## Accessibility ## This Semantic Web Ontology document (for self-hosted Medical Records) was written with a [faithful rendition](http://www.w3.org/2004/01/rdxh/spec#sec_rend) (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: * Markdown * RDF Vocabularies: [SKOS](http://www.w3.org/TR/swbp-skos-core-spec) / Ontology of Biomedical Investigation ([OBO](http://obi.sourceforge.net/)) vocabulary / Dublin Core ([DC](http://dublincore.org/documents/dces/)) .. and generates a host XHTML document with the following (embeded) formats: * GRDDL (OWL RDF/XML) * Manchester OWL [Syntax](http://owl-workshop.man.ac.uk/acceptedLong/submission_9.pdf) * LaTex (eventually)
## 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](http://www.hl7.org/library/data-model/RIM/C30202/rim.htm)) with more expressive [foundational](http://ontology.buffalo.edu/bio/OBR.pdf) ontologies of biology (both domain-agnostic and those specific to the domains of life sciences and healthcare) through the use of the criteria [outlined](http://www.pkc.com/papers/pomr.pdf) 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 ## > The fundamental motivation for the design and philosophy of the Problem-Oriented Medical Record (POMR) > is the belief that the medical record is the central medium of communication and the first repository > of knowledge in the practice of clinical medicine ## KR Methodology ## Elisabeth Bayegan's methodology (outlined in full within her PhD [thesis](http://www.idi.ntnu.no/~bayegan/pub/ebthesis.pdf)) 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 ## GALEN's role classes are used heavily to categorize (for instance): * Clinical social roles (physician, nurse, patient, etc..) * Other roles: DiagnosisRole, SignRole, SymptomRole, .. ## OBO Links ## The dependent OBO ontologies can be [browsed](http://www.bioontology.org/ncbo/faces/pages/ontology_list.xhtml) ## Anatomical Ontology ## Foundational Model of Anatomy [FMA](http://www.bioontology.org/ncbo/faces/pages/ontology_details.xhtml?ontology_display_name=FMA) is adopted for describing anatomical constructs. ## Papers and References ## * [A Problem Oriented Approach to the Computerized Patient Record](http://www.pkc.com/papers/pomr.pdf) * [A Strategy for Improving and Integrating Biomedical Ontologies](http://ontology.buffalo.edu/bio/OBR.pdf) * [HL7 RIM: An Incoherent Standard](http://ontology.buffalo.edu/HL7/doublestandards.pdf) * [DOLCE: Descriptive Ontology of Linguistics and Cognitive Engineering](http://www.loa-cnr.it/DOLCE.html) * [Ontologies for Knowledge Representation in a Computer-Based Patient Record](http://www.idi.ntnu.no/~bayegan/pub/bayegan_ictai02.pdf) * [Open Galen](http://www.co-ode.org/galen) * [Laboratory for Applied Ontology- Medical Theories](http://www.loa-cnr.it/medicine) * [http://www.hl7.org/library/data-model/RIM/C30202/rim.htm](HL7 Reference Information Model) * [HL7 Clinical Document Architecture, Release 2.](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16221939&query_hl=1) * [Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain](http://ontology.buffalo.edu/bfo/Terminology_for_Ontologies.pdf) * [Time Ontology in OWL](http://www.w3.org/TR/owl-time/)
Problem-oriented Medical Record Ontology
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.
