en
Gustavo Carvalho
Regina Hurley
Sebastian Deusing
Shane Babcock
Barry Smith
John Beverley
http://creativecommons.org/licenses/by/4.0/
The Virus Infectious Disease Ontology (VIDO) is an extension of the Infectious Disease Ontology (IDO). VIDO follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by specific viruses and associated virus diseases. Other terms are defined as cross-products of terms from Foundry ontologies to the extent possible.
http://example.com/bfo-spec-label
Person:Alan Ruttenberg
http://purl.obolibrary.org/VIDO_0001123
Infectious disease inhering in a virus disorder that is a disorder due to the presence of the virus.
http://purl.obolibrary.org/VIDO_0001123
http://purl.obolibrary.org/obo/vido.owl
http://purl.obolibrary.org/VIDO_0001123
John Beverley
http://purl.obolibrary.org/VIDO_0001123
viral disease
obo:APOLLO_SV_00000075
Objective specification that is realized by processes that are able or likely to stop the spread of a disease in a population.
obo:APOLLO_SV_00000075
http://purl.obolibrary.org/obo/apollo-sv.owl
obo:APOLLO_SV_00000075
infectious disease control objective specification
obo:APOLLO_SV_00000086
Plan specification whose objective specification is an infectious disease control objective specification.
obo:APOLLO_SV_00000086
http://purl.obolibrary.org/obo/apollo-sv.owl
obo:APOLLO_SV_00000086
infectious disease control strategy
obo:APOLLO_SV_00000174
Algorithm that models the progress of a transmissible disease in a population.
obo:APOLLO_SV_00000174
http://purl.obolibrary.org/obo/apollo-sv.owl
obo:APOLLO_SV_00000174
disease transmission model
obo:APOLLO_SV_00000229
Infectious disease control strategy that has an action specification that is realized in closing facilities where organisms congregate during times when the facilities normally would be open.
obo:APOLLO_SV_00000229
http://purl.obolibrary.org/obo/apollo-sv.owl
obo:APOLLO_SV_00000229
place closure control strategy
obo:APOLLO_SV_00000230
Infectious disease control strategy that has an action specification that is realized in isolating organsims who are infectious.
obo:APOLLO_SV_00000230
http://purl.obolibrary.org/obo/apollo-sv.owl
obo:APOLLO_SV_00000230
case isolation control strategy
obo:APOLLO_SV_00000308
Infectious disease control strategy that has a vector control action specification as part.
obo:APOLLO_SV_00000308
http://purl.obolibrary.org/obo/apollo-sv.owl
obo:APOLLO_SV_00000308
vector control strategy
obo:APOLLO_SV_00000327
Infectious disease control strategy whereby organisms who have had contact with infectious organisms but are not symptomatic or otherwise known to be infectious are prevented from having contact with other susceptible organisms.
obo:APOLLO_SV_00000327
http://purl.obolibrary.org/obo/apollo-sv.owl
obo:APOLLO_SV_00000327
quarantine control strategy
obo:APOLLO_SV_00000541
Objective specification whose endpoint is human awareness of the level of a particular disease in a particular population of a given biological taxon during some time interval.
obo:APOLLO_SV_00000541
http://purl.obolibrary.org/obo/apollo-sv.owl
obo:APOLLO_SV_00000541
disease surveillance objective specification
obo:APOLLO_SV_00000550
Infectious disease control strategy that identifies and treats contacted organisms in a host population.
obo:APOLLO_SV_00000550
http://purl.obolibrary.org/obo/apollo-sv.owl
obo:APOLLO_SV_00000550
contact tracing
obo:BFO_0000001
entity
obo:BFO_0000001
Entity
obo:BFO_0000001
Julius Caesar
obo:BFO_0000001
Verdi’s Requiem
obo:BFO_0000001
the Second World War
obo:BFO_0000001
your body mass index
obo:BFO_0000001
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
http://purl.obolibrary.org/obo/bfo/axiom/0000004
per discussion with Barry Smith
http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
obo:BFO_0000001
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
http://purl.obolibrary.org/obo/bfo/axiom/001-001
obo:BFO_0000001
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
obo:BFO_0000001
obo:bfo.owl
obo:BFO_0000001
entity
obo:BFO_0000002
continuant
obo:BFO_0000002
Continuant
obo:BFO_0000002
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.
obo:BFO_0000002
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
http://purl.obolibrary.org/obo/bfo/axiom/0000007
obo:BFO_0000002
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
http://purl.obolibrary.org/obo/bfo/axiom/008-002
obo:BFO_0000002
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])
http://purl.obolibrary.org/obo/bfo/axiom/126-001
obo:BFO_0000002
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])
http://purl.obolibrary.org/obo/bfo/axiom/009-002
obo:BFO_0000002
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])
http://purl.obolibrary.org/obo/bfo/axiom/011-002
obo:BFO_0000002
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])
http://purl.obolibrary.org/obo/bfo/axiom/009-002
obo:BFO_0000002
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
http://purl.obolibrary.org/obo/bfo/axiom/126-001
obo:BFO_0000002
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
http://purl.obolibrary.org/obo/bfo/axiom/008-002
obo:BFO_0000002
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
http://purl.obolibrary.org/obo/bfo/axiom/011-002
obo:BFO_0000002
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
obo:BFO_0000002
obo:bfo.owl
obo:BFO_0000002
continuant
obo:BFO_0000003
An entity that has temporal parts and that happens, unfolds or develops through time.
obo:BFO_0000003
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
obo:BFO_0000003
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.
obo:BFO_0000003
obo:bfo.owl
obo:BFO_0000003
occurrent
obo:BFO_0000004
ic
obo:BFO_0000004
IndependentContinuant
obo:BFO_0000004
a chair
obo:BFO_0000004
a heart
obo:BFO_0000004
a leg
obo:BFO_0000004
a molecule
obo:BFO_0000004
a spatial region
obo:BFO_0000004
an atom
obo:BFO_0000004
an orchestra.
obo:BFO_0000004
an organism
obo:BFO_0000004
the bottom right portion of a human torso
obo:BFO_0000004
the interior of your mouth
obo:BFO_0000004
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
http://purl.obolibrary.org/obo/bfo/axiom/017-002
obo:BFO_0000004
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])
http://purl.obolibrary.org/obo/bfo/axiom/134-001
obo:BFO_0000004
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])
http://purl.obolibrary.org/obo/bfo/axiom/018-002
obo:BFO_0000004
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])
http://purl.obolibrary.org/obo/bfo/axiom/134-001
obo:BFO_0000004
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
http://purl.obolibrary.org/obo/bfo/axiom/018-002
obo:BFO_0000004
(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]
http://purl.obolibrary.org/obo/bfo/axiom/017-002
obo:BFO_0000004
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
obo:BFO_0000004
obo:bfo.owl
obo:BFO_0000004
independent continuant
obo:BFO_0000006
s-region
obo:BFO_0000006
SpatialRegion
obo:BFO_0000006
BFO 2 Reference: Spatial regions do not participate in processes.
http://purl.obolibrary.org/obo/bfo/axiom/0000002
per discussion with Barry Smith
obo:BFO_0000006
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.
http://purl.obolibrary.org/obo/bfo/axiom/035-001
obo:BFO_0000006
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])
http://purl.obolibrary.org/obo/bfo/axiom/036-001
obo:BFO_0000006
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
http://purl.obolibrary.org/obo/bfo/axiom/036-001
obo:BFO_0000006
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
http://purl.obolibrary.org/obo/bfo/axiom/035-001
obo:BFO_0000006
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
obo:BFO_0000006
obo:bfo.owl
obo:BFO_0000006
spatial region
http://purl.obolibrary.org/obo/bfo/axiom/119-002
obo:BFO_0000008
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
obo:BFO_0000008
obo:bfo.owl
obo:BFO_0000008
temporal region
obo:BFO_0000009
2d-s-region
obo:BFO_0000009
TwoDimensionalSpatialRegion
obo:BFO_0000009
an infinitely thin plane in space.
obo:BFO_0000009
the surface of a sphere-shaped part of space
http://purl.obolibrary.org/obo/bfo/axiom/039-001
obo:BFO_0000009
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
http://purl.obolibrary.org/obo/bfo/axiom/039-001
obo:BFO_0000009
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
obo:BFO_0000009
obo:bfo.owl
obo:BFO_0000009
two-dimensional spatial region
obo:BFO_0000011
the spatiotemporal region occupied by a human life
obo:BFO_0000011
the spatiotemporal region occupied by a process of cellular meiosis.
obo:BFO_0000011
obo:bfo.owl
obo:BFO_0000011
spatiotemporal region
obo:BFO_0000015
a process of cell-division, \ a beating of the heart
obo:BFO_0000015
a process of meiosis
obo:BFO_0000015
a process of sleeping
obo:BFO_0000015
the course of a disease
obo:BFO_0000015
the flight of a bird
obo:BFO_0000015
the life of an organism
obo:BFO_0000015
your process of aging.
obo:BFO_0000015
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
http://purl.obolibrary.org/obo/bfo/axiom/083-003
obo:BFO_0000015
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])
obo:BFO_0000015
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)
obo:BFO_0000015
obo:bfo.owl
obo:BFO_0000015
process
obo:BFO_0000016
an atom of element X has the disposition to decay to an atom of element Y
obo:BFO_0000016
certain people have a predisposition to colon cancer
obo:BFO_0000016
children are innately disposed to categorize objects in certain ways.
obo:BFO_0000016
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
obo:BFO_0000016
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.
http://purl.obolibrary.org/obo/bfo/axiom/062-002
obo:BFO_0000016
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])
obo:BFO_0000016
obo:bfo.owl
obo:BFO_0000016
disposition
obo:BFO_0000017
the disposition of this piece of metal to conduct electricity.
obo:BFO_0000017
the disposition of your blood to coagulate
obo:BFO_0000017
the function of your reproductive organs
obo:BFO_0000017
the role of being a doctor
obo:BFO_0000017
the role of this boundary to delineate where Utah and Colorado meet
obo:BFO_0000017
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.
http://purl.obolibrary.org/obo/bfo/axiom/058-002
obo:BFO_0000017
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])
obo:BFO_0000017
obo:bfo.owl
obo:BFO_0000017
realizable entity
obo:BFO_0000018
0d-s-region
obo:BFO_0000018
ZeroDimensionalSpatialRegion
http://purl.obolibrary.org/obo/bfo/axiom/037-001
obo:BFO_0000018
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
http://purl.obolibrary.org/obo/bfo/axiom/037-001
obo:BFO_0000018
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
obo:BFO_0000018
obo:bfo.owl
obo:BFO_0000018
zero-dimensional spatial region
obo:BFO_0000019
the ambient temperature of this portion of air
obo:BFO_0000019
the color of a tomato
obo:BFO_0000019
the length of the circumference of your waist
obo:BFO_0000019
the mass of this piece of gold.
obo:BFO_0000019
the shape of your nose
obo:BFO_0000019
the shape of your nostril
http://purl.obolibrary.org/obo/bfo/axiom/055-001
obo:BFO_0000019
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])
obo:BFO_0000019
obo:bfo.owl
obo:BFO_0000019
quality
obo:BFO_0000020
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
obo:BFO_0000020
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.
obo:BFO_0000020
the disposition of this fish to decay
obo:BFO_0000020
the function of this heart: to pump blood
obo:BFO_0000020
the mutual dependence of proton donors and acceptors in chemical reactions [79
obo:BFO_0000020
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
obo:BFO_0000020
the pink color of a medium rare piece of grilled filet mignon at its center
obo:BFO_0000020
the role of being a doctor
obo:BFO_0000020
the shape of this hole.
obo:BFO_0000020
the smell of this portion of mozzarella
obo:BFO_0000020
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
http://purl.obolibrary.org/obo/bfo/axiom/131-004
obo:BFO_0000020
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
http://purl.obolibrary.org/obo/bfo/axiom/050-003
obo:BFO_0000020
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])
obo:BFO_0000020
obo:bfo.owl
obo:BFO_0000020
specifically dependent continuant
obo:BFO_0000023
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.
obo:BFO_0000023
the priest role
obo:BFO_0000023
the role of a boundary to demarcate two neighboring administrative territories
obo:BFO_0000023
the role of a building in serving as a military target
obo:BFO_0000023
the role of a stone in marking a property boundary
obo:BFO_0000023
the role of subject in a clinical trial
obo:BFO_0000023
the student role
obo:BFO_0000023
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.
obo:BFO_0000023
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.
http://purl.obolibrary.org/obo/bfo/axiom/061-001
obo:BFO_0000023
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])
obo:BFO_0000023
obo:bfo.owl
obo:BFO_0000023
role
obo:BFO_0000026
1d-s-region
obo:BFO_0000026
OneDimensionalSpatialRegion
obo:BFO_0000026
an edge of a cube-shaped portion of space.
http://purl.obolibrary.org/obo/bfo/axiom/038-001
obo:BFO_0000026
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])
http://purl.obolibrary.org/obo/bfo/axiom/038-001
obo:BFO_0000026
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
obo:BFO_0000026
obo:bfo.owl
obo:BFO_0000026
one-dimensional spatial region
obo:BFO_0000027
object-aggregate
obo:BFO_0000027
ObjectAggregate
obo:BFO_0000027
a collection of cells in a blood biobank.
obo:BFO_0000027
a swarm of bees is an aggregate of members who are linked together through natural bonds
obo:BFO_0000027
a symphony orchestra
obo:BFO_0000027
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)
obo:BFO_0000027
defined by fiat: the aggregate of members of an organization
obo:BFO_0000027
defined through physical attachment: the aggregate of atoms in a lump of granite
obo:BFO_0000027
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
obo:BFO_0000027
defined via attributive delimitations such as: the patients in this hospital
obo:BFO_0000027
the aggregate of bearings in a constant velocity axle joint
obo:BFO_0000027
the aggregate of blood cells in your body
obo:BFO_0000027
the nitrogen atoms in the atmosphere
obo:BFO_0000027
the restaurants in Palo Alto
obo:BFO_0000027
your collection of Meissen ceramic plates.
http://purl.obolibrary.org/obo/bfo/axiom/0000301
obo:BFO_0000027
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
obo:BFO_0000027
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).
obo:BFO_0000027
obo:bfo.owl
obo:BFO_0000027
object aggregate
obo:BFO_0000028
3d-s-region
obo:BFO_0000028
ThreeDimensionalSpatialRegion
obo:BFO_0000028
a cube-shaped region of space
obo:BFO_0000028
a sphere-shaped region of space,
http://purl.obolibrary.org/obo/bfo/axiom/040-001
obo:BFO_0000028
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
http://purl.obolibrary.org/obo/bfo/axiom/040-001
obo:BFO_0000028
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
obo:BFO_0000028
obo:bfo.owl
obo:BFO_0000028
three-dimensional spatial region
obo:BFO_0000029
a hole in the interior of a portion of cheese
obo:BFO_0000029
a rabbit hole
obo:BFO_0000029
an air traffic control region defined in the airspace above an airport
obo:BFO_0000029
the Grand Canyon
obo:BFO_0000029
the Piazza San Marco
obo:BFO_0000029
the cockpit of an aircraft
obo:BFO_0000029
the hold of a ship
obo:BFO_0000029
the interior of a kangaroo pouch
obo:BFO_0000029
the interior of your office
obo:BFO_0000029
the interior of your refrigerator
obo:BFO_0000029
the lumen of your gut
obo:BFO_0000029
your left nostril (a fiat part – the opening – of your left nasal cavity)
http://purl.obolibrary.org/obo/bfo/axiom/034-002
obo:BFO_0000029
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])
obo:BFO_0000029
obo:bfo.owl
obo:BFO_0000029
site
obo:BFO_0000030
atom
obo:BFO_0000030
cell
obo:BFO_0000030
cells and organisms
obo:BFO_0000030
engineered artifacts
obo:BFO_0000030
grain of sand
obo:BFO_0000030
molecule
obo:BFO_0000030
organelle
obo:BFO_0000030
organism
obo:BFO_0000030
planet
obo:BFO_0000030
solid portions of matter
obo:BFO_0000030
star
obo:BFO_0000030
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.
obo:BFO_0000030
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).
obo:BFO_0000030
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
obo:BFO_0000030
BFO 2 Reference: an object is a maximal causally unified material entity
obo:BFO_0000030
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
obo:BFO_0000030
obo:bfo.owl
obo:BFO_0000030
object
obo:BFO_0000031
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.
obo:BFO_0000031
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
obo:BFO_0000031
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
obo:BFO_0000031
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.
http://purl.obolibrary.org/obo/bfo/axiom/074-001
obo:BFO_0000031
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])
obo:BFO_0000031
obo:bfo.owl
obo:BFO_0000031
generically dependent continuant
obo:BFO_0000034
the function of a hammer to drive in nails
obo:BFO_0000034
the function of a heart pacemaker to regulate the beating of a heart through electricity
obo:BFO_0000034
the function of amylase in saliva to break down starch into sugar
obo:BFO_0000034
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.
obo:BFO_0000034
obo:bfo.owl
obo:BFO_0000034
function
obo:BFO_0000035
the boundary between the 2nd and 3rd year of your life.
http://purl.obolibrary.org/obo/bfo/axiom/084-001
obo:BFO_0000035
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])
obo:BFO_0000035
obo:bfo.owl
obo:BFO_0000035
process boundary
obo:BFO_0000038
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).
obo:BFO_0000038
obo:bfo.owl
obo:BFO_0000038
one-dimensional temporal region
obo:BFO_0000040
material
obo:BFO_0000040
MaterialEntity
obo:BFO_0000040
a flame
obo:BFO_0000040
a forest fire
obo:BFO_0000040
a human being
obo:BFO_0000040
a hurricane
obo:BFO_0000040
a photon
obo:BFO_0000040
a puff of smoke
obo:BFO_0000040
a sea wave
obo:BFO_0000040
a tornado
obo:BFO_0000040
an aggregate of human beings.
obo:BFO_0000040
an energy wave
obo:BFO_0000040
an epidemic
obo:BFO_0000040
the undetached arm of a human being
obo:BFO_0000040
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
obo:BFO_0000040
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
obo:BFO_0000040
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.
obo:BFO_0000040
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.
