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/

protege
type: Ontology
comment: The Protege metadata ontology (in the version that is used inside Protege. Note that this is an OWL Full ontology, with annotation properties that have range and domain restrictions. However, the "official" online release of this file is OWL DL, so that ontologies that use Protege metadata annotations can still be shared as OWL DL.

Non biological entity
type: Class
disjoint with: Biological entity
subclass of: Self standing entity
comment: See biological

Biological entity
type: Class
subclass of: Self standing entity
comment: Biological entities Because this is haveily used for
disjoint with: Non biological entity

Self standing entity
type: Class
disjoint with: Refining entity
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.

Physical thing
type: Class
equivalent class: Class
  intersection of: Discrete entity
  intersection of: Physical entity
  intersection of: Continuant 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

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

Physical entity
type: Class
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.
disjoint with: Non physical entity
subclass of: Self standing entity

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

Stomach pathology
type: Class
version info: ProbeClass:true
comment: Pathology of stomach, analogous to Cardiac_pathology. Again both the syndrome and the physical structure are included for demonstration although a more practical query would include only one or the other.
equivalent class: Class
  intersection of: Restriction
    on property: has normality status
    some values from: pathological
  intersection of: Restriction
    on property: has locus
    some values from: Class
      union of: Stomach
      union of: Restriction
        on property: is_clinical_part_of
        some values from: Stomach
subclass of: Probe

pathological
type: Class
comment: Anything which is diseased in the sense that it requires medical management.
subclass of: non Normal

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

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
inverse of: has_clinical_part

Probe
type: Class
comment: Probes are tests inserted to check classification. Tools are almost ready to have them visible or invisible as required.
version info: ProbeClass:true

Physical continuant entity
type: Class
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.
equivalent class: Class
  intersection of: Continuant entity
  intersection of: Physical entity

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

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.

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

Biological object
type: Class
comment: Should classify under Physical object
equivalent class: Class
  intersection of: Biological entity
  intersection of: Discrete entity
  intersection of: Material entity

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

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

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

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

Probe-Strutural part of Cell
type: Class
equivalent class: Restriction
  some values from: Cell
  on property: is structural part of
comment: Parts of the cell according to the strictness version of part-hood - those things which are unquestionably part of the cell.
version info: ProbeClass:true
subclass of: Probe

is structural part of
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
type: ObjectProperty
inverse of: has structural part

Level adequacy status
type: Class
comment: The level of a process. Used in this demonstration to define Heart Failure.
equivalent class: Class
  union of: super adequate status
  union of: adequate status
  union of: inadequate status
subclass of: Quality status partition

Diabetes process
type: Class
comment: The disease process of diabetes
subclass of: Intrinsically pathological process

Cell membrane
type: Class
subclass of: Restriction
  on property: has topology
  some values from: hollow topology
comment: The membrane enclosing the cell
subclass of: Restriction
  some values from: Cell
  on property: is structural part of
subclass of: Cell part

Cell part
type: Class
disjoint with: Organ
disjoint with: Subdivision of body part
disjoint with: Organ part
comment: A primitive in the FMA. Here defined. There may still be case for distinguishing the primitive Cell_part_NAMED as in GALEN from the defined "Part of Cell".
disjoint with: Cell
equivalent class: Class
  intersection of: Biological object
  intersection of: Restriction
    on property: is part of
    some values from: Cell
disjoint with: Organism
disjoint with: Body part
disjoint with: Macro molecule
disjoint with: Lesion

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

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

Physical discrete entity
type: Class
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.
equivalent class: Class
  intersection of: Physical entity
  intersection of: Discrete entity

Written object
type: Class
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.
subclass of: Physical object
subclass of: Restriction
  some values from: Language oeuvre
  on property: is manifestation of

non Normal
type: Class
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'.
subclass of: Normality status
disjoint with: normal

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

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

Intrinsic property partition
type: Class
subclass of: Refining entity
comment: Intrinsic properties are those which are not "qualities" - laterality, topology, etc. There is usually little point in reifying such properties.

