entity
BFO OWL specification label: entity
BFO CLIF specification label: Entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
editor note: 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
editor note: 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
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
type: Class
subclass of: Thing

continuant
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
definition: 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.
editor note: 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
editor note: 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
imported from: iao.owl
elucidation: 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])
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
type: Class
subclass of: entity
disjoint with: occurrent

occurrent
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
editor note: 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
editor note: 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.
editor note: 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.
editor note: 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.
elucidation: 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])
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
type: Class
subclass of: entity

independent continuant
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: 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])
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (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]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
type: Class
subclass of: continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant

spatial region
BFO OWL specification label: s-region
BFO CLIF specification label: SpatialRegion
editor note: BFO 2 Reference: Spatial regions do not participate in processes.
editor note: 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.
elucidation: 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])
has associated axiom(nl): All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has associated axiom(fol): (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has associated axiom(fol): (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
type: Class
subclass of: immaterial entity
disjoint with: site
disjoint with: continuant fiat boundary

temporal region
BFO OWL specification label: t-region
BFO CLIF specification label: TemporalRegion
editor note: 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
elucidation: 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])
has associated axiom(nl): All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has associated axiom(fol): (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has associated axiom(fol): (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has associated axiom(fol): (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
type: Class
subclass of: occurrent
disjoint with: spatiotemporal region
disjoint with: process
disjoint with: process boundary

two-dimensional spatial region
BFO OWL specification label: 2d-s-region
BFO CLIF specification label: TwoDimensionalSpatialRegion
example of usage: an infinitely thin plane in space.
example of usage: the surface of a sphere-shaped part of space
elucidation: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has associated axiom(fol): (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region

spatiotemporal region
BFO OWL specification label: st-region
BFO CLIF specification label: SpatiotemporalRegion
example of usage: the spatiotemporal region occupied by a human life
example of usage: the spatiotemporal region occupied by a process of cellular meiosis.
example of usage: the spatiotemporal region occupied by the development of a cancer tumor
elucidation: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has associated axiom(nl): All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has associated axiom(nl): Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has associated axiom(nl): Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has associated axiom(nl): Every spatiotemporal region occupies_spatiotemporal_region itself.
has associated axiom(nl): Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has associated axiom(fol): (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has associated axiom(fol): (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has associated axiom(fol): (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
type: Class
subclass of: occurrent

process
BFO OWL specification label: process
BFO CLIF specification label: Process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
definition: 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])
editor note: 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)
imported from: bfo.owl
imported from: oae.owl
imported from: obi.owl
imported from: ro.owl
has associated axiom(fol): (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]
type: Class
subclass of: occurrent

disposition
BFO OWL specification label: disposition
BFO CLIF specification label: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: 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.
imported from: ogms.owl
elucidation: 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])
has associated axiom(nl): 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])
has associated axiom(fol): (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]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
type: Class
subclass of: realizable entity
disjoint with: role

realizable entity
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: 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.
imported from: dron.owl
imported from: envo.owl
imported from: obi.owl
imported from: ogms.owl
imported from: The Ontology of Medically Related Social Entities
imported from: opmi.owl
elucidation: 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])
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (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]
has associated axiom(fol): (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]
type: Class
subclass of: specifically dependent continuant
disjoint with: quality

zero-dimensional spatial region
BFO OWL specification label: 0d-s-region
BFO CLIF specification label: ZeroDimensionalSpatialRegion
elucidation: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region

quality
BFO OWL specification label: quality
BFO CLIF specification label: Quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
elucidation: 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])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (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]
type: Class
subclass of: specifically dependent continuant

specifically dependent continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
example of usage: 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
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: 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.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: 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])
editor note: 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.
has associated axiom(fol): (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]
type: Class
subclass of: continuant
disjoint with: generically dependent continuant

role
BFO OWL specification label: role
BFO CLIF specification label: Role
example of usage: 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.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
editor note: 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.
imported from: dron.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: opmi.owl
elucidation: 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])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
type: Class
subclass of: realizable entity

fiat object part
BFO OWL specification label: fiat-object-part
BFO CLIF specification label: FiatObjectPart
example of usage: 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
example of usage: the FMA:regional parts of an intact human body.
example of usage: the Western hemisphere of the Earth
example of usage: the division of the brain into regions
example of usage: the division of the planet into hemispheres
example of usage: the dorsal and ventral surfaces of the body
example of usage: the upper and lower lobes of the left lung
editor note: BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
elucidation: 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])
has associated axiom(fol): (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]
type: Class
subclass of: material entity

one-dimensional spatial region
BFO OWL specification label: 1d-s-region
BFO CLIF specification label: OneDimensionalSpatialRegion
example of usage: an edge of a cube-shaped portion of space.
elucidation: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region

object aggregate
BFO OWL specification label: object-aggregate
BFO CLIF specification label: ObjectAggregate
example of usage: a collection of cells in a blood biobank.
example of usage: a swarm of bees is an aggregate of members who are linked together through natural bonds
example of usage: a symphony orchestra
example of usage: 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)
example of usage: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
example of usage: defined via attributive delimitations such as: the patients in this hospital
example of usage: the aggregate of bearings in a constant velocity axle joint
example of usage: the aggregate of blood cells in your body
example of usage: the nitrogen atoms in the atmosphere
example of usage: the restaurants in Palo Alto
example of usage: your collection of Meissen ceramic plates.
editor note: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
editor note: 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).
definition source: 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.
elucidation: 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])
has associated axiom(fol): (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]
type: Class
subclass of: material entity

three-dimensional spatial region
BFO OWL specification label: 3d-s-region
BFO CLIF specification label: ThreeDimensionalSpatialRegion
example of usage: a cube-shaped region of space
example of usage: a sphere-shaped region of space,
elucidation: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has associated axiom(fol): (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
type: Class
subclass of: spatial region

site
BFO OWL specification label: site
BFO CLIF specification label: Site
example of usage: Manhattan Canyon)
example of usage: a hole in the interior of a portion of cheese
example of usage: a rabbit hole
example of usage: an air traffic control region defined in the airspace above an airport
example of usage: the Grand Canyon
example of usage: the Piazza San Marco
example of usage: the cockpit of an aircraft
example of usage: the hold of a ship
example of usage: the interior of a kangaroo pouch
example of usage: the interior of the trunk of your car
example of usage: the interior of your bedroom
example of usage: the interior of your office
example of usage: the interior of your refrigerator
example of usage: the lumen of your gut
example of usage: your left nostril (a fiat part – the opening – of your left nasal cavity)
elucidation: 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])
has associated axiom(fol): (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
type: Class
subclass of: immaterial entity

object
BFO OWL specification label: object
BFO CLIF specification label: Object
example of usage: atom
example of usage: cell
example of usage: cells and organisms
example of usage: engineered artifacts
example of usage: grain of sand
example of usage: molecule
example of usage: organelle
example of usage: organism
example of usage: planet
example of usage: solid portions of matter
example of usage: star
editor note: BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
editor note: BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
editor note: BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
editor note: BFO 2 Reference: an object is a maximal causally unified material entity
editor note: BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
imported from: dron.owl
imported from: envo.owl
imported from: opmi.owl
elucidation: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
type: Class
subclass of: material entity

generically dependent continuant
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
example of usage: 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.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: 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.
definition: 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])
imported from: iao.owl
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
type: Class
subclass of: continuant

function
BFO OWL specification label: function
BFO CLIF specification label: Function
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
editor note: 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.
elucidation: 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])
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
type: Class
subclass of: disposition

process boundary
BFO OWL specification label: p-boundary
BFO CLIF specification label: ProcessBoundary
example of usage: the boundary between the 2nd and 3rd year of your life.
definition: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has associated axiom(fol): (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has associated axiom(fol): (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
type: Class
subclass of: occurrent

one-dimensional temporal region
BFO OWL specification label: 1d-t-region
BFO CLIF specification label: OneDimensionalTemporalRegion
example of usage: the temporal region during which a process occurs.
editor note: BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
elucidation: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
type: Class
subclass of: temporal region
disjoint with: zero-dimensional temporal region

material entity
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: 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
editor note: 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.
editor note: 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.
imported from: bfo.owl
imported from: dron.owl
imported from: envo.owl
imported from: ero.owl
imported from: oae.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: opmi.owl
elucidation: 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])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (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]
has associated axiom(fol): (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]
type: Class
label: material_entity
subclass of: independent continuant
disjoint with: immaterial entity

has part
type: ObjectProperty
type: TransitiveProperty

realizes
type: ObjectProperty

preceded_by
type: ObjectProperty
type: TransitiveProperty
label: preceded by

continuant fiat boundary
BFO OWL specification label: cf-boundary
BFO CLIF specification label: ContinuantFiatBoundary
definition: b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
editor note: BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
editor note: BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
editor note: Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
has associated axiom(nl): Every continuant fiat boundary is located at some spatial region at every time at which it exists
has associated axiom(fol): (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
type: Class
subclass of: immaterial entity

immaterial entity
BFO OWL specification label: immaterial
BFO CLIF specification label: ImmaterialEntity
editor note: 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
type: Class
subclass of: independent continuant

one-dimensional continuant fiat boundary
BFO OWL specification label: 1d-cf-boundary
BFO CLIF specification label: OneDimensionalContinuantFiatBoundary
example of usage: The Equator
example of usage: all geopolitical boundaries
example of usage: all lines of latitude and longitude
example of usage: the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
example of usage: the median sulcus of your tongue
elucidation: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
has associated axiom(fol): (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
type: Class
subclass of: continuant fiat boundary
disjoint with: two-dimensional continuant fiat boundary
disjoint with: zero-dimensional continuant fiat boundary

process profile
BFO OWL specification label: process-profile
BFO CLIF specification label: ProcessProfile
example of usage: 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
example of usage: 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.
example of usage: 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.
definition: 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])
elucidation: 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])
has associated axiom(fol): (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]
has associated axiom(fol): (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
type: Class
subclass of: process
disjoint with: history

relational quality
BFO OWL specification label: r-quality
BFO CLIF specification label: RelationalQuality
example of usage: 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.
example of usage: a marriage bond, an instance of requited love, an obligation between one person and another.
definition: b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
has associated axiom(fol): (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
type: Class
subclass of: quality

two-dimensional continuant fiat boundary
BFO OWL specification label: 2d-cf-boundary
BFO CLIF specification label: TwoDimensionalContinuantFiatBoundary
elucidation: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
has associated axiom(fol): (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
type: Class
subclass of: continuant fiat boundary

zero-dimensional continuant fiat boundary
BFO OWL specification label: 0d-cf-boundary
BFO CLIF specification label: ZeroDimensionalContinuantFiatBoundary
example of usage: the geographic North Pole
example of usage: the point of origin of some spatial coordinate system.
example of usage: the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
editor note: zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
elucidation: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
has associated axiom(fol): (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
type: Class
subclass of: continuant fiat boundary

zero-dimensional temporal region
BFO OWL specification label: 0d-t-region
BFO CLIF specification label: ZeroDimensionalTemporalRegion
example of usage: a temporal region that is occupied by a process boundary
example of usage: right now
example of usage: the moment at which a child is born
example of usage: the moment at which a finger is detached in an industrial accident
example of usage: the moment of death.
alternative term: temporal instant.
imported from: obi.owl
imported from: opmi.owl
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
type: Class
subclass of: temporal region

BFO OWL specification label
editor preferred label: BFO OWL specification label
definition: 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.
curator note: Really of interest to developers only
type: AnnotationProperty
sub property of: label

BFO CLIF specification label
editor preferred label: BFO CLIF specification label
definition: Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
definition source: Person:Alan Ruttenberg
curator note: Really of interest to developers only
type: AnnotationProperty
sub property of: label

history
BFO OWL specification label: history
BFO CLIF specification label: History
elucidation: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
type: Class
subclass of: process

molecular entity
editor preferred label: molecular entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
editor note: We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
imported from: chebi.owl
imported from: dron.owl
imported from: obi.owl
imported from: opmi.owl
has exact synonym: molecular entity
has_obo_namespace: chebi_ontology
has_related_synonym: entidad molecular
has_related_synonym: entidades moleculares
has_related_synonym: entite moleculaire
has_related_synonym: molecular entities
has_related_synonym: molekulare Entitaet
id: CHEBI:23367
in subset: 3 STAR
type: Class
subclass of: object
subclass of: material entity
subclass of: chemical entity

chemical entity
definition: A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
imported from: chebi.owl
imported from: dron.owl
imported from: opmi.owl
has exact synonym: chemical entity
has_obo_namespace: chebi_ontology
id: CHEBI:24431
in subset: 3 STAR
type: Class
subclass of: material entity

secondary identifier
definition: An identifier(s) (ID), if any, other than the organization's Unique Protocol Identification Number or the NCT number that is assigned to the clinical study. This includes any unique clinical study identifiers assigned by other publicly available clinical trial registries. If the clinical study is funded in whole or in part by a U.S. Federal Government agency, the complete grant or contract number must be submitted as a Secondary ID.
definition: Other identifiers besides the Trial Identifying Number allocated by the Primary Registry, if any.
type: Class
subclass of: information content entity

Australian New Zealand clinical trials registry identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in the Australian New Zealand clinical trials registry (ANZCTR). The format for the registry number is “ACTRN” followed by a 14-digit number, e.g., ACTRN12620000457943.
has exact synonym: ANZCTR identifier
type: Class
subclass of: Clinical Trial Registry Identifier

Australian New Zealand clinical trials registry
definition: Australian New Zealand Clinical Trials Registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: ANZCTR
type: Class
subclass of: primary registry

Peruvian clinical trial registry identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in the Peruvian clinical trial registry (REPEC). The format for the registry number is “PER-” followed by a 3-digit number, followed by a hyphen, followed by a 2-digit number e.g., PER-010-20.
has exact synonym: REPEC identifier
type: Class
subclass of: Clinical Trial Registry Identifier

masking design
definition: The party or parties involved in the clinical trial who are prevented from having knowledge of the interventions assigned to individual participants.
has_related_synonym: blinding
has_related_synonym: masking
type: Class
subclass of: study design

non-random allocation
definition: Participants are expressly assigned to intervention groups through a non-random method, such as physician choice
has exact synonym: non-randomized
has exact synonym: nonrandomized
type: Class
subclass of: Allocation

study summary result
definition: A study record that includes the summary results posted in the ClinicalTrials.gov results database. Summary results information includes participant flow, baseline characteristics, outcome measures, and adverse events (including serious adverse events).
has exact synonym: summary results
type: Class
subclass of: report

secondary outcome measure information
definition: A description of each secondary outcome measure (or for observational studies, specific secondary measurement[s] or observation[s] used to describe patterns of diseases or traits or associations with exposures, risk factors or treatment). Each secondary outcome measure information includes title, description and time frame.
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
has_related_synonym: key secondary outcome
type: Class
subclass of: outcome specification

Iranian registry of clinical trials
definition: The Iranian registry of clinical trials is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: IRCT
type: Class
subclass of: primary registry

other outcome measure information
definition: Any other measurements, excluding post-hoc measures, that will be used to evaluate the intervention(s) or, for observational studies, that are a focus of the study. Each primary outcome measure information includes title, description and time frame.
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
has exact synonym: other pre-specified outcome measures
type: Class
subclass of: outcome specification

Indian clinical trials registry
definition: The Indian clinical trials registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: CTRI
has exact synonym: clinical trials registry - India
type: Class
subclass of: primary registry

The Netherlands national trial register
definition: The Netherlands national trial register is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: NTR
type: Class
subclass of: primary registry

Iranian registry of clinical trials identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in the Iranian registry of clinical trials (IRCT). The format for the registry number is “IRCT” followed by a 14-digit number, one letter and again one or two numbers, e.g., IRCT20100228003449N29.
has exact synonym: IRCT identifier
type: Class
subclass of: Clinical Trial Registry Identifier

German clinical trials register identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in the German clinical trials register (DRKS). The format for the registry number is “DRKS” followed by a 8-digit number, e.g., DRKS00000494.
has exact synonym: DRKS identifier
type: Class
subclass of: Clinical Trial Registry Identifier

Cuban public registry of clinical trials
definition: The Cuban public registry of clinical trials is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: RPCEC
type: Class
subclass of: primary registry

clinical trial outcome measurement
definition: For clinical trials, a planned measurement described in the protocol that is used to determine the effect of an intervention/treatment on participants. For observational studies, a measurement or observation that is used to describe patterns of diseases or traits, or associations with exposures, risk factors, or treatment. Types of outcome measures include primary outcome measure and secondary outcome measure.
has exact synonym: outcome measure
has exact synonym: outcome measurement
type: Class
subclass of: assay

Pan African clinical trial registry
definition: The Pan African clinical trial registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: PACTR
type: Class
subclass of: primary registry

The Netherlands national trial register identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in the The Netherlands national trial register (NTR). The format for the registry number is “NTR” followed by a 1 to 4-digit number, e.g., NL8498.
has exact synonym: NTR identifier
type: Class
subclass of: Clinical Trial Registry Identifier

JAPIC clinical trials registry
definition: The JAPIC (Japan Pharmaceutical Information Center) clinical trials registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: JapicCTI
type: Class
subclass of: primary registry

Pan African clinical trial registry identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in the Pan African clinical trial register. The format for the registry number is “KCT” followed by a 15-digit number, e.g., PACTR202004893013257.
has exact synonym: PACTR identifier
type: Class
subclass of: Clinical Trial Registry Identifier

Chinese clinical trail registry identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in the Chinese clinical trials register (ChiCTR). The format for the registry number is “ChiCTR” followed by a 10-digit number, e.g., ChiCTR2000031589.
alternative term: ChiCTR identifier
has exact synonym: Chinese Clinical Trial Register number
type: Class
subclass of: Clinical Trial Registry Identifier

Lebanese clinical trials registry
definition: The Lebanese clinical trials registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: LBCTR
type: Class
subclass of: primary registry

German clinical trials register
definition: German clinical trials register is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: DRKS
type: Class
subclass of: primary registry

JMACCT clinical trials registry
definition: The JMACCT (Japan Medical Association, Center for Clinical Trials) clinical trials registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: JMACCT
type: Class
subclass of: primary registry

age_between_18_and_64
has exact synonym: adult (18-64)
type: Class
subclass of: Age

number of participants
definition: The actual total number of participants that are enrolled in a clinical study
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
has_related_synonym: enrollment
has_related_synonym: sample size
type: Class
subclass of: data item

Brazilian clinical trial registry identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in Brazilian Registry of Clinical Trials (ReBEC). The format for the ReBEC registry number is “RBR-” followed by 6 characters, e.g., RBR-4hb9qs.
has exact synonym: Brazilian Registry of Clinical Trials identifier
has exact synonym: ReBEC identifier
type: Class
subclass of: Clinical Trial Registry Identifier

clinical trial phase 2/3
definition: Clinical trial phase that is a combination of phases 2 and 3.
has exact synonym: Phase 2/3
has exact synonym: Phase 2/Phase 3
has exact synonym: Phase I/II
type: Class
subclass of: clinical trial phase

study result
definition: data item ....
type: Class
subclass of: data item

healthy volunteer criterion
definition: A type of eligibility criteria that indicates whether people who do not have the condition/disease being studied can participate in that clinical study.
definition: Indication that participants who do not have a disease or condition, or related conditions or symptoms, under study in the clinical study are permitted to participate in the clinical study.
has exact synonym: accepts healthy volunteers
type: Class
subclass of: inclusion criterion

age_between_birth_and_17_years
has exact synonym: child (birth-17)
type: Class
subclass of: Age

primary outcome measure information
definition: A description of each primary outcome measure (or for observational studies, specific key measurement[s] or observation[s] used to describe patterns of diseases or traits or associations with exposures, risk factors or treatment). Each primary outcome measure information includes title, description and time frame.
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
has_related_synonym: primary end point
has_related_synonym: primary outcome(s)
type: Class
subclass of: outcome specification

EU clinical trials register
definition: The EU clinical trials register is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: EU-CTR
type: Class
subclass of: primary registry

