upper.owl
type: Ontology
comment: Double click on rdfs:comment at left This is a demonstration ontology reconstructing much of the OpenGALEN Upper Ontology in OWL-DL. Detailed comments are included with classes and properties along with demonstration notions preceded with the prefix "Probe_". The ontology is provided strictly "as is" and without guarantees. It is still in progress and will be updated from time to time. The ontology is free for use with acknowledgement to OpenGALEN and the University of Manchester. All material copyright University of Manchester. A discussion is available in "Patterns, Properties and Minimizing Commitment: Reconstruction of the GALEN Upper Ontology in OWL" Alan L Rector and Jeremy Rogers, to be presented at the Workshop on Core Ontologies (CORONT) in conjunction with the European Knowledge Acquisition Workshop (EKAW-2004), Northampton, UK. All material available from http://www.cs.man.ac.uk/~rector/ontologies/sample-top-bio/

dependence_property
type: ObjectProperty

Inverse Refining property
type: ObjectProperty
comment: See Refining Property
inverse of: Refining property

Inverse Relational property
type: ObjectProperty
comment: See Relational Property
inverse of: Relational property
domain: Self Standing Entity
range: Self Standing Entity

Refining property
type: ObjectProperty
comment: Properties linking self-standing entities to refining entities or refining entities to each other.
sub property of: dependence_property
domain: Domain Entity
range: Refining Entity

Relational property
type: ObjectProperty
comment: Properties linking self-standing entities
range: Self Standing Entity
domain: Self Standing Entity

acts on
type: ObjectProperty
comment: Acts on substrate Pumping acts_on blood.
sub property of: has participant

affects
type: ObjectProperty
comment: Subvariety of acts_on which indicates actual effect on the thing acted on - creation, modification, etc. A sub of has_locus. Otherwise, everything acted on by the process would become the locus. Counterexample - heart failure. The pumping acts on blood but is adequate. It affects circulation. This is a variant of the GALEN version which achieved many of the same effects via the propagates_via axiom.
sub property of: acts on
sub property of: has locus

has actor
type: ObjectProperty
comment: The actor in a process. If the Heart is the actor in a pathological process then it is a locus of the pathology - see Circulatory_failure_due_to_cardiac_failure
domain: Occurrent Entity
sub property of: has locus
sub property of: has participant

has agent
type: ObjectProperty
comment: Whereas actors can be either occurrents or continants. Agents - the initator, must be a continuant. Occurrents that have agents are known as Acts.
range: Potential Agent
sub property of: has actor

has discrete part
type: ObjectProperty
type: TransitiveProperty
comment: The relations between distinct things - i.e. things that have a distinct shape a well defined numbers of parts and their parts - see is_subdivision_of
sub property of: has structural part

has_clinical_part
type: ObjectProperty
type: TransitiveProperty
comment: The usual meaning of partonomy - including functional and physical partonomy but excluding membership. In general faults etc of gross parts are faults of the whole. Whereas this is not true of the more general is_part_of relation. (Known as "is_clinical_part_of" in reconstruction of GALEN)
sub property of: has part
inverse of: is_clinical_part_of

has location
type: ObjectProperty
type: TransitiveProperty
comment: Most general notion of location. Not necessarily physical NOT GALEN "hasLocation"
sub property of: Relational property

has locus
type: ObjectProperty
type: TransitiveProperty
comment: GALEN 'hasLocation' - locus of pathology. NB because of differences between sanctioning and domain/range constraints, must always ask for has_normality pathological & hasLocus...
sub property of: has location
inverse of: is locus of

has manifestation
type: ObjectProperty
comment: Relation between a pattern or agent and its manifestation. Whether agents are patterns/information or not has been left open. A subproperty of has_location because the agent is co-located with its manifestation.
range: Physical Entity
sub property of: has location
inverse of: is manifestation of
sub property of: is non physical aspect of
domain: Class
  union of: Pattern
  union of: Potential Agent