http://purl.obolibrary.org/obo/bfo/axiom/019-002
obo:BFO_0000040
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])
http://purl.obolibrary.org/obo/bfo/axiom/020-002
obo:BFO_0000040
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
http://purl.obolibrary.org/obo/bfo/axiom/021-002
obo:BFO_0000040
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
http://purl.obolibrary.org/obo/bfo/axiom/019-002
obo:BFO_0000040
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
http://purl.obolibrary.org/obo/bfo/axiom/021-002
obo:BFO_0000040
(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]
http://purl.obolibrary.org/obo/bfo/axiom/020-002
obo:BFO_0000040
(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]
obo:BFO_0000040
obo:bfo.owl
obo:BFO_0000040
material entity
obo:BFO_0000050
is part of
obo:BFO_0000050
my brain is part of my body (continuant parthood, two material entities)
obo:BFO_0000050
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
obo:BFO_0000050
this day is part of this year (occurrent parthood)
obo:BFO_0000050
a core relation that holds between a part and its whole
obo:BFO_0000050
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
obo:BFO_0000050
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
obo:BFO_0000050
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
obo:BFO_0000050
part_of
obo:BFO_0000050
obo:RO_0001901
obo:BFO_0000050
part of
obo:BFO_0000050
http://www.obofoundry.org/ro/#OBO_REL:part_of
obo:BFO_0000051
has part
obo:BFO_0000051
my body has part my brain (continuant parthood, two material entities)
obo:BFO_0000051
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
obo:BFO_0000051
this year has part this day (occurrent parthood)
obo:BFO_0000051
a core relation that holds between a whole and its part
obo:BFO_0000051
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
obo:BFO_0000051
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
obo:BFO_0000051
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
obo:BFO_0000051
has_part
obo:BFO_0000051
obo:RO_0001901
obo:BFO_0000051
has part
obo:BFO_0000054
realized in
obo:BFO_0000054
this disease is realized in this disease course
obo:BFO_0000054
this fragility is realized in this shattering
obo:BFO_0000054
this investigator role is realized in this investigation
obo:BFO_0000054
is realized by
obo:BFO_0000054
realized_in
obo:BFO_0000054
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
obo:BFO_0000054
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
obo:BFO_0000054
obo:bfo.owl
obo:BFO_0000054
realized in
obo:BFO_0000055
realizes
obo:BFO_0000055
this disease course realizes this disease
obo:BFO_0000055
this investigation realizes this investigator role
obo:BFO_0000055
this shattering realizes this fragility
obo:BFO_0000055
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
obo:BFO_0000055
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
obo:BFO_0000055
obo:iao.owl
obo:BFO_0000055
realizes
obo:BFO_0000062
preceded by
obo:BFO_0000062
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
obo:BFO_0000062
is preceded by
obo:BFO_0000062
preceded_by
obo:BFO_0000062
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
obo:BFO_0000062
preceded by
obo:BFO_0000063
precedes
obo:BFO_0000063
precedes
obo:BFO_0000066
occurs in
obo:BFO_0000066
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
obo:BFO_0000066
occurs_in
obo:BFO_0000066
unfolds in
obo:BFO_0000066
unfolds_in
obo:BFO_0000066
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
obo:BFO_0000066
obo:bfo.owl
obo:BFO_0000066
occurs in
obo:BFO_0000067
site of
obo:BFO_0000067
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
obo:BFO_0000067
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
obo:BFO_0000067
obo:bfo.owl
obo:BFO_0000067
contains process
http://purl.obolibrary.org/obo/bfo/axiom/080-003
obo:BFO_0000134
To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003])
http://purl.obolibrary.org/obo/bfo/axiom/081-003
obo:BFO_0000134
To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])
obo:BFO_0000141
immaterial
obo:BFO_0000141
ImmaterialEntity
obo:BFO_0000141
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
obo:BFO_0000141
obo:bfo.owl
obo:BFO_0000141
immaterial entity
obo:BFO_0000144
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
obo:BFO_0000144
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.
obo:BFO_0000144
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.
http://purl.obolibrary.org/obo/bfo/axiom/093-002
obo:BFO_0000144
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])
obo:BFO_0000144
obo:bfo.owl
obo:BFO_0000144
process profile
obo:BFO_0000148
the moment at which a child is born
obo:BFO_0000148
the moment at which a finger is detached in an industrial accident
obo:BFO_0000148
the moment of death.
http://purl.obolibrary.org/obo/bfo/axiom/102-001
obo:BFO_0000148
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
http://purl.obolibrary.org/obo/bfo/axiom/102-001
obo:BFO_0000148
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
obo:BFO_0000148
obo:bfo.owl
obo:BFO_0000148
zero-dimensional temporal region
obo:BFO_0000179
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.
obo:BFO_0000179
Really of interest to developers only
obo:BFO_0000179
BFO OWL specification label
obo:BFO_0000180
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
obo:BFO_0000180
Person:Alan Ruttenberg
obo:BFO_0000180
Really of interest to developers only
obo:BFO_0000180
BFO CLIF specification label
http://purl.obolibrary.org/obo/bfo/axiom/138-001
obo:BFO_0000182
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])
obo:BFO_0000182
obo:bfo.owl
obo:BFO_0000182
history
obo:BFO_999999
John Beverley
obo:BFO_999999
Not sure if this has an IRI yet, so I supplied a placeholder.
obo:BFO_999999
occupies temporal region
obo:CARO_0000000
Material entity part of or substance produced by a multicellular organism with granularity above the level of a protein complex.
obo:CARO_0000000
Anatomical entities - like other material entities - may have immaterial parts.
obo:CARO_0000000
obo:caro.owl
obo:CARO_0000000
anatomical entity
obo:CHEBI_16991
Nucleic acid composed of nucleotides containing deoxyribose and linked by phosphodiester bonds.
obo:CHEBI_16991
http://purl.obolibrary.org/obo/chebi.owl
obo:CHEBI_16991
deoxyribonucleic acid
obo:CHEBI_23367
Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc.
obo:CHEBI_23367
obo:chebi.owl
obo:CHEBI_23367
molecular entity
obo:CHEBI_24432
Role inhering in a molecular entity or part of that entity, realized in biological processes.
obo:CHEBI_24432
http://purl.obolibrary.org/obo/chebi.owl
obo:CHEBI_24432
biological role
obo:CHEBI_33696
Macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases.
obo:CHEBI_33696
http://purl.obolibrary.org/obo/chebi.owl
obo:CHEBI_33696
nucleic acid
obo:CHEBI_33697
Nucleic acid composed of nucleotides containing ribose and linked by phosphodiester bonds.
obo:CHEBI_33697
http://purl.obolibrary.org/obo/chebi.owl
obo:CHEBI_33697
ribonucleic acid
obo:CHEBI_33839
Molecular entity of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
obo:CHEBI_33839
http://purl.obolibrary.org/obo/chebi.owl
obo:CHEBI_33839
macromolecule
obo:CHEBI_36080
Biological macromolecule consisting of one polypeptide chain synthesized at the ribosome.
obo:CHEBI_36080
http://purl.obolibrary.org/obo/chebi.owl
obo:CHEBI_36080
protein
obo:CHEBI_4705
DNA consisting of two parallel strands joined by hydrogen bonds between complementary purines and pyrimidines.
obo:CHEBI_4705
http://purl.obolibrary.org/obo/chebi.owl
obo:CHEBI_4705
double-stranded DNA
obo:CL_0000000
Material entity that is part of or derived from an organism, with maximally connected cell compartments surrounded by a plasma membrane.
obo:CL_0000000
This should be an inferred subclass of BFO:object. -John
obo:CL_0000000
obo:cl.owl
obo:CL_0000000
cell
obo:ERO_0000006
Processed material bearing a reagent role.
obo:ERO_0000006
http://purl.obolibrary.org/obo/ero.owl
obo:ERO_0000006
reagent
obo:ERO_0000008
Reagent that is comprised of immunoglobulins produced by B cells in response to an antigen.
obo:ERO_0000008
http://purl.obolibrary.org/obo/ero.owl
obo:ERO_0000008
antibody reagent
obo:ERO_0000337
Assay used to determine viral titers.
obo:ERO_0000337
http://purl.obolibrary.org/obo/ero.owl
obo:ERO_0000337
viral plaque assay
obo:ERO_0000347
Planned process used to influence one or more factors in a research study, and the independent variable in an interventional study wherein the influence is measured or evaluated.
obo:ERO_0000347
http://purl.obolibrary.org/obo/ero.owl
obo:ERO_0000347
John Beverley
obo:ERO_0000347
intervention
obo:ERO_0000671
Assay analyzing blood serum and other bodily fluids, to detect the presence of serum antibodies.
obo:ERO_0000671
http://purl.obolibrary.org/obo/ero.owl
obo:ERO_0000671
serology assay
obo:ERO_0001362
Assay measuring the concentration of a substance in a material by exploiting binding between an analyte and a corresponding detection antibody.
obo:ERO_0001362
http://purl.obolibrary.org/obo/ero.owl
obo:ERO_0001362
immunoassay
obo:FBdv_00005259
Temporal subdivision of a developmental process.
obo:FBdv_00005259
John Beverley
obo:FBdv_00005259
http://purl.obolibrary.org/obo/ido.owl
obo:FBdv_00005259
generative stage
obo:GEO_000000370
Material entity that is (1) a bona fide or fiat object part of the crust, any bodies of liquid on or contained within the crust, or planetary boundary layer (if present) of a terrestrial planet (including Earth), dwarf planet, exoplanet, natural satellite, planetesimal, or small Solar System body, and that (2) overlaps the planetary surface (including having a boundary that coincides with part of the planetary surface).
obo:GEO_000000370
http://purl.obolibrary.org/obo/GEO
obo:GEO_000000370
geographical entity
obo:GEO_000000371
Geographical entity that has at least one bona fide boundary.
obo:GEO_000000371
http://purl.obolibrary.org/obo/GEO
obo:GEO_000000371
geographical feature
obo:GEO_000000372
Geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface.
obo:GEO_000000372
http://purl.obolibrary.org/obo/GEO
obo:GEO_000000372
geographical region
obo:GO_0002250
Immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
obo:GO_0002250
obo:go.owl
obo:GO_0002250
adaptive immune response
obo:GO_0002443
Process involved in the carrying out of an immune response by a leukocyte.
obo:GO_0002443
obo:go.owl
obo:GO_0002443
leukocyte mediated immunity
obo:GO_0006955
Immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
obo:GO_0006955
obo:go.owl
obo:GO_0006955
immune response
obo:GO_0006959
Immune response mediated through a body fluid.
obo:GO_0006959
obo:go.owl
obo:GO_0006959
humoral immune response
obo:GO_0008150
Process specifically pertinent to the functioning of functionally integrated units.
obo:GO_0008150
obo:go.owl
obo:GO_0008150
biological process
obo:GO_0019028
Protein surrounding virion nucleic acid in some virus particles.
obo:GO_0019028
http://purl.obolibrary.org/obo/go.owl
obo:GO_0019028
viral capsid
obo:GO_0019031
Macromolecule lipid bilayer of a virion surrounding capsid.
obo:GO_0019031
http://purl.obolibrary.org/obo/go.owl
obo:GO_0019031
viral envelope
obo:GO_0019061
Virus generative stage during which an incoming virus is disassembled in the host cell to release a replication-competent viral genome.
obo:GO_0019061
http://purl.obolibrary.org/obo/go.owl
obo:GO_0019061
virus uncoating stage
obo:GO_0019062
Virus generative stage during which a virion protein binds to molecules on the host surface or host cell surface projection.
obo:GO_0019062
http://purl.obolibrary.org/obo/go.owl
obo:GO_0019062
virus attachment stage
obo:GO_0019068
Virus developmental stage during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed.
obo:GO_0019068
http://purl.obolibrary.org/obo/go.owl
obo:GO_0019068
virus synthesis stage
obo:GO_0019081
Virus generative stage during which viral mRNA is translated into viral protein, using the host cellular machinery.
obo:GO_0019081
http://purl.obolibrary.org/obo/go.owl
obo:GO_0019081
virus translation stage
obo:GO_0019083
Virus developmental stage during which a viral genome, or part of a viral genome, is transcribed within the host cell.
obo:GO_0019083
http://purl.obolibrary.org/obo/go.owl
obo:GO_0019083
virus transcription stage
obo:GO_0019814
Protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
obo:GO_0019814
obo:go.owl
obo:GO_0019814
immunoglobulin complex
obo:GO_0019815
Immunoglobulin complex present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
obo:GO_0019815
obo:go.owl
obo:GO_0019815
B cell receptor complex
obo:GO_0032502
Biological process whose specific outcome is the progression of a functional, integrated, unit.
obo:GO_0032502
obo:go.owl
obo:GO_0032502
developmental process
obo:GO_0032991
Stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
obo:GO_0032991
obo:go.owl
obo:GO_0032991
macromolecular complex
obo:GO_0042101
Protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
obo:GO_0042101
obo:go.owl
obo:GO_0042101
T cell receptor complex
obo:GO_0044403
Process carried out by gene products in an organism or acellular structure that enables the entity to engage in a symbiotic relationship with an organism.
obo:GO_0044403
John Beverley
obo:GO_0044403
http://purl.obolibrary.org/obo/go.owl
obo:GO_0044403
symbiotic process
obo:GO_0044406
Attachment of a symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly.
obo:GO_0044406
obo:go.owl
obo:GO_0044406
adhesion of symbiont to host
obo:GO_0044409
Penetration by an organism into the body, tissues, or cells of the host organism.
obo:GO_0044409
obo:go.owl
obo:GO_0044409
entry into host
obo:GO_0044411
Penetration by an organism into its host organism via active breaching of the physical barriers of the host organism.
obo:GO_0044411
obo:go.owl
obo:GO_0044411
entry into host through host barriers
obo:GO_0045087
Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
obo:GO_0045087
obo:go.owl
obo:GO_0045087
innate immune response
obo:GO_0046718
Virus generative stage during which a virion or viral nucleic acid breaches the barriers of a host.
obo:GO_0046718
http://purl.obolibrary.org/obo/go.owl
obo:GO_0046718
virus penetration stage
obo:GO_0046727
Protein subunit comprising viral capsid.
obo:GO_0046727
http://purl.obolibrary.org/obo/go.owl
obo:GO_0046727
capsomere
obo:GO_0048519
Process that stops, prevents, or reduces the frequency, rate or extent of a biological process.
obo:GO_0048519
obo:go.owl
obo:GO_0048519
negative regulation of biological process
obo:GO_0048525
Process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process in which a virus is a participant.
obo:GO_0048525
obo:go.owl
obo:GO_0048525
negative regulation of viral process
obo:GO_0050777
Process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
obo:GO_0050777
obo:go.owl
obo:GO_0050777
negative regulation of immune response
obo:GO_0051093
Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
obo:GO_0051093
obo:go.owl
obo:GO_0051093
negative regulation of developmental process
obo:GO_0051234
Process that localizes a substance or cellular component via movement, tethering or selective degradation.
obo:GO_0051234
obo:go.owl
obo:GO_0051234
establishment of localization
obo:GO_0065007
Process that modulates a measurable attribute of any biological process, quality or function.
obo:GO_0065007
obo:go.owl
obo:GO_0065007
biological regulation
obo:GO_19076
Virus generative stage involving dissemination of mature virus particles from the host cell, by cell lysis or the budding of virus particles from the cell membrane.
obo:GO_19076
http://purl.obolibrary.org/obo/go.owl
obo:GO_19076
virus release stage
obo:IAO_0000002
example to be eventually removed
obo:IAO_0000005
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.
obo:IAO_0000005
http://purl.obolibrary.org/obo/iao.owl
obo:IAO_0000005
objective specification
obo:IAO_0000007
Directive information entity that describes an action the bearer will take
obo:IAO_0000007
http://purl.obolibrary.org/obo/iao.owl
obo:IAO_0000007
action specification
obo:IAO_0000030
information content entity
obo:IAO_0000064
Plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
obo:IAO_0000064
http://purl.obolibrary.org/obo/iao.owl
obo:IAO_0000064
algorithm
obo:IAO_0000103
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
obo:IAO_0000103
Person:Alan Ruttenberg
obo:IAO_0000103
failed exploratory term
obo:IAO_0000104
Directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications.
obo:IAO_0000104
http://purl.obolibrary.org/obo/iao.owl
obo:IAO_0000104
plan specification
obo:IAO_0000111
editor preferred term
obo:IAO_0000111
obo:IAO_0000122
obo:IAO_0000111
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
obo:IAO_0000111
PERSON:Daniel Schober
obo:IAO_0000111
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
obo:IAO_0000111
obo:iao.owl
obo:IAO_0000111
editor preferred term
obo:IAO_0000112
example
obo:IAO_0000112
obo:IAO_0000122
obo:IAO_0000112
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.
obo:IAO_0000112
PERSON:Daniel Schober
obo:IAO_0000112
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
obo:IAO_0000112
obo:iao.owl
obo:IAO_0000112
example of usage
obo:IAO_0000113
in branch
obo:IAO_0000113
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
obo:IAO_0000113
GROUP:OBI
obo:IAO_0000113
OBI_0000277
obo:IAO_0000113
in branch
obo:IAO_0000114
has curation status
obo:IAO_0000114
PERSON:Alan Ruttenberg
obo:IAO_0000114
PERSON:Bill Bug
obo:IAO_0000114
PERSON:Melanie Courtot
obo:IAO_0000114
OBI_0000281
obo:IAO_0000114
has curation status
obo:IAO_0000115
definition
obo:IAO_0000115
obo:IAO_0000122
obo:IAO_0000115
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
obo:IAO_0000115
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
obo:IAO_0000115
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.
obo:IAO_0000115
PERSON:Daniel Schober
obo:IAO_0000115
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
obo:IAO_0000115
obo:iao.owl
obo:IAO_0000115
definition
obo:IAO_0000115
definition
obo:IAO_0000115
textual definition
obo:IAO_0000116
editor note
obo:IAO_0000116
obo:IAO_0000122
obo:IAO_0000116
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.
obo:IAO_0000116
PERSON:Daniel Schober
obo:IAO_0000116
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
obo:IAO_0000116
obo:iao.owl
obo:IAO_0000116
editor note
obo:IAO_0000117
term editor
obo:IAO_0000117
obo:IAO_0000122
obo:IAO_0000117
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
obo:IAO_0000117
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
obo:IAO_0000117
PERSON:Daniel Schober
obo:IAO_0000117
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
obo:IAO_0000117
obo:iao.owl
obo:IAO_0000117
term editor
obo:IAO_0000118
alternative term
obo:IAO_0000118
obo:IAO_0000125
obo:IAO_0000118
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
obo:IAO_0000118
PERSON:Daniel Schober
obo:IAO_0000118
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
obo:IAO_0000118
obo:iao.owl
obo:IAO_0000118
alternative term
obo:IAO_0000119
definition source
obo:IAO_0000119
obo:IAO_0000122
obo:IAO_0000119
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
obo:IAO_0000119
PERSON:Daniel Schober
obo:IAO_0000119
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
obo:IAO_0000119
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
obo:IAO_0000119
obo:iao.owl
obo:IAO_0000119
definition source
obo:IAO_0000120
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
obo:IAO_0000120
metadata complete
obo:IAO_0000121
term created to ease viewing/sort terms for development purpose, and will not be included in a release
obo:IAO_0000121
organizational term
obo:IAO_0000122
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
obo:IAO_0000122
ready for release
obo:IAO_0000123
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
obo:IAO_0000123
metadata incomplete
obo:IAO_0000124
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
obo:IAO_0000124
uncurated
obo:IAO_0000125
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
obo:IAO_0000125
pending final vetting
obo:IAO_0000224
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
obo:IAO_0000224
PERSON: Alan Ruttenberg
obo:IAO_0000224
PERSON: Melanie Courtot
obo:IAO_0000224
core
obo:IAO_0000226
placeholder removed
obo:IAO_0000227
An editor note should explain what were the merged terms and the reason for the merge.
obo:IAO_0000227
terms merged
obo:IAO_0000228
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
obo:IAO_0000228
term imported
obo:IAO_0000229
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
obo:IAO_0000229
term split
obo:IAO_0000231
has obsolescence reason
obo:IAO_0000231
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
obo:IAO_0000231
PERSON:Alan Ruttenberg
obo:IAO_0000231
PERSON:Melanie Courtot
obo:IAO_0000231
has obsolescence reason
obo:IAO_0000232
curator note
obo:IAO_0000232
obo:IAO_0000122
obo:IAO_0000232
An administrative note of use for a curator but of no use for a user
obo:IAO_0000232
PERSON:Alan Ruttenberg
obo:IAO_0000232
obo:iao.owl
obo:IAO_0000232
curator note
obo:IAO_0000233
term tracker item
obo:IAO_0000233
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
obo:IAO_0000233
obo:IAO_0000125
obo:IAO_0000233
An IRI or similar locator for a request or discussion of an ontology term.
obo:IAO_0000233
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
obo:IAO_0000233
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
obo:IAO_0000233
The 'tracker item' can associate a tracker with a specific ontology term.
obo:IAO_0000233
term tracker item
obo:IAO_0000234
obo:IAO_0000125
obo:IAO_0000234
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
obo:IAO_0000234
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
obo:IAO_0000234
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
obo:IAO_0000234
The 'term requester' can credit the person, organization or project who request the ontology term.
obo:IAO_0000234
ontology term requester
obo:IAO_0000410
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
obo:IAO_0000410
Alan Ruttenberg
obo:IAO_0000410
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
obo:IAO_0000410
universal
obo:IAO_0000411
is denotator type
obo:IAO_0000411
relates an class defined in an ontology, to the type of it's denotator
obo:IAO_0000411
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
obo:IAO_0000411
Alan Ruttenberg
obo:IAO_0000411
is denotator type
obo:IAO_0000412
imported from
obo:IAO_0000412
obo:IAO_0000125
obo:IAO_0000412
For external terms/classes, the ontology from which the term was imported
obo:IAO_0000412
PERSON:Alan Ruttenberg
obo:IAO_0000412
PERSON:Melanie Courtot
obo:IAO_0000412
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
obo:IAO_0000412
obo:iao.owl
obo:IAO_0000412
imported from
obo:IAO_0000420
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
obo:IAO_0000420
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
obo:IAO_0000420
Alan Ruttenberg
obo:IAO_0000420
defined class
obo:IAO_0000421
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
obo:IAO_0000421
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
obo:IAO_0000421
Alan Ruttenberg
obo:IAO_0000421
named class expression
obo:IAO_0000423
Terms with this status should eventually replaced with a term from another ontology.
obo:IAO_0000423
Alan Ruttenberg
obo:IAO_0000423
group:OBI
obo:IAO_0000423
to be replaced with external ontology term
obo:IAO_0000424
expand expression to
obo:IAO_0000424
ObjectProperty: RO_0002104
Label: has plasma membrane part
Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
obo:IAO_0000424
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
obo:IAO_0000424
Chris Mungall
obo:IAO_0000424
expand expression to
obo:IAO_0000425
expand assertion to
obo:IAO_0000425
ObjectProperty: RO???
