AFO Foundational Ontology
type: Ontology
version info: TODO: Restrictions for precedes / preceded_by?
version info: TODO: Which relation should be used between a region and an object? contained_in?
version info: TODO: rdfs:comments for all properties.
creator: Matthias Samwald
comment: Design goals of the AFO: * Granularity independence. * Ability to fully represent time in standard OWL through "full temporary parts" of physical objects ('4D view'). * Best possible interoperability with BFO and ontologies based on BFO without introduction of logical inconsistencies. * Direct integration of the OBO Relation Ontology into AFO and best possible interoperability with ontologies that are based on the OBO Relation Ontology. * A generic transitive property called ("has part (etc.)" that is a superclass of all properties that imply parthood and containment between objects and processes. * Focus on the most basic useful ontological constructs and distinctions. * Defined deadline for ontology modifications: full stability of ontology structure and namespace after September 15, 2007.
comment: Note: Some relations have been added under the obofoundry RO namespace that are not currently part of the original RO ontology (e.g. "has_function"). It is expected that these relations will be added to the original RO ontology in the future.
version info: TODO: space-time-region migth be replaced with the corresponding class from BFO if this is deemed consistent.
date: 2007
comment: created by Matthias Samwald

Disposition, function, role
type: Class
disjoint with: Physical quality
comment: Examples: the role of being a doctor, the function of the reproductive organs, the disposition of blood to coagulate, the disposition of metal to conduct electricity
disjoint with: Physical object, part of physical object, aggregate of physical objects, site
disjoint with: Information content entity
disjoint with: Digital entity
disjoint with: Process, arbitrary part of process, aggregate of processes, processual context
subclass of: Restriction
  all values from: Process, arbitrary part of process, aggregate of processes, processual context
  on property: realized as
subclass of: Thing
disjoint with: Space-time region

Physical quality
type: Class
disjoint with: Digital entity
disjoint with: Information content entity
disjoint with: Space-time region
subclass of: Restriction
  all values from: Class
    union of: Physical object, part of physical object, aggregate of physical objects, site
    union of: Process, arbitrary part of process, aggregate of processes, processual context
  on property: towards
comment: "Examples: the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee" (from the definition of BFO).
subclass of: Restriction
  on property: inheres in
  all values from: Class
    union of: Physical object, part of physical object, aggregate of physical objects, site
    union of: Process, arbitrary part of process, aggregate of processes, processual context
    union of: Space-time region
disjoint with: Process, arbitrary part of process, aggregate of processes, processual context
disjoint with: Physical object, part of physical object, aggregate of physical objects, site
subclass of: Thing
disjoint with: Disposition, function, role

Physical object, part of physical object, aggregate of physical objects, site
type: Class
subclass of: Restriction
  all values from: Physical object, part of physical object, aggregate of physical objects, site
  on property: derives from
subclass of: Thing
disjoint with: Information content entity
subclass of: Restriction
  on property: location of
  all values from: Physical object, part of physical object, aggregate of physical objects, site
disjoint with: Space-time region
disjoint with: Digital entity
subclass of: Restriction
  all values from: Class
  on property: preceded by (etc.)
subclass of: Restriction
  some values from: Space-time region
  on property: part of (etc.)
subclass of: Restriction
  all values from: Physical object, part of physical object, aggregate of physical objects, site
  on property: derived into
subclass of: Restriction
  all values from: Space-time region
  on property: contained in
subclass of: Restriction
  on property: transformation of
  all values from: Physical object, part of physical object, aggregate of physical objects, site
subclass of: Restriction
  on property: part of (etc.)
  all values from: Class
disjoint with: Physical quality
subclass of: Class
  complement of: Restriction
    some values from: Thing
    on property: has participant
disjoint with: Process, arbitrary part of process, aggregate of processes, processual context
subclass of: Restriction
  all values from: Class
    union of: Physical quality
    union of: Disposition, function, role
  on property: bearer of quality, disposition, role or function
subclass of: Restriction
  on property: located in
  all values from: Physical object, part of physical object, aggregate of physical objects, site
subclass of: Restriction
  all values from: Class
  on property: precedes (etc.)
disjoint with: Disposition, function, role
subclass of: Restriction
  all values from: Physical object, part of physical object, aggregate of physical objects, site
  on property: adjacent to
subclass of: Restriction
  all values from: Physical object, part of physical object, aggregate of physical objects, site
  on property: transforms into
comment: Examples for objects: "an organism, a heart, a chair, a lung, an apple" Examples for aggregates of objects: "a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital" Examples of arbitrary parts of objects: "upper and lower lobes of the left lung, the dorsal and ventral surfaces of the body, the east side of Saarbruecken, the lower right portion of a human torso" Examples of sites: "a city, a nasal cavity, a blood vein, an environment, sinuses, canals, ventricles, the lumen of the gastrointestinal tract, the location of the battle of Austerlitz, the interior of the aorta, the room in which one is located, the top of one's desk including the things that are on it and the atmosphere surrounding them" (examples from the definition of BFO) NOTE: contrary to BFO, objects in AFO can have temporal parts
subclass of: Restriction
  all values from: Class
    union of: Physical object, part of physical object, aggregate of physical objects, site
    union of: Process, arbitrary part of process, aggregate of processes, processual context
  on property: has part (etc.)
subclass of: Restriction
  all values from: Process, arbitrary part of process, aggregate of processes, processual context
  on property: participates in