has outcome
type: ObjectProperty
version info: TODO: Consider whether to place under affects. should has_outcome be a child of has_locus.
comment: has_outcome The general outcome of an act. Should probably be a sub of affects. Still being chased.
domain: Occurrent Entity
sub property of: acts on

has participant
type: ObjectProperty
comment: Relation betwen occurrents and either continuants or other occurrents.
domain: Occurrent Entity
sub property of: Relational property

has physical location
type: ObjectProperty
type: TransitiveProperty
comment: Physical location
sub property of: has location
inverse of: is physical location of

includes
type: ObjectProperty
comment: relation between syndrome and the different pathologies. The Subproperty includes_specifically is a sub of has_locus. So in general a syndrome or "Clinical Situation" can include things which it is not a disease of - e.g. Diabetes should not be a renal or eye disease, although the total syndrome includes these things, at least as possibilities. However, in this version this broader version of includes is not used.
sub property of: has member

includes specifically
type: ObjectProperty
type: FunctionalProperty
comment: The specific version of includes which points to the causative or key pathology. Follows GALEN naming conventions. Alternatives welcome.
sub property of: has locus
sub property of: includes

is connected to
type: ObjectProperty
comment: Connection. Not symmetric in GALEN because GALEN handled symmetric properties badly.
sub property of: has physical location

is contained in
type: ObjectProperty
type: TransitiveProperty
comment: Containment. In this veresion must be contained in a cavity. This is more pedantic than GALEN. Note containment implies location but not partonomy
domain: Material Entity
inverse of: contains
sub property of: has location

is embodied as
type: ObjectProperty
comment: The relation between an agent and the physical manifestation
sub property of: is non physical aspect of

is grain of
type: ObjectProperty
type: FunctionalProperty
comment: Membership of collective. Grains of sand - beach. Molecules - substances is_grain_of is the fundamental entity for spanning levels of granularity. A grain is a
range: Collective
domain: Physical Thing
inverse of: has grain
sub property of: is member of

is_clinical_part_of
type: ObjectProperty
type: TransitiveProperty
comment: The usual meaning of partonomy - including functional and physical partonomy but excluding membership. In general faults etc of gross parts are faults of the whole. Whereas this is not true of th emore general is_part_of relation. (Known as "is_clinical_part_of" in reconstruction of GALEN)
sub property of: is part of

is in group of
type: ObjectProperty
comment: Group membership as in goose - flock of geese.
sub property of: is member of

is member of
type: ObjectProperty
comment: Membership - not standard partonomy and not included in clinical partonomy
range: Complex
sub property of: is part of

is non physical aspect of
type: ObjectProperty
comment: The top property linking non-physical to physical entities. More a convenience for organisation than a property to be used. We are agnostic about whether one non_physical entity can be linked to other non-physical entities. Hence the range is merely self-standing entity.
domain: Non Physical Entity
sub property of: Relational property
range: Self Standing Entity
inverse of: has non physical aspect

is_of
type: ObjectProperty
description: The property that links regions to the things they are regions of, and more generally modalities and related dependent notions to their kernel notions
sub property of: dependence_property
domain: Dependent Entity
range: Self Standing Entity

is outcome of
type: ObjectProperty
comment: Outcome of process. Has additional parent has_locus to get reasoning right in absence of more sophisticated rules.
range: Occurrent Entity
domain: Self Standing Entity
sub property of: has locus
inverse of: has outcome
sub property of: is acted on by

is part of
type: ObjectProperty
comment: Generic partonomy including membership.
domain: Self Standing Entity
inverse of: has part
sub property of: has physical location

is portion of
type: ObjectProperty
type: InverseFunctionalProperty
comment: The relation between two mass entities which are mixed or parts.
range: Mass Entity
domain: Mass Entity
sub property of: is structural part of

is quality of
type: ObjectProperty
type: InverseFunctionalProperty
comment: GALEN isFeatureOf Children for each quality to control cardinality. Links features to self-standing entities. Placed in this way around to make child of
domain: Quality
sub property of: Relational property
range: Self Standing Entity
inverse of: has quality

is role played by
type: ObjectProperty
comment: Link between a role and the things that play that role. In this direction to be consistent with location and manifestation
sub property of: is non physical aspect of