An activity associated with the clinical care process model
### GALEN Definition NAMEDVolitionalAct newSub ClinicalAct. ### Knowledge Representation for Relevance Ranking of Patient-Record Contents in Primary-Care Situations Elisabeth Bayegan follows the clinical headings set as a framework for a class of 'clinical acts': > The NHS Clinical Headings Project’s main objective has been to identify a limited number of headings that will perform > the jobs that are needed for clinical communicationand navigation and that can be agreed upon by every participant > involved in clinical communication. The project produced a well-established framework of clinical headings > compatible with HL7 and CEN TC251’s standardization work on electronic patient records. Clinical Headings refer > to a set of words and phrases that clinicians use to name sections of their communications (e.g., symptoms, examination > findings, test results, diagnosis, etc.). Clinical headings have no formal syntax or definition, therefore, our content > ontology represents the formal data structures needed to strictly define concepts in the patient record. Her methodology (outlined in full within her PhD [thesis](http://www.idi.ntnu.no/~bayegan/pub/ebthesis.pdf)) is followed as a means for capturing clinical content in an RDF knowledge base. The support for a abstract clinical workflow is also an asset in possible combinations with the HCLS Advanced Clinical Protocols and Pathways ontology being developed in the W3C. ### Care Acts and Agents - Modeling the Clinical Workflow Bayegan: > We distinguish between the direct observations (the patient's problem statement and > physician's observations) and the interpretations that are done on these observations > (assessment, diagnostics, and treatment actions). This distinction between the input > to a process and the actions based on the input is also reflected in our CareActType > ontology (Figure 8.5). The CareActType ontology has four main classes that jut out > from the root concept THING (1) case history, (2) assessment, (3) diagnosis, and > (4) treatment. The former class represents the information input to the care process, > while the three latter classes represent the actions done in the care process (i.e., based > on interpretations). ### Connections to DOLCE's Plan Ontology ### See: [edns:activity][activity]
Should this be a subclass of edns:activity (provide linkage to DOLCE's more generic workflow semantics)? The participant restriction becomes redundant if so
Corresponds (at least syntactically) with the HL7 RIM Act Class, insofar as it is the class of clinical recordings (a REPRESENTATIONAL ARTIFACT) of a natural phenomenon (cpr:medical-problem, cpr:clinical-act, and anything else of clinical relevance) by an individual. Collections of such recordings, each of which is related to a person, manifests as the patient record.
### Reconciling HL7 RIM Inconsistencies The *cpr:clinical-description* class is an attempt to reconcile the ontological inconsistencies with the archetype of a recording of an act and the thing the recording describes (which could be either a continuant / endurant or an occurrant / perdurant). ### about > The relation between information objects and entities they are about. The difference with 'expresses' is that the last > requires a situation to be about something. E.g. Dante's Comedy is about facts like Dante's travel to the hereafter. > The Comedy expresses a script as well as various related meanings, while the facts talked about are not 'expressed'. > Given that descriptions are expressed by at least one IO, and that interpretations of IOs requires conceiving a description, > and the (plausible) claim that being about something can only be done in context, i.e. within a situation, we can propose > that the conceived description is satisfied by the situation (the context) of the entity the IO is about.On this basis, > about would result to be a mediated relation. This is still a proposal, then we keep about here as a primitive for some time. ### depiction > An information realization consisting of depicted images/signs of any sort (e.g. graffiti, drawings, inscriptions, pictures, > sculptures, etc.), which are inscripted on a medium that lasts longer than the depicting act. It also includes any early form > of inscripted iconic expression, which can be considered as original bodily expressions. ### REPRESENTATIONAL ARTIFACT > A representation that is fixed in some medium in such a way that it can serve to make the cognitive representations existing in the minds of separate > subjects publicly accessible in some enduring fashion. Examples are: a text, a diagram, a map legend, a list, a clinical record, or a controlled > vocabulary. ### Act (HL7 RIM) > A record of something that is being done, has been done, can be done, or is intended or requested to be done. One of the goals of this ontology is to facilitate the use of owl-time constructs to express temporal qualities using foundational ontology terms such as: * has-quality As such time:TemporalEntity serves as a syntactic proxy for temporal-quality
Should clinical-descriptions *only* be about people, problems, or acts?
The extension of this class does not include intent or requests ala HL7 RIM
With regards to temporal provenance, a clinical description can be associated with a date (of initial creation or last modification). This is not to be confused with the temporal qualities of the phenomenon it describes.
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.
Relation between a phenomena and the clinical-description which records it in a patient record
Relation between a clinical-description and what it describes
Identification of a disease from its symptoms
### Diagnosis Role Both GALEN and OBI define diagnosis roles: ### GALEN Diagnosis (Phenomenon whichG playsConsultationRole DiagnosisRole) name Diagnosis. ### OBI Diagnosis Role (OBI_159) > A diagnostic role is a role which is assigned to an entity when it is used to identify the nature or cause of some phenomenon (i.e. a diagnosis). - http://wordnet.princeton.edu/perl/webwn?s=diagnosis
This may eventually be aligned with obi:OBI_159
Any activity which is undertaken to find out more information about a patient/client's state of health and social well-being
### GALEN Defnition(s) (ClinicalAct whichG isToDetermine Phenomenon) name InvestigationAct. (ClinicalAct whichG hasSubprocess ExaminingProcess) name ExaminationAct. ### DOLCE's Definition of an information realization > Any physical entity that realizes an information object.
