Sivaram Arabandi Last modification: Feb. 11, 2013 Sivaram Arabandi editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term example A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> editor note editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note curator note is denotator type relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg is denotator type imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property part_of antisymmetric property xsd:true use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) Person:Alan Ruttenberg has ID digit count Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID range allocated to Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) is allocated id range Add as annotation triples in the granting ontology Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg is allocated id range has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg term replaced by Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. Person:Alan Ruttenberg has ID prefix The user-preferred unit for measuring the values of a muo:qualityValue subproperty (e.g. weight). This information is used by the conversion service to convert a value expressed in one unit to the preferred one. Preferred Unit The physical quality measured by a muo:qualityValue subproperty (e.g. weight). Property Measures Quality 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 relates a Blood Pressure state to its value. relates a Patient to a body postion. relates a Diastolic Blood Pressure state to its value. relates a quantity, amount, quality etc to a judged or interpreted level or position (increased, decreased,normal etc). relates a Systolic Blood Pressure state to its value. relates a data item to a count of specific things number of body part or location where the procedure was performed This property relates a unit with another unit from which the former is derived. For instance, square meter derives from meter. Derives from The unit used in the measurement of a particular quality value Measured in The physical quality the unit is able to measure. Measures quality The modifier prefix that applies to a derived unit of measurement Unit prefix The quality value of a measurable physical quality of an entity or phenomenon. Quality value Inverse relation of inheresIn. Relates an independent continuant to a dependent one (e.g. quality, state, function, or disposition). Formerly "has inherence". bearer of relates a place with an entity which occurs, inheres, or is part of it see property chain: a participant of a process at a given time is located where the process is located. has locus inheresIn relates a dependent continuant (a state, quality, property, function, disposition) with the independent continuant it depends on. inverse of hasInherence inheres in relates an entity with the place it occurs, inheres, or is part of locus of most general relation that relates an entity with its physical location spatially related to 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 See SNOMED-CT: the directional, relational, or spatial access to the site of a surgical procedure approach site The relation which holds between representational artifacts and the people who compose them composed by 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 A relation that holds between a cpr:procedure and an entity such that the procedure is advisable by virtue of the entity has indication Relate a clinical diagnoses to the diseases they hypothesize exists in the patient hypothesized problem Relates a representational artifact with the process that is responsible for its creation output of 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. a representation of A relation that holds between a representational artifact and the person it represents (or a part of whom it represents subject of clinical record part of OBO_REL:0000012 http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity relationship Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum adjacent_to OBO_REL:0000022 relationship agent_in OBO_REL:0000010 http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 C contained_in C' if and only if: given any instance 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' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.) relationship Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): contained_in OBO_REL:0000011 relationship contains OBO_REL:0000016 relationship derived_into OBO_REL:0000015 http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'. derived_from relationship Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant. derives_from OBO_REL:0000024 relationship See reasons for obsoletion of improper_part_of has_improper_part OBO_REL:0000005 relationship has_integral_part OBO_REL:0000025 http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 As for part_of, with the additional constraint that subject and object may be identical relationship OBSOLETE. The definition is "As for part_of, with the additional constraint that subject and object may be identical". However, part_of is already reflexive, therefore improper_part_of is identical to part_of. If read differently, as "improper_part_of is part_of but not proper_part_of",improper_part_of becomes identity. So, improper_part_of is either identical to part_of or to identity, and not an intuitive synonym for either of them. [Robert Hoehndorf] improper_part_of OBO_REL:0000004 http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 C integral_part_of C' if and only if: C part_of C' AND C' has_part C relationship integral_part_of OBO_REL:0000008 http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 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.) relationship Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus located_in OBO_REL:0000009 relationship location_of OBO_REL:0000002 http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 For continuants: C part_of 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 *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) relationship Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell. part_of OBO_REL:0000017 http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. relationship An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. preceded_by OBO_REL:0000018 relationship precedes OBO_REL:0000006 http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 As for part_of, with the additional constraint that subject and object are distinct relationship proper_part_of http://purl.org/obo/owl/GOC#GOC_cjm GOC:cjm A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances. relationship this relation was superfluous, so it has been obsoleted relationship OBO_REL:0000014 relationship Obsoleted transformed_into Alternate (standarized) symbol of the entity Alternate Symbol The dimensional size of a simple derived unit, i.e., the exponent of the dimension in the dimensional equation. For instance, for square meters, the dimensional size is two. Dimensional size Modification factor that multiples the base value of the unit Factor The time of a particular quality value (e.g. the weight of Carlos yesterday). In Time Standarized symbol of the entity Preferred Symbol starts no earlier than starts no later than stops no earlier than stops no later than SDO:AHI_Arousal Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with Arousals, and 2. hypopneas that are associated with Arousals. This includes all desaturation levels. Apnea Hypopnea Index (AHI) with Arousals SDO:AHI_Arousal_or_HbO2_2_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with Arousals, 2. apneas that are associated with at least a 2% HbO2 desaturation, 3. hypopneas that are associated with Arousals, and 4. hypopneas that are associated with at least a 2% HbO2 desaturation Apnea Hypopnea Index (AHI) with Arousals or 2% or more HbO2 desaturation SDO:AHI_Arousal_or_HbO2_3_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with Arousals, 2. apneas that are associated with at least a 3% HbO2 desaturation, 3. hypopneas that are associated with Arousals, and 4. hypopneas that are associated with at least a 3% HbO2 desaturation Apnea Hypopnea Index (AHI) with Arousals or 3% or more HbO2 desaturation SDO:AHI_Arousal_or_HbO2_4_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with Arousals, 2. apneas that are associated with at least a 4% HbO2 desaturation, 3. hypopneas that are associated with Arousals, and 4. hypopneas that are associated with at least a 4% HbO2 desaturation Apnea Hypopnea Index (AHI) with Arousals or 4% or more HbO2 desaturation SDO:AHI_Arousal_or_HbO2_5_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with Arousals, 2. apneas that are associated with at least a 5% HbO2 desaturation, 3. hypopneas that are associated with Arousals, and 4. hypopneas that are associated with at least a 5% HbO2 desaturation Apnea Hypopnea Index (AHI) with Arousals or 5% or more HbO2 desaturation SDO:AHI_HbO2_2_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with at least a 2% HbO2 desaturation, and 2. hypopneas that are associated with at least a 2% HbO2 desaturation Apnea Hypopnea Index (AHI) with 2% or more HbO2 desaturation SDO:AHI_HbO2_3_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with at least a 3% HbO2 desaturation, and 2. hypopneas that are associated with at least a 3% HbO2 desaturation Apnea Hypopnea Index (AHI) with 3% or more HbO2 desaturation SDO:AHI_HbO2_4_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with at least a 4% HbO2 desaturation, and 2. hypopneas that are associated with at least a 4% HbO2 desaturation Apnea Hypopnea Index (AHI) with 4% or more HbO2 desaturation SDO:AHI_HbO2_5_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with at least a 5% HbO2 desaturation, and 2. hypopneas that are associated with at least a 5% HbO2 desaturation Apnea Hypopnea Index (AHI) with 5% or more HbO2 desaturation SDO:AHI_NREM Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with NREM sleep stage, and 2. hypopneas that are associated with NREM sleep stage. This includes all desaturation levels. Apnea hypopnea index (AHI) during NREM sleep SDO:AHI_NREM_HbO2_2_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with NREM sleep stage and at least a 2% HbO2 desaturation, and 2. hypopneas that are associated with NREM sleep stage and at least a 2% HbO2 desaturation. Apnea hypopnea index (AHI) during NREM sleep with 2% or more HbO2 desaturation SDO:AHI_NREM_HbO2_3_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with NREM sleep stage and at least a 3% HbO2 desaturation, and 2. hypopneas that are associated with NREM sleep stage and at least a 3% HbO2 desaturation. Apnea hypopnea index (AHI) during NREM sleep with 3% or more HbO2 desaturation SDO:AHI_NREM_HbO2_4_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with NREM sleep stage and at least a 4% HbO2 desaturation, and 2. hypopneas that are associated with NREM sleep stage and at least a 4% HbO2 desaturation. Apnea hypopnea index (AHI) during NREM sleep with 4% or more HbO2 desaturation SDO:AHI_NREM_HbO2_5_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with NREM sleep stage and at least a 5% HbO2 desaturation, and 2. hypopneas that are associated with NREM sleep stage and at least a 5% HbO2 desaturation. Apnea hypopnea index (AHI) during NREM sleep with 5% or more HbO2 desaturation SDO:AHI_NonSupine Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas recorded when the patient was in a non-supine body position 2. hypopneas recorded when the patient was in a non-supine body position None-supine body position includes prone, left or right lateral recumbent positions This includes all desaturation levels. Apnea Hypopnea Index (AHI) in non-supine position SDO:AHI_NonSupine_HbO2_2_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with at least a 2% HbO2 desaturation with patient in a non-supine body position 2. hypopneas that are associated with at least a 2% HbO2 desaturation with patient in a non-supine body position None-supine body position includes prone, left or right lateral recumbent positions Apnea Hypopnea Index (AHI) in non-supine position with 2% or more HbO2 desaturation SDO:AHI_NonSupine_HbO2_3_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with at least a 3% HbO2 desaturation with patient in a non-supine body position 2. hypopneas that are associated with at least a 3% HbO2 desaturation with patient in a non-supine body position None-supine body position includes prone, left or right lateral recumbent positions Apnea Hypopnea Index (AHI) in non-supine position with 3% or more HbO2 desaturation SDO:AHI_NonSupine_HbO2_4_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with at least a 4% HbO2 desaturation with patient in a non-supine body position 2. hypopneas that are associated with at least a 4% HbO2 desaturation with patient in a non-supine body position None-supine body position includes prone, left or right lateral recumbent positions Apnea Hypopnea Index (AHI) in non-supine position with 4% or more HbO2 desaturation SDO:AHI_NonSupine_HbO2_5_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with at least a 5% HbO2 desaturation with patient in a non-supine body position 2. hypopneas that are associated with at least a 5% HbO2 desaturation with patient in a non-supine body position None-supine body position includes prone, left or right lateral recumbent positions Apnea Hypopnea Index (AHI) in non-supine position with 5% or more HbO2 desaturation SDO:AHI_OSAF_SHF_HbO2_3_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. obstructive apneas, and 2. hypopneas that are associated with at least a 3% HbO2 desaturation. Apnea Hypopnea Index (AHI) with obstructive apnea and hypopnea with 3% or more HbO2 desaturation SDO:AHI_OSAF_SHF_HbO2_4_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. obstructive apneas, and 2. hypopneas that are associated with at least a 4% HbO2 desaturation. Apnea Hypopnea Index (AHI) with obstructive apnea and hypopnea with 4% or more HbO2 desaturation SDO:AHI_REM Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with REM sleep stage, and 2. hypopneas that are associated with REM sleep stage. This includes all desaturation levels. Apnea hypopnea index (AHI) during REM sleep SDO:AHI_REM_HbO2_2_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with REM sleep stage and at least a 2% HbO2 desaturation, and 2. hypopneas that are associated with REM sleep stage and at least a 2% HbO2 desaturation. Apnea hypopnea index (AHI) during REM sleep with 2% or more HbO2 desaturation SDO:AHI_REM_HbO2_3_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with REM sleep stage and at least a 3% HbO2 desaturation, and 2. hypopneas that are associated with REM sleep stage and at least a 3% HbO2 desaturation. Apnea hypopnea index (AHI) during REM sleep with 3% or more HbO2 desaturation SDO:AHI_REM_HbO2_4_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with REM sleep stage and at least a 4% HbO2 desaturation, and 2. hypopneas that are associated with REM sleep stage and at least a 4% HbO2 desaturation. Apnea hypopnea index (AHI) during REM sleep with 4% or more HbO2 desaturation SDO:AHI_REM_HbO2_5_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with REM sleep stage and at least a 5% HbO2 desaturation, and 2. hypopneas that are associated with REM sleep stage and at least a 5% HbO2 desaturation. Apnea hypopnea index (AHI) during REM sleep with 5% or more HbO2 desaturation SDO:AHI_Supine Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas recorded when the patient was in a supine body position, and 2. hypopneas recorded when the patient was in a supine body position. This includes all desaturation levels. Apnea Hypopnea Index (AHI) in supine position SDO:AHI_Supine_HbO2_2_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with at least a 2% HbO2 desaturation with patient in a supine body position 2. hypopneas that are associated with at least a 2% HbO2 desaturation with patient in a supine body position Apnea Hypopnea Index (AHI) in supine position with 2% or more HbO2 desaturation SDO:AHI_Supine_HbO2_3_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with at least a 3% HbO2 desaturation with patient in a supine body position 2. hypopneas that are associated with at least a 3% HbO2 desaturation with patient in a supine body position Apnea Hypopnea Index (AHI) in supine position with 3% or more HbO2 desaturation SDO:AHI_Supine_HbO2_4_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with at least a 4% HbO2 desaturation with patient in a supine body position 2. hypopneas that are associated with at least a 4% HbO2 desaturation with patient in a supine body position Apnea Hypopnea Index (AHI) in supine position with 4% or more HbO2 desaturation SDO:AHI_Supine_HbO2_5_pc_desat Calculated Apnea Hypopnea Index (AHI) based on: 1. apneas that are associated with at least a 5% HbO2 desaturation with patient in a supine body position 2. hypopneas that are associated with at least a 5% HbO2 desaturation with patient in a supine body position Apnea Hypopnea Index (AHI) in supine position with 5% or more HbO2 desaturation SDO:AI_CSAF Calculated Apnea Index (AI) based on central sleep apnea finding Central Apnea Index (CAI) SDO:AI_CSAF_Arousal_or_HbO2_4_pc_desat Calculated Apnea Index (AI) based on: 1. central sleep apnea findings that are associated with arousals, and 2. central sleep apnea findings that are associated with at least a 4% HbO2 desaturation Central Apnea Index (CAI) with Arousals or 4% or more HbO2 desaturation SDO:AI_CSAF_HbO2_4_pc_desat Calculated Apnea Index (AI) based on central sleep apnea findings that are associated with at least a 4% HbO2 desaturation Central Apnea Index (CAI) with 4% or more HbO2 desaturation SDO:AI_OSAF Calculated Apnea Index (AI) based on obstructive sleep apnea finding Obstructive Apnea Index (OAI) SDO:AI_OSAF_Arousal_or_HbO2_4_pc_desat Calculated Apnea Index (AI) based on: 1. obstructive sleep apnea findings that are associated with arousals, and 2. obstructive sleep apnea findings that are associated with at least a 4% HbO2 desaturation Obstructive Apnea Index (OAI) with Arousals or 4% or more HbO2 desaturation SDO:AI_OSAF_HbO2_4_pc_desat Calculated Apnea Index (AI) based on obstructive sleep apnea findings that are associated with at least a 4% HbO2 desaturation Obstructive Apnea Index (OAI) with 4% or more HbO2 desaturation SDO:AbdominalRespiratoryExcursionFinding A respiratory finding representing the amplitude of movement of the abdomen