Label: spatially disjoint from
Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
obo:IAO_0000425
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
obo:IAO_0000425
Chris Mungall
obo:IAO_0000425
expand assertion to
obo:IAO_0000426
first order logic expression
obo:IAO_0000426
PERSON:Alan Ruttenberg
obo:IAO_0000426
first order logic expression
obo:IAO_0000427
antisymmetric property
obo:IAO_0000427
part_of antisymmetric property xsd:true
obo:IAO_0000427
use boolean value xsd:true to indicate that the property is an antisymmetric property
obo:IAO_0000427
Alan Ruttenberg
obo:IAO_0000427
antisymmetric property
obo:IAO_0000428
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
obo:IAO_0000428
Alan Ruttenberg
obo:IAO_0000428
group:OBI
obo:IAO_0000428
requires discussion
obo:IAO_0000589
OBO foundry unique label
obo:IAO_0000589
obo:IAO_0000125
obo:IAO_0000589
An alternative name for a class or property which is unique across the OBO Foundry.
obo:IAO_0000589
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
obo:IAO_0000589
PERSON:Alan Ruttenberg
obo:IAO_0000589
PERSON:Bjoern Peters
obo:IAO_0000589
PERSON:Chris Mungall
obo:IAO_0000589
PERSON:Melanie Courtot
obo:IAO_0000589
GROUP:OBO Foundry <http://obofoundry.org/>
obo:IAO_0000589
OBO foundry unique label
obo:IAO_0000596
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"
obo:IAO_0000596
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
obo:IAO_0000596
Person:Alan Ruttenberg
obo:IAO_0000596
has ID digit count
obo:IAO_0000597
Datatype: idrange:1
Annotations: 'has ID range allocated to': "Chris Mungall"
EquivalentTo: xsd:integer[> 2151 , <= 2300]
obo:IAO_0000597
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
obo:IAO_0000597
Person:Alan Ruttenberg
obo:IAO_0000597
has ID range allocated to
obo:IAO_0000598
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"
obo:IAO_0000598
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
obo:IAO_0000598
Person:Alan Ruttenberg
obo:IAO_0000598
has ID policy for
obo:IAO_0000599
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/>
Annotations:
'has ID prefix': "http://purl.obolibrary.org/obo/RO_"
'has ID digit count' : 7,
rdfs:label "RO id policy"
'has ID policy for': "RO"
obo:IAO_0000599
Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created.
obo:IAO_0000599
Person:Alan Ruttenberg
obo:IAO_0000599
has ID prefix
obo:IAO_0000600
elucidation
obo:IAO_0000600
person:Alan Ruttenberg
obo:IAO_0000600
Person:Barry Smith
obo:IAO_0000600
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
obo:IAO_0000600
obo:iao.owl
obo:IAO_0000600
elucidation
obo:IAO_0000601
has associated axiom(nl)
obo:IAO_0000601
Person:Alan Ruttenberg
obo:IAO_0000601
Person:Alan Ruttenberg
obo:IAO_0000601
An axiom associated with a term expressed using natural language
obo:IAO_0000601
obo:iao.owl
obo:IAO_0000601
has associated axiom(nl)
obo:IAO_0000602
has associated axiom(fol)
obo:IAO_0000602
Person:Alan Ruttenberg
obo:IAO_0000602
Person:Alan Ruttenberg
obo:IAO_0000602
An axiom expressed in first order logic using CLIF syntax
obo:IAO_0000602
obo:iao.owl
obo:IAO_0000602
has associated axiom(fol)
obo:IAO_0000603
is allocated id range
obo:IAO_0000603
Add as annotation triples in the granting ontology
obo:IAO_0000603
Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
obo:IAO_0000603
PERSON:Alan Ruttenberg
obo:IAO_0000603
is allocated id range
obo:IAO_0010000
has axiom id
obo:IAO_0010000
Person:Alan Ruttenberg
obo:IAO_0010000
Person:Alan Ruttenberg
obo:IAO_0010000
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
obo:IAO_0010000
obo:iao.owl
obo:IAO_0010000
has axiom label
obo:IAO_0100001
term replaced by
obo:IAO_0100001
obo:IAO_0000125
obo:IAO_0100001
Add as annotation triples in the granting ontology
obo:IAO_0100001
Use on obsolete terms, relating the term to another term that can be used as a substitute
obo:IAO_0100001
Person:Alan Ruttenberg
obo:IAO_0100001
Person:Alan Ruttenberg
obo:IAO_0100001
term replaced by
obo:IDO-COVID-19_0001287
John Beverley
obo:IDO-COVID-19_0001287
SARS-COV-2 Infection
obo:IDO-COVID-19_0001301
John Beverley
obo:IDO-COVID-19_0001301
United States
obo:IDO-COVID-19_0001302
John Beverley
obo:IDO-COVID-19_0001302
Canada
obo:IDO-COVID-19_0001362
Virus which infects and replicates within or on fungi.
obo:IDO-COVID-19_0001362
http://purl.obolibrary.org/obo/vido.owl
obo:IDO-COVID-19_0001362
John Beverley
obo:IDO-COVID-19_0001362
mycovirus
obo:IDO_0000400
A role borne by an organism in symbiosis.
obo:IDO_0000400
Albert Goldfain
obo:IDO_0000400
Alexander Diehl
obo:IDO_0000400
Lindsay Cowell
obo:IDO_0000400
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000400
symbiont role
obo:IDO_0000401
Symbiont role borne by an organism in which both symbionts derive a growth, survival, or fitness advantage from symbiosis.
obo:IDO_0000401
Albert Goldfain
obo:IDO_0000401
Alexander Diehl
obo:IDO_0000401
Lindsay Cowell
obo:IDO_0000401
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000401
mutualist role
obo:IDO_0000402
Symbiont role borne by an organism that derives a growth, survival, or fitness advantage from symbiosis, while the other symbiont is neither advantaged nor disadvantaged.
obo:IDO_0000402
Albert Goldfain
obo:IDO_0000402
Alexander Diehl
obo:IDO_0000402
Lindsay Cowell
obo:IDO_0000402
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000402
commensal role
obo:IDO_0000403
Symbiont role borne by an organism that derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced.
obo:IDO_0000403
Albert Goldfain
obo:IDO_0000403
Alexander Diehl
obo:IDO_0000403
Lindsay Cowell
obo:IDO_0000403
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000403
parasite role
obo:IDO_0000406
Infectious disposition to become part of a disorder only in organisms whose defenses are compromised.
obo:IDO_0000406
Albert Goldfain
obo:IDO_0000406
Alexander Diehl
obo:IDO_0000406
Lindsay Cowell
obo:IDO_0000406
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000406
opportunistic infectious disposition
obo:IDO_0000407
Infectious disposition to become part of a disorder in immunocompetent organisms.
obo:IDO_0000407
Albert Goldfain
obo:IDO_0000407
Alexander Diehl
obo:IDO_0000407
Lindsay Cowell
obo:IDO_0000407
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000407
A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts.
obo:IDO_0000407
primary infectious disposition
obo:IDO_0000408
Host role borne by an organism whose extended organism provides an environment supportive for the survival, growth, maturation, or reproduction of an object contained as a proper part.
obo:IDO_0000408
Albert Goldfain
obo:IDO_0000408
Alexander Diehl
obo:IDO_0000408
Lindsay Cowell
obo:IDO_0000408
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000408
symbiont host role
obo:IDO_0000409
Symbiont host role borne by an organism iwhose partner in symbiosis reaches developmental maturity or reproduces sexually in the host.
obo:IDO_0000409
Albert Goldfain
obo:IDO_0000409
Alexander Diehl
obo:IDO_0000409
Lindsay Cowell
obo:IDO_0000409
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000409
definitive host role
obo:IDO_0000410
Symbiont host role borne by an organism whose partner in symbiosis utilizes the host to undergo a developmental stage transition, and the host is required for continuation of the partner's life cycle.
obo:IDO_0000410
Albert Goldfain
obo:IDO_0000410
Alexander Diehl
obo:IDO_0000410
Lindsay Cowell
obo:IDO_0000410
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000410
intermediate host role
obo:IDO_0000412
Symbiont host role borne by an organism whose partner in symbiosis has the infectious disposition but cannot be transmitted from the host to the partner's definitive host.
obo:IDO_0000412
Albert Goldfain
obo:IDO_0000412
Alexander Diehl
obo:IDO_0000412
Lindsay Cowell
obo:IDO_0000412
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000412
dead-end host role
obo:IDO_0000414
Pathogen host role borne by an organism whose extended organism contains an infectious agent.
obo:IDO_0000414
Albert Goldfain
obo:IDO_0000414
Alexander Diehl
obo:IDO_0000414
Lindsay Cowell
obo:IDO_0000414
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000414
infectious agent host role
obo:IDO_0000415
Host role borne by an organism or acellular structure having a pathogen as part.
obo:IDO_0000415
Albert Goldfain
obo:IDO_0000415
Alexander Diehl
obo:IDO_0000415
Lindsay Cowell
obo:IDO_0000415
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000415
pathogen host role
obo:IDO_0000419
A pathogen vector role borne by an organism in virtue of the fact that the pathogen does not multiply in or on the vector.
obo:IDO_0000419
Albert Goldfain
obo:IDO_0000419
Alexander Diehl
obo:IDO_0000419
Lindsay Cowell
obo:IDO_0000419
passive carrier
obo:IDO_0000419
mechanical vector role
obo:IDO_0000420
A pathogen vector role borne by an organism in virtue of the fact that the pathogen multiplies in the vector.
obo:IDO_0000420
Albert Goldfain
obo:IDO_0000420
Alexander Diehl
obo:IDO_0000420
Lindsay Cowell
obo:IDO_0000420
biological vector role
obo:IDO_0000421
A pathogen transporter role borne by an entity in virtue of the fact that the entity is not a complete organism.
obo:IDO_0000421
I don't understand the rdfs comment indicating drinking water bears the infected agent vehicle role, but neither of the subtypes. Presumably, if an infectious agent is present in drinking water, then it bears a fomite role. Drinking water is, in fact, a classic example. -John Beverley
obo:IDO_0000421
I've expanded this definition and label to cover infectious agent pathogens and infectious structure pathogens. -John Beverley
obo:IDO_0000421
Albert Goldfain
obo:IDO_0000421
Alexander Diehl
obo:IDO_0000421
Lindsay Cowell
obo:IDO_0000421
Drinking water bears the infectious agent vehicle role, but does not bear either of the subtype roles.
obo:IDO_0000421
pathogen vehicle role
obo:IDO_0000422
A pathogen vehicle role borne by an entity in virtue of the fact that the entity is living or contains living cells other than those that have the infectious disposition.
obo:IDO_0000422
Albert Goldfain
obo:IDO_0000422
Alexander Diehl
obo:IDO_0000422
Lindsay Cowell
obo:IDO_0000422
Examples include blood, serum, tissue, or fresh produce.
obo:IDO_0000422
biological vehicle role
obo:IDO_0000423
An infectious agent vehicle role borne by an entity in virtue of the fact that the entity is not alive.
obo:IDO_0000423
Albert Goldfain
obo:IDO_0000423
Alexander Diehl
obo:IDO_0000423
Lindsay Cowell
obo:IDO_0000423
fomite role
obo:IDO_0000424
Role borne by a material entity in which pathogens can persist, and from which they can be transmitted to hosts.
obo:IDO_0000424
Albert Goldfain
obo:IDO_0000424
Alexander Diehl
obo:IDO_0000424
Lindsay Cowell
obo:IDO_0000424
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000424
reservoir of pathogen role
obo:IDO_0000425
Disposition borne by a biological macromolecule produced by a pathogen that is a disposition to undergo processes that increase the pathogen's virulence.
obo:IDO_0000425
Albert Goldfain
obo:IDO_0000425
Alexander Diehl
obo:IDO_0000425
Lindsay Cowell
obo:IDO_0000425
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000425
The virulence factor disposition is typically realized in processes that improve survival of the pathogen in a host, increase the likelihood of transmission to a host, or cause pathological processes in a host.
obo:IDO_0000425
virulence factor disposition
obo:IDO_0000426
Disposition to cause I) malfunction of cells, ii) damage to extracellular matrix, or iii) damage of cells to a degree that can result in cell death.
obo:IDO_0000426
Albert Goldfain
obo:IDO_0000426
Alexander Diehl
obo:IDO_0000426
Lindsay Cowell
obo:IDO_0000426
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000426
toxin disposition
obo:IDO_0000427
Toxin disposition to damage cells or extracellular matrix by a direct enzymatic process.
obo:IDO_0000427
Albert Goldfain
obo:IDO_0000427
Alexander Diehl
obo:IDO_0000427
Lindsay Cowell
obo:IDO_0000427
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000427
exotoxin disposition
obo:IDO_0000430
Role borne by an anatomical entity that serves as the site through which a pathogen enters a host.
obo:IDO_0000430
Albert Goldfain
obo:IDO_0000430
Alexander Diehl
obo:IDO_0000430
Lindsay Cowell
obo:IDO_0000430
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000430
pathogen portal of entry role
obo:IDO_0000431
Role borne by an anatomical entity that serves as the site through which a pathogen exits a host.
obo:IDO_0000431
Albert Goldfain
obo:IDO_0000431
Alexander Diehl
obo:IDO_0000431
Lindsay Cowell
obo:IDO_0000431
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000431
pathogen portal of exit role
obo:IDO_0000434
Role borne by an infectious disorder whose host has another, distinct, infectious disorder - neither arising from the other through metastasis - which emerged after this infectious disorder was established due to increased host susceptibility to infectious disorders.
obo:IDO_0000434
Albert Goldfain
obo:IDO_0000434
Alexander Diehl
obo:IDO_0000434
Lindsay Cowell
obo:IDO_0000434
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000434
primary infection role
obo:IDO_0000435
Role borne by an infectious disorder whose host has another, distinct, primary infectious disorder - neither arising from the other through metastasis - which emerged after the primary infectious disorder was established due to increased host susceptibility to infectious disorders.
obo:IDO_0000435
Albert Goldfain
obo:IDO_0000435
Alexander Diehl
obo:IDO_0000435
Lindsay Cowell
obo:IDO_0000435
secondary infection role
obo:IDO_0000436
Disease whose physical basis is an infectious disorder.
obo:IDO_0000436
Albert Goldfain
obo:IDO_0000436
Alexander Diehl
obo:IDO_0000436
Lindsay Cowell
obo:IDO_0000436
tranmissible disease
obo:IDO_0000436
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000436
infectious disease
obo:IDO_0000437
Disposition borne by a macromolecule that is the disposition to participate in adherence to a host.
obo:IDO_0000437
Albert Goldfain
obo:IDO_0000437
Alexander Diehl
obo:IDO_0000437
Lindsay Cowell
obo:IDO_0000437
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000437
adhesion disposition
obo:IDO_0000438
Disposition borne by a biological macromolecule that is the disposition to facilitate breach of and entry through host barriers.
obo:IDO_0000438
Albert Goldfain
obo:IDO_0000438
Alexander Diehl
obo:IDO_0000438
Lindsay Cowell
obo:IDO_0000438
Invasion factor; invasin
obo:IDO_0000438
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000438
invasion disposition
obo:IDO_0000444
Disposition inhering in an acellular structure or organism, with a part having a disposition to mitigate damage to the entity from invasive or internal threats, which is realized in one or more negative biological regulation process.
obo:IDO_0000444
Albert Goldfain
obo:IDO_0000444
Alexander Diehl
obo:IDO_0000444
Lindsay Cowell
obo:IDO_0000444
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000444
Examples include the following: CCR5 mutations protect T cells from HIV invasion. A tumor cell's resistance to chemotherapy protects the cell from damage by the drug (although this harms the patient). An insect's resistance to insecticide protects it from the insecticide.
obo:IDO_0000444
protective resistance
obo:IDO_0000445
Protective resistance that mitigates the damaging effects of a drug.
obo:IDO_0000445
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000445
Albert Goldfain
obo:IDO_0000445
Alexander Diehl
obo:IDO_0000445
Lindsay Cowell
obo:IDO_0000445
resistance to drug
obo:IDO_0000446
Protective resistance that inheres in an organism and mitigates the damaging effects of a pathogen.
obo:IDO_0000446
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000446
Albert Goldfain
obo:IDO_0000446
Alexander Diehl
obo:IDO_0000446
Lindsay Cowell
obo:IDO_0000446
resistance to pathogen
obo:IDO_0000447
Collective resistance disposition that inheres in an organism population where the proportion of the population with immunity to an infectious agent is high resulting in a low number of transmissions from hosts to susceptible individuals.
obo:IDO_0000447
Albert Goldfain
obo:IDO_0000447
Alexander Diehl
obo:IDO_0000447
Lindsay Cowell
obo:IDO_0000447
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000447
herd immunity to infectious organism
obo:IDO_0000448
Resistance to pathogen that inheres in an organism due to immune system components in its extended organism.
obo:IDO_0000448
Albert Goldfain
obo:IDO_0000448
Alexander Diehl
obo:IDO_0000448
Lindsay Cowell
obo:IDO_0000448
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000448
immunity to pathogen
obo:IDO_0000449
Immunity to pathogen that results in elimination of the infectious agent from the host.
obo:IDO_0000449
Albert Goldfain
obo:IDO_0000449
Alexander Diehl
obo:IDO_0000449
Lindsay Cowell
obo:IDO_0000449
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000449
Sterilizing immunity is typically conferred by neutralizing antibodies.
