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 See Refining Property See Relational Property Properties linking self-standing entities to refining entities or refining entities to each other. Properties linking self-standing entities Acts on substrate Pumping acts_on blood. 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. 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 Whereas actors can be either occurrents or continants. Agents - the initator, must be a continuant. Occurrents that have agents are known as Acts. 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 has_clinical_part 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) Most general notion of location. Not necessarily physical NOT GALEN "hasLocation" GALEN 'hasLocation' - locus of pathology. NB because of differences between sanctioning and domain/range constraints, must always ask for has_normality pathological & hasLocus... 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. TODO: Consider whether to place under affects. should has_outcome be a child of has_locus. has_outcome The general outcome of an act. Should probably be a sub of affects. Still being chased. Relation betwen occurrents and either continuants or other occurrents. Physical location 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. The specific version of includes which points to the causative or key pathology. Follows GALEN naming conventions. Alternatives welcome. Connection. Not symmetric in GALEN because GALEN handled symmetric properties badly. Containment. In this veresion must be contained in a cavity. This is more pedantic than GALEN. Note containment implies location but not partonomy The relation between an agent and the physical manifestation 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_clinical_part_of 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) Group membership as in goose - flock of geese. Membership - not standard partonomy and not included in clinical partonomy 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. is_of The property that links regions to the things they are regions of, and more generally modalities and related dependent notions to their kernel notions Outcome of process. Has additional parent has_locus to get reasoning right in absence of more sophisticated rules. Generic partonomy including membership. The relation between two mass entities which are mixed or parts. GALEN isFeatureOf Children for each quality to control cardinality. Links features to self-standing entities. Placed in this way around to make child of Link between a role and the things that play that role. In this direction to be consistent with location and manifestation 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. The relation between 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. 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) 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. Act An occurrent that has an agent. Activity Level The level of activity of a process. Amongst other statuses takes Level_adequacy_status Afrtistic Style Agent An actual agent - the agent of some real occurrent. Aggregation Anything that brings together things of a given sort. Aggregations are always defined using universal rather than existential restrictions Area Extent Area Unit Artifact 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 Book Oeuvre Building Building Entity 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 A space or hole. "Cavity" is the common anatomic phrase. Classical Cluster Ad hoc grouping - taken from FMA Collective 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 A collection of signals that are made of (has_constituent) sound Compass Positional Relation Complex Anything that is in any way aggregated Continuant Entity Continuant or Endurant. Entities that persists in time but has parts in space. As opposed to Occurrent Creation Act The act of creating, specifically of a pattern. The act of "Creation" will remain otherwise unanalysed in this version. Dependent Entity Discrete Entity Countable entities - people, buildings, organs, etc. Domain Entity 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 Energy Essay Oeuvre Exam Oeuvre Folk Group A discrete collection of things - flocks etc. Also includes Handout Oeuvre Hollow Object Intrinsic Property Partition Intrinsic properties are those which are not "qualities" - laterality, topology, etc. There is usually little point in reifying such properties. Jazz Journal Copy Language Oeuvre Anything oevre that depends on language, whether written or spoken. Clearly an entire subontology couold be developed here. Laterality Sidedness - the left/right hand Left Right Symmetry 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 Level Adequacy Status The level of a process. Used in this demonstration to define Heart Failure. Line The line formed by some physical marks or markers, for example a crease. Linear Extent Literary Style Machine Made Entity Anything that is made. Made artefacts other than things like Bonzai trees or ornamental gardens, etc. Mass Entity Measurable entities - water, air,blood, tissue, etc. as opposed to Discrete_entities Mass Physical Continuant Material Building Part The actual material Material Entity An physical entity that has mass/energy as opposed to holes ("cavities") lines, etc. Material Machine Part The actual material Modifier 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 Musical Style Non Material Building Part Non Material Entity 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 Non_physical_discrete_entity Non Physical Discrete Entity Only boundaries are marked as discrete. Patterns and Organisations should probably also be discrete but requires more consideration. Non Physical Entity See Physical_entity Normality Status 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 Things that happen - processes, events, and activities Occurents - have duration - have parts in time as well as space. as opposed to Continuant Oeuvre '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 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 Pamphlet Copy Part Of Building Note - not all parts of buildings are material. Part Of Machine Note - not all parts of buildings are material. Pattern 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 The act of performing. "Performance" will be left otherwise uninterpreted in this version. Performance Oeuvre Person 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 Photocopy Of A Professors Hand Out Physical Continuant Entity 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 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 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 Physical Mass Entity Physical Object Physical Role Physical Thing 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 A flat surface Play Oeuvre Poem Oeuvre Pop Positional Relation Potential Agent 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 Psycho Social Role Quality Quality Status Partition 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 Quantities have a magnitude and units. They are not so much modifiers as there is no other obvious place for them. Refining Entity All entities which are dependent modifiers - roughly speaking value types and values. (See SWBP note on value partitions) Region 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 Reified relations. Primarily in biology "Qualities" but might also be other forms of relationship Role Played "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 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 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 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 Sound Energy Spatio-temporal-entity A placeholder for points and spatio-temporal notions other than extents. Spatio-temporal-extent 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 Used in clinical systems. Also a useful demonstration of how negation can be used in complex ways, so included here. Style System Functional system Temporal Extents Topology Value Partition 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 Unit Units should, by rights be individuals. Only the classes are actually given. Value 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 Volume Extents Volume Unit Written Object 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 Behind Closed Hollow Topology Hollow Topology In Front Of Inadequate Status Intrinsically Non Normal Left Laterality Mirror Image Symmetry Non Normal 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 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 Right Laterality Single Membrane Topology Solid Topology Super Adequate Status To The East Of To The Left Of To The North Of To The Right Of To The South Of To The West Of Tubular Topology Unpaired Symmetry Owl:Thing