is structural part of
type: ObjectProperty
type: TransitiveProperty
comment: Structural partonomy not including membership. Structural partonomy in GALEN does not cross scales. The domain of of independent entity forces bunches of things, etc. to be independent even though the parent notion of bunch is not.
sub property of: is_clinical_part_of

is subdivision of
type: ObjectProperty
type: TransitiveProperty
comment: The relation between
inverse of: has subdivision
sub property of: is structural part of

occupies
type: ObjectProperty
comment: The relation of an agent to its official 'residence' or buildings which it occupies. Applies to both organisations and individuals. For an organisation, may be considered locative. However, the legal location of an organisation is a tricky matter which we defer here. Note the range is too broad, but it is easier to say any building entity than to make it more precise.
range: Building Entity
domain: Potential Agent
sub property of: Relational property
inverse of: is occupied by

owns
type: ObjectProperty
comment: Only agents can own things. Just about anything except a person can be owned. (Even a person's body, after they are dead is owned in English law, and a person owns their body and body parts under many jurisdictions before death)
domain: Potential Agent
sub property of: Relational property
range: Class
  intersection of: Self Standing Entity
  intersection of: Class
    complement of: Person

has magnitude
type: DatatypeProperty
comment: The numeric value of a quantity. Cannot have place in the hierarchy parallel to that of has_unit, because a data type property cannot be the subproperty of an object property or vice versa.
domain: Quantity
range: float

Act
type: Class
equivalent class: Class
  intersection of: Occurrent Entity
  intersection of: Restriction
    on property: has agent
    some values from: Potential Agent
comment: An occurrent that has an agent.

Activity Level
type: Class
subclass of: Quality
comment: The level of activity of a process. Amongst other statuses takes Level_adequacy_status

Afrtistic Style
type: Class
subclass of: Style

Agent
type: Class
equivalent class: Class
  intersection of: Potential Agent
  intersection of: Restriction
    on property: is agent of
    some values from: Occurrent Entity
comment: An actual agent - the agent of some real occurrent.

Aggregation
type: Class
subclass of: Complex
disjoint with: Relation
comment: Anything that brings together things of a given sort. Aggregations are always defined using universal rather than existential restrictions

Area Extent
type: Class
subclass of: Spatio-temporal-extent
subclass of: Restriction
  on property: has quantity
  all values from: Class
    intersection of: Quantity
    intersection of: Restriction
      on property: has units
      all values from: Area Unit

Area Unit
type: Class
subclass of: Unit

Artifact
type: Class
equivalent class: Class
  intersection of: Continuant Entity
  intersection of: Restriction
    on property: is outcome of
    some values from: Act
comment: The notion of "Artifact" is of something created by an Act (by definition performed by some "Potential_agent"). In this version Artifacts are required to be continuants, but even this limitations is not definite. A performance is certainly artefactual. This limits the Artefact to the script and not the performance. I think that is the usual meaning of the word, but others may choose to differ. Certainly the notion of a "Continuant that is the outcome of some Act" is useful. Whether the labelling is correct or not remains to be discussed.

Book Copy
type: Class
subclass of: Written Object

Book Oeuvre
type: Class
subclass of: Language Oeuvre

Building
type: Class
subclass of: Building Entity
subclass of: Material Entity

Building Entity
type: Class
subclass of: Discrete Entity
subclass of: Made Entity
comment: Must be part of Physical_discrete_continuant_entity rather than physical object, because some parts of buildings are the spaces. Spaces are non-material, so building parts can't all be material.

Cavity
type: Class
subclass of: Non Material Entity
comment: A space or hole. "Cavity" is the common anatomic phrase.

Classical
type: Class
subclass of: Musical Style

Cluster
type: Class
subclass of: Group
comment: Ad hoc grouping - taken from FMA

Collective
type: Class
subclass of: Aggregation
subclass of: Continuant Entity
subclass of: Mass Entity
comment: A collection of grains at one level of granularity that make up a mass entity at the next - i.e. an entity where it is the behaviour of the collective of grains that is important rather than the behaviour of the individual grains is unimportant In general, informally "multiple of" can be read as a pluraliser, i.e. "Multiple has_grain only Red_cell" = "Red cells" Note that multiples are always formed with universal restrictions rather than existential. IE multiples are homogeneous.