obo:IDO_0000449
sterilizing immunity to infectious agent
obo:IDO_0000450
Disposition borne by a material entity to establish localization in or produce toxins that can be transmitted to an organism or acellular structure, either of which may form disorder in the entity or immunocompetent members of the entity’s species.
obo:IDO_0000450
Albert Goldfain
obo:IDO_0000450
Alexander Diehl
obo:IDO_0000450
Lindsay Cowell
obo:IDO_0000450
pathogenicity
obo:IDO_0000450
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000450
pathogenic disposition
obo:IDO_0000451
Disposition borne by a pathogen that is the disposition to penetrate the epithelial barriers of an organism of another species.
obo:IDO_0000451
Albert Goldfain
obo:IDO_0000451
Alexander Diehl
obo:IDO_0000451
Lindsay Cowell
obo:IDO_0000451
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000451
invasive disposition
obo:IDO_0000453
Infectious disposition to be transmitted from an infected, non-human host to a human host.
obo:IDO_0000453
Albert Goldfain
obo:IDO_0000453
Alexander Diehl
obo:IDO_0000453
Lindsay Cowell
obo:IDO_0000453
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000453
zoonotic disposition
obo:IDO_0000454
Infectious disposition to be transmitted from an infected, human host to a non-human host.
obo:IDO_0000454
Albert Goldfain
obo:IDO_0000454
Alexander Diehl
obo:IDO_0000454
Lindsay Cowell
obo:IDO_0000454
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000454
An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis.
obo:IDO_0000454
reverse zoonotic disposition
obo:IDO_0000455
Disposition that inheres in a collection of entities in virtue of the individual dispositions of the constituents of that collection.
obo:IDO_0000455
Albert Goldfain
obo:IDO_0000455
Alexander Diehl
obo:IDO_0000455
Lindsay Cowell
obo:IDO_0000455
This should be pushed up to: http://purl.obolibrary.org/obo/bfo.owl
obo:IDO_0000455
collective disposition
obo:IDO_0000456
Organism that is experiencing immunosuppression.
obo:IDO_0000456
Albert Goldfain
obo:IDO_0000456
Alexander Diehl
obo:IDO_0000456
Lindsay Cowell
obo:IDO_0000456
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000456
immunosuppressed organism
obo:IDO_0000457
Organism that has immunocompetence.
obo:IDO_0000457
Albert Goldfain
obo:IDO_0000457
Alexander Diehl
obo:IDO_0000457
Lindsay Cowell
obo:IDO_0000457
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000457
immunocompetent organism
obo:IDO_0000458
Disposition that inheres in a pathogen host and is a disposition to horizontally transmit that pathogen to organisms of the same species as the host, through casual contact, with a high likelihood of realization.
obo:IDO_0000458
Albert Goldfain
obo:IDO_0000458
Alexander Diehl
obo:IDO_0000458
Lindsay Cowell
obo:IDO_0000458
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000458
contagiousness
obo:IDO_0000459
Host that contains a colony in or on its extended organism.
obo:IDO_0000459
Albert Goldfain
obo:IDO_0000459
Alexander Diehl
obo:IDO_0000459
Lindsay Cowell
obo:IDO_0000459
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000459
colonized host
obo:IDO_0000463
Quality that inheres in an infectious agent or infectious structure and is the likelihood that the agent or structure will undergo a horizontal transmission process.
obo:IDO_0000463
Albert Goldfain
obo:IDO_0000463
Alexander Diehl
obo:IDO_0000463
Lindsay Cowell
obo:IDO_0000463
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000463
The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening.
obo:IDO_0000463
infectious pathogen transmissibility
obo:IDO_0000464
Quality that inheres in a pathogen and is the liklihood that the infectious disposition will be realized upon exposure of a susceptible organism.
obo:IDO_0000464
Albert Goldfain
obo:IDO_0000464
Alexander Diehl
obo:IDO_0000464
Lindsay Cowell
obo:IDO_0000464
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000464
This quality is measured by the proportion of exposed who become infected.
obo:IDO_0000464
infectivity
obo:IDO_0000466
Quality that inheres in a pathogen and is the degree to which realizations of the infectious disease caused by the pathogen become severe or fatal.
obo:IDO_0000466
Albert Goldfain
obo:IDO_0000466
Alexander Diehl
obo:IDO_0000466
Lindsay Cowell
obo:IDO_0000466
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000466
This quality is measured by the proportion of clinically apparent cases that are severe or fatal.
obo:IDO_0000466
virulence
obo:IDO_0000467
Quality that inheres in an entity and is the degree to which it can be harmed by another entity.
obo:IDO_0000467
Albert Goldfain
obo:IDO_0000467
Alexander Diehl
obo:IDO_0000467
Lindsay Cowell
obo:IDO_0000467
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000467
Low susceptibility is often referred to as resistance. In this sense, resistance is a quality.
obo:IDO_0000467
susceptibility
obo:IDO_0000468
Susceptibility that inheres in an organism and is the degree to which it can be harmed by an infectious agent.
obo:IDO_0000468
Albert Goldfain
obo:IDO_0000468
Alexander Diehl
obo:IDO_0000468
Lindsay Cowell
obo:IDO_0000468
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000468
susceptibility to infectious agent
obo:IDO_0000469
Susceptibility that is the degree to which an entity can be harmed or inhibited from surviving by a drug.
obo:IDO_0000469
Albert Goldfain
obo:IDO_0000469
Alexander Diehl
obo:IDO_0000469
Lindsay Cowell
obo:IDO_0000469
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000469
drug susceptibility
obo:IDO_0000470
Drug susceptibility that inheres in an infectious agent and is the degree to which the infectious agent can be harmed or inhibited from surviving by a drug.
obo:IDO_0000470
Albert Goldfain
obo:IDO_0000470
Alexander Diehl
obo:IDO_0000470
Lindsay Cowell
obo:IDO_0000470
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000470
drug susceptibility of infectious agent
obo:IDO_0000471
Infection comprised of infectious organisms from different species.
obo:IDO_0000471
John Beverley
obo:IDO_0000471
complex infection
obo:IDO_0000472
Infection in which pathogen parts persist in the extracellular space of the host.
obo:IDO_0000472
Albert Goldfain
obo:IDO_0000472
Alexander Diehl
obo:IDO_0000472
Lindsay Cowell
obo:IDO_0000472
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000472
extracellular infection
obo:IDO_0000473
Infection in which pathogen parts persist inside host cells.
obo:IDO_0000473
Albert Goldfain
obo:IDO_0000473
Alexander Diehl
obo:IDO_0000473
Lindsay Cowell
obo:IDO_0000473
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000473
intracellular infection
obo:IDO_0000474
Infection for which the infectious agents or structures that are part of the infection are distributed throughout the host.
obo:IDO_0000474
John Beverley
obo:IDO_0000474
systematic infection
obo:IDO_0000475
Infection for which the infectious agents or structures that are part of the infection are limited to a relatively small area of the host's body.
obo:IDO_0000475
local infection
obo:IDO_0000477
Infectious disease course that begins soon after infection is established and progresses rapidly to severe stages.
obo:IDO_0000477
Albert Goldfain
obo:IDO_0000477
Alexander Diehl
obo:IDO_0000477
Lindsay Cowell
obo:IDO_0000477
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000477
acute infectious disease course
obo:IDO_0000479
Quality that inheres in an organism population and is the number of realizations of an infectious disease for which the infectious disease course begins during a specified period of time.
obo:IDO_0000479
Albert Goldfain
obo:IDO_0000479
Alexander Diehl
obo:IDO_0000479
Lindsay Cowell
obo:IDO_0000479
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000479
A particular instance of infectious disease incidence will depend on a type of infectious disease, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure.
obo:IDO_0000479
infectious disease incidence
obo:IDO_0000480
Quality that inheres in an organism population and is the number of organisms in the population that become infected with a pathogen during a specified period of time.
obo:IDO_0000480
Albert Goldfain
obo:IDO_0000480
Alexander Diehl
obo:IDO_0000480
Lindsay Cowell
obo:IDO_0000480
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000480
A particular instance of infection incidence will depend on a type of infectious agent, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure.
obo:IDO_0000480
infection incidence
obo:IDO_0000481
Quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time and in whom the infectious disease begins during the specified period of time.
obo:IDO_0000481
Albert Goldfain
obo:IDO_0000481
Alexander Diehl
obo:IDO_0000481
Lindsay Cowell
obo:IDO_0000481
cumulative incidence of infectious disease
obo:IDO_0000481
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000481
An instance of infectious disease incidence proportion is measured by dividing a measure of an instance of infectious disease incidence by the number of members of the population in which the infectious disease course had not begun at the beginning of the specified period of time over which the incidence was measured.
obo:IDO_0000481
infectious disease incidence proportion
obo:IDO_0000482
Quality that inheres in an organism population and is the proportion of members of the population not infected at the beginning of a specified period of time who become infected during the specified period of time.
obo:IDO_0000482
Albert Goldfain
obo:IDO_0000482
Alexander Diehl
obo:IDO_0000482
Lindsay Cowell
obo:IDO_0000482
cumulative incidence of infection
obo:IDO_0000482
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000482
An instance of infection incidence proportion is measured by dividing a measure of an instance of infection incidence by the number of members of the population not infected at the beginning of the specified period of time over which the incidence was measured.
obo:IDO_0000482
infection incidence proportion
obo:IDO_0000483
Quality that inheres in an organism population and is the infectious disease incidence proportion per unit time.
obo:IDO_0000483
Albert Goldfain
obo:IDO_0000483
Alexander Diehl
obo:IDO_0000483
Lindsay Cowell
obo:IDO_0000483
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000483
An instance of infectious disease incidence rate is measured by dividing a measure of an instance of the infectious disease incidence proportion by the length of the period of time over which the incidence was measured.
obo:IDO_0000483
infectious disease incidence rate
obo:IDO_0000484
Quality that inheres in an organism population and is the infection incidence proportion per unit time.
obo:IDO_0000484
Albert Goldfain
obo:IDO_0000484
Alexander Diehl
obo:IDO_0000484
Lindsay Cowell
obo:IDO_0000484
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000484
An instance of infection incidence rate is measured by dividing a measure of an instance of infection incidence proportion by the length of the period of time over which the incidence was measured.
obo:IDO_0000484
infection incidence rate
obo:IDO_0000485
Quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time.
obo:IDO_0000485
Albert Goldfain
obo:IDO_0000485
Alexander Diehl
obo:IDO_0000485
Lindsay Cowell
obo:IDO_0000485
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000485
Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease prevalence will depend on a type of infectious disease, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics.
obo:IDO_0000485
infectious disease prevalence
obo:IDO_0000486
Quality that inheres in an organism population and is the number of organisms in the population infected with a pathogen at a specified time.
obo:IDO_0000486
Albert Goldfain
obo:IDO_0000486
Alexander Diehl
obo:IDO_0000486
Lindsay Cowell
obo:IDO_0000486
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000486
Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infection prevalence will depend on a type of infectious agent, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics.
obo:IDO_0000486
infection prevalence
obo:IDO_0000487
Quality that inheres in an organism population and is the number of organisms in the population who have, at any point during their lives, been bearers of an infectious disease and experienced realization of the disease.
obo:IDO_0000487
Albert Goldfain
obo:IDO_0000487
Alexander Diehl
obo:IDO_0000487
Lindsay Cowell
obo:IDO_0000487
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000487
Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease lifetime prevalence will depend on a type of infectious disease and a population. Actual measures of prevalence are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics.
obo:IDO_0000487
infectious disease lifetime prevalence
obo:IDO_0000488
Quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for a pathogen in their serum at a specified time.
obo:IDO_0000488
Albert Goldfain
obo:IDO_0000488
Alexander Diehl
obo:IDO_0000488
Lindsay Cowell
obo:IDO_0000488
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000488
Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious agent seroprevalence will depend on a type of infectious agent and a population. Actual measures of seroprevalence are based only on tested individuals and usually specify a geographic location. Other constraints may include population demographics.
obo:IDO_0000488
pathogen seroprevalence
obo:IDO_0000489
Quality that inheres in an organism population and is the per capita number of deaths in the population resulting from an infectious disease over a specified period of time.
obo:IDO_0000489
Albert Goldfain
obo:IDO_0000489
Alexander Diehl
obo:IDO_0000489
Lindsay Cowell
obo:IDO_0000489
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000489
A particular instance of infectious disease mortality rate will depend on a type of infectious disease and a population. Actual measures of mortality rate are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. Mortality rate is typically expressed in units of deaths per 1000 individuals per year.
obo:IDO_0000489
infectious disease mortality rate
obo:IDO_0000490
Quality that inheres in an organism population in virtue of the fact that infections of the type that causes an infectious disease are maintained in the population via intra-population transmission or by transmission from a local reservoir.
obo:IDO_0000490
Albert Goldfain
obo:IDO_0000490
Alexander Diehl
obo:IDO_0000490
Lindsay Cowell
obo:IDO_0000490
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000490
A particular instance of infectious disease endemicity will depend on a type of infectious agent and a population. The population may be specified by temporal, geographic, or demographic constraints. Infectious diseases that are typical or common to a particular population are referred to as endemic.
obo:IDO_0000490
infectious disease endemicity
obo:IDO_0000494
Quality that inheres in an organism population by virtue of the fact that realizations of an infectious disease occur in the population with a fluctuating prevalence.
obo:IDO_0000494
Albert Goldfain
obo:IDO_0000494
Alexander Diehl
obo:IDO_0000494
Lindsay Cowell
obo:IDO_0000494
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000494
Sporadic quality of infectious disease is relational to previous prevalence of the disease.
obo:IDO_0000494
infectious disease sporadicity
obo:IDO_0000495
Disease course that is the realization of an infectious disease.
obo:IDO_0000495
Albert Goldfain
obo:IDO_0000495
Alexander Diehl
obo:IDO_0000495
Lindsay Cowell
obo:IDO_0000495
infectious disease course
obo:IDO_0000496
Chronic infectious disease course that does not progress to severe stages for a long period of time.
obo:IDO_0000496
Albert Goldfain
obo:IDO_0000496
Alexander Diehl
obo:IDO_0000496
Lindsay Cowell
obo:IDO_0000496
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000496
long-term non-progressing infectious disease course
obo:IDO_0000497
Process by which an organism acquires immunity to an infectious agent.
obo:IDO_0000497
Albert Goldfain
obo:IDO_0000497
Alexander Diehl
obo:IDO_0000497
Lindsay Cowell
obo:IDO_0000497
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000497
immunization against infectious agent
obo:IDO_0000498
Immunization that begins with exposure of an organism to antigen and results in immunity against an infectious agent.
obo:IDO_0000498
Albert Goldfain
obo:IDO_0000498
Alexander Diehl
obo:IDO_0000498
Lindsay Cowell
obo:IDO_0000498
inoculation
obo:IDO_0000498
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000498
active immunization against infectious agent
obo:IDO_0000499
Active immunization that begins with exposure of an organism to a vaccine.
obo:IDO_0000499
Albert Goldfain
obo:IDO_0000499
Alexander Diehl
obo:IDO_0000499
Lindsay Cowell
obo:IDO_0000499
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000499
vaccination against infectious agent
obo:IDO_0000500
Active immunization that begins with exposure to smallpox in the form of a scab from a pustule and results in immunity against smallpox.
obo:IDO_0000500
Albert Goldfain
obo:IDO_0000500
Alexander Diehl
obo:IDO_0000500
Lindsay Cowell
obo:IDO_0000500
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000500
variolation
obo:IDO_0000501
Immunization that begins with transfer to an organism of molecules not produced by that organism and that confer immunity against an infectious agent.
obo:IDO_0000501
Albert Goldfain
obo:IDO_0000501
Alexander Diehl
obo:IDO_0000501
Lindsay Cowell
obo:IDO_0000501
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000501
passive immunization against infectious agent
obo:IDO_0000502
Process of infectious disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population.
obo:IDO_0000502
Albert Goldfain
obo:IDO_0000502
Alexander Diehl
obo:IDO_0000502
Lindsay Cowell
obo:IDO_0000502
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000502
infectious disease epidemic
obo:IDO_0000503
Process in which multiple infectious disease epidemics of the same type of infectious disease unfold over overlapping periods of time and affect organism populations located in different geographic regions, including different countries and continents.
obo:IDO_0000503
Albert Goldfain
obo:IDO_0000503
Alexander Diehl
obo:IDO_0000503
Lindsay Cowell
obo:IDO_0000503
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000503
infectious disease pandemic
obo:IDO_0000504
Disorder that is part of an extended organism which has an infectious pathogen part, that exists as a result of a process of formation of disorder initiated by the infectious pathogen.
obo:IDO_0000504
Albert Goldfain
obo:IDO_0000504
Alexander Diehl
obo:IDO_0000504
Lindsay Cowell
obo:IDO_0000504
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000504
infectious disorder
obo:IDO_0000506
Infection that has as part bacteria located in the blood.
obo:IDO_0000506
Albert Goldfain
obo:IDO_0000506
Alexander Diehl
obo:IDO_0000506
Lindsay Cowell
obo:IDO_0000506
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000506
bacteremia
obo:IDO_0000509
obo:ido.owl
obo:IDO_0000509
Aggregate of organisms of the same species.
obo:IDO_0000509
Albert Goldfain
obo:IDO_0000509
Alexander Diehl
obo:IDO_0000509
Lindsay Cowell
obo:IDO_0000509
The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age.
obo:IDO_0000509
organism population
obo:IDO_0000511
obo:ido.owl
obo:IDO_0000511
Organism population whose members have an infection.
obo:IDO_0000511
Albert Goldfain
obo:IDO_0000511
Alexander Diehl
obo:IDO_0000511
Lindsay Cowell
obo:IDO_0000511
infected population
obo:IDO_0000512
obo:ido.owl
obo:IDO_0000512
Organism population in whose members an infectious disease is being realized.
obo:IDO_0000512
Albert Goldfain
obo:IDO_0000512
Alexander Diehl
obo:IDO_0000512
Lindsay Cowell
obo:IDO_0000512
diseased population
obo:IDO_0000513
obo:ido.owl
obo:IDO_0000513
Organism population whose members each have an infectious disposition.
obo:IDO_0000513
Albert Goldfain
obo:IDO_0000513
Alexander Diehl
obo:IDO_0000513
Lindsay Cowell
obo:IDO_0000513
infectious agent population
obo:IDO_0000514
obo:ido.owl
obo:IDO_0000514
Organism population whose members are not infected with an infectious agent and who lack immunity to the infectious agent.
obo:IDO_0000514
Albert Goldfain
obo:IDO_0000514
Alexander Diehl
obo:IDO_0000514
Lindsay Cowell
obo:IDO_0000514
at-risk population
obo:IDO_0000514
susceptible population
obo:IDO_0000515
obo:ido.owl
obo:IDO_0000515
Organism population whose members are participating in non-parasitic symbiosis with a particular host.
obo:IDO_0000515
Albert Goldfain
obo:IDO_0000515
Alexander Diehl
obo:IDO_0000515
Lindsay Cowell
obo:IDO_0000515
normal resident microflora population
obo:IDO_0000515
An infectious organism population (IDO:0000513) (1) that is not part of any infection (IDO:0000586), (2) whose members are participating in a process of symbiosis (GO:0044403) with the same host, and (3) whose members are organisms of types among the normal resident microbiota for the type of host organism.
obo:IDO_0000515
normal resident microbiota population
obo:IDO_0000519
One-dimensional temporal region beginning with the extablishment of an infectious agent or structure in a host and ending with the onset of symptoms in the host.
