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apollo_sv-base.obo
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format-version: 1.2
data-version: apollo_sv/releases/2024-04-19/apollo_sv-base.owl
remark: When citing Apollo-SV, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/apollo_sv.owl. When referencing a specific component of the Apollo-SV such as a class, object property, annotation property, or individual, use the component's Uniform Resource Identifier (URI).
ontology: apollo_sv/apollo_sv-base
property_value: http://purl.org/dc/elements/1.1/contributor "Amanda Hicks" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "John Levander" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Josh Hanna" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Matt Diller" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Mike Wagner" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Shawn T. Brown" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "William R. Hogan" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "Mathias Brochhausen" xsd:string
property_value: http://purl.org/dc/elements/1.1/title "Apollo Structured Vocabulary (Apollo-SV)" xsd:string
property_value: http://purl.org/dc/elements/1.1/type IAO:8000001
property_value: http://purl.org/dc/terms/description "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation." xsd:string
property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by/4.0/" xsd:string
property_value: owl:versionInfo "2023-01-10" xsd:string
property_value: owl:versionInfo "2024-04-19" xsd:string
property_value: RTS:00000001 "C87985BA-6A8A-483A-A6B6-63975101F672" xsd:string
property_value: RTS:00000002 "082D5D78-D916-457E-B4FD-365F86F45B30" xsd:string
[Term]
id: APOLLO_SV:00000000
name: purely intentional entity
def: "A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an \"act\") that is laden with determinate, uniformily structured content." []
comment: MB: Right now we represent 'purely intentional entities' as siblings to 'information content entities'. Given their nature I am not entirly sure that this is correct. It seems that both 'information content entity' and 'simulation' are subclass to 'purely intentional entity'.
is_a: BFO:0000031
property_value: http://purl.org/dc/elements/1.1/source "Ingarden, R. (1964) Der Streit um die Existenz der Welt I. Existentalontologie. Max Niemeyer, Tübingen." xsd:string
property_value: http://purl.org/dc/elements/1.1/source "Ingarden, R. (1965a) Das literarische Kunstwerk. 3. Auflage. Max Niemeyer, Tübingen." xsd:string
property_value: http://purl.org/dc/elements/1.1/source "Ingarden, R. (1965b) Der Streit um die Existenz der Welt II/1. Formalontologie 1. Teil. Max Niemeyer, Tübingen." xsd:string
property_value: http://purl.org/dc/elements/1.1/source "Johansson I. (2009) Proof of the existence of universals – and Roman Ingarden's Ontology. Metaphysica. International Journal for Ontology & Metaphysics. 10, 65-87" xsd:string
property_value: http://purl.org/dc/elements/1.1/source "Thomasson AL. \"Ingarden and the Ontology of Cultural Objects.\" In: Chrudziminski A (ed.): Existence, Culture, and Person. The Ontology of Roman Ingarden. Frankfurt: ontos, 2005, 115-136." xsd:string
property_value: IAO:0000600 "A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an \"act\") that is laden with determinate, uniformily structured content." xsd:string
[Term]
id: APOLLO_SV:00000001
name: epidemic model
def: "A disease transmission model whose concretization is realized as a simulation of infectious disease epidemic or infectious disease pandemic." []
is_a: APOLLO_SV:00000174 ! disease transmission model
property_value: IAO:0000117 "William Hogan and Michael Wagner" xsd:string
property_value: IAO:0000600 "An algorithm the concretizations of which models the transmission of transmissible disease." xsd:string
[Term]
id: APOLLO_SV:00000002
name: basic reproduction number
def: "The average number of transmissions of an infectious agent from an infectious organism to a susceptible organism within a completely susceptible population." []
comment: MB: Here we run into the well know DL problem that we cannot specify that the infectious agent that is transmitted is of the same type that the infectious agent the population is susceptible to.
