BFO OWL specification label
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO CLIF specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
editor preferred label
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example
example of usage
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
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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.
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.
definition editor
term editor
Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
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.
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative label
alternative term
A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
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
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
curator note
An administrative note of use for a curator but of no use for a user
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
imported from
For external terms/classes, the ontology from which the term was imported
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:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
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
has associated axiom(nl)
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
Used to capture development notes and design decisions or questions. All annotations using this property should be removed before publishing / releasing the ontology to the public (but ideally retained in some place as valuable documentation).
SEPIO_editor_note
For use in the EMBL-EBI ArrayExpress interface.
has database cross reference
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
An alternative label for a given entity such as a commonly used abbreviation or synonym.
Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software.
has exact synonym
comment
A human-readable name for the subject.
label
alternate name
derived_from
derived from
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
For use in research contexts the minimum age needs to be specified.
A cognitive representation of themselves by a person or a group about themselves.
This entity is more than self-identity of an individual as it includes group identity.
An identity that a person has about themselves.
The term 'self' sounds tautologous but is required to reflect the fact that this is not identity in terms of who you are but how you represent yourself to yourself.
The cognitive representation includes multiple aspects and some of these are social. For example, group memberships, cultural norms. Collective identity as a shared attribute of group is related to this but is separate.
A person between 13 and 19 years of age.
A person who is between the ages of 13 and 19.
A mixed study design in which two or more groups experience the same study processes but in a different order.
A non-interventional study design in which study participants who have been identified as having (case) or not having (control) some characteristic of interest are compared on other characteristics to establish whether these are associated with being a case or control.
A study design in which study participants are not planned to experience an intervention as a part of the study process.
A study design in which measurements taken on the same study participants at two or more different times in different circumstances are compared.
An interventional study design in which participants are randomly allocated to receive one of two or more interventions or no intervention using a study randomisation process.
A study design in which measurements taken on two or more groups of study participants at two or more times are compared allowing differences to be assessed between groups and over time.
A study design that includes specification of some intervention as part of the study process.
controlled trial, study with at least one comparator group
A randomised controlled trial design in which participants are randomised to study on more than one occasion during the study.
sequential multiple randomised controlled trial design
A randomised controlled trial design in which pre-existing groups of participants are randomly allocated to intervention arms
cRCT, CRT, cluster-randomised controlled intervention trial, cluster-randomised controlled trial
cluster randomised controlled trial design
An interventional study design in which participants are allocated to receive one or two or more interventions or no intervention using a quasi-random process.
quasi-randomised controlled trial design
An interventional study design in which all the participants receive the same type of intervention.
A repeated measures study design involving multiple repeated measurements taken in each of two or more conditions facilitating inferential statistical analyses to be undertaken to output statistical parameters from data sets for each individual participant.
A temporal interval between the end of one intervention and the beginning of another in a cross-over research study
A health status in which the person presents fewer or lower intensity of symptoms compared to their previous symptom presentation, and the current symptoms minimally interfere with their life.
A health status in which the symptoms of a person suffering from a disorder have reverted from a desired level to an undesired level.
Learning that involves changing the strength of association between two or more mental processes.
While associative learning is often defined as learning an association between a stimulus and response, the stimulus has to be perceived. Therefore, associative learning is between perceiving or processing information about a stimulus (a mental process) and one or more other mental processes. The label 'associative learning' is also used for a behaviour change technique (BCT) in the BCT Taxonomy v1 (Michie et al., 2013). The definition for this BCT reads as follows: 'Present a neutral stimulus jointly with a stimulus that already elicits the behavior repeatedly until the neutral stimulus elicits that behavior.' As indicated by the definition, the BCT is the deliberate presentation of a stimulus, whereas the MoA is a learning process that occurs in the brain.
A BCI attribute that is its temporal organisation.
A data item that is the number of contact events in an intervention temporal part.
A BCI schedule of delivery in which the frequency and duration of BCI temporal parts are uniform across the course of a BCI or BCI part.
A BCI schedule of delivery in which the frequency and duration of contact events differ over the course of a temporal part or BCI.
This includes individual people, groups of people, and organisations.
A role played by a person, population or organisation that provides a BCI.
A behaviour change intervention source role that inheres in a person.
An attribute of a BCI delivery that is the physical or informational medium through which a BCI is provided.
behaviour change intervention mode of delivery
Mode of delivery that involves devices or substances that alter bodily processes or structure.
Is intended to be disjoint from informational mode of delivery.
Somatic mode of delivery that involves ingestion of a chemical into the body.
Ingestion mode of delivery that involves ingestion of a chemical through the skin.
Somatic mode of delivery that involves ingestion of a chemical through the stomach or intestine.
Ingestion mode of delivery that involves absorption of a chemical through the lining of the buccal cavity.
Ingestion mode of delivery that involves absorption of a chemical through the upper airways or lungs by inspiration.
Ingestion mode of delivery that involves a chemical being introduced into body tissue through a hollow needle that punctures the skin.
Ingestion mode of delivery that involves a device that is worn on the body.
Includes as parts social setting and physical setting.
An aggregate of entities that form the environment in which a BCI is provided.
A personal attribute that is a time quality inhering in a person by virtue of how long the person has existed.
A personal attribute that is the state of an individual's mental or physical condition.
A bodily quality based on reproductive function or organs.
A biological sex associated with the ability to produce female gametes.
A biological sex associated with the ability to produce male gametes.
A health status attribute that is having been prescribed the use of one or more drugs to improve, maintain or protect one's health.
This includes the following subclasses: 1) BCI effect estimate type -the type of statistic used to represent the difference (e.g. odds ratio, mean difference), 2) BCI effect estimate value – the datum that represents the difference (e.g. 1.35), 3) BCI effect estimate uncertainty type – the type of statistic used to represent the range of uncertainty of the value (e.g. 95% confidence interval see STATO), and 4) the BCI effect estimate uncertainty value - the datum representing the uncertainty (e.g. 1.20-1.55).
A behaviour change intervention evaluation finding that characterises the difference between BCI outcome estimates of two BCI scenarios.
An intervention evaluation finding that characterises the difference between intervention outcome estimates of two intervention scenarios.
behaviour change intervention effect estimate
An evaluation finding that is the output of a BCI evaluation study.
An evaluation finding that is the output of an intervention evaluation study.
behaviour change intervention evaluation finding
A geographical location of a country where the intervention takes place.
A healthcare facility that is run by a care home organization and is the bearer of a care home function.
A clinic providing healthcare services to people in a certain area
A healthcare facility to treat patients in the community without them staying overnight.
A healthcare facility where dental healthcare is provided.
A facility in which formal education is provided to a student population.
A facility used by a group of people living in the same place or having a particular characteristic in common.
A facility used as an outlet for shopping.
A facility of a room, set of rooms, or building used as a place for commercial, professional, or bureaucratic work.
A facility where individuals are being reprimanded, detained or imprisoned.
A facility of a building or group of buildings where goods are manufactured or assembled chiefly by machine
A facility relating to or characteristic of soldiers or armed forces
Methods of traveling from one place to another.