UMIN clinical trials registry
definition: The UMIN (University Hospital Medical Information Network Center) clinical trials registry is a Japanese primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: UMIN CTR
type: Class
subclass of: primary registry

age_older_than_64
has exact synonym: older adult (65+)
type: Class
subclass of: Age

outcome measure result
definition: Data generated from measurement of experimental variables in a study, or for observational studies, from descriptions of patterns of diseases or traits or associations with exposures, risk factors or treatment.
type: Class
subclass of: report

human subjects protection review board status
definition: Indicate whether a clinical study has been reviewed and approved by at least one human subjects protection review board or such review is not required per applicable law (for example, 21 CFR Part 56, 45 CFR Part 46, or other applicable regulation).
type: Class
subclass of: status

Korean clinical trials registry
definition: ClinicalTrials.gov is a registry of clinical trials.
definition: The Korean clinical trials registry (Clinical Research Information Service (CRiS), Republic of Korea) is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: CRiS
has exact synonym: Clinical Research Information Service, Republic of Korea
type: Class
subclass of: primary registry

phase not applicable
definition: Trials without phases (for example, studies of devices or behavioral interventions).
has exact synonym: N/A
type: Class
subclass of: clinical trial phase

retrospective study design
definition: Look back using observations collected predominantly prior to subject selection and enrollment
type: Class
subclass of: study design

International standard randomised controlled trial register identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in the international standard randomised controlled trial register (ISRCT). The format for the registry number is “ISRCTN” followed by a 8-digit number, e.g., ISRCTN14966673.
has exact synonym: ISRCTN
has exact synonym: International Standard Randomised Controlled Trial Number
type: Class
subclass of: Clinical Trial Registry Identifier

clinical trial phase 1/2
definition: Clinical trial phase that is a combination of phases 1 and 2.
has exact synonym: Phase 1/2
has exact synonym: Phase 1/Phase 2
has exact synonym: Phase I/II
type: Class
subclass of: clinical trial phase

prospective study design
definition: Look forward using periodic observations collected predominantly following subject enrollment
type: Class
subclass of: study design

Thai clinical trials registry identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in the Thai clinical trials registry (TCTR). The format for the registry number is “TCTR” followed by a 11-digit number, e.g., TCTR20200405001
has exact synonym: TCTR identifier
type: Class
subclass of: Clinical Trial Registry Identifier

Chinese clinical trial registry
definition: The Chinese clinical trial registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: ChiCTR
type: Class
subclass of: primary registry

Thai clinical trials registry
definition: The Thai clinical trials registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: TCTR
type: Class
subclass of: primary registry

outcome specification
definition: A description of the outcome measure in an interventional study or for observational studies, specific key measurement[s] or observation[s] used to describe patterns of diseases or traits or associations with exposures, risk factors or treatment.
type: Class
subclass of: directive information entity

Indian clinical trial registry identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in the Indian clinical trial register. The format for the registry number is “CRTI/” followed by a 4-digit number, followed by a slash, followed a 2-digit number, followed by a slash, followed a 6-digit number, e.g., CTRI/2020/03/024402.
has exact synonym: CRTI identifier
has exact synonym: Clinical Trials Registry - India identifier
type: Class
subclass of: Clinical Trial Registry Identifier

Brazilian clinical trials registry
definition: The Brazilian clinical trials registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: ReBec
type: Class
subclass of: primary registry

jRCT clinical trial identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in the Japan Registry of Clinical Trials (jRCT). The format for the registry number is “jRCTs” followed by a 9-digit number, e.g., JPRN-jRCTs031190227
has exact synonym: Japan registry of clinical trials identifier
type: Class
subclass of: Japan clinical trial identifier

Cuban public registry of clinical trials identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in the Cuban public registry of clinical trials (RPCEC). The format for the registry number is “RPCEC” followed by a 8-digit number, e.g., RPCEC00000306.
has exact synonym: RPCEC identifier
type: Class
subclass of: Clinical Trial Registry Identifier

Lebanese clinical trials registry identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in the Lebanese clinical trials registry (LBCTR). The format for the registry number is “LBCTR” followed by a 10-digit number, e.g., LBCTR2020043459.
type: Class
see also: LBCTR identifier
subclass of: Clinical Trial Registry Identifier

primary registry
definition: A primary registry is clinical trial registry in the WHO registry network that meet specific criteria for content, quality and validity, accessibility, unique identification, technical capacity and administration. Primary registries also meet the requirements of the International Clinical Trials Registry Platform (ICMJE).
type: Class
subclass of: ClinicalTrial.gov registry

Peruvian clinical trial registry
definition: The Peruvian clinical trial registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: REPEC
type: Class
subclass of: primary registry

Sri Lanka clinical trials registry
definition: The Sri Lanka clinical trials registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: SLCTR
type: Class
subclass of: primary registry

ClinicalTrial.gov registry
definition: ClinicalTrials.gov is a registry for clinical trials.
has exact synonym: ClinicalTrials.gov
type: Class
subclass of: clinical trials registry organization

clinical trials registry organization
definition: A clinical trials registry organization is an organization that enables the registration and documentation of clinical trials.
has exact synonym: clinical trials registry
type: Class
subclass of: registry

clinical trial enrollment
type: Class
subclass of: human subject enrollment

clinical trial participant
type: Class
subclass of: human subject

healthy enrollee
type: Class
subclass of: human subject

enrolled patient
type: Class
subclass of: human subject

placebo medical intervention
type: Class
subclass of: medical intervention

outcome measurement datum
type: Class
subclass of: data item

primary outcome measurement datum
type: Class
subclass of: outcome measurement datum

secondary outcome measurement datum
type: Class
subclass of: outcome measurement datum

investigational molecular entity
type: Class
subclass of: molecular entity

drug clinical trial
type: Class
subclass of: clinical trial

clinical trial sponsor role
type: Class
subclass of: sponsor role

procedure clinical trIal
type: Class
subclass of: feasibility study

double blinded design
definition: a study design in which neither the subjects nor the investigators are permitted to know which subject is receiving which treatment
has exact synonym: double-blind
has exact synonym: double-blinded
type: Class
subclass of: masking design

single blinded design
definition: a study design in which only the investigators are permitted to know which subject is receiving which treatment
has exact synonym: double blind
has exact synonym: double blinded
type: Class
subclass of: masking design

open blinded design
definition: a study design in which the subjects and the investigators are permitted to know which subject is receiving which treatment
has exact synonym: open blind
has exact synonym: open label
type: Class
subclass of: masking design

sequential design
definition: Groups of participants are assigned to receive interventions based on prior milestones being reached in the study, such as in some dose escalation and adaptive design studies
type: Class
subclass of: intervention design

single arm design
definition: study design with a single group (arm)
has exact synonym: sinlge arm
type: Class
subclass of: intervention design

primary outcome measurement
type: Class
subclass of: clinical trial outcome measurement

secondary outcome measurement
type: Class
subclass of: clinical trial outcome measurement

clinical trial primary purpose specification
definition: The main objective of the intervention(s) being evaluated by the clinical trial.
alternative term: primary purpose of clinical trial
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
type: Class
subclass of: objective specification

clinical trial phase
definition: The quality of a clinical trial that studies a drug or biological product. The phase is based on the study's objective, the number of participants, and other characteristics. According to USA FDA, there are five phases: Early Phase 1 (formerly listed as Phase 0), Phase 1, Phase 2, Phase 3, and Phase 4.
definition editor: Leon Li, Asiyah Lin, Oliver He
alternative term: clinical trial stage
definition source: https://www.clinicaltrials.gov/ct2/help/glossary/phase
has_narrow_synonym: phase
type: Class
subclass of: process quality

clinical trial early phase 1
definition: A clinical trial phase that is designed to use an investigational agent that is available only in very limited quantities and which has never previously given to humans or for which there is extremely limited human experience. Phase 0 clinical trials are intended to enable researchers to understand the path of the drug in the body and its efficacy. Adverse event reporting in Phase 0 trials is expedited. [def-source: NCI]
definition editor: Leon Li, Asiyah Lin, Oliver He
alternative term: Early Phase 1
alternative term: Pre-Clinical Phase
alternative term: clinical trial phase 0
definition source: http://purl.obolibrary.org/obo/NCIT_C54721
definition source: https://en.wikipedia.org/wiki/Clinical_trial
UMLS_CUI: C1882358
NCIT code: C54721
type: Class
subclass of: clinical trial phase

clinical trial phase 1
definition: A clinical trial phase that represents the first-in-man trial, which tests within a small group of people (typically 20-80) to evaluate safety, determine safe dosage ranges, and begin to identify side effects. A drug's side effects could be subtle or long term, or may only happen with a few people, so phase 1 trials are not expected to identify all side effects.
definition editor: Leon Li, Asiyah Lin, Oliver He
alternative term: Phase 1
alternative term: Phase I
definition source: Phase I Trial
definition source: https://en.wikipedia.org/wiki/Clinical_trial
UMLS_CUI: C0920321
NCIT code: C15600
type: Class
subclass of: clinical trial phase

clinical trial phase 2
definition: A clinical trial phase that is designed to study a biomedical or behavioral intervention in a larger group of people (several hundred), to evaluate the drug's effectiveness for a particular indication in patients with the disease or condition under study, and to determine the common short-term side effects and risks associated with the intervention. [def-source: NCI]
definition editor: Leon Li, Asiyah Lin, Oliver He
alternative term: Phase II
definition source: Phase II Trial
definition source: https://en.wikipedia.org/wiki/Clinical_trial
UMLS_CUI: C0282460
NCIT code: C15601
type: Class
subclass of: clinical trial phase

clinical trial phase 3
definition: A clinical trial phase that is designed to investigate the efficacy of the biomedical or behavioral intervention in large groups of human subjects (from several hundred to several thousand), to confirm efficacy, to monitor adverse reactions to the new medication or treatment regimen with respect to long-term use and by comparing the intervention to other standard or experimental interventions as well as to a placebo. [def-source: NCI]
definition editor: Leon Li, Asiyah Lin, Oliver He
alternative term: Phase III
definition source: Phase III Trial
definition source: https://en.wikipedia.org/wiki/Clinical_trial
UMLS_CUI: C0282461
NCIT code: C15602
type: Class
subclass of: clinical trial phase

clinical trial phase 4
definition: A clinical trial phase that is designed for a randomized, controlled trial to evaluate the long-term safety and efficacy of a drug for a given indication. Often they are designed to study side effects that may have become apparent after the phase III study was completed. [def-source: NCI]
definition editor: Leon Li, Asiyah Lin, Oliver He
alternative term: Phase IV
definition source: https://en.wikipedia.org/wiki/Clinical_trial
UMLS_CUI: C0282462
NCIT code: C15603
type: Class
subclass of: clinical trial phase

Early Phase 1 clinical trial
definition: A clinical trial that is at Early Phase 1 or Phase 0
definition: A clinical trial that is at an Early Phase i or Phase 0, which is designed to use an investigational agent that is available only in very limited quantities and which has never previously given to humans or for which there is extremely limited human experience. Phase 0 clinical trials are intended to enable researchers to understand the path of the drug in the body and its efficacy. Adverse event reporting in Phase 0 trials is expedited. [def-source: NCI]
definition: Exploratory trials, involving very limited human exposure, with no therapeutic or diagnostic intent (e.g., screening studies, microdose studies). (Formerly listed as "Phase 0")
definition editor: Leon Li, Asiyah Lin, Oliver He
alternative term: Phase 0 clinical trial
alternative term: Phase 0 trial
alternative term: Pre-Clinical Trial
definition source: http://purl.obolibrary.org/obo/NCIT_C54721
definition source: https://en.wikipedia.org/wiki/Clinical_trial
type: Class
subclass of: clinical trial
equivalent class: Restriction
  on property: has process quality
  some values from: clinical trial early phase 1

European clinical trial registry identifier
example of usage: EudraCT Number: 2007-002422-29
definition editor: Qingliang Leon Li, Asiyah Yu Lin, Oliver He
alternative term: EudraCT identifier
definition source: https://en.wikipedia.org/wiki/EudraCT
definition source: https://www.clinicaltrialsregister.eu/ctr-search/search
type: Class
subclass of: Clinical Trial Registry Identifier

Japan clinical trial identifier
definition editor: Qingliang Leon Li, Asiyah Yu Lin, Oliver He
definition source: https://pubchem.ncbi.nlm.nih.gov/source/NIPH%20Clinical%20Trials%20Search%20of%20Japan
definition source: https://rctportal.niph.go.jp/en/
type: Class
subclass of: Clinical Trial Registry Identifier

JAPIC clinical trial identifier
definition editor: Qingliang Leon Li, Asiyah Yu Lin, Oliver He
alternative term: JapicCTI
definition source: https://rctportal.niph.go.jp/en/
type: Class
subclass of: Clinical Trial Registry Identifier

JMACCT clinical trial identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in JMACCT. The format for the JMACCT registry number is “JMA-IIA” followed by a 5-digit number, e.g., JMA-IIA00391.
definition editor: Qingliang Leon Li, Asiyah Yu Lin, Oliver He
alternative term: JMACCT
definition source: https://rctportal.niph.go.jp/en/
type: Class
subclass of: Japan clinical trial identifier

UMIN-CTR clinical trial identifier
definition: A Japan clinical trial identifier provided by the University Hospital Medical Information Network Center (UMIN-CTR)
definition editor: Qingliang Leon Li, Asiyah Yu Lin, Oliver He
alternative term: UMIN
definition source: https://rctportal.niph.go.jp/en/
type: Class
subclass of: Japan clinical trial identifier

USA National Clinical Trial identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in the ClinicalTrials.gov. The format for the ClinicalTrials.gov registry number is “NCT” followed by an 8-digit number, e.g.: NCT00000419.
definition editor: Qingliang Leon Li, Asiyah Yu Lin, Oliver He
alternative term: NCT identifier
alternative term: NCT number
alternative term: National Clinical Trial identifier
definition source: https://clinicaltrials.gov/ct2/about-site/link-to
definition source: https://www.nlm.nih.gov/bsd/policy/clin_trials.html
type: Class
subclass of: Clinical Trial Registry Identifier

study start date
definition: The date on which a study starts
type: Class
subclass of: zero-dimensional temporal region

clinical trial primary completion date
definition: The date that the final participant was examined or received an intervention for the purposes of final collection of data for the primary outcome, whether the clinical study concluded according to the pre-specified protocol or was terminated. In the case of clinical studies with more than one primary outcome measure with different completion dates, this term refers to the date on which data collection is completed for all of the primary outcomes.
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
has exact synonym: primary completion
type: Class
subclass of: study completion date

clinical trial study completion date
definition: The date the final participant was examined or received an intervention for purposes of final collection of data for the primary and secondary outcome measures and adverse events (for example, last participant’s last visit), whether the clinical study concluded according to the pre-specified protocol or was terminated.
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
has exact synonym: completion date
type: Class
subclass of: study completion date

title of clinical trial
definition: A textual entity that is the title of a clinical trial
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
type: Class
subclass of: textual entity

lay title of clinical trial
definition: A title of clinical trial that is meant for lay people understanding
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
has exact synonym: brief title
has exact synonym: lay title
has exact synonym: public title
type: Class
subclass of: title of clinical trial

official title of clinical trial
definition: A title of clinical trial that is recorded as official
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
has exact synonym: full title
has exact synonym: scientific title
type: Class
subclass of: title of clinical trial

clinical trial
definition: a clinical trial is a medical interventional study where participants are assigned prospectively to an intervention or interventions according to a protocol to evaluate the safety and efficacy of the intervention(s) on biomedical or other health related outcomes. The Interventions include but are not restricted to drugs, cells and other biological products, surgical procedures, radiologic procedures, devices, behavioral treatments, process-of-care changes, preventive care, etc.
definition editor: Oliver He, Asiyah Yu Lin, Qingliang Li
alternative term: interventional trial
definition source: https://clinicaltrials.gov/ct2/search/map
definition source: https://en.wikipedia.org/wiki/Clinical_trial
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
definition source: https://www.who.int/ictrp/en/
type: Class
subclass of: Interventional Study

drug product
definition: a material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role
definition editor: William Hogan
imported from: dron.owl
creator: William Hogan
type: Class
subclass of: material entity

epidemiological study
editor preferred label: epidemiological study
example of usage: A study of the populations and demographic of the avian flu.
has curation status: IAO_0000120
definition: A human study of diseases in populations of humans or other animals, specifically how, when and where they occur. Epidemiological studies can never prove causation, epidemiological evidence can only show that this risk factor is correlated with a higher incidence of disease in the population exposed to that risk factor. The higher the correlation the more certain the association, but it cannot prove the causation.
definition editor: PERSON: Karen Corday
definition source: http://pmep.cce.cornell.edu/profiles/extoxnet/TIB/epidemiology.html
imported from: ero.owl
type: Class
subclass of: human subject study

ERO_0000348
definition: single group of individuals with specific characteristics.

medical device
example of usage: A blood pressure monitor is a medical device.
has curation status: IAO_0000120
definition: An instrument used in the diagnosis of disease or other conditions or for use in the care, treatment, or prevention of disease that does not achieve any of its primary intended purposes by chemical action or by being metabolized.
definition editor: PERSON: Nicole Vasilevsky
definition source: http://medical-dictionary.thefreedictionary.com/medical+device
imported from: ero.owl
type: Class
subclass of: material entity

feasibility study
has curation status: metadata incomplete
definition: A preliminary study to determine the practicability of a proposed health program or procedure or of a larger study and to appraise the factors that may influence its practicability. A feasibility study aims to discover those things which may affect successful study conduct on a larger scale.
definition editor: PERSON: Melanie Wilson
definition source: Dictionary of Epidemiology, 5th edition.
imported from: ero.owl
type: Class
subclass of: human subject study

registry
has curation status: metadata incomplete
definition: An organization dedicated to the collection, storage and dissemination of a set of scientific or clinical data.
definition editor: PERSON: Nicole Vasilevsky
definition source: PERSON: Scott Hoffmann
imported from: ero.owl
type: Class
subclass of: organization

objective specification
editor preferred label: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has curation status: ready for release
definition: A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
editor note: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
editor note: 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
editor note: Answers the question, why did you do this experiment?
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Barry Smith
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
alternative term: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
imported from: iao.owl
type: Class
subclass of: directive information entity

action specification
example of usage: Pour the contents of flask 1 into flask 2
has curation status: ready for release
definition: A directive information entity that describes an action the bearer will take.
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
imported from: iao.owl
type: Class
subclass of: directive information entity

data item
editor preferred label: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: pending final vetting
definition: 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.
editor note: 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.
editor note: 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.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: 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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
alternative term: data
imported from: iao.owl
imported from: ogms.owl
type: Class
subclass of: information content entity

information content entity
editor preferred label: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: ready for release
definition: A generically dependent continuant that is about some thing.
definition: An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
editor note: 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).
editor note: 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.
definition editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
imported from: dron.owl
imported from: envo.owl
imported from: iao.owl
imported from: ico.owl
imported from: obi.owl
imported from: ogms.owl
imported from: The Ontology of Medically Related Social Entities
imported from: ontoneo.owl
imported from: opmi.owl
imported from: pdro.owl
type: Class
subclass of: generically dependent continuant

directive information entity
has curation status: ready for release
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 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.
editor note: 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.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: 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
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
imported from: iao.owl
imported from: obi.owl
type: Class
subclass of: information content entity

curation status specification
editor preferred label: curation status specification
has curation status: pending final vetting
definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
definition editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266
imported from: iao.owl
type: Class
subclass of: data about an ontology part

report
editor preferred label: report
example of usage: Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
has curation status: pending final vetting
definition: a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)
editor note: 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.
editor note: 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
editor note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
editor note: 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
editor note: disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
definition editor: PERSON:Chris Stoeckert
definition source: GROUP: OBI
definition source: OBI_0000099
imported from: iao.owl
type: Class
subclass of: document

data about an ontology part
definition: data about an ontology part is a data item about a part of an ontology, for example a term
definition editor: Person:Alan Ruttenberg
imported from: iao.owl
type: Class
subclass of: data item

plan specification
editor preferred label: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: ready for release
definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
editor note: 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.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
imported from: obi.owl
type: Class
comment: 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
subclass of: directive information entity

editor preferred label
editor preferred label: editor preferred label
editor preferred label: editor preferred term
editor preferred label: editor preferred term~editor preferred label
has curation status: ready for release
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
type: AnnotationProperty
label: editor preferred term
label: editor preferred term~editor preferred label

example of usage
editor preferred label: example
editor preferred label: example of usage
has curation status: ready for release
definition: 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
definition: 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.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
type: AnnotationProperty

has curation status
editor preferred label: has curation status
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bill Bug
definition editor: PERSON:Melanie Courtot
definition source: OBI_0000281
type: AnnotationProperty

definition
editor preferred label: definition
editor preferred label: textual definition
has curation status: ready for release
definition: A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
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.
definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 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.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
has exact synonym: DEFINITION
type: AnnotationProperty
label: textual definition

editor note
editor preferred label: editor note
has curation status: ready for release
definition: 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: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
database_cross_reference: IAO:0000116
has_obo_namespace: uberon
id: editor_note
is metadata tag: 1
shorthand: editor_note
type: AnnotationProperty

definition editor
editor preferred label: definition editor
editor preferred label: term editor
has curation status: ready for release
definition: 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
definition: 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
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
type: AnnotationProperty
label: term editor

alternative term
editor preferred label: alternative term
has curation status: pending final vetting
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
type: AnnotationProperty

definition source
editor preferred label: definition source
has curation status: ready for release
definition: 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
definition: 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
definition editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
type: AnnotationProperty

ready for release
type: curation status specification
type: NamedIndividual
type: Thing

metadata incomplete
type: curation status specification
type: NamedIndividual
type: Thing

pending final vetting
type: curation status specification
type: NamedIndividual
type: Thing

is about
type: ObjectProperty

curator note
editor preferred label: curator note
has curation status: ready for release
definition: An administrative note of use for a curator but of no use for a user
definition editor: PERSON:Alan Ruttenberg
database_cross_reference: IAO:0000232
has_obo_namespace: uberon
id: curator_notes
is metadata tag: 1
shorthand: curator_notes
type: AnnotationProperty
label: curator notes

term tracker item
editor preferred label: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
has curation status: pending final vetting
definition: An IRI or similar locator for a request or discussion of an ontology term.
definition editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
type: AnnotationProperty
comment: The 'tracker item' can associate a tracker with a specific ontology term.

