional spatial dimension but no mass. Old name: immaterial anatomical entity

immaterial three dimensional physical entity
type: Class
subclass of: immaterial object
definition: three-dimensional space

information object
type: Class
subclass of: particular
subclass of: Restriction
  on property: has part
  all values from: information object
subclass of: Class
  complement of: Restriction
    on property: is bearer of
    some values from: physical mass
subclass of: Restriction
  on property: is part of
  all values from: information object
subclass of: Restriction
  on property: is included in
  all values from: Class
    union of: information object
    union of: material object
subclass of: Class
  complement of: Restriction
    on property: is bearer of
    some values from: physical volume
definition: Piece of information (not necessarily human) , as it exists independently of any potential material carrier.

instantaneus process
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: projects onto
    all values from: point in time
definition: What happens at one point in time, typically a process boundary

life
type: Class
subclass of: process
definition: The whole process which is characterized by the existence of a physical entity. E.g. the life process of an orgamism perdures as long as this entity exists. The life lx of the continuant entity x does not have any process segment which does not x as participant.

material object
type: Class
subclass of: particular
subclass of: Restriction
  on property: is bearer of
  all values from: Class
    union of: disposition
    union of: information object
    union of: object quality
    union of: role
subclass of: Restriction
  on property: includes
  all values from: entity at some time
subclass of: Restriction
  on property: includes
  all values from: Class
    union of: disposition
    union of: immaterial object
    union of: information object
    union of: material object
    union of: quality
    union of: role
subclass of: Restriction
  on property: is included in
  all values from: entity at some time
subclass of: Restriction
  on property: has granular part
  all values from: material object
subclass of: Restriction
  on property: has component part
  all values from: material object
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

mono molecular entity
type: Class
subclass of: compound
definition: A mono-molecular entity is a self connected compound of two atoms or more which exhibit at least one covalent bound. Molecular entities can be isolated molecules or parts of molecules (groups, residue). They may be electrically neutral or not. In biological systems molecular entities generally occur in very high quantities. In text, references to chemicals are often ambiguous. When we state "water has a molecular weight of 18" we refer to single water molecules. However, saying that "water has a density of 1kg/dm³" under certain conditions then we make a statement about pluralities of water molecules each of which has water molecules as "grains" Old name: molecular entity The upper bound of monomolecular entities is shallow. Strictly even a diamond crystal would be a monomolecular entity. One argument against this idea is that a diamond crystal is still a diamond crystal if you take away some portions. This is not the case with a classical molecule.

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

object quality
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  all values from: Class
    union of: immaterial object
    union of: material object
disjoint with: process quality
definition: quality that inheres in an object

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

one dimensional physical entity
type: Class
subclass of: immaterial object
definition: line or curve

organism
type: Class
subclass of: structured biological entity
definition: Entire autonomous biological structure.
see also: FMAID:256135 Body

organism part
type: Class
subclass of: structured biological entity
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.

particular
type: Class
definition: From an universalist point of view most BioTop classes can be considered the extension of universals. However, BioTop does not claim that all of its classes are the extension of universals and is agnostic with regard to the existence of universals and the delineation between universals and non-universals.

physical boundary
type: Class
subclass of: immaterial object
subclass of: Restriction
  on property: is boundary of
  all values from: Class
    union of: immaterial object
    union of: material object
definition: A independent physical entity that bounds or demarcates some other physical entity. Commonly viewed as a lower-dimensional part, the the notion of physical boundary here also encompasses ill-delimited spaces that fulfill the same function, e.g. biological joints.

physical force
type: Class
subclass of: process quality
definition: force as defined by physics (mass + acceleration)

physical length
type: Class
subclass of: object quality
definition: physical length (e.g. in meters)

physical mass
type: Class
subclass of: object quality
subclass of: Restriction
  on property: inheres in
  all values from: material object
definition: Mass (gravity independent) - not weight. Measured in g, kg, ...

