definition
editor note
alternative term
editor preferred term
example of usage
part of
Intended meaning: Ambiguous between continuant-parthood and occurrent-parthood. domain: continuant range: continuant time: at some time domain: occurrent range: occurrent time: atemporal
Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell.
part_of
has part
has_part
inheres in
Intended meaning: domain: specifically dependent continuant range: independent continuant time: at all times A specifically dependent continuant A inheres in its independent continuant B at all times during which A exists.
inheres_in
bearer of
Intended meaning: domain: independent continuant range: specifically dependent continuant time: at some time
bearer_of
is bearer of
realized in
Intended meaning: domain: realizable entity range: processual entity time: atemporal
is realized by
realized_in
realizes
Intended meaning: domain: processual entity range: realizable entity time: atemporal
participates in
Intended meaning: domain: continuant and (not spatial region) range: processual entity time: at some time
participates_in
has participant
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
Intended meaning: domain: processual entity range: continuant and (not spatial region) time: at some time
has_participant
concretized by
Intended meaning: domain: generically dependent continuant range: specifically dependent continuant time: at some time
concretized_by
is concretized by
concretizes
Intended meaning: domain: specifically dependent continuant range: generically dependent continuant time: at some time
is concretization of
preceded by
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
Intended meaning: domain: occurrent range: occurrent time: atemporal
is preceded by
preceded_by
precedes
occurs in
Intended meaning: domain: occurrent range: independent continuant time: atemporal
occurs_in
unfolds in
unfolds_in
function of
Intended meaning: domain: function range: independent continuant time: at all times
function_of
quality of
Intended meaning: domain: quality range: independent continuant time: at all times
quality_of
role of
Intended meaning: domain: role range: independent continuant time: at all times
role_of
has function
Intended meaning: domain: independent continuant range: function time: at some time
has_function
has quality
Intended meaning: domain: independent continuant range: quality time: at some time
has_quality
has role
Intended meaning: domain: independent continuant range: role time: at some time
has_role
disposition of
Intended meaning: domain: disposition range: independent continuant time: at all times
disposition_of
has disposition
Intended meaning: domain: independent continuant range: disposition time: at some time
has_disposition
adjacent to
Intended meaning: domain: independent continuant range: independent continuant time: at some time
Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum
adjacent_to
is adjacent to
derives from
Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants 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 continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.
Intended meaning: domain: material entity range: material entity time: atemporal
derives_from
derived into
derived_into
has agent
has_agent
agent in
agent_in
integral part of
integral_part_of
has integral part
has_integral_part
location of
Intended meaning: domain: spatial region range: continuant time: at some time
location_of
proper part of
proper_part_of
has proper part
has_proper_part
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) time: at some time
contained_in
contains
Intended meaning: domain: spatial region or site (immaterial continuant) range: material entity time: at some time
transformation of
When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.
transformation_of
transformed into
Obsolete in OBO_REL.
has improper part
Ambiguous between continuant-parthood and occurrent-parthood. domain: continuant range: continuant time: at some time domain: occurrent range: occurrent time: atemporal
OBSOLETE: See reasons for obsoletion of improper_part_of.
has_improper_part
improper part of
OBSOLETE. The definition is "As for part_of, with the additional constraint that subject and object may be identical". However, part_of is already reflexive, therefore improper_part_of is identical to part_of. If read differently, as "improper_part_of is part_of but not proper_part_of",improper_part_of becomes identity. So, improper_part_of is either identical to part_of or to identity, and not an intuitive synonym for either of them. [Robert Hoehndorf]
improper_part_of
relationship
located in
Intended meaning: domain: continuant range: spatial region time: at some time
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
located_in
entity
continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
a heart
a person
a symphony orchestra
endurant
the color of a tomato
the disposition of blood to coagulate
the lawn and atmosphere in front of our building
the mass of a cloud
occurrent
An entity that has temporal parts and that happens, unfolds or develops through time.
a surgical operation as processual context for a nosocomical infection
perdurant
the life of an organism
the most interesting part of Van Gogh's life
the spatiotemporal context occupied by a process of cellular meiosis
the spatiotemporal region occupied by the development of a cancer tumor
independent continuant
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
a chair
a leg
an organism
substantial entity
the bottom right portion of a human torso
dependent continuant
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
spatial region
A continuant that is neither bearer of quality entities nor inheres in any other entities.