Forms of transportation that run on fixed routes and are available to the public, usually for a set fare
A form of transportation owned by an individual for individual or group use.
A form of transportation delivering interventions in transient locations.
A form of transporation which can transport patients for health treatment, and in some instances will also provide out-of-hospital healthcare to the patient.
A site which is an outdoor location outside of a building.
An outdoor environment set in an expanse of water.
An outdoor environment for the passage of persons or cyclists on land
A place designed and staffed to house and treat individuals that need assistance with mental dysfunctions
A planned process that is the smallest part of BCI content that is observable, replicable and on its own has the potential to bring about behaviour change.
A data item that is the output of an intervention evaluation study.
Also referred to in definitions as human behaviour or just behaviour.
A bodily process of a human that involves co-ordinated contraction of striated muscles controlled by the brain.
it is concerned with moving skeletal parts to which it is usually attached.' (https://www.collinsdictionary.com/dictionary/english/striped-muscle)
Striated muscles referred to in the definition do not ordinarily involve cardiac muscles. Behaviours are usually in response to an internal or external stimuli. Every behaviour is associated with mental processes, but not every mental process is associated with behaviour. For instance, a verbal communication behaviour will involve mental processes to produce speech. However, mental processes associated with listening can occur without a person performing a behaviour. 'behaviours' can involve a series of activities (e.g., more granular behaviours). 'A 'striated muscle' can defined as 'a type of contractile tissue that is marked by transverse striations
A position-related behaviour in which muscles are used by a person to move themselves relative to the immediate environment or part of it.
An individual human behaviour that involves maintenance or improvement of flexibility, strength, balance or cardiovascular fitness.
An individual human behaviour that involves taking defensive action in order to avoid stimuli judged as aversive by the person.
A uniform process aggregate whose member parts are behaviours of the same type and in the same person.
- For any x and y in P where x does not equal y, if x occupies_spatiotemporal_region s, then y occupies_spatiotemporal_region t and s does not equal t
- For any pi in P, s is participant_in pi
- P is the set {p1, ... pn} of process aggregate member parts of b
b is a behaviour pattern means: - b is instance_of uniform process aggregate
The term 'pattern' is used to refer to several processes (individual human behaviours) of the same type being repeated overtime. This class is intended to include behaviours that can usefully be characterised in terms of frequency and pattern of enactment with a temporal start and end of the series. This means that the series can be terminated (e.g. stopping smoking), interrupted (e.g. abstaining from alcohol consumption for a month), and changed in frequency (e.g. cutting down on snacks).
An occurrent consisting exactly of a plurality of processes that are process_aggregate_member_parts_of that occurrent for all times at which it exists.
Process aggregate extends BFO in the same way that object aggregate extends its coverage of material entities. It is required to be able to classify occurrents such as behaviour patterns that are repeated occurrences of classes of process that have properties such as average frequency of occurrence (not to be confused with frequency as a process profile) and temporal patterning of occurrences.
A locomotive behaviour that involves moving at a regular pace by lifting and setting down each foot in turn, never having both feet off the ground at once.
A planned process that has the aim of influencing an outcome.
A research study that aims to assess attributes of an intervention with regards to their positive or negative value.
A process that is influenced by an intervention.
This is intended to provide a user-friendly way of representing the way in which processes are manifest. This is somewhat similar to, but not the same as, the class 'specifically dependent continuant' in Basic Formal Ontology which provides a way of representing features of material entities such as age and size. It is formally equivalent to process profile in Basic Formal Ontology.
A process profile that is an attribute of a process.
A mental process in which a lasting mental or behavioural change occurs as the result of experience.
The class 'learning' from the Gene Ontology was not reused but adapted for the Mechanism of Action (MoA) Ontology, as the Gene Ontology only focuses on learning adaptive behaviours in order to be relevant to all organisms.
A process aggregate whose member parts are of the same type.
u is a uniform process aggregate means: • u instance_of process aggregate • P is the set {p1,…pn} of process aggregate member parts of u • X is some descendant of process • Each of {p1,…pn} in P is instance_of X
A specifically dependent continuant that inheres in a person.
Attributes included under this header are age, immigration, social and economic conditions.
A process attribute whose bearer is a behaviour change intervention.
A belief about one's position in life in relation to one's goals, expectations, standards and concerns.
An individual human behaviour that relates to the enactor's posture or location.
An individual human behaviour that relates to some subjective experience of the behaving person.
creating a data set
A planned process that has a data set as its specified output.
William R. Hogan
data set creation
dataset creation
dataset creating
entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
An entity is anything that exists or has existed or will exist.
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entities
entitātem
continuant
An 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.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R.
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in 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.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
specifically dependent continuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
A 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.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object
fiat object part
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
A three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof.
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
A one-dimensional temporal region is a temporal region that is extended.
material entity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.
A member of the class of thienopyrans that is 4,7-dihydro-5H-thieno[2,3-c]pyran substituted by a (methylamino)methyl at position 7S. It is a trace amine-associated receptor 1 and serotonin 5-HT1A receptors agonist that has demonstrated efficacy in the treatment of patients with schizophrenia.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
A cyclic compound having as ring members atoms of carbon and at least of one other element.
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
An organosulfur compound is a compound containing at least one carbon-sulfur bond.
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
A p-block molecular entity containing any pnictogen.
Any p-block molecular entity containing a chalcogen.
A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.
Any molecule that consists of a series of atoms joined together to form a ring.
A molecule that features two fused rings.
A polycyclic compound in which at least one of the rings contains at least one non-carbon atom.
A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom.
A main group molecular entity that contains one or more atoms of a p-block element.
Any organic molecule that consists of atoms connected in the form of a ring.
Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene.
Any heteroorganic entity containing at least one carbon-nitrogen bond.
A mood-stimulating drug used primarily in the treatment of affective disorders and related conditions.
A class of drugs producing both physiological and psychological effects through a variety of mechanisms involving the central nervous system.
A loosely defined grouping of drugs that have effects on psychological function.
A traditional grouping of drugs said to have a soothing or calming effect on mood, thought or behaviour.
An agent that controls agitated psychotic behaviour, alleviate acute psychotic states, reduce psychotic symptoms, and exert a quieting effect.
A loosely defined group of drugs that tend to reduce the activity of the central nervous system.
Any molecular entity consisting of more than one atom.
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
An organochalcogen compound containing at least one carbon-oxygen bond.
Any organic heterocyclic compound containing at least one ring oxygen atom.
Cholesterol esters and free cholesterol which are contained in or bound to very low density lipoproteins (VLDL).
very-low-density lipoprotein cholesterol
Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL).
Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL).
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
Any steroid based on a cholestane skeleton and its derivatives.
Cholesterol esters and free cholesterol which are contained in or bound to lipoproteins.
Any molecular entity that contains carbon.
A compound formally derived from ammonia by replacing two hydrogen atoms by organyl groups.
A cyclic compound having as ring members atoms of at least two different elements.
A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.
A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind.
A mixture composed of two or more diastereoisomers (stereoisomers not related as mirror images).