physical volume
type: Class
subclass of: object quality
definition: Volume of three-dimensional objects - third potency of length

plan
type: Class
subclass of: information object
subclass of: Restriction
  on property: represents
  all values from: process
definition: A plan is a series of steps to be carried out in order to achiev a goal. Plans can only be realized by processes

plan execution
type: Class
subclass of: Class
  intersection of: action
  intersection of: Restriction
    on property: has outcome
    some values from: process
  intersection of: Restriction
    on property: has patient
    some values from: plan

plurality of organisms
type: Class
subclass of: collective material entity
subclass of: Restriction
  on property: has granular part
  all values from: organism
definition: Collection of two or more organisms of the same sort.

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

poly molecular composite entity
type: Class
subclass of: compound
definition: An object which contains several molecules, has direct parts (components) of different types and which changes its ontological nature if subdivided. It must have clear unity and identity criteria.

process
type: Class
subclass of: particular
subclass of: Restriction
  on property: projects onto
  all values from: temporal region
subclass of: Restriction
  on property: projects onto
  some values from: temporal region
subclass of: Restriction
  on property: is part of
  all values from: process
subclass of: Restriction
  on property: includes
  all values from: Class
    union of: process
    union of: process quality
subclass of: Restriction
  on property: has participant
  some values from: Thing
subclass of: Restriction
  on property: has part
  all values from: process
subclass of: Restriction
  on property: is bearer of
  all values from: process quality
subclass of: Restriction
  on property: realization of
  all values from: disposition
prior version: processual entity
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.

process quality
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: inheres in
    some values from: process
subclass of: Restriction
  on property: inheres in
  all values from: process
definition: quality that inheres in a process

quality
type: Class
subclass of: particular
subclass of: Restriction
  on property: has part
  all values from: quality
subclass of: Restriction
  on property: is included in
  all values from: Class
    union of: immaterial object
    union of: material object
    union of: process
    union of: quality
subclass of: Restriction
  on property: projects onto
  all values from: value region
subclass of: Restriction
  on property: is part of
  all values from: quality
definition: A quality is a dependent entity that is exhibited if it inheres in some other entity or entities at all.

role
type: Class
subclass of: particular
subclass of: Restriction
  on property: has part
  all values from: role
subclass of: Restriction
  on property: is part of
  all values from: role
definition: A role is a realizable entity the manifestation of which brings about some result or end that is not essential to its bearer in virtue of the kind of thing that it is, but that can be served or participated in by that kind of continuant entity in some kinds of natural, social or institutional contexts.

structured biological entity
type: Class
subclass of: poly molecular composite entity
subclass of: Restriction
  on property: at some time
  some values from: Restriction
    on property: is part of
    some values from: organism
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

taxon quality
type: Class
subclass of: object quality
subclass of: Restriction
  on property: projects onto
  all values from: taxon value region
definition: The quality of one or more biological organisms, as well as of parts of organism of partaining to a biological taxon. [steschu20080127]

taxon value region
type: Class
subclass of: value region
subclass of: Restriction
  on property: is projection of
  all values from: taxon quality
definition: abstract region in which the values of biological taxa are located (cf. Schulz et.al ISMB 2008). Biological taxa can be ascribed not only to organisms but also to ogranism parts, derivates, as well as populations.

temporal region
type: Class
subclass of: particular
subclass of: Restriction
  on property: has part
  all values from: temporal region
subclass of: Restriction
  on property: is part of
  all values from: temporal region
prior version: temporal entity, time
definition: Point or interval on the time axis

time interval
type: Class
subclass of: temporal region
definition: the interval between two time points

two dimensional physical entity
type: Class
subclass of: immaterial object
definition: plane

value region
type: Class
subclass of: particular
subclass of: Restriction
  on property: is projection of
  all values from: quality
subclass of: Restriction
  on property: includes
  all values from: quality
definition: A value region is an abstract region in which (non quantitative) values of qualities are located.

wave
type: Class
subclass of: immaterial object
definition: (wikipedia) disturbance that propagates through space and time, usually with transference of energy