obo:IDO_0000519
Albert Goldfain
obo:IDO_0000519
Alexander Diehl
obo:IDO_0000519
Lindsay Cowell
obo:IDO_0000519
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000519
incubation interval
obo:IDO_0000520
One-dimensional temporal region during which a pathogen host bears a contagiousness disposition.
obo:IDO_0000520
Albert Goldfain
obo:IDO_0000520
Alexander Diehl
obo:IDO_0000520
Lindsay Cowell
obo:IDO_0000520
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000520
communicability interval
obo:IDO_0000522
Organism bearing a symbiont role.
obo:IDO_0000522
Albert Goldfain
obo:IDO_0000522
Alexander Diehl
obo:IDO_0000522
Lindsay Cowell
obo:IDO_0000522
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000522
symbiont
obo:IDO_0000523
Organism that can only reach developmental maturity, replicate, or persist in symbiosis.
obo:IDO_0000523
Albert Goldfain
obo:IDO_0000523
Alexander Diehl
obo:IDO_0000523
Lindsay Cowell
obo:IDO_0000523
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000523
obligatory symbiont
obo:IDO_0000524
Symbiont bearing a mutualist role.
obo:IDO_0000524
Albert Goldfain
obo:IDO_0000524
Alexander Diehl
obo:IDO_0000524
Lindsay Cowell
obo:IDO_0000524
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000524
mutualist
obo:IDO_0000525
Symbiont bearing a commensal role.
obo:IDO_0000525
Albert Goldfain
obo:IDO_0000525
Alexander Diehl
obo:IDO_0000525
Lindsay Cowell
obo:IDO_0000525
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000525
commensal
obo:IDO_0000526
Symbiont bearing a parasite role.
obo:IDO_0000526
Albert Goldfain
obo:IDO_0000526
Alexander Diehl
obo:IDO_0000526
Lindsay Cowell
obo:IDO_0000526
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000526
parasite
obo:IDO_0000528
Material entity bearing a pathogenic disposition.
obo:IDO_0000528
Albert Goldfain
obo:IDO_0000528
Alexander Diehl
obo:IDO_0000528
Lindsay Cowell
obo:IDO_0000528
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000528
pathogen
obo:IDO_0000530
Pathogen bearing a primary infectious disposition.
obo:IDO_0000530
Albert Goldfain
obo:IDO_0000530
Alexander Diehl
obo:IDO_0000530
Lindsay Cowell
obo:IDO_0000530
principal pathogen
obo:IDO_0000530
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000530
primary pathogen
obo:IDO_0000531
Object bearing a host role.
obo:IDO_0000531
Albert Goldfain
obo:IDO_0000531
Alexander Diehl
obo:IDO_0000531
Lindsay Cowell
obo:IDO_0000531
http://purl.obolibrary.org/obo/ido.owl
This should be pushed to an upper-level ontology.
obo:IDO_0000531
host
obo:IDO_0000532
Host bearing a definitive host role.
obo:IDO_0000532
Albert Goldfain
obo:IDO_0000532
Alexander Diehl
obo:IDO_0000532
Lindsay Cowell
obo:IDO_0000532
primary host
obo:IDO_0000532
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000532
definitive host
obo:IDO_0000533
Host bearing an intermediate host role.
obo:IDO_0000533
Albert Goldfain
obo:IDO_0000533
Alexander Diehl
obo:IDO_0000533
Lindsay Cowell
obo:IDO_0000533
secondary host
obo:IDO_0000533
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000533
intermediate host
obo:IDO_0000535
Host bearing a dead-end host role.
obo:IDO_0000535
Albert Goldfain
obo:IDO_0000535
Alexander Diehl
obo:IDO_0000535
Lindsay Cowell
obo:IDO_0000535
incidental host
obo:IDO_0000535
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000535
dead-end host
obo:IDO_0000537
Pathogen host bearing an infectious agent host role.
obo:IDO_0000537
Albert Goldfain
obo:IDO_0000537
Alexander Diehl
obo:IDO_0000537
Lindsay Cowell
obo:IDO_0000537
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000537
infectious agent host
obo:IDO_0000538
Host bearing a pathogen host role.
obo:IDO_0000538
Albert Goldfain
obo:IDO_0000538
Alexander Diehl
obo:IDO_0000538
Lindsay Cowell
obo:IDO_0000538
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000538
pathogen host
obo:IDO_0000539
Infectious agent host bearing the infectious agent carrier role.
obo:IDO_0000539
Albert Goldfain
obo:IDO_0000539
Alexander Diehl
obo:IDO_0000539
Lindsay Cowell
obo:IDO_0000539
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000539
asymptomatic infectious agent carrier
obo:IDO_0000543
Pathogen transporter bearing a pathogen vehicle role.
obo:IDO_0000543
Albert Goldfain
obo:IDO_0000543
Alexander Diehl
obo:IDO_0000543
Lindsay Cowell
obo:IDO_0000543
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000543
pathogen vehicle
obo:IDO_0000544
Pathogen vehicle bearing a fomite role.
obo:IDO_0000544
Albert Goldfain
obo:IDO_0000544
Alexander Diehl
obo:IDO_0000544
Lindsay Cowell
obo:IDO_0000544
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000544
fomite
obo:IDO_0000545
Material entity bearing a pathogen reservoir role.
obo:IDO_0000545
Albert Goldfain
obo:IDO_0000545
Alexander Diehl
obo:IDO_0000545
Lindsay Cowell
obo:IDO_0000545
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000545
infectious agent reservoir
obo:IDO_0000547
A macromolecule produced by a pathogen and that has a virulence factor disposition.
obo:IDO_0000547
Albert Goldfain
obo:IDO_0000547
Alexander Diehl
obo:IDO_0000547
Lindsay Cowell
obo:IDO_0000547
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000547
virulence factor
obo:IDO_0000548
Biological macromolecule that has an invasion disposition.
obo:IDO_0000548
Albert Goldfain
obo:IDO_0000548
Alexander Diehl
obo:IDO_0000548
Lindsay Cowell
obo:IDO_0000548
invasin
obo:IDO_0000548
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000548
invasion factor
obo:IDO_0000549
Molecular entity that has a toxin disposition.
obo:IDO_0000549
Albert Goldfain
obo:IDO_0000549
Alexander Diehl
obo:IDO_0000549
Lindsay Cowell
obo:IDO_0000549
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000549
toxin
obo:IDO_0000550
Toxin bearing an exotoxin disposition.
obo:IDO_0000550
Albert Goldfain
obo:IDO_0000550
Alexander Diehl
obo:IDO_0000550
Lindsay Cowell
obo:IDO_0000550
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000550
exotoxin
obo:IDO_0000551
Exotoxin bearing an enterotoxin disposition.
obo:IDO_0000551
Albert Goldfain
obo:IDO_0000551
Alexander Diehl
obo:IDO_0000551
Lindsay Cowell
obo:IDO_0000551
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000551
enterotoxin
obo:IDO_0000552
Toxin bearing an endotoxin disposition that is a structural component of a pathogen and is released from the pathogen only upon cytolysis.
obo:IDO_0000552
Albert Goldfain
obo:IDO_0000552
Alexander Diehl
obo:IDO_0000552
Lindsay Cowell
obo:IDO_0000552
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000552
endotoxin
obo:IDO_0000553
Anatomical entity bearing a pathogen portal of entry role.
obo:IDO_0000553
Albert Goldfain
obo:IDO_0000553
Alexander Diehl
obo:IDO_0000553
Lindsay Cowell
obo:IDO_0000553
obo:ido.owl
obo:IDO_0000553
pathogen portal of entry
obo:IDO_0000554
Anatomical entity bearing a pathogen portal of exit role.
obo:IDO_0000554
Albert Goldfain
obo:IDO_0000554
Alexander Diehl
obo:IDO_0000554
Lindsay Cowell
obo:IDO_0000554
obo:ido.owl
obo:IDO_0000554
pathogen portal of exit
obo:IDO_0000557
Biological macromolecule that has an adhesion disposition.
obo:IDO_0000557
Albert Goldfain
obo:IDO_0000557
Alexander Diehl
obo:IDO_0000557
Lindsay Cowell
obo:IDO_0000557
adhesin
obo:IDO_0000557
adhesion molecule
obo:IDO_0000557
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000557
adhesion factor
obo:IDO_0000566
Infectious disorder bearing a primary infection role.
obo:IDO_0000566
Albert Goldfain
obo:IDO_0000566
Alexander Diehl
obo:IDO_0000566
Lindsay Cowell
obo:IDO_0000566
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000566
primary infection
obo:IDO_0000567
Infectious disorder bearing a secondary infection role.
obo:IDO_0000567
Albert Goldfain
obo:IDO_0000567
Alexander Diehl
obo:IDO_0000567
Lindsay Cowell
obo:IDO_0000567
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000567
secondary infection
obo:IDO_0000568
Infectious disease inhering in an infectious disorder composed of pathogens having zoonotic dispositions.
obo:IDO_0000568
Albert Goldfain
obo:IDO_0000568
Alexander Diehl
obo:IDO_0000568
Lindsay Cowell
obo:IDO_0000568
zoonosis
obo:IDO_0000570
Infection that is part of an asymptomatic carrier.
obo:IDO_0000570
Albert Goldfain
obo:IDO_0000570
Alexander Diehl
obo:IDO_0000570
Lindsay Cowell
obo:IDO_0000570
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000570
subclinical infection
obo:IDO_0000571
Material entity bearing protective resistance.
obo:IDO_0000571
Albert Goldfain
obo:IDO_0000571
Alexander Diehl
obo:IDO_0000571
Lindsay Cowell
obo:IDO_0000571
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000571
resistant entity
obo:IDO_0000576
Immunity to pathogen that inheres in an organism in virtue of germline encoded components that directly recognize components of potential pathogens.
obo:IDO_0000576
Albert Goldfain
obo:IDO_0000576
Alexander Diehl
obo:IDO_0000576
Lindsay Cowell
obo:IDO_0000576
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000576
innate immunity to infectious agent
obo:IDO_0000578
Immunity to pathogen that inheres in an organism in virtue of components of its circulating body fluid, e.g. blood, lymph, hemolymph.
obo:IDO_0000578
Albert Goldfain
obo:IDO_0000578
Alexander Diehl
obo:IDO_0000578
Lindsay Cowell
obo:IDO_0000578
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000578
"Circulating body fluid" refers to blood, lymph, and hemolymph.
obo:IDO_0000578
humoral immunity to infectious agent
obo:IDO_0000579
Immunity to pathogen that inheres in an organism in virtue of its leukocytes.
obo:IDO_0000579
Albert Goldfain
obo:IDO_0000579
Alexander Diehl
obo:IDO_0000579
Lindsay Cowell
obo:IDO_0000579
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000579
leukocyte-mediated immunity to infectious agent
obo:IDO_0000580
Immunity to pathogen that inheres in an organism in virtue of antibodies not produced by that organism.
obo:IDO_0000580
Albert Goldfain
obo:IDO_0000580
Alexander Diehl
obo:IDO_0000580
Lindsay Cowell
obo:IDO_0000580
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000580
passive immunity to infectious agent
obo:IDO_0000581
Resistance to drug that mitigates the damaging effects of an antibiotic.
obo:IDO_0000581
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000581
Albert Goldfain
obo:IDO_0000581
Alexander Diehl
obo:IDO_0000581
Lindsay Cowell
obo:IDO_0000581
antibiotic resistance
obo:IDO_0000583
Pathogen whose infection incidence is increasing following its first introduction into a new host Species.
obo:IDO_0000583
Albert Goldfain
obo:IDO_0000583
Alexander Diehl
obo:IDO_0000583
Lindsay Cowell
obo:IDO_0000583
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000583
emerging pathogen
obo:IDO_0000584
Toxin bearing a cytotoxin disposition.
obo:IDO_0000584
Albert Goldfain
obo:IDO_0000584
Alexander Diehl
obo:IDO_0000584
Lindsay Cowell
obo:IDO_0000584
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000584
cytotoxin
obo:IDO_0000585
Collective disposition to initiate processes that result in a disorder.
obo:IDO_0000585
Albert Goldfain
obo:IDO_0000585
Alexander Diehl
obo:IDO_0000585
Lindsay Cowell
obo:IDO_0000585
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000585
collective pathogenic disposition
obo:IDO_0000586
Part of an organism that itself is part of an extended organism with a pathogen as part, which participates in the formation of the infection.
obo:IDO_0000586
Albert Goldfain
obo:IDO_0000586
Alexander Diehl
obo:IDO_0000586
Lindsay Cowell
obo:IDO_0000586
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000586
infection
obo:IDO_0000587
Resistance to pathogen that inheres in an organism due to an allele or combination of alleles in its genome.
obo:IDO_0000587
Albert Goldfain
obo:IDO_0000587
Alexander Diehl
obo:IDO_0000587
Lindsay Cowell
obo:IDO_0000587
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000587
The resistance of individuals to HIV invasion oonferred by particular CCR5 alleles is an example. Resistance against malaria conferred by the sickle cell gene is another.
obo:IDO_0000587
genetic resistance to pathogen
obo:IDO_0000588
Collective disposition the realization of which mitigates the damaging effects of some entity on members of the collection.
obo:IDO_0000588
Albert Goldfain
obo:IDO_0000588
Alexander Diehl
obo:IDO_0000588
Lindsay Cowell
obo:IDO_0000588
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000588
collective resistance disposition
obo:IDO_0000589
Organism that has an immunodeficiency.
obo:IDO_0000589
Albert Goldfain
obo:IDO_0000589
Alexander Diehl
obo:IDO_0000589
Lindsay Cowell
obo:IDO_0000589
immunocompromised organism
obo:IDO_0000589
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000589
immunodeficient organism
obo:IDO_0000590
Infectious disease course that unfolds over a long period of time.
obo:IDO_0000590
Albert Goldfain
obo:IDO_0000590
Alexander Diehl
obo:IDO_0000590
Lindsay Cowell
obo:IDO_0000590
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000590
chronic infectious disease course
obo:IDO_0000592
obo:ido.owl
obo:IDO_0000592
Organism population whose members have acquired immunity to an infectious agent.
obo:IDO_0000592
Albert Goldfain
obo:IDO_0000592
Alexander Diehl
obo:IDO_0000592
Lindsay Cowell
obo:IDO_0000592
immune population
obo:IDO_0000593
One-dimensional temporal region during which a transmission process occurs.
obo:IDO_0000593
Albert Goldfain
obo:IDO_0000593
Alexander Diehl
obo:IDO_0000593
Lindsay Cowell
obo:IDO_0000593
This should be imported from: http://purl.obolibrary.org/obo/trans.owl
obo:IDO_0000593
transmission interval
obo:IDO_0000596
Organism that has an infectious disposition.
obo:IDO_0000596
This is an inferred subclass of pathogen.
obo:IDO_0000596
Albert Goldfain
obo:IDO_0000596
Alexander Diehl
obo:IDO_0000596
Lindsay Cowell
obo:IDO_0000596
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000596
infectious agent
obo:IDO_0000603
Process by which an infectious agent or infectious structure, established in a host, becomes part of an infection in the host.
obo:IDO_0000603
Albert Goldfain
obo:IDO_0000603
Alexander Diehl
obo:IDO_0000603
Lindsay Cowell
obo:IDO_0000603
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000603
process of establishing an infection
obo:IDO_0000604
Establishment of localization in host process in which an organism or acellular structure establishes a colony in or on a host.
obo:IDO_0000604
Albert Goldfain
obo:IDO_0000604
Alexander Diehl
obo:IDO_0000604
Lindsay Cowell
obo:IDO_0000604
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000604
colonization of host
obo:IDO_0000606
Colonization of host process that results in a clinically abnormal colony.
obo:IDO_0000606
Albert Goldfain
obo:IDO_0000606
Alexander Diehl
obo:IDO_0000606
Lindsay Cowell
obo:IDO_0000606
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000606
establishment of a clinically abnormal colony
obo:IDO_0000607
Process in which an entity comes into being as a result of the process.
obo:IDO_0000607
Albert Goldfain
obo:IDO_0000607
Alexander Diehl
obo:IDO_0000607
Lindsay Cowell
obo:IDO_0000607
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000607
production
obo:IDO_0000608
Production process in which a participant creates a copy of itself.
obo:IDO_0000608
Albert Goldfain
obo:IDO_0000608
Alexander Diehl
obo:IDO_0000608
Lindsay Cowell
obo:IDO_0000608
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000608
replication
obo:IDO_0000610
Process that attenuates an immune response.
obo:IDO_0000610
Albert Goldfain
obo:IDO_0000610
Alexander Diehl
obo:IDO_0000610
Lindsay Cowell
obo:IDO_0000610
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000610
immunosuppression
obo:IDO_0000611
Immunosuppression which unfolds as part of the natural self-regulation of an immune response.
obo:IDO_0000611
Albert Goldfain
obo:IDO_0000611
Alexander Diehl
obo:IDO_0000611
Lindsay Cowell
obo:IDO_0000611
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000611
physiologic immunosuppression
obo:IDO_0000612
Immunosuppression process which arises as the result of a disorder.
obo:IDO_0000612
Albert Goldfain
obo:IDO_0000612
Alexander Diehl
obo:IDO_0000612
Lindsay Cowell
obo:IDO_0000612
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000612
pathologic immunosuppression
obo:IDO_0000615
obo:ido.owl
obo:IDO_0000615
Organism population persisting in a site it has colonized.
obo:IDO_0000615
Albert Goldfain
obo:IDO_0000615
Alexander Diehl
obo:IDO_0000615
Lindsay Cowell
obo:IDO_0000615
colony
obo:IDO_0000616
Colony whose members are infectious agents.
obo:IDO_0000616
Albert Goldfain
obo:IDO_0000616
Alexander Diehl
obo:IDO_0000616
Lindsay Cowell
obo:IDO_0000616
infectious agent colony
obo:IDO_0000617
Disorder of an immune system component that results in defective functioning of the immune system.
obo:IDO_0000617
Albert Goldfain
obo:IDO_0000617
Alexander Diehl
obo:IDO_0000617
Lindsay Cowell
obo:IDO_0000617
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000617
immunodeficiency
obo:IDO_0000618
Disposition inhering in an organism that is the disposition to mount a normal immune response.
obo:IDO_0000618
Albert Goldfain
obo:IDO_0000618
Alexander Diehl
obo:IDO_0000618
Lindsay Cowell
obo:IDO_0000618
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000618
immunocompetence
obo:IDO_0000619
Disposition whose realization negatively regulates an immune response.
obo:IDO_0000619
Albert Goldfain
obo:IDO_0000619
Alexander Diehl
obo:IDO_0000619
Lindsay Cowell
obo:IDO_0000619
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000619
immunosuppressive disposition
obo:IDO_0000621
Immunity to pathogen that inheres in an organism in virtue of antigen receptors encoded by somatically diversified genes in the organism's genome and expressed by cells that have undergone selection during a primary immune response in that organism.
obo:IDO_0000621
Albert Goldfain
obo:IDO_0000621
Alexander Diehl
obo:IDO_0000621
Lindsay Cowell
obo:IDO_0000621
adaptive immunity to infectious agent
obo:IDO_0000621
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000621
acquired immunity to infectious agent
obo:IDO_0000623
Infectious disposition to be transmitted from one organism to another of the same species by horizontal transmission.
obo:IDO_0000623
Albert Goldfain
obo:IDO_0000623
Alexander Diehl
obo:IDO_0000623
Lindsay Cowell
obo:IDO_0000623
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000623
communicability
obo:IDO_0000625
Establishment of localization process in which a material entity reaches a site in or on a host in which it can survive, grow, multiply, or mature.
