Alan Rector Alan Ruttenberg Andrew Spear Michel Dumontier Pierre Grenon Sivaram Arabandi Songmao Zhang Chimezie Ogbuji Holger Stenzhorn application/rdf+xml http://www.ifomis.org/bfo/1.1 en Institute for Formal Ontology and Medical Information Science (IFOMIS) http://creativecommons.org/licenses/by/3.0 Barry Smith and Pierre Grenon: "The Cornucopia of Formal Ontological Relations" Barry Smith: "Against Fantology" Barry Smith: "Basic Tools of Formal Ontology" Barry Smith: "Beyond Concepts: Ontology as Reality Representation" Pierre Grenon and Barry Smith: "SNAP and SPAN: Towards Geospatial Dynamics" Pierre Grenon, Barry Smith and Louis Goldberg: "Biodynamic Ontology: Applying BFO in the Biomedical Domain" Pierre Grenon: "BFO in a Nutshell: A Bi-categorial Axiomatization of BFO and Comparison with DOLCE" Pierre Grenon: "Nuts in BFO's Nutshell: Revisions to the Bi-categorial Axiomatization of BFO" Pierre Grenon: "Spatio-temporality in Basic Formal Ontology: SNAP and SPAN, Upper-Level Ontology, and Framework for Formalization" Basic Formal Ontology (BFO) The CPR ontology has as its domain of discourse, the domain of clinical medicine and the related information content and other ”digital entities” that comprise CPR content. It is intended for use as a coordinate system for managing or eliciting precise meanings of terminology used by healthcare professionals within subdomains of clinical medicine for (meaningful) use in an application. This OWL ontology imports BFO, the OBO relationship ontology, and others. It formally defines a focused, core set of patient care concept archetypes [Jung, C.] replicated in various patient record terminology systems, and bioinformatic literature. This core is defined in RDF and follows the normalization principles of rigorous formal ontologies [Rector, A.]. It is can be used by patients who are medical laymen but informaticians themselves in building large, meaningfully useful web portal infrastructure for patient-controlled healthcare record systems. A formal, uniform list of archetypal artifacts in Computer-based Patient Records 1.1.1 Last modification: July 31th, 2011 Chimezie Ogbuji Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. An entity responsible for making contributions to the content of the resource. Contributor Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges. The extent or scope of the content of the resource. Coverage Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. An entity primarily responsible for making the content of the resource. Creator Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). The physical or digital manifestation of the resource. Format Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN). An unambiguous reference to the resource within a given context. Resource Identifier Recommended best practice is to use RFC 3066 [RFC3066], which, in conjunction with ISO 639 [ISO639], defines two- and three-letter primary language tags with optional subtags. Examples include "en" or "eng" for English, "akk" for Akkadian, and "en-GB" for English used in the United Kingdom. A language of the intellectual content of the resource. Language Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity. An entity responsible for making the resource available Publisher Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a related resource. Relation Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource. Information about rights held in and over the resource. Rights Management The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. The topic of the content of the resource. Subject and Keywords Typically, a Title will be a name by which the resource is formally known. A name given to the resource. Title Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element. The nature or genre of the content of the resource. Resource Type acts on acts on acts on acted on http://www.hl7.org/library/data-model/RIM/C30202/rim.htm#Procedure-targetSiteCode-att The anatomical site or system that is the focus of the procedure. acts on anatomy is approach via is approach via is approach via was approached via See SNOMED-CT: the directional, relational, or spatial access to the site of a surgical procedure approach site composed by composed by composed by composed by The relation which holds between representational artifacts and the people who compose them composed by has finding site has finding site has finding site had finding site http://www.hl7.org/library/data-model/RIM/C30202/rim.htm#Observation-targetSiteCode-att .. specifying detail about the anatomical site or system that is the focus of the observation. Corresponds with SNOMED-CT findingSite relation has finding site indicated by indicated by indicated by indicated by A relation that holds between a cpr:procedure and an entity such that the procedure is advisable by virtue of the entity indicated by plays role plays role plays role plays role plays role hypothesized problem hypothesized problem hypothesized problem hypothesized problem Relate a clinical diagnoses to the diseases they hypothesize exists in the patient hypothesized problem caused by caused by caused by caused by is caused by contraindicates by contraindicates contraindicates contraindicated indicates indicates indicates indicates is the output of is the output of is the output of was the output of Relates a representational artifact with the process that is responsible for its creation output of represents represents represents represented It is same as Information Artifact Ontology's 'is about' property [http://purl.obofoundry.org/obo/IAO_0000136] Representational artifacts stand in the cpr:representationOf relation to entities in the world. Note, this relation is somewhat similar to the relation which holds between web representations and the resources they describe [Walsh, N - Jacobs, I]. The relation ontology (RO) does not have a suitable place for this. describes / is a representation of represented by represented by represented by represented by has (as a subject of the record) has (as a subject of the record) has (as a subject of the record) has (as a subject of the record) A relation that holds between a representational artifact and the person it represents (or a part of whom it represents subject of clinical record actively participates in actively