Information content entity
type: Class
disjoint with: Disposition, function, role
disjoint with: Physical object, part of physical object, aggregate of physical objects, site
disjoint with: Physical quality
disjoint with: Process, arbitrary part of process, aggregate of processes, processual context
disjoint with: Space-time region
disjoint with: Digital entity

Digital entity
type: Class
disjoint with: Physical quality
disjoint with: Process, arbitrary part of process, aggregate of processes, processual context
disjoint with: Disposition, function, role
disjoint with: Physical object, part of physical object, aggregate of physical objects, site
disjoint with: Space-time region
disjoint with: Information content entity
comment: Two digital entities are the same if they are bite-wise identical.

Process, arbitrary part of process, aggregate of processes, processual context
type: Class
subclass of: Restriction
  all values from: Physical quality
  on property: bearer of quality, disposition, role or function
subclass of: Restriction
  all values from: Class
  on property: precedes (etc.)
subclass of: Restriction
  all values from: Class
    union of: Physical object, part of physical object, aggregate of physical objects, site
    union of: Process, arbitrary part of process, aggregate of processes, processual context
  on property: regulated by
disjoint with: Disposition, function, role
subclass of: Restriction
  on property: precedes
  all values from: Process, arbitrary part of process, aggregate of processes, processual context
disjoint with: Physical quality
subclass of: Restriction
  on property: preceded by
  all values from: Process, arbitrary part of process, aggregate of processes, processual context
disjoint with: Physical object, part of physical object, aggregate of physical objects, site
subclass of: Restriction
  on property: has part
  all values from: Process, arbitrary part of process, aggregate of processes, processual context
subclass of: Restriction
  on property: has part (etc.)
  all values from: Class
    union of: Physical object, part of physical object, aggregate of physical objects, site
    union of: Process, arbitrary part of process, aggregate of processes, processual context
disjoint with: Space-time region
disjoint with: Information content entity
subclass of: Restriction
  all values from: Process, arbitrary part of process, aggregate of processes, processual context
  on property: regulates
subclass of: Restriction
  on property: has participant
  all values from: Physical object, part of physical object, aggregate of physical objects, site
subclass of: Restriction
  all values from: Class
  on property: preceded by (etc.)
comment: Examples of processes: "the life of an organism, the process of sleeping, the process of cell-division" Examples of arbitrary parts of processes: "chewing during a meal, the middle part of a rainstorm, the worst part of a heart-attack, the most interesting part of Van Gogh's life" Examples of aggregates of processes: "the beating of the hearts of each of seven individuals in the room, the playing of each of the members of an orchestra, a process of digestion and a process of thinking taken together" Examples of processual contexts: "a surgical operation as processual context for a nosocomical infection, a routine check-up as processual context for the finding of a tumor, a clinical trial as processual context for the discovery of a new treatment or drug" (from the definition of BFO)
disjoint with: Digital entity
subclass of: Thing