property_value: APOLLO_SV:0000040 "basicReproductionNumbers" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000600 "The number of organisms that each infected organism infects in a completely susceptible population during its infectious period." xsd:string
[Term]
id: APOLLO_SV:00000003
name: population immunity survey
def: "A population survey that assesses the level of immunity against a particular pathogen in a specified population." []
comment: Comment from Mike (to do!):\nI checked because an infection and immunity census would involve two different census methods. One would be some kind of disease surveillance that counts infections. The other is some kind of immunity census process based on seroprevalence studies or vaccination registries.
is_a: APOLLO_SV:00000152 ! population survey
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000600 "A population survey that assesses the level of immunity against a particular pathogen in a specified population." xsd:string
[Term]
id: APOLLO_SV:00000005
name: simulating of process of type X
def: "a planned process that (1) has at least one process part that has as participants representations of participants (in place of those participants) of processes of type X, and where all such process parts substitute for parts of processes of type X, and (2) is carried out for the purpose of planning for processes of type X, learning more about processes of type X, or teaching about processes of type X." []
comment: For example, in a simulated volcano eruption, representations of lava, lava tubes, vents, etc. take the place of actual lava, lava tubes, vents, etc.\n\nEven in the case of a simulated disaster scenario where actual ambulances, fire trucks, and people participate, representations of catastrophic events and injuries, etc. take the place of real ones.
is_a: OBI:0000011
property_value: APOLLO_SV:0000040 "simulating of process of type X" xsd:string
property_value: IAO:0000600 "A process that replaces the essential participants of another type of process with representations of those participants." xsd:string
[Term]
id: APOLLO_SV:00000006
name: simulation requester identifier
def: "An identifier that refers to the legal person that commissions a simulation process." []
comment: Class was originally created to correspond with a complex type from Apollo XSD v3.1.0.
is_a: IAO:0020000
property_value: IAO:0000600 "An identifier that refers to the person or organization who is requesting one or more executions of the simulator software." xsd:string
[Term]
id: APOLLO_SV:00000007
name: simulation software application
def: "A software application that provides a model of a real phenomenon based on a set of mathematical formulas." []
is_a: IAO:0000594
property_value: APOLLO_SV:0000040 "simulator" xsd:string
property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Simulation_software" xsd:string
property_value: IAO:0000600 "A software application that provides a model of a real phenomenon based on a set of mathematical formulas." xsd:string
[Term]
id: APOLLO_SV:00000008
name: software development
def: "A planned process that has specified output a software product and that involves the creation of source code." []
is_a: OBI:0000011
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Software_development" xsd:string
property_value: IAO:0000600 "A planned process resulting in a software product involving the creation of source code." xsd:string
[Term]
id: APOLLO_SV:00000009
name: simulator developer identifier
def: "An identifier that refers to the legal person that creates and maintains a simulator." []
is_a: APOLLO_SV:00000105 ! software developer identifier
property_value: IAO:0000600 "An identifier that refers to the person or organization who is responsible for the simulator. It is intended to uniquely identify a person or organization. That said, we do not plan to control the namespace for simulator developer at this point in development. We will add our ideas about alternatives at a future date." xsd:string
[Term]
id: APOLLO_SV:00000010
name: simulator identifier
def: "An identifier that refers to all version of a specific simulator." []
is_a: APOLLO_SV:00000109 ! software identifier
intersection_of: IAO:0020000
intersection_of: IAO:0000219 APOLLO_SV:00000007 ! simulation software application
relationship: BFO:0000050 APOLLO_SV:00000054 ! complete simulator identifier
relationship: IAO:0000219 APOLLO_SV:00000007 ! simulation software application
property_value: IAO:0000600 "An identifier that refers to all versions of a specific simulator, such as “FRED”. We intend that it uniquely identify a simulator when combined with simulator developer. For example, the combination www.psc.edu/FRED would differentiate the FRED simulator created by a Pittsburgh organization from another “FRED” simulator maintained elsewhere. The implementation of namespace control for simulator name (i.e., making sure that they don’t use “FRED” twice) is the responsibility of simulator developer." xsd:string
[Term]
id: APOLLO_SV:00000011
name: control strategy reactive start time information
def: "A control strategy start time information item that is based on a condition that triggers the control strategy." []
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000600 "A control strategy start time information item that is based on a condition that triggers the control strategy." xsd:string
is_obsolete: true
[Term]
id: APOLLO_SV:00000012
name: simulation time step value