Collective Of Sound Signals
type: Class
subclass of: Collective
subclass of: Restriction
  on property: has grain
  all values from: Class
    intersection of: Signal
    intersection of: Restriction
      on property: has constituent
      some values from: Sound Energy
comment: A collection of signals that are made of (has_constituent) sound

Compass Positional Relation
type: Class
subclass of: Positional Relation

Complex
type: Class
subclass of: Self Standing Entity
comment: Anything that is in any way aggregated

Continuant Entity
type: Class
subclass of: Self Standing Entity
disjoint with: Occurrent Entity
comment: Continuant or Endurant. Entities that persists in time but has parts in space. As opposed to Occurrent

Creation Act
type: Class
subclass of: Act
comment: The act of creating, specifically of a pattern. The act of "Creation" will remain otherwise unanalysed in this version.

Dependent Entity
type: Class
subclass of: Domain Entity

Discrete Entity
type: Class
subclass of: Self Standing Entity
disjoint with: Mass Entity
comment: Countable entities - people, buildings, organs, etc.

Domain Entity
type: Class
comment: See comment under Metadata tab for ontology documentation. (double click on rdfs:comment) Domain_entity is the top proper entity in the ontology. We recommend defining a top entity within the ontology because: a) It is often useful to define other entities either for debugging purposes (probes) or to simulate individuals, etc. b) Some tools treat the immediate children of owl:Thing peculirarly.

Duration Unit
type: Class
subclass of: Unit

Energy
type: Class
subclass of: Mass Entity
subclass of: Occurrent Entity

Essay Oeuvre
type: Class
subclass of: Language Oeuvre

Exam Oeuvre
type: Class
subclass of: Language Oeuvre

Folk
type: Class
subclass of: Musical Style

Group
type: Class
subclass of: Aggregation
subclass of: Continuant Entity
subclass of: Discrete Entity
comment: A discrete collection of things - flocks etc. Also includes

Handout Oeuvre
type: Class
subclass of: Language Oeuvre

Hollow Object
type: Class
equivalent class: Class
  intersection of: Physical Object
  intersection of: Restriction
    on property: has topology
    some values from: Hollow Topology

Intrinsic Property Partition
type: Class
subclass of: Refining Entity
disjoint with: Modifier
comment: Intrinsic properties are those which are not "qualities" - laterality, topology, etc. There is usually little point in reifying such properties.

Jazz
type: Class
subclass of: Musical Style

Journal Copy
type: Class
subclass of: Written Object

Language Oeuvre
type: Class
subclass of: Oeuvre
comment: Anything oevre that depends on language, whether written or spoken. Clearly an entire subontology couold be developed here.

Laterality
type: Class
equivalent class: Class
  union of: Left Laterality
  union of: Right Laterality
subclass of: Selector
comment: Sidedness - the left/right hand

Left Right Symmetry
type: Class
equivalent class: Class
  union of: Paired Symmetry
  union of: Unpaired Symmetry
subclass of: Intrinsic Property Partition
comment: Used in anatomy to identify parts of the body which have left and right versions, which may be different (e.g. the, lungs, the hemispheres of the brain) or mirror images of each other, e.g. hands, arms, etc.

Length Unit
type: Class
subclass of: Unit

Level Adequacy Status
type: Class
equivalent class: Class
  union of: Adequate Status
  union of: Inadequate Status
  union of: Super Adequate Status
subclass of: Quality Status Partition
comment: The level of a process. Used in this demonstration to define Heart Failure.

Line
type: Class
subclass of: Non Material Entity
comment: The line formed by some physical marks or markers, for example a crease.