participates in actively participates in actively participates in is located in is located in is located in was located in part of a part of a part of a part of starts no earlier than starts no earlier than starts no earlier than starts no earlier than starts no earlier than starts no later than starts no later than starts no later than starts no later than starts no later than stops no earlier than stops no earlier than stops no earlier than stops no earlier than stops no earlier than stops no later than stops no later than stops no later than stops no later than stops no later than physical qualities physical quality physical quality muo:PhysicalQuality muo:Prefix muo:QualityValue unit of measurements unit of measurement unit of measurement muo:UnitOfMeasurement case history case history cpr:anamnesis The case history of a medical patient as recalled by the patient -- Wordnet case history anatomical boundary entities immaterial anatomical entities anatomical boundary entity immaterial anatomical entity anatomical boundary entity immaterial anatomical entity cpr:anatomical-boundary-entity http://sigpubs.biostr.washington.edu/archive/00000135/ FMA: Immaterial anatomical entity of one less dimension than the anatomical entity it bounds or demarcates from another anatomical entity. Examples: surface of heart, surface of epithelial cell, cervicothoracic plane, supra-orbital notch, costal margin, apex beat, Sylvian point. Anatomical boundary entity anatomical spaces anatomical space anatomical space cpr:anatomical-space http://sigpubs.biostr.washington.edu/archive/00000135/ FMA: Non-material physical anatomical entity of three dimensions, which is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more body substances or anatomical structures. Examples: celom, thoracic cavity, lesser sac of peritoneum, cavity of right atrium, lumen of aorta, mediastinum, anterior compartment of forearm, intervertebral foramen. Anatomical space anatomical Structures anatomical Structure anatomical Structure cpr:anatomical-structure http://sigpubs.biostr.washington.edu/archive/00000135/ FMA: Material anatomical entity which has inherent 3D shape; is generated by coordinated expression of the organism's own structural genes; its parts are spatially related to one another in patterns determined by coordinated gene expression. Examples: heart, right ventricle, mitral valve, myocardium, endothelium, lymphocyte, fibroblast, thorax, cardiovascular system, hemoglobin, T cell receptor. Anatomical Structure anatomical surfaces anatomical surface anatomical surface cpr:anatomical-surface http://sigpubs.biostr.washington.edu/archive/00000135/ FMA: Non-material physical anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures. Examples: body surface, epigastrium, precordium, right iliac fossa. Anatomical surface http://purl.org/obo/owl/FMA#FMA_24137 bodily features bodily feature bodily feature cpr:bodily-feature Physical component, bodily qualities, and bodily processes ( of an organism ) bodily feature clinical acts clinical act clinical act cpr:clinical-act http://www.cycfoundation.org/concepts/MedicalCareEvent A collection of events. Each instance of medical care is an event in which a medical care professional provides a medical service to some human or animal patient(s). Clinical Act clinical administrations clinical administration clinical administration cpr:clinical-administration-act http://www.nhsia.nhs.uk/headings/pages/draftinfo.asp Any administrative act undertaken by a clinician, that supports the assessment or treatment of a patient/client, but which in itself is not investigatory or therapeutic. Clinical administration clinical hypothesis-generating acts clinical hypothesis-generating act clinical hypothesis-generating act cpr:clinical-analysis-act Clinical hypothesis-generating act clinical diagnoses clinical diagnosis clinical diagnosis cpr:clinical-diagnosis http://dictionary.webmd.com/terms/diagnosis The determination of the nature of a disease, injury, or congenital defect. clinical diagnosis http://www.bmj.com/cgi/content/full/324/7339/729 http://www.loa-cnr.it/medicine/clin-act/class46.html clinical examinations clinical examination clinical examination cpr:clinical-examination http://en.wikipedia.org/wiki/Clinical_examination The process by which a health care provider investigates the body of a patient for signs of disease Clinical examination clinical phenotypes clinical phenotype clinical phenotype cpr:clinical-phenotype A constellation of those types of bodily features that are associated with a disorder at each stage of its development. clinical phenotype clinician roles clinician role clinician role cpr:clinician-role Role played by people who participate in clinical activities (typically Nurse, Physician / Doctor,etc.) Clinician role computer systems computer system computer system cpr:computer-system EHR entities EHR entity EHR entity cpr:cpr-entities "EHR entities" data entities data entity data entity cpr:data-entity diagnostic images diagnostic image diagnostic image cpr:diagnostic-image http://www.hl7.org/library/data-model/RIM/C30202/rim.htm#DiagnosticImage-cls diagnostic procedures diagnostic procedure diagnostic procedure cpr:diagnostic-procedure Diagnostic procedure extra-organismal continuants extra-organismal continuant extra-organismal continuant cpr:extra-organismal-continuant http://ontology.buffalo.edu/bio/OBR.pdf Aggregates of organismal continuants Extra-organismal continuants images image image cpr:image http://wordnet.princeton.edu/perl/webwn?s=image A visual representation (of an object or scene or person or abstraction) produced on a surface image immaterial anatomical continuants immaterial anatomical continuant immaterial anatomical continuant cpr:immaterial-anatomical-continuant From FMA: Physical anatomical entity which is a three-dimensional space, surface, line or point associated with a material physical anatomical entity. Examples: body space, surface of heart, costal margin, apex of right lung, anterior compartment of right arm. Comment Immaterial anatomical continuant http://purl.org/obo/owl/FMA#FMA_71917 immaterial pathological continuants immaterial pathological continuant immaterial pathological continuant cpr:immaterial-pathological-continuant http://ontology.buffalo.edu/bio/OBR.pdf