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.
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
BFO CLIF specification label
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example
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.
example of usage
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
curator note
An administrative note of use for a curator but of no use for a user
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
term tracker item
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
The 'term requester' can credit the person, organization or project who request the ontology term.
ontology term requester
is denotator type
relates an class defined in an ontology, to the type of it's denotator
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
expand assertion to
ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
Chris Mungall
first order logic expression
antisymmetric property
part_of antisymmetric property xsd:true
use boolean value xsd:true to indicate that the property is an antisymmetric property
Alan Ruttenberg
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
PERSON:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO"
Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits)
has ID digit count
Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms
has ID range allocated to
Relating an ontology used to record id policy to the ontology namespace whose policy it manages
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.
has ID prefix
elucidation
person:Alan Ruttenberg
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
has associated axiom(nl)
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
is allocated id range
Add as annotation triples in the granting ontology
Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
has axiom id
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom label
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
temporal interpretation
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
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.
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
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'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
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.
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'.
has_part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[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])
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
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
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])
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
preceded by
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.
is preceded by
preceded_by
precedes
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
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
Not sure if this has an IRI yet, so I supplied a placeholder.
occupies temporal region
results in
has specified input
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.
is specified input of
has specified output
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.
is specified output of
inheres in
this fragility inheres in this vase
this red color inheres in this apple
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
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
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
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.
bearer_of
is bearer of
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
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.
is role of
role_of
role of
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
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.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
disposition of
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
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
location_of
location of
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
located_in
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
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
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates
x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y
negatively regulates (process to process)
negatively regulates
x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y
positively regulates (process to process)
positively regulates
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.
has output
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.
every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
results in formation of
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
Infectious disease inhering in a virus disorder that is a disorder due to the presence of the virus.
viral disease
Objective specification that is realized by processes that are able or likely to stop the spread of a disease in a population.
infectious disease control objective specification
Plan specification whose objective specification is an infectious disease control objective specification.
infectious disease control strategy
Algorithm that models the progress of a transmissible disease in a population.
disease transmission model
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.
place closure control strategy
Infectious disease control strategy that has an action specification that is realized in isolating organsims who are infectious.
case isolation control strategy
Infectious disease control strategy that has a vector control action specification as part.
vector control strategy
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.
quarantine control strategy
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.
disease surveillance objective specification
Infectious disease control strategy that identifies and treats contacted organisms in a host population.
contact tracing
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
temporal region
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
two-dimensional spatial region
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
spatiotemporal region
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
realizable entity
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
zero-dimensional spatial region
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
quality
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
specifically dependent continuant
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
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.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
role
an edge of a cube-shaped portion of space.
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])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
one-dimensional spatial region
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
object aggregate
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
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])
site
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
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.
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).
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
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
object
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
Continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
function
the boundary between the 2nd and 3rd year of your life.
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])
process boundary
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).
one-dimensional temporal region
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
process profile
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
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])
history
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
Anatomical entities - like other material entities - may have immaterial parts.
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
Nucleic acid composed of nucleotides containing deoxyribose and linked by phosphodiester bonds.
deoxyribonucleic acid
This is a suggested revision to the ChEBI definition.
John Beverley
Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc.
Role inhering in a molecular entity or part of that entity, realized in biological processes.
biological role
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
Macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases.
nucleic acid
Nucleic acid composed of nucleotides containing ribose and linked by phosphodiester bonds.
ribonucleic acid
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.
macromolecule
A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
protein
DNA consisting of two parallel strands joined by hydrogen bonds between complementary purines and pyrimidines.
double-stranded DNA
This is a suggestion for the ChEBI definition of this term, since it currently lacks a definition.
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
This should be an inferred subclass of BFO:object. -John
Processed material bearing a reagent role.
reagent
Reagent that is comprised of immunoglobulins produced by B cells in response to an antigen.
antibody reagent
This term should be move from ERO to VIDO.
viral plaque assay
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.
intervention
Assay analyzing blood serum and other bodily fluids, to detect the presence of serum antibodies.
serology assay
Assay measuring the concentration of a substance in a material by exploiting binding between an analyte and a corresponding detection antibody.
immunoassay
Temporal subdivision of a developmental process.
generative stage
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).
Process involved in the carrying out of an immune response by a leukocyte.
Immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
Immune response mediated through a body fluid.
Process specifically pertinent to the functioning of functionally integrated units.
Protein surrounding virion nucleic acid in some virus particles.
The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
viral capsid
This is a suggested revision to the GO definition and hierarchy placement.
Macromolecule lipid bilayer of a virion surrounding capsid.
The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
viral envelope
Virus generative stage during which an incoming virus is disassembled in the host cell to release a replication-competent viral genome.
virus uncoating stage
This is a suggested revision to the GO definition.
Virus generative stage during which a virion protein binds to molecules on the host surface or host cell surface projection.
virus attachment stage
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.
virus synthesis stage
Virus generative stage during which viral mRNA is translated into viral protein, using the host cellular machinery.
virus translation stage
Virus developmental stage during which a viral genome, or part of a viral genome, is transcribed within the host cell.
virus transcription stage
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.
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.
Biological process whose specific outcome is the progression of a functional, integrated, unit.
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.
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.
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.
symbiotic process
Attachment of a symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly.
Penetration by an organism into the body, tissues, or cells of the host organism.
Penetration by an organism into its host organism via active breaching of the physical barriers of the host organism.
Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
Virus generative stage during which a virion or viral nucleic acid breaches the barriers of a host.
virus penetration stage
Protein subunit comprising viral capsid.
capsomere
Process that stops, prevents, or reduces the frequency, rate or extent of a biological process.
negative regulation of biological process
Process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process in which a virus is a participant.
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.
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).
negative regulation of developmental process
Process that localizes a substance or cellular component via movement, tethering or selective degradation.
Process that modulates a measurable attribute of any biological process, quality or function.
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.
virus release stage
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.
objective specification
Directive information entity that describes an action the bearer will take
action specification
information content entity
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.
algorithm
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.
plan specification
Virus which infects and replicates within or on fungi.
mycovirus
A role borne by an organism in symbiosis.
symbiont role
Symbiont role borne by an organism in which both symbionts derive a growth, survival, or fitness advantage from symbiosis.
mutualist role
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.
commensal role
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.
parasite role
Infectious disposition to become part of a disorder only in organisms whose defenses are compromised.
opportunistic infectious disposition
Infectious disposition to become part of a disorder in immunocompetent organisms.
A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts.
primary infectious disposition
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.
symbiont host role
Symbiont host role borne by an organism iwhose partner in symbiosis reaches developmental maturity or reproduces sexually in the host.
definitive host role
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.
intermediate host role
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.
dead-end host role
Pathogen host role borne by an organism whose extended organism contains an infectious agent.
infectious agent host role
Host role borne by an object having a pathogen as part or an borne by an organism having a pathogen as part of its extended organism.
pathogen host role
A pathogen vector role borne by an organism in virtue of the fact that the pathogen does not multiply in or on the vector.
mechanical vector role
A pathogen vector role borne by an organism in virtue of the fact that the pathogen multiplies in the vector.
biological vector role
A pathogen transporter role borne by an entity in virtue of the fact that the entity is not a complete organism.
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
I've expanded this definition and label to cover infectious agent pathogens and infectious structure pathogens. -John Beverley
Drinking water bears the infectious agent vehicle role, but does not bear either of the subtype roles.
pathogen vehicle role
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.
Examples include blood, serum, tissue, or fresh produce.
biological vehicle role
An infectious agent vehicle role borne by an entity in virtue of the fact that the entity is not alive.
fomite role
Role borne by a material entity in which pathogens can persist, and from which they can be transmitted to hosts.
reservoir of pathogen role
Disposition borne by a biological macromolecule produced by a pathogen that is a disposition to undergo processes that increase the pathogen's virulence.
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.
virulence factor disposition
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.
toxin disposition
Toxin disposition to damage cells or extracellular matrix by a direct enzymatic process.
exotoxin disposition
Role borne by an anatomical entity that serves as the site through which a pathogen enters a host.
pathogen portal of entry role
Role borne by an anatomical entity that serves as the site through which a pathogen exits a host.
pathogen portal of exit role
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.
primary infection role
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.
secondary infection role
Disease whose physical basis is an infectious disorder.
tranmissible disease
infectious disease
Disposition borne by a macromolecule that is the disposition to participate in adherence to a host.
adhesion disposition
Disposition borne by a biological macromolecule that is the disposition to facilitate breach of and entry through host barriers.
invasion disposition
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.