textual entity
editor preferred label: textual entity
example of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
has curation status: metadata incomplete
definition: 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.
editor note: 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.
editor note: 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.
definition editor: PERSON: Lawrence Hunter
alternative term: text
imported from: obi.owl
type: Class
subclass of: information content entity

document
editor preferred label: document
example of usage: A journal article, patent application, laboratory notebook, or a book
has curation status: IAO_0000120
definition: A collection of information content entities intended to be understood together as a whole
definition editor: PERSON: Lawrence Hunter
imported from: iao.owl
type: Class
subclass of: information content entity

imported from
editor preferred label: imported from
has curation status: pending final vetting
definition: For external terms/classes, the ontology from which the term was imported
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
type: AnnotationProperty

postal address
has curation status: metadata incomplete
definition: A textual entity that is used as directive to deliver something to a person, or organization
editor note: 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59
imported from: obi.owl
type: Class
subclass of: textual entity

email address
editor preferred label: email address
has curation status: metadata incomplete
editor note: Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583
definition editor: Person:Alan Ruttenberg
definition editor: Person:Chris Stoeckart
imported from: obi.owl
type: Class
subclass of: contact person information

centrally registered identifier
example of usage: The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
has curation status: IAO_0000120
definition: An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
editor note: 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
editor note: Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
editor note: Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bill Hogan
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Melanie Courtot
alternative term: CRID
definition source: Original proposal from Bjoern, discussions at IAO calls
imported from: iao.owl
has_narrow_synonym: Primary Registry and Trial Identifying Number
type: Class
subclass of: information content entity

elucidation
editor preferred label: elucidation
definition editor: person:Alan Ruttenberg
definition source: Person:Barry Smith
elucidation: 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
type: AnnotationProperty

has associated axiom(nl)
editor preferred label: has associated axiom(nl)
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom associated with a term expressed using natural language
type: AnnotationProperty

has associated axiom(fol)
editor preferred label: has associated axiom(fol)
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom expressed in first order logic using CLIF syntax
type: AnnotationProperty

has axiom label
type: AnnotationProperty

contact affiliation
definition: Home institution of the contact person.
imported from: ms.owl
database_cross_reference: value-type:xsd:string
has_obo_namespace: MS
id: MS:1000590
type: Class
subclass of: textual entity

root
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: all
type: Class
subclass of: material entity

cellular organisms
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:1
has_obo_namespace: ncbi_taxonomy
has_related_synonym: biota
type: Class
subclass of: root

Eukaryota
imported from: ncbitaxon.owl
has_rank: NCBITaxon superkingdom
database_cross_reference: GC_ID:1
database_cross_reference: PMID:23020233
database_cross_reference: PMID:30257078
has exact synonym: eucaryotes
has exact synonym: eukaryotes
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Eucarya
has_related_synonym: Eucaryotae
has_related_synonym: Eukarya
has_related_synonym: Eukaryotae
has_related_synonym: eukaryotes
type: Class
subclass of: cellular organisms

Mammalia
imported from: ncbitaxon.owl
has_rank: NCBITaxon class
database_cross_reference: GC_ID:1
has exact synonym: mammals
has_obo_namespace: ncbi_taxonomy
has_related_synonym: mammals
type: Class
subclass of: Vertebrata <vertebrates>

Vertebrata <vertebrates>
imported from: ncbitaxon.owl
database_cross_reference: GC_ID:1
has exact synonym: Vertebrata
has exact synonym: vertebrates
has_obo_namespace: ncbi_taxonomy
has_related_synonym: vertebrates
type: Class
subclass of: Eukaryota

Homo sapiens
editor preferred label: Homo sapiens
alternative term: human
alternative term: human being
alternative term: man
alternative term: person
imported from: envo.owl
imported from: ncbitaxon.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: opmi.owl
has_rank: NCBITaxon species
database_cross_reference: GC_ID:1
has exact synonym: human
has exact synonym: man
has_obo_namespace: ncbi_taxonomy
has_related_synonym: Home sapiens
has_related_synonym: Homo sampiens
has_related_synonym: Homo sapeins
has_related_synonym: Homo sapian
has_related_synonym: Homo sapians
has_related_synonym: Homo sapien
has_related_synonym: Homo sapience
has_related_synonym: Homo sapiense
has_related_synonym: Homo sapients
has_related_synonym: Homo sapines
has_related_synonym: Homo spaiens
has_related_synonym: Homo spiens
has_related_synonym: Humo sapiens
has_related_synonym: humans
type: Class
subclass of: Mammalia

Has_NICHD_Parent
definition: A property created to allow the source NICHD to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are the contributing source.
definition: An association created to allow the source NICHD to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are a contributing source.
code: A11
Semantic_Type: Conceptual Entity
Preferred_Name: Has_NICHD_Parent
has exact synonym: Has_NICHD_Parent
type: AnnotationProperty
range: anyURI

Clinical Trial Final Report
definition: Records containing any interim or final results, as well as clinical and statistical descriptions, presentations, analyses and interpretations of any therapeutic, prophylactic, or diagnostic agent used in human subjects in a clinical trial.
imported from: ncit.owl
code: C115575
Semantic_Type: Intellectual Product
Preferred_Name: Clinical Trial Final Report
UMLS_CUI: C3889645
Contributing_Source: CDISC-GLOSS
Contributing_Source: CareLex
ALT_DEFINITION: A written description of a trial/study of any therapeutic, prophylactic, or diagnostic agent conducted in human subjects, in which the clinical and statistical description, presentations, and analyses are fully integrated into a single report. [ICH E3]
ALT_DEFINITION: Subcategory name for the eTMF domain used to classify clinical study report documents.
has exact synonym: CTrial Fin Rept Subcat
has exact synonym: Central Trial Final Reports Subcategory
has exact synonym: Clinical Trial Final Report
has exact synonym: Reports
has exact synonym: final report
in subset: NCIT C114548
in subset: NCIT C61410
in subset: NCIT C67497
type: Class
subclass of: report

Patient Registry Study
definition: An observational study that is also considered to be a Patient Registry. This type of study should only be registered once in the Protocol Registration and Results System (PRS), by the sponsor responsible for the primary data collection and analysis.
definition: Observational studies which include an organized system that uses observational methods to collect uniform data (clinical and other) prospectively for a population defined by a particular disorder/disease, condition (including susceptibility to a disorder), or exposure (including products, health care services, and/or procedures) and that serves a predetermined scientific, clinical, or policy purpose. Patient registries may be single purpose or on-going data collection programs that address one or more questions. (AHRQ)
imported from: ncit.owl
code: C129000
Semantic_Type: Research Activity
Preferred_Name: Patient Registry Study
UMLS_CUI: C0920631
Contributing_Source: CDISC
ALT_DEFINITION: Observational studies which include an organized system that uses observational methods to collect uniform data (clinical and other) prospectively for a population defined by a particular disorder/disease, condition (including susceptibility to a disorder), or exposure (including products, health care services, and/or procedures) and that serves a predetermined scientific, clinical, or policy purpose. Patient registries may be single purpose or on-going data collection programs that address one or more questions. (AHRQ)
has exact synonym: PATIENT REGISTRY
has exact synonym: Patient Registry Study
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66830
in subset: NCIT C99077
type: Class
subclass of: Observational Study

Device Feasibility Study
definition: An intervention of a device product is being evaluated to determine the feasibility of the product or to test a prototype device and not health outcomes. Such studies are conducted to confirm the design and operating specifications of a device before beginning a full clinical trial. (ClinicalTrials.gov)
imported from: ncit.owl
code: C139174
Semantic_Type: Research Activity
Preferred_Name: Device Feasibility Study
NCI_META_CUI: CL526612
Contributing_Source: CDISC
ALT_DEFINITION: An intervention of a device product is being evaluated to determine the feasibility of the product or to test a prototype device and not health outcomes. Such studies are conducted to confirm the design and operating specifications of a device before beginning a full clinical trial. (ClinicalTrials.gov)
has exact synonym: DEVICE FEASIBILITY
has exact synonym: Device Feasibility
has exact synonym: Device Feasibility Study
in subset: NCIT C132298
in subset: NCIT C147067
in subset: NCIT C61410
in subset: NCIT C66736
in subset: NCIT C66830
type: Class
subclass of: feasibility study

Study Type
definition: The nature of the investigation or the investigational use for which clinical study is being done.
imported from: ncit.owl
code: C142175
Semantic_Type: Research Activity
Preferred_Name: Study Type
NCI_META_CUI: CL540168
Contributing_Source: CDISC
ALT_DEFINITION: Describes the role the study plays in determining the interventions a subject receives.
has exact synonym: STYPE
has exact synonym: Study Type
in subset: NCIT C132298
in subset: NCIT C142191
in subset: NCIT C61410
in subset: NCIT C66738
in subset: NCIT C66830
in subset: NCIT C67152
type: Class
subclass of: planned process

Random Allocation
definition: Participants are assigned to intervention groups by chance
definition: The process of resource distribution that is done by chance.
imported from: ncit.owl
code: C142660
Semantic_Type: Activity
Preferred_Name: Random Allocation
NCI_META_CUI: CL540611
Contributing_Source: CDISC-GLOSS
ALT_DEFINITION: Assignment of subjects to treatment (or control) groups in an unpredictable way. NOTE: in a blinded study, assignment sequences are concealed, but available for disclosure in the event a subject has an adverse experience.
has exact synonym: Random Allocation
has exact synonym: random allocation
has exact synonym: randomized
in subset: NCIT C61410
in subset: NCIT C67497
type: Class
subclass of: Allocation

Study Primary Purpose
definition: The main objective of the intervention(s) being evaluated by the clinical trial.
definition: The principal reason or intention for the execution of an interventional or non-interventional clinical study.
imported from: ncit.owl
code: C147141
Semantic_Type: Idea or Concept
Preferred_Name: Study Primary Purpose
NCI_META_CUI: CL545057
Contributing_Source: CDISC
ALT_DEFINITION: The principal reason or intention for the execution of an interventional or non-interventional clinical study. (NCI)
has exact synonym: Study Primary Purpose
in subset: NCIT C132298
in subset: NCIT C147066
in subset: NCIT C61410
type: Class
subclass of: plan specification

Gene Therapy
definition: Application of genetic material (usually DNA) into cells in order to permanently correct an inherited disease or acquired disease.
imported from: ncit.owl
code: C15238
Semantic_Type: Therapeutic or Preventive Procedure
Display_Name: Gene Therapy
Preferred_Name: Gene Therapy
UMLS_CUI: C0017296
Contributing_Source: CDISC
Contributing_Source: CTRP
ALT_DEFINITION: Application of genetic material into cells in order to correct an inherited or acquired disease.
ALT_DEFINITION: Treatment of human disease by gene transfer.
ALT_DEFINITION: Treatment that alters a gene. In studies of gene therapy for cancer, researchers are trying to improve the body's natural ability to fight the disease or to make the cancer cells more sensitive to other kinds of therapy.
Legacy_Concept_Name: Gene_Therapy
DesignNote: Gene therapy techniques attempt to replace a faulty or missing gene associated with a particular disease, mediate localized delivery of a protein producing specified therapeutic effects, or introduce new cellular functions.
has exact synonym: DNA Therapy
has exact synonym: GENETIC
has exact synonym: Gene Therapy
has exact synonym: Gene Transfer Procedure
has exact synonym: Gene transfer
has exact synonym: Genetic
has exact synonym: Intervention, Genetic
has exact synonym: Molecular Biology, Gene Therapy
has exact synonym: gene therapy
in subset: NCIT C116977
in subset: NCIT C118169
in subset: NCIT C61410
in subset: NCIT C66830
in subset: NCIT C99078
type: Class
subclass of: medical intervention

Health Services Research
definition: A multidisciplinary field of inquiry that examines the costs, quality, accessibility, delivery, organization, financing, and outcomes of health care services.
definition: One or more interventions for evaluating the delivery, processes, management, organization, or financing of healthcare.
imported from: ncit.owl
code: C15245
Semantic_Type: Research Activity
Preferred_Name: Health Services Research
UMLS_CUI: C0018757
Contributing_Source: CDISC
ALT_DEFINITION: A type of study designed to evaluate the delivery, processes, management, organization or financing of health care. (ClinicalTrials.gov)
Legacy_Concept_Name: Health_Services_Research
has exact synonym: HEALTH SERVICES RESEARCH
has exact synonym: Health Services Research
in subset: NCIT C132298
in subset: NCIT C147067
in subset: NCIT C61410
in subset: NCIT C66736
in subset: NCIT C66830
type: Class
subclass of: Study Primary Purpose

Surgical Procedure
definition: A diagnostic or treatment procedure performed by manual and/or instrumental means, often involving an incision and the removal or replacement of a diseased organ or tissue; of or relating to or involving or used in surgery or requiring or amenable to treatment by surgery.
imported from: ncit.owl
Has_NICHD_Parent: NCIT C25218
code: C15329
Semantic_Type: Health Care Activity
Display_Name: Surgical Procedure
Preferred_Name: Surgical Procedure
UMLS_CUI: C0543467
Contributing_Source: CPTAC
Contributing_Source: CTRP
Contributing_Source: NICHD
ALT_DEFINITION: A procedure to remove or repair a part of the body or to find out whether disease is present. An operation.
Legacy_Concept_Name: Surgical_Procedure
NICHD_Hierarchy_Term: Surgical Procedure
Maps_To: Surgery
Maps_To: Surgically Treated
has exact synonym: Operation
has exact synonym: Surgery
has exact synonym: Surgical
has exact synonym: Surgical Interventions
has exact synonym: Surgical Procedure
has exact synonym: Surgical Procedures
has exact synonym: Surgically
has exact synonym: Type of Surgery
has exact synonym: surgery
in subset: NCIT C116977
in subset: NCIT C118169
in subset: NCIT C156952
in subset: NCIT C156953
in subset: NCIT C156954
in subset: NCIT C157524
in subset: NCIT C157526
in subset: NCIT C157527
in subset: NCIT C157528
in subset: NCIT C157529
in subset: NCIT C157530
in subset: NCIT C157532
in subset: NCIT C157533
in subset: NCIT C157534
in subset: NCIT C159412
in subset: NCIT C90259
type: Class
subclass of: medical procedure

Phase I Trial
definition: A clinical research protocol designed to test a new biomedical intervention in a small group of people for the first time. A Phase I trial can be to establish the toxicity of a new treatment with escalating intensity of the treatment administered and/or to determine the side effects of a new treatment for a particular indication in subjects.
definition: Includes initial studies to determine the metabolism and pharmacologic actions of drugs in humans, the side effects associated with increasing doses, and to gain early evidence of effectiveness; may include healthy participants and/or patients.
imported from: ncit.owl
code: C15600
Semantic_Type: Research Activity
Preferred_Name: Phase I Trial
UMLS_CUI: C0920321
Contributing_Source: CDISC
Contributing_Source: CDISC-GLOSS
ALT_DEFINITION: The first step in testing a new treatment in humans. These studies test the best way to give a new treatment (for example, by mouth, intravenous infusion, or injection) and the best dose. The dose is usually increased a little at a time in order to find the highest dose that does not cause harmful side effects. Because little is known about the possible risks and benefits of the treatments being tested, phase I trials usually include only a small number of patients who have not been helped by other treatments.
ALT_DEFINITION: The initial introduction of an investigational new drug into humans. Phase 1 studies are typically closely monitored and may be conducted in patients or normal volunteer subjects. NOTE: These studies are designed to determine the metabolism and pharmacologic actions of the drug in humans, the side effects associated with increasing doses, and, if possible, to gain early evidence on effectiveness. During Phase 1, sufficient information about the drug's pharmacokinetics and pharmacological effects should be obtained to permit the design of well-controlled, scientifically valid Phase 2 studies. The total number of subjects and patients included in Phase 1 studies varies with the drug, but is generally in the range of 20 to 80. Phase 1 studies also include studies of drug metabolism, structure-activity relationships, and mechanism of action in humans, as well as studies in which investigational drugs are used as research tools to explore biological phenomena or disease processes. [after FDA CDER handbook, ICH E8]
ALT_DEFINITION: The initial introduction of an investigational new drug into humans. Phase 1 studies are typically closely monitored and may be conducted in patients or normal volunteer subjects. NOTE: These studies are designed to determine the metabolism and pharmacologic actions of the drug in humans, the side effects associated with increasing doses, and, if possible, to gain early evidence on effectiveness. During Phase 1, sufficient information about the drug's pharmacokinetics and pharmacological effects should be obtained to permit the design of well-controlled, scientifically valid, Phase 2 studies. The total number of subjects and patients included in Phase I studies varies with the drug, but is generally in the range of 20 to 80. Phase 1 studies also include studies of drug metabolism, structure-activity relationships, and mechanism of action in humans, as well as studies in which investigational drugs are used as research tools to explore biological phenomena or disease processes. [After FDA CDER Handbook, ICH E8] (CDISC glossary)
Legacy_Concept_Name: Phase_I_Trial
has exact synonym: 1
has exact synonym: Clinical Trials, Phase I
has exact synonym: Early-Stage Clinical Trials
has exact synonym: PHASE I TRIAL
has exact synonym: Phase 1 Study
has exact synonym: Phase I Clinical Trials
has exact synonym: Phase I Protocol
has exact synonym: Phase I Study
has exact synonym: Phase I Trial
has exact synonym: Trial Phase 1
has exact synonym: phase 1
has exact synonym: phase I trial
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66737
in subset: NCIT C66830
in subset: NCIT C67497
type: Class
subclass of: clinical trial

