Problem-oriented Medical Record Ontology

foaf	http://xmlns.com/foaf/0.1/
owl	http://www.w3.org/2002/07/owl#
p5	http://www.loa-cnr.it/ontologies/TemporalRelations.owl#
daml	http://www.daml.org/2001/03/daml+oil#
p3	http://www.loa-cnr.it/ontologies/FunctionalParticipation.owl#
wn	http://xmlns.com/wordnet/1.6/
dc	http://purl.org/dc/elements/1.1/
rim	http://wopeg.he.agfa.be/rules/RIMV3OWL#
galen	http://www.co-ode.org/ontologies/galen#
plan	http://www.loa-cnr.it/ontologies/Plans.owl
None	http://www.geneontology.org/owl#
p4	http://www.loa-cnr.it/ontologies/SpatialRelations.owl#
inf	http://www.loa-cnr.it/ontologies/InformationObjects.owl#
skos	http://www.w3.org/2004/02/skos/core#
edns	http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#
xml	http://www.w3.org/XML/1998/namespace
obo	http://www.geneontology.org/owl#
p1	http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#
dol	http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#
temp	http://www.loa-cnr.it/ontologies/TemporalRelations.owl#
rdfs	http://www.w3.org/2000/01/rdf-schema#
wot	http://xmlns.com/wot/0.1/
obi	http://obi.sourceforge.net/ontology/OBI.owl#
bfo	http://www.ifomis.org/bfo/1.0/snap#
p2	http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#
rdf	http://www.w3.org/1999/02/22-rdf-syntax-ns#
sem	http://www.loa-cnr.it/ontologies/SemioticCommunicationTheory.owl#
common	http://www.loa-cnr.it/ontologies/CommonSenseMapping.owl#
xsd	http://www.w3.org/2001/XMLSchema#
time	http://www.w3.org/2006/time#
cpr	http://purl.org/cpr/0.5#

This Semantic Web Ontology document (for self-hosted Medical Records) was written with a faithful rendition (GRDDL) in mind for consumption by Semantic Web Agents, lay people, logicians, and more ubiquitous markup user agents.

It is generated by a Python software library which takes an OWL/XML document with the following additional (embedded) formats:

Definition

The goal is to define a minimal set of terms that connect representations from well defined healthcare information & process models (such as HL7 RIM) with more expressive foundational ontologies of biology (both domain-agnostic and those specific to the domains of life sciences and healthcare) through the use of the criteria outlined in the traditional Problem-oriented Medical Record structure.

Meeting CPR Requirements

This is an attempt to demonstrate how a few best practices in ontology and software engineering can be applied to address the problem of the lack of a unified vocabulary for Computer-based Patient Records (CPR)

Problem-oriented Medical Record Methodology

KR Methodology

Elisabeth Bayegan's methodology (outlined in full within her PhD thesis) is followed as a means for capturing clinical content in an RDF knowledge base with syntactic and semantic extensions for DLP (and RIF?) expressivity (RDFLib)

KR (Description Logic) Syntax

Wherever possible, the Manchester OWL Syntax (@@TODO References) is adopted to capture axiomatic semantics of DL terminologies.

GALEN' Role classes

OBO Links

Anatomical Ontology

Foundational Model of Anatomy FMA is adopted for describing anatomical constructs.