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
A diastereoisomeric mixture of approximately equal amounts of all four possible diastereoisomers of 4-(1-hydroxy-2-{[4-(4-hydroxyphenyl)butan-2-yl]amino}ethyl)phenol.
A diastereoisomeric mixture of approximately equal amounts of all four possible diastereoisomers of 4-(1-hydroxy-2-{[4-(4-hydroxyphenyl)butan-2-yl]amino}ethyl)phenol. A beta-adrenergic agonist, it is used (generally as the hydrochloride salt) as a feed additive for use in pigs and other livestock to promote protein deposition, resulting in leaner meat. The R,R diastereoisomer, butopamine, is responsible for most of the leanness-enhancing effects. While use of ractopamine has been banned in over 120 countries including throughout the EU, in the US it used in an estimated 80% of all beef, pork and turkey production.
( -)-all-rac-p-hydroxy-alpha-({[3-(p-hydroxyphenyl)-1-methylpropyl]amino}methyl)benzyl alcohol, ractopamine, ractopamina, ractopaminum
A quantitative or qualitative value which is the result of an act of assessing a morphological or physiological state or property in a single individual or sample or a group of individuals or samples, based on direct observation or experimental manipulation.
Any value resulting from the quantification of a morphological or physiological parameter pertaining to the heart and/or blood vessels.
Any measurement of components of the electrical conduction system of the heart.The electrical conduction system of the heart transmits signals generated usually by the sinoatrial node to cause contraction of the heart muscle.
QT interval corrected for heart rate calculated by the QT interval divided by the square root of the interval from one QRS complex to the onset of the next QRS complex measured in seconds.
Any measurement of a structural part of a system of the body that is composed of tissues and cells that enable it to perform a particular function.
This is not the same term as the original "heart measurement". That term is now "heart morphological measurement".
A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification.
An astrononmical body part which delimited by physical discontinuities with its surroundings.
This class is being depopulated and will be filled only with inferred subclasses. Please do not use this for direct annotation, favouring instead a more descriptive subclass.
An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature.
A construction which enables the movement of humans, their animals or their vehicles.
An open way for the passage of vehicles, persons, or animals on land
A construction that has been assembled by deliberate human effort.
"constructed" should probably be made something like a quality and this class obsoleted or filled only by inference
A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a body of wate
A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a body of water.
An area in which grasses (Graminae) are a significant component of the vegetation
Land having a cover of trees, shrubs, or both.
An area with a high density of trees. A small forest may be called a wood
The definitions of forest can vary greatly, and different classes will be needed to support the major categories. Tree cover alone is not enough to distinguish between forests and plantations. The international definition proposed by the 2010 FAO Forestry Resource Assessment: "land spanning more than 0.5 ha with trees higher than 5 metres and canopy cover of more than 10 percent, or trees able to reach these thresholds in situ . It does not include land that is predominantly under agricultural or urban land use." - FAO. 2010. Global forest resources assessment 2010, Main report, FAO Forestry Paper 163. Rome.
A part of an astronomical body which is primarily composed of solid material.
A facility, permanent or temporary, on land, in air, space or water, where scientific research or measurements can be undertaken
A bounded area of land, or water, usually in its natural or semi-natural (landscaped) state and set aside for some purpose, usually to do with recreation or conservation
A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein.
Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition.
A material part of an astronomical body.
Also note that some astronomical body parts (ABPs) may have fiat boundaries: if there's strong debate about where an ABP begins or ends (over and above fuzzy boundaries), with different official classifications setting different thresholds or limits, axiomatise the class with fiat boundaries of the appropriate dimension.
Note that material entities may have immaterial entities (e.g. sites) as parts.
This class includes material parts of astronomical bodies. Immaterial parts, such as magnetospheres, are represented as sites under the influence of magnetic fields.Please post countercases in the ENVO tracker for revision of this hierarchy if needed.
Material parts of astronomical bodies generally have boundaries formed by discontinuities in qualities, composition, or other physical characterisitcs. These boundaries are sometimes sharp, and sometimes diffuse, with different classification systems and communities declaring varying thresholds (e.g. for where a shoreline, forest, or other entity begins and ends). However, some boundaries are declared by fiat - that is, by arbitrary human convention or decree - particularly by regulatory or other authorities and communities of practice. The classes in this hierarchy attempt to offer generalisable definitions that allow multiple classfiication systems to map to and interoperate through. If desired, we can create classes that declare thresholds used by a given authority or community under the more generic ones, annotated with source information.
astronomical body part
An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it.
terrestrial environmental zone
A construction which comprises a durable surface layer overlying a solid surface intended to sustain vehicular or foot traffic.
constructed pavement
A vegetated area is a geographic feature which has ground cover dominated by plant communities.
A part of an astronomical body which is composed of a continuous medium bearing liquid, gaseous, and solid material in variable quantities.
compound astronomical body part
A material entity which has been assembled through the intentional, instinctual, or deliberately programmed efforts of an organism or machine.
construction
A landform which occurs on the surface of an astronomical body.
geographic feature
The usage of "surface" here aligns with that of planetary surface: in contact with the atmosphere or space. The extent of the "surface" can vary. For rocky planets like Earth, astrogeologists consider the crust as the surface.
surface landform
A solid astronomical body part which has been formed from and is composed primarily of the matter of that astronomical body.
Landforms may be natural or anthropogenic. This term has often has loose usage when referencing entities which are either subterranean or submerged below water bodies. In some cases, oceans themselves are considered landforms. Here, we have provided subclasses to resolve this ambiguity, but place oceans and other water bodies elsewhere.In later revisions, this hiearchy is likely to be reordered based on the formation processes of the entities within it.
landform
A reference to a place on the Earth, by its name or by its geographical location
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
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 that reliably tends to produce (approximately) truthful statements.
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.
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.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
An information entity is an entity that represents information about some other entity. For example, a measurement, a clustered data set.
an information content entity is an entity that is generically dependent on some material entity and stands in relation of aboutness to some entity
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
PERSON: Bjoern Peters
directive information entity
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Alan Ruttenberg
Clint Dowland
OBI Plan and Planned Process branch
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
measurement datum
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A data item that is a recording of the output of an assay.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
person:Chris Stoeckert
textual entity
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
PERSON: Lawrence Hunter
text
citation
Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
A textual entity intended to identify a particular publication.
A textual entity intended to identify a particular institution.
A textual entity that denotes a particular in reality.
A textual entity documenting the source of funding that supported some study.
funding source declaration textual entity
A textual entity that discusses work from other publications and expresses their relevancy to the content of a document.
An anatomical structure in which there inheres the disposition to be the agent of a mental process.
mental functioning related anatomical structure
An extended organism that is a member of the species Homo sapiens.
A bodily process that occurs in the brain, and that can of itself be conscious, or can give rise to a process that can of itself be conscious or can give rise to behaviour.
A 'mental process' is a subclass of 'bodily process', as mental processes occur within the body, specifically involving the brain.
A bodily process which brings into being, sustains or modifies a cognitive representation or a behavior inducing state.