Linear Extent
type: Class
subclass of: Spatio-temporal-extent
subclass of: Restriction
  on property: has quantity
  all values from: Class
    intersection of: Quantity
    intersection of: Restriction
      on property: has units
      all values from: Length Unit

Literary Style
type: Class
subclass of: Style

Machine
type: Class
subclass of: Building Entity
subclass of: Material Entity

Made Entity
type: Class
subclass of: Artifact
subclass of: Physical Thing
comment: Anything that is made. Made artefacts other than things like Bonzai trees or ornamental gardens, etc.

Mass Entity
type: Class
subclass of: Self Standing Entity
comment: Measurable entities - water, air,blood, tissue, etc. as opposed to Discrete_entities

Mass Physical Continuant
type: Class
equivalent class: Class
  intersection of: Continuant Entity
  intersection of: Mass Entity
  intersection of: Physical Entity

Material Building Part
type: Class
equivalent class: Class
  intersection of: Material Entity
  intersection of: Part Of Building
comment: The actual material

Material Entity
type: Class
subclass of: Physical Continuant Entity
comment: An physical entity that has mass/energy as opposed to holes ("cavities") lines, etc.

Material Machine Part
type: Class
equivalent class: Class
  intersection of: Material Entity
  intersection of: Part Of Machine
subclass of: Part Of Machine
comment: The actual material

Modifier
type: Class
subclass of: Refining Entity
comment: Modifiers are the common modifiers which change the state of a quality or other aspect of a self-standing entity. In many cases it is worth representing the "quality" as a class.

Musical Oeuvre
type: Class
subclass of: Oeuvre

Musical Style
type: Class
subclass of: Style

Non Material Building Part
type: Class
equivalent class: Class
  intersection of: Non Material Entity
  intersection of: Part Of Building

Non Material Entity
type: Class
subclass of: Physical Continuant Entity
comment: Physical entities that do not have mass but are defined by other phyhsical entities, e.g. a planar surface defined by a table.

Non Material Machine Part
type: Class
equivalent class: Class
  intersection of: Non Material Entity
  intersection of: Part Of Machine
subclass of: Part Of Machine

Non_physical_discrete_entity
type: Class
label: Non Physical Discrete Entity
equivalent class: Class
  intersection of: Discrete Entity
  intersection of: Non Physical Entity
comment: Only boundaries are marked as discrete. Patterns and Organisations should probably also be discrete but requires more consideration.

Non Physical Entity
type: Class
subclass of: Self Standing Entity
disjoint with: Physical Entity
comment: See Physical_entity

Normality Status
type: Class
equivalent class: Class
  union of: Non Normal
  union of: Normal
subclass of: Status Partition
comment: Normality_status is a special status for biomedical ontologies. It has a much more complex structure than most other status, but is a good demonstration of the advantages of using "value partitions" rather than simple values. NB - essentially a value partition - two values plus a covering axiom.

Occurrent Entity
type: Class
subclass of: Self Standing Entity
comment: Things that happen - processes, events, and activities Occurents - have duration - have parts in time as well as space. as opposed to Continuant

Oeuvre
type: Class
equivalent class: Class
  intersection of: Pattern
  intersection of: Restriction
    on property: is outcome of
    some values from: Act
comment: 'Oeuvre' is the french word for "work" in the sense of "work of art" or "work of literature". It is used here to avoid the English homonym of "work" as a verb or the type of working that we do for a living. In this version we will take a very simple versio and just define written, musical and visual oeuvre without trying to analyse them further.

Organisation
type: Class
subclass of: Group
subclass of: Non Physical Entity
subclass of: Potential Agent
subclass of: Restriction
  on property: has member
  all values from: Potential Agent
comment: Organisations are here taken as being co-extensive with the group of agents that make them up - which can of course be empty. Alternatively we could take the Organisation as independent and constituted by the group of agents. One might also wish to argue that an organisation has to be an actual agent - in effect that it has to do something - but it is more that it is empowered to do things than that it does them which seems to count.

Organisational Role
type: Class
subclass of: Role Played

Pamphlet Copy
type: Class
subclass of: Written Object

Part Of Building
type: Class
subclass of: Building Entity
comment: Note - not all parts of buildings are material.