Papers and References

Class Hierarchy

Property / Relation Hierarchy

We distinguish between a quality (e.g., the color of a specific rose), and its value (e.g., a particular shade of red). The latter is called quale, and describes the position of an individual quality within a certain conceptual space (called here quality space) Gardenfors (2000). So when we say that two roses have (exactly) the same color, we mean that their color qualities, which are distinct, have the same position in the color space, that is they have the same color quale. Qualities can be seen as the basic entities we can perceive or measure: shapes, colors, sizes, sounds, smells, as well as weights, lengths, electrical charges... 'Quality' is often used as a synonymous of 'property', but this is not the case in this upper ontology: qualities are particulars, properties are universals. Qualities inhere to entities: every entity (including qualities themselves) comes with certain qualities, which exist as long as the entity exists. An endurant of type e1 metaphorically plays a role (defined in a description d2), when that role comes from a metaphorical mapping between the description d1 that grants a unity criterion to endurants of type e1, and another description d2 that grants a unity criterion to endurants of type e2. A role r characterizes a collection c when proper subsets of the members of c play different roles r,...,rn that are all used by a same description or deputed by a same figure. An abstract merging task is a merging aimed at 'formally' joining the tasks that are direct successor to a case task. Differently from synchronization tasks, which are expected to be executed, abstract mergings only provide abstract boundaries to a task structure, because in a case task, only one action task is supposed to be executed. An endurant having a direct physical (at least spatial) quality. A task defined in a plan assessment. 'Component' is a proper part with a role (or function) in a system or a context. Roles can be different for the same entity, and the evaluation of them changes according to the kind of entity. For instance, components of endurants can 'play functional roles' in a whole, while components of perdurants are the essential 'episodes' in their whole.As a functional part relation, component is not transitive, because functions depend on intentions and/or designs, and something intentionally essential for a direct whole, can be non-essential for another, indirect whole. 2 2 agent_in A quality space is a topologically maximal region. The constraint of maximality cannot be given completely in OWL, but a constraint is given that creates a partition out of all quality spaces (e.g. no two quality spaces can overlap mereologically). This is the immediate relation between roles and endurants. A role classifies the position (function, use, relevance, ...) of an endurant within a context (description). Roles can be ordered, interdependent, at different layers. etc. Total constant participation applied to the mereological sum of the perdurants in which an endurant participates. A temporal region, measured according to a calendar. A Perdurant that exemplifies the intentionality of an agent. Could it be aborted, incomplete, mislead, while remaining a (potential) accomplishment ... The point here is that having a result depends on a method, then an action remains an action under incomplete results. As a matter of fact, if we neutralize intentionality, a purely topological, post-hoc view is at odds with the notion of incomplete accomplishments. Being about an antity with the main purpose of conventionally naming that entity. Typically, proper nouns identify entities. A parameter valued by regions that are used asindicators for some behaviour or event to be checked. This is the immediate relation between courses and perdurants. A course can be either atomic, being a simple 'perdurant role', or it can be complex, thus creating an abstract ordering over a temporal or causal sequence of processes or actions. The ontology of plans develops in detail intentional complex courses. AKA Agentive-role.A role that can only be played by agents. A concept that classifies (in particular, it 'sequences') perdurants (processes, events, or states), as a component of some description. Courses are the descriptive counterpart of perdurants, and, since perdurants have endurants as participants, they are usually the function of some role. A region at which only temporal qualities can be directly located. It assumes a metrics for time. Analytical location holding between physical endurants and physical regions. A state related to planning. It is sequenced by 'deliberation task', and is preceded by a decision activity. When a plan is 'private', a decision state is cognitive, otherwise it depends on some cognitive state. A non-social relation(ship): formal, linguistic, etc. It is considered here a theory, because relations are established in order to give an ordering to some reality. Specialization as reification of a partial-order relation between type- or set-reified social objects, i.e. descriptions, concepts, and collections.For example, concepts that are apparently classified by other concepts; e.g. a manager that plays the role of buyer, where the role manager actually specializes the role buyer. Descriptions can be specialized by other descriptions that specialize their concepts. For descriptions, an intention to specialize must be present (unless purely formal theories are considered, but even in this case a criterion of relevance is usually active). Specialization does not imply expansion (proper part) for descriptions. If there exists a concept that is defined by the specialized description, which is not d-used in the specializing one, the second only specializes a part of the first. If there exists a concept that is defined by the specializing description, which is not d-used by the specialized one, the first both specializes and expands the second. Examples of Social Descriptions are laws, norms, shares, peace