def: "A numeral that is part of a simulation time step action specification." []
is_a: IAO:0000029
property_value: APOLLO_SV:0000040 "numberOfUnitsOfTimeInOneSimulatorStep" xsd:string
property_value: IAO:0000600 "A number of time step units in a time step of a simulation. \n\nFor example, if the time step is 6 hours, then this value is 6.\n" xsd:string
[Term]
id: APOLLO_SV:00000013
name: simulator version identifier
def: "An identifier that, as part of a complete simulator identifier, refers to one specific version of a simulator software." []
is_a: IAO:0020000
relationship: BFO:0000050 APOLLO_SV:00000054 ! complete simulator identifier
property_value: IAO:0000600 "An identifier that refers to a unique version of a simulator. Simulator version distinguishes, for example, version “2.0” from “2.0.b”" xsd:string
[Term]
id: APOLLO_SV:00000014
name: simulation time step unit
def: "A time unit that is part of a simulation time step action specification." []
is_a: UO:0000003
property_value: APOLLO_SV:0000040 "unitOfTimeForSimulatorTimeStep" xsd:string
property_value: IAO:0000600 "A unit of time for each time step of a simulation, such as “hours” or “days”." xsd:string
[Term]
id: APOLLO_SV:00000015
name: simulation run length
def: "The action specification that specifies the number of time steps a simulation is going to run." []
is_a: APOLLO_SV:00000793 ! epidemic simulator action specification
relationship: BFO:0000051 APOLLO_SV:00000068 ! simulation time step action specification
property_value: APOLLO_SV:0000040 "runLength" xsd:string
property_value: IAO:0000600 "The number of time steps in a simulator run.\n\nFor example, if run length is 10 and the time step is 6 hours, then the simulator will simulate a 60-hour period that begins at simulator time zero.\n" xsd:string
[Term]
id: APOLLO_SV:00000016
name: infectious period duration
def: "A duration of the parts of an infection during which the host bears an infectious disposition in a population of hosts." []
comment: MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs.
is_a: APOLLO_SV:00000243 ! duration
property_value: APOLLO_SV:0000040 "infectiousPeriodDuration" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000600 "A period when an individual of a particular species, who is infected with a particular pathogen, is able to infect susceptible organisms of a particular species.\n\nNote that the susceptible and infectious organisms can be of different species." xsd:string
[Term]
id: APOLLO_SV:00000017
name: latent period duration
def: "A duration of the time interval between the host acquiring an infection and the host bearing a contagiousness disposition during the same disease course within a population of hosts." []
comment: MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs
comment: The duration of the period between when an organism becomes infected and when it becomes infectious.
is_a: APOLLO_SV:00000243 ! duration
property_value: APOLLO_SV:0000040 "latentPeriodDuration" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000600 "A period during which an organism of a particular species, who is infected with a particular pathogen, is not yet able to infect susceptible organisms of a particular species. \n\nNote that the susceptible and infected organisms can be of different species.\n\n" xsd:string
[Term]
id: APOLLO_SV:00000018
name: count of simulated susceptible population
is_a: APOLLO_SV:00000617 ! population count
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
[Term]
id: APOLLO_SV:00000019
name: count of simulated exposed population
is_a: APOLLO_SV:00000617 ! population count
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
[Term]
id: APOLLO_SV:00000020
name: count of simulated contagious population
is_a: APOLLO_SV:00000617 ! population count
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
[Term]
id: APOLLO_SV:00000021
name: count of simulated resistant population
is_a: APOLLO_SV:00000617 ! population count
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
[Term]
id: APOLLO_SV:00000022
name: count of simulated population
def: "The count of (simulated organisms) in a simulated population." []
comment: MW: I know this causes problems with our set-theoretic definition. Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step. \n\nAny ideas? I’ve considered and rejected allowing individual organisms to be fractional. Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’\n
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000600 "The number of simulated organisms in a simulated population. The number does not have to be an integer. " xsd:string
[Term]
id: APOLLO_SV:00000023
name: vaccination dose schedule
def: "An action specification comprising the number of doses and their timing for a vaccination of an individual organism against a specific infectious agent." []
is_a: APOLLO_SV:00000084 ! control strategy dose schedule
property_value: IAO:0000600 "A vaccination schedule specifies the intended timing of initial and subsequent booster doses of vaccine for an individual organism. " xsd:string
[Term]
id: APOLLO_SV:00000024
name: vaccination compliance
def: "The fraction expressing the probability that an organism who is eligible according to a particular vaccination policy will be consented for that vaccination." []
comment: MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for a vaccination against the members that are eligible and consented the vaccination. There is a class "eligibility rule" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.