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

Probe located in skull
type: Class
version info: ProbeClass:true
subclass of: Probe
comment: Everything located in the skull Includes the brain which is contained in the cranial cavity but not a part of the skull.
equivalent class: Restriction
  some values from: Skull
  on property: has location

Skull
type: Class
comment: The skull is actually a set of bones.
subclass of: Specified set

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

Line
type: Class
disjoint with: Plane
subclass of: Non material entity
comment: The line formed by some physical marks or markers, for example a crease.
disjoint with: Cavity

Plane
type: Class
comment: A flat surface
disjoint with: Cavity
subclass of: Non material entity
disjoint with: Line

Non material entity
type: Class
subclass of: Physical continuant entity
disjoint with: Material 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.

Cavity
type: Class
disjoint with: Plane
disjoint with: Line
comment: A space or hole. "Cavity" is the common anatomic phrase.
subclass of: Non material entity

Specified set
type: Class
subclass of: Group
comment: Set in FMA sense of a specified list with a specific number. NOT a mathematical set.

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

Potential agent
type: Class
subclass of: Continuant entity
subclass of: Discrete 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.
subclass of: Self standing entity

Heart pathology
type: Class
equivalent class: Class
  intersection of: Restriction
    some values from: pathological
    on property: has normality status
  intersection of: Restriction
    some values from: Class
      union of: Heart
      union of: Restriction
        some values from: Heart
        on property: is part of
    on property: has locus
comment: Any pathology in the heart. Includes both the processes and the syndromes. A sensible interface would ask for one or the other, but they are both included here for demonstration purposes. Note that Circulatory_failure_due_to_heart_failure is included. This is the reason for having has_actor imply has_locus. This is a mild over-generalisation and will lead to some over inclusion.
subclass of: Probe
version info: ProbeClass:true

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

Oeuvre
type: Class
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.
equivalent class: Class
  intersection of: Pattern
  intersection of: Restriction
    on property: is outcome of
    some values from: Act

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

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

Biological Cavity
type: Class
equivalent class: Class
  intersection of: Biological entity
  intersection of: Cavity
comment: See cavity

Organelle
type: Class
subclass of: Continuant entity
subclass of: Material entity
subclass of: Discrete entity
comment: Any of the various independent bodies in the cell - mitihorndria, chloroplasts etc. There is some disagreement as to whether the nucleus should be classified as an organelle. Here it is not.
subclass of: Biological entity

Nexus
type: Class
subclass of: Group
comment: Specific complex lijnked by some fundamental principle as in Syndromes. Also dualities such as ulcer and ulceration which are here not distinguished from other syndromes but might be in a more pedantic version. Also this version does not distinguish arbitrary syndromes such as Tetrology of Falot from systematic syndromes, such as all the things that fit together around Diabetes.

Cytoplasm
type: Class
subclass of: Continuant entity
subclass of: Restriction
  on property: is functional part of
  some values from: Cell
subclass of: Restriction
  some values from: Intracellular compartment
  on property: is contained in
subclass of: Mass entity
subclass of: Physical entity
subclass of: Biological entity
comment: The stuff that fills the cell

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

Mass entity
type: Class
subclass of: Self standing entity
disjoint with: Discrete entity
comment: Measurable entities - water, air,blood, tissue, etc. as opposed to Discrete_entities

Material building part
type: Class
comment: The actual material
equivalent class: Class
  intersection of: Part of building
  intersection of: Material entity

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

Selector
type: Class
subclass of: Intrinsic property partition
disjoint with: Left right symmetry
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.

Left right symmetry
type: Class
disjoint with: Topology value partition
equivalent class: Class
  union of: unpaired symmetry
  union of: paired symmetry
disjoint with: Selector
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.
subclass of: Intrinsic property partition

Topology value partition
type: Class
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.
disjoint with: Left right symmetry
subclass of: Intrinsic property partition
disjoint with: Selector

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.