Examples include thinking, feeling pain, remembering and emotion as occurrent experiences.
Mental processes can vary in the degree to which they involve consciousness. A 'mental process' is a subclass of 'bodily process', as mental processes occur within the body, specifically involving the brain.
Mental processes can varying in the degree to which they involve consciousness.
GO:0050890, cognition, defined as `The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.'
A dependent continuant which is about a portion of reality.
A representation which specifically depends on an anatomical structure in the cognitive system of an organism.
A bodily disposition is a disposition that inheres in some extended organism. Examples are: my disposition to catch a cold when exposed to a virus, my ability to speak the English language.
A disposition that inheres in some extended organism.
Bodily disposition includes features that can be used in a specific context, such as a person's strength, but not a person's weight. A person has a specific weight independent of the circumstances they are in.
Extended organism refers to an organism and its microbiome (e.g., the bacteria that live in one's digestive system) Bodily disposition would include features, such as a person's strength (which can be used in a specific context), but not weight. A person would have a certain weight independent of most circumstances they are in.
Extended organism refers to an organism and its microbiome (e.g., the bacteria that live in one's digestive system).
bodily disposition
A bodily disposition that is realized in a mental process.
A mental disposition is a bodily disposition that is realized in a mental process.
'Mental disposition' is a subclass of 'bodily disposition', as mental dispositions occur in the body.
Mental disposition' is a subclass of 'bodily disposition', as mental dispositions occur in the body.
mental disposition
A mental disposition to represent a proposition to be true.
Judging is a mental process that brings a belief into existence. Judging differently may also bring that belief out of existence. An act of believing is just thinking about a belief. Beliefs typically cause us to behave in ways that are characteristic with the content of that belief. However, this is not a necessary feature for the existence of the belief.
belief
A bodily quality is a quality that inheres in some extended organism.
bodily quality
An information content entity that represents a type of scale on which a variable is measured, including nominal, ordinal, interval, ratio.
A data transformation that is used to calculate the power of a statistical analysis.
A quantitative confidence value that refers to an interval give values within which there is a high probability (95 percent by convention) that the true population value can be found.
A quantitative confidence value that measures the variability of data around the mean.
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
A data item that is derived from a statistical data analysis.
Jie Zheng, Yongqun He, Marcy Harris, Asiyah Yu Lin
WEB: http://en.wikipedia.org/wiki/Statistic
WEB: http://www.ask.com/question/what-is-numerical-data
derived data from statistical analysis
A data item that is derived from an inferential statistical data analysis.
WEB: http://psc.dss.ucdavis.edu/sommerb/sommerdemo/stat_inf/intro.htm
derived data from inferential statistical analysis
A confidence interval with 95 percent probability that the true population value can be found.
A data item that is produced as the output of a data transformation.
transformed data item
planned process
Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
A processual entity that realizes a plan which is the concretization of a plan specification.
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
completely executed planned process
quantitative confidence value
A data item which is used to indicate the degree of uncertainty about a measurement.
A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution.
A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
selection criterion
rats should be aged between 6 and 8 weeks and weight between 180-250grams
A directive information entity which defines and states a principle of standard by which selection process may take place.
Person: Philippe Rocca-Serra
selection rule
OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A planned process that produces output data from input data.
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
arithmetic mean calculation
An arithmetic mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
Monnie McGee
PERSON: James Malone
PERSON: Monnie McGee
From Monnie's file comments - need to add moment_calculation and center_calculation roles but they don't exist yet - (editor note added by James Jan 2008)
averaging data transformation
An averaging data transformation is a data transformation that has objective averaging.
center calculation data transformation
A center calculation data transformation is a data transformation that has objective of center calculation.
descriptive statistical calculation data transformation
A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design.
eligibility criterion
PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
an eligibility criterion (rule) is_a selection criterion which defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process.
eligibility rule
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
inclusion criterion
PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) .
An eligibility criterion which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process.
an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study.
inclusion condition
inclusion rule
exclusion rule
PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months.
An eligibility criterion which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process.
an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study
exclusion criterion
A series of statements representing health-relevant qualities of a patient and of a patient's family.
A process experienced by the patient, which can only be experienced by the patient, that is hypothesized to be clinically relevant.
A process in which at least one bodily component of an organism participates.
A process in which at least one bodily component of an organsim participates.
From OGMS: http://purl.obolibrary.org/obo/OGMS_0000060
The phrase 'bodily component of an organism’ in the definition refers to ‘a part of the body’.
A bodily process that is clinically abnormal.
The representation of a conclusion of a diagnostic process.
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.
From OGMS: http://purl.obolibrary.org/obo/OGMS_0000087
A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient
A data item that is about a patient and is the specified output of a health care process assay or diagnostic process
clinical data item
A diagnosis that is the outcome of a diagnostic process targeting a second or additional health problem.
Alice Nzinga
Mathias Brochhausen
secondary infection, nosocomial infection
amended from http://en.wikipedia.org/wiki/Comorbidity
It is argued that Comorbidity occurs due to a disposition established by a prior infection with a pathogenic organism of a different kind.
Relation between person and diagnosis needs to be specified
comorbidity
A material entity that is a human made strcuture with firm connection between its foundation and the ground.
"Building" is a subclass of this.
This type of entity is referred to as "Bauwerk" or "Bauliche Anlage".
architectural structure
An architectural structure that bears some function.
Ontology of Medically Related Social Entities
facility
A facility that is run by a hospital organization, such as emergency departments, outpatient clinics and rehabilitation and is the bearer of a hospital function
A health care facility that bears the function to provide acute and intensive healthcare services and that is run by a hospital organization and is the bearer of a hospital function.
William Hogan
hospital facility
A facility that’s administered by a health care organisation for the purpose of providing health care to a patient population
A facility bearing the function to provide healthcare and that is administered by a health care organization for the purpose of providing health care to a patient or patient population.
health care facility
A health care facility that bears a function to provide healthcare to the sick or terminally ill
Emma Norris
Human Behaviour Change Project
hospice facility
A facility to assist in physical or addiction recovery
rehabilitation facility
a health care facility that also bears a residence function and thus one in which the patients are also residents of the facility
community living health care facility
residential facility
A facility that has at least one housing unit as part in which a person or persons live
Modified version of definition provided by Human Behaviour Change Project
status
The current stage of a clinical study and whether it is or will be open for enrollment
The current stage of a clinical study and whether it is or will be open for enrolment.
study status
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
A physical quality inhering in a bearer that has mass near a gravitational body.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
A health care facility whose function is to store, prepare, dispense, and monitor the usage of pharmaceutical drugs among patients in a given area or encountered in a given health care provider organization
Un établissement de santé qui a pour fonction d'entreposer, préparer, distribuer et surveiller l'utilisation des médicaments parmi les patients d'une zone géographique donnée ou suivis dans une organisation de soin donnée.
pharmacy facility
établissement de pharmacologie
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].