Dependent, pathological, organismal continuants whose existence depends on corresponding independent continuant entities. Spaces, lines, surfaces, and points Immaterial pathological continuant infectious diseases infectious disease infectious disease cpr:infectious-disease infectious disease laboratory tests laboratory test laboratory test cpr:laboratory-test A quantitative or qualitative test of a substance (especially an ore or a drug) to determine its components; Laboratory test laboratory test findings laboratory test finding laboratory test finding cpr:laboratory-test-finding The representation of a quality of a specimen, and thereby a patient, that is the output of a laboratory test Laboratory test finding cpr:linguistic-construct longitudinal patient medical histories longitudinal patient medical history longitudinal patient medical history cpr:longitudinal-patient-medical-history The aggregate of all healthcare activities associated with a particular patient. Longitudinal healthcare process aggregate material pathological entities material pathological entity material pathological entity cpr:material-pathological-entity http://ontology.buffalo.edu/bio/OBR.pdf Those independent organismal continuants that result from processes other than those governed by the organisms structural genes. What Virchow had in mind was that pathological changes in the structure and function of cells and tissues constitute the disease entity.. (Caroline Whitbeck) the morphologic changes seen at the tissue level or the cellular level that are characteristic features of a disease. Material pathological entity medical devices medical device medical device cpr:medical-device medical device medical history screening acts medical history screening act medical history screening act cpr:medical-history-screening-act http://en.wikipedia.org/wiki/Medical_history Any diagnostic act which attempts to determine / realize anamnesis Medical history screening act http://wordnet.princeton.edu/perl/webwn?s=anamnesis medical therapies medical therapy medical therapy cpr:medical-therapy Medical therapy medications medication medication cpr:medication http://dictionary.webmd.com/terms/medication http://www.loa-cnr.it/medicine/biologic-substances/class18.html A medicinal substance, or medicament. 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. Medication http://www.co-ode.org/ontologies/galen#Drug http://www.loa-cnr.it/medicine/biologic-substances/class18.html cpr:metadata-entity All these are about describing the artefact itself. Use "puns" for the members of these now that they are available in OWL organismal process aggregates organismal process aggregate organismal process aggregate cpr:organismal-process-aggregate http://ontology.buffalo.edu/bio/OBR.pdf Organismal process aggregate pathological dispositions pathological disposition pathological disposition cpr:pathological-disposition A disposition (i) to undergo pathological processes that (ii) exists in an organism caused by one or more etiologic agents (iii) typically involving an identifiable group of signs and symptoms and (iv) consistent physiological or anatomical alterations Pathological disposition (disease) pathological processes pathological process pathological process cpr:pathological-process http://ontology.buffalo.edu/bio/OBR.pdf Pathological process pathological roles pathological role pathological role cpr:pathological-role http://ontology.buffalo.edu/bio/OBR.pdf Pathological role patients patient patient cpr:patient A person who participates in a healthcare act while playing the patient role. Directly corresponds with the Patient and MedicalPatient classes in GALEN / Cyc Patient patient records patient record patient record cpr:patient-record an electronic document (a representational artifact) which captures clinically relevant data about a specific patient and is primarily comprised of one or more cpr:clinical-artifacts. patient record patient roles patient role patient role cpr:patient-role Role played by people who are the recipient of healthcare services Patient role person person person cpr:person Human / person http://reliant.teknowledge.com/DAML/SUMO.owl#Human http://www.co-ode.org/ontologies/galen#Person http://www.cycfoundation.org/concepts/Person pharmacological substances pharmacological substance pharmacological substance cpr:pharmacological-substance physical anatomical entities physical anatomical entity physical anatomical entity cpr:physical-anatomical-entity http://sigpubs.biostr.washington.edu/archive/00000135/ FMA: Anatomical entity which has three or fewer spatial dimensions. Examples: hemoglobin molecule, mitochondrion, hepatocyte, erythrocyte, heart, head, blood, urine, peritoneal cavity, diaphragmatic surface of heart, inferior margin of liver, apex of lung. Physical anatomical entity physical therapies physical therapy physical therapy cpr:physical-therapy http://dictionary.webmd.com/terms/physical-therapy Treatment of pain, disease, or injury by physical means Physical therapy physicians physician physician cpr:physician http://dictionary.webmd.com/terms/physician A doctor; a person who has been educated, trained, and licensed to practice the art and science of medicine. Physician physician roles physician role physician role cpr:physician-role Role played by physicians who participate in clinical activities Physician role physiological dispositions physiological disposition physiological disposition cpr:physiological-disposition http://www.ifomis.uni-saarland.de/projects/bfo/manual/ Causes a specific physiological process or transformation in the object in which it inheres, under specific circumstances and in conjunction with the laws of nature. Physiological disposition physiological processes physiological process physiological process cpr:physiological-process http://ontology.buffalo.edu/bio/OBR.pdf Physiological process physiological roles physiological role physiological role cpr:physiological-role Physiological role psychological therapies psychological therapy psychological therapy cpr:psychological-therapy Psycholoical therapy representational artifacts representational artifact representational artifact cpr:representational-artifact http://ontology.buffalo.edu/bfo/Terminology_for_Ontologies.pdf 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. Representational