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.
protective resistance
Protective resistance that mitigates the damaging effects of a drug.
resistance to drug
Protective resistance that inheres in an organism and mitigates the damaging effects of a pathogen.
resistance to pathogen
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.
herd immunity to infectious organism
Resistance to pathogen that inheres in an organism due to immune system components in its extended organism.
immunity to pathogen
Immunity to pathogen that results in elimination of the infectious agent from the host.
Sterilizing immunity is typically conferred by neutralizing antibodies.
sterilizing immunity to infectious agent
Disposition borne by a material entity to establish localization in and result in formation of disorder in a host or immunocompetent members of the same species as the host.
pathogenicity
pathogenic disposition
Disposition borne by a pathogen that is the disposition to penetrate the epithelial barriers of an organism of another species.
invasive disposition
Infectious disposition to be transmitted from an infected, non-human host to a human host.
zoonotic disposition
Infectious disposition to be transmitted from an infected, human host to a non-human host.
An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis.
reverse zoonotic disposition
Disposition that inheres in a collection of entities in virtue of the individual dispositions of the constituents of that collection.
This should be pushed up to: http://purl.obolibrary.org/obo/bfo.owl
collective disposition
Organism that is experiencing immunosuppression.
immunosuppressed organism
Organism that has immunocompetence.
immunocompetent organism
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.
contagiousness
Host that contains a colony in or on its extended organism.
colonized host
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.
The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening.
infectious pathogen transmissibility
Quality that inheres in a pathogen and is the liklihood that the infectious disposition will be realized upon exposure of a susceptible organism.
This quality is measured by the proportion of exposed who become infected.
infectivity
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.
This quality is measured by the proportion of clinically apparent cases that are severe or fatal.
virulence
Quality that inheres in an entity and is the degree to which it can be harmed by another entity.
Low susceptibility is often referred to as resistance. In this sense, resistance is a quality.
susceptibility
Susceptibility that inheres in an organism and is the degree to which it can be harmed by an infectious agent.
susceptibility to infectious agent
Susceptibility that is the degree to which an entity can be harmed or inhibited from surviving by a drug.
drug susceptibility
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.
drug susceptibility of infectious agent
Infection comprised of infectious organisms from different species.
complex infection
Infection in which pathogen parts persist in the extracellular space of the host.
extracellular infection
Infection in which pathogen parts persist inside host cells.
intracellular infection
Infection for which the infectious agents or structures that are part of the infection are distributed throughout the host.
systematic infection
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.
local infection
Infectious disease course that begins soon after infection is established and progresses rapidly to severe stages.
acute infectious disease course
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.
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.
infectious disease incidence
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.
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.
infection incidence
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.
cumulative incidence of infectious disease
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.
infectious disease incidence proportion
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.
cumulative incidence of infection
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.
infection incidence proportion
Quality that inheres in an organism population and is the infectious disease incidence proportion per unit time.
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.
infectious disease incidence rate
Quality that inheres in an organism population and is the infection incidence proportion per unit time.
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.
infection incidence rate
Quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time.
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.
infectious disease prevalence
Quality that inheres in an organism population and is the number of organisms in the population infected with a pathogen at a specified time.
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.
infection prevalence
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.
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.
infectious disease lifetime prevalence
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.
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.
pathogen seroprevalence
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.
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.
infectious disease mortality rate
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.
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.
infectious disease endemicity
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.
Sporadic quality of infectious disease is relational to previous prevalence of the disease.
infectious disease sporadicity
Disease course that is the realization of an infectious disease.
infectious disease course
Chronic infectious disease course that does not progress to severe stages for a long period of time.
long-term non-progressing infectious disease course
Process by which an organism acquires immunity to an infectious agent.
immunization against infectious agent
Immunization that begins with exposure of an organism to antigen and results in immunity against an infectious agent.
inoculation
active immunization against infectious agent
Active immunization that begins with exposure of an organism to a vaccine .
vaccination against infectious agent
Active immunization that begins with exposure to smallpox in the form of a scab from a pustule and results in immunity against smallpox.
variolation
Immunization that begins with transfer to an organism of molecules not produced by that organism and that confer immunity against an infectious agent.
passive immunization against infectious agent
Process of infectious disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population.
infectious disease epidemic
Infectious disease epidemic during which statistically significant increases of infectious disease incidences 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.
infectious disease pandemic
Disorder that is part of an organism whose extended organism has some infectious agent or structure as part, which participates in the formation of infection.
infectious disorder
Infection that has as part bacteria located in the blood.
bacteremia
Aggregate of organisms of the same species.