obo:IDO_0000625
Albert Goldfain
obo:IDO_0000625
Alexander Diehl
obo:IDO_0000625
Lindsay Cowell
obo:IDO_0000625
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000625
establishment of localization in host
obo:IDO_0000626
Process by which a disorder comes into existence.
obo:IDO_0000626
Albert Goldfain
obo:IDO_0000626
Alexander Diehl
obo:IDO_0000626
Lindsay Cowell
obo:IDO_0000626
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000626
appearance of disorder
obo:IDO_0000627
Infectious disorder that is the physical basis for an unfolding acute infectious disease course.
obo:IDO_0000627
Albert Goldfain
obo:IDO_0000627
Alexander Diehl
obo:IDO_0000627
Lindsay Cowell
obo:IDO_0000627
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000627
acute infection
obo:IDO_0000628
Infection that persists for an extended period of time.
obo:IDO_0000628
John Beverley
obo:IDO_0000628
chronic infection
obo:IDO_0000629
Role borne by either an organism whose extended organism contains a distinct material entity, or an acellular structure containing a distinct material entity, realized in use of that structure or organism as a site of reproduction or replication.
obo:IDO_0000629
Albert Goldfain
obo:IDO_0000629
Alexander Diehl
obo:IDO_0000629
Lindsay Cowell
obo:IDO_0000629
This should be pushed to: http://purl.obolibrary.org/obo/ogms.owl
obo:IDO_0000629
host role
obo:IDO_0000630
Infection resulting from a transmission process that unfolds in a hospital.
obo:IDO_0000630
Albert Goldfain
obo:IDO_0000630
Alexander Diehl
obo:IDO_0000630
Lindsay Cowell
obo:IDO_0000630
nosocomial infection
obo:IDO_0000630
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000630
hospital-acquired infection
obo:IDO_0000631
Infection resulting from a transmission process that did not unfold in a health care facility.
obo:IDO_0000631
Albert Goldfain
obo:IDO_0000631
Alexander Diehl
obo:IDO_0000631
Lindsay Cowell
obo:IDO_0000631
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000631
community-acquired infection
obo:IDO_0000632
Toxin bearing a neurotoxin disposition.
obo:IDO_0000632
Albert Goldfain
obo:IDO_0000632
Alexander Diehl
obo:IDO_0000632
Lindsay Cowell
obo:IDO_0000632
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000632
neurotoxin
obo:IDO_0000633
Infection established as a result of spread from another infection in a non-adjacent location in the extended organism of the host.
obo:IDO_0000633
John Beverley
obo:IDO_0000633
metastatic infection
obo:IDO_0000635
Role borne by a material entity that contains a site from which an infectious agent is transmitted.
obo:IDO_0000635
Albert Goldfain
obo:IDO_0000635
Alexander Diehl
obo:IDO_0000635
Lindsay Cowell
obo:IDO_0000635
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000635
source of infection role
obo:IDO_0000638
Infection resulting from a transmission process that unfolds in a nursing home.
obo:IDO_0000638
Albert Goldfain
obo:IDO_0000638
Alexander Diehl
obo:IDO_0000638
Lindsay Cowell
obo:IDO_0000638
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000638
nursing-home acquired infection
obo:IDO_0000639
Pathogen disposed to infect human hosts.
obo:IDO_0000639
Albert Goldfain
obo:IDO_0000639
Alexander Diehl
obo:IDO_0000639
Lindsay Cowell
obo:IDO_0000639
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000639
infectious human pathogen
obo:IDO_0000640
Immunodeficiency that is not caused by a genetic predisposition.
obo:IDO_0000640
Albert Goldfain
obo:IDO_0000640
Alexander Diehl
obo:IDO_0000640
Lindsay Cowell
obo:IDO_0000640
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000640
Causes of acquired immunodeficiences include infection and drug treatments (e.g. chemotherapy).
obo:IDO_0000640
acquired immunodeficiency
obo:IDO_0000642
Infection comprised of infectious organisms or structures all of the same Species.
obo:IDO_0000642
simple infection
obo:IDO_0000643
Pathogen whose infection incidence is increasing in a host population as a result of changes in the biology of the host or pathogen, or changes in their interactions.
obo:IDO_0000643
Albert Goldfain
obo:IDO_0000643
Alexander Diehl
obo:IDO_0000643
Lindsay Cowell
obo:IDO_0000643
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000643
re-emerging pathogen
obo:IDO_0000650
Colonization of host in a human.
obo:IDO_0000650
Albert Goldfain
obo:IDO_0000650
Alexander Diehl
obo:IDO_0000650
Lindsay Cowell
obo:IDO_0000650
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000650
colonization of human
obo:IDO_0000651
Immunodeficiency that exists in an organism because of a genetic predisposition.
obo:IDO_0000651
Albert Goldfain
obo:IDO_0000651
Alex Diehl
obo:IDO_0000651
Lindsay Cowell
obo:IDO_0000651
congenital immunodeficiency
obo:IDO_0000651
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000651
primary immunodeficiency
obo:IDO_0000653
Infectious disease inhering in an infectious disorder composed of pathogens bearing reverse zoonotic dispositions.
obo:IDO_0000653
Albert Goldfain
obo:IDO_0000653
Alex Diehl
obo:IDO_0000653
Lindsay Cowell
obo:IDO_0000653
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000653
reverse zoonosis
obo:IDO_0000654
Pathogen with an opportunistic infectious disposition.
obo:IDO_0000654
Albert Goldfain
obo:IDO_0000654
Alex Diehl
obo:IDO_0000654
Lindsay Cowell
obo:IDO_0000654
opportunist
obo:IDO_0000654
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000654
opportunistic pathogen
obo:IDO_0000655
Disposition to undergo a transmission process.
obo:IDO_0000655
Albert Goldfain
obo:IDO_0000655
Alex Diehl
obo:IDO_0000655
Lindsay Cowell
obo:IDO_0000655
This should be pushed to: http://purl.obolibrary.org/obo/trans.owl
obo:IDO_0000655
transmissibility disposition
obo:IDO_0000656
Pathogen transmission process in which a pathogen is transmitted from one host to another of the same species, and the two hosts are not in a parent-child relationship.
obo:IDO_0000656
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000656
horizontal pathogen transmission process
obo:IDO_0000657
Process that results in death.
obo:IDO_0000657
Alex Diehl
obo:IDO_0000657
Lindsay Cowell
obo:IDO_0000657
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000657
process that results in death
obo:IDO_0000659
Organism that is not infected with an infectious agent and lacks protective immunity to the infectious agent.
obo:IDO_0000659
Alex Diehl
obo:IDO_0000659
Lindsay Cowell
obo:IDO_0000659
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000659
susceptible organism
obo:IDO_0000660
results in
obo:IDO_0000663
Process that stops, prevents, or reduces the frequency, rate or extent of a life-sustaining process.
obo:IDO_0000663
Alex Diehl
obo:IDO_0000663
Lindsay Cowell
obo:IDO_0000663
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000663
negative regulation of life-sustaining process
obo:IDO_0000664
has_material_basis_in
obo:IDO_0000665
Material entity bearing a source of infection role.
obo:IDO_0000665
Albert Goldfain
obo:IDO_0000665
Alex Diehl
obo:IDO_0000665
Lindsay Cowell
obo:IDO_0000665
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0000665
source of infection
obo:IDO_0001000
John Beverley
obo:IDO_0001000
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001000
infectious disease incidence profile
obo:IDO_0001001
John Beverley
obo:IDO_0001001
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001001
infectious disease incidence proportion profile
obo:IDO_0001002
John Beverley
obo:IDO_0001002
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001002
infectious disease incidence rate profile
obo:IDO_0001005
Immunosuppressed organism that is experiencing pathologic immunosuppression.
obo:IDO_0001005
Alex Diehl
obo:IDO_0001005
Lindsay Cowell
obo:IDO_0001005
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001005
negative regulation of establishment of localization
obo:IDO_0001005
pathologically immunosuppressed organism
obo:IDO_0001007
Process that stops, prevents, or reduces the frequency, rate or extent of a production process.
obo:IDO_0001007
John Beverley
obo:IDO_0001007
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001007
negative regulation of production
obo:IDO_0001008
Process that stops, prevents, or reduces the frequency, rate or extent of a replication process.
obo:IDO_0001008
John Beverley
obo:IDO_0001008
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001008
negative regulation of replication
obo:IDO_0001009
Process boundary that marks the start of the life cycle of a pathogen.
obo:IDO_0001009
Alex Diehl
obo:IDO_0001009
John Beverley
obo:IDO_0001009
Lindsay Cowell
obo:IDO_0001009
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001009
pathogen birth process boundary
obo:IDO_0001010
Process boundary that marks the end of the life cycle of a pathogen.
obo:IDO_0001010
John Beverley
obo:IDO_0001010
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001010
pathogen death process boundary
obo:IDO_0001011
Pathologically immunosuppressed organism that is experiencing drug-based immunosuppression.
obo:IDO_0001011
Alex Diehl
obo:IDO_0001011
Lindsay Cowell
obo:IDO_0001011
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001011
drug-based immunosuppressed organism
obo:IDO_0001025
Disposition to kill fungi.
obo:IDO_0001025
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001025
John Beverley
obo:IDO_0001025
fungicidal disposition
obo:IDO_0001027
Disposition to kill bacteria.
obo:IDO_0001027
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001027
John Beverley
obo:IDO_0001027
bactericidal disposition
obo:IDO_0001028
Disposition to inhibit the reproduction of bacteria.
obo:IDO_0001028
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001028
John Beverley
obo:IDO_0001028
bacteriostatic disposition
obo:IDO_0001029
Disposition to kill parasites.
obo:IDO_0001029
We use parasite in the sense of organisms that are parasitic in humans.
obo:IDO_0001029
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001029
John Beverley
obo:IDO_0001029
parasiticidal disposition
obo:IDO_0001030
Disposition to inhibit the reproduction of parasites.
obo:IDO_0001030
'Parasite' is used in the sense of eukaryotic organisms that are parasitic in humans.
obo:IDO_0001030
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001030
John Beverley
obo:IDO_0001030
parasitostatic disposition
obo:IDO_0001040
Static agent bearing a bacteriostatic disposition.
obo:IDO_0001040
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001040
John Beverley
obo:IDO_0001040
bacteriostatic
obo:IDO_0001041
Cidal agent with a bactericidal disposition that is realized in a process of killing bacteria.
obo:IDO_0001041
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001041
John Beverley
obo:IDO_0001041
bactericidal
obo:IDO_0001054
Acellular structure that has an infectious disposition.
obo:IDO_0001054
This is an inferred subclass of pathogen.
obo:IDO_0001054
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001054
John Beverley
obo:IDO_0001054
infectious structure
obo:IDO_0001065
obo:ido.owl
obo:IDO_0001065
Aggregate of acellular structures.
obo:IDO_0001065
John Beverley
obo:IDO_0001065
acellular structure aggregate
obo:IDO_0001083
Zero-dimensional temporal region occupied by a pathogen birth process boundary.
obo:IDO_0001083
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001083
John Beverley
obo:IDO_0001083
pathogen birth temporal region
obo:IDO_0001085
Zero-dimensional temporal region occupied by a pathogen death process boundary.
obo:IDO_0001085
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001085
John Beverley
obo:IDO_0001085
pathogen death temporal region
obo:IDO_0001088
prions
obo:IDO_0001088
viruses
obo:IDO_0001088
Self-replicating organic structure comprised of acellular organic parts.
obo:IDO_0001088
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001088
John Beverley
obo:IDO_0001088
acellular self-replicating organic structure
obo:IDO_0001089
Material entity with a cidal agent disposition that is realized in a process of killing bacteria, fungi, parasites, or viruses.
obo:IDO_0001089
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001089
John Beverley
obo:IDO_0001089
cidal agent
obo:IDO_0001090
Material entity bearing a static agent disposition.
obo:IDO_0001090
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001090
John Beverley
obo:IDO_0001090
static agent
obo:IDO_0001091
Disposition to inhibit the reproduction of bacteria, fungi, or parasites, or inhibit the replication of viruses.
obo:IDO_0001091
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001091
John Beverley
obo:IDO_0001091
static agent disposition
obo:IDO_0001092
Disposition to kill bacteria, fungi, parasites, or viruses.
obo:IDO_0001092
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001092
John Beverley
obo:IDO_0001092
cidal agent disposition
obo:IDO_0001093
Pathogen host bearing an infectious structure host role.
obo:IDO_0001093
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001093
John Beverley
obo:IDO_0001093
infectious structure host
obo:IDO_0001094
Pathogen host role borne by an object or organism whose extended organism contains an infectious structure.
obo:IDO_0001094
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001094
John Beverley
obo:IDO_0001094
infectious structure host role
obo:IDO_0001095
Material entity bearing a pathogen transporter role.
obo:IDO_0001095
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001095
John Beverley
obo:IDO_0001095
pathogen transporter
obo:IDO_0001096
Role borne by a material entity in or on which a pathogen is located, from which the pathogen may be transmitted to a new host.
obo:IDO_0001096
John Beverley
obo:IDO_0001096
pathogen transporter role
obo:IDO_0001109
Pathogen generative stage that is a temporal subdivision of an infectious agent developmental process.
obo:IDO_0001109
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001109
John Beverley
obo:IDO_0001109
infectious agent generative stage
obo:IDO_0001110
Pathogen generative stage that is a temporal subdivision of an infectious structure developmental process.
obo:IDO_0001110
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001110
John Beverley
obo:IDO_0001110
infectious structure generative stage
obo:IDO_0001111
Generative stage that is a temporal subdivision of a pathogen developmental process.
obo:IDO_0001111
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001111
John Beverley
obo:IDO_0001111
pathogen generative stage
obo:IDO_0001124
Pathogen host role borne by an organism whose extended organism contains a pathogen bearing an infectious disposition towards the host, and the host has no symptoms of the infectious disease caused by the pathogen.
obo:IDO_0001124
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001124
John Beverley
obo:IDO_0001124
asymptomatic carrier role
obo:IDO_0001126
Pathogen host with an infection as part but exhibits no signs or symptoms.
obo:IDO_0001126
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001126
John Beverley
obo:IDO_0001126
asymptomatic carrier
obo:IDO_0001127
Infectious structure host bearing an asymptomatic carrier role.
obo:IDO_0001127
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001127
John Beverley
obo:IDO_0001127
asymptomatic infectious structure carrier
obo:IDO_0001133
Pathogen host role borne by an organism whose extended organism contains a pathogen bearing an infectious disposition towards the host, and the host has manifested symptoms of the infectious disease caused by the pathogen.
obo:IDO_0001133
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001133
John Beverley
obo:IDO_0001133
symptomatic carrier role
obo:IDO_0001134
Pathogen host with infection as part that exhibits symptoms.
obo:IDO_0001134
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001134
John Beverley
obo:IDO_0001134
symptomatic carrier
obo:IDO_0001163
Toxin disposition realized in processes resulting in damage to host cells.
obo:IDO_0001163
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001163
John Beverley
obo:IDO_0001163
cytotoxin disposition
obo:IDO_0001164
Toxin disposition realized in damaging or interfering with the function of nerve tissue.
obo:IDO_0001164
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001164
John Beverley
obo:IDO_0001164
neurotoxin disposition
obo:IDO_0001165
Toxin disposition that is a structural component of a pathogen and is realized only during cytolsis.
obo:IDO_0001165
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001165
John Beverley
obo:IDO_0001165
endotoxin disposition
obo:IDO_0001166
Exotoxin disposition ithat is realized in a process of damaging intestinal mucosa cells.
obo:IDO_0001166
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001166
John Beverley
obo:IDO_0001166
enterotoxin disposition
obo:IDO_0001167
Infectious structure host bearing a symptomatic carrier role.
obo:IDO_0001167
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001167
John Beverley
obo:IDO_0001167
symptomatic infectious structure carrier
obo:IDO_0001168
Infectious agent host bearing an infectious agent carrier role.
obo:IDO_0001168
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001168
John Beverley
obo:IDO_0001168
symptomatic infectious agent carrier
obo:IDO_0001172
obo:ido.owl
obo:IDO_0001172
Acellular structure aggregate whose members are infectious structures.
obo:IDO_0001172
John Beverley
obo:IDO_0001172
infectious structure aggregate
obo:IDO_0001196
Pathogen transporter bearing a pathogen vector role.
obo:IDO_0001196
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001196
John Beverley
obo:IDO_0001196
pathogen vector
obo:IDO_0001197
Pathogen vector bearing a biological vector role.
obo:IDO_0001197
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001197
John Beverley
obo:IDO_0001197
biological vector
obo:IDO_0001198
Pathogen vector bearing a mechanical vector role.
obo:IDO_0001198
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001198
John Beverley
obo:IDO_0001198
mechanical vector
obo:IDO_0001199
Pathogen vehicle bearing a biological vehicle role.
obo:IDO_0001199
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001199
John Beverley
obo:IDO_0001199
biological vehicle
obo:IDO_0001335
Establishment of localization in or on a human host.
obo:IDO_0001335
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001335
John Beverley
obo:IDO_0001335
establishment of localization in human host
obo:IDO_0001343
Process beginning with the establishing of an infection in a host and ending when the host becomes contagious, during which pathogens are multiplying in the host.
obo:IDO_0001343
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001343
John Beverley
obo:IDO_0001343
latency process
obo:IDO_0001344
Process boundary that marks the start of an infection, latency process, and incubation process.
obo:IDO_0001344
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001344
John Beverley
obo:IDO_0001344
infection start process boundary
obo:IDO_0001345
Process boundary marking the end of a latency period.
obo:IDO_0001345
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001345
John Beverley
obo:IDO_0001345
latency end process boundary
obo:IDO_0001346
Process boundary marking the end of an incubation period.
obo:IDO_0001346
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001346
John Beverley
obo:IDO_0001346
incubation end process boundary
obo:IDO_0001348
Zero-dimensional temporal region occupied by an infection start process boundary.
obo:IDO_0001348
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001348
John Beverley
obo:IDO_0001348
infection start temporal region
obo:IDO_0001349
Zero-dimensional temporal region occupied by an infection end process boundary.
obo:IDO_0001349
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001349
John Beverley
obo:IDO_0001349
infection end temporal region
obo:IDO_0001350
Zero-dimensional temporal region occupied by a latency end process boundary.
obo:IDO_0001350
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001350
John Beverley
obo:IDO_0001350
latency end temporal region
obo:IDO_0001351
Zero-dimensional temporal region occupied by a communicability end process boundary.
obo:IDO_0001351
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001351
John Beverley
obo:IDO_0001351
communicability end temporal region
obo:IDO_0001352
Zero-dimensional temporal region occupied by an incubation end process boundary.
obo:IDO_0001352
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001352
John Beverley
obo:IDO_0001352
incubation end temporal region
obo:IDO_0001353
Zero-dimensional temporal region occupied by a communicability start process boundary.
obo:IDO_0001353
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001353
John Beverley
obo:IDO_0001353
communicability start temporal region
obo:IDO_0001354
Process boundary marking the start of a latency interval.
obo:IDO_0001354
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001354
John Beverley
obo:IDO_0001354
latency start process boundary
obo:IDO_0001355
Process boundary marking the start of an incubation interval.
obo:IDO_0001355
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001355
John Beverley
obo:IDO_0001355
incubation start process boundary
obo:IDO_0001356
Process boundary marking the start of a communicability interval.
obo:IDO_0001356
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001356
John Beverley
obo:IDO_0001356
communicability start process boundary
obo:IDO_0001357
Process boundary marking the end of a communicability interval.
obo:IDO_0001357
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001357
John Beverley
obo:IDO_0001357
communicability end process boundary
obo:IDO_0001374
Biological role borne by a molecular entity that serves as the site on an antigen realized in immune system recognition and binding by antibodies.