on inhalation and exhalation Abdominal respiratory excursion finding SDO:Absence http://www.co-ode.org/ontologies/galen#absence Absence SDO:African African Black race Negroid race SDO:AgeAtDiagnosis Recorded age of a patient at the time a diagnosis was made. Age at time of Diagnosis SDO:AgeAtTimeOfProcedure Recorded age when a patient underwent a procedure (test, study etc). Age at time of Procedure Age at time of Study Age at time of Test 0.0 120.0 SDO:AgeFinding Age SDO:Airflow Airflow SDO:AirflowMeter Airflow meter SDO:AlphaWave MeSH ID: D000513 Definition: One of four types of brain waves characterized by a relatively high voltage or amplitude and a frequency of 8-13 Hz. They constitute the majority of waves recorded by EEG registering the activity of the parietal and occipital lobes when the individual is awake, but relaxed with the eyes closed. [MeSH] Alpha wave SDO:AmericanIndian American Indian Native american SDO:Amplitude magnitude of change in the oscillating variable, with each oscillation, within an oscillating system. [Wikipedia] Amplitude SDO:AnkleBrachialPressureIndex (sdo: BloodPressureSystolic_Supine_Lowerlimb)/(sdo: BloodPressureSystolic_Supine_Upperlimb) Calculation: supine systolic blood pressure at the ankle (higher of the dorsalis pedis or posterior tibial artery) divided by supine systolic blood pressure in the arms. Definition: ratio of the blood pressure in the lower limbs to the blood pressure in the upper limbs. Ankle to Brachial pressure index (ABPI, ABI) Ankle arm index SDO:Apnea a state in which there is complete cessation of breathing Apnea SDO:ApneaFinding Respiratory airflow amplitude reduced to 10% or less compared to baseline. Apnea can be voluntary or involuntary. Apnea finding 0 250 SDO:ApneaHypopneaIndex (sdo:NumberOfSleepApneaFindings + sdo:NumberOfSleepHypopneaFindings)/(sdo:TotalSleepTime) Calculation: total number of apneas and hypopneas divided by the number of hours of sleep. Definition: number of apneas and hypopneas per hour of sleep. Apnea hypopnea index (AHI) SDO:ApneaIndex (sdo:NumberOfSleepApneaFindings)/(sdo:TotalSleepTime) Calculation: total number of apneas divided by the number of hours of sleep. Definition: number of apneas per hour of sleep Apnea Index (AI) SDO:Asian http://www.ebi.ac.uk/efo/EFO_0002753 Denotes a person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent, including Cambodia, China, India, Japan, Korea, Malaysia, Mongolia, Pakistan, the Philippine Islands, Thailand, and Vietnam. Asian Black race Negroid race SDO:AsianOrPacificIslander A group that has as its members people belonging to either Asian or PacificIslander racial groups Asian or Pacific islander SDO:AutonomicNervousSystemDisorder Autonomic (Visceral) nervous system disorder SDO:BaselineHemoglobinOxygenSaturation Baseline hemoglobin oxygen saturation SDO:BaselineRespiratoryAirflowAmplitude A baseline value for respiratory amplitude determined as (1) an average of all measurements performed during the test, or (2) an average of measurements obtained during a period of known quite breathing Baseline respiratory flow amplitude finding SDO:BetaWave MeSH ID: D001611 Definition: Brain waves with frequency greater than 13 Hz seen on EEG during wakefulness. [MeSH] Beta wave SDO:BilateralLowerLimbMovementDuringSleep Bilateral lower limb movement finding SDO:BilateralUpperLimbMovementDuringSleep Bilateral upper limb movement finding SDO:BiologicalEventRecord a record of a single occurrence of a biological process Biological event SDO:BiologicalSex http://purl.org/obo/owl/PATO#0000047 Definition: An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. [PATO] Biological Sex SDO:BiologicalState Definition: static condition that inheres in a biological entity. SDO:BloodPressureDecreased An interpretation of decreased blood pressure. Blood pressure (BP) decreased Low Blood Pressure (BP) SDO:BloodPressureDiastolic Diastolic pressure is minimum pressure in the arteries, which occurs near the beginning of the cardiac cycle when the ventricles are filled with blood. [Wikipedia] Blood pressure - diastolic Diastolic Blood Pressure (BP) SDO:BloodPressureDiastolic_Average (sdo:Mean(sdo:BloodPressureDiastolic)) An average of 2 or more Diastolic pressure measurements taken over a period of time Average diastolic blood pressure (BP) SDO:BloodPressureDiastolic_Sitting Diastolic blood pressure measured in a seated patient Blood pressure - diastolic - sitting body position Diastolic Blood Pressure (BP) - Sitting position SDO:BloodPressureFinding a grouping term for all the Blood pressure related findings Blood pressure finding 0 300 SDO:BloodPressureFindingValue An objective measure of Blood pressure in mm Hg. blood pressure finding value SDO:BloodPressureFunction Pressure exerted on vessel walls by the flow of blood. This commonly refers to the systemic arterial blood pressure but can also include pulmonary as well as venous pressure. Blood pressure (BP)function SDO:BloodPressureIncreased An interpretation of increased blood pressure. Note: this is not a diagnosis of HTN. Blood pressure (BP) increased Elevated Blood Pressure (BP) 0 300 SDO:BloodPressureMeasure An objective measure of Blood pressure in mm Hg. blood pressure measure SDO:BloodPressureMeasurementProcedure Blood pressure measurement procedure SDO:BloodPressureState Refers to a blood pressure state. Blood pressure (BP) value SDO:BloodPressureSystolic Systolic pressure is peak pressure in the arteries, which occurs near the end of the cardiac cycle when the ventricles are contracting. [Wikipedia] Blood pressure - systolic Systolic Blood Pressure (BP) SDO:BloodPressureSystolic_Average (sdo:Mean(sdo:BloodPressureSystolic)) An average of 2 or more Systolic pressure measurements taken over a period of time Average systolic blood pressure (BP) SDO:BloodPressureSystolic_Sitting Systolic blood pressure measured in a seated patient Blood pressure - systolic - sitting body position Systolic Blood Pressure (BP) - sitting position SDO:BloodPressureSystolic_Supine Systolic blood pressure measured in a supine patient Blood pressure - systolic - supine body position Systolic Blood Pressure (BP) - supine position SDO:BloodPressureSystolic_Supine_Lowerlimb Systolic blood pressure measured in the Leg of a supine patient Blood pressure - systolic in lower limb - supine body position Supine ankle Blood Pressure (BP) Systolic Blood Pressure (BP) in leg - supine position SDO:BloodPressureSystolic_Supine_Upperlimb Systolic blood pressure measured in the Arm of a supine patient Blood pressure - systolic in upper limb - supine body position Supine arm Blood Pressure (BP) Systolic Blood Pressure (BP) in arm - supine position SDO:Bloodflow Bloodflow 0.0 100.0 SDO:BodyMassIndexFinding (sdo:WeightFinding / (sdo:HeightFinding * sdo:HeightFinding) ) Calculation: Metric BMI Formula ( Weight in Kilograms / ( Height in Meters ) x ( Height in Meters ) ) Body Mass Index (BMI) finding SDO:BodyPosition Refers to the configuration of the human body. It is often used interchangably with the term 'Posture' Body position Posture SDO:BodyPosition-LeftLateral Position of a person lying down with left-side downward. Body position - left lateral Left lateral recumbent position SDO:BodyPosition-Prone Position of a person lying flat, face downward. Body position - prone SDO:BodyPosition-Recumbent Etymology: Latin recumbent-, recumbens, present participle of recumbere to lie down, from re- + -cumbere to lie down; Body position - recumbent SDO:BodyPosition-RightLateral Position of a person lying down with right-side downward. Body position - right lateral Right lateral recumbent position SDO:BodyPosition-Sitting Body position - sitting SDO:BodyPosition-Standing Body position - standing SDO:BodyPosition-Supine Position of a person lying flat, face upward. Body position - supine SDO:BodyPositionFinding Describes the configuration of an individual's body i.e. standing, supine, sitting etc Body position finding SDO:BrainWavePattern patterns of electrical activity of the brain Brain wave pattern SDO:BreathingProcess Process of taking air into the lungs and letting air out Breathing process SDO:CardiacElectricalConductanceTest Diagnostic test of the Cardiac electrical activity Cardiac electrical conductance tests SDO:CardiacElectrophysiologyTest minimally invasive procedure to study the electrical conduction system of the heart. It is performed in a CATH lab. Cardiac Electrophysiology (EP) study SDO:CardiovascularDisease SDO:CardiovascularDisorder Cardiovascular system disorder SDO:CardiovascularEventRecord SDO:CardiovascularSystemFunction functions that are part of the Cardiovascular system Cardiovascular system function SDO:CardiovascularSystemState Refers to a configuration of the cardiovascular system. Cardiovascular system state SDO:CardiovascularSystemTest cardiovascular system test SDO:Caucasian http://www.ebi.ac.uk/efo/EFO_0002754 Denotes person with European, Middle Eastern, or North African ancestral origin who identifies, or is identified, as White. Caucasian Occidental White race SDO:CentralNervousSystemDisorder disorders of the brain and spinal cord. Central nervous system (CNS) disorder SDO:CentralSleepApneaDisorder Recurrent cessation of respiration during sleep with the apnea having no associated ventilatory effort. Central sleep apnea (CSA) disorder SDO:CentralSleepApneaFinding-AASM_2007 A sleep apnea associated with an absent inspiratory effort throughout the entire period of absent airflow Central sleep apnea (CSA) finding SDO:Central_tendency http://purl.org/net/OCRe/statistics.owl#Central_tendency Central tendency SDO:CognitiveDisorder Disorder of Cognition SDO:ConsciousnessFinding Consciousness finding SDO:ConsciousnessFunction Definition: the awareness or perception of the environment and of one's own mental processes. Consciousness function SDO:ConsciousnessProcess Consciousness process SDO:ConsciousnessState Conciousness state SDO:ContinuousPositiveAirwayPressureVentilationTest a diagnostic test measuring the response of the respiratory system to Continuous positive airway pressure ventilation (CPAP) Continuous positive airway pressure (CPAP) ventilation test SDO:CorticalBasalGanglionicDegeneration Rare progressive neurodegenerative disease involving the cerebral cortex and the basal ganglia. It is characterized by marked disorders in movement and cognitive dysfunction. Cortical basal ganglionic degeneration (CBGD) Corticobasal degeneration (CBD) SDO:CranialNerveDisorders disorders involving the cranial nerves Cranial nerve disorders SDO:CurrentChronologicalAge Current age of a patient calculated using the current date and the patient's date of birth Current chronological age Current age SDO:DateOfBirth Date of birth (DoB) Birth date SDO:Decreased Decreased Lowered SDO:DeltaWave MeSH ID: D003700 Definition: One of the four types of brain waves seen on EEG characterized by a high amplitude and a frequency of 4 Hz and below. They are considered the "deep sleep waves" observed during sleep in dreamless states, infancy, and in some brain disorders. [MeSH] Delta wave SDO:Dementia Definition: an acquired deterioration in cognitive abilities that impairs the successful performance of activities of daily living. [Harrison's Principles of Internal Medicine, 17e] Dementia is a non-specific illness syndrome (set of signs and symptoms) in which affected areas of cognition may be memory, attention, language, and problem solving. It is normally required to be present for at least 6 months to be diagnosed; cognitive dysfunction which has been seen only over shorter times, particularly less than weeks, must be termed delirium. [Wikipedia] Dementia SDO:DiagnosisDate date on which a disease or disorder was diagnosed Diagnosis date SDO:DiagnosticEquipment Diagnostic equipment or device SDO:DiastolicArterialHypertension A disorder of the systemic arterial system that manifests as a persistent increase in diastolic arterial pressure above the normal values for age and sex. Diastolic arterial hypertension (HTN) SDO:Dispersion http://purl.org/net/OCRe/statistics.owl#Disperion Dispersion SDO:Distributional_metric http://purl.org/net/OCRe/statistics.owl#Distributional_metric A way to summarize one aspect of a distribution. Distributional metric SDO:ElectroCardiographyFinding Electrocardiography finding ECG finding EKG finding SDO:ElectroEncephalographyFinding Electroencephalography (EEG) finding SDO:ElectroMyographyFinding Electromyography (EMG) finding SDO:ElectroOculographyFinding Electrooculography (EOG) finding SDO:Electrocardiogram a recording of the electrical activity of the heart produced by Electrocardiography. Electrocardiogram (ECG, EKG) SDO:Electrocardiography the measurement of electrical activity of the heart and the recording of such activity as a visual trace. Electrocardiography (ECG, EKG) test SDO:Electroencephalogram a recording of the electrical activity of the brain produced by Electroencephalography. Electroencephalogram (EEG) SDO:Electroencephalography the measurement of electrical activity in different parts of the brain and the recording of such activity as a visual trace. Electroencephalography (EEG) test SDO:Electromyogram a recording of the electrical activity produced by skeletal muscles and measured by Electromyography. Electromyogram (EMG) SDO:Electromyography the measurement of electrical activity produced by skeletal muscles and the recording of such activity as a visual trace. Electromyography (EMG) test SDO:Electrooculogram a recording of the resting potential of the retina produced by electrooculography and used to measure eye movements. Electrooculogram (EOG) SDO:Electrooculography A technique for measuring the resting potential of the retina. The resulting signal is called the electrooculogram. The main applications are in ophthalmological diagnosis and in recording eye movements. Unlike the electroretinogram, the EOG does not represent the response to individual visual stimuli. [Wikipedia] Electrooculography (EOG) test SDO:ElectrophysiologyFinding Electrophysiological finding SDO:ElectrophysiologyTest Diagnostic tests of the electrical activity in various regions of the body Electrophysiology test SDO:EndocrineDisease 0 24 SDO:EpworthSleepinessScale Measure of daytime sleepiness on a scale of 0 to 24 by use of a very short questionnaire. This can be helpful in diagnosing sleep disorders. It was introduced in 1991 by Dr Murray Johns of Epworth Hospital in Melbourne, Australia. The questionnaire asks the subject to rate his or her probability of falling asleep on a scale of increasing probability from 0 to 3 in eight different situations.[1] The scores for the eight questions are added to obtain a single number. A number in the range 0–9 is considered to be normal while a number in the range 10–24 is considered to indicate that specialist medical advice should be recommended. he Epworth sleepiness scale has been validated primarily in obstructive sleep apnea. It is used to measure excessive daytime sleepiness and is repeated after the administration of treatment (e.g., CPAP) to document improvement of symptoms. In narcolepsy, the Epworth sleepiness scale has both a high specificity (100%) and sensitivity (93.5%).[ [Wikepedia] Epworth Sleepiness Scale (ESS) SDO:EsophagealManometer Esophageal manometer SDO:EsophagealManometry Measurement of the pressure changes in the lumen of the esophagus is the gold standard for detecting and quantifying respiratory effort. These pressure changes are reflective of the changes in intrathoracic pressure which in turn are reflective of the inspiratory effort. Esophageal manometry SDO:EthnicGroup http://www.ebi.ac.uk/efo/EFO_0001799 A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (MSH); A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP) An ethnic group is a population whose members have a common heritage that is real or presumed such as common culture, language, religion, behaviour or biological trait. Ethnic group Ethnicity SDO:EthnicityFinding Describes the specific ethnic group that an individual belongs to. Ethnicity finding SDO:EventDate Date when an Event took place (i.e a specific instance of a processual entity) Event date SDO:EventID an identifier representing an event uniquely within a record keeping system Event ID SDO:EventRecord a record (representation artifact) of a process or procedure that has taken place Event record SDO:ExhalationProcess Process of letting air out of the lungs Exhalation process Expiration SDO:ExhaledMinuteVolume Exhaled minute volume SDO:Existentiality http://www.co-ode.org/ontologies/galen#Existentiality existentiality SDO:Exponential http://purl.org/net/OCRe/statistics.owl#Exponential Exponential SDO:FallingAsleepState Definition: a state of conciousness during which there is a person is feeling increasingly sleepy i.e. transitioning from a Wake state to a Sleep state. Falling asleep state Sleepy SDO:Female http://purl.org/obo/owl/PATO#0000383 Definition: A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. [PATO:0000383] Female sex Woman SDO:FemalePseudohermaphrodite http://purl.org/obo/owl/PATO#0001829 Definition: A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of female and external sexual characteristics of male. [PATO:0001829] Female pseudohermaphrodite SDO:FileSetReference an identifier representing a set of files uniquely within a record keeping system File set reference File path SDO:Flow movement typical of fluids (gases, liquids) and is expressed as volume of a liquid or gas that is moving per unit of time. Flow SDO:FlowMeasuringInstrument Flow measuring instrument SDO:Frequency http://purl.org/obo/owl/PATO#0000044 A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time. Frequency SDO:GammaWave Brain waves with frequency range approximately 30–100 Hz. Gamma rhythms are thought to represent binding of different populations of neurons together into a network for the purpose of carrying out a certain cognitive or motor function. [Wikipedia] Gamma wave SDO:GasExchangeFunction the function of exchange of gases at the alveolar membrane Gas exchange function SDO:GenderFinding Gender of an individual. Gender is the wide set of characteristics that are seen to distinguish between female and male members of a species. In ordinary speech, it is used interchangeably with "sex" to denote the condition of being male or female. [Wikipedia] Gender finding SDO:GeneralClinicalFinding General clinical finding SDO:GeneticSex Definition: sex as determined by the presence of the