artifact http://www.cycfoundation.org/concepts/InformationBearingThing http://www.loa-cnr.it/ontologies/InformationObjects.owl#linguistic-object http://www.w3.org/TR/webarch/#def-representation screening acts screening act screening act cpr:screening-act http://www.pkc.com/papers/pomr.pdf Process of data collection with pre-defined and standardized screening questionnaires in order to discover problems. http://www.loa-cnr.it/medicine/medical-procedures/class2.html self examinations self examination self examination cpr:self-examination Examination performed by a patient on their his or herself to determine the nature or identity of a disease or disorder substance administrations substance administration substance administration cpr:substance-administration http://www.hl7.org/library/data-model/RIM/C30202/rim.htm#SubstanceAdministration-cls Drug adminstration Substance adminstration http://www.co-ode.org/ontologies/galen#DrugAdministration patient's record of a symptoms patient's record of a symptom patient's record of a symptom cpr:symptom-recording Recording of a bodily feature of a patient as observed by the patient as a result of a self examination or elicitation of anamnesis and hypothesized (by the patient) to be a manifestation of a disease. patient's record of a symptom syndromes syndrome syndrome cpr:syndrome therapeutic acts therapeutic act therapeutic act cpr:therapeutic-act http://www.nhsia.nhs.uk/headings/pages/draftinfo.asp Any activity which is undertaken to maintain or improve a patient/client's state of health and well-being, relieve distress or reduce risk Therapeutic act obo:ObsoleteClass obo:Subset obo:Synonym obo:SynonymType entities entity entity bfo:Entity entity continuants continuant continuant snap:Continuant Definition: An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. Examples: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra, the disposition of blood to coagulate, the lawn and atmosphere in front of our building Synonyms: endurant continuant dependent continuants dependent continuant dependent continuant snap:DependentContinuant Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities. dependent_continuant dispositions disposition disposition snap:Disposition Definition: A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C. Examples: the disposition of vegetables to decay when not refrigerated, the disposition of a vase to brake if dropped, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease, the disposition of metal to conduct electricity. disposition snap:FiatObjectPart Definition: A material entity [snap:MaterialEntity] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities. Examples: upper and lower lobes of the left lung, the dorsal and ventral surfaces of the body, the east side of Saarbruecken, the lower right portion of a human torso Synonyms: fiat substance part fiat_object_part snap:Function Definition: A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for. Examples: the function of a birth canal to enable transport, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc., the function of reproduction in the transmission of genetic material, the digestive function of the stomach to nutriate the body, the function of a hammer to drive in nails, the function of a computer program to compute mathematical equations, the function of an automobile to provide transportation, the function of a judge in a court of law function snap:GenericallyDependentContinuant Definition: A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time. Examples: a certain PDF file that exists in different and in several hard drives generically_dependent_continuant snap:IndependentContinuant Definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything. Examples: an organism, a heart, a leg, a person, a symphony orchestra, a chair, the bottom right portion of a human torso, the lawn and atmosphere in front of our building Synonyms: substantial entity independent_continuant snap:MaterialEntity Definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. Examples: collection of random bacteria, a chair, dorsal surface of the body material_entity objects object object snap:Object Definition: A material entity [snap:MaterialEntity] that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time. Examples: an organism, a heart, a chair, a lung, an apple Synonyms: substance object object aggregates object aggregate object aggregate snap:ObjectAggregate Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries. Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital Synonyms: substance aggregate object_aggregate snap:ObjectBoundary Comment: Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal. Definition: An independent continuant [snap:IndependentContinuant] that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [snap:Object] entities that exist at exactly the point where the object [snap:Object] is separated off from the rest of the existing entities in the world. Examples: the surface of the skin, the surface of the earth, the surface of the interior of the stomach, the outer surface of a cell or cell wall Synonyms: substance boundary object_boundary snap:OneDimensionalRegion Definition: A spatial region [snap:SpatialRegion] with one dimension. Examples: the part of space that is a line stretching from one end of absolute space to the other, an edge of a cube-shaped part of space one_dimensional_region qualities quality quality snap:Quality Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property). Examples: the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee quality snap:RealizableEntity Comment: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized. Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap:Continuant] entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. Examples: the role of being a doctor, the function of the reproductive organs, the disposition of blood to coagulate, the disposition of metal to conduct electricity realizable_entity snap:Role Definition: A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts. Examples: the role of a person as a surgeon, the role of a chemical compound in an experiment, the role of a patient relative as defined by a hospital administrative form, the role of a woman as a legal mother in the context of system of laws, the role of a biological grandfather as legal guardian in the context of a system of laws, the role of ingested matter in digestion, the role of a student in a university role snap:Site Comment: An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are site [snap:Site] entities) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class). Definition: An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [snap:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [snap:Site] entities are entities that can be occupied by other continuant [snap:Continuant] entities. Examples: a particular room in a particular hospital, Maria's nostril or her intestines for a variety of bacteria. site snap:SpatialRegion Comment: All instances of continuant [snap:Continuant] are spatial entities, that is, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself. Comment: An instance of spatial region [snap:SpatialRegion] is a part of space. All parts of space are spatial region [snap:SpatialRegion] entities and only spatial region [snap:SpatialRegion] entities are parts of space. Space is the entire extent of the spatial universe, a designated individual, which is thus itself a spatial region [snap:SpatialRegion]. Comment: Space and spatial region [snap:SpatialRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called "absolutist" or "the container view". In BFO, the class site [snap:Site] allows for a so-called relational view of space, that is to say, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site [snap:Site] are not spatial region [snap:SpatialRegion] entities, they are nevertheless spatial entities. Definition: A continuant [snap:Continuant] that is neither bearer of quality [snap:Quality] entities nor inheres in any other entities. Examples: the sum total of all space in the universe, parts of the sum total of all space in the universe spatial_region snap:SpecificallyDependentContinuant Definition: A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. Examples: the mass of a cloud, the smell of mozzarella, the liquidity of blood, the color of a tomato, the disposition of fish to decay, the role of being a doctor, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc. Synonyms: property, trope, mode specifically_dependent_continuant snap:ThreeDimensionalRegion Definition: A spatial region [snap:SpatialRegion] with three dimensions. Examples: a cube-shaped part of space, a sphere-shaped part of space three_dimensional_region snap:TwoDimensionalRegion Definition: A spatial region [snap:SpatialRegion] with two dimensions. Examples: the surface of a cube-shaped part of space, the surface of a sphere-shaped part of space, the surface of a rectilinear planar figure-shaped part of space two_dimensional_region snap:ZeroDimensionalRegion Definition: A spatial region [snap:SpatialRegion] with no dimensions. Examples: a point zero_dimensional_region span:ConnectedSpatiotemporalRegion Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has temporal and spatial dimensions such that all points within the spatiotemporal region are mediately or immediately connected to all other points within the same spatiotemporal region [span:SpatiotemporalRegion]. Examples: the spatial and temporal location of an individual organism's life, the spatial and temporal location of the development of a fetus connected_spatiotemporal_region span:ConnectedTemporalRegion Definition: A temporal region [span:TemporalRegion] every point of which is mediately or immediately connected with every other point of which. Examples: the 1970s years, the time from the beginning to the end of a heart attack, the time taken up by cellular meiosis connected_temporal_region span:FiatProcessPart Definition: A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities. Examples: chewing during a meal, the middle part of a rainstorm, the worst part of a heart-attack, the most interesting part of Van Gogh's life fiat_process_part span:Occurrent Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants. Examples: the life of an organism, a surgical operation as processual context for a nosocomical infection, the spatiotemporal context occupied by a process of cellular meiosis, the most interesting part of Van Gogh's life, the spatiotemporal region occupied by the development of a cancer tumor Synonyms: perdurant occurrent span:Process Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities. Examples: the life of an organism, the process of sleeping, the process of cell-division process span:ProcessAggregate Definition: A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries. Examples: the beating of the hearts of each of seven individuals in the room, the playing of each of the members of an orchestra, a process of digestion and a process of thinking taken together process_aggregate span:ProcessBoundary Definition: A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary. Examples: birth, death, the forming of a synapse, the onset of REM sleep, the detaching of a finger in an industrial accident, the final separation of two cells at the end of cell-division, the incision at the beginning of a surgery process_boundary span:ProcessualContext Comment: An instance of a processual context [span:ProcessualContext] is a mixture of processual entity [span:ProcessualEntity] which stand as surrounding environments for other processual entity [span:ProcessualEntity] entities. The class processual context [span:ProcessualContext] is the analogous among occurrent [span:Occurrent] entities to the class site [snap:Site] among continuant [snap:Continuant] entities. Definition: An occurrent [span:Occurrent] consisting of a characteristic spatial shape inhering in some arrangement of other occurrent [span:Occurrent] entities. Processual context [span:ProcessualContext] entities are characteristically entities at or in which other occurrent [span:Occurrent] entities can be located or occur. Examples: The processual context for a given manipulation occurring as part of an experiment is made of processual entities which occur in parallel, are not necessarily all parts of the experiment themselves and may involve continuant [snap:Continuant] entities which are in the spatial vicinity of the participants in the experiment. processual_context