comment: MW: I still see enough similarities at the abstract level among some control measures that we might add the concepts “Control measure compliance”, “Control measure efficacy” and “control measure efficacy delay.” We could then post-coordinate particular control measures such as vaccine.\n\nIt is worth noting that there are control measures such as closing schools that are not applied at the individual level. We have not represented those control measures yet.\n
is_a: OBI:0302867
property_value: IAO:0000600 "The fraction of individuals in a population who are eligible according to a particular vaccination policy and will accept vaccination assuming no supply constraint." xsd:string
[Term]
id: APOLLO_SV:00000025
name: vaccination efficacy
def: "The infectious disease treatment efficacy of a vaccine." []
comment: need to generate class restriction. Something like:\n\n'is realized by' some (processual_entity and (has_participant some ('Anatomical structure' and ('is physical basis of' some 'protective resistance'))\n\nwe'd also like to say that the protective resistance disposition began to exist during the process. \n\ncan't recall whether we should use process or processual_entity for future BFO compatibility.
comment: Notes: \n1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer
is_a: APOLLO_SV:00000227 ! infectious disease treatment efficacy
property_value: APOLLO_SV:0000040 "vaccinationEfficacies" xsd:string
property_value: IAO:0000600 "The degree to which a particular vaccination reduces the probability that a vaccinated individual will have a particular vaccination preventable outcome." xsd:string
[Term]
id: APOLLO_SV:00000026
name: facility survey
def: "A planned process involving counting numbers of facilities in a specific region." []
is_a: OBI:0000011
property_value: IAO:0000600 "A planned process involving counting numbers of facilities in a specific region." xsd:string
[Term]
id: APOLLO_SV:00000027
name: school facility census
comment: Motivating use case is Synthia synthetic population data.
is_a: APOLLO_SV:00000173 ! census
intersection_of: APOLLO_SV:00000173 ! census
intersection_of: IAO:0000136 OMRSE:00000064
intersection_of: OBI:0000312 APOLLO_SV:00000026 ! facility survey
intersection_of: OBI:0000312 APOLLO_SV:00000026 {all_only="true"} ! facility survey
relationship: IAO:0000136 OMRSE:00000064
relationship: OBI:0000312 APOLLO_SV:00000026 ! facility survey
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
[Term]
id: APOLLO_SV:00000029
name: infectious disease control strategy execution
def: "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease. " []
is_a: OBI:0000011
property_value: IAO:0000600 "A process that is applied to a population with the goal of preventing, or mitigating the severity of an infectious disease. " xsd:string
[Term]
id: APOLLO_SV:00000030
name: hospital patient population
comment: Key motivating use case was Synthia synthetic population data.