realized as
type: ObjectProperty
inverse of: realization of

Space-time region
type: Class
disjoint with: Physical quality
disjoint with: Physical object, part of physical object, aggregate of physical objects, site
subclass of: Restriction
  all values from: Class
    union of: Physical object, part of physical object, aggregate of physical objects, site
    union of: Process, arbitrary part of process, aggregate of processes, processual context
    union of: Space-time region
  on property: precedes (etc.)
disjoint with: Disposition, function, role
disjoint with: Digital entity
subclass of: Restriction
  on property: preceded by (etc.)
  all values from: Class
    union of: Physical object, part of physical object, aggregate of physical objects, site
    union of: Process, arbitrary part of process, aggregate of processes, processual context
    union of: Space-time region
comment: A region (or regions) of space during a certain timespan (or certain timespans). There is no requirement for spatial or temporal connectedness, i.e., a space-time-region can be made up of several, non-connected space-time-regions; and it can exist at several, non-connected time spans.
disjoint with: Process, arbitrary part of process, aggregate of processes, processual context
subclass of: Restriction
  all values from: Class
    union of: Physical object, part of physical object, aggregate of physical objects, site
    union of: Process, arbitrary part of process, aggregate of processes, processual context
    union of: Space-time region
  on property: has part (etc.)
subclass of: Thing
disjoint with: Information content entity

bearer of quality, disposition, role or function
type: ObjectProperty
inverse of: inheres in

precedes (etc.)
type: ObjectProperty
comment: " <precedes (etc.)> " means that the end of the existance of A precedes the start of the existance of . and can be processes, objects or space-time regions.
inverse of: preceded by (etc.)

regulated by
type: ObjectProperty
inverse of: regulates

precedes
type: TransitiveProperty
sub property of: precedes (etc.)
type: ObjectProperty
inverse of: preceded by
comment: " <precedes> " means that the end of the existance of A precedes the start of the existance of . and have to be processes.
range: Process, arbitrary part of process, aggregate of processes, processual context
domain: Process, arbitrary part of process, aggregate of processes, processual context

preceded by
type: TransitiveProperty
inverse of: precedes
type: ObjectProperty
domain: Process, arbitrary part of process, aggregate of processes, processual context
range: Process, arbitrary part of process, aggregate of processes, processual context
sub property of: preceded by (etc.)

has part
type: TransitiveProperty
sub property of: has part (etc.)
type: ObjectProperty
inverse of: part of

has part (etc.)
type: TransitiveProperty
comment: A relationship that unifies several similar relationships into one: "has part", "has participant", "contains", "has agent", and "location of". Note: "<object123 > <has part (etc.)> <a process123>" means that some (or all) parts of object123 participate in process123.
type: ObjectProperty
inverse of: part of (etc.)

regulates
type: ObjectProperty
inverse of: regulated by

has participant
type: ObjectProperty
sub property of: has part (etc.)
inverse of: participates in

preceded by (etc.)
type: ObjectProperty
inverse of: precedes (etc.)

towards
type: ObjectProperty
comment: TODO: OBOL namespace?
comment: A relation between a relational quality and an entity.

inheres in
type: ObjectProperty
inverse of: bearer of quality, disposition, role or function

derives from
type: TransitiveProperty
type: ObjectProperty
inverse of: derived into

location of
type: TransitiveProperty
inverse of: located in
sub property of: has part (etc.)
type: ObjectProperty

part of (etc.)
type: TransitiveProperty
type: ObjectProperty
inverse of: has part (etc.)

derived into
type: TransitiveProperty
type: ObjectProperty
inverse of: derives from

contained in
type: ObjectProperty
sub property of: part of (etc.)
inverse of: contains

transformation of
type: TransitiveProperty
inverse of: transforms into
type: ObjectProperty

located in
type: TransitiveProperty
sub property of: part of (etc.)
inverse of: location of
type: ObjectProperty

adjacent to
type: SymmetricProperty
type: ObjectProperty

transforms into
type: ObjectProperty
inverse of: transformation of

participates in
type: ObjectProperty
sub property of: part of (etc.)
inverse of: has participant

contains
type: ObjectProperty
inverse of: contained in
sub property of: has part (etc.)