A G-protein coupled receptor that contains the 7 transmembrane receptor (rhodopsin family) domain (Pfam:PF00001), which includes 7 transmembrane helices (TMI-TM7) with 3 intracellular loops (IL1-IL3) and 3 extracellular loops (EL1-EL3) between the helices. The amino-terminal region is extracellular and the carboxyl-terminal region is intracellular. Rhodopsin-like G-protein coupled receptors (GPCRs) are unique among the several classes of GPCRs in that most have a very short amino-terminal segment and several characteristic sequence motifs, particularly NSxxNPxxY in TM7 and D/E-R-Y/F between TM3 and loop IL2. Most bind their ligands within a cavity between the TM regions.
Category=family. Classification based on GRAFS system. [PMID:12761335]
rhodopsin-like G-protein coupled receptor
A rhodopsin-like G-protein coupled receptor that is related to trace amine-associated receptor 1 (TAAR1) and characterized by the sequence motif NSxxNPxx[YH]xxx[YF]xWF overlapping TM7.
A rhodopsin-like G-protein coupled receptor that is related to trace amine-associated receptor 1 (TAAR1) and characterized by the sequence motif NSxxNPxx[YH]xxx[YF]xWF overlapping TM7. Trace amines are biogenic amines present in very low levels in mammalian tissues. Their physiological roles in mammals are poorly understood. Some of them are neurotransmitters in invertebrates. Ligands are currently known for only two TAARs, TAAR1 in human, rat, and mouse, and TAAR4 in rat.
trace-amine-associated receptor, trace amine associated receptor
A trace amine receptor that is a member of a subfamily comprising TAAR1, TAAR2, TAAR3P and TAAR4.
A trace amine-associated receptor 1-4 that is a translation product of the human TAAR1 gene or a 1:1 ortholog thereof.
A trace amine-associated receptor 1-4 that is a translation product of the human TAAR1 gene or a 1:1 ortholog thereof. The preferred ligands of the human protein are trace amines, including beta-phenylethylamine, p-tyramine, octopamine and tryptamine. It is unresponsive to amines such as epinephrine and histamine and only partially activated by dopamine and serotonine.
An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.
A protein that has G protein-coupled receptor (GPCR) activity. Each GPCR consists of a single polypeptide with an extracellular N-terminus, an intracellular C-terminus and seven hydrophobic transmembrane domains (TM1-TM7) linked by three extracellular loops (ECL1-ECL3) and three intracellular loops (ICL1-ICL3). GPCRs function as part of a heterotrimeric complex to transmit an extracellular signal across the membrane by activating an associated G-protein via the exchange of GDP for GTP on the alpha subunit.
A molecular entity that minimally consists of a protein.
Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565).
A planned process executed in the performance of scientific research wherein systematic investigations are performed to establish facts and reach new conclusions about phenomena in the world.
Data generation process are typically experimental studies or observations, but can include any process generating information used to evaluate a claim. This is an organizational class that groups more specific types of such processes that are most commonly used in generating data used as evidence to support claims. These processes produce informational artifacts such as measured data values, derived statistical calculations and confidence measures, or statements representing summaries or conclusions drawn from such data.
research activity
A planned process that executes some study design or protocol to generate scientific data that is interpreted to test or generate a hypothesis.
Explore the classification of study types here as a possibility to implement in SEPIO. https://mcw.libguides.com/evidencebased/studies Useful because these map to the strength of the evidence each might provide.
A research study is considered broadly to be any scientific activity aimed at answering a research question. Studies can be simple or complex, depending on the scope of the question being explored and the extent of resources deployed in doing so. They may include a full research investigation, a set of experiments, or a single experiment or assay. Regardless, that act of summarizing any results as a finding statement is considered part of the study.
A research study is considered broadly to be any scientific activity aimed at answering a research question. Studies can be simple or complex, depending on the scope of the question being explored and the extent of resources deployed in doing so. They may include a full research investigation, a set of related experiments, or a single experiment or assay. Regardless, that act of summarizing any results as a finding statement is considered part of the study. 'Study' here is broadly considered to include any defined activity performed to address a scientific question or generate a scientific hypothesis. It covers scientific inquiry at different scales of complexity, from a single assay, experiment or observation, to a complex research investigation addressing a broader scientific question. Studies can be based on a broad range of methods, including in silico algorithms, in vitro or in vivo experimentation on model systems, clinical studies on human subjects, or curation and analysis of existing knowledge, e.g. from publications, datasets, or knowledegbases, to derive novel insight.
research study
A data item which denotes the smallest value found in a dataset or resulting from a calculation.
a minimum value is a data item which denotes the smallest value found in a dataset or resulting from a calculation.
Alejandra Gonzalez-Beltran
Philippe Rocca-Serra
STATO
minimum value
A data item which denotes the largest value found in a dataset or resulting from a calculation.
maximum value is a data item which denotes the largest value found in a dataset or resulting from a calculation.
maximum value
A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s.
review formal definition as both numerator and denominator should be of the same type, not just some data item
adapted from Wolfram Alpha: https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig76g7
prevalence is a ratio formed by the number of subjects diagnosed with a disease divided by the total population size.
adapted from: https://www.health.ny.gov/diseases/chronic/basicstat.htm
prevalence
An experimental factor in Array Express which are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This upper level class is really used to give a root class from which applications can rely on and not be tied to upper ontology classses which do change.
Concept naming convention is lower case natural naming with spaces, when necessary captials should be used, for example disease factor, HIV, breast carcinoma, Ewing's sarcoma
A measurement is an information entity that is a recording of the output of a measurement such as produced by an instrument.
A cardiovascular measurement is a measurement of some part of the cardiovascular system and is typically used in the process of disease diagnosis in human patients.
A measurement quantifying some blood cell, or component.
Hemoglobin measurement is a measure of the quantity of the metallo protein hemoglobin in blood often used in the diagnosis of anaemia.
A triglyceride measurement is a quantification of triglycerides in some body fluid, used as a biomarker for cardiovascular disease.
A quantification of glycated A1c hemoglobin in blood used as an index for blood glucose level over several months.
Glycated hemoglobin is preferred over glycosylated hemoglobin to reflect the correct (non-enyzmatic) process. Early literature often used glycosylated as it was unclear which process was involved until further research was performed. The terms are still sometimes used interchangeably in English language literature. (See https://en.wikipedia.org/wiki/Glycated_hemoglobin)
Is the quantification of some glycoprotein.
A total cholesterol measurement is the quantification of cholesterol in blood, total cholesterol is defined as the sum of HDL, LDL, and VLDL.
The measurement of LDL cholesterol in blood used as a risk indicator for heart disease.
low density lipoprotein cholesterol measurement
The measurement of HDL cholesterol in blood used as a risk indicator for heart disease.
high density lipoprotein cholesterol measurement
The determination of the amount of hormone present in a sample.
Is the quantification of some lipoprotein
Is a quantification of some protein, typically obtained from an individual with the intention of using the measurement in some diagnostic process.