All instances of continuant are spatial entities, that is, they enter in the relation of (spatial) location with spatial region entities. As a particular case, the exact spatial location of a spatial region is this region itself.
An instance of spatial region is a part of space. All parts of space are spatial region entities and only spatial region entities are parts of space. Space is the entire extent of the spatial universe, a designated individual, which is thus itself a spatial region.
Comment: Space and spatial region entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called "absolutist" or "the container view". In BFO, the class site allows for a so-called relational view of space, that is to say, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site are not spatial region entities, they are nevertheless spatial entities.
parts of the sum total of all space in the universe
spatial_region
the sum total of all space in the universe
processual entity
A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
process
the process of cell-division
the process of sleeping
temporal region
All instances of occurrent are temporal entities, that is, they enter in the relation of (temporal) location with temporal region entities. As a particular case, the exact spatiotemporal location of a temporal region is this region itself. Continuant entities are not temporal entities in the technical sense just explained; they are related to time in a different way, not through temporal location but through a relation of existence at a time or during a period of time (see continuant).
An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe, a designated individual, which is thus a temporal region itself.
An occurrent that is part of time.
Time and temporal region entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called "absolutist" or "the container view" in analogy to what is traditionally the case with space (see spatial region).
the duration of a surgical procedure
the moment of death
the time it takes to run a marathon
two dimensional region
A spatial region with two dimensions.
the surface of a cube-shaped part of space
the surface of a rectilinear planar figure-shaped part of space
the surface of a sphere-shaped part of space
two_dimensional_region
scattered spatiotemporal region
A spatiotemporal region that has spatial and temporal dimensions and every spatial and temporal point of which is not connected with every other spatial and temporal point of which.
the space and time occupied by the individual games of the World Cup
the space and time occupied by the individual liaisons in a romantic affair
spatiotemporal region
All instances of occurrent are spatiotemporal entities, that is, they enter in the relation of (spatiotemporal) location with spatiotemporal region entities. As a particular case, the exact spatiotemporal location of a spatiotemporal region is this region itself.
An occurrent at or in which processual entity entities can be located.
Spacetime and spatiotemporal region entities are entities in their own rights which exist independently of any entities which can be located at them. This view of spacetime can be called "absolutist" or "the container view". In BFO, the class processual context allows for a so-called relational view of spacetime, that is to say, a view according to which spatiotemporality is a matter of relative location between entities and not a matter of being tied to spacetime. In BFO, the bridge between these two views is secured through the fact that instances of processual context are too spatiotemporal entities.
the spatiotemporal region occupied by a human life
spatiotemporal instant
A connected spatiotemporal region at a specific moment.
the spatiotemporal region occupied by a single instantaneous temporal slice (part) of a process
connected spatiotemporal region
A spatiotemporal region that has temporal and spatial dimensions such that all points within the spatiotemporal region are mediately or immediately connected to all other points within the same spatiotemporal region.
the spatial and temporal location of an individual organism's life
the spatial and temporal location of the development of a fetus
process aggregate
A processual entity that is a mereological sum of process entities and possesses non-connected boundaries.
a process of digestion and a process of thinking taken together
the beating of the hearts of each of seven individuals in the room
the playing of each of the members of an orchestra
disposition
A realizable entity that essentially causes a specific process or transformation in the object in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object) has the disposition D to (transform, initiate a process) R under conditions C.
the disposition of a patient with a weakened immune system to contract disease
the disposition of a vase to brake if dropped
the disposition of metal to conduct electricity
the disposition of vegetables to decay when not refrigerated
realizable entity
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
If a realizable entity inheres in a continuant, this does not imply that it is actually realized.
the function of the reproductive organs
the role of being a doctor
zero dimensional region
A spatial region with no dimensions.
a point
zero_dimensional_region
quality
A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property).
the ambient temperature of air
the circumference of a waist
the mass of a piece of gold
the shape of a nose
the weight of a chimpanzee
specifically dependent continuant
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
mode
property
the disposition of fish to decay
the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
the liquidity of blood
the smell of mozzarella
trope
temporal instant
A connected temporal region comprising a single moment of time.