Phase II Trial
definition: A clinical research protocol designed to study a biomedical or behavioral intervention in a larger group of people (several hundred), to evaluate the drug's effectiveness for a particular indication in patients with the disease or condition under study, and to determine the common short-term side effects and risks associated with the intervention.
definition: Includes controlled clinical studies conducted to evaluate the effectiveness of the drug for a particular indication or indications in participants with the disease or condition under study and to determine the common short-term side effects and risks.
imported from: ncit.owl
code: C15601
Semantic_Type: Research Activity
Preferred_Name: Phase II Trial
UMLS_CUI: C0282460
Contributing_Source: CDISC
Contributing_Source: CDISC-GLOSS
ALT_DEFINITION: A study to test whether a new treatment has an anticancer effect (for example, whether it shrinks a tumor or improves blood test results) and whether it works against a certain type of cancer.
ALT_DEFINITION: Controlled clinical studies conducted to evaluate the effectiveness of the drug for a particular indication or indications in patients with the disease or condition under study and to determine the common short-term side effects and risks associated with the drug. NOTE: Phase 2 studies are typically well controlled, closely monitored, and conducted in a relatively small number of patients, usually involving no more than several hundred subjects. [after FDA CDER handbook, ICH E8]
ALT_DEFINITION: Phase 2. Controlled clinical studies conducted to evaluate the effectiveness of the drug for a particular indication or indications in patients with the disease or condition under study and to determine the common short-term side effects and risks associated with the drug. NOTE: Phase 2 studies are typically well controlled, closely monitored, and conducted in a relatively small number of patients, usually involving no more than several hundred subjects. [After FDA CDER Handbook, ICH E8] (CDISC glossary)
Legacy_Concept_Name: Phase_II_Trial
has exact synonym: 2
has exact synonym: Clinical Trials, Phase II
has exact synonym: PHASE II TRIAL
has exact synonym: Phase 2 Study
has exact synonym: Phase II Clinical Trial
has exact synonym: Phase II Protocol
has exact synonym: Phase II Study
has exact synonym: Phase II Trial
has exact synonym: Trial Phase 2
has exact synonym: phase 2
has exact synonym: phase II trial
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66737
in subset: NCIT C66830
in subset: NCIT C67497
type: Class
subclass of: clinical trial

Phase III Trial
definition: A clinical research protocol designed to investigate the efficacy of the biomedical or behavioral intervention in large groups of human subjects (from several hundred to several thousand), to confirm efficacy, to monitor adverse reactions to the new medication or treatment regimen with respect to long-term use and by comparing the intervention to other standard or experimental interventions as well as to a placebo.
definition: Includes trials conducted after preliminary evidence suggesting effectiveness of the drug has been obtained, and are intended to gather additional information to evaluate the overall benefit-risk relationship of the drug.
imported from: ncit.owl
code: C15602
Semantic_Type: Research Activity
Preferred_Name: Phase III Trial
UMLS_CUI: C0282461
Contributing_Source: CDISC
Contributing_Source: CDISC-GLOSS
ALT_DEFINITION: A study to compare the results of people taking a new treatment with the results of people taking the standard treatment (for example, which group has better survival rates or fewer side effects). In most cases, studies move into phase III only after a treatment seems to work in phases I and II. Phase III trials may include hundreds of people.
ALT_DEFINITION: Phase 3. Studies are expanded controlled and uncontrolled trials. They are performed after preliminary evidence suggesting effectiveness of the drug has been obtained, and are intended to gather the additional information about effectiveness and safety that is needed to confirm efficacy and evaluate the overall benefit-risk relationship of the drug and to provide an adequate basis for physician labeling. NOTE: Phase 3 studies usually include from several hundred to several thousand subjects. [After FDA CDER Handbook, ICH E8] (CDISC glossary)
ALT_DEFINITION: Studies are expanded controlled and uncontrolled trials. They are performed after preliminary evidence suggesting effectiveness of the drug has been obtained and are intended to gather the additional information about effectiveness and safety that is needed to confirm efficacy and evaluate the overall benefit-risk relationship of the drug and to provide an adequate basis for physician labeling. NOTE: Phase 3 studies usually include from several hundred to several thousand subjects. [after FDA CDER handbook, ICH E8]
Legacy_Concept_Name: Phase_III_Trial
has exact synonym: 3
has exact synonym: Clinical Trials, Phase III
has exact synonym: PHASE III TRIAL
has exact synonym: Phase 3 Study
has exact synonym: Phase III Clinical Trial
has exact synonym: Phase III Protocol
has exact synonym: Phase III Study
has exact synonym: Phase III Trial
has exact synonym: Phase III Trials
has exact synonym: Trial Phase 3
has exact synonym: phase 3
has exact synonym: phase III trial
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66737
in subset: NCIT C66830
in subset: NCIT C67497
type: Class
subclass of: clinical trial

Phase IV Trial
definition: A randomized, controlled trial that is designed to evaluate the long-term safety and efficacy of a drug for a given indication. Often they are designed to study side effects that may have become apparent after the phase III study was completed.
definition: Studies of FDA-approved drugs to delineate additional information including the drug's risks, benefits, and optimal use.
imported from: ncit.owl
code: C15603
Semantic_Type: Research Activity
Preferred_Name: Phase IV Trial
UMLS_CUI: C0282462
Contributing_Source: CDISC
Contributing_Source: CDISC-GLOSS
ALT_DEFINITION: After a treatment has been approved and is being marketed, it is studied in a phase IV trial to evaluate side effects that were not apparent in the phase III trial. Thousands of people are involved in a phase IV trial.
ALT_DEFINITION: Phase 4. Postmarketing (Phase 4) studies to delineate additional information about the drug's risks, benefits, and optimal use that may be requested by regulatory authorities in conjunction with marketing approval. NOTE: These studies could include, but would not be limited to, studying different doses or schedules of administration than were used in Phase 2 studies, use of the drug in other patient populations or other stages of the disease, or use of the drug over a longer period of time. [After FDA CDER Handbook, ICH E8] (CDISC glossary)
ALT_DEFINITION: Post approval studies to delineate additional information about the drug's risks, benefits, and optimal use that may be requested by regulatory authorities in conjunction with marketing approval. NOTE: These studies could include, but would not be limited to, studying different doses or schedules of administration than were used in Phase 2 studies, use of the drug in other patient populations or other stages of the disease, or use of the drug over a longer period of time. [after FDA CDER handbook, ICH E8]
Legacy_Concept_Name: Phase_IV_Trial
has exact synonym: 4
has exact synonym: Clinical Trials, Phase IV
has exact synonym: PHASE IV TRIAL
has exact synonym: Phase 4 Study
has exact synonym: Phase IV Clinical Trials
has exact synonym: Phase IV Study
has exact synonym: Phase IV Trial
has exact synonym: Trial Phase 4
has exact synonym: phase 4
has exact synonym: phase IV trial
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66737
in subset: NCIT C66830
in subset: NCIT C67497
type: Class
subclass of: clinical trial

Phase I/II Trial
definition: A clinical research protocol designed to study the safety, dosage levels and response to new treatment. Phase I/II trials combine a Phase I and a Phase II trial of the same treatment into a single protocol.
definition: Trials that are a combination of phases 1 and 2.
imported from: ncit.owl
code: C15693
Semantic_Type: Research Activity
Preferred_Name: Phase I/II Trial
UMLS_CUI: C1519043
Contributing_Source: CDISC
ALT_DEFINITION: A class of clinical study that combines elements characteristic of traditional Phase I and Phase II trials. See also Phase I, Phase II.
ALT_DEFINITION: A trial to study the safety, dosage levels, and response to a new treatment.
Legacy_Concept_Name: Phase_I_II_Trial
has exact synonym: 1-2
has exact synonym: PHASE I/II TRIAL
has exact synonym: Phase I/II Trial
has exact synonym: Phase I/II trial
has exact synonym: Trial Phase 1-2
has exact synonym: Trial Phase 1/2
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66737
in subset: NCIT C66830
type: Class
subclass of: clinical trial

Phase II/III Trial
definition: A type of clinical study that combines elements characteristic of traditional Phase II and Phase III trials.
definition: Trials that are a combination of phases 2 and 3.
imported from: ncit.owl
code: C15694
Semantic_Type: Research Activity
Preferred_Name: Phase II/III Trial
UMLS_CUI: C1519042
Contributing_Source: CDISC
ALT_DEFINITION: A class of clinical study that combines elements characteristic of traditional Phase II and Phase III trials.
ALT_DEFINITION: A trial to study response to a new treatment and the effectiveness of the treatment compared with the standard treatment regimen.
Legacy_Concept_Name: Phase_II_III_Trial
has exact synonym: 2-3
has exact synonym: PHASE II/III TRIAL
has exact synonym: Phase II/III Trial
has exact synonym: Trial Phase 2-3
has exact synonym: Trial Phase 2/3
has exact synonym: phase II/III trial
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66737
in subset: NCIT C66830
type: Class
subclass of: clinical trial

Basic Research
definition: Fundamental research designed to obtain or increase general scientific knowledge.
definition: One or more interventions for examining the basic mechanism of action (for example, physiology or biomechanics of an intervention).
imported from: ncit.owl
code: C15714
Semantic_Type: Research Activity
Preferred_Name: Basic Research
UMLS_CUI: C0681833
Contributing_Source: CDISC
ALT_DEFINITION: A type of study designed to examine the basic mechanism of action (e.g., physiology, biomechanics) of an intervention. (ClinicalTrials.gov)
Legacy_Concept_Name: Basic_Science
has exact synonym: BASIC SCIENCE
has exact synonym: Basic Research
has exact synonym: Basic Science
has exact synonym: Basic Science Research
in subset: NCIT C132298
in subset: NCIT C147067
in subset: NCIT C61410
in subset: NCIT C66736
in subset: NCIT C66830
type: Class
subclass of: Study Primary Purpose

Observational Study
definition: Studies among cancer patients and healthy populations that involve no intervention or alteration in the status of the participants.
imported from: ncit.owl
code: C16084
Semantic_Type: Research Activity
Preferred_Name: Observational Study
UMLS_CUI: C1518527
Contributing_Source: CDISC
ALT_DEFINITION: A type of study in which individuals are observed or certain outcomes are measured. No attempt is made to affect the outcome (for example, no treatment is given).
ALT_DEFINITION: Studies in which biomedical and/or health outcomes are assessed in pre-defined groups of individuals. Subjects in the study may receive diagnostic, therapeutic, or other interventions, but the investigator does not assign specific interventions to the subjects of the study.
Legacy_Concept_Name: Observational_Study
has exact synonym: OBSERVATIONAL
has exact synonym: Observational Study
has exact synonym: Observational Trial
has exact synonym: observational study
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66830
in subset: NCIT C99077
type: Class
subclass of: human subject study

Condition or Disease under Study
definition: Primary disease(s) or condition(s) being studied in the trial, or the focus of the study. (clinicaltrials.gov)
definition: The disease, disorder, syndrome, illness, or injury that is being studied. On ClinicalTrials.gov, conditions may also include other health-related issues, such as lifespan, quality of life, and health risks.
definition: The name(s) of the disease(s) or condition(s) studied in the clinical study, or the focus of the clinical study. Use, if available, appropriate descriptors from NLM's Medical Subject Headings (MeSH)-controlled vocabulary thesaurus or terms from another vocabulary, such as the Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT), that has been mapped to MeSH within the Unified Medical Language System (UMLS) Metathesaurus.
imported from: ncit.owl
code: C161319
Semantic_Type: Qualitative Concept
Preferred_Name: Condition or Disease under Study
Contributing_Source: CDISC
ALT_DEFINITION: Primary disease(s) or condition(s) being studied in the trial, or the focus of the study. (clinicaltrials.gov)
has exact synonym: Condition or Disease under Study
has exact synonym: Primary Disease or Condition Being Studied in the Trial, or the Focus of the Study
has exact synonym: health condition(s) or problem(s) studied
has exact synonym: target disease
has_narrow_synonym: condition
in subset: NCIT C132298
in subset: NCIT C160921
in subset: NCIT C61410
type: Class
subclass of: medical condition

Personal Attribute
definition: The distinguishing qualities or prominent aspects of an individual person.
imported from: ncit.owl
imported from: opmi.owl
code: C19332
Semantic_Type: Organism Attribute
Preferred_Name: Personal Attribute
UMLS_CUI: C0681884
Legacy_Concept_Name: Personal_Attribute
has exact synonym: Personal
has exact synonym: Personal Attribute
has exact synonym: Subject Characteristics
type: Class
subclass of: information content entity

Age
definition: A type of eligibility criteria that indicates the age a person must be to participate in a clinical study.
definition: How long something has existed; elapsed time since birth.
imported from: ncit.owl
imported from: opmi.owl
Has_NICHD_Parent: NCIT C89335
code: C25150
Semantic_Type: Organism Attribute
Preferred_Name: Age
UMLS_CUI: C0001779
Contributing_Source: CDISC
Contributing_Source: FDA
Contributing_Source: NICHD
ALT_DEFINITION: How long something has existed; elapsed time since birth. (NCI)
ALT_DEFINITION: The time elapsed since birth.
Legacy_Concept_Name: Age
NICHD_Hierarchy_Term: Chronological Age
has exact synonym: AGE
has exact synonym: Age
has exact synonym: Aged
has exact synonym: Chronological Age
has exact synonym: Postnatal Age
has exact synonym: age
in subset: NCIT C118466
in subset: NCIT C19752
in subset: NCIT C54447
in subset: NCIT C61410
in subset: NCIT C77526
in subset: NCIT C83187
in subset: NCIT C83188
in subset: NCIT C90007
in subset: NCIT C90009
in subset: NCIT C90259
type: Class
subclass of: Personal Attribute

Clinical Study Protocol
definition: A formal document that describes a complete plan of research activity in the framework of a clinical study; specifically, the study objective(s), design, methodology, eligibility requests for prospective subjects and controls; intervention regimen(s), proposed methods of analysis of data; statistical considerations, and organization of the study. The protocol usually also provides the background and rationale for the trial, but these could be represented in other protocol referenced documents.
imported from: ncit.owl
code: C25320
Semantic_Type: Intellectual Product
Preferred_Name: Clinical Study Protocol
UMLS_CUI: C1507394
Contributing_Source: BRIDG
Contributing_Source: CDISC-GLOSS
Contributing_Source: CareLex
ALT_DEFINITION: A detailed plan of a scientific or medical experiment, treatment, or procedure. In clinical trials, it states what the study will do, how it will be done, and why it is being done. It explains how many people will be in the study, who is eligible to take part in it, what study drugs or other interventions will be given, what tests will be done and how often, and what information will be collected.
ALT_DEFINITION: A discrete, structured plan (that persists over time) of a formal investigation to assess the utility, impact, pharmacological, physiological, and/or psychological effects of a particular treatment, procedure, drug, device, biologic, food product, cosmetic, care plan, or subject characteristic. NOTE(S): The term "protocol" is somewhat overloaded and must be qualified to provide semantic context. Therefore the term "study protocol" was chosen to disambiguate it from other protocols. In previous versions of BRIDG, there was one class for StudyProtocol. However this too represented multiple distinct aspects of the semantics of study protocol, each of which have now been split into separate classes:- The StudyProtocol class represents the content of the study protocol and can exist even before the information is put into document form. - The details of the structured plan for the study protocol are represented by the StudyProtocolVersion, so named because any aspect of the definition can change from version to version. These details include, but are not limited to, the characteristics, specifications, objective(s), background, the pre-study/study/post-study portions of the plan (including the design, methodology, statistical considerations, organization).- The protocol and its versions can each be represented in document form, respectively StudyProtocolDocument and StudyProtocolDocumentVersion. A StudyProtocolDocument groups the various document versions (StudyProtocolDocumentVersions).- The conduct of a study based on a study protocol definition is represented by the StudyExecution class.
ALT_DEFINITION: A formal document that describes a complete plan of research activity in the framework of a clinical study; specifically, the study objective(s), design, methodology, eligibility requests for prospective subjects and controls; intervention regimen(s), proposed methods of analysis of data; statistical considerations, and organization of the study. The protocol usually also provides the background and rationale for the trial, but these could be represented in other protocol referenced documents. [NCI]
ALT_DEFINITION: See protocol.
Legacy_Concept_Name: Protocol
has exact synonym: Clinical Study Protocol
has exact synonym: Clinical Trial Protocol
has exact synonym: Full Protocol
has exact synonym: Prot
has exact synonym: Protocol
has exact synonym: Protocol Amendment
has exact synonym: Study Protocol
has exact synonym: StudyProtocol
has exact synonym: Trial Protocol
has exact synonym: clinical protocol
has exact synonym: protocol
in subset: NCIT C114548
in subset: NCIT C159501
in subset: NCIT C159503
in subset: NCIT C61410
in subset: NCIT C67497
type: Class
subclass of: Study Protocol
subclass of: Restriction
  on property: has part
  some values from: secondary outcome measure information
subclass of: Restriction
  on property: has part
  some values from: primary outcome measure information

Sponsor
definition: A person or organization that supports or champions something.
imported from: ncit.owl
code: C48355
Semantic_Type: Human
Preferred_Name: Sponsor
UMLS_CUI: C1711305
Legacy_Concept_Name: Sponsor
has exact synonym: Applicant
has exact synonym: Sponsor
type: Class
subclass of: Homo sapiens

Diagnosis Study
definition: A type of study designed to evaluate method(s) aimed at identifying a disease or condition.
definition: One or more interventions are being evaluated for identifying a disease or health condition.
imported from: ncit.owl
code: C49653
Semantic_Type: Research Activity
Preferred_Name: Diagnosis Study
UMLS_CUI: C1704656
Contributing_Source: CDISC
ALT_DEFINITION: A type of study designed to evaluate intervention(s) aimed at identifying a disease or condition.
Legacy_Concept_Name: Diagnosis_Study
has exact synonym: DIAGNOSIS
has exact synonym: Diagnosis Study
has exact synonym: Diagnostic Study
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66736
in subset: NCIT C66739
in subset: NCIT C66830
type: Class
subclass of: Study Primary Purpose

Treatment Study
definition: A type of study protocol designed to evaluate intervention(s) for disease treatment.
definition: One or more interventions are being evaluated for treating a disease, syndrome, or condition.
imported from: ncit.owl
code: C49656
Semantic_Type: Research Activity
Preferred_Name: Treatment Study
UMLS_CUI: C3161471
Contributing_Source: CDISC
ALT_DEFINITION: A type of study designed to evaluate intervention(s) for treatment of disease, syndrome or condition.
Legacy_Concept_Name: Treatment_Study
has exact synonym: TREATMENT
has exact synonym: Therapy Trial
has exact synonym: Treatment Study
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66736
in subset: NCIT C66739
in subset: NCIT C66830
type: Class
subclass of: Study Primary Purpose

Prevention Study
definition: A type of study protocol designed to evaluate intervention(s) for disease prevention.
definition: One or more interventions are being assessed for preventing the development of a specific disease or health condition.
imported from: ncit.owl
code: C49657
Semantic_Type: Research Activity
Preferred_Name: Prevention Study
UMLS_CUI: C1706420
Contributing_Source: CDISC
ALT_DEFINITION: A type of study designed to identify actions necessary to permanently eliminate or reduce the long-term risk to human life as a result of a particular medication or treatment regimen.
Legacy_Concept_Name: Prevention_Study
has exact synonym: PREVENTION
has exact synonym: Prevention Study
has exact synonym: Preventive Clinical Trial
has exact synonym: Prophylaxis Study
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66736
in subset: NCIT C66739
in subset: NCIT C66830
type: Class
subclass of: Study Primary Purpose

Planned Subject Number
definition: The number of subjects entered in a clinical trial.
imported from: ncit.owl
code: C49692
Semantic_Type: Group Attribute
Preferred_Name: Planned Subject Number
UMLS_CUI: C1709561
Contributing_Source: CDISC
Contributing_Source: CDISC-GLOSS
ALT_DEFINITION: The number of subjects in a class or group (including the total for the entire trial) intended to be enrolled in a trial to reach the planned sample size. Target enrollments are set so that statistical and scientific objectives of a trial will have a likelihood of being met as determined by agreement, algorithm, or other specified process.
ALT_DEFINITION: The planned number of subjects to be entered in a clinical trial. (NCI)
Legacy_Concept_Name: Planned_Subject_Number
has exact synonym: Anticipated Enrollment
has exact synonym: PLANSUB
has exact synonym: Planned Enrollment
has exact synonym: Planned Number of Subjects
has exact synonym: Planned Subject Number
has exact synonym: Target Enrollment
has exact synonym: target enrollment
has exact synonym: target number
has exact synonym: target size
in subset: NCIT C132298
in subset: NCIT C147066
in subset: NCIT C61410
in subset: NCIT C66738
in subset: NCIT C66830
in subset: NCIT C67152
in subset: NCIT C67497
type: Class
subclass of: data item