an impairment of health or a condition of abnormal functioning
### Alignment with OBI **TODO** Align with OBI_155 once it settles ### Ontology of Biomedical Reality > Relying on the FMAs definition of anatomical structure, we distinguish anatomical (normal) > from pathological (abnormal) material entities; the latter resulting from processes other than those > governed by the organism’s structural genes. We also extend the FMAs representation of material entities
This may eventually be aligned with obi:OBI_155
Relation between a medical sign and the entity which causes the objective indication interpreted by a clinician
A quantitative or qualitative test of a substance (especially an ore or a drug) to determine its components;
### Wordnet Defnitions Assay: > A quantitative or qualitative test of a substance (especially an ore or a drug) to determine its components; > frequently used to test for the presence or concentration of infectious agents or antibodies etc.) Diagnostic test: > An assay conducted for diagnostic purposes.
Placeholder for medical devices ontology
Any diagnostic act which attempts to determine / realize anamnesis
### WIkipedia Definition > The medical history or anamnesis[1] of a patient is information gained by a physician or other > healthcare professional by asking specific questions, either of the patient or of other people > who know the person and can give suitable information (in this case, it is sometimes called heteroanamnesis), > with the aim of obtaining information useful in formulating a diagnosis and providing medical care > to the patient. This kind of information is called the symptoms, in contrast with clinical signs, > which are ascertained by direct examination. Rather than explicitely referring (within the patient record) to instances of a class called 'history' (which act as input to activities in the care process), information-objects realized by instances of this class are assumed to be considered a case history (relative - temporaly - to the screening acts)
The class of entities or particulars which play a galen:SignOrSymptomRole or a galen:DiagnosisRole
### POMR Definition Consists mainly of problems that clearly require the intervention of a health care professional. These include acute problems requiring hospitalization and chronic problems requiring long-term management. Such problems usually offer at least some risk of impairment or disability especially if diagnosis or management is not handled properly. ### Relation to GALEN's "Basic Template for Signs and Symptoms" This 'defined class' can be considered equivalent to GALEN's SignSymptomOrDiagnosis.
Does the POMR methodology require that all medical-problems are occurrents? Do they include endurants (continuants) and / or qualities?
Is galen:hasSeverity an appropriate relation to use to capture the severity of medical problems
An "objective" (determined by a clnician) indication of some medical fact or quality that is detected by a physician during a physical examination of a patient
### Wordnet Wordnet definition of a medical sign: > .. any objective evidence of the presence of a disorder or disease ### Wikipedia Wikipedia [definition](http://en.wikipedia.org/wiki/Medical_sign) > a medical sign is an objective indication of some medical fact or quality > that is detected by a physician during a physical examination of a patient—such > as elevated blood pressure, or a clubbing of the fingers (which may be a sign > of lung disease), or arcus senilis. ### Representation Theory - Laboratory for Applied Ontology (LOA) : Medical Theories > In principle, a theory of signs admits that anything can be used to describe anything else. > In practice, there are severe limitations on the use of some entity as interpretant of another, > and these limitations derive from the cultural and local context, from the symbolic system used, > and from the cognitive and ontological underlying motivations. This is a theory which only > describes the use of signs as a post-hoc issue, after some intentionality has decided what is an > interpretant of what. Interpretant is a relation which holds between any two entities, where the > first is used to describe or explain the second. There are background conditions for being an > interpretant: an agent should be aware of both the interpretant and the reference, and a context > should encompass the agent and the entities involved. Interpretant is reflexive, while symmetry > and transitivity are debatable. Symmetry seems inappropriate, since usually some entity is USED > as interpretant, and the process is not reverted (not an equivalence). Transitivity holds only > if metaphor and metonymy are discarded as possible sense sources in the domain of interpretation.
Are class axioms in conflict? *Any* interpretation by a doctor is a medical sign, but *all* medical signs must be medical problems?
(medicine) something that treats or prevents or alleviates the symptoms of disease
### Laboratory for Applied Ontology (LOA) > A substance used in the treatment, diagnosis, prevention, or analysis of normal and abnormal body function. This includes substances that occur naturally in the body and are administered therapeutically.