The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age.
organism population
Organism population whose members have an infection.
infected population
Organism population in whose members an infectious disease is being realized.
diseased population
Organism population whose members each have an infectious disposition.
infectious agent population
Organism population whose members are not infected with an infectious agent and who lack immunity to the infectious agent.
at-risk population
susceptible population
Organism population whose members are participating in non-parasitic symbiosis with a particular host.
normal resident microflora population
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.
normal resident microbiota population
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.
incubation interval
One-dimensional temporal region during which a pathogen host bears a contagiousness disposition.
communicability interval
Organism bearing a symbiont role.
symbiont
Organism that can only reach developmental maturity, replicate, or persist in symbiosis.
obligatory symbiont
Symbiont bearing a mutualist role.
mutualist
Symbiont bearing a commensal role.
commensal
Symbiont bearing a parasite role.
parasite
Material entity bearing a pathogenic disposition.
pathogen
Pathogen bearing a primary infectious disposition.
primary pathogen
Object bearing a host role.
http://purl.obolibrary.org/obo/ido.owl This should be pushed to an upper-level ontology.
host
Host bearing a definitive host role.
primary host
definitive host
Host bearing an intermediate host role.
secondary host
intermediate host
Host bearing a dead-end host role.
incidental host
dead-end host
Pathogen host bearing an infectious agent host role.
infectious agent host
Host bearing a pathogen host role.
pathogen host
Infectious agent host bearing the infectious agent carrier role.
asymptomatic infectious agent carrier
Pathogen transporter bearing a pathogen vehicle role.
pathogen vehicle
Pathogen vehicle bearing a fomite role.
fomite
Material entity bearing a pathogen reservoir role.
infectious agent reservoir
A macromolecule produced by a pathogen and that has a virulence factor disposition.
virulence factor
Biological macromolecule that has an invasion disposition.
invasin
invasion factor
Molecular entity that has a toxin disposition.
toxin
Toxin bearing an exotoxin disposition.
exotoxin
Exotoxin bearing an enterotoxin disposition.
enterotoxin
Toxin bearing an endotoxin disposition that is a structural component of a pathogen and is released from the pathogen only upon cytolysis.
endotoxin
Anatomical entity bearing a pathogen portal of entry role.
pathogen portal of entry
Anatomical entity bearing a pathogen portal of exit role.
pathogen portal of exit
Biological macromolecule that has an adhesion disposition.
adhesin
adhesion molecule
adhesion factor
Infectious disorder bearing a primary infection role.
primary infection
Infectious disorder bearing a secondary infection role.
secondary infection
Infectious disease inhering in an infectious disorder composed of pathogens having zoonotic dispositions.
zoonosis
Infection that is part of an asymptomatic carrier.
subclinical infection
Material entity bearing protective resistance.
resistant entity
Immunity to pathogen that inheres in an organism in virtue of germline encoded components that directly recognize components of potential pathogens.
innate immunity to infectious agent
Immunity to pathogen that inheres in an organism in virtue of components of its circulating body fluid, e.g. blood, lymph, hemolymph.
"Circulating body fluid" refers to blood, lymph, and hemolymph.
humoral immunity to infectious agent
Immunity to pathogen that inheres in an organism in virtue of its leukocytes.
leukocyte-mediated immunity to infectious agent
Immunity to pathogen that inheres in an organism in virtue of antibodies not produced by that organism.
passive immunity to infectious agent
Resistance to drug that mitigates the damaging effects of an antibiotic.
antibiotic resistance
Pathogen whose infection incidence is increasing following its first introduction into a new host Species.
emerging pathogen
Toxin bearing a cytotoxin disposition.
cytotoxin
Collective disposition to initiate processes that result in a disorder.
collective pathogenic disposition
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.
infection
Resistance to pathogen that inheres in an organism due to an allele or combination of alleles in its genome.