span:ProcessualEntity Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. Examples: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird processual_entity span:ScatteredSpatiotemporalRegion Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has spatial and temporal dimensions and every spatial and temporal point of which is not connected with every other spatial and temporal point of which. Examples: the space and time occupied by the individual games of the World Cup, the space and time occupied by the individual liaisons in a romantic affair scattered_spatiotemporal_region span:ScatteredTemporalRegion Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which. Examples: the time occupied by the individual games of the World Cup, the time occupied by the individual liaisons in a romantic affair scattered_temporal_region span:SpatiotemporalInstant Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] at a specific moment. Examples: the spatiotemporal region occupied by a single instantaneous temporal slice (part) of a process spatiotemporal_instant span:SpatiotemporalInterval Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] that endures for more than a single moment of time. Examples: the spatiotemporal region occupied by a process or by a fiat processual part spatiotemporal_interval span:SpatiotemporalRegion Comment: All instances of occurrent [span:Occurrent] are spatiotemporal entities, that is, they enter in the relation of (spatiotemporal) location with spatiotemporal region [span:SpatiotemporalRegion] entities. As a particular case, the exact spatiotemporal location of a spatiotemporal region [span:SpatiotemporalRegion] is this region itself. Comment: An instance of the spatiotemporal region [span:SpatiotemporalRegion] is a part of spacetime. All parts of spacetime are spatiotemporal region [span:SpatiotemporalRegion] entities and only spatiotemporal region [span:SpatiotemporalRegion] entities are parts of spacetime. In particular, neither spatial region [snap:SpatialRegion] entities nor temporal region [span:TemporalRegion] entities are in BFO parts of spacetime. Spacetime is the entire extent of the spatiotemporal universe, a designated individual, which is thus itself a spatiotemporal region [span:SpatiotemporalRegion]. Spacetime is among occurrents the analogous of space among continuant [snap:Continuant] entities. Comment: Spacetime and spatiotemporal region [span:SpatiotemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of spacetime can be called "absolutist" or "the container view". In BFO, the class processual context [span:ProcessualContext] allows for a so-called relational view of spacetime, that is to say, a view according to which spatiotemporality is a matter of relative location between entities and not a matter of being tied to spacetime. In BFO, the bridge between these two views is secured through the fact that instances of processual context [span:ProcessualContext] are too spatiotemporal entities. Definition: An occurrent [span:Occurrent] at or in which processual entity [span:ProcessualEntity] entities can be located. Examples: the spatiotemporal region occupied by a human life, the spatiotemporal region occupied by the development of a cancer tumor, the spatiotemporal context occupied by a process of cellular meiosis spatiotemporal_region span:TemporalInstant Definition: A connected temporal region [span:ConnectedTemporalRegion] comprising a single moment of time. Examples: right now, the moment at which a finger is detached in an industrial accident, the moment at which a child is born, the moment of death temporal_instant span:TemporalInterval Definition: A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time. Examples: any continuous temporal duration during which a process occurs temporal_interval span:TemporalRegion Comment: All instances of occurrent [span:Occurrent] are temporal entities, that is, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant]. Comment: An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe, a designated individual, which is thus a temporal region itself. Comment: Time and temporal region [span:TemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called "absolutist" or "the container view" in analogy to what is traditionally the case with space (see spatial region [snap:SpatialRegion]. Definition: An occurrent [span:Occurrent] that is part of time. Examples: the time it takes to run a marathon, the duration of a surgical procedure, the moment of death temporal_region owl:Thing From SNOMED-CT: [..] the action being performed to accomplish the procedure. It does not include the surgical approach (e.g. translumbar), equipment (e.g. sutures), or physical forces (e.g. laser energy). The criteria that restricts instances of this defined class to only include those that are 'of' an organism was not axiomatized Those processes which either take place within the human organism or are processes of causal interaction in which the human organism is involved. Activities in the primary-care process are divided into two types of activities, administrative activities and clinical (encounter) activities. We have focused on the latter group of activities, activities that are relevant for medical decision making; where the clinical activities are dependent on information from the patient-record system. We say that the clinical activities belong to the clinical encounter. The division of activities into two different types, administrative and clinical, is in accordance with the HL7 RIM That which is discovered by direct observation or measurement of an organism attribute or condition, including the clinical history of the patient. The history of the presence of a disease is a 'Finding' and is distinguished from the disease itself. Note, the criteria regarding hypothesis of clinical significance is not axiomatized 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. the process of inquiry aimed at discovering the causes and mechanisms of a patient's disease insofar as this information is needed to inform treatment and management decisions to achieve the best medical outcome for the patient, and to prevent the disease in others. The type of nucleic acid containing deoxyribose as the sugar component and found principally in the nuclei (chromatin, chromosomes) and mitochondria of animal and plant cells, usually loosely bound