Allocation
definition: The distribution of resources over various time periods, products, operations, or investments.
definition: The method by which participants are assigned to arms in a clinical trial.
imported from: ncit.owl
code: C52580
Semantic_Type: Activity
Preferred_Name: Allocation
UMLS_CUI: C1706778
Contributing_Source: CDISC
ALT_DEFINITION: The process of assigning subjects to particular treatment groups or cohorts in a clinical study.
Legacy_Concept_Name: Allocation
has exact synonym: Allocation
has exact synonym: Subject Allocation
in subset: NCIT C132298
in subset: NCIT C147066
in subset: NCIT C61410
type: Class
subclass of: intervention design

Contact Information
definition: Information regarding the means of contacting a person or group.
imported from: ncit.owl
code: C60776
Semantic_Type: Conceptual Entity
Preferred_Name: Contact Information
UMLS_CUI: C1880174
Legacy_Concept_Name: Contact_Information
has exact synonym: Contact Info
has exact synonym: Contact Information
type: Class
subclass of: textual entity

Clinical Study Sponsor
definition: An entity such as an individual, company, institution, group, or organization which takes responsibility for the initiation, management, and/or financing of a clinical study. The sponsor does not actually conduct the investigation unless the sponsor is a sponsor-investigator. A person other than an individual (e.g., corporation or agency) that uses one or more of its own employees to conduct research it has initiated is considered to be a sponsor, and the employees are considered to be investigators. [21 CFR P.50.3(k)] [21 CFR P.50.102(j)] [21 CFR P.312.3]
imported from: ncit.owl
code: C70793
Semantic_Type: Health Care Related Organization
Preferred_Name: Clinical Study Sponsor
UMLS_CUI: C2347796
Contributing_Source: CDISC
Contributing_Source: CDISC-GLOSS
Contributing_Source: CareLex
ALT_DEFINITION: An entity that is responsible for the initiation, management, and/or financing of a clinical study.
ALT_DEFINITION: An entity that is responsible for the initiation, management, and/or financing of a clinical study.[NCI]
ALT_DEFINITION: An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. NOTE: If there is also a secondary sponsor, the responsible entity would be considered the primary sponsor. A corporation or agency whose employees conduct the investigation is considered a sponsor and the employees are considered investigators. [After ICH E6, WHO, 21 CFR 50.3 (e), and after IDMP] See also secondary sponsor.
Legacy_Concept_Name: Clinical_Study_Sponsor
has exact synonym: CLINICAL STUDY SPONSOR
has exact synonym: Clinical Study Sponsor
has exact synonym: SPONSOR
has exact synonym: Sponsor
has exact synonym: Study Sponsor
has exact synonym: sponsor
in subset: NCIT C114548
in subset: NCIT C132298
in subset: NCIT C154681
in subset: NCIT C61410
in subset: NCIT C66738
in subset: NCIT C66830
in subset: NCIT C67152
in subset: NCIT C67497
in subset: NCIT C78735
in subset: NCIT C83187
in subset: NCIT C83188
type: Class
subclass of: Sponsor

Study Protocol
definition: The formal plan of an experiment or research activity, including the objective, rationale, design, materials and methods for the conduct of the study; intervention description, and method of data analysis.
definition: The written description of the clinical study, including objective(s), design, and methods. It may also include relevant scientific background and statistical considerations (if the protocol document includes the statistical analysis plan, use "Study Protocol with SAP and/or ICF" option). Note: All amendments approved by a human subjects protection review board (if applicable), before the time of submission and that apply to all clinical trial Facility Locations must be included.
imported from: ncit.owl
code: C70817
Semantic_Type: Intellectual Product
Preferred_Name: Study Protocol
UMLS_CUI: C2348563
Contributing_Source: CDISC
ALT_DEFINITION: The formal plan of an experiment or research activity, including the objective, rationale, design, materials and methods for the conduct of the study, intervention description, and method of data analysis.
Legacy_Concept_Name: Study_Protocol
has exact synonym: Protocol
has exact synonym: Study Protocol
in subset: NCIT C132298
in subset: NCIT C132310
in subset: NCIT C61410
type: Class
subclass of: protocol

Blinded Clinical Study
definition: A clinical study that is designed using a procedure in which one or more parties to the study [subject(s), investigator(s), monitor, or/and data analyst(s)] are kept unaware of the treatment assignment(s).
imported from: ncit.owl
code: C70840
Semantic_Type: Research Activity
Preferred_Name: Blinded Clinical Study
UMLS_CUI: C2347038
Contributing_Source: CDISC-GLOSS
ALT_DEFINITION: A study in which the subject, the investigator, or anyone assessing the outcome is unaware of the treatment assignment(s). NOTE: Blinding is used to reduce the potential for bias. [Modified ICH E6 Glossary] See also blinding/masking, double-blind study, single-blind study, triple-blind study; contrast with open-label or unblinded study.
ALT_DEFINITION: A type of study in which the patients (single-blinded) or the patients and their doctors (double-blinded) do not know which drug or treatment is being given. The opposite of a blinded study is an open label study.
Legacy_Concept_Name: Blinded_Clinical_Study
has exact synonym: Blind Clinical Study
has exact synonym: Blinded Clinical Study
has exact synonym: Blinded Clinical Trial
has exact synonym: Masked Clinical Study
has exact synonym: blinded study
in subset: NCIT C61410
in subset: NCIT C67497
type: Class
subclass of: Interventional Study

Screening Study
definition: Clinical studies testing the efficacy of devices, techniques, procedures, or tests for the purpose of detecting the presence of disease, usually before there are any symptoms.
definition: One or more interventions are assessed or examined for identifying a condition, or risk factors for a condition, in people who are not yet known to have the condition or risk factor.
imported from: ncit.owl
code: C71485
Semantic_Type: Research Activity
Preferred_Name: Screening Study
UMLS_CUI: C2348164
Contributing_Source: CDISC
Contributing_Source: CDISC-GLOSS
ALT_DEFINITION: A type of study designed to assess or examine methods of identifying a condition (or risk factors for a condition) in people who are not yet known to have the condition (or risk factor). (Clinicaltrials.gov)
ALT_DEFINITION: Trials conducted to detect persons with early, mild, and asymptomatic disease.
Legacy_Concept_Name: Screening_Study
has exact synonym: SCREENING
has exact synonym: Screening Study
has exact synonym: Screening Trial
has exact synonym: screening trials
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66736
in subset: NCIT C66830
in subset: NCIT C67497
type: Class
subclass of: Study Primary Purpose

Supportive Care Study
definition: Clinical studies intended to improve the comfort and quality of life for the patient using drugs, nutritional, dietary, behavioral or other interventions.
definition: One or more interventions are evaluated for maximizing comfort, minimizing side effects, or mitigating against a decline in the participant's health or function.
imported from: ncit.owl
code: C71486
Semantic_Type: Research Activity
Preferred_Name: Supportive Care Study
UMLS_CUI: C2348611
Contributing_Source: CDISC
ALT_DEFINITION: A type of study designed to evaluate one or more interventions where the primary intent is to maximize comfort, minimize side effects or mitigate against a decline in the subject's health or function. In general, supportive care interventions are not intended to cure a disease. (ClinicalTrials.gov)
Legacy_Concept_Name: Supportive_Care_Study
has exact synonym: SUPPORTIVE CARE
has exact synonym: Supportive Care Study
has exact synonym: Supportive Care Trial
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66736
in subset: NCIT C66830
type: Class
subclass of: Study Primary Purpose

Factorial Study
definition: A type of clinical study in which two or more treatments are given alone and in combination, such that all possible combinations are represented across the treatment arms, and are compared in parallel against the study control group.
definition: Two or more interventions, each alone and in combination, are evaluated in parallel against a control group
imported from: ncit.owl
code: C82638
Semantic_Type: Research Activity
Preferred_Name: Factorial Study
UMLS_CUI: C2826344
Contributing_Source: CDISC
ALT_DEFINITION: Two or more interventions, each alone or in combination, are evaluated in parallel against a control group. This study design allows for the comparison of active drug to placebo, presence of drug-drug interactions, and comparison of active drugs against each other.
Legacy_Concept_Name: Factorial_Study
has exact synonym: FACTORIAL
has exact synonym: Factorial Study
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66830
in subset: NCIT C77526
in subset: NCIT C89967
in subset: NCIT C99076
type: Class
subclass of: Interventional Study

Collaborator
definition: Any of two or more parties working jointly towards a common goal.
imported from: ncit.owl
code: C84336
Semantic_Type: Conceptual Entity
Preferred_Name: Collaborator
UMLS_CUI: C2827395
has exact synonym: Collaborator
type: Class
subclass of: Homo sapiens

Test Facility Country
definition: The country in which the test is conducted.
imported from: ncit.owl
code: C90467
Semantic_Type: Geographic Area
Preferred_Name: Test Facility Country
UMLS_CUI: C2983675
Contributing_Source: CDISC
ALT_DEFINITION: The country of the place in which a nonclinical laboratory study takes place, i.e., actually uses the test article in a test system. Testing facility includes any establishment required to register under section 510 of the act that conducts nonclinical laboratory studies and any consulting laboratory described in section 704 of the act that conducts such studies. Testing facility encompasses only those operational units that are being or have been used to conduct nonclinical laboratory studies. (FDA)
has exact synonym: TFCNTRY
has exact synonym: Test Facility Country
in subset: NCIT C61410
in subset: NCIT C77526
in subset: NCIT C90007
in subset: NCIT C90009
type: Class
subclass of: Contact Information

Test Facility Name
definition: The name of the place in which a test is conducted.
imported from: ncit.owl
code: C90469
Semantic_Type: Intellectual Product
Preferred_Name: Test Facility Name
UMLS_CUI: C2983677
Contributing_Source: CDISC
ALT_DEFINITION: The name of the place in which a nonclinical laboratory study takes place, i.e., actually uses the test article in a test system. Testing facility includes any establishment required to register under section 510 of the act that conducts nonclinical laboratory studies and any consulting laboratory described in section 704 of the act that conducts such studies. Testing facility encompasses only those operational units that are being or have been used to conduct nonclinical laboratory studies. (FDA)
has exact synonym: TSTFNAM
has exact synonym: Test Facility Name
in subset: NCIT C61410
in subset: NCIT C77526
in subset: NCIT C90007
in subset: NCIT C90009
type: Class
subclass of: Contact Information

Study Condition
definition: A condition that is a focus of the study.
imported from: ncit.owl
code: C93360
Semantic_Type: Qualitative Concept
Preferred_Name: Study Condition
UMLS_CUI: C2985574
Contributing_Source: BRIDG
ALT_DEFINITION: A condition that is a focus of the study.
has exact synonym: Study Condition
has exact synonym: StudyCondition
in subset: NCIT C159501
in subset: NCIT C159503
type: Class
subclass of: condition

Interventional Study
definition: Studies in which individuals are assigned by an investigator based on a protocol to receive specific interventions. Subjects may receive diagnostic, therapeutic or other types of interventions. The assignment of the intervention may or may not be random. The individuals are then followed and biomedical and/or health outcomes are assessed.
imported from: ncit.owl
code: C98388
Semantic_Type: Research Activity
Preferred_Name: Interventional Study
UMLS_CUI: C3274035
Contributing_Source: CDISC
Contributing_Source: CDISC-GLOSS
ALT_DEFINITION: A trial which intervenes with the inviolability of the trial subject for the purpose of the investigation. For example, the administration of an investigational medical product to the trial subject or use of some extra means of intervention (i.e., samples, tests, or questionnaires) that would not otherwise be used. [Clinical Trial Directive EC/20/2001 definitions]
ALT_DEFINITION: Studies in which individuals are assigned by an investigator based on a protocol to receive specific interventions. Subjects may receive diagnostic, therapeutic or other types of interventions. The assignment of the intervention may or may not be random. The individuals are then followed and biomedical and/or health outcomes are assessed.
has exact synonym: INTERVENTIONAL
has exact synonym: Interventional Study
has exact synonym: interventional clinical trial
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66830
in subset: NCIT C67497
in subset: NCIT C99077
type: Class
subclass of: human subject study

Clinical Trial Registry Identifier
definition: A sequence of letters, numbers, or other characters that uniquely identifies a clinical trial within a clinical trial registry.
imported from: ncit.owl
code: C98714
Semantic_Type: Intellectual Product
Preferred_Name: Clinical Trial Registry Identifier
UMLS_CUI: C3274381
Contributing_Source: CDISC
ALT_DEFINITION: Identification numbers assigned to the protocol by clinicaltrials.gov, EudraCT, or other registries.
has exact synonym: Clinical Trial Registry Identifier
has exact synonym: REGID
has exact synonym: Registry Identifier
has exact synonym: Trial Identifying Number
in subset: NCIT C61410
in subset: NCIT C66738
in subset: NCIT C66830
in subset: NCIT C67152
type: Class
subclass of: centrally registered identifier

Expanded Access Study
definition: An investigational drug product (including biological product) available through expanded access for patients who do not qualify for enrollment in a clinical trial. Expanded Access includes all expanded access types under section 561 of the Federal Food, Drug, and Cosmetic Act: (1) for individual patients, including emergency use; (2) for intermediate-size patient populations; and (3) under a treatment IND or treatment protocol.
definition: Studies that provide a means for obtaining an experimental drug or device for patients who are not adequately treated by existing therapy, who do not meet the eligibility criteria for enrollment, or who are otherwise unable to participate in another clinical study. Expanded Access studies include individual-patient IND, treatment IND, compassionate use, emergency use or continued access.
imported from: ncit.owl
code: C98722
Semantic_Type: Research Activity
Preferred_Name: Expanded Access Study
UMLS_CUI: C3274389
Contributing_Source: CDISC
ALT_DEFINITION: Studies that provide a means for obtaining an experimental drug or device for patients who are not adequately treated by existing therapy, who do not meet the eligibility criteria for enrollment, or who are otherwise unable to participate in another clinical study. Expanded Access studies include individual-patient IND, treatment IND, compassionate use, emergency use or continued access.
has exact synonym: EXPANDED ACCESS
has exact synonym: Expanded Access Study
in subset: NCIT C132298
in subset: NCIT C61410
in subset: NCIT C66830
in subset: NCIT C99077
type: Class
subclass of: human subject study

Intervention Type
definition: For each intervention studied in the clinical study, the general type of intervention.
definition: The kind of product or procedure studied in a trial.
imported from: ncit.owl
code: C98747
Semantic_Type: Functional Concept
Preferred_Name: Intervention Type
UMLS_CUI: C3274412
Contributing_Source: CDISC
ALT_DEFINITION: The kind of product or procedure studied in a trial.
has exact synonym: INTTYPE
has exact synonym: Intervention Type
has_narrow_synonym: intervention
in subset: NCIT C61410
in subset: NCIT C66738
in subset: NCIT C66830
in subset: NCIT C67152
type: Class
subclass of: planned process

Primary Outcome Measure
definition: The primary measurement(s) or observation(s) used to measure the effect of experimental variables in a study, or for observational studies, to describe patterns of diseases or traits or associations with exposures, risk factors or treatment. These are the outcome measures used to assess the primary objective(s).
imported from: ncit.owl
code: C98772
Semantic_Type: Intellectual Product
Preferred_Name: Primary Outcome Measure
UMLS_CUI: C3274433
Contributing_Source: CDISC
ALT_DEFINITION: The primary measurement(s) or observation(s) used to measure the effect of experimental variables in a study, or for observational studies, to describe patterns of diseases or traits or associations with exposures, risk factors or treatment. These are the outcome measures used to assess the primary objective(s).
has exact synonym: OUTMSPRI
has exact synonym: PRIMARY OUTCOME MEASURE
has exact synonym: Primary Outcome Measure
in subset: NCIT C117745
in subset: NCIT C61410
in subset: NCIT C66738
in subset: NCIT C66830
in subset: NCIT C67152
in subset: NCIT C81222
type: Class
subclass of: data item

Secondary Outcome Measure
definition: Other key measures that will be used to evaluate the intervention(s) or, for observational studies, that are a focus of the study. These are the outcome measures used to assess the secondary objective(s).
imported from: ncit.owl
code: C98781
Semantic_Type: Intellectual Product
Preferred_Name: Secondary Outcome Measure
UMLS_CUI: C3274440
Contributing_Source: CDISC
ALT_DEFINITION: Secondary measures that will be used to evaluate the intervention(s) or, for observational studies, that are a focus of the study. These are the outcome measures used to assess the secondary objective(s).
has exact synonym: OUTMSSEC
has exact synonym: SECONDARY OUTCOME MEASURE
has exact synonym: Secondary Outcome Measure
in subset: NCIT C117745
in subset: NCIT C61410
in subset: NCIT C66738
in subset: NCIT C66830
in subset: NCIT C67152
in subset: NCIT C81222
type: Class
subclass of: data item

code
read only: true
definition: A property representing a concept unique identifier within the NCI Enterprise Vocabulary Service's NCI Thesaurus.
code: NHC0
Preferred_Name: code
has exact synonym: code
type: AnnotationProperty
range: string

Semantic_Type
definition: A property that represents a description of the sort of thing or category to which a concept belongs in the context of the UMLS semantic network.
definition: The semantic type describes the sort of thing or category to which a concept belongs in the context of the UMLS semantic network.
code: P106
Semantic_Type: Conceptual Entity
Display_Name: Semantic Type
Preferred_Name: Semantic_Type
DesignNote: In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS.
has exact synonym: Semantic_Type
type: AnnotationProperty
range: NCIT Semantic Type-enum

Display_Name
definition: A property representing an alternative Preferred Name for use in some NCI systems.
definition: Provides an alternative Preferred Name for use in some NCI systems.
code: P107
Semantic_Type: Conceptual Entity
Display_Name: Display Name
Preferred_Name: Display_Name
has exact synonym: Display Name
has exact synonym: Display_Name
type: AnnotationProperty
range: string

Preferred_Name
definition: A property representing the word or phrase that NCI uses by preference to refer to the concept.
definition: The word or phrase that NCI uses by preference to refer to the concept.
code: P108
Semantic_Type: Conceptual Entity
Display_Name: Preferred Name
Preferred_Name: Preferred_Name
has exact synonym: Preferred Name
has exact synonym: Preferred Term
has exact synonym: Preferred_Name
type: AnnotationProperty
range: string

UMLS_CUI
definition: A property representing the concept unique identifier (CUI) assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept.
definition: Concept Unique Identifiers, or CUIs, are concept numbers assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept.
code: P207
Semantic_Type: Conceptual Entity
Display_Name: UMLS CUI
Preferred_Name: UMLS_CUI
has exact synonym: UMLS_CUI
type: AnnotationProperty
range: string

NCI_META_CUI
definition: A property representing the concept unique identifier (CUI) for those concepts that appear in NCI Metathesaurus but not in the National Library of Medicine Unified Medical Language System (NLM UMLS).
code: P208
Semantic_Type: Conceptual Entity
Display_Name: NCI Metathesaurus CUI
Preferred_Name: NCI_META_CUI
has exact synonym: NCI_META_CUI
type: AnnotationProperty
range: string

Contributing_Source
definition: A property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake.
definition: This property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake.
code: P322
Semantic_Type: Conceptual Entity
Display_Name: Contributing Source
Preferred_Name: Contributing_Source
has exact synonym: Contributing_Source
type: AnnotationProperty
range: NCIT Contributing Source-enum

ALT_DEFINITION
definition: A property representing the English language definition of a concept from a source other than NCI.
definition: English language definitions of what a source other than NCI means by the concept. These are limited to 1024 characters. They include information about the definition's source in a form that can easily be interpreted by software.
code: P325
Semantic_Type: Conceptual Entity
Display_Name: [source] Definition
Preferred_Name: ALT_DEFINITION
has exact synonym: ALT_DEFINITION
type: AnnotationProperty
range: NCIT textArea

Legacy_Concept_Name
read only: true
definition: A property representing a retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding.
definition: A retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding.
code: P366
Semantic_Type: Conceptual Entity
Preferred_Name: Legacy Concept Name
has exact synonym: Legacy Concept Name
type: AnnotationProperty
range: string