Part Of Machine
type: Class
subclass of: Building Entity
comment: Note - not all parts of buildings are material.

Pattern
type: Class
subclass of: Continuant Entity
subclass of: Non Physical Entity
comment: Patterns are general forms and scripts including 'oeuvres' - the abstractions for intellectual outputs. These were not developed in GALEN and so are left undeveloped here. There is also an argument, according to Barry Smith, for using pattern rather than complexes for Diseases/Clinical situations. However, this leaves us with three entities at least for each disease. Furthermore, we talk of the duration etc. of a disaease which seems to apply more sensibly to the process.

Performance Act
type: Class
subclass of: Act
comment: The act of performing. "Performance" will be left otherwise uninterpreted in this version.

Performance Oeuvre
type: Class
subclass of: Oeuvre

Person
type: Class
subclass of: Physical Object
subclass of: Potential Agent
comment: The agentive aspect of a person. That which ceases to exist when the person dies. It is difficult to avoid some degree of dualism.

Photocopy
type: Class
subclass of: Written Object

Photocopy Of A Professors Hand Out
type: Class
equivalent class: Class
  intersection of: Photocopy
  intersection of: Restriction
    on property: is manifestation of
    some values from: Class
      intersection of: Handout Oeuvre
      intersection of: Restriction
        on property: is outcome of
        some values from: Class

Physical Continuant Entity
type: Class
equivalent class: Class
  intersection of: Continuant Entity
  intersection of: Physical Entity
comment: A common parent for material and non-material physical things. No obvious label has been suggested other than the literal one given here. However, it is very useful, even necessary that includes both material things and the holes and other non-material entities defined by the material things.

Physical Discrete Entity
type: Class
equivalent class: Class
  intersection of: Discrete Entity
  intersection of: Physical Entity
comment: Discrete physical things, whether occurrents or continuants, whether material or non-material. This may be redundant, depending on ones views of mass occurrents such as "walking", "digesting", "talking", etc.

Physical Entity
type: Class
subclass of: Self Standing Entity
comment: Those things that are manifest physically - both occurrrents and continuants but not abstractions such as ideas, patterns, etc. This ontology is specifically silent on whether "Agents" are physical or not in order to be able to fit in with ontologies which make either choice.

Physical Manifestation Of Oeuvre
type: Class
equivalent class: Class
  intersection of: Physical Object
  intersection of: Restriction
    on property: is manifestation of
    some values from: Oeuvre
subclass of: Restriction
  on property: is outcome of
  some values from: Act

Physical Mass Entity
type: Class
equivalent class: Class
  intersection of: Mass Entity
  intersection of: Physical Entity

Physical Object
type: Class
equivalent class: Class
  intersection of: Discrete Entity
  intersection of: Material Entity

Physical Role
type: Class
subclass of: Role Played

Physical Thing
type: Class
equivalent class: Class
  intersection of: Continuant Entity
  intersection of: Discrete Entity
  intersection of: Physical Entity
comment: Material_or_non_material - includes both objects and holes, lines, etc. We don't have a convenient inclusive label. We've used "Physical thing" as less bad than others. "Physical_feature" has too many misleading connotations.

Plane
type: Class
subclass of: Non Material Entity
comment: A flat surface

Play Oeuvre
type: Class
subclass of: Language Oeuvre

Poem Oeuvre
type: Class
subclass of: Language Oeuvre

Pop
type: Class
subclass of: Musical Style

Positional Relation
type: Class
subclass of: Relation

Potential Agent
type: Class
subclass of: Continuant Entity
subclass of: Discrete Entity
subclass of: Self Standing Entity
comment: Potential_agent serves as the domain for has_agent. The list of potential agents is deliberately left open and no statement is made about whether they need by physical or not. Alternatively one could leave the domain of has_agent as simply discrete continuant.

Print Out Copy
type: Class
subclass of: Written Object

Psycho Social Role
type: Class
subclass of: Role Played

Quality
type: Class
subclass of: Relation

Quality Status Partition
type: Class
subclass of: Status Partition
comment: Quality_status_partitions are the vast majority of status partitions which go with qualities. Only a single example, "Level" is given here, but most clinical features such as body temperature, height, weight, pulse rate, etc. would be treated as "qualities". Each would have its own "Quality" defined under self-standing entities and a set of mutually exclusive statuses.