is_a: OMRSE:00000023
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
[Term]
id: APOLLO_SV:00000031
name: simulated population
def: "A simulation of a population or populations of organisms of a particular biological taxon that simulates a particular type of event or types of event that occur in a specified time interval." []
is_a: APOLLO_SV:00000070 ! simulation
intersection_of: APOLLO_SV:00000067 PCO:0000000 ! simulates
intersection_of: RO:0000056 APOLLO_SV:00000005 ! simulating of process of type X
relationship: APOLLO_SV:00000067 PCO:0000000 ! simulates
relationship: RO:0000056 APOLLO_SV:00000005 ! simulating of process of type X
property_value: APOLLO_SV:0000040 "simulatorReferencablePopulation" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000600 "A simulated population is a set of simulated organisms. The set can be null (e.g., the set of 200 year-old H. sapiens). A simulated population can include more than one species, in which case it may be convenient to define each species as a simulated population and form the overall simulated population by set union. Similarly, it may be convenient to define sociodemographic or geographic strata within a simulated population as simulated populations and obtain the overall simulated population by set union. See examples in “Programmer’s Guide, page x)" xsd:string
[Term]
id: APOLLO_SV:00000032
name: count
def: "A measurement datum that is the output of counting." []
is_a: IAO:0000109
intersection_of: IAO:0000027
intersection_of: OBI:0000312 APOLLO_SV:00000033 ! counting
relationship: OBI:0000312 APOLLO_SV:00000033 ! counting
property_value: APOLLO_SV:0000040 "count" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000600 "A measurement datum that is the output of counting." xsd:string
[Term]
id: APOLLO_SV:00000033
name: counting
def: "The planned process of finding the number of elements in a finite set of objects." []
is_a: OBI:0000011
intersection_of: OBI:0000011
intersection_of: OBI:0000299 APOLLO_SV:00000032 ! count
relationship: OBI:0000299 APOLLO_SV:00000032 ! count
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Counting" xsd:string
property_value: IAO:0000600 "The planned process of finding the number of elements in a finite set of objects." xsd:string
[Term]
id: APOLLO_SV:00000034
name: simulation of organism
comment: a simulation that is about an organism
is_a: APOLLO_SV:00000070 ! simulation
intersection_of: APOLLO_SV:00000067 OBI:0100026 {all_some="true"} ! simulates
intersection_of: RO:0000056 APOLLO_SV:00000005 ! simulating of process of type X
relationship: APOLLO_SV:00000067 OBI:0100026 ! simulates
relationship: RO:0000056 APOLLO_SV:00000005 ! simulating of process of type X
[Term]
id: APOLLO_SV:00000036
name: normal distribution
def: "A continuous parametric probability distribution that is uniform; centered around the mean, parameter μ; and whose spread of standard deviations, parameter σ, adheres to the empirical rule." []
is_a: APOLLO_SV:00000251 ! continuous parametric probability distribution
property_value: APOLLO_SV:0000040 "NormalDistribution" xsd:string
property_value: IAO:0000600 "A continuous probability distribution in which the parameter μ is the mean or expectation of the distribution and the parameter σ is its standard deviation" xsd:string
[Term]
id: APOLLO_SV:00000038
name: simulation of exposed organism
def: "A simulation of an infectious agent host that is not contagious and is part of a simulated population." []
is_a: APOLLO_SV:00000034 ! simulation of organism
property_value: IAO:0000600 "A simulated organism in a simulated population that has acquired a particular simulated disease but is not yet able to transmit the disease to another simulated organism." xsd:string
[Term]
id: APOLLO_SV:00000039
name: simulated population location identifier
def: "An identifier that refers to a geographical location to be used as location of a population in a simulation." []
is_a: IAO:0020000
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000600 "An identifier referring to geographical location of a simulated population. Our intent is for the location identifiers to be INCITS codes." xsd:string
[Term]
id: APOLLO_SV:00000040
name: simulation of infectious organism
def: "A simulation of an infectious organism host that is contagious." []
is_a: APOLLO_SV:00000034 ! simulation of organism
property_value: IAO:0000600 "A simulated organism in a simulated population that has acquired a particular simulated disease and is able to transmit the disease to another simulated organism." xsd:string
[Term]
id: APOLLO_SV:00000041
name: simulation of recovered organism
def: "A simulated organism in a simulated population that is not susceptible. " []
is_a: APOLLO_SV:00000034 ! simulation of organism