NICHD_Hierarchy_Term
definition: A property representing a term chosen by NICHD to be used in the representation of the NICHD hierarchy.
code: P371
Semantic_Type: Conceptual Entity
Preferred_Name: NICHD_Hierarchy_Term
Contributing_Source: NICHD
has exact synonym: NICHD_Hierarchy_Term
type: AnnotationProperty
range: string

Maps_To
definition: A property representing that a term in another terminology has been mapped to a term in NCIt and describes the relationship between the mapped terms.
code: P375
Semantic_Type: Conceptual Entity
Preferred_Name: Maps_To
has exact synonym: Maps_To
type: AnnotationProperty
range: NCIT textArea

DesignNote
definition: A property representing notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept.
definition: Design notes are notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept.
code: P98
Semantic_Type: Conceptual Entity
Display_Name: DesignNote
Preferred_Name: DesignNote
has exact synonym: DesignNote
type: AnnotationProperty
range: string

adverse event
definition: Any untoward or unfavorable medical occurrence in a participant, including any abnormal sign (for example, abnormal physical exam or laboratory finding), symptom, or disease, temporally associated with the participant’s participation in the research, whether or not considered related to the participant’s participation in the research
definition: a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event.
editor note: Melanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'.
editor note: YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device.
editor note: YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention.
editor note: YH: In development of OAE, we initially use vaccine adverse event as our use case. A vaccine adverse event is associated with a vaccination (i.e. a medical intervention), regardless of whether it is considered vaccine-related, and includes any side effect, injury, toxicity, or sensitivity reaction or significant failure of immunization (i.e., a pharmacologic action). Ref: Baylor NW and Midthum K. Regulation and testing of vaccines. In: Vaccines (Editors: Plotkin S, Orenstein W, and Offit P). 2008. p1623.
editor note: YH: The current term 'adverse event' is different from the term definition shown in our paper: He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. OAE: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full lenghth conference proceeding paper. We made the name changing in order to make OAE cover the broader sense of the 'adverse event' which does not assume definite causal effect between an adverse event and a medical intervention. In current definition, the adverse event emphasizes the time association and assumes a likelihood of such a causal association. This term 'adverse event' is stil under the OGMS:pathological bodily process. The 'adverse event' defined in the above paper has now been changed to a new term: 'causal adverse event'. See more information in the new publication: Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29 doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740.
editor note: YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events.
editor note: YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'.
definition editor: Yongqun He
alternative term: AE
alternative term: adverse reaction
definition source: WEB: http://en.wikipedia.org/wiki/Adverse_event
definition source: WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm
definition source: WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068
imported from: oae.owl
type: Class
comment: The OAE official website is: http://www.oae-ontology.org/.
subclass of: pathological bodily process
subclass of: Restriction
  on property: preceded_by
  some values from: medical intervention

medical intervention
definition: A process or action that is the focus of a clinical study. Interventions include drugs, medical devices, procedures, vaccines, and other products that are either investigational or already available. Interventions can also include noninvasive approaches, such as education or modifying diet and exercise.
definition: medical intervention is a planned process that has the goal of diagnosing, preventing or relieving illness or injury.
editor note: The act of intervening, interfering or interceding with the intent of modifying the outcome. In medicine, an intervention is usually undertaken to help treat or cure a condition. For example, "Acupuncture as a therapeutic intervention is widely practiced in the United States," Reference: http://www.medterms.com/script/main/art.asp?articlekey=34214 . Some interventions can be used for diagnosis.
definition editor: YH
definition source: WEB: http://wiki.answers.com/Q/What_is_medical_intervention
imported from: oae.owl
imported from: The Ontology of Medically Related Social Entities
imported from: opmi.owl
has exact synonym: Intervention(s)
type: Class
subclass of: planned process

drug administration
definition: a medical intervention where a patient is administered with a drug
definition editor: YH
imported from: oae.owl
type: Class
subclass of: medical intervention

therapeutic intervention
definition: a medical intervention that is used for therapeutic purpose
definition editor: YH
imported from: oae.owl
type: Class
subclass of: medical intervention

medical procedure
definition: a medical intervention that refers to any series of pre-defined steps that should be followed to achieve a desired result.
definition editor: YH, SS
definition source: WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm
imported from: oae.owl
type: Class
subclass of: medical intervention

planned process
editor preferred label: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: ready for release
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
editor note: '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.)
editor note: 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.
definition editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: 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)
imported from: dron.owl
imported from: envo.owl
imported from: ico.owl
imported from: oae.owl
imported from: obi.owl
imported from: The Ontology of Medically Related Social Entities
imported from: opmi.owl
imported from: vo.owl
type: Class
subclass of: process
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification

investigation
editor preferred label: investigation
example of usage: Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
has curation status: ready for release
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
definition editor: Bjoern Peters
definition source: OBI branch derived
curator note: Could add specific objective specification
curator note: Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
imported from: obi.owl
imported from: opmi.owl
ISA alternative term: study
type: Class
subclass of: planned process

assay
editor preferred label: assay
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
has curation status: ready for release
definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
editor note: 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
definition editor: PlanAndPlannedProcess Branch
alternative term: measuring
alternative term: scientific observation
definition source: OBI branch derived
imported from: obi.owl
ISA alternative term: study assay
IEDB alternative term: any method
type: Class
subclass of: planned process

responsible party role
editor preferred label: responsible party role
example of usage: he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm
has curation status: IAO_0000120
definition: a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
definition editor: Person: Jennifer Fostel
alternative term: responsible party
definition source: OBI
imported from: obi.owl
type: Class
subclass of: investigation agent role

intervention design
editor preferred label: intervention design
example of usage: PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
has curation status: pending final vetting
definition: A description of the manner in which the clinical trial will be conducted.
definition: An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
definition editor: Philppe Rocca-Serra
definition source: OBI branch derived
imported from: obi.owl
has exact synonym: Interventional Study Design
has exact synonym: intervention model
type: Class
subclass of: study design

investigation agent role
editor preferred label: investigation agent role
example of usage: The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
has curation status: ready for release
definition: A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
editor note: Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
editor note: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
definition editor: GROUP: Role Branch
alternative term: investigator
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
imported from: obi.owl
imported from: opmi.owl
ISA alternative term: study person role
type: Class
comment: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
subclass of: role

sponsor role
editor preferred label: sponsor role
has curation status: IAO_0000120
definition: a responsible party role involved with any of the following activities: initiating, managing and funding a study
definition editor: Person: Jennifer Fostel
alternative term: sponsor
curator note: CDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigators
imported from: obi.owl
imported from: opmi.owl
type: Class
subclass of: responsible party role

organization
editor preferred label: organization
example of usage: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
has curation status: ready for release
definition: An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
editor note: BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Philippe Rocca-Serra
definition editor: PERSON: Susanna Sansone
definition source: GROUP: OBI
imported from: obi.owl
type: Class
subclass of: material entity

protocol
editor preferred label: protocol
example of usage: PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
has curation status: ready for release
definition: A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
imported from: obi.owl
ISA alternative term: study protocol
type: Class
subclass of: plan specification

has_specified_input
type: ObjectProperty

informed consent process
editor preferred label: informed consent process
has curation status: ready for release
definition: A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate.
editor note: 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity.
definition editor: Person:Alan Ruttenberg
definition source: http://clinicaltrials.gov/ct2/info/glossary#informed
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
imported from: obi.owl
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: Homo sapiens
subclass of: Restriction
  on property: has participant
  some values from: Restriction
    on property: has role
    some values from: investigation agent role

device
editor preferred label: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
has curation status: ready for release
definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor note: 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent…
definition editor: PERSON: Helen Parkinson
alternative term: instrument
definition source: OBI development call 2012-12-17.
imported from: obi.owl
type: Class
subclass of: material entity

country name
editor preferred label: country name
has curation status: IAO_0000120
definition: A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography.
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
definition source: Website: http://en.wikipedia.org/wiki/Country
imported from: obi.owl
NIAID GSCID-BRC alternative term: Specimen Collection Location - Country
Source: NIAID GSCID-BRC
type: Class
subclass of: textual entity

selection criterion
editor preferred label: selection criterion
example of usage: rats should be aged between 6 and 8 weeks and weight between 180-250grams
has curation status: ready for release
definition: A directive information entity which defines and states a principle of standard by which selection process may take place.
definition editor: Person: Philippe Rocca-Serra
alternative term: selection rule
definition source: OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/
imported from: obi.owl
type: Class
subclass of: directive information entity

ISA alternative term
editor preferred label: ISA alternative term
has curation status: ready for release
definition: An alternative term used by the ISA tools project (http://isa-tools.org).
editor note: Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
definition editor: Person: Alejandra Gonzalez-Beltran
definition editor: Person: Philippe Rocca-Serra
definition source: ISA tools project (http://isa-tools.org)
type: AnnotationProperty
sub property of: alternative term

NIAID GSCID-BRC alternative term
editor preferred label: NIAID GSCID-BRC alternative term
has curation status: ready for release
definition: An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
type: AnnotationProperty
sub property of: alternative term

selection
editor preferred label: selection
example of usage: PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect.
has curation status: ready for release
definition: A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria.
editor note: this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary)
definition editor: Person: Philippe Rocca-Serra
alternative term: selection process
definition source: OBI
imported from: obi.owl
type: Class
subclass of: planned process

value specification
editor preferred label: value specification
example of usage: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
has curation status: ready for release
definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
editor note: This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
definition editor: PERSON:Bjoern Peters
imported from: obi.owl
type: Class
subclass of: information content entity

age group inclusion criterion
editor preferred label: age group inclusion criterion
example of usage: "18-33 years old"
has curation status: metadata incomplete
definition: A type of eligibility criteria that indicates the age a person must be to participate in a clinical study. This may be indicated by a specific age or the following age groups. The age groups are: Child (birth-17), Adult (18-64), Older Adult (65+).
definition: An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process.
definition editor: Mathias Brochhausen
term tracker item: #839
imported from: obi.owl
has exact synonym: ages eligible for study
type: Class
subclass of: inclusion criterion
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: minimum age value specification
  intersection of: Restriction
    on property: has part
    some values from: maximum age value specification

minimum age value specification
editor preferred label: minimum age value specification
has curation status: metadata incomplete
definition: A value specifcation that specifies the youngest age when specifying an age range.
definition: The numerical value, if any, for the minimum age a potential participant must meet to be eligible for the clinical study.
definition editor: Mathias Brochhausen
imported from: obi.owl
has exact synonym: minimum age
type: Class
subclass of: value specification

maximum age value specification
editor preferred label: maximum age value specification
has curation status: metadata incomplete
definition: A value specifcation that specifies the oldest age when specifying an age range.
definition: The numerical value, if any, for the maximum age a potential participant can be to be eligible for the clinical study.
definition editor: Mathias Brochhausen
imported from: obi.owl
has exact synonym: maximum age
type: Class
subclass of: value specification

sex inclusion criterion
editor preferred label: sex inclusion criterion
example of usage: "included males and females", "included male patients"
has curation status: metadata incomplete
definition: A type of eligibility criteria that indicates the sex of people who may participate in a clinical study (all, female, male). Sex is a person's classification as female or male based on biological distinctions. Sex is distinct from gender-based eligibility.
definition: An inclusion criterion that defines and states one or more sexes which, if met, makes an entity suitable for a given task or participation in a given process.
definition editor: Mathias Brochhausen
imported from: obi.owl
has exact synonym: sexes eligible for study
type: Class
subclass of: inclusion criterion

case-control study design
editor preferred label: case-control study design
has curation status: IAO_0000120
definition: A study design that entails the creation of two types of roles, such that each participant under investigation bears one or the other. What distinguishes the two types of roles is an 'outcome', which is associated with participants that have the case role but not associated with participants that have the control role. A case-control study examines the hypothesis that the presence of the outcome in case participants is associated with an 'exposure' that is not associated with control participants.
definition editor: John Judkins, Bjoern Peters
definition source: Wikipedia, OBI
imported from: obi.owl
type: Class
subclass of: study design

observation design
editor preferred label: observation design
example of usage: PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
has curation status: pending final vetting
definition: observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
definition editor: Philippe Rocca-Serra
definition source: OBI branch derived
imported from: obi.owl
type: Class
subclass of: study design

study design
editor preferred label: study design
example of usage: a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
has curation status: ready for release
definition: 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.
editor note: Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
definition editor: PERSON: Chris Stoeckert
alternative term: experimental design
curator note: rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
imported from: obi.owl
imported from: omiabis.owl
type: Class
subclass of: plan specification

repeated measure design
editor preferred label: repeated measure design
example of usage: PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations.
has curation status: IAO_0000120
definition: a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs
definition editor: PlanAndPlannedProcess Branch
definition source: http://www.holah.karoo.net/experimentaldesigns.htm
imported from: obi.owl
type: Class
subclass of: intervention design

cross over design
editor preferred label: cross over design
example of usage: PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity.
has curation status: IAO_0000120
definition: Participants receive one of two (or more) alternative interventions during the initial phase of the study and receive the other intervention during the second phase of the study
definition: a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control
definition editor: Philippe Rocca-Serra
definition source: (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html)
imported from: obi.owl
type: Class
subclass of: repeated measure design

n-to-1 design
editor preferred label: n-to-1 design
has curation status: pending final vetting
definition: N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993).
definition editor: Philippe Rocca-Serra
definition source: Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm)
imported from: obi.owl
type: Class
subclass of: cross over design

parallel group design
editor preferred label: parallel group design
example of usage: PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR.
has curation status: pending final vetting
definition: 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. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment
definition: Participants are assigned to one of two or more groups in parallel for the duration of the study
definition editor: Philippe Rocca-Serra
alternative term: independent measure design
definition source: http://www.holah.karoo.net/experimentaldesigns.htm
imported from: obi.owl
type: Class
subclass of: study design

factorial design
editor preferred label: factorial design
example of usage: PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.
has curation status: pending final vetting
definition: Two or more interventions, each alone and in combination, are evaluated in parallel against a control group
definition: factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable.
definition editor: Philippe Rocca-Serra
definition source: http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment)
imported from: obi.owl
type: Class
subclass of: study design

eligibility criterion
editor preferred label: eligibility criterion
example of usage: PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
has curation status: ready for release
definition: A limited list of criteria for selection of participants in the clinical study, provided in terms of inclusion and exclusion criteria and suitable for assisting potential participants in identifying clinical studies of interest.
definition: The key requirements that people who want to participate in a clinical study must meet or the characteristics they must have. Eligibility criteria consist of both inclusion criteria (which are required for a person to participate in the study) and exclusion criteria (which prevent a person from participating). Types of eligibility criteria include whether a study accepts healthy volunteers, has age or age group requirements, or is limited by sex
definition: 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.
definition editor: Person: Philippe Rocca-Serra
alternative term: eligibility rule
definition source: Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
imported from: obi.owl
type: Class
subclass of: selection criterion

inclusion criterion
editor preferred label: inclusion criterion
example of usage: 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) .
has curation status: pending final vetting
definition: A type of eligibility criteria. These are the reasons that a person is allowed to participate in a clinical study.
definition: 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.
definition editor: Person: Philippe Rocca-Serra
alternative term: inclusion condition
alternative term: inclusion rule
definition source: Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
imported from: obi.owl
has exact synonym: key inclusion criteria
type: Class
subclass of: eligibility criterion

exclusion criterion
editor preferred label: exclusion rule
example of usage: 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.
has curation status: pending final vetting
definition: A type of eligibility criteria. These are reasons that a person is not allowed to participate in a clinical study.
definition: 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
definition editor: Person: Philippe Rocca-Serra
definition source: Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
imported from: obi.owl
has exact synonym: key exclusion criteria
type: Class
subclass of: eligibility criterion

human subject enrollment
editor preferred label: human subject enrollment
example of usage: enlisting familiy members of HIV patients into a study
has curation status: ready for release
definition: A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent.
editor note: As with group assignment, should the specified output here be an organism which bears a role
definition editor: Bjoern Peters
definition source: IEDB
curator note: criteria come from plan / clinical trial branch
imported from: obi.owl
type: Class
subclass of: selection

IEDB alternative term
editor preferred label: IEDB alternative term
has curation status: ready for release
definition: An alternative term used by the IEDB.
definition editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
type: AnnotationProperty
sub property of: alternative term

clinical finding
definition: A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-07-19T10:18:02Z
imported from: ogms.owl
type: Class
subclass of: data item

clinical history
definition: A series of statements representing health-relevant qualities of a patient and of a patient's family.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-07-19T10:18:59Z
imported from: ogms.owl
type: Class
subclass of: data item

preclinical finding
definition: A representation of a quality of a patient that is (1) recorded by a clinician because the quality is hypothesized to be of clinical significance and (2) refers to qualities obtaining in the patient prior to their becoming detectable in a clinical history taking or physical examination.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T10:22:44Z
imported from: ogms.owl
type: Class
subclass of: data item

disease
definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:21:20Z
imported from: ogms.owl
type: Class
subclass of: disposition

bodily process
definition editor: Albert Goldfain
curator note: creation date: 2009-06-23T11:53:49Z
imported from: oae.owl
imported from: ogms.owl
type: Class
subclass of: process

pathological bodily process
definition: A bodily process that is clinically abnormal.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:54:29Z
imported from: oae.owl
imported from: ogms.owl
type: Class
subclass of: bodily process

diagnosis
definition: 1. the determination of the nature of a case of disease. 2. the art of distinguishing one disease from another.
definition: The representation of a conclusion of a diagnostic process.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T12:42:23Z
imported from: ogms.owl
type: Class
subclass of: data item

longitudinal study design
definition: A study design that involves repeated observations of the same entity over time. In the biobank context, longitudinal studies sample a group of people in a given time period, and study them at intervals by the acquisition and analyses of data and/or samples over time.
definition editor: Alice Nzinga
imported from: omiabis.owl
type: Class
subclass of: study design

cohort study design
definition: A longitudinal study that aims to study a case-defined population who presently have a certain condition or recepient of a particular treatment that are followed over time and are compared with a similar group who do not have condition.
imported from: omiabis.owl
type: Class
subclass of: longitudinal study design

role in human social processes
definition: A role inhering in an entity realized by social interactions in human society.
definition editor: Mathias Brochhausen
imported from: The Ontology of Medically Related Social Entities
type: Class
comment: Previous definition: A role played by an entity in human social processes.
subclass of: role

legal person role
definition: A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law.
definition editor: Mathias Brochhausen
definition source: Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
imported from: The Ontology of Medically Related Social Entities
type: Class
comment: We are aware of the fact that Wikipedia's definition differs from ours by saying that "Legal personality (...) is the characteristic of a non-living entity regarded by law to have the status of personhood" (http://en.wikipedia.org/wiki/Legal_personality) However, Shaw explicates: "In any legal system, certain entities, whether they be individuals or companies, will be regarded as possessing rights and duties enforceable at law. Thus an individual may prosecute or be prosecuted for assault and a company can sue for breach of contract. They are able to do this because the law recognises them as 'legal persons' possessing the capacity to have and to maintain certain rights, and being subject to perform specific duties. (...) In municipal law individuals, limited companies and public corporations are recognized as each possessing a distinct legal personality, the terms of which are circumscribed by the relevant legislation" (Shaw MN: International Law. Sixth Edition. Cambridge University Press, Cambridge, 2008). We hold that Shaw's position is ontological more prolific since it not only allows to explain how groups of individuals become recognized as unities at law, but also how different individuals can hold different legal personality roles (always against the context of one legal system). The latter will proof useful when dealing with the representing comatous patients or minorsat law in ontologies.
subclass of: role in human social processes

telephone number
definition: A telephone number is a sequence of digits assigned to a fixed-line telephone subscriber station connected to a telephone line or to a wireless electronic telephony device, such as a radio telephone or a mobile telephone, or to other devices for data transmission via the public switched telephone network (PSTN) or other public and private networks.
definition editor: Oliver He
alternative term: phone number
definition source: https://en.wikipedia.org/wiki/Telephone_number
imported from: opmi.owl
type: Class
subclass of: contact person information

contact name
definition: The textual name of the contact person or organization
imported from: opmi.owl
type: Class
subclass of: Contact Information

medical condition
definition: The medical state or condition of a patient
definition editor: Oliver He, Edison Ong
alternative term: medical state
definition source: https://en.wikipedia.org/wiki/Medical_state
imported from: opmi.owl
type: Class
subclass of: realizable entity

investigator
definition: A person who performs an investigation task and takes the role of an investigator role.
imported from: opmi.owl
type: Class
subclass of: Homo sapiens

clinical investigator
definition: An investigator who is involved in a clinical trial and is responsible for ensuring that an investigation is conducted according to the signed investigator statement, the investigational plan, and applicable regulations; for protecting the rights, safety, and welfare of subjects under the investigator's care; and for the control of drugs under investigation.
definition editor: Oliver He
definition source: https://en.wikipedia.org/wiki/Clinical_investigator
imported from: opmi.owl
type: Class
subclass of: investigator

clinical trial start date
definition: The (estimated) date on which the clinical study is open for recruitment of participants, or the actual date on which the first participant is enrolled.
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
imported from: opmi.owl
has exact synonym: date of first enrollment
has exact synonym: study start
type: Class
subclass of: study start date

study completion date
definition: The date on which a study completes
definition: The date the final participant was examined or received an intervention for purposes of final collection of data for the primary and secondary outcome measures and adverse events (for example, last participant’s last visit), whether the clinical study concluded according to the pre-specified protocol or was terminated.
definition editor: Oliver He
imported from: opmi.owl
has exact synonym: Completion Date
has exact synonym: study completion
type: Class
subclass of: zero-dimensional temporal region

date of registration
definition: The date on which the study sponsor or investigator first submitted a study record to ClinicalTrials.gov. There is typically a delay of a few days between the first submitted date and the record's availability on ClinicalTrials.gov (the first posted date).
definition: a date when a registration occurs
imported from: opmi.owl
has exact synonym: First submitted
has exact synonym: date of registration in primary registry
type: Class
subclass of: zero-dimensional temporal region

recruitment status
definition: The current stage of a clinical study and whether it is or will be open for enrollment
definition: The recruitment status for the clinical study as a whole, based upon the status of the individual sites. If at least one facility in a multi-site clinical study has an Individual Site Status of "Recruiting," then the Overall Recruitment Status for the study must be "Recruiting."
definition editor: Oliver He
definition source: https://clinicaltrials.gov/ct2/help/glossary/recruitment-status
imported from: opmi.owl
type: Class
subclass of: status

status
definition editor: Oliver He, Edison Ong
imported from: opmi.owl
type: Class
subclass of: realizable entity

study status
definition: The current stage of a clinical study and whether it is or will be open for enrollment
definition editor: Oliver He
definition source: https://clinicaltrials.gov/ct2/help/glossary/recruitment-status
imported from: opmi.owl
type: Class
subclass of: status