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.
genetic resistance to pathogen
Collective disposition the realization of which mitigates the damaging effects of some entity on members of the collection.
collective resistance disposition
Organism that has an immunodeficiency.
immunocompromised organism
immunodeficient organism
Infectious disease course that unfolds over a long period of time.
chronic infectious disease course
Organism population whose members have acquired immunity to an infectious agent.
immune population
One-dimensional temporal region during which a transmission process occurs.
This should be imported from: http://purl.obolibrary.org/obo/trans.owl
transmission interval
Organism that has an infectious disposition.
This is an inferred subclass of pathogen.
infectious agent
Process by which an infectious agent or infectious structure, established in a host, becomes part of an infection in the host.
process of establishing an infection
Establishment of localization in host process in which an organism or acellular structure establishes a colony in or on a host.
colonization of host
Colonization of host process that results in a clinically abnormal colony.
establishment of a clinically abnormal colony
Process in which an entity comes into being as a result of the process.
production
Production process in which a participant creates a copy of itself.
replication
Process that attenuates an immune response.
immunosuppression
Immunosuppression which unfolds as part of the natural self-regulation of an immune response.
physiologic immunosuppression
Immunosuppression process which arises as the result of a disorder.
pathologic immunosuppression
Organism population persisting in a site it has colonized.
colony
Colony whose members are infectious agents.
infectious agent colony
Disorder of an immune system component that results in defective functioning of the immune system.
immunodeficiency
Disposition inhering in an organism that is the disposition to mount a normal immune response.
immunocompetence
Disposition whose realization negatively regulates an immune response.
immunosuppressive disposition
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.
adaptive immunity to infectious agent
acquired immunity to infectious agent
Infectious disposition to be transmitted from one organism to another of the same species by horizontal transmission.
communicability
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.
establishment of localization in host
Process by which a disorder comes into existence.
appearance of disorder
Infectious disorder that is the physical basis for an unfolding acute infectious disease course.
acute infection
Infection that persists for an extended period of time.
chronic infection
Role borne by an acellular structure containing a material entity other than the structure, or organism whose extended organism contains a material entity other than the organism, realized in use of that structure or organism as a site of reproduction or replication.
This should be pushed to: http://purl.obolibrary.org/obo/ogms.owl
host role
Infection resulting from a transmission process that unfolds in a hospital.
nosocomial infection
hospital-acquired infection
Infection resulting from a transmission process that did not unfold in a health care facility.
community-acquired infection
Toxin bearing a neurotoxin disposition.
neurotoxin
Infection established as a result of spread from another infection in a non-adjacent location in the extended organism of the host.
metastatic infection
Role borne by a material entity that contains a site from which an infectious agent is transmitted.
source of infection role
Infection resulting from a transmission process that unfolds in a nursing home.
nursing-home acquired infection
Pathogen disposed to infect human hosts.
infectious human pathogen
Immunodeficiency that is not caused by a genetic predisposition.
Causes of acquired immunodeficiences include infection and drug treatments (e.g. chemotherapy).
acquired immunodeficiency
Infection comprised of infectious organisms or structures all of the same Species.
simple infection
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.
re-emerging pathogen
Colonization of host in a human.
colonization of human
Immunodeficiency that exists in an organism because of a genetic predisposition.
Infectious disease inhering in an infectious disorder composed of pathogens bearing reverse zoonotic dispositions.
Pathogen with an opportunistic infectious disposition.
Disposition to undergo a transmission process.
This should be pushed to: http://purl.obolibrary.org/obo/trans.owl
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.
horizontal pathogen transmission process
Organism that is not infected with an infectious agent and lacks protective immunity to the infectious agent.
Process that stops, prevents, or reduces the frequency, rate or extent of a life-sustaining process.
negative regulation of life-sustaining process
Material entity bearing a source of infection role.
Process that stops, prevents, or reduces the frequency, rate or extent of a production process.
negative regulation of production
Process that stops, prevents, or reduces the frequency, rate or extent of a replication process.
negative regulation of replication
Process boundary that marks the start of the life cycle of a pathogen.
pathogen birth process boundary
Process boundary that marks the end of the life cycle of a pathogen.
pathogen death process boundary
fungicidal disposition
bactericidal disposition
Disposition to inhibit the reproduction of bacteria.
bacteriostatic disposition
We use parasite in the sense of organisms that are parasitic in humans.
parasiticidal disposition
Disposition to inhibit the reproduction of parasites.