XX (female) or the XY (male) genotype in somatic cells, without regard to phenotypic manifestations. [http://medical-dictionary.thefreedictionary.com/Biological+sex] Chromosomal Sex Genetic Sex 0.0 250.0 SDO:HeightFinding Height finding SDO:HematologicalEventRecord SDO:HematologicalFunction Hematological function SDO:HematologicalLabTestFinding Definition: A finding that is the output of a laboratory test/procedure on a Hematological specimen Hematological lab test finding 0 100 SDO:HemoglobinOxygenDesaturationFinding (sdo:BaselineHemoglobinOxygenSaturation - sdo:HemoglobinOxygenDesaturationFinding) Definition: Percentage of hemoglobin in blood that is NOT bound to oxygen. Hemoglobin Oxygen (O2) desaturation finding 2 SDO:HemoglobinOxygenDesaturation_2_percent_or_more Definition: A recording of a hemoglobin oxygen desaturation equal to or greater than 2% Hemoglobin oxygen (O2) desaturation 2% or more 3 SDO:HemoglobinOxygenDesaturation_3_percent_or_more Definition: A recording of a hemoglobin oxygen desaturation equal to or greater than 3% Hemoglobin oxygen (O2) desaturation 3% or more 4 SDO:HemoglobinOxygenDesaturation_4_percent_or_more Definition: A recording of a hemoglobin oxygen desaturation equal to or greater than 3% Hemoglobin oxygen (HB O2) desaturation 4% or more 5 SDO:HemoglobinOxygenDesaturation_5_percent_or_more Definition: A recording of a hemoglobin oxygen desaturation equal to or greater than 3% Hemoglobin oxygen (HB O2) desaturation 5% or more 0 100 SDO:HemoglobinOxygenSaturationFinding Definition: Percentage of hemoglobin in blood bound to oxygen Hemoglobin Oxygen (HB O2) saturation finding SDO:Hermaphrodite http://purl.org/obo/owl/PATO#0001340 Definition: A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. [PATO:0001340] Hermaphrodite SDO:Hispanic In the U.S., Latin American derived populations are grouped in a "Hispanic" or "Latino" ethnicity. Hispanic Latino SDO:HistoryOfAntiHypertensiveUse a clinical history finding where a patient reports of taking anti-Hypertensive medication(s) in the past.The value space for this is present/absent (or true/false). History of Anti-Hypertensive use SDO:HistoryOfHypertension a clinical history finding where a patient reports of a diagnosis of Hypertension (disorder) at some time in the past.The value space for this is present/absent (or true/false). History of Hypertension (HTN) SDO:HistoryOfSnoring a clinical history finding where a patient reports of a history of snoring.The value space for this is present/absent (or true/false). History of Snoring SDO:Hypersomnia Definition: Excessive sleepiness Hypersomnia SDO:Hypopnea a state of breathing that is very shallow or has an abnormally low respiratory rate. Hypopnea SDO:HypopneaFinding Respiratory airflow amplitude more than 10% but less than 70% of baseline Hypopnea finding SDO:HypopneaIndex (sdo:NumberOfSleepHypopneaFindings)/(sdo:TotalSleepTime) Calculation: total number of hypopneas divided by the number of hours of sleep. Definition: number of hypopneas per hour of sleep Hypopnea Index (HI) SDO:Increased Increased Raised SDO:Index a number or formula expressing some property, ratio, measure etc., of something indicated e.g.: index of growth; index of intelligence. Something that serves to guide, point out, or otherwise facilitate reference: - a number derived from a formula, used to characterize a set of data - is way for summarization of data (dimension reduction) - Curtis Tatsuoka Index SDO:InhalationProcess Process of taking air into the lungs Inhalation process Inspiration SDO:InhaledMinuteVolume Inhaled minute volume SDO:Interquartile_range http://purl.org/net/OCRe/statistics.owl#Interquartile_range Interquartile range SDO:IntranasalPressureTransducer Intranasal pressure transducer SDO:K-complex A well delineated negative sharp wave immediately followed by a positive component standing out from the background EEG, with total duration >=0.5 seconds, usually maximal in amplitude when recorded using formal derivations. [AASM 2007 Manual] K complex SDO:Lambda http://purl.org/net/OCRe/statistics.owl#Lambda Lambda SDO:LeftLowerLimbMovementDuringSleep Left lower limb movement finding SDO:LeftUpperLimbMovementDuringSleep Left upper limb movement finding SDO:Level level SDO:LewyBodyDisease The clinical syndrome is characterized by visual hallucinations, parkinsonism, fluctuating alertness, falls, and often REM sleep behavior disorder. The key neuropathologic feature is the presence of Lewy bodies throughout the cortex, amygdala, cingulate cortex, and substantia nigra. Lewy body disease (LBD) Cortical lewy body disease (CLBD) Dementia with Lewy bodies Diffuse lewy body disease (DLBD) SDO:LimbMovementDuringSleep Limb movement during sleep SDO:LimbMovementFinding Limb movement (LM) finding SDO:LowerLimbMovementDuringSleep Lower limb movement finding Leg movement finding SDO:Male http://purl.org/obo/owl/PATO#0000384 Definition: A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. [PATO:0000384] Male sex Man SDO:MalePseudohermaphrodite http://purl.org/obo/owl/PATO#0001828 Definition: A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of male and external sexual characteristics of female. [PATO:0001828] Male pseudohermaphrodite SDO:MaximumHemoglobinOxygenSaturation Maximum hemoglobin oxygen (HB O2) saturation SDO:Mean http://purl.org/net/OCRe/statistics.owl#Mean Mean Average SDO:MeanArterialBloodPressure (sdo:BloodPressureDiastolic + 1/3 (sdo:BloodPressureSystolic - sdo:BloodPressureDiastolic)) The mean arterial pressure (MAP) is the average over a cardiac cycle and is determined by the cardiac output (CO), systemic vascular resistance (SVR), and central venous pressure (CVP) MAP = (CO * SVR) + CVP MAP can be approximately determined from measurements of the systolic pressure (Psys) and the diastolic pressure (Pdia) while there is a normal resting heart rate, MAP = Pdia + 1/3(Psys - Pdia) [Wikipedia] Mean arterial blood pressure (BP) SDO:MeanHbO2SaturationDuringNREMSleep Mean Hemoglobin Oxygen Saturation during NREM sleep SDO:MeanHbO2SaturationDuringREMSleep Mean Hemoglobin Oxygen Saturation during REM sleep SDO:MeanHbO2SaturationDuringSleep Mean Hemoglobin Oxygen (HB O2) Saturation during Sleep SDO:MeanHemoglobinOxygenSaturation Mean hemoglobin oxygen (HB O2) saturation SDO:Median http://purl.org/net/OCRe/statistics.owl#Median Median SDO:MedicationDate date on which a medication was administered Medication date SDO:MinimumHbO2SaturationDuringNREMSleep Minimum Hemoglobin Oxygen (HB O2) Saturation during NREM sleep SDO:MinimumHbO2SaturationDuringREMSleep Minimum Hemoglobin Oxygen (HB O2) Saturation during REM Sleep SDO:MinimumHbO2SaturationDuringSleep Minimum Hemoglobin Oxygen (HB O2) Saturation during Sleep SDO:MinimumHemoglobinOxygenSaturation Minimum hemoglobin oxygen (HB O2) saturation SDO:MixedRace A group that has as its members people belonging to two or more Racial groups at the same time. E.g.: an individual with one African parent and one Caucasian parent. There can be various combinations of the mixing of racial groups. Mixed race SDO:MixedSleepApneaFinding-AASM_2007 A sleep apnea associated with an absent inspiratory effort initially, followed by resumption of inspiratory effort in the second half Mixed sleep apnea (MSA) finding SDO:Mode http://purl.org/net/OCRe/statistics.owl#Mode Mode SDO:MovementDisorder Definition: neurological conditions that affect the speed, fluency, quality and ease of movement. Movement disorder SDO:MultipleSleepLatencyTest A validated, objective measure of the ability or tendency to fall asleep under stardardized conditions. [Sleep Medicine Essentials - Teofilo L. Lee-Chiong] Multiple Sleep Latency Test (MSLT) SDO:MultipleSystemAtrophy Definition: a sporadic, progressive, neurodegenerative disease of undetermined etiology, characterized clinically by extrapyramidal, pyramidal, cerebellar, and autonomic dysfunction in any combination (Consensus Committees representing the American Autonomic Society and. the American Academy of Neurology in 1996 and 1998). [eMedicine] Multiple System Atrophy (MSA) SDO:NREMSleepArousalIndex Definition: number of arousal events per hour of NREM sleep NREM sleep arousal index Sleep arousal index during NREM sleep SDO:NamedHypopneaFinding SDO:NamedSleepApneaFinding SDO:Narcolepsy The cardinal features of narcolepsy are Cataplexy, Hypnagogic hallucinations, Excessive daytime sleepiness, Sleep paralysis, and Sleep disruption Narcolepsy SDO:NasalThermistor Nasal thermistor SDO:NasalThermocouple Nasal thermocouple SDO:NervousSystemDisease SDO:NervousSystemDisorder Nervous system disorder SDO:NervousSystemFinding SDO:NervousSystemFunction Nervous system function SDO:NervousSystemProcess Nervous system process SDO:NervousSystemState SDO:NeuroelectrophysiologyTest Diagnostic test of the Nervous system electrical activity Neuroelectrophysiology test SDO:NeurologicalEventRecord SDO:NonRapidEyeMovementSleep NREM sleep is characterized by a lack of rapid eye movements. Non-rapid eye movement (NREM) sleep SDO:NonRapidEyeMovementSleep-N1 American Academy of Sleep Medicine (AASM), 2007 AASM 2007 NREM sleep Stage 1, Rechtschaffen and Kales (R&K) NREM sleep Stage 1 Alpha rhythm is attenuated and replaced by low amplitude, mixed frequency activity (Theta waves). Non-rapid eye movement (NREM) sleep - stage N1 Stage N1 sleep SDO:NonRapidEyeMovementSleep-N2 American Academy of Sleep Medicine (AASM), 2007 AASM 2007 NREM sleep Stage 2, Rechtschaffen and Kales (R&K) NREM sleep Stage 2 Sleep spindles and K-complexes unassociated with arousals is characteristic of stage N2 sleep. Non-rapid eye movement (NREM) sleep - stage N2 Stage N2 sleep SDO:NonRapidEyeMovementSleep-N3 American Academy of Sleep Medicine (AASM), 2007 AASM 2007 NREM sleep Stage 3 Non-rapid eye movement (NREM) sleep - stage N3 Deep sleep Slow wave sleep (SWS) Stage N3 sleep SDO:NonRapidEyeMovementSleep-Stage3 Rechtschaffen and Kales (R&K) standardization, 1968 Rechtschaffen and Kales (R&K) NREM sleep Stage 3 Non-rapid eye movement (NREM) sleep - stage 3 NREM Stage 3 sleep SDO:NonRapidEyeMovementSleep-Stage4 Rechtschaffen and Kales (R&K) NREM sleep Stage 4 Non-rapid eye movement (NREM) sleep - stage 4 NREM Stage 4 sleep SDO:Normal Normal 0 2000 SDO:NumberOfSleepApneaFindings count of the apnea events occuring during a sleep study Number of sleep apnea findings SDO:NumberOfSleepApneaFindings_2_pc_desat count of the apnea events occuring during a sleep study that are associated with a 2% HbO2 desaturation Number of sleep apnea findings associated with 2% HbO2 desaturation SDO:NumberOfSleepApneaFindings_3_pc_desat count of the apnea events occuring during a sleep study that are associated with a 3% HbO2 desaturation Number of sleep apnea findings associated with 3% HbO2 desaturation SDO:NumberOfSleepApneaFindings_4_pc_desat count of the apnea events occuring during a sleep study that are associated with a 4% HbO2 desaturation Number of sleep apnea findings associated with 4% HbO2 desaturation SDO:NumberOfSleepApneaFindings_5_pc_desat count of the apnea events occuring during a sleep study that are associated with a 5% HbO2 desaturation Number of sleep apnea findings associated with 5% HbO2 desaturation SDO:NumberOfSleepApneaFindings_Arousal count of the apnea events occuring during a sleep study that are associated with an arousal Number of sleep apnea findings associated with arousal SDO:NumberOfSleepApneaFindings_NonSupine count of the apnea events that occur while the patient is in a non-supine body position (prone, left or right lateral recumbent) Number of sleep apnea findings associated with a non-supine body position SDO:NumberOfSleepApneaFindings_Supine count of the apnea events that occur while the patient is in a supine body position Number of sleep apnea findings associated with supine body position 0 2000 SDO:NumberOfSleepHypopneaFindings count of the hypopnea events occuring during a sleep study Number of sleep hypopnea findings SDO:NumberOfSleepHypopneaFindings_2_pc_desat count of the hypopnea events occuring during a sleep study that are associated with a 2% HbO2 desaturation Number of sleep hypopnea findings associated with 2% HbO2 desaturation SDO:NumberOfSleepHypopneaFindings_3_pc_desat count of the hypopnea events occuring during a sleep study that are associated with a 3% HbO2 desaturation Number of sleep hypopnea findings associated with 3% HbO2 desaturation SDO:NumberOfSleepHypopneaFindings_4_pc_desat count of the hypopnea events occuring during a sleep study that are associated with a 4% HbO2 desaturation Number of sleep hypopnea findings associated with 4% HbO2 desaturation SDO:NumberOfSleepHypopneaFindings_5_pc_desat count of the hypopnea events occuring during a sleep study that are associated with a 5% HbO2 desaturation Number of sleep hypopnea findings associated with 5% HbO2 desaturation SDO:NumberOfSleepHypopneaFindings_Arousal count of the hypopnea events occuring during a sleep study that are associated with an arousal Number of sleep hypopnea findings associated with arousal SDO:NumberOfSleepHypopneaFindings_NonSupine count of the hypopnea events that occur while the patient is in a non-supine body position (prone, left or right lateral recumbent) Number of sleep hypopnea findings associated with a non-supine body position SDO:NumberOfSleepHypopneaFindings_Supine count of the hypopnea events that occur while the patient is in a supine body position Number of sleep hypopnea findings associated with supine body position SDO:ObstructiveSleepApneaDisorder Recurrent episodes of complete (apnea) or partial (hypopnea) upper airway obstruction occuring during sleep. Obstructive sleep apnea (OSA) disorder SDO:ObstructiveSleepApneaFinding-AASM_2007 A sleep apnea associated with normal or increased inspiratory effort throughout the entire period of absent airflow Obstructive sleep apnea (OSA) finding SDO:OperationDate Operation date Surgery date SDO:OralThermistor SDO:OralThermocouple Oral thermocouple SDO:OxygenTransport Oxygen transport in Blood SDO:PacificIslander a geographic term to describe the Austronesian inhabitants of any of the three major sub-regions of Oceania: Polynesia, Melanesia and Micronesia. Polynesia: The islands scattered across a triangle covering the east-central region of the Pacific Ocean. The triangle is bounded by the Hawaiian islands in the north, New Zealand in the west, and Easter Island in the east. The rest of Polynesia comprises Samoan islands (American Samoa and Samoa), the Cook Islands, French Polynesia (Tahiti and The Society Islands, Marquesas Islands, Austral Islands, and the Tuamotu Archipelago), Niue Island, Tokelau and Tuvalu, Tonga, Wallis and Futuna, and Pitcairn Island. Melanesia: The island of New Guinea, the Bismarck and Louisiade archipelagos, the Admiralty Islands, and Bougainville Island (which make up the independent state of Papua New Guinea), the Solomon Islands, the Santa Cruz Islands (part of the Solomon Islands), New Caledonia and Loyalty Islands, Vanuatu (formerly New Hebrides), Fiji, Norfolk Island, and various smaller islands. Micronesia: The islands of Kiribati, Guam, Nauru, the Commonwealth of the Northern Marianas, the Republic of the Marshall Islands, Palau, and the Federated States of Micronesia (Yap, Chuuk, Pohnpei, and Kosrae, all in the Caroline Islands). Pacific islander SDO:Parasomnia Definition: sleep disorders that involve abnormal and unnatural movements, behaviors, emotions, perceptions, and dreams that occur while falling asleep, sleeping, between sleep stages, or arousal from sleep [Wikipedia]. Parasomnia SDO:ParkinsonDisease Parkinson disease Idiopathic Parkinson's disease Paralysis agitans Parkinson's disease Primary parkinsonism SDO:Parkinsonism Definition: a neurological syndrome characterized by tremor, hypokinesia, rigidity, and postural instability. Parkinsonism SDO:PatientID an identifier representing a patient uniquely within a record keeping system Patient ID SDO:PercentTimeInNREMSleep (sdo:TimeInNREMSleep / sdo:TotalSleepTime) Percentage time in NREM sleep SDO:PercentTimeInNREMSleep-Stage1 Percentage time in NREM sleep - Stage 1 SDO:PercentTimeInNREMSleep-Stage2 Percentage time in NREM sleep - Stage 2 SDO:PercentTimeInNREMSleep-Stage3 Percentage time in NREM sleep - Stage 3 SDO:PercentTimeInNREMSleep-Stage4 Percentage time in NREM sleep - Stage 4 SDO:PercentTimeInREMSleep (sdo:TimeInREMSleep / sdo:TotalSleepTime) Percentage time in REM sleep 0 100 SDO:PercentTimeInSleep Percent time in sleep SDO:PeriodicBilateralLowerLimbMovementDuringSleep Periodic bilateral lower limb movement during sleep SDO:PeriodicBilateralUpperLimbMovementDuringSleep Periodic bilateral upper limb movement during sleep SDO:PeriodicLeftLowerLimbMovementDuringSleep Periodic left lower limb movement during sleep SDO:PeriodicLeftUpperLimbMovementDuringSleep Periodic left upper limb movement during sleep SDO:PeriodicLimbMovementDisorder Periodic limb movement disorder is characterized by periodic episodes of repetitive, highly stereotyped, limb movements that occur during sleep (PLMS) and by clinical sleep disturbance that cannot be accounted for by another primary sleep disorder. Periodic limb movement disorder (PLMD) Nocturnal myoclonus syndrome SDO:PeriodicLimbMovementDuringSleep Periodic limb movement during sleep (PLMS) 4 SDO:PeriodicLimbMovementFinding Periodic limb movement (PLM) finding Periodic leg movement (PLM) finding 0 200 SDO:PeriodicLimbMovementIndex Nnumber of limb movements during each hour of sleep Periodic leg movement (PLM) index SDO:PeriodicLowerLimbMovementDuringSleep Periodic lower limb movement during sleep Periodic leg movement during sleep SDO:PeriodicRightLowerLimbMovementDuringSleep Periodic right lower limb movement during sleep SDO:PeriodicRightUpperLimbMovementDuringSleep Periodic right upper limb movement during sleep SDO:PeriodicUpperLimbMovementDuringSleep Periodic upper limb movement during sleep SDO:PeripheralNervousSystemDisorder SDO:PhenotypicSex http://purl.org/obo/owl/PATO#0001894 Definition: the phenotypic manifestations of sex determined by endocrine influences. [http://medical-dictionary.thefreedictionary.com/Biological+sex] Phenotypic Sex SDO:PhysicalLength Length SDO:Pneumotachometer Pneumotachometer SDO:Polysomnogram a digital recording that is an output of polysomnography procedure and has as its parts - Electroencephaplogram (EEG), Electrooculogram (EOG), Electromyogram (EMG), Electrocardiogram (EKG), Respiratory Airflow, Respiratory Effort, Oxygen saturation and Body