NCIT code
definition: An annotation property that refers to a code defined by NCIT
type: AnnotationProperty

combinational intervention
definition: Combining a drug and device, a biological product and device; a drug and biological product; or a drug, biological product, and device
definition editor: Leon Li, Asiyah Lin, Oliver He
imported from: opmi.owl
type: Class
subclass of: medical intervention

has process quality
type: ObjectProperty

behavioral intervention
definition: A medical intervention that involves a behavioral process to control, prevent, or treat a behavior problem.
definition editor: Leon Li, Asiyah Lin, Oliver He
definition source: https://www.understood.org/en/learning-attention-issues/treatments-approaches/educational-strategies/behavior-intervention-plans-what-you-need-to-know
imported from: opmi.owl
has exact synonym: behavioral
type: Class
subclass of: medical intervention

human subject
imported from: opmi.owl
type: Class
subclass of: Homo sapiens

contact person
example of usage: In clinicaltrials.gov, contact information character limits: First Name: 62 characters Last Name: 62 characters Degree: 30 characters Phone: 30 characters Phone Ext: 14 characters Email: 254 characters Citation: https://prsinfo.clinicaltrials.gov/definitions.html#StudyOfficials
definition: A person who serves as a contact role and has disclosed specified information to be reached. Usually the contact information, such as email and phone number, is provided.,
editor note: Leon, Asiyah, Oliver: Since each contact needs to provide some contact information, we may need to define the contact information.
definition editor: Leon Li, Asiyah Lin, Oliver He
definition source: https://prsinfo.clinicaltrials.gov/definitions.html#StudyOfficials
imported from: opmi.owl
type: Class
subclass of: Homo sapiens

facility contact
definition: A contact person for each facility participating in a study.
definition editor: Leon Li, Asiyah Lin, Oliver He
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
imported from: opmi.owl
type: Class
subclass of: contact person

contact of scientific queries
definition editor: Leon Li, Asiyah Lin, Oliver He
definition source: https://prsinfo.clinicaltrials.gov/definitions.html#StudyOfficials
imported from: opmi.owl
type: Class
subclass of: contact person

investigator role
definition: An investigation agent role that is taken by a human individual
definition editor: Leon Li, Asiyah Lin, Oliver He
alternative term: human investigator role
imported from: opmi.owl
type: Class
subclass of: investigation agent role

contact person role
definition: a role taken by a person who serves as a contact for some process.
definition editor: Leon Li, Asiyah Lin, Oliver He
imported from: opmi.owl
type: Class
subclass of: role

contact for public queries
definition editor: Leon Li, Asiyah Lin, Oliver He
definition source: https://prsinfo.clinicaltrials.gov/definitions.html#StudyOfficials
imported from: opmi.owl
type: Class
subclass of: contact person

central contact person of study
definition: A person to whom questions concerning enrollment at any location of the study can be addressed.
definition editor: Leon Li, Asiyah Lin, Oliver He
alternative term: central contact person
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
imported from: opmi.owl
type: Class
subclass of: contact person

contact person information
definition: information content entity about a contact person
definition editor: Leon Li, Asiyah Lin, Oliver He
imported from: opmi.owl
type: Class
subclass of: information content entity

primary sponsor role
definition: A sponsor role taken by an individual, organization, group or other legal entity which takes responsibility for initiating, managing and/or financing a study. The Primary Sponsor is responsible for ensuring that the trial is properly registered. The Primary Sponsor may or may not be the main funder.
definition editor: Leon Li, Asiyah Lin, Oliver He
definition source: https://www.who.int/ictrp/network/trds/en/
imported from: opmi.owl
type: Class
subclass of: sponsor role

secondary sponsor role
definition: A sponsor role taken by an additional individual, organization or another legal person, if any, that has agreed with the primary sponsor to take on responsibilities of sponsorship.
definition editor: Leon Li, Asiyah Lin, Oliver He
alternative term: collaborator role
definition source: https://www.who.int/ictrp/network/trds/en/
imported from: opmi.owl
type: Class
comment: A secondary sponsor may have agreed to: - take on all the responsibilities of sponsorship jointly with the primary sponsor; or - form a group with the Primary Sponsor in which the responsibilities of sponsorship are allocated among the members of the group; or - act as the Primary Sponsor’s legal representative in relation to some or all of the trial sites. by WHO (https://www.who.int/ictrp/network/trds/en/)
comment: In clinicaltrials.gov, the secondary sponsor role can be taken by a project collaborator (Reference: https://prsinfo.clinicaltrials.gov/trainTrainer/WHO-ICMJE-ClinTrialsgov-Cross-Ref.pdf). However, a secondary sponsor may serve as a collaborator role, but a collaborator may not serve as a secondary sponsor role.
subclass of: sponsor role

principal investigator role
definition: An investigator role taken by an individual who is designated as responsible party by the sponsor
definition editor: Leon Li, Asiyah Lin, Oliver He
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
imported from: opmi.owl
type: Class
subclass of: investigator role

sponsor investigator role
definition: An investigator role taken by an individual who both initiates and conducts the study
definition editor: Leon Li, Asiyah Lin, Oliver He
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
imported from: opmi.owl
type: Class
subclass of: investigator role

investigation collaborator role
definition: An investigation agent role taken by an agent (an individual, organization, group or another legal entity) who provides support to an investigation. The support may include funding, design, implementation, data analysis or reporting. The responsible party is responsible for confirming all collaborators before listing them.
definition editor: Leon Li, Asiyah Li, Oliver He
alternative term: collaborator role
definition source: https://prsinfo.clinicaltrials.gov/definitions.html#Collaborators
definition source: https://www.who.int/ictrp/network/trds/en/
imported from: opmi.owl
type: Class
comment: A secondary sponsor may serve as a collaborator role. However, a collaborator may not serve as a secondary sponsor role.
subclass of: investigation agent role

human subject study
definition: A systematic, scientific investigation that can be either interventional or observational and involves human beings as research subjects. Human subject research can be either medical (clinical) research or non-medical (e.g., social science) research.
definition editor: Oliver He
alternative term: human investigation
alternative term: human study
definition source: https://en.wikipedia.org/wiki/Human_subject_research
imported from: opmi.owl
type: Class
subclass of: investigation

biological sex
definition: An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000047
in subset: attribute slim
type: Class
subclass of: organismal quality

female
definition: A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000383
in subset: mpath slim
in subset: value slim
type: Class
subclass of: phenotypic sex

male
definition: A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000384
in subset: mpath slim
in subset: value slim
type: Class
subclass of: phenotypic sex

process quality
definition: A quality which inheres in an process.
imported from: pato.owl
has_alternative_id: PATO:0001239
has_alternative_id: PATO:0001240
has exact synonym: quality of a process
has exact synonym: quality of occurrent
has exact synonym: quality of process
has exact synonym: relational quality of occurrent
has_obo_namespace: quality
id: PATO:0001236
type: Class
comment: See comments of relational quality of a physical entity.
subclass of: quality

physical object quality
definition: A quality which inheres in a continuant.
imported from: pato.owl
has_alternative_id: PATO:0001237
has_alternative_id: PATO:0001238
database_cross_reference: snap:Quality
has exact synonym: monadic quality of a continuant
has exact synonym: multiply inhering quality of a physical entity
has exact synonym: quality of a continuant
has exact synonym: quality of a single physical entity
has exact synonym: quality of an object
has exact synonym: quality of continuant
has_narrow_synonym: monadic quality of an object
has_narrow_synonym: monadic quality of continuant
has_obo_namespace: quality
id: PATO:0001241
type: Class
comment: 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.
subclass of: quality

phenotypic sex
definition: An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0001894
in subset: attribute slim
type: Class
subclass of: biological sex

organismal quality
definition: A quality that inheres in an entire organism or part of an organism.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0001995
type: Class
subclass of: physical object quality

condition
has curation status: metadata incomplete
definition: An information content entity that describes some relationships between some entities and whose truthfullness is a prerequisite for something.
definition: Une entité de contenu informationnel qui décrit des relations entre certaines entités et dont la véracité est un prérequis pour quelque chose. @fr
imported from: pdro.owl
type: Class
subclass of: information content entity

has participant
type: ObjectProperty

concretizes
type: ObjectProperty

has role
type: ObjectProperty

has active ingredient
example of usage: Any portion of roundup 'has active ingredient' some glyphosate
definition: A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.
imported from: ro.owl
has exact synonym: has active substance
has_related_synonym: has active pharmaceutical ingredient
type: ObjectProperty
inverse of: active ingredient in

active ingredient in
type: ObjectProperty

vaccination
definition: a medical intervention that involves in adding vaccine into a host (e.g., human, mouse) in vivo with the intent to invoke an adaptive immune response.
imported from: oae.owl
imported from: vo.owl
type: Class
subclass of: medical intervention

phase 1 vaccine trial
definition: A vaccine clinical trial that investigates the safety profile of a vaccine in a small group (10-50) of healthy volunteers.
definition editor: YH
imported from: vo.owl
type: Class
subclass of: vaccine clinical trial

phase 2 vaccine trial
definition: A vaccine clinical trial that studies vaccine efficacy with a target population (numbering 50-100). Different dosage levels will also be explored at this stage to determine the optimum dose.
definition editor: YH
imported from: vo.owl
type: Class
subclass of: vaccine clinical trial

phase 3 vaccine trial
definition: A vaccine clinical trial that takes the trial to a large-scale safety and efficacy study in a relevant patient population, usually in excess of 3,000.
definition editor: YH
imported from: vo.owl
type: Class
subclass of: vaccine clinical trial

phase 4 vaccine trial
definition: The final stage of vaccine clinical evaluation. Phase IV occurs after a vaccine or therapy is licensed and is being used by large numbers of people. These studies are not always required or completed.
definition editor: YH
imported from: vo.owl
type: Class
subclass of: vaccine clinical trial

vaccine clinical trial
definition: A processual entity by which a vaccine is tested clinically for safety and effectiveness. Clinical trials are conducted in phases. Classically, clinical trials unfold in three phases in order to gather data and information about a vaccine and its performance. This will form the basis of a dossier submitted to regulatory authorities by way of an application for licensure. After a vaccine is licensed and is being used by large numbers of people, a Phase IV study may or may not be taken for vaccine clinical evaluation.
editor note: Most vaccines against a pathogen (e.g., HIV) are not tested by vaccinating people and then deliberately exposing them to virulent pathogen (e.g., HIV). This strategy is never for a vaccine against a disease as serious as HIV. The best way to determine if a vaccine is effective is to test it in a randomized, controlled, double-blind clinical trial. This type of trial is often referred to as the gold standard in medical research and provides the strongest evidence for the efficacy of a vaccine.
definition editor: YH
imported from: vo.owl
type: Class
subclass of: human subject study

CTO: Core Ontology of Clinical Trials
contributor: Asiyah Yu Lin (CDRH, Food and Drug Administration)
contributor: Astghik Sargsyan (Fraunhofer SCAI)
contributor: Geena Mariya Jose (Causality Biomodels)
contributor: Leon Li (NIH)
contributor: Oliver He (University of Michigan)
contributor: Shounak Baksi (Causality Biomodels)
description: The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials.
creator: Alpha Tom Kodamullil (Fraunhofer SCAI)
creator: Johannes Darms (Fraunhofer SCAI)
creator: Stephan Gebel (Fraunhofer SCAI)
creator: Sumit Madan (Fraunhofer SCAI)
license: http://creativecommons.org/licenses/by/4.0
type: Ontology
version info: Version Release: 1.0.0

has_rank
definition: A metadata relation between a class and its taxonomic rank (eg species, family)
has_obo_namespace: ncbi_taxonomy
type: AnnotationProperty

Description
description: Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
type: AnnotationProperty
comment: An account of the content of the resource.

Source
description: The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
type: AnnotationProperty
comment: A reference to a resource from which the present resource is derived.

Case control study
definition: Group of individuals with specific characteristics (for example, conditions or exposures) compared to group(s) with different characteristics, but otherwise similar.

Case crossover study
definition: Characteristics of case immediately prior to disease onset (sometimes called the hazard period) compared to characteristics of same case at a prior time (that is, control period).

Cohort study
definition: Group of individuals, initially defined and composed, with common characteristics (for example, condition, birth year), who are examined or traced over a given time period.

Parallel group study
definition: Participants are assigned to one of two or more groups in parallel for the duration of the study

Crossover study
definition: Participants receive one of two (or more) alternative interventions during the initial phase of the study and receive the other intervention during the second phase of the study

Single group study
definition: Clinical trials with a single arm

has_alternative_id
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has exact synonym
definition: A property representing a 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.
definition: 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: FULL_SYN
has exact synonym: Synonym with Source Data
type: AnnotationProperty
label: has_exact_synonym

has_narrow_synonym
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

in subset
definition: An association that connects the concept defining a particular terminology subset with concepts that belong to this subset.
definition: Used to associate the concept defining a particular terminology subset with concepts that belong to this subset.
has exact synonym: Concept_In_Subset
type: AnnotationProperty
label: in_subset

shorthand
type: AnnotationProperty

label
editor preferred label: label
type: AnnotationProperty

Korean clinical trial registry identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in the Korean Clinical Research Information Service (CRIS). The format for the registry number is “KCT” followed by a 7-digit number, e.g., KCT0004537.
has exact synonym: CRIS identifier

Sri Lanka clinical trials registry identifier
definition: A centrally registered identifier that is assigned for a specific clinical trial registered in the Sri Lanka clinical trials registry (SLCTR ). The format for the registry number is “SLCTR /” followed by a 4-digit number, followed by a slash, followed a 3-digit number, e.g., SLCTR/2020/010
has exact synonym: SLCTR identifier

jRTC clinical trials register
definition: The jRTC (Japan Registry of Clinical Trials) clinical trial registry is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: Japan Registry of Clinical Trials
has exact synonym: jRTC

International standard randomised controlled trial register
definition: The international standard randomised controlled trial register is a primary clinical trial registry recognised by WHO and ICMJE that enables the registration of clinical trials.
has exact synonym: ISRCTN

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith
annotated property: editor note
annotated source: entity
annotated target: 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

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002
annotated property: has associated axiom(fol)
annotated source: continuant
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001
annotated property: definition
annotated source: continuant fiat boundary
annotated target: b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000008
annotated property: editor note
annotated source: continuant fiat boundary
annotated target: Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001
annotated property: has associated axiom(fol)
annotated source: continuant fiat boundary
annotated target: (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001
annotated property: elucidation
annotated source: one-dimensional continuant fiat boundary
annotated target: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001
annotated property: has associated axiom(fol)
annotated source: one-dimensional continuant fiat boundary
annotated target: (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002
annotated property: definition
annotated source: process profile
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005
annotated property: elucidation
annotated source: process profile
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005
annotated property: has associated axiom(fol)
annotated source: process profile
annotated target: (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]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002
annotated property: has associated axiom(fol)
annotated source: process profile
annotated target: (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001
annotated property: definition
annotated source: relational quality
annotated target: b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001
annotated property: has associated axiom(fol)
annotated source: continuant
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001
annotated property: has associated axiom(fol)
annotated source: relational quality
annotated target: (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001
annotated property: elucidation
annotated source: two-dimensional continuant fiat boundary
annotated target: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001
annotated property: has associated axiom(fol)
annotated source: two-dimensional continuant fiat boundary
annotated target: (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000001
comment: requested by Melanie Courtot
annotated property: editor note
annotated source: zero-dimensional continuant fiat boundary
annotated target: zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001
annotated property: elucidation
annotated source: zero-dimensional continuant fiat boundary
annotated target: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001
annotated property: has associated axiom(fol)
annotated source: zero-dimensional continuant fiat boundary
annotated target: (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001
annotated property: elucidation
annotated source: zero-dimensional temporal region
annotated target: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001
annotated property: has associated axiom(fol)
annotated source: zero-dimensional temporal region
annotated target: (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/138-001
annotated property: elucidation
annotated source: history
annotated target: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: secondary identifier
annotated target: An identifier(s) (ID), if any, other than the organization's Unique Protocol Identification Number or the NCT number that is assigned to the clinical study. This includes any unique clinical study identifiers assigned by other publicly available clinical trial registries. If the clinical study is funded in whole or in part by a U.S. Federal Government agency, the complete grant or contract number must be submitted as a Secondary ID.

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith
annotated property: editor note
annotated source: occurrent
annotated target: 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.

Axiom
definition source: https://www.who.int/ictrp/network/trds/en/
annotated property: definition
annotated source: secondary identifier
annotated target: Other identifiers besides the Trial Identifying Number allocated by the Primary Registry, if any.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: masking design
annotated target: The party or parties involved in the clinical trial who are prevented from having knowledge of the interventions assigned to individual participants.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: non-random allocation
annotated target: Participants are expressly assigned to intervention groups through a non-random method, such as physician choice

Axiom
definition source: https://clinicaltrials.gov/ct2/about-studies/glossary
annotated property: definition
annotated source: study summary result
annotated target: A study record that includes the summary results posted in the ClinicalTrials.gov results database. Summary results information includes participant flow, baseline characteristics, outcome measures, and adverse events (including serious adverse events).

Axiom
annotated property: has_related_synonym
annotated source: secondary outcome measure information
annotated target: key secondary outcome

Axiom
definition source: https://clinicaltrials.gov/ct2/about-studies/glossary
annotated property: definition
annotated source: clinical trial outcome measurement
annotated target: For clinical trials, a planned measurement described in the protocol that is used to determine the effect of an intervention/treatment on participants. For observational studies, a measurement or observation that is used to describe patterns of diseases or traits, or associations with exposures, risk factors, or treatment. Types of outcome measures include primary outcome measure and secondary outcome measure.