Pattern
type: Class
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.
subclass of: Continuant entity

Collective
type: Class
subclass of: Aggregation
subclass of: Continuant 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.
subclass of: Mass entity

Inflammation process
type: Class
subclass of: Intrinsically pathological process
comment: Inflammation

Probe Cliincal part of Skull
type: Class
equivalent class: Restriction
  some values from: Skull
  on property: is_clinical_part_of
subclass of: Probe
comment: The major parts of the skull including structural and functional - in this case in demo only structural parts. Excludes the Brain because the Brain is contained in rather than part of the skull.
version info: ProbeClass:true

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.

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.

Modifier
type: Class
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.
subclass of: Refining entity

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

intrinsically pathological
type: Class
subclass of: intrinsically non Normal
comment: Always pathological, e.g. of tumours.
subclass of: pathological

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

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

Artifact
type: Class
disjoint with: Natural non biological entity
equivalent class: Class
  intersection of: Continuant entity
  intersection of: Restriction
    some values from: Act
    on property: is outcome of
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.

Natural non biological entity
type: Class
disjoint with: Artifact
subclass of: Non biological entity
comment: All those things created by potential agents, whether people or others. We leave open the issue of whether animals can be agents and the authors of artefacts.

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

Normality status
type: Class
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.
subclass of: Status partition
equivalent class: Class
  union of: normal
  union of: non Normal

Probe-Clinical part of Cell
type: Class
version info: ProbeClass:true
equivalent class: Restriction
  on property: is_clinical_part_of
  some values from: Cell
comment: Parts of the cell at the a single granularity
subclass of: Probe

normal
type: Class
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.
subclass of: Normality status
disjoint with: non Normal

Non physical entity
type: Class
comment: See Physical_entity
subclass of: Self standing entity
disjoint with: Physical entity

Complex
type: Class
subclass of: Self standing entity
comment: Anything that is in any way aggregated

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

Signal
type: Class
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.
subclass of: Discrete entity
subclass of: Physical entity

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

Cardiac failure
type: Class
comment: NB - Fudged because of bug. that doesn't translate pathology propagation axiom properly to DIG interface
equivalent class: Class
  intersection of: Cardiac pumping
  intersection of: Restriction
    on property: has outcome
    some values from: Class
      intersection of: Circulation of blood
      intersection of: Restriction
        on property: has level quality
        some values from: Class
      intersection of: Restriction
        on property: has normality status
        some values from: pathological

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.

Person agent
type: Class
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.

has agent
type: ObjectProperty
sub property of: has actor
inverse of: is agent of
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

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

ClinicalSituation
type: Class
comment: "Clinical Situation" in GALEN Effectively "Disease" as opposed to the simple process or lesion at the heart of the disease. Hence we have both "Pericarditis_syndrome" and "Pericarditis_process" Likewise, both "Ulcer of stomach" and "Ulcer_of_stomach_syndrome" which includes the process and might include the pain and other things that go with it. Note thatt his simplified version just has a single level of "includes" property for syndromes. By rights, there should be two levels - one for the defining conditions and one for everything else. See 'Nexus'
subclass of: Nexus

Ulceration process
type: Class
subclass of: Intrinsically pathological process
comment: The process of ulceration - as opposed to the ulcer that is the outcome of that process

includes
type: ObjectProperty
sub property of: has member
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.

Physiologic process
type: Class
comment: Any of the usual processes of physiology, growth, circulation, movement, etc.
subclass of: Biological physical occurrent

Syndrome including pathology axiom
type: Class
comment: An axiom that a Syndrome that includes anything pathological is itself pathological A good example of why we need to be able to make axioms either anonymous or at least invisible.
subclass of: Restriction
  on property: has normality status
  some values from: pathological
equivalent class: Class
  intersection of: ClinicalSituation
  intersection of: Restriction
    some values from: Restriction
      on property: has normality status
      some values from: pathological
    on property: includes

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.