Quantity
type: Class
subclass of: Modifier
comment: Quantities have a magnitude and units. They are not so much modifiers as there is no other obvious place for them.

Refining Entity
type: Class
subclass of: Dependent Entity
disjoint with: Self Standing Entity
comment: All entities which are dependent modifiers - roughly speaking value types and values. (See SWBP note on value partitions)

Region
type: Class
subclass of: Dependent Entity
description: A arbitrary or humanly defined division of a physical object. Typically might be bounded by things or be characterised by being the left or right side, front or back, upper or lower half, etc. In a sense related portion

Relation
type: Class
subclass of: Complex
comment: Reified relations. Primarily in biology "Qualities" but might also be other forms of relationship

Role Played
type: Class
subclass of: Pattern
comment: "Roles" are summarisers which indecated what roles a entity plays in different situations. To emphasize this aspect and reduce ambiguity, we use the suffixe "_played". (This leads to some ugly exprssions of the form "...plays_role x_played". So normally, specific roles are given just the suffix "_role", e.g. "Music_role", "Catalyst_role" etc. In some cases such as "Music_role" or "Literature_role" they are natural kinds that probably can't be defined. In other cases such as "Catalyst role", it may be that they could be defined, but for the purposes of this ontology we choose not to do so. Note also that most roles are actually with respect to some other individual, agent, or situation. Arguable all roles have this feature. The importantance of roles is that they allow the same thing play more than one role - e.g. a ring tone to play both a music role and a signalling role. Note that Roles are disjoint, but the property plays_role is multi-valued (not functional). Hence the same entity can play many roles simultaneously.

Selector
type: Class
subclass of: Intrinsic Property Partition
disjoint with: Topology Value Partition
comment: Selectors are things that select one of a finite list of things rather than actually modifying something. Examples are left_hand or "left laterality" vs "right laterality" , ordinals that number parts of the body such as the spine, etc.

Self Standing Entity
type: Class
subclass of: Domain Entity
comment: Entities which can stand on their own. Primitive self-standing entities in the upper ontology come in disjoint pairs. In the domain ontology they form disjoint non-exhaustive trees. The pairs show up poorly because the windows are ordered alphabetically. However, they can be identified by the disjoint axioms (lower right hand corner of this tab). The disjoint pairs are deiberately not exhaustive - i.e. we defer the issue of whether everything must be either physical or non-physical etc. This allows defering commitment on such issues as whether sets of physical things are themselves physical, etc. This is a matter on which other ontologies differe. Also no opposite for 'Complex' is provided, again to defer decisions. 'Biological' is included for convenience in a BioMedical ontology. In general it should be possible to classify a self-standing entity by asking questions about the basic dichotomies and subdichotomies Asa matter of style in this version, dichotomies have been represented as a pair of disjoint entities but have not been made exhaustive, e.g. it would be possible for something to be neither physical nor non-physical. This is part of the policy of deliberately deferring ontological commitments.

Signal
type: Class
subclass of: Discrete Entity
subclass of: Physical Entity
subclass of: Restriction
  on property: is manifestation of
  some values from: Pattern
comment: Signals are discrete occurrents that are manifestations information - i.e. are the manifestation of a pattern. Signals have to be carried by something - i.e. constituted by some underlying mass medium, e.g. a form of energy.

Situated Positional Relation
type: Class
subclass of: Positional Relation

Sound Energy
type: Class
subclass of: Energy

Spatio-temporal-entity
type: Class
subclass of: Physical Discrete Entity
comment: A placeholder for points and spatio-temporal notions other than extents.

Spatio-temporal-extent
type: Class
subclass of: Spatio-temporal-entity
comment: Subsumes extents of any diimensionality. The important cases are covered currently. Could be defined in terms of dimensionality in a future version. Spatio-temporal extents should be capable of taking magnitude values, and indeed this can be entered in Protege, but they will not perform as expected with the classifier. However, they are created for purposes of illustration.