position. Polysomnogram (PSG) Sleep study SDO:Polysomnography a multi-parametric test used in the study of sleep and as a diagnostic tool in sleep medicine. [Wikipedia] It typically records: 1. Electroencephaplogram (EEG) 2. Electrooculogram (EOG) 3. Electromyogram (EMG) - Chin and Limb 4. Electrocardiogram (EKG) 5. Respiratory Airflow 6. Respiratory Effort 7. Oxygen saturation 8. Body position Polysomnography (PSG) test Sleep study procedure SDO:PolysomnographyFinding A finding that is the output of a Polysomnography procedure. Polysomnography (PSG) finding Sleep study finding SDO:PolysomnographyMeasure measure of sleep that is an extension of the scored events i.e. derived by further analysis of the scored events Polysomnography measure SDO:PolysomnographyWithCPAPTitrationTest a diagnostic test to evaluate the effect of CPAP during Polysomnography on the quality of sleep to establish a treatment regimen Polysomnography with CPAP Titration SDO:Presence http://www.co-ode.org/ontologies/galen#presence Presence SDO:Pressure http://purl.org/obo/owl/PATO#0001025 A physical quality which inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. Pressure SDO:PressureMeasuringInstrument Pressure measuring instrument Manometer SDO:ProcedureDate date on which a procedure was performed Procedure date SDO:ProcedureEventRecord a record of a single occurence of a procedure Procedure event SDO:PseudobulbarPalsy Definition: bilateral impairment of the function of the lower cranial nerves 9, 10, 11 and 12 which control the muscles of eating, swallowing and talking. It is the result of an upper motor neuron lesion to the corticobulbar pathways in the pyramidal tract. [Wikipedia] Pseudobulbar palsy SDO:Pseudohermaphrodite http://purl.org/obo/owl/PATO#0001827 Definition: A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of one sex and external sexual characteristics of the other sex. [PATO:0001827] Pseudohermaphrodite SDO:QualityValue the value of a quality and consists of a numeric value and a measurement unit. quality value SDO:REMSleepArousalIndex Definition: number of arousal events per hour of REM sleep REM sleep arousal index SDO:REMSleepBehaviorDisorder Definition: RBD is characterized by abnormal behaviors emerging during REM sleep that cause injury or sleep disruption. REM sleep behavior disorder (RBD) Rapid eye movement sleep behavior disorder (RBD) SDO:RaceFinding Describes the specific racial group that an individual belongs to. Race finding SDO:RacialGroup http://www.ebi.ac.uk/efo/EFO_0001432 An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. A race is a popluation categorized on the basis of various sets of heritable characteristics. Race Racial group SDO:Range http://purl.org/net/OCRe/statistics.owl#Range Range SDO:RapidEyeMovementDuringSleep Rapid eye movement finding SDO:RapidEyeMovementSleep REM sleep is characterized by low amplitude, mixed frequency waves associated with rapid eye movements. Rapid eye movement (REM) sleep Stage R sleep 0 100 SDO:RespiratoryAirflowAmplitudeFinding This is a relative measure of airflow using the amplitude of the inspiratory waveform Respiratory flow amplitude finding 10 SDO:RespiratoryAirflowAmplitude_10_percent_or_less 10 30 SDO:RespiratoryAirflowAmplitude_11_to_30_percent 10 50 SDO:RespiratoryAirflowAmplitude_11_to_50_percent 10 70 SDO:RespiratoryAirflowAmplitude_11_to_70_percent SDO:RespiratoryAirflowFinding Respiratory airflow finding SDO:RespiratoryAirflowRate This is an absolute measure of airflow during breathing and is measured by spirometry or plethysmography Respiratory airflow rate SDO:RespiratoryAirflowTest Respiratory airflow measurement test SDO:RespiratoryDisease 0 250 SDO:RespiratoryDisturbanceIndex Definition: total number of apneas, hypopneas and respiratory effort related arousals (RERAs) divided by the number of hours of sleep. Respiratory disturbance index (RDI) 1 SDO:RespiratoryEffortAmplitudeAbsent An absent respiratory effort amplitude Respiratory effort amplitude absent SDO:RespiratoryEffortAmplitudeDecreased A respiratory effort amplitude which is relative low compared to average or normal. Respiratory effort amplitude decreased 0 100 SDO:RespiratoryEffortAmplitudeFinding measures the amplitude change in the depth of an inspiratory effort Respiratory effort amplitude finding SDO:RespiratoryEffortAmplitudeIncreased A respiratory effort amplitude which is greater compared to average or normal. Respiratory effort amplitude increased SDO:RespiratoryEffortAmplitudeNormal A respiratory effort amplitude which is average or normal. Respiratory effort amplitude normal SDO:RespiratoryEffortFinding Definition: depth of inspiration measures the depth of an inspiratory effort (an instance of the inspiratory process) Respiratory effort finding SDO:RespiratoryEffortPressureFinding pressure finding used as a quantitative measure of the respiratory effort. This is often measured in the esophagus and reflects the intrathoracic pressure. Respiratory effort pressure finding SDO:RespiratoryEffortTest Respiratory effort measurement test SDO:RespiratoryEventRecord SDO:RespiratoryFinding SDO:RespiratoryFunctionTest Respiratory function test SDO:RespiratoryImpedancePlethysmography Evaluation of respiratory excursions using bands placed around the chest and abdomen Respiratory impedance plethysmography SDO:RespiratoryInductancePlethysmography Respiratory inductance plethysmography (RIP) SDO:RespiratoryLabTestFinding Respiratory lab test finding SDO:RespiratoryMinuteVolume volume of air that is inhaled or exhaled per unit of time Respiratory minute volume SDO:RespiratoryMovementExcursionFinding A respiratory finding representing the amplitude of movement of chest and diaphragm on inhalation and exhalation Respiratory movement excursion finding SDO:RespiratoryMovementFinding A respiratory finding representing the movement of chest and diaphragm on inhalation and exhalation Respiratory movement finding SDO:RespiratoryMovementSymmetryFinding A respiratory finding representing the symmetry of movement of chest and diaphragm on inhalation and exhalation Respiratory movement symmetry finding SDO:RespiratoryRateFinding Definition: Frequency of breathing (measured as number of breaths taken per 1 min) Respiratory rate finding SDO:RespiratoryRhythmFinding Respiratory rhythm or pattern SDO:RespiratorySystemFunction Respiratory system function Breathing function SDO:RespiratorySystemProcess Respiratory system process SDO:RespiratorySystemState SDO:RespiratorySystemTest Respiratory system test SDO:RespiratoryVolumeFinding SDO:RespiratoryVolumeTest Respiratory volume measurement test SDO:RestlessLegsSyndrome Restless legs syndrome is a disorder characterized by sensory symptoms and motor disturbances of the limbs, mainly during rest Restless legs syndrome (RLS) Wittmaack-Ekbom's syndrome SDO:RightLowerLimbMovementDuringSleep Right lower limb movement finding SDO:RightUpperLimbMovementDuringSleep Right upper limb movement finding SDO:SleepApneaDisorder a sleep disorder characterized by pauses in breathing during sleep Sleep apnea disorder SDO:SleepApneaFinding A finding of apnea occuring during a state of sleep Sleep apnea finding 10 SDO:SleepApneaFinding-AASM_2007 AASM Manual for Scoring Sleep, 2007 - Recommended defintion Airflow reduction >= 90% of baseline lasting for atleast 10 seconds Sensor to detect apnea: Oronasal thermal sensor Apnea finding - AASM manual 2007 definition SDO:SleepArousalFinding Definition: abrupt change from sleep to wakefulness Sleep arousal finding 3 10 SDO:SleepArousalFinding-AASM_2007 during sleep stages N1, N2, N3 or R if there is an abrupt shift of EEG frequency including alpha, theta and/or frequencies greater than 16 Hz (but not spindles) that lasts at least 3 seconds, with at least 10 seconds of stable sleep preceding the change. Scoring of arousal during REM requires a concurrent increase in submental EMG lasting at least 1 second. Sleep arousal finding - AASM 2007 0 250 SDO:SleepArousalIndex Definition: number of arousal events per hour of sleep Sleep arousal index SDO:SleepDisorder Definition: disorders related to the sleep function Sleep related disorders 0 600 SDO:SleepDuration an EEG finding that describes the temporal aspects of sleep such as 'total sleep time', 'time in REM sleep' etc. Sleep duration finding SDO:SleepFinding represents the sleep state Sleep finding SDO:SleepFunction Sleep function SDO:SleepHypopneaFinding A hypopnea occuring during a period of sleep Sleep hypopnea finding 10 SDO:SleepHypopneaFinding-AASM_2007-1 AASM Manual for Scoring Sleep, 2007 - Recommended defintion Airflow reduction >= 30% of baseline lasting for atleast 10 seconds HbO2 desaturation >= 4% from baseline Sensor to detect hypopnea: Nasal air pressure transducer Sleep hypopnea finding - AASM manual 2007 definition 1 10 SDO:SleepHypopneaFinding-AASM_2007-2 AASM Manual for Scoring Sleep, 2007 - Alternative defintion Airflow reduction >= 50% of baseline lasting for atleast 10 seconds HbO2 desaturation >= 3% from baseline Sleep hypopnea finding - AASM manual 2007 definition 2 10 SDO:SleepHypopneaFinding-Adult Sleep hypopnea finding - Adult 8 SDO:SleepHypopneaFinding-CHAT Airflow <= 50% of baseline for atleast 5 sec
 + 3 % Desaturation or Arousal Sleep hypopnea finding - CHAT 8 SDO:SleepHypopneaFinding-Child Sleep hypopnea finding - Child 5 SDO:SleepHypopneaFinding-SAC Airflow <= 50% of baseline for atleast 5 sec Sleep hypopnea finding - SAC 0 600 SDO:SleepOnsetLatency Time taken to fall asleep. Formally sleep latency is measured from the time of 'lights out' until the first epoch of any stage of sleep. [Sleep Medicine Essentials - Teofilo L. Lee-Chiong] Sleep onset latency SDO:SleepOnsetTime an event marking the date and time of onset of sleep. AASM 2007 defintion: The start of the first epoch scored as any stage other than stage W Sleep onset time SDO:SleepProcess mechanism of sleep Sleep process SDO:SleepRelatedBreathingDisorder Sleep related breathing disorder (SBD) Sleep disordered breathing (SDB) SDO:SleepRelatedFinding SDO:SleepRelatedMovementDisorder Condition characterized by relatively simple, usually stereotyped, movements that disturb sleep or by other sleep related monophasic movement disorders such as related leg cramps. Sleep related movement disorder SDO:SleepSpindle A train of distinct waves with frequency 11-16 Hz (most commonly 12-14 Hz) with a duration >=0.5 seconds, usually maximal in amplitude using central derivations. [AASM 2007 Manual] Sleep spindle SDO:SleepState Definition: a state of conciousness during which there is a decreased or no awareness of the surroundings. Asleep Sleep state SDO:SleepStudyScoringAct the act of analysis and scoring of events in a Polysomnogram Sleep study scoring SDO:SnoringProcess vibration of respiratory structures and the resulting sound, due to obstructed air movement during breathing while sleeping [Wikipedia] Snoring process SDO:SpinalNerveDisorders SDO:SplitNightPolysomnography a sleep study that involves that includes CPAP titration for part of the study time Split Night Polysomnography Split Night Study SDO:Statistical_artifact http://purl.org/net/OCRe/statistics.owl#Statistical_concept Statistical concept SDO:StudyDate Study date SDO:SystemicArterialHypertension A disorder of the systemic arterial system that manifests as a persistent increase in arterial pressure (diastolic and/or systolic) above the normal values for age and sex. Systemic arterial hypertension (HTN) SDO:SystolicArterialHypertension A disorder of the systemic arterial system that manifests as a persistent increase in systolic arterial pressure above the normal values for age and sex. Systolic arterial hypertension (HTN) SDO:TestDate Test date SDO:ThetaWave MeSH ID: D013826 Definition: One of four types of brain waves, characterized by a frequency of 4-7 Hz, usually observed in the temporal lobes when the individual is awake, but relaxed and sleepy. [MeSH] Theta wave SDO:ThoracicRespiratoryExcursionFinding A respiratory finding representing the amplitude of movement of the chest on inhalation and exhalation Thoracic respiratory excursion finding SDO:TimeInNREMSleep Portion of the total sleep time that was spent in NREM sleep Time in NREM Sleep SDO:TimeInREMSleep Portion of the total sleep time that was spent in REM sleep Time in REM Sleep SDO:TotalSleepTime The total period of time between falling asleep and final waking up (often this same as 'lights on'). This includes the short periods of wakeful states that occur between periods of sleep. Total sleep time (TST) SDO:UpperLimbMovementDuringSleep Upper limb movement finding SDO:ValuePartition value partition SDO:Variance http://purl.org/net/OCRe/statistics.owl#Variance Variance SDO:VentilationFunction the function of movement of gas in and out of the lungs Ventilation function SDO:VertexSharpWavePattern Sharply contoured waves with duration <0.5 seconds maximal over the central region and distinguishable from the background activity. [AASM 2007 Manual] Vertex sharp wave (V wave) pattern SDO:VolumeMeasuringInstrument SDO:WakeFinding represents the waking state, ranging from full alertness through early stages of drowsiness. In stage W, the majority of individuals with eyes closed will demonstrate Alpha rhythm over the occipital region. The EEG pattern with eyes open consists of low amplitude activity (chiefly beta and alpha frequencies) without the rhythmicity of alpha rhythm. Wakefulness finding SDO:WakeFunction Wake function SDO:WakeState Definition: a state of conciousness during which there is an awareness of the surroundings. Wake state Awake Stage W Wake state SDO:WakefulnessProcess Wakefulness process Arousal process SDO:WakingUpState Definition: a state of conciousness during which there is a person is feeling increasingly awake i.e. transitioning from a Sleep state to a Wake state. Waking up state Arousal 0.0 200.0 SDO:WeightFinding Weight finding UnitsOntology:Non-SI_unit Certain units that are not part of the International System of Units, i.e., they are outside the SI, but are important and widely used. [http://physics.nist.gov/cuu/Units/outside.html] Non-SI unit UnitsOntology:SI_system modern form of the metric system and is generally a system devised around the convenience of the number ten. [http://en.wikipedia.org/wiki/International_System_of_Units] SI system (le Système international d'unités) UnitsOntology:US_length_unit The system for measuring length in the United States customary system is based on the inch, foot, yard, and mile, which are the only four customary length measurements in everyday use. Since July 1, 1959, these have been defined on the basis of 1 yard = 0.9144 meters except for some applications in surveying. [http://en.wikipedia.org/wiki/United_States_customary_units#Units_of_length] US length unit UnitsOntology:US_mass_unit There have historically been five different English systems of mass: tower, apothecaries', troy, avoirdupois, and metric. Of these, it is the avoirdupois system which is the most common system of weights in the U.S., although Troy weight is still used to weigh precious metals. The avoirdupois (pronounced /ˌævərdəˈpɔɪz/; French pronunciation: [avwaʀdypwɑ]) system is a system of weights (or, properly, mass) based on a pound of sixteen ounces. [http://en.wikipedia.org/wiki/United_States_customary_units#Units_of_mass] US mass unit UnitsOntology:US_ounce (unit:gram / 28.34952) ounce (oz) UnitsOntology:US_pound (unit:US_ounce / 16) (unit:gram / 453.59237) pound (lb) UnitsOntology:area_density_unit http://purl.org/obo/owl/UO#UO_0000054 Definition: A density unit which is a standard measure of the mass exerting an influence on a given area. [Wikipedia] area density unit mass per unit area unit UnitsOntology:base_unit http://purl.org/obo/owl/UO#UO_0000045 Definition: A unit which is one of a particular measure to which all measures of that type can be related. [NIST] base unit UnitsOntology:centimeter (unit:meter * 100) http://purl.org/obo/owl/UO#UO_0000015 Definition: A length unit which is equal to one hundredth of a meter or 10^[-2] m. [NIST] centimeter cm UnitsOntology:count http://purl.org/obo/owl/UO#UO_0000189 Definition: A dimensionless unit which denotes a simple count of things. [MGED] count score tally UnitsOntology:cubic_meter (unit:liter / 1000) http://purl.org/obo/owl/UO#UO_0000096 Definition: A volume unit which is equal to the volume of a cube with edges one meter in length. One cubic meter equals to 1000 liter.s [NIST] cubic meter m^[3] UnitsOntology:day (unit:hour / 24) http://purl.org/obo/owl/UO#UO_0000033 Definition: A time unit which is equal to 24 hours. [Wikipedia] day UnitsOntology:decibel http://purl.org/obo/owl/UO#UO_0000259 Definition: The decibel (dB) is a logarithmic unit of measurement that expresses the magnitude of a physical quantity (usually power or intensity) relative to a specified or implied reference level. Since it expresses a ratio of two quantities with the same unit, it is a dimensionless unit. A decibel is one tenth of a bel, a seldom-used unit. [Wikipedia] An ratio unit which is an indicator of sound power per unit area. [techtarget] decibel dB UnitsOntology:density_unit http://purl.org/obo/owl/UO#UO_0000182 Definition: A derived unit which is a standard measure of the influence exerted by some mass. [Wikipedia] density unit UnitsOntology:derived_unit http://purl.org/obo/owl/UO#UO_0000046 Definition: A unit which is derived from base units. [Wikipedia] derived unit UnitsOntology:dimensionless_unit http://purl.org/obo/owl/UO#UO_0000186 Definition: A derived unit which is a standard measure of physical quantity consisting of only a numerical number without any units. [Wikipedia] dimensionless unit UnitsOntology:english_system refers to the historical units of measurement in medieval England, which evolved as a combination of the Anglo-Saxon and Roman systems of units. [http://en.wikipedia.org/wiki/English_unit] types of English system: Imperial system: is a system of units, first defined in the British Weights and Measures Act of 1824, later refined (until 1959) and reduced. [http://en.wikipedia.org/wiki/Imperial_unit] United States customary units: most commonly used system of measurement in the United States. It is similar but not identical to the British Imperial units. The vast majority of U.S. customary units have been defined in terms of the meter and the kilogram since the Mendenhall Order of 1893 (and, in practice, for many years before that date). [http://en.wikipedia.org/wiki/United_States_customary_units] English