'Parasite' is used in the sense of eukaryotic organisms that are parasitic in humans.
parasitostatic disposition
Static agent bearing a bacteriostatic disposition.
bacteriostatic
Cidal agent with a bactericidal disposition that is realized in a process of killing bacteria.
bactericidal
Self-replicating organic structure that has an infectious disposition.
infectious structure
Object aggregate that consists of acellular self-replicating organic structures.
acellular self-replicating organic structure aggregate
Zero-dimensional temporal region occupied by a pathogen birth process boundary.
pathogen birth temporal region
Zero-dimensional temporal region occupied by a pathogen death process boundary.
pathogen death temporal region
prions
viruses
Object consisting of an organic structure that is able to initiate replication of its structure in a host.
Yongqun He
self-replicating organic structure
Material entity with a cidal agent disposition that is realized in a process of killing bacteria, fungi, parasites, or viruses.
cidal agent
Material entity bearing a static agent disposition.
static agent
Disposition to inhibit the reproduction of bacteria, fungi, or parasites, or inhibit the replication of viruses.
static agent disposition
Disposition to kill bacteria, fungi, parasites, or viruses.
cidal agent disposition
Pathogen host bearing an infectious structure host role.
infectious structure host
Pathogen host role borne by an object or organism whose extended organism contains an infectious structure.
infectious structure host role
Material entity bearing a pathogen transporter role.
pathogen transporter
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.
pathogen transporter role
Pathogen generative stage that is a temporal subdivision of an infectious agent developmental process.
infectious agent generative stage
Pathogen generative stage that is a temporal subdivision of an infectious structure developmental process.
infectious structure generative stage
Generative stage that is a temporal subdivision of a pathogen developmental process.
pathogen generative stage
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.
asymptomatic carrier role
Pathogen host with an infection as part but exhibits no signs or symptoms.
asymptomatic carrier
Infectious structure host bearing an asymptomatic carrier role.
asymptomatic infectious structure carrier
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.
symptomatic carrier role
Pathogen host with infection as part that exhibits symptoms.
symptomatic carrier
Toxin disposition realized in processes resulting in damage to host cells.
cytotoxin disposition
Toxin disposition realized in damaging or interfering with the function of nerve tissue.
neurotoxin disposition
Toxin disposition that is a structural component of a pathogen and is realized only during cytolsis.
endotoxin disposition
Exotoxin disposition ithat is realized in a process of damaging intestinal mucosa cells.
enterotoxin disposition
Infectious structure host bearing a symptomatic carrier role.
symptomatic infectious structure carrier
Infectious agent host bearing an infectious agent carrier role.
symptomatic infectious agent carrier
Self-replicating organic structure aggregate whose members are infectious structures.
infectious structure aggregate
Pathogen transporter bearing a pathogen vector role.
pathogen vector
Pathogen vector bearing a biological vector role.
biological vector
Pathogen vector bearing a mechanical vector role.
mechanical vector
Pathogen vehicle bearing a biological vehicle role.
biological vehicle
Establishment of localization in or on a human host.
establishment of localization in human host
One-dimensional temporal region beginning with the establishing of an infection in a host and ending when the host becomes contagious.
latency interval
Process boundary that marks the start of an infection, latency process, and incubation process.
infection start process boundary
Process boundary marking the end of a latency period.
latency end process boundary
Process boundary marking the end of an incubation period.
incubation end process boundary
Zero-dimensional temporal region occupied by an infection start process boundary.
infection start temporal region
Zero-dimensional temporal region occupied by an infection end process boundary.
infection end temporal region
Zero-dimensional temporal region occupied by a latency end process boundary.
latency end temporal region
Zero-dimensional temporal region occupied by a communicability end process boundary.
communicability end temporal region
Zero-dimensional temporal region occupied by an incubation end process boundary.
incubation end temporal region
Zero-dimensional temporal region occupied by a communicability start process boundary.
communicability start temporal region
Process boundary marking the start of a latency interval.