obo:IDO_0001374
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001374
John Beverley
obo:IDO_0001374
epitope role
obo:IDO_0001377
Surveillance process aiming to produce information about one or several objects, in the form of microorganisms, which have the role of pathogen.
obo:IDO_0001377
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001377
pathogen surveillance
obo:IDO_0001378
Surveillance process aiming to produce information about one or several objects, in the form of arthropods, which have the role of serving as biological pathogen vectors.
obo:IDO_0001378
http://purl.obolibrary.org/obo/ido.owl
obo:IDO_0001378
vector surveillance
obo:NCBITaxon_10239
Acellular structure with RNA or DNA genetic material which uses host metabolic resources for RNA or DNA replication.
obo:NCBITaxon_10239
The mass noun term label imported from the NCBITaxon "Viruses" has been replaced with the count noun "virus", to align with BFO.
obo:NCBITaxon_10239
obo:ncbitaxon.owl
obo:NCBITaxon_10239
virus
obo:NCBITaxon_2
obo:ncbitaxon.owl
obo:NCBITaxon_2
bacteria
obo:NCBITaxon_2169561
Human Immunodeficiency Virus
obo:NCBITaxon_2169561
Virus with genetic material encoded in single-stranded RNA that replicates using reverse transcriptase to convert positive-sense RNA to DNA.
obo:NCBITaxon_2169561
http://purl.obolibrary.org/obo/NCBITaxon_2169561
obo:NCBITaxon_2169561
Baltimore Classification Group VI
obo:NCBITaxon_2169561
John Beverley
obo:NCBITaxon_2169561
single-stranded RNA retrovirus
obo:NCBITaxon_2731342
Parvovirus
obo:NCBITaxon_2731342
Virus with genetic material encoded in single-stranded DNA and replicates using DNA polymerase.
obo:NCBITaxon_2731342
http://purl.obolibrary.org/obo/NCBITaxon_2731342
obo:NCBITaxon_2731342
Baltimore Classification Group II
obo:NCBITaxon_2731342
John Beverley
obo:NCBITaxon_2731342
single-stranded DNA virus
obo:NCBITaxon_2759
obo:ncbitaxon.owl
obo:NCBITaxon_2759
eukaryota
obo:NCBITaxon_35237
Adenovirus
obo:NCBITaxon_35237
Poxvirus
obo:NCBITaxon_35237
Virus that has its genetic material encoded in double-stranded DNA and replicates using DNA polymerase.
obo:NCBITaxon_35237
http://purl.obolibrary.org/obo/NCBITaxon_35237
obo:NCBITaxon_35237
Baltimore Classification Group I
obo:NCBITaxon_35237
John Beverley
obo:NCBITaxon_35237
double-stranded DNA virus
obo:NCBITaxon_35268
Hepatitus B Virus
obo:NCBITaxon_35268
Virus with genetic material that is encoded in double-stranded DNA and replicates through single-stranded RNA intermediate.
obo:NCBITaxon_35268
http://purl.obolibrary.org/obo/NCBITaxon_35268
obo:NCBITaxon_35268
Baltimore Classification Group VII
obo:NCBITaxon_35268
Pararetrovirus
obo:NCBITaxon_35268
John Beverley
obo:NCBITaxon_35268
double-stranded DNA retrovirus
obo:NCBITaxon_35278
Coronavirus
obo:NCBITaxon_35278
Picornavirus
obo:NCBITaxon_35278
Virus with genetic material encoded in single-stranded RNA that can be translated directly into proteins.
obo:NCBITaxon_35278
http://purl.obolibrary.org/obo/NCBITaxon_35278
obo:NCBITaxon_35278
Baltimore Classification Group IV
obo:NCBITaxon_35278
John Beverley
obo:NCBITaxon_35278
positive-sense single-stranded RNA virus
obo:NCBITaxon_35301
Rhabdovirus
obo:NCBITaxon_35301
Virus with genetic material encoded in single-stranded RNA that can be translated into proteins only after transcription by RNA polymerase.
obo:NCBITaxon_35301
http://purl.obolibrary.org/obo/NCBITaxon_35301
obo:NCBITaxon_35301
Baltimore Classification Group V
obo:NCBITaxon_35301
John Beverley
obo:NCBITaxon_35301
negative-sense single-stranded RNA virus
obo:NCBITaxon_35325
Reovirus
obo:NCBITaxon_35325
Virus with genetic material encoded in double-stranded RNA.
obo:NCBITaxon_35325
http://purl.obolibrary.org/obo/NCBITaxon_35325
obo:NCBITaxon_35325
Baltimore Classification Group III
obo:NCBITaxon_35325
John Beverley
obo:NCBITaxon_35325
double-stranded RNA virus
obo:NCBITaxon_36469
Acellular structure that consists of an abnormally folded protein which replicates by by transmitting its abnormal structure to other proteins.
obo:NCBITaxon_36469
John Beverley
obo:NCBITaxon_36469
http://purl.obolibrary.org/obo/ncbitaxon.owl
obo:NCBITaxon_36469
prion
obo:NCBITaxon_9606
obo:ncbitaxon.owl
obo:NCBITaxon_9606
homo sapiens
obo:OBI_0000011
Process that realizes a plan which is the concretization of a plan specification.
obo:OBI_0000011
http://purl.obolibrary.org/obo/obi.owl
obo:OBI_0000011
planned process
obo:OBI_0000047
Material entity that is created or changed during material processing.
obo:OBI_0000047
http://purl.obolibrary.org/obo/obi.owl
obo:OBI_0000047
processed material
obo:OBI_0000070
Planned process with the objective to produce information about some evaluant.
obo:OBI_0000070
http://purl.obolibrary.org/obo/obi.owl
obo:OBI_0000070
assay
obo:OBI_0000086
Role inhering in a molecular entity when the molecular entity is used to produce a chemical reaction to detect, measure, or produce other substances.
obo:OBI_0000086
http://purl.obolibrary.org/obo/obi.owl
obo:OBI_0000086
reagent role
obo:OBI_0000094
Planned process which results in physical changes in a specified input material.
obo:OBI_0000094
http://purl.obolibrary.org/obo/obi.owl
obo:OBI_0000094
material processing
obo:OBI_0000237
Biological role inhering in some molecular entity, that stimulates an immune response when identified by the immune systems cells.
obo:OBI_0000237
http://purl.obolibrary.org/obo/obi.owl
obo:OBI_0000237
John Beverley
obo:OBI_0000237
antigen role
obo:OBI_0000293
http://purl.obolibrary.org/obo/obi.owl
obo:OBI_0000293
has specified input
obo:OBI_0000295
Participates in relation between a planned process and a continuant participating in that process that is not created during the process, where the presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
obo:OBI_0000295
http://purl.obolibrary.org/obo/obi.owl
obo:OBI_0000295
is specified input of
obo:OBI_0000299
http://purl.obolibrary.org/obo/obi.owl
obo:OBI_0000299
has specified output
obo:OBI_0000312
Participates in relation between a planned process and a continuant participating in that process where the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
obo:OBI_0000312
http://purl.obolibrary.org/obo/obi.owl
obo:OBI_0000312
is specified output of
obo:OBI_0000406
Double stranded DNA that is the specified output of a polymerase chain reaction
obo:OBI_0000406
http://purl.obolibrary.org/obo/obi.owl
obo:OBI_0000406
PCR product
obo:OBI_0000415
Enzymatic amplification in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication.
obo:OBI_0000415
http://purl.obolibrary.org/obo/obi.owl
obo:OBI_0000415
polymerase chain reaction
obo:OBI_0000552
Material processing amplifying cDNA during a PCR reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity.
obo:OBI_0000552
http://purl.obolibrary.org/obo/obi.owl
obo:OBI_0000552
reverse transcribed PCR
obo:OBI_0100026
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
obo:OBI_0100026
obo:obi.owl
obo:OBI_0100026
organism
obo:OBI_0600058
Material processing using enzymes to increase the number of molecules of a material entity.
obo:OBI_0600058
http://purl.obolibrary.org/obo/obi.owl
obo:OBI_0600058
enzymatic amplification
obo:OBI_1110001
Molecular entity bearing the epitope role.
obo:OBI_1110001
http://purl.obolibrary.org/obo/obi.owl
obo:OBI_1110001
John Beverley
obo:OBI_1110001
epitope
obo:OBI_1110034
Molecular entity bearing an antigen role.
obo:OBI_1110034
http://purl.obolibrary.org/obo/obi.owl
obo:OBI_1110034
antigen
obo:OGMS_0000020
Process experienced by a patient which can only be experienced by the patient, that is hypothesized to be clinically relevant.
obo:OGMS_0000020
obo:ogms.owl
obo:OGMS_0000020
symptom
obo:OGMS_0000031
Disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
obo:OGMS_0000031
obo:ogms.owl
obo:OGMS_0000031
disease
obo:OGMS_0000045
Material entity that is a clinically abnormal part of an extended organism.
obo:OGMS_0000045
obo:ogms.owl
obo:OGMS_0000045
disorder
obo:OGMS_0000063
Totality of all processes through which a given disease instance is realized.
obo:OGMS_0000063
obo:ogms.owl
obo:OGMS_0000063
disease course
obo:OGMS_0000087
Object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism.
obo:OGMS_0000087
obo:ogms.owl
obo:OGMS_0000087
extended organism
obo:OMRSE_00000061
Material entity that is a human made structure with firm connection between its foundation and the ground.
obo:OMRSE_00000061
http://purl.obolibrary.org/obo/OMRSE
obo:OMRSE_00000061
architectural structure
obo:OMRSE_00000062
Architectural structure that bears some function.
obo:OMRSE_00000062
http://purl.obolibrary.org/obo/OMRSE
obo:OMRSE_00000062
facility
obo:OMRSE_00000063
Facility that is run by a hospital organization and is the bearer of a hospital function.
obo:OMRSE_00000063
http://purl.obolibrary.org/obo/OMRSE
obo:OMRSE_00000063
hospital facility
obo:OMRSE_00000102
Facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population.
obo:OMRSE_00000102
http://purl.obolibrary.org/obo/OMRSE
obo:OMRSE_00000102
healthcare facility
obo:RO_0000052
inheres in
obo:RO_0000052
this fragility inheres in this vase
obo:RO_0000052
this red color inheres in this apple
obo:RO_0000052
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
obo:RO_0000052
A dependent inheres in its bearer at all times for which the dependent exists.
obo:RO_0000052
inheres_in
obo:RO_0000052
obo:RO_0001901
obo:RO_0000052
inheres in
obo:RO_0000053
bearer of
obo:RO_0000053
this apple is bearer of this red color
obo:RO_0000053
this vase is bearer of this fragility
obo:RO_0000053
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
obo:RO_0000053
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
obo:RO_0000053
bearer_of
obo:RO_0000053
is bearer of
obo:RO_0000053
obo:RO_0001901
obo:RO_0000053
bearer of
obo:RO_0000056
participates in
obo:RO_0000056
this blood clot participates in this blood coagulation
obo:RO_0000056
this input material (or this output material) participates in this process
obo:RO_0000056
this investigator participates in this investigation
obo:RO_0000056
a relation between a continuant and a process, in which the continuant is somehow involved in the process
obo:RO_0000056
participates_in
obo:RO_0000056
participates in
obo:RO_0000057
has participant
obo:RO_0000057
this blood coagulation has participant this blood clot
obo:RO_0000057
this investigation has participant this investigator
obo:RO_0000057
this process has participant this input material (or this output material)
obo:RO_0000057
a relation between a process and a continuant, in which the continuant is somehow involved in the process
obo:RO_0000057
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
obo:RO_0000057
has_participant
obo:RO_0000057
http://www.obofoundry.org/ro/#OBO_REL:has_participant
obo:RO_0000057
has participant
obo:RO_0000058
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
obo:RO_0000058
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
obo:RO_0000058
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
obo:RO_0000058
is concretized as
obo:RO_0000059
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
obo:RO_0000059
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
obo:RO_0000059
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
obo:RO_0000059
concretizes
obo:RO_0000079
this catalysis function is a function of this enzyme
obo:RO_0000079
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
obo:RO_0000079
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
obo:RO_0000079
function_of
obo:RO_0000079
is function of
obo:RO_0000079
function of
obo:RO_0000080
this red color is a quality of this apple
obo:RO_0000080
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
obo:RO_0000080
A quality inheres in its bearer at all times for which the quality exists.
obo:RO_0000080
is quality of
obo:RO_0000080
quality_of
obo:RO_0000080
quality of
obo:RO_0000081
this investigator role is a role of this person
obo:RO_0000081
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
obo:RO_0000081
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
obo:RO_0000081
is role of
obo:RO_0000081
role_of
obo:RO_0000081
role of
obo:RO_0000085
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
obo:RO_0000085
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
obo:RO_0000085
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
obo:RO_0000085
has_function
obo:RO_0000085
has function
obo:RO_0000086
this apple has quality this red color
obo:RO_0000086
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
obo:RO_0000086
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
obo:RO_0000086
has_quality
obo:RO_0000086
has quality
obo:RO_0000087
this person has role this investigator role (more colloquially: this person has this role of investigator)
obo:RO_0000087
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
obo:RO_0000087
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
obo:RO_0000087
has_role
obo:RO_0000087
has role
obo:RO_0000091
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
obo:RO_0000091
has disposition
obo:RO_0000092
disposition of
obo:RO_0001000
this cell derives from this parent cell (cell division)
obo:RO_0001000
this nucleus derives from this parent nucleus (nuclear division)
obo:RO_0001000
obo:IAO_0000125
obo:RO_0001000
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
obo:RO_0001000
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
obo:RO_0001000
derives_from
obo:RO_0001000
derives from
obo:RO_0001001
this parent cell derives into this cell (cell division)
obo:RO_0001001
this parent nucleus derives into this nucleus (nuclear division)
obo:RO_0001001
obo:IAO_0000125
obo:RO_0001001
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
obo:RO_0001001
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
obo:RO_0001001
derives_into
obo:RO_0001001
derives into
obo:RO_0001015
is location of
obo:RO_0001015
my head is the location of my brain
obo:RO_0001015
this cage is the location of this rat
obo:RO_0001015
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
obo:RO_0001015
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
obo:RO_0001015
location_of
obo:RO_0001015
obo:RO_0001901
obo:RO_0001015
location of
obo:RO_0001025
located in
obo:RO_0001025
my brain is located in my head
obo:RO_0001025
this rat is located in this cage
obo:RO_0001025
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
obo:RO_0001025
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
obo:RO_0001025
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
obo:RO_0001025
located_in
obo:RO_0001025
obo:RO_0001901
obo:RO_0001025
http://www.obofoundry.org/ro/#OBO_REL:located_in
obo:RO_0001025
located in
obo:RO_0001900
temporal interpretation
obo:RO_0001900
https://github.com/oborel/obo-relations/wiki/ROAndTime
obo:RO_0001901
## Elucidation
This is used when the statement/axiom is assumed to hold true 'eternally'
## How to interpret (informal)
First the "atemporal" FOL is derived from the OWL using the standard
interpretation. This axiom is temporalized by embedding the axiom
within a for-all-times quantified sentence. The t argument is added to
all instantiation predicates and predicates that use this relation.
## Example
Class: nucleus
SubClassOf: part_of some cell
forall t :
forall n :
instance_of(n,Nucleus,t)
implies
exists c :
instance_of(c,Cell,t)
part_of(n,c,t)
## Notes
This interpretation is *not* the same as an at-all-times relation
obo:RO_0001901
axiom holds for all times
obo:RO_0001902
## Elucidation
This is used when the first-order logic form of the relation is
binary, and takes no temporal argument.
## Example:
Class: limb
SubClassOf: develops_from some lateral-plate-mesoderm
forall t, t2:
forall x :
instance_of(x,Limb,t)
implies
exists y :
instance_of(y,LPM,t2)
develops_from(x,y)
obo:RO_0001902
relation has no temporal argument
obo:RO_0002000
the surface of my skin is a 2D boundary of my body
obo:RO_0002000
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
obo:RO_0002000
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
obo:RO_0002000
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
obo:RO_0002000
2D_boundary_of
obo:RO_0002000
boundary of
obo:RO_0002000
is 2D boundary of
obo:RO_0002000
is boundary of
obo:RO_0002000
obo:RO_0001901
obo:RO_0002000
2D boundary of
obo:RO_0002002
my body has 2D boundary the surface of my skin
obo:RO_0002002
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
obo:RO_0002002
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
obo:RO_0002002
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
obo:RO_0002002
has boundary
obo:RO_0002002
has_2D_boundary
obo:RO_0002002
obo:RO_0001901
obo:RO_0002002
has 2D boundary
obo:RO_0002211
obo:IAO_0000125
obo:RO_0002211
x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y
obo:RO_0002211
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
obo:RO_0002211
Chris Mungall
obo:RO_0002211
David Hill
obo:RO_0002211
Tanya Berardini
obo:RO_0002211
http://purl.obolibrary.org/obo/ro/docs/causal-relations
obo:RO_0002211
GO
obo:RO_0002211
Regulation precludes parthood; the regulatory process may not be within the regulated process.
obo:RO_0002211
regulates (processual)
obo:RO_0002211
false
obo:RO_0002211
regulates
obo:RO_0002212
obo:IAO_0000125
obo:RO_0002212
x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y
obo:RO_0002212
Chris Mungall
obo:RO_0002212
http://purl.obolibrary.org/obo/ro/docs/causal-relations
obo:RO_0002212
negatively regulates (process to process)
obo:RO_0002212
negatively regulates
obo:RO_0002213
x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y
obo:RO_0002213
Chris Mungall
obo:RO_0002213
http://purl.obolibrary.org/obo/ro/docs/causal-relations
obo:RO_0002213
positively regulates (process to process)
obo:RO_0002213
positively regulates
obo:RO_0002234
obo:IAO_0000125
obo:RO_0002234
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
obo:RO_0002234
Chris Mungall
obo:RO_0002234
produces
obo:RO_0002234
has output
obo:RO_0002297
an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
obo:RO_0002297
every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
obo:RO_0002297
obo:IAO_0000125
obo:RO_0002297
Chris Mungall
obo:RO_0002297
GOC:mtg_berkeley_2013
obo:RO_0002297
results_in_formation_of
obo:RO_0002297
results in formation of
obo:RO_0002350
An organism that is a member of a population of organisms
obo:RO_0002350
is member of is a mereological relation between a item and a collection.
obo:RO_0002350
is member of
obo:RO_0002350
member part of
obo:RO_0002350
SIO
obo:RO_0002350
obo:RO_0001901
obo:RO_0002350
member of
obo:RO_0002351
has member is a mereological relation between a collection and an item.
obo:RO_0002351
SIO
obo:RO_0002351
obo:RO_0001901
obo:RO_0002351
has member
obo:TRANS_0000000
Process in which a pathogen is transmitted directly or indirectly to a new host.
obo:TRANS_0000000
TRANS includes a sibling class of 'indirect' labeled 'direct', and these terms mirror standard definitions of 'direct transmission' and 'indirect transmission' in the literature. However, in the literature and in TRANS the definitions seem confused. For example, direct transmission is claimed to involve direct contact, yet respiratory droplet spread from a host - which plausibly involves a vehicle - is counted as direct rather than indirect transmission. We will follow standard use in part, adopting indirect transmission, but not direct, and defining a term for contact transmission.
obo:TRANS_0000000
obo:trans.owl
obo:TRANS_0000000
pathogen transmission process
obo:TRANS_0000002
Pathogen transmission process in which a pathogen is indirectly transferred to a host by intermediary vehicles or vectors.