property_value: IAO:0000600 "A simulated organism in a simulated population that is neither susceptible, exposed, nor infectious for a particular simulated disease. \nNote that the name for this concept, were it to be named based on its intent, would be ‘immune.’ However, in the practice domain of epidemiology this concept is traditionally termed ‘recovered.’ The problem with the traditional name is that organisms can be considered ‘recovered’ by virtue of having been vaccinated, which differs from lay usage.\n" xsd:string
[Term]
id: APOLLO_SV:00000042
name: simulation of disease
def: "A representation of a disposition realized in a represented disease course that at least part of the simulated population is represented as participating in." []
is_a: APOLLO_SV:00000070 ! simulation
property_value: APOLLO_SV:0000040 "disease" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000600 "The disease being simulated." xsd:string
[Term]
id: APOLLO_SV:00000043
name: reproduction number
def: "The average value of transmissions of the infectious agent from one infected organism to another, resulting in an infection. " []
property_value: APOLLO_SV:0000040 "ReproductionNumber" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000600 "The number of susceptible organisms that each infected organism infects. ‘Infects’ carries the same meaning as ‘exposes’ in epidemic simulations such as SEIR simulation." xsd:string
[Term]
id: APOLLO_SV:00000044
name: nursery school student population
comment: Key motivating use case was Synthia synthetic population data.
is_a: APOLLO_SV:00000178 ! school student population
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
[Term]
id: APOLLO_SV:00000045
name: obsolete asymptomatic infection fraction
def: "The fraction given to express the probability that an organism will become infected, but stay asymptomatic." []
is_a: ObsoleteClass
property_value: APOLLO_SV:0000040 "asymptomatic infection fraction" xsd:string
property_value: IAO:0000600 "The fraction of infectious individuals who do not develop symptoms during the course of their infections." xsd:string
is_obsolete: true
[Term]
id: APOLLO_SV:00000046
name: vaccine supply schedule
def: "An action specification giving the number of doses of vaccine to be made available over a specific time period." []
is_a: APOLLO_SV:00000795 ! individual treatment control strategy action specification
property_value: IAO:0000600 "The counts of vaccine doses that become available in a specific population location during (at the start of would be unambiguous) each simulator time step." xsd:string
[Term]
id: APOLLO_SV:00000047
name: vaccination administration capacity
def: "An action specification giving the number of vaccinations possible in a population during a specific time interval." []
is_a: APOLLO_SV:00000795 ! individual treatment control strategy action specification
property_value: IAO:0000600 "The counts of individuals that could be vaccinated in a population location per time step unit in the absence of any vaccine supply constraints. It represents the capacity of medical system to vaccinate individuals." xsd:string
[Term]
id: APOLLO_SV:00000048
name: antiviral treatment efficacy
def: "The infectious disease treatment efficacy of an antiviral drug." []
comment: MB: For DL reasons the easiest way to formalize the definition was to assume only organism that are either host or not immune undergo antiviral treatment. Is that adequate? I assume this'll create problems…
is_a: APOLLO_SV:00000227 ! infectious disease treatment efficacy
property_value: APOLLO_SV:0000040 "AntiviralTreatmentEfficacy" xsd:string
property_value: IAO:0000600 "The degree to which a particular antiviral drug reduces the probability that a treated individual will have a particular preventable outcome.\n\nPreventable outcomes include but are not limited to infection, infectiousness, symptoms, and hospitalization." xsd:string
[Term]
id: APOLLO_SV:00000049
name: antiviral efficacy delay
def: "The value of the time interval between an organism's taking antivirals against a specific infectious agent and the organism’s losing its infectious agent host role. " []
is_a: APOLLO_SV:00000243 ! duration
property_value: IAO:0000600 "The duration of time (expressed in time steps) between initiation of a particular antiviral treatment to an organism and when the organism becomes non infectious or, if the antiviral is being administered prophylactically, protected from infection. " xsd:string
[Term]
id: APOLLO_SV:00000050
name: antiviral compliance
def: "The fraction expressing the probability that an organism will be consented to receive antiviral treatment when eligible." []
comment: MB: This class is still awaiting its class restriction. It should be restricted as being about a population that has members that are eligible for an antiviral treatment against the members that are eligible and consented the antiviral treatment. There is a class "eligibility rule" in OBI (http://purl.obolibrary.org/obo/OBI_0500026), but it is restricted by definition to studies. I put in an issue in the OBI issue tracker. The consenting process and its specified outcome should be done in d-acts, but needs to be done properly.