Probe-Clinical Part of heart
type: Class
comment: Probes for the clinical parts of the heart. This includes both functional and structural parthood. This is what a doctor would expect to see, including Pericarditis - i.e. an inflammation of the covering of the heart. Strictly speaking, the Pericardium is, however, a spearate organ, so according to the FMA view, it does not form part of the heart.
equivalent class: Restriction
  on property: is_clinical_part_of
  some values from: Heart
subclass of: Probe
version info: ProbeClass:true

has actor
type: ObjectProperty
sub property of: has locus
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 participant
inverse of: is actor in

Probe structural part of heart
type: Class
subclass of: Probe
version info: ProbeClass:true
equivalent class: Restriction
  on property: is structural part of
  some values from: Heart
comment: The structural parts of the heart. Essentially the FMA view of what should be part of the heart, excluding individual cardiac cells etc. which require the still broader is_part_of relation.

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

Pericarditis process
type: Class
comment: Inflammation of the covering of the heart (the "pericardium")
equivalent class: Class
  intersection of: Inflammation process
  intersection of: Restriction
    on property: affects
    some values from: Pericardium

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

affects
type: ObjectProperty
inverse of: is affected by
sub property of: acts on
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: has locus

Pathological process
type: Class
comment: The process aspect of disease or disorder, e.g. Diabetes, High blood pressure, the growth of a tumour, ulceration, etc. See Pathological.
equivalent class: Class
  intersection of: Biological physical occurrent
  intersection of: Restriction
    some values from: pathological
    on property: has normality status

Probe-Part of Cell
type: Class
subclass of: Probe
version info: ProbeClass:true
equivalent class: Restriction
  some values from: Cell
  on property: is part of
comment: All parts of the cell across granularities

Organisation
type: Class
subclass of: Potential agent
subclass of: Non physical entity
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.
subclass of: Group

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

is quality of
type: ObjectProperty
range: Self standing entity
domain: Quality
sub property of: Relational property
inverse of: has quality
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
type: InverseFunctionalProperty

Relational property
type: ObjectProperty
inverse of: Inverse Relational property
comment: Properties linking self-standing entities
domain: Self standing entity
range: Self standing entity

Inverse Relational property
type: ObjectProperty
comment: See Relational Property
range: Self standing entity
domain: Self standing entity
inverse of: Relational property

owns
type: ObjectProperty
range: Class
  intersection of: Self standing entity
  intersection of: Class
    complement of: Person agent
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)
sub property of: Relational property
domain: Potential agent
inverse of: is owned by

is non physical aspect of
type: ObjectProperty
inverse of: has non physical aspect
range: Self standing entity
sub property of: Relational property
domain: Non physical entity
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.

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

has_clinical_part
type: ObjectProperty
sub property of: has part
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)
inverse of: is_clinical_part_of
type: TransitiveProperty

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

Refining property
type: ObjectProperty
domain: Domain entity
comment: Properties linking self-standing entities to refining entities or refining entities to each other.
range: Refining entity
inverse of: Inverse Refining property

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

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

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.
sub property of: has location
domain: Class
  union of: Pattern
  union of: Potential agent
sub property of: is non physical aspect of
range: Physical entity
inverse of: is manifestation of

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

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

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

is grain of
type: ObjectProperty
range: Collective
sub property of: is member of
type: FunctionalProperty
inverse of: has grain
domain: Physical thing
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

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

occupies
type: ObjectProperty
range: Building entity
domain: Potential agent
inverse of: is occupied by
sub property of: Relational property
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.

has discrete part
type: ObjectProperty
sub property of: has structural part
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
type: TransitiveProperty

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

has magnitude
type: DatatypeProperty
range: float
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