system of measurement UnitsOntology:event_count Definition: A dimensionless count unit which denotes the number of occurrences of an event. event count number of events UnitsOntology:event_frequency Definition: the number of occurrences of an event within a fixed time interval. [Wikipedia] Event frequency UnitsOntology:events_per_day (unit:events_per_hour * 24) Definition: number of events occurring in 1 day. Events per day UnitsOntology:events_per_hour (unit:events_per_minute * 60) Definition: number of events occurring in 1 hour. Events per hour UnitsOntology:events_per_minute (unit:events_per_second * 60) Definition: number of events occurring in 1 minute. Events per minute UnitsOntology:events_per_month (unit:events_per_day * 30) Definition: number of events occurring in 1 month. Events per month UnitsOntology:events_per_second Definition: number of events occurring in 1 second. Events per second UnitsOntology:events_per_week (unit:events_per_day * 7) Definition: number of events occurring in 1 week. Events per week UnitsOntology:events_per_year (unit:events_per_day * 365.25) Definition: number of events occurring in 1 year. Events per year UnitsOntology:foot (unit:inch / 12) (unit:meter / 0.3048) foot (ft) UnitsOntology:fraction http://purl.org/obo/owl/UO#UO_0000191 Definition: A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator). [Wikipedia] fraction UnitsOntology:frequency_unit http://purl.org/obo/owl/UO#UO_0000105 Definition: A derived unit which is a standard measure of the number of repetitive actions in a particular time. [NIST] frequency unit UnitsOntology:gram (unit:kilogram * 1000) http://purl.org/obo/owl/UO#UO_0000021 Definition: A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. [NIST] gram g UnitsOntology:hertz http://purl.org/obo/owl/UO#UO_0000106 Definition: A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. [NIST] hertz Hz UnitsOntology:hour (unit:minute / 60) http://purl.org/obo/owl/UO#UO_0000032 Definition: A time unit which is equal to 3600 seconds or 60 minutes. [Wikipedia] hour h UnitsOntology:inch (unit:millimeter / 25.4) inch (in) UnitsOntology:kilogram http://purl.org/obo/owl/UO#UO_0000009 Definition: A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. [NIST] kilogram kg UnitsOntology:kilogram_per_square_meter http://purl.org/obo/owl/UO#UO_0000086 Definition: An area density unit which is equal to the mass of an object in kilograms divided by the surface area in meters squared. [NIST] kilogram per square meter kg/m^[2] UnitsOntology:length_unit http://purl.org/obo/owl/UO#UO_0000001 Definition: A base unit which is a standard measure of the distance between two points. [Wikipedia] length unit UnitsOntology:liter http://purl.org/obo/owl/UO#UO_0000099 Definition: A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. [NIST] liter L UnitsOntology:liter_per_minute Definition: liter per minute l/m liter/min UnitsOntology:mass_unit http://purl.org/obo/owl/UO#UO_0000002 Definition: A base unit which is a standard measure of the amount of matter/energy of a physical object. [Wikipedia] mass unit UnitsOntology:meter http://purl.org/obo/owl/UO#UO_0000008 Definition: A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. [NIST] meter m UnitsOntology:metric_system an international decimalised system of measurement. [http://en.wikipedia.org/wiki/Metric_system] Metric system of measurement UnitsOntology:mile (unit:meter / 1609.344) (unit:yard / 1760) mile (mi) UnitsOntology:milligram (unit:gram * 1000) http://purl.org/obo/owl/UO#UO_0000022 Definition: A mass unit which is equal to one thousandth of a gram or 10^[-3] g. [NIST] milligram mg UnitsOntology:millimeter (unit:meter * 1000) http://purl.org/obo/owl/UO#UO_0000016 Definition: A length unit which is equal to one thousandth of a meter or 10^[-3] m. [NIST] millimeter mm UnitsOntology:millimeters_of_mercury Pressure exerted by a column of mercury. One mmHg (millimeter of mercury) is equal to one torr (133.322 Pa). millimeters of mercury mm Hg Millimeters of Mercury UnitsOntology:minute (unit:second / 60) http://purl.org/obo/owl/UO#UO_0000031 Definition: A time unit which is equal to 60 seconds. [Wikipedia] minute min UnitsOntology:month (unit:day / 30) http://purl.org/obo/owl/UO#UO_0000035 Definition: A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which is science is taken to be equal to 30 days. [Wikipedia] month UnitsOntology:named_ratio grouping for some special types of ratios UnitsOntology:non-SI_pressure_unit Pressure units that are not part of the SI system but are widely used. non-SI pressure unit UnitsOntology:pascal http://purl.org/obo/owl/UO#UO_0000110 Definition: A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2]. pascal Pa UnitsOntology:percent (unit:fraction * 100) http://purl.org/obo/owl/UO#UO_0000187 Definition: A dimensionless ratio unit which denotes numbers as fractions of 100. [Wikipedia] percent % UnitsOntology:pressure_unit http://purl.org/obo/owl/UO#UO_0000109 Definition: A derived unit which is a standard measure of the force applied to a given area. pressure unit UnitsOntology:ratio http://purl.org/obo/owl/UO#UO_0000190 Definition: A dimensionless unit which denotes an amount or magnitude of one quantity relative to another. [Wikipedia] ratio UnitsOntology:scale Definition: A dimensionless ratio unit which relates the part (the numerator) to a specified, fixed whole (the denominator). E.g. in a map, a scale of 1:10,000 may mean something like 1 centimeter on the map is equivalent to 100 meters on the ground. scale UnitsOntology:second http://purl.org/obo/owl/UO#UO_0000010 Definition: A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. [NIST] second s UnitsOntology:time_unit http://purl.org/obo/owl/UO#UO_0000003 Definition: A base unit which is a standard measure of the dimension in which events occur in sequence. [Wikipedia] time unit UnitsOntology:unit http://purl.org/obo/owl/UO#UO_0000000 Definition: A unit of measurement is a standardized quantity of a physical quality. [Wikipedia] Unit of measurement UnitsOntology:united_states_customary_units most commonly used system of measurement in the United States. It is similar but not identical to the British Imperial units. The vast majority of U.S. customary units have been defined in terms of the meter and the kilogram since the Mendenhall Order of 1893 (and, in practice, for many years before that date). [http://en.wikipedia.org/wiki/United_States_customary_units] United States customary units American system English units UnitsOntology:volume_flow_unit Definition: the volume of fluid which passes through a given surface per unit time. [Wikipedia] volume flow unit UnitsOntology:volume_unit http://purl.org/obo/owl/UO#UO_0000095 Definition: A derived unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas. [NIST] volume unit UnitsOntology:week (unit:day / 7) http://purl.org/obo/owl/UO#UO_0000034 Definition: A time unit which is equal to 7 days. [Wikipedia] week UnitsOntology:yard (unit:foot / 3) (unit:meter / 0.9144) yard (yd) UnitsOntology:year (unit:day / 365.25) http://purl.org/obo/owl/UO#UO_0000036 Definition: A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. [Wikipedia] year Alpha 2 adrenergic agonist DPP-4 inhibitor Abciximab Acarbose Acetohexamide Adenosine diphosphate (ADP) receptor inhibitor Adenosine reuptake inhibitor Adrenergic receptor antagonists Aldomet Aldosterone antagonist Alpha-adrenoceptor agonist Alpha-glucosidase inhibitor Alpha adrenergic receptor antagonist Alpha blocker Amlodipine Amylin analog Angiotensin-Converting Enzyme (ACE) inhibitor antihypertensive formulation made up of Angiotensin-Converting Enzyme (ACE) inhibitor + Diuretic Angiotensin-Converting Enzyme (ACE) inhibitor AND Diuretic Angiotensin II receptor antagonist antihypertensive formulation made up of Angiotensin II receptor antagonist + Diuretic Angiotensin II receptor antagonist AND Diuretic Anticoagulant SNOMED-concept_id: 63094006 Anticonvulsant SNOMED-concept_id: 358926001 Antidementia drug RxNorm-RXCUI: 927 SNOMED-concept_id: 36236003 Antidepressant Antidiabetic agent SNOMED-concept_id: 58050004 Antiparkinsonian drug Antiplatelet drug SNOMED-concept_id: 255635008 drug used in the treatment of symptoms of anxiety Anxiolytic Apresoline Aspirin Atenolol Autonomic agent Benazepril SNOMED-concept_id: 16047007 five intrinsic benzodiazepine effects: anxiolytic, amnesic, sedative/hypnotic, anticonvulsant and muscle relaxant. Benzodiazepine Beta adrenergic receptor antagonist Beta blocker Biguanide Calan Calcium channel blocker Capoten Captopril SNOMED-concept_id: 40820003 Carbamazepine Cardiovascular system (CVS) drug Cardizem Central nervous system (CNS) drug Centrally acting hypotensive agent Brand names: Diuril Chlorothiazide Chlorpropamide Cilostazol SNOMED-concept_id: 96236000 Clobazam SNOMED-concept_id: 69708003 Clonazepam SNOMED-concept_id: 62782004 Clonidine Clopidogrel two or more drugs that are used in combination to reduce blood pressure combination hypotensive agent combination antihypertensive agent Corgard Cyclooxygenase inhibitor SNOMED-concept_id: 48546005 Diazepam Diltiazem Dipyridamole Diuretic Donepezil Donezepil (misspelling) SNOMED-concept_id: 384952006 Dopamine agonist Enalapril Endocrine system drug Eptifibatide Exenatide Felodipine Fosinopril Furosemide (frusemide) SNOMED-concept_id: 108402001 Gabapentin Gliclazide Glimepiride Glipizide Glyburide Glycoprotein IIB/IIIA inhibitor Hematologic drug Hydralazine Brand names: Apo-Hydro, Aquazide H, Dichlotride, Hydrodiuril, HydroSaluric, Microzide, Esidrex, Oretic Hydrochlorothiazide (HCTZ, HCT, HZT) SNOMED-concept_id: 321088006 drug whose primary function is to induce sleep Hypnotic agent or drug whose primary function is to reduce blood pressure Hypotensive agent Antihypertensive agent Incretin mimetic agent Inderal Insulin Lasix SNOMED-concept_id: 15383004 Levodopa L-3-hydroxytyrosine L-Dopa Liraglutide Lisinopril Loop diuretic Lopresor SNOMED-concept_id: 19225000 Lorazepam Meglitinide SNOMED-concept_id: 419304003 Melatonin agonist Metformin SNOMED-concept_id: 84078002 Methyldopa Metoprolol Miglitol SNOMED-concept_id: 71770007 Monoamine oxidase inhibitor (MAOI) Nadolol Nateglinide Brand names: Adalat, Nifedical, Procardia Nifedipine Oxyprenolol Perindopril Phenformin Phosphodiesterase inhibitor Pindolol Pioglitazone Potassium sparing diuretic SNOMED-concept_id: 108471007 Pramipexole Pramlintide Prasugrel Procardia Propranolol drugs that exert an effect on the mental state Psychoactive agent Psychotherapeutic agent Quinapril SNOMED-concept_id: 419588002 Ramelteon Ramipril Repaglinide SNOMED-concept_id: 108473005 Ropinirole Rosiglitazone Saxagliptin SNOMED-concept_id: 349859000 Sedative SNOMED-concept_id: 349854005 Selective serotonin re-uptake inhibitor (SSRI) Serotonin-specific reuptake inhibitor (SSRI) Serotonin-norepinephrine reuptake inhibitor (SNRI) Sitagliptin Sulfonylurea Sulphonamide diuretic Sympathomimetic agent Adrenergic agent Tenormin Thiazide diuretic Thiazolidinedione Thrombolytic agent Ticlopidine Timolol Tirofiban Tolazamide Tolbutamide Trandolapril SNOMED-concept_id: 33219003 Tricyclic antidepressant Troglitazone Vasodilator Vasotec Brand names: Isoptin, Verelan, Verelan PM, Calan, Bosoptin, Covera-HS Verapamil Vildagliptin Zestril IAO:0000027 a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. OBO:imported 'http://purl.obolibrary.org/obo/iao.owl' data item IAO:0000030 an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity OBO:sourced 'OBI:0000142' information content entity IAO:0000078 curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification IAO:0000102 data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part IAO:0000225 obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification IAO:0000409 The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type OGMS:0000013 Albert Goldfain creation date: 2009-06-23T10:17:44Z obsolete_representation OGMS:0000014 A representation of a bodily feature of a patient that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:18:02Z clinical finding OGMS:0000015 A series of statements representing health-relevant features of a patient and of a patient's family. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:18:59Z clinical history OGMS:0000016 A representation of the clinically significant bodily features of a patient that is inferred from the totality of clinical findings about the given patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:20:20Z clinical picture OGMS:0000017 A representation of an image that supports an inference to an assertion about some quality of a patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:21:10Z image finding OGMS:0000018 A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:21:58Z laboratory finding OGMS:0000019 A representation of a bodily feature of a patient that is (1) recorded by a clinician because the feature is hypothesized to be of clinical significance and (2) refers to features obtaining in the patient prior to their becoming detectable in a clinical history taking or physical examination. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:22:44Z preclinical finding OGMS:0000020 A bodily feature of a patient that is observed by the patient and is hypothesized by the patient to be a realization of a disease. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:02:10Z symptom OGMS:0000021 note: defined class Albert Goldfain creation date: 2009-06-23T11:09:37Z bodily feature of a patient OGMS:0000022 A bodily feature of a patient that is (a) a deviation from clinical normality that exists in virtue of the realization of a disease and (b) is observable. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:12:33Z manifestation of a disease OGMS:0000023 A (combination of) bodily feature(s) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:13:49Z phenotype OGMS:0000024 A bodily feature of a patient that is observed in a physical examination and is deemed by the clinician to be of clinical significance. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:14:36Z sign OGMS:0000025 A manifestation of a disease that is detectable in a clinical history taking or physical examination. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:15:43Z clinical manifestation of a disease OGMS:0000026 A manifestation of a disease that exists prior to the time at which it would be detected in a clinical history taking or physical examination, if the patient were to present to a clinician. A realization of a disease that exists prior to its becoming detectable in a clinical history taking or physical examination. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:16:50Z preclinical manifestation of a disease OGMS:0000027 A clinically abnormal phenotype. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:18:05Z clinical phenotype OGMS:0000028 A clinically abnormal phenotype that is characteristic of a single disease. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:18:39Z disease phenotype OGMS:0000029 A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:19:17Z vital sign OGMS:0000030 A disposition in an organism that constitutes an increased risk of the organism's subsequently developing the disease X. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:20:25Z predisposition to disease of type X OGMS:0000031 A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:21:20Z disease OGMS:0000032 Albert Goldfain creation date: 2009-06-23T11:22:01Z homeostasis OGMS:0000033 A predisposition to disease of type X whose physical basis is a constitutional abnormality in an organism's genome. This abnormality is the physical basis for the increased risk of acquiring the disease X. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:23:07Z genetic predisposition to disease of type X OGMS:0000034 A disease whose physical basis is an acquired genetic disorder. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:24:05Z acquired genetic disease OGMS:0000035 A disease whose physical basis is a constitutional genetic disorder. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:24:59Z constitutional genetic disease OGMS:0000036 A disease whose physical basis is an infectious disorder. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:25:51Z obsolete_infectious disease OGMS:0000037 Homeostasis that is clinically abnormal for an organism of a given type and age in a given environment. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:26:44Z abnormal homeostasis OGMS:0000038 Homeostasis of a type that is not clinically abnormal. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:27:28Z normal homeostasis OGMS:0000039 A quality which is an spatial arrangement or distribution of a(n) independent continuant(s) across a Three Dimensional Region. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:36:24Z configuration OGMS:0000040 A configuration which deviates in some way from a canonical configuration for a particular organism. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:36:58Z pathological physical configuration OGMS:0000045 A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:39:44Z disorder OGMS:0000046 A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:40:27Z epigenetic disorder OGMS:0000047 A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:41:14Z genetic disorder OGMS:0000048 A disorder whose etiology includes the presence of a pathogenic organism within a host organism or an abnormal imbalance in the normal resident organismal flora. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:41:45Z obsolete_infectious disorder OGMS:0000049 A disorder consisting in the presence of a pathogenic organism within a host organism that occurs due to the disposition established by a prior infection with a pathogenic organism of a different kind. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:42:20Z obsolete_secondary infection OGMS:0000050 A genetic disorder acquired by a single cell in an organism that leads to a population of cells within the organism bearing the disorder. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:43:09Z acquired genetic disorder OGMS:0000051 A genetic disorder inherited during conception that is part of all cells in the organism. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:43:44Z constitutional genetic disorder OGMS:0000054 A fiat process part which involves the execution of a standardized protocol for measuring qualities of a patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:47:06Z obsolete_standardized clinical process OGMS:0000055 An interview in which a clinician elicits a clinical history from a patient or from a third party who is reporting on behalf of the patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:49:16Z clinical history taking OGMS:0000056 A measurement assay that has as input a patient-derived specimen, and as output a result that represents a quality of the specimen. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:49:49Z laboratory test OGMS:0000057 A sequence of acts of observing and measuring bodily features of a patient performed by a clinician; measurements may occur with and without elicitation. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:50:18Z physical examination OGMS:0000059 A process in an organism that leads to a subsequent disorder. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:53:07Z etiological process OGMS:0000060 Albert Goldfain creation date: 2009-06-23T11:53:49Z bodily process OGMS:0000061 A bodily process that is clinically abnormal. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:54:29Z pathological bodily process OGMS:0000063 The totality of all processes through which a given disease instance is realized. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:55:44Z disease course OGMS:0000064 A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:56:26Z chronic disease course OGMS:0000065 A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, involve an increasing deviation from homeostasis. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:57:09Z progressive disease course OGMS:0000066 A disease course that terminates in a return to normal homeostasis. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:57:44Z transient disease course OGMS:0000067 Albert Goldfain creation date: 2009-06-23T11:58:22Z _undefined primitive term OGMS:0000068 Albert Goldfain creation date: 2009-06-23T11:58:39Z obsolete_bodily feature OGMS:0000069 Albert Goldfain creation date: 2009-06-23T11:59:24Z clinically abnormal OGMS:0000070 Albert Goldfain creation date: 2009-06-23T12:00:09Z physical basis OGMS:0000071 Albert Goldfain creation date: 2009-06-23T12:00:39Z realization OGMS:0000073 The representation of a conclusion of an interpretive process that has as input a clinical picture of a given patient and as output an assertion (diagnostic statement) to the effect that the patient has a disease of such and such a type. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T12:42:23Z diagnosis OGMS:0000074 A value for a quality reported in a lab report and asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-26T10:31:34Z normal value OGMS:0000075 Albert Goldfain creation date: 2009-07-08T12:20:49Z obsolete_infection OGMS:0000077 TODO: Define, relate to disorder, and place in the OGMS hierarchy. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:14:59Z pathological formation OGMS:0000078 An anatomical structure (FMA) is pathological whenever (1) it has come into being as a result of changes in some pre-existing canonical anatomical structure, (2) through processes other than the expression of the normal complement of genes of an organism of the given type, and (3) is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:14:05Z pathological anatomical structure OGMS:0000079 TODO: Define, relate to disorder, and place in the OGMS hierarchy. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:15:17Z portion of pathological body substance OGMS:0000080 A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:17:07Z pathological transformation OGMS:0000081 A pathological bodily process in which matter is reorganized in such a way as to give rise to new pathological formations which take the place of entities existing earlier. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:17:24Z pathological derivation OGMS:0000082 TODO: Define. Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:17:47Z pathological invasion OGMS:0000083 TODO: Define. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=26 creation date: 2009-11-24T04:51:11Z physical examination finding OGMS:0000084 An aggregate of organisms of the same type. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=33 creation date: 2009-11-24T04:51:11Z organism population OGMS:0000085 TODO: Define. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=13 creation date: 2009-11-24T04:51:11Z pain OGMS:0000086 A clinical picture that is an association of symptoms, signs and other clinical findings that collectively indicate or characterize a disease or disorder. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=32 creation date: 2009-11-24T04:51:11Z syndrome OGMS:0000087 An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=3 creation date: 2010-01-25T04:51:11Z extended organism OGMS:0000088 A communication from a patient about something they perceive as being abnormal about their body or life. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=12 creation date: 2010-01-25T04:51:11Z patient symptom report OGMS:0000089 A structurally anomalous part of an organism acquired during fetal development and present at birth (but not necessarily hereditary) which is hypothesized to be harmful for the organism. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=28 creation date: 2010-03-31T04:51:11Z congenital malformation OGMS:0000090 A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T04:51:11Z treatment OGMS:0000091 A processual entity during which a patient participating in a disease course gradually returns to participating in a canonical life course. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T04:51:11Z convalescence OGMS:0000092 A processual entity which has as parts all the processes in which a given organism is participant. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=38 creation date: 2010-03-31T04:51:11Z life course OGMS:0000093 A hypothesis about the course of a disease. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T12:42:23Z prognosis muo:BaseUnit Base units are units that have not been derived from any other unit. In turn, base units can be used to derive other measurement units. Base units are units that have not been derived from any other unit. In turn, base units can be used to derive other measurement units. The International System of Units (SI), recognizes several base units for base physical qualities assumed to be mutually independent. Base unit Base unit of measurement muo:ComplexDerivedUnit Units that are derived from two or more measurement units (i.e. a derived unit which is defined by means of more than one unit in its dimensional equation). For instance, the complex derived unit meter per second squared is defined by a dimensional equation with two units: m and s2. Complex derived unit of measurement muo:DerivedUnit Some physical qualities (such as area, acceleration, etc.), called derived physical qualities, are defined in terms of base qualities via a system of dimensional equations. The derived units for derived qualities are obtained from these equations combinated with the base units. Derived unit of measurement muo:MetricUnit FIX Metric unit muo:PhysicalQuality The physical qualities such as mass, weight, speed, etc. are kind of properties that can be quantified i.e. that can be perceived, measured or even calculated. The concept of physical quality is similar to the notion of quality, used in metrology, the science of measurement. We distinguish between: 1) A physical quality in the general sense: a kind of physical property ascribed to phenomena that can be quantified for a particular phenomenon (e.g. length and electrical charge); 2) A physical quantity in the particular sense: a quantifiable property ascribed to a particular phenomenon (e.g. the weight of my device). MUO only uses physical quantities in the general sense. Physical quality muo:Prefix A prefix (also known as a metric prefix) is a name or associated symbol that precedes a unit of measure (or its symbol) to form a decimal multiple or submultiple. Prefixes are used to reduce the quantity of zeroes in numerical equivalencies. For instance, 1000 meters can be written as 1 kilometer, using the prefix kilo, a symbol to represent the number 1000. Prefix muo:QualityValue The value of an individual quality, for instance, the weight of an individual object. If we consider metrology, the value of a physical quality Q is expressed as the product of a numerical value {Q} and a physical unit [Q]: Q = {Q} x [Q]. In MUO, the class muo:QualityValue is used to represent the values of qualities, Q. Instances of this class are related with 1) exactly one unit, suitable for measure the physical quality (meters for length, grams for weight, etc), by means of the property muo:measuredIn, [Q]; 2) a number, which express the relationship between the value and the unit by means of the rdf:value property, {Q}; 3) a time, which expresses the quality value along the line of time. Quality values can be temporalized, but this is not always necessary. Quality value muo:SIUnit Unit belonging to the International System of Units. The SI recognizes several base and derived units for some physical qualities assumed to be mutually independent. SI unit muo:SimpleDerivedUnit Units that are derived from exactly one base unit. There are two main possibilities. On one hand, there are units that are derived by adding a prefix to the unit. The prefix is a name or associated symbol (e.g. kilo) that precedes a unit of measure (e.g. meter) to form a decimal multiple or submultiple (e.g. Kilometer). Derived units, obtained by the application of a prefix, measure the same physical quality as its base unit. On the other hand, there are another kind of simple derived units that are also obtained from exactly one base unit but they measure a different physical quality. They are obtained by changing the exponent of the unit in the dimensional equation. For instance, this is how square meters are derived from meters. This exponent is represented in MUO with the datatype property muo:dimensionalSize. Combining this two patterns we can represent units that are obtained from a prefix and that have a dimension size different from 1, for instance, the unit square kilometer. Derived unit of measurement made out of exactly one base unit muo:UnitOfMeasurement Measurement units are standards for measurement of physical properties or qualities. Every unit is related to a particular kind of property. For instance, the meter unit is uniquely related to the length property. Under our ontological approach, units are abstract spaces used as a reference metrics for quality spaces, such as physical qualia, and they are counted by some number. For instance, weight-units define some quality spaces for the weight-quality where specific weights of objects, like devices or persons, are located by means of comparisons with the proper weight-value of the selected weight-unit. Unit of measurement An action is a processual entity that that is promoted by an agent, having a clear role distinction between agent and patient action Producing a direct effect on affecting the quality of having a livespan age quality a function that inheres in some structured biological entity. biological function The whole process from origin to death of an organism biological life Process specific for biological systems. biological processual entity space that is located inside a biological entity biological space Mereological Sum of multiple grains of the same sort without clear identity and unity criteria. Whether or not the grains are considered of the same sort depends on the view. Therefore this class does not really make a clear categorial distinction, because all matter can be described as a collection of atoms. As a consequence, these classes are not fully defined. The fuzzyness of this class is due to the "same sort" criterion. collective material entity the role a human plays as active part in a health system health professional role A role an entity plays as an actor or participant in processes that assess or influence the health status of an organism. health related role human EXAMPLE OF POPULATION human population Continuant entity that has neither a mass nor a volume and which do not inhere in other entities. immaterial nonphysical entity Physical spaces that have a threedimensional spatial dimension but no mass. Old name: immaterial anatomical entity immaterial physical entity three-dimensional space immaterial three dimensional physical entity Piece of information (not necessarily human) , as it exists independently of any potential material carrier. information entity Living complex biological system which functions as a stable whole. In contrast to colonial organisms their components generally cannot survive on their own. We conceive organisms in a material sense. Therefore we do not assume any ontological difference between a unicellular organism and the cell it is made of. "Colonial Organism" are not considered Organisms. We here include viruses into the category of organisms. Organism in an inactive form which are not dead are considered living organisms. Whether a living organism coincides with its body or hasPart its body, is controversial. We use "hasPhysicalPart" for relating organism to body. Being reflexive, this would not be incompatible with a view in which a living organism is a body. living organism organism The role that determines the occupation that characterizes the daily life of a human being or animal. occupational role any biological process that involves a whole organism organism process Mass (gravity independent) - not weight. Measured in g, kg, ... physical mass Collection of two or more organisms of the same sort. plurality of organisms An object which contains several molecules, has direct parts (components) of different types and which changes its ontological nature if subdivided. It must have clear unity and identity criteria. poly molecular composite entity Collection of Organisms of a defined taxon living in a given geographic area. In contrast to the "official" definition ("same species") this definition is broader and corresponds better to the use of the term in some contexts (e.g. "mixed population of 2 species") all child classes of population are only meant as examples demonstrating how population classes can be postcoordinated population A role is a realizable entity the manifestation of which brings about some result or end that is not essential to its bearer in virtue of the kind of thing that it is, but that can be served or participated in by that kind of continuant entity in some kinds of natural, social or institutional contexts. role Corresponds to FMA anatomical structure but extends to any kind of orgnaism: Material anatomical entity which is generated by coordinated expression of the organism's own genes that guide its morphogenesis; has inherent 3D shape; its parts are connected and 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. Old name: anatomical structure structured biological entity The case history of a medical patient as recalled by the patient -- Wordnet case history 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 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 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 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 Physical component, bodily qualities, and bodily processes ( of an organism ) bodily feature 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 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 act 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 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 A constellation of those types of bodily features that are associated with a disorder at each stage of its development. clinical phenotype Role played by people who participate in clinical activities (typically Nurse, Physician / Doctor,etc.) Clinician role http://www.hl7.org/library/data-model/RIM/C30202/rim.htm#DiagnosticImage-cls Diagnostic procedure http://ontology.buffalo.edu/bio/OBR.pdf Aggregates of organismal continuants Extra-organismal continuants Normal homeostasis 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 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 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 A quantitative or qualitative test of a substance (especially an ore or a drug) to determine its components; Laboratory test The representation of a quality of a specimen, and thereby a patient, that is the output of a laboratory test Laboratory test finding The aggregate of all healthcare activities associated with a particular patient. Longitudinal healthcare process aggregate 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 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 therapy 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 http://ontology.buffalo.edu/bio/OBR.pdf Organismal process aggregate 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) http://ontology.buffalo.edu/bio/OBR.pdf Pathological process http://ontology.buffalo.edu/bio/OBR.pdf Pathological role 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 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 record Role played by people who are the recipient of healthcare services Patient role Human / person http://reliant.teknowledge.com/DAML/SUMO.owl#Human http://www.co-ode.org/ontologies/galen#Person http://www.cycfoundation.org/concepts/Person 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 http://dictionary.webmd.com/terms/physical-therapy Treatment of pain, disease, or injury by physical means Physical therapy 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 Role played by physicians who participate in clinical activities Physician role 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 http://ontology.buffalo.edu/bio/OBR.pdf Physiological process Physiological role Psycholoical therapy 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 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 Examination performed by a patient on their his or herself to determine the nature or identity of a disease or disorder 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 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. 