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 &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; 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