Ontology
comment: Double click on rdfs:comment at left This is a demonstration top ontology for biomedicine reconstructing built along the lines of DOLCE but also reimplementing 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 the University of Manchester and CO-ODE project. (c) University of Manchester 2005 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/
imports: protege

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

Self standing entity
type: Class
disjoint with: Refining 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
subclass of: Domain entity

Stomach pathology
type: Class
version info: ProbeClass:true
equivalent class: Class
  intersection of: Restriction
    some values from: pathological
    on property: has normality status
  intersection of: Restriction
    on property: has locus
    some values from: Class
      union of: Stomach
      union of: Restriction
        on property: is clinically part of
        some values from: Stomach
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.
subclass of: Probe

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 clinically part of
type: ObjectProperty
inverse of: has clinical part
sub property of: is generic part of
comment: The usual clinical meaning of partonomy - including functional and physical partonomy but excluding membership - which effectively excludes malfufunction of individual cells but not of multiples of cells.

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

Normality value
type: Class
equivalent class: Class
  union of: normal
  union of: non Normal
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.
subclass of: Quality partition

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

Physical entity
type: Class
comment: Those things that are manifest physically - both occurrrents and continuants but not abstractions such as ideas, patterns, etc. GALEN 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

Probe-Strutural part of Cell 2
type: Class
version info: ProbeClass:true
equivalent class: Restriction
  some values from: Cell
  on property: is structural part of
subclass of: Probe

is structural part of
type: TransitiveProperty
domain: Physical continuant
sub property of: has physical location
type: ObjectProperty
range: Physical continuant
inverse of: has structural part
comment: Structural partonomy not including membership. Structural partonomy in does not cross levels of collectivity. NB that Structural partonomy also has parents in both generic_part and physical_location. This is because the notion of partonomy used here to include the usual clinical use includes both functional and structural parthood, but functional parthood does not involve physical location.
sub property of: is clinically part of

is functional part of
type: ObjectProperty
sub property of: is clinically part of
comment: Functional parthood - does not imply physical location although many functional parts are co-located with physical parts. Includes both parthod as in the the thyroid gland is funcitonally part of theendocrine system and the ligament is part of the knee joint. The first includes structural parthood, the second does not.
inverse of: has functional part

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

includes specifically
type: ObjectProperty
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.
inverse of: is included in specifically

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

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

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

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

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.
equivalent class: Class
  intersection of: ClinicalSituation
  intersection of: Restriction
    some values from: Restriction
      some values from: pathological
      on property: has normality status
    on property: includes
subclass of: Restriction
  some values from: pathological
  on property: has normality status

includes
type: ObjectProperty
inverse of: is included in
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.

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

Group
type: Class
subclass of: Complex
comment: A discrete collection of things - flocks etc. Also called "Determinate Collective" in recent papers.
subclass of: Continuant entity
subclass of: Discrete entity

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. All modifiers in the current version consist of quality partitions, although one could argue that Normality_value is sufficiently different to deserve a categorty of its own. This step left in only for analysis

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-Clinical Part of heart
type: Class
equivalent class: Restriction
  on property: is clinically part of
  some values from: Heart
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.
version info: ProbeClass:true
subclass of: Probe

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

Cell membrane
type: Class
subclass of: Restriction
  some values from: hollow topology
  on property: has 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 generic part of
    some values from: Cell
disjoint with: Organism
disjoint with: Body part
disjoint with: Macro molecule
disjoint with: Lesion

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.

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
sub property of: has participant
inverse of: is actor in
domain: Occurrent entity

Probe structural part of heart
type: Class
subclass of: Probe
equivalent class: Restriction
  some values from: Heart
  on property: is structural part of
version info: ProbeClass:true
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

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.

is contained in
type: ObjectProperty
domain: Material entity
inverse of: contains
sub property of: has physical 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
range: Class
  union of: Cavity
  union of: Hollow object
type: TransitiveProperty

Probe located in skull
type: Class
version info: ProbeClass:true
equivalent class: Restriction
  some values from: Skull
  on property: has location
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.

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

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.

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

Heart pathology
type: Class
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.
equivalent class: Class
  intersection of: Restriction
    some values from: pathological
    on property: has normality status
  intersection of: Restriction
    on property: has locus
    some values from: Class
      union of: Heart
      union of: Restriction
        on property: is generic part of
        some values from: Heart
subclass of: Probe
version info: ProbeClass:true

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

Complex
type: Class
subclass of: Self standing entity
comment: Anything that is in any way aggregated or dependent on something else. There is an argument about whether qualities should be under Complex or sedparate. Likewise for relations. No strong ontological commitment is made or intended. However, it is much easier to understand the top ontology by putting in a branch at this level. Note tha there is no notion of Non-complex. Whereas all of the other notions in the upper level can be treated as principled dichotomies. There are too many arguments about 'complexes' to do so without making premature ontological commitments.

Organelle
type: Class
subclass of: Continuant entity
subclass of: Material entity
subclass of: Discrete entity
subclass of: Self standing entity
subclass of: Restriction
  on property: is grain of
  some values from: Class
    intersection of: Bunch
    intersection of: Restriction
      all values from: Organelle
      on property: has grain
    intersection of: Restriction
      some values from: Cell
      on property: is functional part of
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

Bunch
type: Class
comment: Fl.ocks of geese, schools of fish, etc.
subclass of: Group

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

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

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

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

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

Quality partition
type: Class
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.
subclass of: Modifier

Collective
type: Class
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 collectives are always formed with universal restrictions rather than existential. IE multiples are homogeneous.
subclass of: Complex
subclass of: Mass entity

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

Probe Cliincal part of Skull
type: Class
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.
equivalent class: Restriction
  some values from: Skull
  on property: is clinically part of
version info: ProbeClass:true

Probe-Part of Cell
type: Class
subclass of: Probe
version info: ProbeClass:true
equivalent class: Restriction
  on property: is generic part of
  some values from: Cell

Probe-Clinical part of Cell
type: Class
version info: ProbeClass:true
equivalent class: Restriction
  some values from: Cell
  on property: is clinically part of
subclass of: Probe

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
        some values from: pathological
        on property: has normality status

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

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

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

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

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

has physical location
type: ObjectProperty
inverse of: is physical location of
sub property of: has location
type: TransitiveProperty
comment: Physical location - but includes connectedness which the OBO relations do not. This is arguable. However, in most applications,

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

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

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