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 .. A boundary class .. Abdominal wall .. A boundary class .. Mediastinal artery Left bronchial artery Segment of tracheobronchial tree Third posterior intercostal artery Fourth posterior intercostal artery Fifth posterior intercostal artery Sixth posterior intercostal artery Seventh posterior intercostal artery Eighth posterior intercostal artery Ninth posterior intercostal artery Tenth posterior intercostal artery Eleventh posterior intercostal artery .. A boundary class .. Organ with organ cavity which is connected to the optic nerve. Examples: There are only two eyeballs, the right and the left eyeballs.. Eyeball .. A boundary class .. Diaphragm Cephalic vein Cardinal organ part which is bounded predominantly by bonafide boundaries. Examples: lobe of lung, osteon, acinus, submucosa, anterior leaflet of mitral valve, capsule of kidney, cortical bone, muscle fasciculus. Organ component Vascular tree, the organ parts of which are veins. Examples: There are only three canonical instances, systemic venous tree (organ), pulmonary venous tree (organ) and portal venous tree (organ). Venous tree organ .. A boundary class .. Median nerve Inferior phrenic artery Lumbar artery Right first lumbar artery Right second lumbar artery Right third lumbar artery Right fourth lumbar artery Left first lumbar artery Left second lumbar artery Left third lumbar artery Left fourth lumbar artery Right inferior phrenic artery Left inferior phrenic artery .. A boundary class .. Superior mesenteric artery Inferior mesenteric artery Renal artery Right renal artery Left renal artery Middle suprarenal artery Right middle suprarenal artery Left middle suprarenal artery Median sacral artery Testicular artery Right testicular artery Left testicular artery Ovarian artery Right ovarian artery Left ovarian artery .. A boundary class .. Common iliac artery Right common iliac artery Left common iliac artery First lumbar artery Second lumbar artery Third lumbar artery Fourth lumbar artery .. A boundary class .. Subdivision of free lower limb, which is the proximal segment of a lower limb and links the free lower limb to the trunk; it is demarcated by the plane of the surface of the acetabular fossa from the free lower limb; together with the free lower limb, it constitutes the lower limb. Examples: There are only two instances, right and left pelvic girdles. Pelvic girdle .. A boundary class .. Muscle layer of renal pelvis Subdivision of abdomen Subdivision of thorax .. A boundary class .. Anatomical structure, which is the maximal aggregate manifestation of an individual member of the species Homo sapiens; it is completely surrounded by skin. Examples: There is only one human body. Body Muscle layer of region of ureter Gray matter component of neuraxis which is located in the interior of the neuraxis. Example: thalamus, dentate nucleus, ventral horn of spinal cord. Internal gray matter component Gray matter component of neuraxis which is located on the surface of the neuraxis. Example: cerebral cortex, cerebellar cortex. External gray matter component .. A boundary class .. Brachial artery Branch of brachial artery Deep brachial artery Superior ulnar collateral artery Inferior ulnar collateral artery Set of organ parts Basilic vein Tributary of subclavian vein Brachial vein Subdivision of body proper .. A boundary class .. Skeletal system Free limb segment Cerebral white matter Subdivision of thorax, which is the anterolateral part of the thorax and is demarcated from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the back of the thorax, it constitutes the thorax. Examples: There is only one chest. Chest Subdivision of head .. A boundary class .. Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. Face .. A boundary class .. Subdivision of thorax which is anterior to the plane of the posterior boundary of the middle mediastinum. Anterior chest .. A boundary class .. Subdivision of limb, which is the proximal segment of a limb and links the free limb to the trunk; it is demarcated by the plane of the surfaces of the glenoid and acetabular fossae from the free limb; together with the free limb, it constitutes the limb. Examples: There are only four instances, right and left pectoral girdles and right and left pelvic girdles. Limb girdle .. A boundary class .. Subdivision of limb, which is distal to the limb girdle and demarcated by the plane of the surfaces of the glenoid and acetabular fossae from the limb girdle; together with the limb girdle, it constitutes the limb. Examples: There are only four instances, right and left free upper limbs and right and left free lower limbs. Free limb .. A boundary class .. Free limb, which is distal to the pectoral girdle and demarcated by the plane of the surface of the glenoid fossa from the pectoral girdle; together with the pectoral girdle, it constitutes the upper limb. Examples: There are only two instances, right and left free upper limbs. Free upper limb .. A boundary class .. Free limb, which is distal to the pelvic girdle and demarcated by the plane of the surface of the acetabular fossa from the pelvic girdle; together with the pelvic girdle, it constitutes the lower limb. Examples: There are only two instances, right and left free lower limbs. Free lower limb Arm Subdivision of trunk .. A boundary class .. Back of trunk .. A boundary class .. Thoracolumbar fascia .. A boundary class .. Thoracic part of tracheobronchial tree Investing fascia Tubular organ part, the wall and lumen of which are continuous with those of the ventricles of the heart, directly or indirectly through branches of the aorta and pulmonary trunk. Examples: bronchial artery, hepatic artery, coronary artery, truncus anterior of right pulmonary artery, aorta. Arterial trunk Right bronchial artery .. A boundary class .. Musculocutaneous nerve .. A boundary class .. Radial nerve Hollow tree, the organ parts of which are arteries, veins or lymphatic vessels. Examples: systemic arterial tree (organ), portal venous tree (organ), thoracic duct tree. Vascular tree Segment of artery Segment of vein .. A boundary class .. Ulnar nerve .. A boundary class .. Aorta Subdivision of hemolymphoid system .. A boundary class .. Brachiocephalic artery .. A boundary class .. Common carotid artery .. A boundary class .. Right common carotid artery .. A boundary class .. Subclavian artery .. A boundary class .. Left common carotid artery Left first bronchial artery Left second bronchial artery Esophageal artery Posterior intercostal artery Right third posterior intercostal artery Right fourth posterior intercostal artery Right fifth posterior intercostal artery Right sixth posterior intercostal artery Right seventh posterior intercostal artery Right eighth posterior intercostal artery Right ninth posterior intercostal artery Right tenth posterior intercostal artery Right eleventh posterior intercostal artery Left third posterior intercostal artery Left fourth posterior intercostal artery Left fifth posterior intercostal artery Left sixth posterior intercostal artery Left seventh posterior intercostal artery Left eighth posterior intercostal artery Left ninth posterior intercostal artery Subdivision of cardiovascular system .. A boundary class .. Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs. Pulmonary vascular system .. A boundary class .. Subdivision of cardiovascular system which has as its parts the left side of heart and the systemic arterial tree. Systemic arterial system .. A boundary class .. Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava. Systemic venous system Subdivision of nervous system Subdivision of respiratory system .. A boundary class .. Subdivision of respiratory system which consists of the nose, nasopharynx, oropharynx and larynx Upper respiratory tract .. A boundary class .. Subdivision of respiratory system which consists of the tracheobronchial tree, right lung and left lung. Lower respiratory tract Left tenth posterior intercostal artery Vascular tree, the organ parts of which are arteries. Examples: There are only two canonical instances, systemic arterial tree (organ) and pulmonary arterial tree (organ). Arterial tree organ .. A boundary class .. Arterial tree organ connected to the right ventricle. Examples: There is only one pulmonary arterial tree (organ). Pulmonary arterial tree organ Left eleventh posterior intercostal artery Subcostal artery Right subcostal artery *Subdivision of face which consists of the nasal skeleton, nasal septum and nasal cavity. .. A boundary class .. Nose Left subcostal artery .. A boundary class .. Left subclavian artery .. A boundary class .. Left superior intercostal vein Systemic artery which supplies the heart. Coronary artery Arterial tree (organ) connected to the left ventricle. Examples: There is only one systemic arterial tree (organ). Systemic arterial tree .. A boundary class .. Venous tree (organ) connected to the left atrium. Examples: There are four pulmonary venous trees; right superior pulmonary vein, right inferior pulmonary vein, left superior pulmonary vein and left inferior pulmonary vein. Pulmonary venous tree organ .. A boundary class .. Superior pulmonary vein .. A boundary class .. Right superior pulmonary vein Systemic arterial trunk Segment of central retinal artery Intraocular part of central retinal artery .. A boundary class .. Coronary artery which emerges from the anterior aortic sinus, between the right auricle and the pulmonary trunk, and supplies the right side of the heart. Right coronary artery .. A boundary class .. Coronary artery which emerges from the left posterior aortic sinus, between the left auricle and the pulmonary trunk, and supplies the left side of the heart. Left coronary artery .. A boundary class .. Subdivision of thorax which includes all structures from the skin to the costal pleura. Examples: There is only one chest wall. Chest wall .. A boundary class .. Nonparenchymatous organ that primarily consists of skeletal muscle tissue aggregated into macroscopic fasciculi by connective tissue; together with other muscles, it constitutes the muscular system. Examples: biceps, diaphragm, masseter, right third external intercostal muscle, external oblique, levator ani, serratus anterior. Muscle organ Nonparenchymatous organ that consists of organ parts composed of various types of connective tissue; it surrounds and interconnects various organs and body parts, and establishes the anatomical integrity of body parts and organ systems. Examples: superficial fascia, investing fascia, fat pad. Fascia organ .. A boundary class .. Subdivision of arterial tree (organ) which consists of branching sets of tubes (arterial trunk) that form a tree; together with other arterial trees (organ part), it constitutes an arterial tree (organ). Examples: pulmonary arterial tree, right coronary arterial tree, superior mesenteric tree. Artery .. A boundary class .. Subdivision of venous tree (organ) which consists of branching sets of tubes (venous trunks) that form a tree; together with other venous trees (organ part), it constitutes a venous tree (organ). Examples: subclavian venous tree, jugular tree, extrahepatic portal tree, common iliac venous tree. Vein .. A boundary class .. Celiac artery Organ component of neuraxis that has as its parts gray matter and white matter that surround the cerebral ventricular system; Examples: There is only one brain. Brain .. A boundary class .. Cranial nerve which connects the midbrain to the extra-ocular and intra-ocular muscles. Oculomotor nerve Trochlear nerve Trigeminal nerve Abducens nerve Facial nerve Vestibulocochlear nerve Glossopharyngeal nerve Hypoglossal nerve Right spinal accessory nerve Left spinal accessory nerve Tributary of dural venous sinus Tributary of cavernous sinus Tributary of superior ophthalmic vein Ciliary vein Scleral venous sinus Tributary of anterior ciliary vein Segment of central retinal vein Intraocular part of central retinal vein Subdivision of face .. A boundary class .. Eyelid .. A boundary class .. Upper eyelid .. A boundary class .. Lower eyelid Eye .. A boundary class .. Subdivision of head which consists of the neurocranium and all layers superficial to it including the cranial cavity and its contents. Examples: There is only one head proper. Head proper Material anatomical entity which consists of the maximum number of discontinuous members of the same class. Examples: set of cranial nerves, ventral branches of aorta, set of mammary arteries, thoracic viscera, dental arcade. Anatomical set Solid organ which consists of parenchyma and connective tissue stroma; the stroma subdivides the parenchyma into lobes, segments, lobules, acini, or cortex and medulla. Examples: lung, liver, spleen, kidney, parathyroid gland. Parenchymatous organ Parenchymatous organ the stroma of which subdivides the parenchyma into lobes, segments, lobules and acini. Examples: lung, liver, lactiferous gland, testis. Lobular organ Solid organ which consists of organ parts that are arranged as fascicles or sheets. Examples: muscle (organ), ligament (organ), membrane (organ), skin, viscerocranial mucosa. Nonparenchymatous organ Organ the unshared parts of which do not surround macroscopic anatomical spaces; only its shared parts (subdivisions of hollow tree organs) contain anatomical spaces. Examples: lung, liver, thymus, ovary, muscle (organ), meninx, superficial fascia, skin. Solid organ Organ the unshared parts of which surround one or more macroscopic anatomical spaces. Examples: neuraxis, tooth, esophagus, heart, long bone, corpus spongiosum of penis. Cavitated organ Cavitated organ in which its unshared parts surround one continuous anatomical space. Examples: stomach, urinary bladder, esophagus, uterine tube. Organ with organ cavity Cavitated organ in which its unshared parts surround two or more macroscopic anatomical spaces. Examples: heart, long bone, corpus spongiosum of penis, bulb of vestibule. Organ with cavitated organ parts .. A boundary class .. Organ with organ cavity which consists of gray matter and white matter. Examples: There is only one neuraxis. Neuraxis Organ with organ cavity, which consists of an arborizing set of tubular organ parts, the walls of which are continuous and surround a continuous lumen. Examples: systemic arterial tree (organ), tracheobronchial tree, biliary tree. Hollow tree organ .. A boundary class .. Vagus nerve Investing fascia of limb .. A boundary class .. Investing fascia of lower limb Muscle organ which is a part of the trunk. Examples: external intercostal muscle, external oblique, levator ani. Muscle of trunk .. A boundary class .. Neural tree (organ) which is directly continuous with the spinal cord. Examples: Fifth cervical spinal nerve, third lumbar spinal nerve. Spinal nerve Cervical nerve .. A boundary class .. Thoracic nerve .. A boundary class .. Lumbar nerve Fat body .. A boundary class .. Sacral nerve .. A boundary class .. Coccygeal nerve Variant spinal nerve Neural tree organ which is continuous with the brain. Examples: Trochlear nerve, facial nerve. Cranial nerve Orbital fat body .. A boundary class .. First thoracic nerve .. A boundary class .. Right first thoracic nerve .. A boundary class .. Left first thoracic nerve .. A boundary class .. Right second thoracic nerve .. A boundary class .. Left second thoracic nerve .. A boundary class .. Right third thoracic nerve .. A boundary class .. Left third thoracic nerve .. A boundary class .. Neural tree organNonparenchymatous organ which has as its parts an aggregate of neurons (nuclei or ganglia) and their axons which are grouped into fasciculi by connective tissue to form elongated, cable-like structures that are arranged into a tree. Examples: vagus nerve, cervical spinal nerve, T2 spinal nerve (including the nuclei and ganglia of these nerves). Neural tree organ .. A boundary class .. Twelfth thoracic nerve Subdivision of front of abdomen .. A boundary class .. Second thoracic nerve .. A boundary class .. Third thoracic nerve .. A boundary class .. First lumbar nerve .. A boundary class .. Second lumbar nerve 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 .. A boundary class .. One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter. Cerebral hemisphere .. A boundary class .. Right twelfth thoracic nerve Subdivision of telencephalon which is one of five subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries. Lobe of cerebral hemisphere Frontal lobe is the anterior-most of five lobes of the cerebral hemisphere. It is bounded by the central sulcus on its posterior border and by the longitudinal cerebral fissure on its medial border. Frontal lobe Temporal lobe is the ventrolateral lobe of five lobes comprising each cerebral hemisphere. It is bounded dorsally by the lateral fissure and posteriorly by an arbitrary border shared with the occipital lobe. Temporal lobe .. A boundary class .. Left twelfth thoracic nerve Cerebral cortex .. A boundary class .. Superior frontal gyrus .. A boundary class .. Middle frontal gyrus .. A boundary class .. Inferior frontal gyrus .. A boundary class .. Straight gyrus .. A boundary class .. Precentral gyrus .. A boundary class .. Superior temporal gyrus .. A boundary class .. Middle temporal gyrus .. A boundary class .. Inferior temporal gyrus .. A boundary class .. Fusiform gyrus .. A boundary class .. Anterior transverse temporal gyrus .. A boundary class .. Posterior transverse temporal gyrus .. A boundary class .. Parahippocampal gyrus .. A boundary class .. Anterior commissure .. A boundary class .. Fornix of forbrain is an organ subdivision of the telencephalon which is made up primarily of myelinated axonal neural tissue. The fornix is an arch-shaped fiber bundle connecting Ammon's horn of the hippocampus with the mammillary nuclei of the hypothalamus and anterior nuclei of the thalamus. Fornix of forebrain .. A boundary class .. Organ component of neuraxis that has as its parts the telencephalon, diencephalon, lateral ventricles and third ventricle. Examples: There is only one forebrain. Forebrain .. A boundary class .. Organ component of neuraxis that has as its parts the tectum, cerebral peduncle, midbrain tegmentum and cerebral aqueduct. Examples: There is only one midbrain. Midbrain Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures. There is only one telencephalon. Telencephalon .. A boundary class .. Rostral segment of the hindbrain that has as its parts the pons and the cerebellum. Metencephalon Lateral orbital gyrus Medial orbital gyrus .. A boundary class .. Wall of respiratory bronchiole .. A boundary class .. Wall of terminal bronchiole .. A boundary class .. Fourth thoracic nerve .. A boundary class .. Right fourth