latency start process boundary
Process boundary marking the start of an incubation interval.
incubation start process boundary
Process boundary marking the start of a communicability interval.
communicability start process boundary
Process boundary marking the end of a communicability interval.
communicability end process boundary
Biological role borne by a molecular entity that serves as the site on an antigen realized in immune system recognition and binding by antibodies.
epitope role
Surveillance process aiming to produce information about one or several objects, in the form of microorganisms, which have the role of pathogen.
pathogen surveillance
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.
vector surveillance
Self-replicating organic structure comprised of acellular organic parts.
acellular self-replicating organic structure
Object aggregate that consists of self-replicating organic structures.
self-replicating organic structure aggregate
Acellular self-replicating organic structure with RNA or DNA genetic material which uses host metabolic resources for RNA or DNA replication.
The mass noun term label imported from the NCBITaxon "Viruses" has been replaced with the count noun "virus", to align with BFO.
Virus with genetic material encoded in single-stranded RNA that replicates using reverse transcriptase to convert positive-sense RNA to DNA.
single-stranded RNA retrovirus
Virus with genetic material encoded in single-stranded DNA and replicates using DNA polymerase.
single-stranded DNA virus
Virus that has its genetic material encoded in double-stranded DNA and replicates using DNA polymerase.
double-stranded DNA virus
Virus with genetic material that is encoded in double-stranded DNA and replicates through single-stranded RNA intermediate.
double-stranded DNA retrovirus
Virus with genetic material encoded in single-stranded RNA that can be translated directly into proteins.
positive-sense single-stranded RNA virus
Virus with genetic material encoded in single-stranded RNA that can be translated into proteins only after transcription by RNA polymerase.
negative-sense single-stranded RNA virus
Virus with genetic material encoded in double-stranded RNA.
double-stranded RNA virus
Acellular self-replicating organic structure that consists of an abnormally folded protein which replicates by by transmitting its abnormal structure to other proteins.
prion
Process that realizes a plan which is the concretization of a plan specification.
planned process
Material entity that is created or changed during material processing.
processed material
Planned process with the objective to produce information about some evaluant.
assay
Role inhering in a molecular entity when the molecular entity is used to produce a chemical reaction to detect, measure, or produce other substances.
reagent role
Planned process which results in physical changes in a specified input material.
material processing
Biological role inhering in some molecular entity, that stimulates an immune response when identified by the immune systems cells.
antigen role
Double stranded DNA that is the specified output of a polymerase chain reaction
PCR product
Enzymatic amplification in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication.
polymerase chain reaction
Material processing amplifying cDNA during a PCR reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity.
reverse transcribed PCR
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.
Object 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.
This is a suggested revision to the OBI definition and hierarchy placement. Using OBI was a deliberate choice over CARO, for reasons discussed here: 10.31219/osf.io/5bx8c
Material processing using enzymes to increase the number of molecules of a material entity.
enzymatic amplification
Material entity bearing the epitope role.
epitope
Material entity bearing an antigen role.
antigen
Process experienced by a patient which can only be experienced by the patient, that is hypothesized to be clinically relevant.
Disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
Material entity that is a clinically abnormal part of an extended organism.
Totality of all processes through which a given disease instance is realized.
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.
Material entity that is a human made structure with firm connection between its foundation and the ground.
architectural structure
Architectural structure that bears some function.
facility
Facility that is run by a hospital organization and is the bearer of a hospital function.
hospital facility
Facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population.
healthcare facility
Process in which a pathogen is transmitted directly or indirectly to a new host.
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.
This is a suggested revision of the TRANS definition.
Pathogen transmission process in which a pathogen is indirectly transferred to a host by intermediary vehicles or vectors.
Pathogen transmission process in which a pathogen is transferred to a host through surface-to-surface contact.
contact pathogen transmission process
Indirect pathogen transmission process in which a pathogen is transmitted from a host expelling respiratory droplets to another host.
droplet pathogen transmission process
A fluid that is composed of blood plasma and erythrocytes.