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
connected temporal region
A temporal region every point of which is mediately or immediately connected with every other point of which.
the 1970s years
the time from the beginning to the end of a heart attack
the time taken up by cellular meiosis
role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
the role of a biological grandfather as legal guardian in the context of a system of laws
the role of a chemical compound in an experiment
the role of a patient relative as defined by a hospital administrative form
the role of a person as a surgeon
the role of a student in a university
the role of a woman as a legal mother in the context of system of laws
the role of ingested matter in digestion
fiat object part
A material entity that is part of an object but is not demarcated by any physical discontinuities.
fiat substance part
the dorsal and ventral surfaces of the body
the east side of Saarbruecken
the lower right portion of a human torso
upper and lower lobes of the left lung
object boundary
An independent continuant that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object entities that exist at exactly the point where the object is separated off from the rest of the existing entities in the world.
Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.
substance boundary
the outer surface of a cell or cell wall
the surface of the earth
the surface of the interior of the stomach
the surface of the skin
one dimensional region
A spatial region with one dimension.
an edge of a cube-shaped part of space
one_dimensional_region
the part of space that is a line stretching from one end of absolute space to the other
object aggregate
A material entity that is a mereological sum of separate object entities and possesses non-connected boundaries.
a collection of random bacteria
a flock of geese
a group of commuters on the subway
a heap of stones
substance aggregate
the patients in a hospital
three dimensional region
A spatial region with three dimensions.
a cube-shaped part of space
a sphere-shaped part of space
three_dimensional_region
site
An independent continuant consisting of a characteristic spatial shape in relation to some arrangement of other continuant entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site entities are entities that can be occupied by other continuant entities.
An instance of Site is a mixture of independent continuant entities which act as surrounding environments for other independent continuant entities, most importantly for instances of object. A site is typically made of object or fiat object part entities and a surrounding medium in which is found an object occupying the site. Independent continuant entities may be associated with others (which, then, are sites) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site entities are not to be confused with spatial region entities. In BFO, site allows for a so-called relational view of space which is different from the view corresponding to the class spatial region (see the comment on this class).
Maria's nostril or her intestines for a variety of bacteria
a particular room in a particular hospital
object
A material entity that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object entities is independent of that of other entities and can be maintained through time.
a lung
an apple
substance
generically dependent continuant
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
a certain PDF file that exists in different and in several hard drives
scattered temporal region
A temporal region every point of which is not mediately or immediately connected with every other point of which.
the time occupied by the individual games of the World Cup
the time occupied by the individual liaisons in a romantic affair
fiat process part
A processual entity that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities.
chewing during a meal
the middle part of a rainstorm
the worst part of a heart-attack
function
A realizable entity the manifestation of which is an essentially end-directed activity of a continuant entity in virtue of that continuant entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
the digestive function of the stomach to nutriate the body
the function of a birth canal to enable transport
the function of a computer program to compute mathematical equations
the function of a hammer to drive in nails
the function of a judge in a court of law
the function of an automobile to provide transportation
the function of reproduction in the transmission of genetic material
process boundary
A processual entity that is the fiat or bona fide instantaneous temporal process boundary.
birth
death
the detaching of a finger in an industrial accident
the final separation of two cells at the end of cell-division
the forming of a synapse
the incision at the beginning of a surgery
the onset of REM sleep
spatiotemporal interval
A connected spatiotemporal region that endures for more than a single moment of time.
the spatiotemporal region occupied by a process or by a fiat processual part
temporal interval
A connected temporal region lasting for more than a single moment of time.
any continuous temporal duration during which a process occurs
material entity
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
Material entity subsumes object, fiat object part, and object aggregate, which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
collection of random bacteria
dorsal surface of the body
processual context
An instance of a processual context is a mixture of processual entity which stand as surrounding environments for other processual entity entities. The class processual context is the analogous among occurrent entities to the class site among continuant entities.
An occurrent consisting of a characteristic spatial shape inhering in some arrangement of other occurrent entities. Processual context entities are characteristically entities at or in which other occurrent entities can be located or occur.
The processual context for a given manipulation occurring as part of an experiment is made of processual entities which occur in parallel, are not necessarily all parts of the experiment themselves and may involve continuant [snap:Continuant] entities which are in the spatial vicinity of the participants in the experiment.