thoracic nerve .. A boundary class .. Left fourth thoracic nerve .. A boundary class .. Fifth thoracic nerve .. A boundary class .. Right fifth thoracic nerve .. A boundary class .. Left fifth thoracic nerve Biological entity, which constitutes the structural organization of a biological organism, or is an attribute of that organization. Examples: cell, heart, head, peritoneal cavity, apex of lung, anatomical term, sagittal plane. Anatomical entity .. A boundary class .. Sixth thoracic nerve .. A boundary class .. Right sixth thoracic nerve .. A boundary class .. Left sixth thoracic nerve .. A boundary class .. Seventh thoracic nerve .. A boundary class .. Right seventh thoracic nerve .. A boundary class .. Left seventh thoracic nerve .. A boundary class .. Eighth thoracic nerve .. A boundary class .. Right eighth thoracic nerve .. A boundary class .. Left eighth thoracic nerve .. A boundary class .. Ninth thoracic nerve .. A boundary class .. Right ninth thoracic nerve .. A boundary class .. Left ninth thoracic nerve .. A boundary class .. Tenth thoracic nerve .. A boundary class .. Right tenth thoracic nerve .. A boundary class .. Left tenth thoracic nerve .. A boundary class .. Eleventh thoracic nerve .. A boundary class .. Right eleventh thoracic nerve .. A boundary class .. Left eleventh thoracic nerve .. A boundary class .. Right first lumbar nerve .. A boundary class .. Left first lumbar nerve .. A boundary class .. Right second lumbar nerve .. A boundary class .. Left second lumbar nerve .. A boundary class .. Third lumbar nerve .. A boundary class .. Fourth lumbar nerve .. A boundary class .. Fifth lumbar nerve .. A boundary class .. Right third lumbar nerve .. A boundary class .. Left third lumbar nerve .. A boundary class .. Right fourth lumbar nerve .. A boundary class .. Left fourth lumbar nerve .. A boundary class .. Right fifth lumbar nerve .. A boundary class .. Left fifth lumbar nerve .. A boundary class .. First sacral nerve .. A boundary class .. Second sacral nerve .. A boundary class .. Third sacral nerve .. A boundary class .. Fourth sacral nerve .. A boundary class .. Fifth sacral nerve .. A boundary class .. Right first sacral nerve .. A boundary class .. Left first sacral nerve .. A boundary class .. Right second sacral nerve .. A boundary class .. Left second sacral nerve .. A boundary class .. Right third sacral nerve .. A boundary class .. Left third sacral nerve .. A boundary class .. Right fourth sacral nerve .. A boundary class .. Left fourth sacral nerve .. A boundary class .. Right fifth sacral nerve .. A boundary class .. Left fifth sacral nerve .. A boundary class .. Right coccygeal nerve .. A boundary class .. Left coccygeal nerve First cervical nerve Second cervical nerve Third cervical nerve Fourth cervical nerve Fifth cervical nerve Sixth cervical nerve Seventh cervical nerve Eighth cervical nerve Neural tree (organ) which is directly continuous with the neuraxis. Examples: phrenic nerve, radial nerve, ilioinguinal nerve, sciatic nerve. Peripheral nerve Systemic artery Systemic vein 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. Immaterial physical anatomical entity 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 Physical anatomical entity which has mass. Examples: hemoglobin molecule, mitochondrion, hepatocyte, erythrocyte, heart, head, blood, urine. Material anatomical entity Spinal accessory nerve .. A boundary class .. Wall of lobular bronchiole .. A boundary class .. Anatomical structure, which consists of the maximal set of organ parts so connected to one another that together they constitute a unit of macroscopic anatomy, structurally distinct from other such units. Examples: femur, biceps, liver, heart, skin, tracheobronchial tree, ovary. Organ Anatomical structure, which is a subdivision of a cardinal body part; it may exclude bones; is demarcated from other subdivisions of the same cardinal body part by anatomical surfaces or lines or topographical references; together with other contiguous subdivisions of the same cardinal body part, it constitutes a cardinal body part. Examples: thorax, perineum, back of neck, forearm, hand, phalanx, nose, auricle of ear, scrotum. Subdivision of cardinal body part Anatomical structure, which consists of a specific set of the members of (predominantly) one organ or organ part subclass interconnected by zones of continuity or body substances; is demarcated from other subdivisions of the same organ system by one or more zones of continuity or anatomical lines; together with other subdivisions of the same organ system, it constitutes an organ system. Examples: rib cage, facial skeleton, portal system, central nervous system, upper respiratory tract, muscle group of back. Organ system subdivision Cardinal organ part which is a fiat subdivision of an organ. Examples: lingula of left lung, tail of pancreas, artery, trochanter, nodulus of semilunar valve, right side of heart, duodenum, fundus of stomach. Organ region .. A boundary class .. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata . Examples: There is only one hindbrain. Hindbrain Class of unpaired telencephalic white matter structures consisting of fiber pathways which project across the midsagittal plane and which serve to interconnect telencephalic structures lying within the contralateral cerebral hemisphere. Intercerebral commissure Organ component of neuraxis that has as its parts the cerebellar cortex, cerebellar nuclear complex and cerebellar white matter. Examples: There is only one cerebellum. Cerebellum .. A boundary class .. Bronchial artery Brodmann area Brodmann area 1 Brodmann area 2 Brodmann area 3 Brodmann area 4 Brodmann area 5 Brodmann area 6 Segment of cerebral cortex Brodmann area 7 Brodmann area 8 Brodmann area 9 Brodmann area 10 Brodmann area 11 Brodmann area 12 Brodmann area 13 Brodmann area 14 Brodmann area 15 Brodmann area 16 Brodmann area 17 Brodmann area 18 Brodmann area 19 Brodmann area 20 Brodmann area 21 Brodmann area 22 Brodmann area 23 Brodmann area 24 Brodmann area 25 Brodmann area 26 Brodmann area 27 Brodmann area 28 Brodmann area 29 Brodmann area 30 Brodmann area 31 Brodmann area 32 Brodmann area 33 Brodmann area 34 Brodmann area 35 Brodmann area 36 Brodmann area 37 Brodmann area 38 Brodmann area 39 Brodmann area 40 Brodmann area 41 Brodmann area 42 Brodmann area 43 Brodmann area 44 Brodmann area 45 Brodmann area 46 Brodmann area 47 .. A boundary class .. Pericardial artery Subdivision of subclavian artery Subdivision of internal thoracic artery Set of organs .. A boundary class .. Organ with cavitated organ parts, which is continuous with the systemic and npulmonary arterial and venous trees. Examples: There is only one heart. Heart Caviness neocortex parcellation unit Frontal gyrus 1 (F1) Frontal gyrus 2 (F2) Frontal gyrus 3, pars opercularis (F3o) Angular gyrus (AG) Intracalcarine cortex (CALC) Cingulate gyrus, anterior division (CGa) Cingulate gyrus, posterior division (CGp) Cuneal gyrus (CN) Central opercular cortex (CO) Frontal gyrus 3, pars triangularis (F3t) Frontal medial cortex (FMC) Frontal operculum cortex (FO) Frontal orbital cortex (FOC) Frontal pole (FP) Heschl's gyrus Insula cortex (INS) Juxtaparacentral lobule cortex (JPL) Lingula gyrus (LG) Occipital fusiform gyrus (OF) Lateral occipital cortex, inferior division (OLi) Lateral occipital cortex, superior division (OLs) Occipital pole (OP) Paracingulate gyrus (PAC) Precuneus cortex (PCN) Parahippocampal gyrus, anterior division (PHa) Parahippocampal gyrus, posterior division (PHp) Parietal operculum cortex (PO) Postcentral gyrus (POG) Planum polare (PP) Precentral gyrus (PRG) Planum temporale (PT) Subcallosal cortex (SC) Supracalcarine cortex (SCAL) Supramarginal gyrus, anterior division (SGa) Supramarginal gyrus, posterior division (SGp) Superior parietal lobule (SPL) Superior temporal gyrus, anterior division (T1a) Superior temporal gyrus, posterior division (T1p) Middle temporal gyrus, anterior division (T2a) Middle temporal gyrus, posterior division (T2p) Inferior temporal gyrus, anterior division (T3a) Inferior temporal gyrus, posterior division (T3p) Temporal frontal cortex, anterior division (TFa) Temporal frontal cortex, posterior division (TFp) Middle temporal gyrus, temporoccipital part (TO2) Inferior temporal gyrus, temporoccipital part (TO3) Temporal occipital fusiform cortex (TOF) Temporal pole (TP) Tributary of axillary vein Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. Membrane organ .. A boundary class .. Anatomical structure, which consists of members of predominantly one organ subclass; these members are interconnected by zones of continuity. Examples: skeletal system, cardiovascular system, alimentary system. Organ system Anatomical structure, which has as its parts a maximal set of diverse subclasses of organ and organ part spatially associated with either the skull, the vertebral column or a complete set of bones of the appendicular skeleton; it is partially surrounded by skin and forms a distinct morphological subdivision of the body; together all principal body parts constitute the entire body. Examples: Head, neck, trunk, and the limbs. Cardinal body part Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the skull, it is partially surrounded by skin of head. Examples: There is only one head. Head .. A boundary class .. Nervous system Functional system which consists of structures involved in respiration. Respiratory system Organ system which consists of the heart, the systemic and pulmonary arterial and venous system, the lymphatic and the portal venous system. Cardiovascular system .. A boundary class .. Lymphatic system .. A boundary class .. Subdivision of body proper, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the ribcage, thoracic and lumbar vertebral column, sacrum and coccyx, it is partially surrounded by skin of trunk. Examples: There is only one trunk. Trunk .. A boundary class .. Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with a complete set of bones of the appendicular skeleton, it is partially surrounded by skin of limb. Examples: There are only four instances, right upper and lower limbs and left upper and lower limbs. Limb .. A boundary class .. Upper limb Lower limb .. A boundary class .. Lobular organ the parenchyma of which consists of air-filled alveoli which communicate with the tracheobronchial tree. Examples: There are only two instances, right lung and left lung. Lung .. A boundary class .. Cerebellar cortex .. A boundary class .. Cerebellar nuclear complex .. A boundary class .. Limbic lobe .. A boundary class .. Lung which consists of the right upper lobe, middle lobe and right lower lobe. Right lung .. A boundary class .. Lung which consists of the left upper lobe and left lower lobe. Left lung Cuneate nucleus of spinal cord Accessory cuneate nucleus of spinal cord Gracile nucleus of spinal cord Commissural nucleus of spinal cord Posteromarginal nucleus Nucleus proprius dorsalis Spinal reticular nucleus Dorsal nucleus of Clarke Intermediolateral nucleus Intermediomedial nucleus Lateral cervical nucleus Nucleus cornucommissuralis posterior Nucleus cornucommissuralis anterior .. A boundary class .. Hollow tree organ, the organ parts of which consists of the trachea and right and left bronchial trees. Examples: There is only one tracheobronchial tree. Tracheobronchial tree Medial motor nucleus of spinal cord Lateral motor nucleus of spinal cord Gracile fasciculus of spinal cord Cuneate fasciculus of spinal cord Fasciculus interfascicularis Medial longitudinal fasciculus of spinal cord Dorsal spinocerebellar tract of spinal cord Ventral spinocerebellar tract of spinal cord Lateral corticospinal tract of spinal cord Ventral corticospinal tract of spinal cord Anterolateral corticospinal tract of spinal cord Lateral spinothalamic tract Spinotectal tract of spinal cord Spino-olivary tract of spinal cord Lateral vestibulospinal tract of spinal cord Cuneocerebellar tract of spinal cord Spinocortical tract of spinal cord Tectospinal tract of spinal cord Pontine reticulospinal tract Medullary reticulospinal tract Olivospinal tract of spinal cord Rubrospinal tract of spinal cord Subdivision of lymphoid system .. A boundary class .. Wall of trachea Musculoskeletal system Tract of spinal cord Set of neuraxis structures Fasciculus of spinal cord Organ component of neuraxis that has as its parts gray matter and white matter that surround the central canal. Examples: There is only one spinal cord. Spinal cord Nucleus of neuraxis which is located within the spinal cord. Example: dorsal nucleus of Clarke, Intermediolateral nucleus. Nucleus of spinal cord Subdivision of brachiocephalic vein Subdivision of subclavian vein Subdivision of superior vena caval tree Set of organ subdivisions Set of heterogeneous clusters Set of neural trees Intermediate orbital gyrus Posterior orbital gyrus Anatomical structure, which consists of two or more types of tissues that form a defined structural aggregate in an organ. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas. Cardinal organ part Segment of subclavian artery Proximal free limb segment Cardinal free limb segment Organ component which is part of the brain or spinal cord. Organ component of neuraxis Organ component of neuraxis which is an aggregation of neural axonal tissue. Examples: superior cerebellar peduncle, medial lemniscus, rubrospinal tract, medial longitudinal fasciculus . White matter component of neuraxis Organ component of neuraxis which is an aggregation of neural somatic tissue. Examples: cerebral cortex, thalamus, red nucleus. Gray matter component of neuraxis External matter component of neuraxis which covers extentive regions of the neuraxis. Example: cerebral cortex, cerebellar cortex. Cortex of neuraxis Internal gray matter component of neuraxis which consists of a discrete aggregate of neuronal soma. Example: dentate nucleus, red nucleus. Nucleus of neuraxis Tract of neuraxis Fornix of neuraxis Gyrus of neuraxis Hemisphere of neuraxis Lobe of neuraxis Commissure of neuraxis Set of basal ganglia Fasciculus of neuraxis Internal gray matter component which consists of an assemblage of nuclei of neuraxis. Example: cerebellar nuclear complex, Vestibular nuclear complex. Nuclear complex of neuraxis Region of muscle layer of organ Cardinal organ part which is a fiat subdivision of an organ component. Examples: cervical part of wall of esophagus, mucosa of body of stomach. Region of organ component Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. Organ segment Segment of arterial tree organ Segment of venous tree organ Region of wall of tracheobronchial tree Segment of systemic artery Corpus callosum .. A boundary class .. Subdivision of the trunk, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage; together with the abdomen, pelvis and perineum, it constitutes the trunk. Examples: There is only one thorax. Thorax Subdivision of trunk, which is demarcated from the thorax internally by the inferior surface of the sternocostal part of the diaphragm and externally by the costal margin, from the pelvis by the plane of the superior pelvic aperture and from the lower limbs by the inguinal folds; together with the thorax, pelvis, and perineum, it constitutes the trunk. Examples: There is only one abdomen. Abdomen Membrane organ that surrounds the brain and the spinal cord. Meninx Muscle organ which is a part of the thorax. Examples: external intercostal muscle, diaphragm. Muscle of thorax Muscle of upper limb Muscle of lower limb Limb segment Immune system Peripheral nervous system Autonomic nervous system oboInOwl:DbXref oboInOwl:Definition oboInOwl:OboInOwl oboInOwl:ObsoleteClass oboInOwl:Subset oboInOwl:Synonym oboInOwl:SynonymType entity 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Definition: A spatial region [snap:SpatialRegion] with no dimensions. Examples: a point zero_dimensional_region 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 3 4 5 6 30 50 70 10 90 example to be eventually removed The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot core placeholder removed An editor note should explain what were the merged terms and the reason for the merge. terms merged This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal Alan Ruttenberg defined class A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion 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: Feb. 11, 2013 Sivaram Arabandi Sivaram Arabandi Last modification: Feb. 11, 2013 Sivaram Arabandi Constellation of bodily features Biological process 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 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 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 structure 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) Entity that causes a disease has consequence has contraindication has input surgical method has output Healthcare professional role http://www.loa-cnr.it/ontologies/ExtendedDnS.owl#setting-for 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 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 ..pathological changes in the structure and function of cells and tissues Process of physiological or anatomical alteration as a result of the realization of a pathological disposition (a disease) organism organismal continuant .. the organism which constitutes an etiologic agent (Caroline Whitbeck) pathogen http://www.hl7.org/library/data-model/RIM/C30202/rim.htm#Procedure-cls 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. record clinical situation Sequela Sign recording http://www.loa-cnr.it/Papers/focomf2.pdf A certain enduring constellation of values of an independent continuant's aggregate physical properties. 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 has part OBO_REL:0000021 http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 As for has_participant, but with the additional condition that the component instance is causally active in the relevant process relationship has_agent OBO_REL:0000003 relationship has_part OBO_REL:0000019 http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 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 relationship Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant OBO_REL:0000007 relationship has_proper_part OBO_REL:0000020 relationship participates_in OBO_REL:0000013 http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2. relationship When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes. transformation_of