comment: MW: Since the estimates that modelers use are from real populations, I have two questions:\n1. Should we distinguish between real and simulated population?\n2. If so, do we want to represent a ‘measured’ antiviral compliance number that is a property of a real population and distinguish it from this number that we are using to study what might happen in a simulated population?\n\nMB: This issue will need to be taken care of in the axiomatization of simulated population
is_a: OBI:0302867
property_value: APOLLO_SV:0000040 "antiviral cm compliance" xsd:string
property_value: IAO:0000600 "The fraction of individuals in a simulated population that will accept antiviral treatment if offered. " xsd:string
[Term]
id: APOLLO_SV:00000051
name: antiviral supply schedule
def: "An action specification giving the number of doses of an antiviral to be made available during a specific time interval. " []
is_a: APOLLO_SV:00000795 ! individual treatment control strategy action specification
property_value: IAO:0000600 "Counts of antiviral doses that become available in a specific location per time step unit." xsd:string
[Term]
id: APOLLO_SV:00000052
name: antiviral administration schedule
def: "An action specification that tells the total number of antiviral doses available to be administered to a population during a specific time interval." []
is_a: APOLLO_SV:00000795 ! individual treatment control strategy action specification
property_value: IAO:0000600 "Counts of antiviral doses that can be administered in a specific location per time step unit." xsd:string
[Term]
id: APOLLO_SV:00000053
name: simulation of organism awaiting control measure
def: "A simulated organism that is assumed “eligible, willing and able” to participate with a particular control measure." []
comment: MB: APOLLO_SV_00000053 and APOLLO_SV_00000058 have not been given a class restriction, since they are not expressible in BFO right now, due to their referring to "will". Both classes have been made disjoint in the OWL file, though.
comment: This class will need more ontological reasoning, since the "willing" part of the definition is not representable in BFO to date.
is_a: APOLLO_SV:00000034 ! simulation of organism
disjoint_from: APOLLO_SV:00000058 ! simulation of organism not awaiting control measure
property_value: IAO:0000600 "A simulated organism in a simulated population that is “eligible, willing and able” to participate with a particular simulated control measure." xsd:string
[Term]
id: APOLLO_SV:00000054
name: complete simulator identifier
def: "An identifier that refers to a specific simulator." []
comment: MB: I am not 100% happy with the elucidation. Can't we just say that this is the full identifier identifying the simulator with both its name and its version number?
is_a: IAO:0020000
intersection_of: IAO:0020000
intersection_of: IAO:0000219 APOLLO_SV:00000001 ! epidemic model
relationship: IAO:0000219 APOLLO_SV:00000001 ! epidemic model
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000600 "The combination of simulator developer, simulator name, and simulator version, for example “www.psc.edu/FRED/2.0” The combination is intended to uniquely identify the simulation algorithm that produced output X, given input Y to support scientific audit, error analysis, and reproducibility of results." xsd:string
[Term]
id: APOLLO_SV:00000055
name: epidemic simulating
def: "A simulating of a disease epidemic or pandemic." []
property_value: APOLLO_SV:0000040 "epidemic simulation" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000600 "the process of simulating a disease epidemic or pandemic. This term is not currently used in Apollo-WS." xsd:string
[Term]
id: APOLLO_SV:00000056
name: hospital patient population census
comment: Motivating use case is to cover Synthia data, and possibly configuration/output of the MRSA simulator in the MIDAS community (CA-MRSA Repast).