This is a general class for any measurement of a protein. Do not annotate to this class, request a more specific child term.
quantification of some lipid or lipoprotein
cardiovascular disease biomarkers, such as ST2 cardiac biomarker and C-reactive protein, are used as indicators for cardiovascular disease and as predictors for therapeutic responses
cardiovascular disease biomarker measurement
The quantification of a biomarker used in the diagnosis or management of diabetes mellitus
Quantification of prolactin in a sample.
An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.
Dose of pharmacological substance delivered to an individual.
A written name intended to identify a particular drug.
A data item that is about the number of times a dose of pharmacological substance is delivered during an intervention.
frequency of pharmacological substance dose
A written name intended to identify a particular intervention arm.
A temporal interval between the start and end of an intervention.
A maximum value of the dose of pharmacological substance delivered to individuals in a group.
maximum dose of pharmacological substance
A average value of dose of pharmacological substance delivered to individuals in a group.
average dose of pharmacological substance
A minimum value of the dose of pharmacological substance delivered to individuals in a group.
minimum dose of pharmacological substance
An intervention that has the same or similar appearance and delivery to another intervention but is intended not to have the active content of that intervention.
A measurement data item that is the recording of the output of the Abnormal Involuntary Movement Scale.
Guy, W. (1976). ECDEU assessment manual for psychopharmacology. US Department of Health, Education, and Welfare, Public Health Service, Alcohol, Drug Abuse, and Mental Health Administration, National Institute of Mental Health, Psychopharmacology Research Branch, Division of Extramural Research Programs.
A measure for 'dyskinesias' and 'dyskinesias following an intervention'
Abnormal Involuntary Movement Scale data item
Positive and Negative Syndrome Scale data item that is the recording of the output of the subscale about affective psychotic disorder symptoms.
A measure for 'affective psychotic disorder symptom severity'
Anxiety and depression subscale of Positive and Negative Syndrome Scale data item
Positive and Negative Syndrome Scale data item that is the recording of the output of the subscale about anxiety symptoms.
Anxiety subscale of Positive and Negative Syndrome Scale data item
A measurement data item that is the recording of the output of the Barnes Akathisia Rating Scale.
A measure for 'akathisia' and 'akathisia following an intervention'
A measurement data item that is the recording of the output of the Brief Negative Symptom Scale.
A measure for 'negative psychotic disorder symptom severity'
A measurement data item that is the recording of the output of the Brief Psychiatric Rating Scale.
A measure for 'psychotic disorder symptom severity'
Brief Psychiatric Rating Scale data item
A measurement data item that is the recording of the output of the Clinical Global Impression scale.
Clinical Global Impression data item about the improvement in a person's condition.
Clinical Global Impression – Improvement data item
Clinical Global Impression data item about the severity of a disorder.
Clinical Global Impressions - Severity data item
A measurement data item that is the recording of the output of the Columbia-Suicide Severity Rating Scale.
Columbia-Suicide Severity Rating Scale data item
Columbia-Suicide Severity Rating Scale data item about suicidal ideation.
A measure for 'suicidal ideation' and 'suicidal ideation following intervention'
Columbia-Suicide Severity Rating Scale ideation data item
Columbia-Suicide Severity Rating Scale data item about suicide attempts.
A measure for 'suicidal attempt' and 'suicidal attempt following intervention'
Columbia-Suicide Severity Rating Scale suicide attempt data item
Positive and Negative Syndrome Scale data item that is the recording of the output of the subscale about depression symptoms.
A measure for 'depression symptom severity'
Depression subscale of Positive and Negative Syndrome Scale data item
A measurement data item that is the recording of the output of the EuroQol five dimensions questionnaire-3 levels.
A measure for 'belief about quality of life'
EuroQol five dimensions questionnaire-3 levels data item
A measurement data item that is the recording of the output of the Montgomery and Asberg Depression Rating Scale.
Montgomery and Asberg Depression Rating Scale data item
Positive and Negative Syndrome Scale data item that is the recording of the output of the subscale about negative psychotic disorder symptoms.
Negative subscale of Positive and Negative Syndrome Scale data item
A measurement data item that is the recording of the output of the Personal and Social Performance Scale.
Personal and Social Performance Scale data item
A measurement data item that is the recording of the output of the Positive and Negative Syndrome Scale.
Positive and Negative Syndrome Scale data item
Positive and Negative Syndrome Scale data item that is the recording of the output of the subscale about positive psychotic disorder symptoms.
Positive subscale of Positive and Negative Syndrome Scale data item
A measurement data item that is the recording of the output of the Scale for Assessment of Positive Symptoms for Parkinson's disease.
A measure for 'positive psychotic disorder symptom severity'
Scale for Assessment of Positive Symptoms for Parkinson's disease data item
A measurement data item that is the recording of the output of the Simpson Angus Scale data item.
A measure for 'neuroleptic-induced parkinsonism' and 'neuroleptic-induced parkinsonism following an intervention'
A measurement data item that is the recording of the output of the Neuropsychiatric Inventory Huntington's disease.
The Neuropsychiatric Inventory Huntington's disease data item
A measurement data item that is the recording of the output of the Unified Parkinson's Disease Rating Scale Part 3.
Fahn, S. R. L. E. (1987). Unified Parkinson's disease rating scale. Recent developments in Parkinson's disease, 153-163.
A measure for 'drug-induced movement disorder' and 'drug-induced movement disorder following an intervention'
Unified Parkinson's Disease Rating Scale Part 3 data item
A measurement data item that is the recording of the output of the University of California, San Diego Performance-Based Skills Assessment-Brief.
University of California, San Diego Performance-Based Skills Assessment-Brief
An adverse change in a bodily measurement parameter relating to HbA1c measurement.
An adverse event associated with a change in a person's bodily meeasurement parameters.
Based on http://purl.obolibrary.org/obo/OAE_0000581
adverse change in a bodily measurement parameter
An adverse change in a bodily measurement parameter relating to the body mass index.
An adverse change in a bodily measurement parameter relating to body weight.
An adverse change in a bodily measurement parameter relating to glucose measurement.
An adverse change in a bodily measurement parameter relating to the high density lipoprotein cholesterol measurement.
adverse change in high density lipoprotein cholesterol measurement
An adverse change in a bodily measurement parameter relating to the low density lipoprotein cholesterol measurement.
adverse change in low density lipoprotein cholesterol measurement
An adverse change in a bodily measurement parameter relating to prolactin measurement.
An adverse change in prolactin measurement in people with female gender.
adverse change in prolactin measurement of females
An adverse change in prolactin measurement in people with male gender.
adverse change in prolactin measurement of males
An adverse change in a bodily measurement parameter relating to the total cholesterol measurement.
adverse change in total cholesterol measurement
An adverse change in a bodily measurement parameter relating to triglyceride measurement.
adverse change in triglyceride measurement
A pathological bodily process that occurs after the intervention delivery starts.
A psychotic disorder symptom is characterized by a person experiencing depression, anxiety or low moods.
Symptom severity that is associated with an affective psychotic disorder symptom.
affective psychotic disorder symptom severity
A drug-induced movement disorder following intervention that involves feeling restlessness, increased urges to move and reduced capability to suppress such urges.