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
haemolymphatic fluid
Material 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.
organism substance
Anatomical entity that has mass.
material anatomical entity
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
bodily fluid
A portion of organism substance that secreted_by a respiratory system.
respiratory secretion
Matter ejected from the lungs, bronchi, and trachea, through the mouth.
sputum
Infection that has as part virus particles located in the blood.
viremia
Virus that is in its assembled state consisting of genomic material (DNA or RNA) surrounded by coating molecules.
virion
Cidal agent with a viricidal disposition that is realized in a process of killing viruses.
viricide
Static agent bearing a virostatic disposition.
Replication process in which a virus containing some portion of genetic material inherited from a parent virus is replicated.
virus replication
Disposition to kill viruses.
viricidal disposition
A disposition to inhibit the reproduction of viruses.
virostatic disposition
Acellular self-replicating organic structure aggregate whose members are viruses
virus aggregate
Acellular self-replicating organic structure aggregate whose members are viroids.
viroid aggregate
Acellular self-replicating organic structure aggregate whose members are prions.
prion aggregate
Replication process in which a prion facilitates abnormal folding in proteins resulting in additional, identical, abnormally folded proteins.
prion replication
Infectious structure generative stage that is a temporal subdivision of a virus developmental process.
virus generative stage
Infectious disease whose physical basis is a virus disorder that is clinically abnormal in virtue of the presence of the relevant virus population.
viral disease course
Infectious disorder that exists as a result of a process of formation of disorder initiated by a virus or virus population.
virus disorder
Infectious structure host whose extended organism has some virus part.
virus host
Subclinical infection that is part of a virus host.
subclinical virus infection
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.
respiratory droplet
Respiratory droplet bearing a fomite role.
respiratory droplet fomite
Respiratory droplet fomite with virus part.
respiratory droplet virus fomite
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.
viral pathogenesis
Process of establishing an infection in which a virus participates.
process of establishing viral infection
Cell with an adhesion factor part bearing a viral adhesion disposition
virus adhesion susceptible cell
Adhesion disposition borne by a macromolecule part of a virus that is the disposition to participate in a virus attachment process
viral adhesion disposition
Quality inhering in a portion of fluid that is the proportion of virions to volume of that portion of fluid
viral load
Virus which infects and replicates within or on bacteria or archea.
bacteriophage
Virus which infects and replicates within or on viruses.
virophage
establishment of localization in virus host
oncovirus
Acellular self-replicating organic structure having some arrangement of viral components (e.g. viral capsid, viral DNA/RNA), that is clinically abnormal.
disordered virus
Acellular self-replicating organic structure having some arrangement of protein components, that is clinically abnormal.
disordered prion
One-dimensional temporal region beginning with the establishment of a virus in a host and ending with the first appearance of a virion following viral release.
eclipse interval
Site part of an antigen that is recognized by immune system cells and to which antibodies attach.
epitope site
Infectious disease pandemic 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.
viral disease pandemic
Infectious disease epidemic in which there is a statistically significant increase in the viral disease incidence of a population.
viral disease epidemic
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.
surveillance process
Site generated by morphogenetic or physiologic processes that is bounded by an anatomical surface.
anatomical space
Anatomical space that is part of a cell.
cell space
Disposition to inhibit the reproduction of fungi.
fungistatic disposition
Anatomical space through which a pathogen enters an organism.
pathogen portal of entry site
Anatomical space through which a pathogen exits an organism.
pathogen portal of exit site
Anatomical space in which an infection is located.
site of infection
Anatomical space in which an infection appears in a host organism.
source of infection site
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.
The role is realized in a process that transfers an infectious organism from one location to another.
pathogen vector role
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.
infectious disposition
Disease that occurs in different organs functioning in respiration and consisting especially of the nose, nasal passages, nasopharynx, larynx, trachea, bronchi, and lungs.
respiratory system disease
Respiratory system disease located in the lower respiratory tract.
lower respiratory tract disease
Progressive and life-threatening pulmonary distress in the absence of an underlying pulmonary condition, usually following major trauma or surgery.
acute respiratory distress syndrome
Process that generates the ability of a pathogen to induce disorder in an organism.
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.
pathogenesis
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.
country
Information Content Entity that consists of a set of propositions or images (as in the case of a blueprint) that prescribe some Entity.
directive information content entity
A geospatial region that delimits the authority of a formally constituted government to exercise its control within the bounded area.
geopolitical entity
A site at or near the surface of the Earth.
geospatial region
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])
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])