Status Partition
type: Class
subclass of: Modifier
comment: Used in clinical systems. Also a useful demonstration of how negation can be used in complex ways, so included here.

Style
type: Class
subclass of: Quality

System
type: Class
subclass of: Group
comment: Functional system

Temporal Extents
type: Class
subclass of: Spatio-temporal-extent
subclass of: Restriction
  on property: has quantity
  all values from: Class
    intersection of: Quantity
    intersection of: Restriction
      on property: has units
      all values from: Duration Unit

Topology Value Partition
type: Class
subclass of: Intrinsic Property Partition
comment: General topological characteristics used in anatomy. The most important variants are hollow and solid, but there are many variants, only a few of which are detailed here.

Typscript Copy
type: Class
subclass of: Written Object

Unit
type: Class
subclass of: Modifier
comment: Units should, by rights be individuals. Only the classes are actually given.

Value
type: Class
subclass of: Refining Entity
description: General parent for modifier values. Can be used either with a single property such as "has_quality" as in BFO or with a separate property for each modifier as in the more usual practice.

Visual Oeuvre
type: Class
subclass of: Oeuvre

Volume Extents
type: Class
subclass of: Spatio-temporal-extent
subclass of: Restriction
  on property: has quantity
  all values from: Class
    intersection of: Quantity
    intersection of: Restriction
      on property: has units
      all values from: Volume Unit

Volume Unit
type: Class
subclass of: Unit

Written Object
type: Class
subclass of: Physical Object
subclass of: Restriction
  on property: is manifestation of
  some values from: Language Oeuvre
comment: We could describe this an an object that is the manifestation outcome of writing, or that contains writing, etc. We shall keep the commitments minimal for now as to how the writing got to the physical page - e.g. was it photocopied, printed, etc. Merely by saying that it is the manifestation of an Oeuvre we demand that it be the outcome of some act.

Adequate Status
type: Class
subclass of: Level Adequacy Status

Behind
type: Class
subclass of: Situated Positional Relation

Closed Hollow Topology
type: Class
subclass of: Hollow Topology
disjoint with: Tubular Topology

Hollow Topology
type: Class
subclass of: Topology Value Partition

In Front Of
type: Class
subclass of: Situated Positional Relation

Inadequate Status
type: Class
subclass of: Level Adequacy Status

Intrinsically Non Normal
type: Class
subclass of: Non Normal

Left Laterality
type: Class
subclass of: Laterality
disjoint with: Right Laterality

Mirror Image Symmetry
type: Class
subclass of: Paired Symmetry

Non Normal
type: Class
subclass of: Normality Status
disjoint with: Normal
comment: Anything worth noting as out of the ordinary. There are many different ways of being non_Normal and endless discussions of the variants, but the one thing people seem to be able to agree on is a notion of 'not normal'.

Normal
type: Class
subclass of: Normality Status
comment: Not non-normal - actually better thought of that way although not represented in this form. Those things not worth noting because they are expected and noting them would not, in general, convey useful information unless there were some reason to suspect that in the given circumstances they would be non-normal.

Paired Symmetry
type: Class
subclass of: Left Right Symmetry

Right Laterality
type: Class
subclass of: Laterality

Single Membrane Topology
type: Class
subclass of: Topology Value Partition

Solid Topology
type: Class
subclass of: Topology Value Partition

Super Adequate Status
type: Class
subclass of: Level Adequacy Status

To The East Of
type: Class
subclass of: Compass Positional Relation

To The Left Of
type: Class
subclass of: Situated Positional Relation

To The North Of
type: Class
subclass of: Compass Positional Relation

To The Right Of
type: Class
subclass of: Situated Positional Relation

To The South Of
type: Class
subclass of: Compass Positional Relation

To The West Of
type: Class
subclass of: Compass Positional Relation

Tubular Topology
type: Class
subclass of: Hollow Topology

Unpaired Symmetry
type: Class
subclass of: Left Right Symmetry

Owl:Thing
type: Class