Based on https://www.ncbi.nlm.nih.gov/books/NBK519543/
akathisia following pharmacological intervention
A belief about the degree to which a drug results in harm to a person.
Based on Alshammari, T. M. (2016). Drug safety: The concept, inception and its importance in patients’ health. Saudi Pharmaceutical Journal, 24(4), 405-412.
A belief about about the negative effects of a drug on a person.
belief about drug-related adverse events
A belief about whether the delivered intervention is appropriate based on anticipated or experienced responses to the intervention.
Based on Sekhon, M., Cartwright, M., and Francis, J. J. (2017). Acceptability of healthcare interventions: an overview of reviews and development of a theoretical framework. BMC health services research, 17(1), 1-13.
A belief about the degree to which a drug results in unpleasant or bothersome bodily reactions.
Based on Stanulović, V., Hodolic, M., Mitsikostas, D. D., and Papadopoulos, D. (2022). Drug tolerability: how much ambiguity can be tolerated? A systematic review of the assessment of tolerability in clinical studies. British Journal of Clinical Pharmacology, 88(2), 551-565.
A data item that is derived by dividing the body weight be the square of the body height.
Based on Nuttall F. Q. (2015). Body Mass Index: Obesity, BMI, and Health: A Critical Review. Nutrition today, 50(3), 117–128. https://doi.org/10.1097/NT.0000000000000092
A death following an intervention that involves a participant dying as a result of an accident.
death due to accidents following an intervention
A death following an intervention that results from an illness or its complications or an internal bodily malfunction that is not directly caused by external events.
Based on https://en.wikipedia.org/wiki/Manner_of_death
death due to natural causes following an intervention
A serious adverse event following an intervention that has an outcome of death.
A symptom that is related to a depression diagnosis.
Symptom severity that is associated with a depression symptom.
Symptom severity that is associated with a depression symtom.
An adverse event following a pharmacological intervention that involves reduced abilities to control movements.
extrapyramidal symptom following intervention
Based on https://www.ncbi.nlm.nih.gov/books/NBK534115/
drug-induced movement disorder following intervention
An adverse event following an intervention that involves dyskinesias.
A death following an intervention that involves a participant being intentionally killed by another person.
A health care process that involves a person being admitted to a hospital.
A bodily disposition to realise processes that influence a person's life quality.
A psychotic disorder symptom that is characterized by the absence or decrease in ability or motivation to initiate plans, speak, express emotion of find pleasure.
Based on https://www.psychiatry.org/patients-families/schizophrenia/what-is-schizophrenia
Psychotic disorder symptom severity that is associated with negative psychotic disorder symptoms.
negative psychotic disorder symptom severity
A drug-induced movement disorder following intervention that involves experiencing slowness of movement, tremors and rigidity.
Based on https://link.springer.com/article/10.1007/s007020100006
neuroleptic-induced parkinsonism following intervention
Number of participant drop-out from the intervention as a result the participants experiencing some adverse event.
number of participant drop-out due to adverse events
Number of participant drop-out from the intervention as a result of the intervention failing to produce the desired effect.
number of participant drop-out due to inefficacy
Number of participant drop-out due to adverse events that are experienced following the intervention.
number of participant drop-out due to side-effects
Number of intervention participants who discontinue participating in an intervention.
number of participant drop-out from intervention
An intervention outcome that is positively influenced by the intervention.
A psychotic disorder symptom that is characterized by the presence of hallucinations, delusions, or disorganised thoughts or behaviours.
Psychotic disorder symptom severity that is associated with positive psychotic disorder symptoms.
positive psychotic disorder symptom severity
Symptom severity that is associated with a psychotic disorder symptom.
An adverse event following an intervention that results in death, a life-threatening event, a persistent or significant disability or a birth defect or requires hospitalisation or extends hospitalisation.
Based on http://purl.obolibrary.org/obo/OAE_0000631
serious adverse event following an intervention
A serious adverse event following an intervention that is associated with multiple, persistent or salient negative mental processes.
serious psychological adverse event following an intervention
A serious adverse event following an intervention that is associated with multiple, persistent or salient physical symptoms.
serious somatic adverse event following an intervention
An adverse event following an intervention that involves thoughts about suicide.
Based on http://purl.obolibrary.org/obo/OAE_0001432
suicidal ideation following intervention
An adverse event following an intervention that involves at least one attempted suicide.
Based on http://purl.obolibrary.org/obo/OAE_0001433
A death following an intervention that involves a participant intentionally ending their own life.
A data item that is about the location on the dimension of a symptom.
A data item that is about the severity dimension associated with a symptom.
Death following an intervention that involves a homicide or accidents.
unnatural dealth due to external factors following an intervention
A person who is in the latter end of their lifespan.
A person who has not yet reached maturity.
A clinical history in which there is a history of psychosis experience.
clinical history of psychosis experience
A self-identity as belonging to a group or groups whose members have a common heritage that is real or presumed such as common culture, language, religion, behaviour or biological trait.
A clinical history in which there is a history of only one period of psychosis experience.
A self-identity as having a particular gender, which may or may not correspond with sex assigned at birth.
A clinical history in which a person has more negative than psychotic disorder symptoms.
predominant negative psychotic disorder symptom history
A symptom that involves a person experiencing delusions, hallucinations, conceptual disorganisation or disorganised speech or behaviour
https://www.mind.org.uk/information-support/types-of-mental-health-problems/psychosis/about-psychosis/ DSM V
Hallucinatory behaviour is an example of disorganised behaviour
A psychosis diagnosis that involves the conclusion that a person meets pre-set criteria for schizophrenia as a result of a diagnostic process.
Standard deviation of human age in a population.
A clinical history in which a person has an inadequate response to at least two adequate rials of antipsychotic drugs.
A data item that is about the number of sites.
A psychiatric facility in which patients stay at the facility overnight.
A psychiatric facility to treat patients without them staying overnight.
An aggregate of entities that form the environment in which participants are recruited for a study.
A textual entity intended to identify a particular author.
A blinding process in which the data analysts are not informed about intervention arm assignments until after the data analysis is completed.
blinding data analysts of intervention arm
A blinding process in which sources deliverying the intervention are not informed about which of two or more interventions they are deliverying until after an endpoint has been reached.
blinding intervention source about intervention arm
A blinding process in which the outcome assessors are not informed about which of two or more interventions they are collecting data about until after an endpoint has been reached.
blinding outcome assessor of intervention arm
A blinding process in which participants are not informed about which of two or more interventions they are to experience until after an endpoint has been reached.
blinding participant about intervention arm
A planned process in which information about study arm assignment is withheld from people until they completed their role in the study's data collection or analysis has ended.
"randomised controlled trial design" AND "cross over design"
cross over randomised controlled trial design
"randomised controlled trial design" AND "n-of-1 study design"
n-of-1 randomised controlled trial design
A data item that is about the number of intervention groups in a study.
A related work textual entity that discusses work from other publications done as part of the same research project as the work reported in a document.
Formal citation for a plan specification of the study published as protocol or trial registration.
pre-registered plan specification source
A textual entity documenting the year in which some study was published.