to protein (hence the term deoxyribonucleoprotein); Physical basis for a disease An abnormality in the nucleotide sequence of an oranism's genome that is the etiologic agent for a genetic disease Addresses the shortcoming in the RO in that only continuants can be agents and doesn't support other scenarios where we with to express a causal relationship between processes (for instance) A relation that holds between some entity and a cpr:therapeutic-act such that the therapeutic act is inadvisable by virtue of the entity Relates an (informatics) process with a representational artifact that is acted upon by participants in the process and is a necessary component of the process From SNOMED-CT: [..] the action being performed to accomplish the procedure Relates an (informatics) process with a representational artifact that is the result of actions performed by one or more actors (with an informatics role) that participate A role placed by a professional who provides a medical service .. relating to or denoting any disease or condition that arises spontaneously or for which the cause is unknown Relates a recorded clinical situation with its component parts Relates an investigative act with the entity it seeks to elicit or discover Typically used to relate the quality of a participant in an informatics process that resultes in the representational artifact Note, this defined class is meant to satisfy the historical recommendation of adopting medical record terminology that emphasize the ability to present a clinician with a 'problem list' as part of L. Weed of problem-oriented medical record methodology From SNOMED-CT: [..] morphologic changes seen at the tissue or cellular level that are characteristic features of a disease Relates a processual entity to a point in time that marks the beginning or end of the (approximate) period when the processual entity started or when it ended. These are the 4 points in time that comprise a 'fuzzy' temporal interval Any living individual, whether plant or animal, considered as a whole. Organisms are the prototypical examples of substances, which are maximal connected substantial entities. They are those substantial entities which enjoy a certain rounded- offness or natural completeness, including not only organisms but also cells, rocks, planets, and a range of self-contained artifacts such as a needle or a plastic bag Any virus, microorganism, or other substance causing disease. The intersection of was changed to a unionOf (to address inconsistency) These are clinical artifacts that represent clinical situations involving findings and observables A bodily feature that is a consequence of a disease. Stedman's definition The recording of any abnormality indicative of disease, discoverable on examination of the patient; an objective indication of disease, in contrast to a symptom, which is a subjective indication of disease. Note, here a medical sign is defined as a recording rather than what the recording is a representation of. Per Ferrarario et.al, "Intuitively, we may say that states are cumulative since the mereological sum of two instances of the same occurrence-type maintains the same occurrence-type (e.g the sum of two instances of "desire" is still of the type "desire"). Moreover, states are homeomeric since all their temporal parts are described by the very same expression used for the whole occurrence" 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. A physical sign in which a non-zero value is an indication that the organism is alive Last modification: July 31th, 2011 Chimezie Ogbuji Alan Rector Michel Dumontier Sivaram Arabandi Songmao Zhang Chimezie Ogbuji The CPR ontology has as its domain of discourse, the domain of clinical medicine and the related information content and other ”digital entities” that comprise CPR content. It is intended for use as a coordinate system for managing or eliciting precise meanings of terminology used by healthcare professionals within subdomains of clinical medicine for (meaningful) use in an application. This OWL ontology imports BFO, the OBO relationship ontology, and others. It formally defines a focused, core set of patient care concept archetypes [Jung, C.] replicated in various patient record terminology systems, and bioinformatic literature. This core is defined in RDF and follows the normalization principles of rigorous formal ontologies [Rector, A.]. It is can be used by patients who are medical laymen but informaticians themselves in building large, meaningfully useful web portal infrastructure for patient-controlled healthcare record systems. A formal, uniform list of archetypal artifacts in Computer-based Patient Records Last modification: July 31th, 2011 Chimezie Ogbuji accomplishment actions accomplishment action accomplishment action cpr:SurgicalMethod accomplishment action aggregate bodily features aggregate bodily feature aggregate bodily feature cpr:aggregate-bodily-feature Constellation of bodily features biological processes biological process biological process cpr:biological-process Biological process clinical artifacts clinical artifact clinical artifact cpr:clinical-artifact A class which corresponds (at least syntactically) with the HL7 CDA Entry Act Class, insofar as its members consist of clinical recordings (representational artifacts) of natural phenomena of clinical significance. clinical artifact http://www.hl7.org/library/data-model/RIM/C30202/rim.htm#Act-cls http://xml.coverpages.org/CDA-Release2-Unofficial.html#CDA_Entry_Acts clinical findings clinical finding clinical finding cpr:clinical-finding A representation of a bodily feature of a patient that is recorded by a clinician because the feature is hypothesized to be of clinical significance. clinical finding clinical investigation acts clinical investigation act clinical investigation act cpr:clinical-investigation-act Any activity which is undertaken to find out more information about a patient/client's state of health and social well-being Clinical investigation act DNA structures DNA structure DNA structure cpr:deoxyribonucleic-acid-structure DNA structure etiologic agents etiologic agent etiologic agent cpr:etiologic-agent Toward the end of the nineteenth century the name of a disease came to reflect the type of entity thought to cause it, the so-called