treaties, etc., which are generically dependent on societies.Social descriptions are dependent on a community of agents. A relation holding between non-physical objects and entities whatsoever (thus including non-physical objects themselves). An intuition for the references relation could be that a non-physical object adds 'information' to an entity. In fact, non-physical objects depend on a communication setting. In most cases, this is the characteristic relation that provides a unity criterion to objects, events, etc. For example, cars are objects and not mere aggregates because there is a project, a design, a social value, a functional structure, a personal emotional structure, etc. attached to them. This attachment can be represented by means of 'non-physical objects' that 'reference' cars. The most obvious application is for situations, which do not exist without a description, although they still are extensional entities: a situation without a part is no more the same situation, but a situation is not a mere aggregate, since it has references to a description as its unity criterion. Adding information to an entity can also be thought as an intentional solution to a holistic stance. Defenders of this view -within different frameworks- are Kant, Brentano, Husserl, Gestalt psychologists, Merleau-Ponty ... References is distinguished according to the kinds of non-physical objects and referenced ground entities: referencing between descriptions and situations is called 'SATISFIED-BY', while referencing between description components and situation components is called 'CLASSIFIES'. 'SETTING-FOR' is a referencing relation between a situation and the entities in its setting (it was formerly a constitution relation, but since situation appear to be social objects from the DOLCE viewpoint, the constitution solution is no more applicable). 'EXPRESSES' is bound to information objects and the meaning (description of a representation or conceptualization) in which they are involved. 'REALIZED-BY' is bound to information objects and physical representations that are used to communicate them, etc. 'ABOUT' is bound to information objects and entities whatsoever (aboutness of intentionality). A phenomenon having a physical endurant as participant. integral_part_of C integral_part_of C' if and only if: C part_of C' AND C' has_part C A relation holding between non-physical objects and entities whatsoever (thus including non-physical objects themselves). An intuition for the references relation could be that a non-physical object adds 'information' to an entity. In fact, non-physical objects depend on a communication setting. In most cases, this is the characteristic relation that provides a unity criterion to objects, events, etc. For example, cars are objects and not mere aggregates because there is a project, a design, a social value, a functional structure, a personal emotional structure, etc. attached to them. This attachment can be represented by means of 'non-physical objects' that 'reference' cars. The most obvious application is for situations, which do not exist without a description, although they still are extensional entities: a situation without a part is no more the same situation, but a situation is not a mere aggregate, since it has references to a description as its unity criterion. Adding information to an entity can also be thought as an intentional solution to a holistic stance. Defenders of this view -within different frameworks- are Kant, Brentano, Husserl, Gestalt psychologists, Merleau-Ponty ... References is distinguished according to the kinds of non-physical objects and referenced ground entities: referencing between descriptions and situations is called 'SATISFIED-BY', while referencing between description components and situation components is called 'CLASSIFIES'. 'SETTING-FOR' is a referencing relation between situation and the entities in its setting (it was formerly a constitution relation, but since situation appear to be social objects from the DOLCE viewpoint, the constitution solution is no more applicable). 'EXPRESSES' is bound to information objects and the meaning (description of a representation or conceptualization) in which they are involved. 'REALIZED-BY' is bound to information objects and physical representations that are used to communicate them, etc. 'ABOUT' is bound to information objects and entities whatsoever (aboutness of intentionality). clinical-examination The process by which a health care provider investigates the body of a patient for signs of disease ### Wikipedia definition > Physical examination or clinical examination is the process by which a health care provider investigates the body of a patient for signs > of disease. It generally follows the taking of the medical history - an account of the symptoms > as experienced by the patient. Together with the medical history, the physical examination aids > in determining the correct diagnosis and devising the treatment plan. This data then becomes part of the medical record. location_of A task (as any other concept) can be optional within some plan (or any description). In this case, it can be ignored in plan execution without affecting the satisfaction of the plan.Within plans, an task said to be optional should be placed in a way that preserves the topology (the connectedness) of the maximal task, except for sequential tasks, where it can be skipped without affecting the control structure. In fact, an optional task must either be component of a bag or sequential task, or have the concurrent task or the any-order task as a direct predecessor. 2 The task sequencing a decision to take action in order to start a plan execution. A state of the (embodied) mind A catch-all class for entities from the social world. It includes agentive and non-agentive socially-constructed objects: descriptions, concepts, figures, collections, information objects. It could be equivalent to 'non-physical object', but we leave the possibility open of 'private' non-physical objects.