Axiom
annotated property: has_related_synonym
annotated source: number of participants
annotated target: enrollment

Axiom
annotated property: has_related_synonym
annotated source: number of participants
annotated target: sample size

Axiom
definition source: https://clinicaltrials.gov/ct2/about-studies/glossary
annotated property: definition
annotated source: healthy volunteer criterion
annotated target: A type of eligibility criteria that indicates whether people who do not have the condition/disease being studied can participate in that clinical study.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: healthy volunteer criterion
annotated target: Indication that participants who do not have a disease or condition, or related conditions or symptoms, under study in the clinical study are permitted to participate in the clinical study.

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000012
annotated property: editor note
annotated source: occurrent
annotated target: 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.

Axiom
annotated property: has_related_synonym
annotated source: primary outcome measure information
annotated target: primary end point

Axiom
annotated property: has_related_synonym
annotated source: primary outcome measure information
annotated target: primary outcome(s)

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: human subjects protection review board status
annotated target: Indicate whether a clinical study has been reviewed and approved by at least one human subjects protection review board or such review is not required per applicable law (for example, 21 CFR Part 56, 45 CFR Part 46, or other applicable regulation).

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: phase not applicable
annotated target: Trials without phases (for example, studies of devices or behavioral interventions).

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: retrospective study design
annotated target: Look back using observations collected predominantly prior to subject selection and enrollment

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: prospective study design
annotated target: Look forward using periodic observations collected predominantly following subject enrollment

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: sequential design
annotated target: Groups of participants are assigned to receive interventions based on prior milestones being reached in the study, such as in some dose escalation and adaptive design studies

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Early Phase 1 clinical trial
annotated target: Exploratory trials, involving very limited human exposure, with no therapeutic or diagnostic intent (e.g., screening studies, microdose studies). (Formerly listed as "Phase 0")

Axiom
annotated property: has exact synonym
annotated source: clinical trial study completion date
annotated target: completion date

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/077-002
annotated property: elucidation
annotated source: occurrent
annotated target: 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])

Axiom
annotated property: has_narrow_synonym
annotated source: centrally registered identifier
annotated target: Primary Registry and Trial Identifying Number

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Patient Registry Study
annotated target: An observational study that is also considered to be a Patient Registry. This type of study should only be registered once in the Protocol Registration and Results System (PRS), by the sponsor responsible for the primary data collection and analysis.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Random Allocation
annotated target: Participants are assigned to intervention groups by chance

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Study Primary Purpose
annotated target: The main objective of the intervention(s) being evaluated by the clinical trial.

Axiom
annotated property: has exact synonym
annotated source: Gene Therapy
annotated target: Genetic

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Health Services Research
annotated target: One or more interventions for evaluating the delivery, processes, management, organization, or financing of healthcare.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Phase I Trial
annotated target: Includes initial studies to determine the metabolism and pharmacologic actions of drugs in humans, the side effects associated with increasing doses, and to gain early evidence of effectiveness; may include healthy participants and/or patients.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Phase II Trial
annotated target: Includes controlled clinical studies conducted to evaluate the effectiveness of the drug for a particular indication or indications in participants with the disease or condition under study and to determine the common short-term side effects and risks.

Axiom
comment: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Phase III Trial
annotated target: Includes trials conducted after preliminary evidence suggesting effectiveness of the drug has been obtained, and are intended to gather additional information to evaluate the overall benefit-risk relationship of the drug.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Phase IV Trial
annotated target: Studies of FDA-approved drugs to delineate additional information including the drug's risks, benefits, and optimal use.

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001
annotated property: has associated axiom(nl)
annotated source: occurrent
annotated target: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Phase I/II Trial
annotated target: Trials that are a combination of phases 1 and 2.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Phase II/III Trial
annotated target: Trials that are a combination of phases 2 and 3.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Basic Research
annotated target: One or more interventions for examining the basic mechanism of action (for example, physiology or biomechanics of an intervention).

Axiom
definition source: https://clinicaltrials.gov/ct2/about-studies/glossary
annotated property: definition
annotated source: Condition or Disease under Study
annotated target: The disease, disorder, syndrome, illness, or injury that is being studied. On ClinicalTrials.gov, conditions may also include other health-related issues, such as lifespan, quality of life, and health risks.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Condition or Disease under Study
annotated target: The name(s) of the disease(s) or condition(s) studied in the clinical study, or the focus of the clinical study. Use, if available, appropriate descriptors from NLM's Medical Subject Headings (MeSH)-controlled vocabulary thesaurus or terms from another vocabulary, such as the Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT), that has been mapped to MeSH within the Unified Medical Language System (UMLS) Metathesaurus.

Axiom
annotated property: has exact synonym
annotated source: Condition or Disease under Study
annotated target: health condition(s) or problem(s) studied

Axiom
definition source: https://clinicaltrials.gov/ct2/about-studies/glossary
annotated property: definition
annotated source: Age
annotated target: A type of eligibility criteria that indicates the age a person must be to participate in a clinical study.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Diagnosis Study
annotated target: One or more interventions are being evaluated for identifying a disease or health condition.

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001
annotated property: has associated axiom(nl)
annotated source: occurrent
annotated target: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Treatment Study
annotated target: One or more interventions are being evaluated for treating a disease, syndrome, or condition.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Prevention Study
annotated target: One or more interventions are being assessed for preventing the development of a specific disease or health condition.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Allocation
annotated target: The method by which participants are assigned to arms in a clinical trial.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/results_definitions.html
annotated property: definition
annotated source: Study Protocol
annotated target: The written description of the clinical study, including objective(s), design, and methods. It may also include relevant scientific background and statistical considerations (if the protocol document includes the statistical analysis plan, use "Study Protocol with SAP and/or ICF" option). Note: All amendments approved by a human subjects protection review board (if applicable), before the time of submission and that apply to all clinical trial Facility Locations must be included.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Screening Study
annotated target: One or more interventions are assessed or examined for identifying a condition, or risk factors for a condition, in people who are not yet known to have the condition or risk factor.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Supportive Care Study
annotated target: One or more interventions are evaluated for maximizing comfort, minimizing side effects, or mitigating against a decline in the participant's health or function.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Factorial Study
annotated target: Two or more interventions, each alone and in combination, are evaluated in parallel against a control group

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Expanded Access Study
annotated target: An investigational drug product (including biological product) available through expanded access for patients who do not qualify for enrollment in a clinical trial. Expanded Access includes all expanded access types under section 561 of the Federal Food, Drug, and Cosmetic Act: (1) for individual patients, including emergency use; (2) for intermediate-size patient populations; and (3) under a treatment IND or treatment protocol.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Intervention Type
annotated target: For each intervention studied in the clinical study, the general type of intervention.

Axiom
annotated property: has_narrow_synonym
annotated source: Intervention Type
annotated target: intervention

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001
annotated property: has associated axiom(fol)
annotated source: occurrent
annotated target: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]

Axiom
definition source: https://prsinfo.clinicaltrials.gov/results_definitions.html
annotated property: definition
annotated source: adverse event
annotated target: Any untoward or unfavorable medical occurrence in a participant, including any abnormal sign (for example, abnormal physical exam or laboratory finding), symptom, or disease, temporally associated with the participant’s participation in the research, whether or not considered related to the participant’s participation in the research

Axiom
definition source: https://www.clinicaltrials.gov/ct2/about-studies/glossary
annotated property: definition
annotated source: medical intervention
annotated target: A process or action that is the focus of a clinical study. Interventions include drugs, medical devices, procedures, vaccines, and other products that are either investigational or already available. Interventions can also include noninvasive approaches, such as education or modifying diet and exercise.

Axiom
annotated property: has exact synonym
annotated source: medical intervention
annotated target: Intervention(s)

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: intervention design
annotated target: A description of the manner in which the clinical trial will be conducted.

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001
annotated property: has associated axiom(fol)
annotated source: occurrent
annotated target: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

Axiom
definition source: https://clinicaltrials.gov/ct2/about-studies/glossary
annotated property: definition
annotated source: age group inclusion criterion
annotated target: A type of eligibility criteria that indicates the age a person must be to participate in a clinical study. This may be indicated by a specific age or the following age groups. The age groups are: Child (birth-17), Adult (18-64), Older Adult (65+).

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: minimum age value specification
annotated target: The numerical value, if any, for the minimum age a potential participant must meet to be eligible for the clinical study.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: maximum age value specification
annotated target: The numerical value, if any, for the maximum age a potential participant can be to be eligible for the clinical study.

Axiom
definition source: https://clinicaltrials.gov/ct2/about-studies/glossary
annotated property: definition
annotated source: sex inclusion criterion
annotated target: A type of eligibility criteria that indicates the sex of people who may participate in a clinical study (all, female, male). Sex is a person's classification as female or male based on biological distinctions. Sex is distinct from gender-based eligibility.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: cross over design
annotated target: Participants receive one of two (or more) alternative interventions during the initial phase of the study and receive the other intervention during the second phase of the study

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002
annotated property: definition
annotated source: independent continuant
annotated target: 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])

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: parallel group design
annotated target: Participants are assigned to one of two or more groups in parallel for the duration of the study

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: factorial design
annotated target: Two or more interventions, each alone and in combination, are evaluated in parallel against a control group

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: eligibility criterion
annotated target: A limited list of criteria for selection of participants in the clinical study, provided in terms of inclusion and exclusion criteria and suitable for assisting potential participants in identifying clinical studies of interest.

Axiom
definition source: https://clinicaltrials.gov/ct2/about-studies/glossary
annotated property: definition
annotated source: eligibility criterion
annotated target: The key requirements that people who want to participate in a clinical study must meet or the characteristics they must have. Eligibility criteria consist of both inclusion criteria (which are required for a person to participate in the study) and exclusion criteria (which prevent a person from participating). Types of eligibility criteria include whether a study accepts healthy volunteers, has age or age group requirements, or is limited by sex

Axiom
definition source: https://clinicaltrials.gov/ct2/about-studies/glossary
annotated property: definition
annotated source: inclusion criterion
annotated target: A type of eligibility criteria. These are the reasons that a person is allowed to participate in a clinical study.

Axiom
definition source: http://www.icmje.org/recommendations/ https://www.who.int/ictrp/network/trds/en/
annotated property: has exact synonym
annotated source: inclusion criterion
annotated target: key inclusion criteria

Axiom
definition source: https://clinicaltrials.gov/ct2/about-studies/glossary
annotated property: definition
annotated source: exclusion criterion
annotated target: A type of eligibility criteria. These are reasons that a person is not allowed to participate in a clinical study.

Axiom
definition source: http://www.icmje.org/recommendations/ https://www.who.int/ictrp/network/trds/en/
annotated property: has exact synonym
annotated source: exclusion criterion
annotated target: key exclusion criteria

Axiom
definition source: https://www.clinicaltrialsregister.eu/doc/EU_Clinical_Trials_Register_Glossary.pdf
annotated property: definition
annotated source: diagnosis
annotated target: 1. the determination of the nature of a case of disease. 2. the art of distinguishing one disease from another.

Axiom
annotated property: has exact synonym
annotated source: clinical trial start date
annotated target: date of first enrollment

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/001-001
annotated property: elucidation
annotated source: entity
annotated target: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001
annotated property: has associated axiom(nl)
annotated source: independent continuant
annotated target: 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])

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: study completion date
annotated target: The date the final participant was examined or received an intervention for purposes of final collection of data for the primary and secondary outcome measures and adverse events (for example, last participant’s last visit), whether the clinical study concluded according to the pre-specified protocol or was terminated.

Axiom
annotated property: has exact synonym
annotated source: study completion date
annotated target: Completion Date

Axiom
definition source: https://www.clinicaltrials.gov/ct2/about-studies/glossary
annotated property: definition
annotated source: date of registration
annotated target: The date on which the study sponsor or investigator first submitted a study record to ClinicalTrials.gov. There is typically a delay of a few days between the first submitted date and the record's availability on ClinicalTrials.gov (the first posted date).

Axiom
annotated property: has exact synonym
annotated source: date of registration
annotated target: date of registration in primary registry

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: recruitment status
annotated target: The recruitment status for the clinical study as a whole, based upon the status of the individual sites. If at least one facility in a multi-site clinical study has an Individual Site Status of "Recruiting," then the Overall Recruitment Status for the study must be "Recruiting."

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: combinational intervention
annotated target: Combining a drug and device, a biological product and device; a drug and biological product; or a drug, biological product, and device

Axiom
annotated property: has exact synonym
annotated source: behavioral intervention
annotated target: behavioral

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: ERO_0000348
annotated target: single group of individuals with specific characteristics.

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002
annotated property: has associated axiom(nl)
annotated source: independent continuant
annotated target: 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])

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Case control study
annotated target: Group of individuals with specific characteristics (for example, conditions or exposures) compared to group(s) with different characteristics, but otherwise similar.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Case crossover study
annotated target: Characteristics of case immediately prior to disease onset (sometimes called the hazard period) compared to characteristics of same case at a prior time (that is, control period).

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Cohort study
annotated target: Group of individuals, initially defined and composed, with common characteristics (for example, condition, birth year), who are examined or traced over a given time period.

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Parallel group study
annotated target: Participants are assigned to one of two or more groups in parallel for the duration of the study

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Crossover study
annotated target: Participants receive one of two (or more) alternative interventions during the initial phase of the study and receive the other intervention during the second phase of the study

Axiom
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
annotated property: definition
annotated source: Single group study
annotated target: Clinical trials with a single arm

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001
annotated property: has associated axiom(fol)
annotated source: independent continuant
annotated target: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002
annotated property: has associated axiom(fol)
annotated source: independent continuant
annotated target: (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]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002
annotated property: has associated axiom(fol)
annotated source: independent continuant
annotated target: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000002
comment: per discussion with Barry Smith
annotated property: editor note
annotated source: spatial region
annotated target: 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.

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001
annotated property: elucidation
annotated source: spatial region
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001
annotated property: has associated axiom(nl)
annotated source: spatial region
annotated target: All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001
annotated property: has associated axiom(fol)
annotated source: spatial region
annotated target: (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001
annotated property: has associated axiom(fol)
annotated source: spatial region
annotated target: (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002
annotated property: has associated axiom(fol)
annotated source: continuant
annotated target: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000003
comment: per discussion with Barry Smith
annotated property: editor note
annotated source: temporal region
annotated target: 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

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001
annotated property: elucidation
annotated source: temporal region
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001
annotated property: has associated axiom(nl)
annotated source: temporal region
annotated target: All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002
annotated property: has associated axiom(nl)
annotated source: temporal region
annotated target: Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002
annotated property: has associated axiom(fol)
annotated source: temporal region
annotated target: (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001
annotated property: has associated axiom(fol)
annotated source: temporal region
annotated target: (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001
annotated property: has associated axiom(fol)
annotated source: temporal region
annotated target: (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001
annotated property: elucidation
annotated source: two-dimensional spatial region
annotated target: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001
annotated property: has associated axiom(fol)
annotated source: two-dimensional spatial region
annotated target: (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001
annotated property: elucidation
annotated source: spatiotemporal region
annotated target: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002
annotated property: has associated axiom(fol)
annotated source: continuant
annotated target: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001
annotated property: has associated axiom(nl)
annotated source: spatiotemporal region
annotated target: All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001
annotated property: has associated axiom(nl)
annotated source: spatiotemporal region
annotated target: Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001
annotated property: has associated axiom(nl)
annotated source: spatiotemporal region
annotated target: Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002
annotated property: has associated axiom(nl)
annotated source: spatiotemporal region
annotated target: Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002
annotated property: has associated axiom(fol)
annotated source: spatiotemporal region
annotated target: (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001
annotated property: has associated axiom(fol)
annotated source: spatiotemporal region
annotated target: (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001
annotated property: has associated axiom(fol)
annotated source: spatiotemporal region
annotated target: (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001
annotated property: has associated axiom(fol)
annotated source: spatiotemporal region
annotated target: (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001
annotated property: has associated axiom(fol)
annotated source: spatiotemporal region
annotated target: (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003
annotated property: definition
annotated source: process
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000007
annotated property: editor note
annotated source: continuant
annotated target: 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

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003
annotated property: has associated axiom(fol)
annotated source: process
annotated target: (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]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002
annotated property: elucidation
annotated source: disposition
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002
annotated property: has associated axiom(nl)
annotated source: disposition
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002
annotated property: has associated axiom(fol)
annotated source: disposition
annotated target: (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]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002
annotated property: has associated axiom(fol)
annotated source: disposition
annotated target: (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002
annotated property: elucidation
annotated source: realizable entity
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002
annotated property: has associated axiom(nl)
annotated source: realizable entity
annotated target: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002
annotated property: has associated axiom(fol)
annotated source: realizable entity
annotated target: (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]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002
annotated property: has associated axiom(fol)
annotated source: realizable entity
annotated target: (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]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001
annotated property: elucidation
annotated source: zero-dimensional spatial region
annotated target: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002
annotated property: elucidation
annotated source: continuant
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001
annotated property: has associated axiom(fol)
annotated source: zero-dimensional spatial region
annotated target: (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001
annotated property: elucidation
annotated source: quality
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001
annotated property: has associated axiom(nl)
annotated source: quality
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001
annotated property: has associated axiom(fol)
annotated source: quality
annotated target: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001
annotated property: has associated axiom(fol)
annotated source: quality
annotated target: (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]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003
annotated property: definition
annotated source: specifically dependent continuant
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith
annotated property: editor note
annotated source: specifically dependent continuant
annotated target: 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.

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003
annotated property: has associated axiom(fol)
annotated source: specifically dependent continuant
annotated target: (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]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001
annotated property: elucidation
annotated source: role
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001
annotated property: has associated axiom(fol)
annotated source: role
annotated target: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001
annotated property: has associated axiom(nl)
annotated source: continuant
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004
annotated property: elucidation
annotated source: fiat object part
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004
annotated property: has associated axiom(fol)
annotated source: fiat object part
annotated target: (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]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001
annotated property: elucidation
annotated source: one-dimensional spatial region
annotated target: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001
annotated property: has associated axiom(fol)
annotated source: one-dimensional spatial region
annotated target: (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000011
annotated property: editor note
annotated source: object aggregate
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000301
annotated property: editor note
annotated source: object aggregate
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000300
annotated property: definition source
annotated source: object aggregate
annotated target: 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.

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004
annotated property: elucidation
annotated source: object aggregate
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004
annotated property: has associated axiom(fol)
annotated source: object aggregate
annotated target: (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]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001
annotated property: elucidation
annotated source: three-dimensional spatial region
annotated target: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002
annotated property: has associated axiom(nl)
annotated source: continuant
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001
annotated property: has associated axiom(fol)
annotated source: three-dimensional spatial region
annotated target: (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002
annotated property: elucidation
annotated source: site
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002
annotated property: has associated axiom(fol)
annotated source: site
annotated target: (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/024-001
annotated property: elucidation
annotated source: object
annotated target: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001
annotated property: definition
annotated source: generically dependent continuant
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001
annotated property: has associated axiom(fol)
annotated source: generically dependent continuant
annotated target: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001
annotated property: elucidation
annotated source: function
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001
annotated property: has associated axiom(fol)
annotated source: function
annotated target: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001
annotated property: definition
annotated source: process boundary
annotated target: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002
annotated property: has associated axiom(nl)
annotated source: process boundary
annotated target: Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002
annotated property: has associated axiom(nl)
annotated source: continuant
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002
annotated property: has associated axiom(fol)
annotated source: process boundary
annotated target: (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001
annotated property: has associated axiom(fol)
annotated source: process boundary
annotated target: (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001
annotated property: elucidation
annotated source: one-dimensional temporal region
annotated target: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001
annotated property: has associated axiom(fol)
annotated source: one-dimensional temporal region
annotated target: (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002
annotated property: elucidation
annotated source: material entity
annotated target: 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])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002
annotated property: has associated axiom(nl)
annotated source: material entity
annotated target: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002
annotated property: has associated axiom(nl)
annotated source: material entity
annotated target: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002
annotated property: has associated axiom(fol)
annotated source: material entity
annotated target: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002
annotated property: has associated axiom(fol)
annotated source: material entity
annotated target: (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]

Axiom
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002
annotated property: has associated axiom(fol)
annotated source: material entity
annotated target: (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]