has exemplary spatial part
type: ObjectProperty
sub property of: has exemplary part
sub property of: has constant spatial part
comment: " <has exemplary spatial part> " means that does not only have as a spatial part, but also many additional entities which have a high similarity with . We do not formalize which criteria need to be met for an entity to be 'similar' in this meaning, or which quantity constitues 'many entities'.
comment: Examples: * <a liver> <has exemplary spatial part> <a liver cell> * <a crowd of people> <has exemplary spatial part> <a Person> * <water in a bottle> <has exemplary spatial part> <a water molecule>
inverse of: exemplary spatial part of

has exemplary part
type: ObjectProperty
comment: " <has exemplary part> " means that does not only have as a part, but also many additional entities which have a high similarity with . We do not formalize which criteria need to be met for an entity to be 'similar' in this meaning, or which quantity constitues 'many entities'.
comment: Examples: * <Applause of the audience> <has exemplary part> <handclap>
inverse of: exemplary part of
sub property of: has part

has constant spatial part
type: TransitiveProperty
sub property of: has part
type: ObjectProperty
inverse of: constant spatial part of

exemplary spatial part of
type: ObjectProperty
inverse of: has exemplary spatial part
sub property of: exemplary part of
sub property of: constant spatial part of

has exemplary full temporal part
type: ObjectProperty
comment: " <has exemplary full temporal part> " means that does not only have as a full temporal part, but also many additional entities which have a high similarity with . We do not formalize which criteria need to be met for an entity to be 'similar' in this meaning, or which quantity constitues 'many entities'.
comment: Examples: * <Heart> <has exemplary full temporal part> <Heart during contraction>
sub property of: has exemplary part
sub property of: has full temporal part
inverse of: exemplary temporal part of

has full temporal part
type: TransitiveProperty
sub property of: has part
comment: " <has temporal part> " means that B refers to A at a certain time interval (or at several certain time intervals). The duration of is therefore smaller or equivalent to the duration of . During its existence is made up of ALL the matter of . does not need to be temporally connected, i.e. it can exist in many, non-continuous time intervals that are separated by time intervals where does not exist.
comment: Examples: * <Pop concert> <has temporal part> <first song> * <John Doe> <has temporal part> <John Doe at the age between 15 and 20 years> * <Vienna> <has temporal part> <Vienna in each winter>
inverse of: full temporal part of
type: ObjectProperty

exemplary temporal part of
type: ObjectProperty
sub property of: exemplary part of
sub property of: full temporal part of
inverse of: has exemplary full temporal part

exemplary participant of
type: ObjectProperty
sub property of: participates in
inverse of: has exemplary participant

has exemplary participant
type: ObjectProperty
inverse of: exemplary participant of
comment: " <has exemplary participant> " means that does not only have as a participant, but also many additional entities which have a high similarity with . We do not formalize which criteria need to be met for an entity to be 'similar' in this meaning, or which quantity constitues 'many entities'. Example: * <New York Marathon> <has exemplary participant> <John Doe>
sub property of: has participant

exemplary part of
type: ObjectProperty
sub property of: part of
inverse of: has exemplary part

constant spatial part of
type: TransitiveProperty
inverse of: has constant spatial part
type: ObjectProperty
sub property of: part of

part of
type: TransitiveProperty
inverse of: has part
sub property of: part of (etc.)
type: ObjectProperty

agent in
type: ObjectProperty
inverse of: has agent
sub property of: participates in

has agent
type: ObjectProperty
inverse of: agent in
sub property of: has participant

has topic
type: ObjectProperty
inverse of: is topic of

is topic of
type: ObjectProperty
inverse of: has topic

realization of
type: ObjectProperty
inverse of: realized as

full temporal part of
type: TransitiveProperty
sub property of: part of
type: ObjectProperty
inverse of: has full temporal part

has primary topic
type: FunctionalProperty
inverse of: is primary topic of
sub property of: has topic
type: ObjectProperty

is primary topic of
type: InverseFunctionalProperty
type: ObjectProperty
inverse of: has primary topic
sub property of: is topic of