A generalization of the encoder and decoder roles in Jakobson's theory of communication, which should be played by an agent.

A schedule is a task that cannot be executed twice, since it has a temporal parameter restricted to one value. In other words, a schedule classifies a specific event, which results to be 'scheduled'. When a schedule is complex, all component tasks must be temporally-bound. A plan is a method for executing or performing a procedure or a stage of a procedure. A plan must use both at least one role played by an agent, and at least one task. Finally, a plan has a goal as proper part, and can also have regulations and other descriptions as proper parts. has_participant P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t AKA arbitrary-collection.The mereological sum of any two or more endurants (physical or not). Arbitrary sums have no unity criterion (they are 'extensional'). Within Physical objects, a special place have those to which we ascribe generic intentionality (compatibly to Brentano's distinction i.e., the ability to represent something to oneself, intentionality is here represented as the ability to internally represent a description). In particular, we call Agentive, as opposite to Non-agentive, those that are able to internally represent a plan. In general, we assume that agentive objects are constituted by non-agentive objects: an organism is constituted by bodily organs, a robot is constituted by some machinery, and so on. Among non-agentive physical objects we have for example houses, bodily organs, pieces of wood, etc. A feature that is not part of its host, like a hole in a piece of cheese, the underneath of a table, the front of a house, or the shadow of a tree. A linguistic object consisting of a string (independently of its physical realization). Its topological unity can change according to its physical realization: as a written realization, its boundaries are blank spaces, as a spoken realization, sometimes is silence, sometimes not, and higher order features intervene. Grammatical entities such as nouns, verbs, adjectives, etc. are roles defined by a grammar, and words (or larger linguistic objects) can play those roles in a given language. E.g., the word 'share' can play both 'verb' and 'noun' roles in contemporary English, while the word 'come' can only play the 'verb' role in English, and the 'adverb' or 'conjunction' roles in Italian (but if we consider a word as only realized by phonemes, i.e. if we consider the oral realizations of 'come', there is no common word in the two languages). Within stative occurrences, we distinguish between states and processes according to homeomericity: sitting is classified as a state but running is classified as a process, since there are (very short) temporal parts of a running that are not themselves runnings. In general, processes differ from situations because they are not assumed to have a description from which they depend. They can be sequenced by some course, but they do not require a description as a unifying criterion. On the other hand, at any time, one can conceive a description that asserts the constraints by which a process of a certian type is such, and in this case, it becomes a situation. Since the decision of designing an explicit description that unifies a perdurant depends on context, task, interest, application, etc., when aligning an ontology do DLP, there can be indecision on where to align a process-oriented class. For example, in the WordNet alignment, we have decided to put only some physical processes under 'process', e.g. 'organic process', in order to stress the social orientedness of DLP. But whereas we need to talk explicitly of the criteria by which we conceive organic processes, these will be put under 'situation'. Similar considerations are made for the other types of perdurants in DOLCE. A different notion of event (dealing with change) is currently investigated for further developments: being 'achievement', 'accomplishment', 'state', 'event', etc. can be also considered 'aspects' of processes or of parts of them. For example, the same process 'rock erosion in the Sinni valley' can be conceptualized as an accomplishment (what has brought the current state that e.g. we are trying to explain), as an achievement (the erosion process as the result of a previous accomplishment), as a state (if we collapse the time interval of the erosion into a time point), or as an event (what has changed our focus from a state to another). In the erosion case, we could have good motivations to shift from one aspect to another: a) causation focus, b) effectual focus, c) condensation d) transition (causality). If we want to consider all the aspects of a process together, we need to postulate a unifying descriptive set of criteria (i.e. a 'description'), according to which that process is circumstantiated in a 'situation'. The different aspects will arise as a parts of a same situation. A.K.A. 'selected-by'.The referencing relation between concepts defined by descriptions and constituents of situations. It can be understood as a reification of a 'satisfiability' relation holding between elements of theories and elements of models.It has a time index, but this should not be intended as a partial compresence, since the time only refers to a part of the classified particular life or extension. 1 A boundary here is taken to be a part (mereological treatment). Consequently, in the case of endurants, (reified) boundaries are features. Any method used to enforce communication. 1 Mereological overlap: having a common part. AKA C-Description. A non-physical object that is defined by a description s, and whose function is classifying entities from a ground ontology in order to build situations that can satisfy s. A specialization of the interpreter role, played by the agents trying to conceive the description expressed by some information object created by agents playing the encoder role.

A role played by descriptions only. Usable for metalinguistic notions, like those that deal with granular partitions of knowledge, strata of reality, argumentation, etc. A role created and maintained by a society. Being part at time t. It holds for endurants only. This is important to model parts that can change or be lost over time without affecting the identity of the whole. In FOL, this is expressed as a ternary relation, but in DLs we only can reason with binary relations, then only the necessary axiom of compresence is represented here. This is the immediate relation between roles and endurants. A role classifies the position (function, use, relevance, ...) of an endurant within a context (description). Roles can be ordered, interdependent, at different layers. etc. Any entity e1 is metaphorically mapped to any other entity e2 when one of the concepts that classify e1, e.g. c1, is contextually augmented by another concept c2 from another description. located_in C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.) An event occurring in the (embodied) mind. A saturated plan is a plan that cannot be executed twice, since it defines spatio-temporal parameters restricted to one value, e.g. one of its tasks classifies an event that is valued by a definite temporal value in a definite space region.Of course, in the case of maximal spatio-temporal regions, a saturated plan tends to approximate an abstract plan from the execution viewpoint, but these worst cases are unavoidable when dealing with maximality. A description expressed by a text, and ordered by additional semiotic codes (narratological structures). A location relation bounded to regions and defined analytically through the composition of inherence and q-location. This is the analytical version of 'generic location'. The composition of d-uses and valued-by relations: a description d-uses a parameter that is valued by a region. A relation that holds without additional mediating individuals. In logical terms, a non-composed relation. Descriptions define either concepts or (social) figures. Once defined, they can be d-used by other descriptions.