etiologic agent, and etiology soon came to be definitive (i.e., to be regarded as essential) for those diseases for which it was known, and diagnostic categories were refined to reflect the view that the character of a disease was determined by the character of its etiologic agent, and etiologic classification became the preferred mode of classification. (Caroline Whitbeck) etiologic agent genetic abnormalities genetic abnormality genetic abnormality cpr:genetic-abnormality genetic abnormality causes causes causes is caused causes contraindicated by contraindicated by contraindicated by contraindicated by has contraindication has (as input) has (as input) has (as input) had (as input) has input accomplished via accomplished via accomplished via accomplished via surgical method has (as output) has (as output) has (as output) has (as output) has output healthcare professional roles healthcare professional role healthcare professional role cpr:healthcare-professional-role Healthcare professional role idiopathic diseases idiopathic disease idiopathic disease cpr:idiopathic-disease idiopathic disease has (as a component part) has (as a component part) has (as a component part) has (as a component part) http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#setting-for investigates investigates investigates investigates measurement of measurement of measurement of measurement of A specialization of the representation of relation that holds between a representational artifact and a muo:QualityValue (from the measurement unit ontology): the combination of a numeric value and a unit of measurement measurement of medical problems medical problem medical problem cpr:medical-problem http://www.pkc.com/papers/pomr.pdf .. problems that clearly require the intervention of a health care professional. These include acute problems requiring hospitalization and chronic problems requiring long-term management. medical problem http://www.co-ode.org/ontologies/galen#PathologicalPhenomenon http://www.co-ode.org/ontologies/galen#hasChronicity http://www.co-ode.org/ontologies/galen#hasPathologicalStatus http://www.co-ode.org/ontologies/galen#hasSeverity morphologic alterations morphologic alteration morphologic alteration cpr:morphologic-alteration ..pathological changes in the structure and function of cells and tissues Process of physiological or granularity-agnostic anatomical alteration as a result of the realization of a pathological disposition (a disease) occurs during occurs during occurs during occurred during organisms organism organism cpr:organism organism organismal continuants organismal continuant organismal continuant cpr:organismal-continuant organismal continuant pathogen pathogen pathogen cpr:pathogen .. the organism which constitutes an etiologic agent (Caroline Whitbeck) pathogen procedures procedure procedure cpr:procedure http://www.hl7.org/library/data-model/RIM/C30202/rim.htm#Procedure-cls recorded clinical situations recorded clinical situation recorded clinical situation cpr:recorded-clinical-situation Firstly, the distinction between findings within and without situations can be removed by separating concepts into "kernel concepts"; that represent the entity itself and "recordable concepts"; for situations in which the entity either is, or is not, present. Kernel concepts would then be purely internal. Only recordable concepts would correspond to codes used as statements in Electronic Health Records (EHRs). Each recordable code would represent a class expression for a "Clinical situation"; -- Rector, A. [..] a context model to allow users and/or implementers to specify context [..], without depending on a particular record structure. The Situation with explicit context hierarchy and various attributes assigned to concepts in this hierarchy accomplish this. recorded clinical situation sequelae sequela sequela cpr:sequela Sequela sign recordings sign recording sign recording cpr:sign-recording record of a "clinical sign" states state state cpr:state http://www.loa-cnr.it/Papers/focomf2.pdf A certain enduring constellation of values of an independent continuant's aggregate physical properties. therapeutic procedures therapeutic procedure therapeutic procedure cpr:therapeutic-procedure http://dictionary.webmd.com/terms/surgery An Act whose immediate and primary outcome (post-condition) is the alteration of the physical condition of the subject. The children of this class should be pair-wise disjoint and categorized by the procedure method (essentially an equivalent of the HL7 RIM methodCode procedure attribute) Therapeutic procedure http://www.hl7.org/library/data-model/RIM/C30202/rim.htm#Procedure-cls http://www.loa-cnr.it/medicine/medical-procedures/class15.html vital signs vital sign vital sign cpr:vital-sign determination of temperature, pulse rate, rate of breathing, and level of blood pressure. physical sign indicating life Alan Ruttenberg Andrew Spear Pierre Grenon Holger Stenzhorn application/rdf+xml http://www.ifomis.org/bfo/1.1 en Institute for Formal Ontology and Medical Information Science (IFOMIS) http://creativecommons.org/licenses/by/3.0 Barry Smith and Pierre Grenon: "The Cornucopia of Formal Ontological Relations" Barry Smith: "Against Fantology" Barry Smith: "Basic Tools of Formal Ontology" Barry Smith: "Beyond Concepts: Ontology as Reality Representation" Pierre Grenon and Barry Smith: "SNAP and SPAN: Towards Geospatial Dynamics" Pierre Grenon, Barry Smith and Louis Goldberg: "Biodynamic Ontology: Applying BFO in the Biomedical Domain" Pierre Grenon: "BFO in a Nutshell: A Bi-categorial Axiomatization of BFO and Comparison with DOLCE" Pierre Grenon: "Nuts in BFO's Nutshell: Revisions to the Bi-categorial Axiomatization of BFO" Pierre Grenon: "Spatio-temporality in Basic Formal Ontology: SNAP and SPAN, Upper-Level Ontology, and Framework for Formalization" Basic Formal Ontology (BFO) 1.1.1 has causally active participant has causally active participants has causally active participant had a causally active participant has part has (as a part) has (as a part) had (as a part) has (as a participant) has (as a participant) has (as a participant) had (as a participant) has proper part has (as a proper part) has (as a proper part) had (as a proper part) participates_in participates in participates in participated in