obo:TRANS_0000002
John Beverley
obo:TRANS_0000002
obo:trans.owl
obo:TRANS_0000002
indirect pathogen transmission process
obo:TRANS_0000007
Pathogen transmission process in which a pathogen is transferred to a host through surface-to-surface contact.
obo:TRANS_0000007
http://purl.obolibrary.org/obo/trans.owl
obo:TRANS_0000007
John Beverley
obo:TRANS_0000007
contact pathogen transmission process
obo:TRANS_0000008
Indirect pathogen transmission process in which a pathogen is transmitted from a host expelling respiratory droplets to another host.
obo:TRANS_0000008
http://purl.obolibrary.org/obo/trans.owl
obo:TRANS_0000008
John Beverley
obo:TRANS_0000008
droplet pathogen transmission process
obo:UBERON_0000178
A fluid that is composed of blood plasma and erythrocytes.
obo:UBERON_0000178
obo:uberon.owl
obo:UBERON_0000178
blood
obo:UBERON_0000463
Anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
obo:UBERON_0000463
http://purl.obolibrary.org/obo/uberon.owl
obo:UBERON_0000463
organism substance
obo:UBERON_0006538
Organism substance that is secreted by a respiratory system.
obo:UBERON_0006538
http://purl.obolibrary.org/obo/uberon.owl
obo:UBERON_0006538
respiratory secretion
obo:UBERON_0007311
Matter ejected from the lungs, bronchi, and trachea, through the mouth.
obo:UBERON_0007311
http://purl.obolibrary.org/obo/uberon.owl
obo:UBERON_0007311
sputum
obo:VIDO_0000505
Infection that has as part virus particles located in the blood.
obo:VIDO_0000505
Albert Goldfain
obo:VIDO_0000505
Alexander Diehl
obo:VIDO_0000505
Lindsay Cowell
obo:VIDO_0000505
http://purl.obolibrary.org/obo/ido.owl
obo:VIDO_0000505
viremia
obo:VIDO_0000508
Virus that is in its assembled state consisting of genomic material (DNA or RNA) surrounded by coating molecules.
obo:VIDO_0000508
Albert Goldfain
obo:VIDO_0000508
Alexander Diehl
obo:VIDO_0000508
Lindsay Cowell
obo:VIDO_0000508
obo:VIDO_0000508
virion
obo:VIDO_0000564
Cidal agent with a viricidal disposition that is realized in a process of killing viruses.
obo:VIDO_0000564
Albert Goldfain
obo:VIDO_0000564
Alexander Diehl
obo:VIDO_0000564
Lindsay Cowell
obo:VIDO_0000564
http://purl.obolibrary.org/obo/ido.owl
obo:VIDO_0000564
viricide
obo:VIDO_0001004
Static agent bearing a virostatic disposition.
obo:VIDO_0001004
John Beverley
obo:VIDO_0001004
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001004
virostatic
obo:VIDO_0001016
Replication process in which a virus containing some portion of genetic material inherited from a parent virus is replicated.
obo:VIDO_0001016
John Beverley
obo:VIDO_0001016
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001016
virus replication
obo:VIDO_0001022
Disposition to kill viruses.
obo:VIDO_0001022
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001022
John Beverley
obo:VIDO_0001022
viricidal disposition
obo:VIDO_0001024
A disposition to inhibit the reproduction of viruses.
obo:VIDO_0001024
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001024
John Beverley
obo:VIDO_0001024
virostatic disposition
obo:VIDO_0001066
Acellular structure aggregate whose members are viruses
obo:VIDO_0001066
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001066
John Beverley
obo:VIDO_0001066
virus aggregate
obo:VIDO_0001067
Acellular infectious aggregate whose members are viroids.
obo:VIDO_0001067
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001067
John Beverley
obo:VIDO_0001067
viroid aggregate
obo:VIDO_0001069
Acellular infectious aggregate whose members are prions.
obo:VIDO_0001069
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001069
John Beverley
obo:VIDO_0001069
prion aggregate
obo:VIDO_0001086
Replication process in which a prion facilitates abnormal folding in proteins resulting in additional, identical, abnormally folded proteins.
obo:VIDO_0001086
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001086
John Beverley
obo:VIDO_0001086
prion replication
obo:VIDO_0001114
Infectious structure generative stage that is a temporal subdivision of a virus developmental process.
obo:VIDO_0001114
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001114
John Beverley
obo:VIDO_0001114
virus generative stage
obo:VIDO_0001120
Infectious disease whose physical basis is a virus disorder that is clinically abnormal in virtue of the presence of the relevant virus population.
obo:VIDO_0001120
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001120
John Beverley
obo:VIDO_0001120
viral disease course
obo:VIDO_0001122
Infectious disorder that exists as a result of a process of formation of disorder initiated by a virus.
obo:VIDO_0001122
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001122
John Beverley
obo:VIDO_0001122
virus disorder
obo:VIDO_0001128
Infectious structure host whose extended organism has some virus part.
obo:VIDO_0001128
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001128
John Beverley
obo:VIDO_0001128
virus host
obo:VIDO_0001169
Subclinical infection that is part of a virus host.
obo:VIDO_0001169
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001169
John Beverley
obo:VIDO_0001169
subclinical virus infection
obo:VIDO_0001188
Respiratory secretion composed of a small column of liquid, bounded completely or almost completely by free surfaces which maintains its shape due to the surface tension of the liquid.
obo:VIDO_0001188
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001188
John Beverley
obo:VIDO_0001188
respiratory droplet
obo:VIDO_0001189
Respiratory droplet bearing a fomite role.
obo:VIDO_0001189
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001189
John Beverley
obo:VIDO_0001189
respiratory droplet fomite
obo:VIDO_0001190
Respiratory droplet fomite with virus part.
obo:VIDO_0001190
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001190
John Beverley
obo:VIDO_0001190
respiratory droplet virus fomite
obo:VIDO_0001194
Pathogenesis process realization of a pathogenic disposition inhering in a virus or virus population, having at least the proper process parts: (1) pathogen transmission, (2) establishment of localization in host, (3) process of establishing a viral infection, and (4) appearance of a virus disorder.
obo:VIDO_0001194
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001194
John Beverley
obo:VIDO_0001194
viral pathogenesis
obo:VIDO_0001195
Process of establishing an infection in which a virus participates.
obo:VIDO_0001195
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001195
John Beverley
obo:VIDO_0001195
process of establishing viral infection
obo:VIDO_0001266
Cell with an adhesion factor part bearing a viral adhesion disposition
obo:VIDO_0001266
obo:VIDO_0001266
John Beverley
obo:VIDO_0001266
virus adhesion susceptible cell
obo:VIDO_0001267
Adhesion disposition borne by a macromolecule part of a virus that is the disposition to participate in a virus attachment process
obo:VIDO_0001267
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001267
John Beverley
obo:VIDO_0001267
viral adhesion disposition
obo:VIDO_0001331
Quality inhering in a portion of fluid that is the proportion of virions to volume of that portion of fluid
obo:VIDO_0001331
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001331
John Beverley
obo:VIDO_0001331
viral load
obo:VIDO_0001333
Virus which infects and replicates within or on bacteria or archea.
obo:VIDO_0001333
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001333
This is an inferred subclass of pathogen.
obo:VIDO_0001333
John Beverley
obo:VIDO_0001333
bacteriophage
obo:VIDO_0001334
Virus which infects and replicates within or on viruses.
obo:VIDO_0001334
This is an inferred subclass of pathogen.
obo:VIDO_0001334
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001334
John Beverley
obo:VIDO_0001334
virophage
obo:VIDO_0001336
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001336
John Beverley
obo:VIDO_0001336
establishment of localization in virus host
obo:VIDO_0001361
Virus that causes cancer in hosts.
obo:VIDO_0001361
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001361
John Beverley
obo:VIDO_0001361
oncovirus
obo:VIDO_0001363
Acellular self-replicating organic structure having some clinically abnormal arrangement of viral components (e.g. viral capsid, viral DNA/RNA).
obo:VIDO_0001363
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001363
John Beverley
obo:VIDO_0001363
disordered virus
obo:VIDO_0001364
Acellular structure having some arrangement of protein components, that is clinically abnormal.
obo:VIDO_0001364
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001364
John Beverley
obo:VIDO_0001364
disordered prion
obo:VIDO_0001365
Process beginning with the establishment of a virus in a host and ending with the first appearance of a virion following viral release, during which an infecting virus is uncoating to begin genome replication.
obo:VIDO_0001365
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001365
John Beverley
obo:VIDO_0001365
eclipse process
obo:VIDO_0001372
Site part of an antigen that is recognized by immune system cells and to which antibodies attach.
obo:VIDO_0001372
John Beverley
obo:VIDO_0001372
epitope site
obo:VIDO_0001386
Process in which multiple viral disease epidemics of the same type of viral disease unfold over overlapping periods of time and affect organism populations located in different geographic regions, including different countries and continents.
obo:VIDO_0001386
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001386
John Beverley
obo:VIDO_0001386
viral disease pandemic
obo:VIDO_0001387
Process of viral disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population.
obo:VIDO_0001387
http://purl.obolibrary.org/obo/vido.owl
obo:VIDO_0001387
John Beverley
obo:VIDO_0001387
viral disease epidemic
obo:VSMO_
Planned process with the objective to produce information about some evaluant with the purpose of, if justified by the information gathered, managing, directing, or protecting.
obo:VSMO_
http://purl.obolibrary.org/obo/vsmo.owl
obo:VSMO_
surveillance process
http://purl.obolibrary.org/obo/ido.owl/CARO_0000005
Site generated by morphogenetic or physiologic processes that is bounded by an anatomical surface.
http://purl.obolibrary.org/obo/ido.owl/CARO_0000005
http://purl.obolibrary.org/obo/caro.owl
http://purl.obolibrary.org/obo/ido.owl/CARO_0000005
John Beverley
http://purl.obolibrary.org/obo/ido.owl/CARO_0000005
anatomical space
http://purl.obolibrary.org/obo/ido.owl/CARO_0000062
Anatomical space that is part of a cell.
http://purl.obolibrary.org/obo/ido.owl/CARO_0000062
http://purl.obolibrary.org/obo/caro.owl
http://purl.obolibrary.org/obo/ido.owl/CARO_0000062
cell space
http://purl.obolibrary.org/obo/ido.owl/IDO_0001026
Disposition to inhibit the reproduction of fungi.
http://purl.obolibrary.org/obo/ido.owl/IDO_0001026
http://purl.obolibrary.org/obo/ido.owl
http://purl.obolibrary.org/obo/ido.owl/IDO_0001026
John Beverley
http://purl.obolibrary.org/obo/ido.owl/IDO_0001026
fungistatic disposition
http://purl.obolibrary.org/obo/ido.owl/IDO_0001036
Anatomical space through which a pathogen enters an organism.
http://purl.obolibrary.org/obo/ido.owl/IDO_0001036
http://purl.obolibrary.org/obo/ido.owl
http://purl.obolibrary.org/obo/ido.owl/IDO_0001036
John Beverley
http://purl.obolibrary.org/obo/ido.owl/IDO_0001036
pathogen portal of entry site
http://purl.obolibrary.org/obo/ido.owl/IDO_0001037
Anatomical space through which a pathogen exits an organism.
http://purl.obolibrary.org/obo/ido.owl/IDO_0001037
http://purl.obolibrary.org/obo/ido.owl
http://purl.obolibrary.org/obo/ido.owl/IDO_0001037
John Beverley
http://purl.obolibrary.org/obo/ido.owl/IDO_0001037
pathogen portal of exit site
http://purl.obolibrary.org/obo/ido.owl/IDO_0001072
Anatomical space in which an infection is located.
http://purl.obolibrary.org/obo/ido.owl/IDO_0001072
http://purl.obolibrary.org/obo/ido.owl
http://purl.obolibrary.org/obo/ido.owl/IDO_0001072
John Beverley
http://purl.obolibrary.org/obo/ido.owl/IDO_0001072
site of infection
http://purl.obolibrary.org/obo/ido.owl/IDO_0001107
Anatomical space in which an infection appears in a host organism.
http://purl.obolibrary.org/obo/ido.owl/IDO_0001107
http://purl.obolibrary.org/obo/ido.owl
http://purl.obolibrary.org/obo/ido.owl/IDO_0001107
John Beverley
http://purl.obolibrary.org/obo/ido.owl/IDO_0001107
source of infection site
http://purl.obolibrary.org/obo/ido.owl/IDO_0001130
A pathogen transporter role that is borne by an organism active in the transfer of an infectious agent or infectious structure to an organism of another species in which it can realize its infectious disposition.
http://purl.obolibrary.org/obo/ido.owl/IDO_0001130
John Beverley
http://purl.obolibrary.org/obo/ido.owl/IDO_0001130
The role is realized in a process that transfers an infectious organism from one location to another.
http://purl.obolibrary.org/obo/ido.owl/IDO_0001130
pathogen vector role
http://purl.obolibrary.org/obo/ido.owl/IDO_0001157
Pathogenic disposition borne by a pathogen to be transmitted to a host and become part of an infection in that host or immunocompetent members of the same species as the host.
http://purl.obolibrary.org/obo/ido.owl/IDO_0001157
http://purl.obolibrary.org/obo/ido.owl
http://purl.obolibrary.org/obo/ido.owl/IDO_0001157
John Beverley
http://purl.obolibrary.org/obo/ido.owl/IDO_0001157
infectious disposition
/VIDO_0001355
Infectious disease incidence profile comprised of a series of determinate viral disease incidence qualities caused by a specific virus in a population over time.
/VIDO_0001355
viral disease incidence profile
/VIDO_0001356
Infectious disease incidence proportion profile comprised of a series of viral disease incidence proportion qualities caused by a specific virus per unit time.
/VIDO_0001356
viral disease incidence proportion profile
/VIDO_0001357
Infectious disease incidence rate profile comprised of a series of viral disease rate qualities caused by a specific virus per unit time.
/VIDO_0001357
viral disease incidence rate profile
/VIDO_0001358
One-dimensional temporal region on which a virus is no longer replicating but remains within a host cell and which may be reactivated to begin replication again.
/VIDO_0001358
viral dormancy interval
/VIDO_0001359
Object consisting of an organic structure that is able to initiate replication of its structure in a host.
/VIDO_0001359
self-replicating organic structure
http://www.ebi.ac.uk/efo/EFO_0000684
Disease that occurs in different organs functioning in respiration and consisting especially of the nose, nasal passages, nasopharynx, larynx, trachea, bronchi, and lungs.
http://www.ebi.ac.uk/efo/EFO_0000684
http://www.ebi.ac.uk/efo/efo.owl
http://www.ebi.ac.uk/efo/EFO_0000684
respiratory system disease
http://www.ebi.ac.uk/efo/EFO_0009433
Respiratory system disease located in the lower respiratory tract.
http://www.ebi.ac.uk/efo/EFO_0009433
http://www.ebi.ac.uk/efo/efo.owl
http://www.ebi.ac.uk/efo/EFO_0009433
lower respiratory tract disease
http://www.ebi.ac.uk/efo/EFO_1000637
Progressive and life-threatening pulmonary distress in the absence of an underlying pulmonary condition, usually following major trauma or surgery.
http://www.ebi.ac.uk/efo/EFO_1000637
http://www.ebi.ac.uk/efo/efo.owl
http://www.ebi.ac.uk/efo/EFO_1000637
acute respiratory distress syndrome
oboInOwl:shorthand
shorthand
http://www.informatics.jax.org/vocab/gene_ontology/GO:0009405
Process that generates the ability of a pathogen to induce disorder in an organism.
http://www.informatics.jax.org/vocab/gene_ontology/GO:0009405
Process that is the realization of a pathogenic disposition inhering in an pathogen or pathogen population, having at least the proper process parts: (1) pathogen transmission, (2) establishment of localization in host, (3) process of establishing an infection, and (4) appearance of disorder.
http://www.informatics.jax.org/vocab/gene_ontology/GO:0009405
http://purl.obolibrary.org/obo/go.owl
http://www.informatics.jax.org/vocab/gene_ontology/GO:0009405
John Beverley
http://www.informatics.jax.org/vocab/gene_ontology/GO:0009405
pathogenesis
http://www.ontologyrepository.com/CommonCoreOntologies/Country
A Geopolitical Entity that delimits a Government with effective internal and external sovereignty over the region and its population, and which is not dependent on or subject to any other power or Geopolitical Entity.
http://www.ontologyrepository.com/CommonCoreOntologies/Country
http://www.ontologyrepository.com/CommonCoreOntologies/
http://www.ontologyrepository.com/CommonCoreOntologies/Country
country
http://www.ontologyrepository.com/CommonCoreOntologies/DescriptiveInformationContentEntity
Information Content Entity that consists of a set of propositions that describe some Entity.
http://www.ontologyrepository.com/CommonCoreOntologies/DescriptiveInformationContentEntity
http://www.ontologyrepository.com/CommonCoreOntologies/
http://www.ontologyrepository.com/CommonCoreOntologies/DescriptiveInformationContentEntity
descriptive information content entity
http://www.ontologyrepository.com/CommonCoreOntologies/DesignativeInformationContentEntity
Information Content Entity that consists of a set of symbols that denote some Entity.
http://www.ontologyrepository.com/CommonCoreOntologies/DesignativeInformationContentEntity
http://www.ontologyrepository.com/CommonCoreOntologies/
http://www.ontologyrepository.com/CommonCoreOntologies/DesignativeInformationContentEntity
designative information content entity
http://www.ontologyrepository.com/CommonCoreOntologies/DirectiveInformationContentEntity
Information Content Entity that consists of a set of propositions or images (as in the case of a blueprint) that prescribe some Entity.
http://www.ontologyrepository.com/CommonCoreOntologies/DirectiveInformationContentEntity
http://www.ontologyrepository.com/CommonCoreOntologies/
http://www.ontologyrepository.com/CommonCoreOntologies/DirectiveInformationContentEntity
directive information content entity
http://www.ontologyrepository.com/CommonCoreOntologies/DivisionOfGeopoliticalEntity
A Geospatial Region that is a fiat division of a Geopolitical Entity and not a Geopolitical Entity.
http://www.ontologyrepository.com/CommonCoreOntologies/DivisionOfGeopoliticalEntity
http://www.ontologyrepository.com/CommonCoreOntologies/
http://www.ontologyrepository.com/CommonCoreOntologies/DivisionOfGeopoliticalEntity
division of geopolitical entity
http://www.ontologyrepository.com/CommonCoreOntologies/GeopoliticalEntity
A geospatial region that delimits the authority of a formally constituted government to exercise its control within the bounded area.
http://www.ontologyrepository.com/CommonCoreOntologies/GeopoliticalEntity
http://www.ontologyrepository.com/CommonCoreOntologies/
http://www.ontologyrepository.com/CommonCoreOntologies/GeopoliticalEntity
geopolitical entity
http://www.ontologyrepository.com/CommonCoreOntologies/GeospatialLocation
A Geospatial Region at which an Entity or Event is located.
http://www.ontologyrepository.com/CommonCoreOntologies/GeospatialLocation
http://www.ontologyrepository.com/CommonCoreOntologies/
http://www.ontologyrepository.com/CommonCoreOntologies/GeospatialLocation
geospatial location
http://www.ontologyrepository.com/CommonCoreOntologies/GeospatialRegion
A site at or near the surface of the Earth.
http://www.ontologyrepository.com/CommonCoreOntologies/GeospatialRegion
http://www.ontologyrepository.com/CommonCoreOntologies
http://www.ontologyrepository.com/CommonCoreOntologies/GeospatialRegion
geospatial region
rdfs:label
label