An information object (a obi:digital_entity?) which includes relevant healthcare content about (similar to foaf:primaryTopic) a patient
No longer a subclass of foaf:Document and inf:linguistic-object. Now is a sole subclass of edns:information-object
(a human being) "there was too much for one person to do" - http://wordnet.princeton.edu/perl/webwn?s=person
Therapy that uses physical agents: exercise and massage and other modalities
Process of data collection with pre-defined and standardized screening questionnaires in order to discover problems.
### Problem-oriented Medical Record Definition > .. screening information can be subdivided into at least four major areas: (1) wellness > screening, (2) physical examination, (3) medical history, and (4) mental health screening. > Additional categories or sub-categories may be introduced for special needs (such as breast > cancer screening). For each of these areas we expect to record findings indicating the patient's > current status and condition, and recommended actions (in response to the findings) that may > require follow-up and monitoring. ### Laboratory for Applied Ontology (LOA) - Medical-procedures Theory > A procedure, method, or technique used to determine the nature or identity of a disease or disorder. This excludes procedures which are primarily carried out on specimens in a laboratory. ### HL7 RIM Observation Definition > An Act of recognizing and noting information about the subject, and whose immediate and primary outcome (post-condition) is new data about a subject. ### GALEN Definition ClinicalAct whichG isToDetermine (Existentiality which isExistenceOf PathologicalPhenomenon)) name ScreeningAct. OBO\_REL\_has\_improper\_part is used to relate a screening act with the acts that compose it (history taking and physical examination)
The act of introducing or otherwise applying a substance to the patient
### GALEN Definition (MechanicalPropulsion whichG < actsSpecificallyOn Drug hasUniqueAssociatedDisplacement (Displacement which isDisplacementTo BodyStructure)> ) name DrugAdministration. ### HL7 RIM Defnition (SubstanceAdministration-cls) > The act of introducing or otherwise applying a substance to the subject. > Discussion: The effect of the substance is typically established on a biochemical basis, > however, that is not a requirement. For example, radiotherapy can largely be described in > the same way, especially if it is a systemic therapy such as radio-iodine. This class also > includes the application of chemical treatments to an area.
The act of introducing or otherwise applying a substance to the subject.
How should this relate to the cpr:medication being administered?
A medical procedure involving an incision with instruments; performed to repair damage or arrest disease in a living body)
### GALEN Definition (Process whichG playsClinicalRole SurgicalRole) name SurgicalDeed.
A sensation or change in health function experienced by a patient
### Wordnet Definition See: [symptom](http://wordnet.princeton.edu/perl/webwn?s=symptom) ### Wikipedia Definition See: [Symptom](http://en.wikipedia.org/wiki/Symptom): > Strict ly, a symptom is a sensation or change in health function experienced by a patient. Thus, symptoms may be > loosely classified as strong, mild or weak. In this, medically correct, sense of the word, it is a subjective > report, as opposed to a sign, which is objective evidence of the presence of a disease or disorder. Examples of > symptoms are fatigue/tiredness, pain, or nausea. In contrast, elevated blood pressure, or abnormal appearance of > the retina, would be a medical sign indicating the nature of the disease. ### GALEN (GRAIL) Definition(s) (Phenomenon whichG playsConsultationRole SymptomRole) name Symptom. interpetant-of can be thought of as somewhat related to how isConsultationRolePlayedBy relates a SymptomRole with the phenomenon which 'plays' it
Any activity which is undertaken to maintain or improve a patient/client's state of health and well-being, relieve distress or reduce risk
### Wordnet Definition > ..care provided to improve a situation (especially medical procedures or applications that are intended to relieve illness or injury) ### GALEN Defintion ClinicalAct newSub TreatmentAct. ### NHS Clinical Headings > Any activity which is undertaken to maintain or improve a patient/client's state of health and well-being, relieve distress or reduce risk ### HL7 RIM Definition > An Act whose immediate and primary outcome (post-condition) is the alteration of the physical condition of the subject. ### Laboratory for Applied Ontology (LOA) > A procedure, method, or technique designed to prevent a disease or a disorder, or to improve physical function, or used in the process of treating a disease or injury.
Property relating a foaf:Image to a medical sign it indicates
prednisone 20qOD alternating with 18qOD.