"randomised controlled trial design" AND "parallel group design"
parallel randomised controlled trial design
A study arm designation as a comparator to some intervention arm.
A study arm that is subject to evaluation in an intervention evaluation study.
A temporal interval between the start and end of an intervention contact event.
A planned process that is part of an intervention and is intended to be causally active in influencing its target outcome or outcomes.
A control arm designation where there is no intervention.
An information content entity that is about an intervention scenario and designates it as part of an intervention evaluation study.
A control arm designation where the same content and delivery is already provided as standard practice.
A control arm designation where no intervention prior to the primary outcome follow-up point is delivered but participants in the study arm are informed that they will be entitled to receive an intervention at some time after that point.
A mental disposition that is realised by experiencing low pleasure or interest in response to various positively valenced stimuli.
Symptom severity that is associated with anhedonia.
A data item about the number of heart contractions within a temporal interval.
A quantitative confidence value that denotes the lower endpoint of a 95% confidence interval and indicates the lowest value within a true parameter is likely to reside within the confidence interval.
Based on Ross, S. M. (2017). Estimation. Introductory statistics ( p. 329-380). Academic Press.
Number of intervention participants who discontinue participating in a intervention arm.
number of participant drop-out from intervention arm
A bodily disposition to detect, pursue, learn from, and derive pleasure from stimuli perceived as positive.
Associative learning by which information is acquired regarding the positive outcomes of stimuli and behaviours.
A mental process in which the discrepancy between the predicted and received rewards is signalled.
Based on Schultz, W. (2022). Dopamine reward prediction error coding. Dialogues in clinical neuroscience. RDoC - https://www.nimh.nih.gov/research/research-funded-by-nimh/rdoc/definitions-of-the-rdoc-domains-and-constructs
Time point at which a measurement is taken with reference to a temporal part of the intervention evaluation study.
temporal reference associated with measurement in intervention
A quantitative confidence value that denotes the upper endpoint of a 95% confidence interval and indicates the highest value within a true parameter is likely to reside within the confidence interval.
A data item about the maximum capacity of an individual's body to transport and use oxygen during incremental exercise, which reflects the physical fitness of the individual.
Diagnosis severity relating to an anxiety diagnosis.
A symptom that related to a anxiety diagnosis.
Symptom severity that is associated with a anxiety symtom.
A diagnosis that involves the conclusion that a person meets pre-set criteria for autism spectrum disorder as a result of a diagnostic process.
Diagnosis severity relating to an autism spectrum disorder diagnosis.
autism spectrum disorder diagnosis severity
A measurement data item that is the recording of depression symptom severity.
A data item that is about the severity dimension associated with a diagnosis.
There are different scales for rating severity, which can be indicate differences in severity.
A depression diagnosis that involves the conclusion that a person meets pre-set criteria for dysthymic disorder as a result of a diagnostic process.
persistent depressive disorder diagnosis status
Symptom severity that is associated with insomnia.
A depression diagnosis that involves the conclusion that a person meets pre-set criteria for major depressive disorder as a result of a diagnostic process.
A data item that is about the number of participants in an intervention or part of an intervention at a timepoint.
Number of intervention participants who are part of an intervention arm.
number of participants in intervention arm
Number of intervention participants who were randomly allocated to study arms within an intervention.
number of randomised intervention participants
Diagnosis severity relating to a post-traumatic stress disorder diagnosis.
post-traumatic stress disorder diagnosis severity
A diagnosis that involves the conclusion that a person meets pre-set criteria for post-traumatic stress disorder as a result of a diagnostic process.
post-traumatic stress disorder diagnosis
A measurement data item that is the recording of post-traumatic stress disorder severity level.
post-traumatic stress disorder severity measurement item
Anxiety symptom severity before the intervention delivery begins.
pre-intervention anxiety symptom severity
Autism spectrum diagnosis severity before the intervention delivery begins.
pre-intervention autism spectrum disorder diagnosis severity
Depression symptom severity before an intervention starts.
pre-intervention depression symptom severity
Insomnia symptom severity before the intervention delivery begins.
Personal attribute before the intervention delivery begins.
Baseline clinical variable, baseline variable
Based on https://dictionary.apa.org/baseline-characteristic
Post-traumatic stress disorder diagnosis severity before the intervention delivery begins.
Logical definition was: "post-traumatic stress disorder diagnosis severity" precedes "intervention"
pre-intervention post-traumatic stress disorder diagnosis severity
Substance use severity before the intervention delivery begins.
Prevalence of diagnosis for bipolar disorder.
prevalence of bipolar disorder diagnosis
Prevalence of people diagnosed with a specific disorder.
Prevalence of diagnosis for major depressive disorder.
prevalence of unipolar depression disorder diagnosis
prevalence of major depressive disorder diagnosis
A data item about the frequency of a substance use behaviour or the amount of psychoactive substance ingested into the body.
An aggregate of entities that form the environment in which an intervention is provided.
A textual entity documenting the email address of an author of a publication.
An information content entity that is the language used to express the information in a document.
A symptom that is related to a psychotic disorder diagnosis.
Anxiety symptom severity relating to a post-traumatic stress symptom.
An anxiety symptom that related to a post-traumatic stress disorder diagnosis.
An attribute of a measurement scale that involves the degree to which the outcomes from the scale represent the intended variable or variables.
Based on Price, P. (2015). Research methods in psychology, 2nd Canadian Edition. BCcampus.
A diagnosis that involves the conclusion that a person meets pre-set criteria for depression as a result of a diagnostic process.
Dose of pharmacological substance delivered to individuals within each day.
An adverse event following an intervention that occurs in the digestive system.
digestive system adverse event following intervention
An adverse event following an intervention that involves experiencing dizziness.
A digestive system adverse event following intervention that involves experiencing dry mouth.
A pain following intervention that has an outcome of headache.
An adverse event following an intervention in which there is an inability to fall asleep or to stay asleep as long as desired.
A digestive system adverse event following intervention that has an outcome of nausea, a gastric discomfort associated with the inclination to vomit
An adverse event following an intervention that has an outcome of pain.
A digestive system adverse event following intervention that has an outcome of vomiting, the retrograde expulsion of gastric contents through the oral cavity.
A diagnosis that involves the conclusion that a person meets pre-set criteria for psychosis as a result of a diagnostic process.
The aggregate of human age in a population.
Physical performance behaviour pattern that increases heart rate and respiration while using large muscle groups repetitively and rhythmically.
cardio training, aerobic exercise, aerobics, endurance exercise, endurance training, cardiovascular exercise
A locomotive behaviour that involves trotting or running at a slow and steady pace.
An individual human behaviour pattern that involves repeated physical performance behaviour.
Physical performance behaviour pattern that uses weight, or other forms of resistance, to induce muscle contraction and build strength, anaerobic endurance, and size of skeletal muscles.
A locomotive behaviour that involves moving at a steady pace and speed with long strides such that there is a phase at which all limbs are above the ground.
Individual human behaviour pattern involving consumption behaviour and physical performance behaviour in order to grow muscles.