is_a: APOLLO_SV:00000153 ! population census
intersection_of: APOLLO_SV:00000153 ! population census
intersection_of: IAO:0000136 APOLLO_SV:00000030 ! hospital patient population
relationship: IAO:0000136 APOLLO_SV:00000030 ! hospital patient population
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
[Term]
id: APOLLO_SV:00000058
name: simulation of organism not awaiting control measure
def: "A simulated organism that is assumed “ineligible, unwilling or unable” to participate with a particular control measure." []
comment: MB: APOLLO_SV_00000053 and APOLLO_SV_00000058 have not been given a class restriction, since they are not expressible in BFO right now, due to their referring to "will". Both classes have been made disjoint in the OWL file, though.
comment: This class will need more ontological reasoning, since the "unwilling" part of the definition is not representable in BFO to date.
property_value: IAO:0000600 "A simulated organism in a simulated population that is “ineligible, unwilling or unable” to participate with a particular simulated control measure." xsd:string
[Term]
id: APOLLO_SV:00000059
name: simulation of organism awaiting effect of control measure
def: "A simulated organism that participates in a particular control measure that has not yet been effective." []
is_a: APOLLO_SV:00000034 ! simulation of organism
property_value: IAO:0000600 "This concept represents a simulated organism that has received a control measure such as vaccination in which a period of time must elapse before the benefit of the control measure accrues. A simulated organism is ‘awaiting efficacy’ if ‘efficacy delay’ (e.g. the concept ‘antiviral efficacy delay’ for the particular simulated control measure is greater than the elapsed time between application of the control measure and the current simulated time." xsd:string
[Term]
id: APOLLO_SV:00000060
name: simulation of antiviral control measure
def: "The simulation of an antiviral control measure. " []
comment: MB: For all the antiviral-related classes I referred to ChEBI: Antiviral class. I wasn't able to use the plug-in though (there was a JAVA heap space error, probably due to the size of ChEBI).\nAND (more importantly) I did not re-use any of the ChEBI hierarchy which, even in the BFO version is a mess.\nMaybe we need to discuss this.\n
is_a: APOLLO_SV:00000070 ! simulation
property_value: APOLLO_SV:0000040 "antiviral control measure" xsd:string
property_value: IAO:0000600 "A type of control measure based on administration of chemotherapeutic agents to an infected or high-risk organism that kill or inhibit replication of viruses within a simulated organism." xsd:string
[Term]
id: APOLLO_SV:00000061
name: simulation of vaccination control measure
def: "A simulation of a vaccination control measure." []
is_a: APOLLO_SV:00000070 ! simulation
property_value: APOLLO_SV:0000040 "simulation of vaccination control measure" xsd:string
property_value: IAO:0000600 "A type of control measure that uses vaccination to create immunity in simulated organisms to specific pathogens." xsd:string
[Term]
id: APOLLO_SV:00000062
name: primary school student population
comment: Key motivating use case was Synthia synthetic population data.
is_a: APOLLO_SV:00000178 ! school student population
[Term]
id: APOLLO_SV:00000063
name: simulation of control measure participant
def: "A simulation of an organism in a simulated population that has participated in an epidemic control measure." []
is_a: APOLLO_SV:00000034 ! simulation of organism
property_value: IAO:0000600 "A simulated organism in a simulated population has participated in a particular simulated control measure. (e.g. an organism received antiviral treatment)" xsd:string
[Term]
id: APOLLO_SV:00000064
name: simulation time series
def: "A time sampled measurement data set, where the position in the sequence of each data item corresponds to a specific time_step of the simulation." []
comment: MB: The ontological status of simulations (Thoughts)\n\nOne property that seems to be common among simulations in comparison to many other fictions is the fact that the chronological order of the simulated purely intentional entities is not changed in the process of simulating.\n\nWhile in many pieces of fiction the order in which the purely intentional entities are created can vary, this is not the case for simulations.\n
is_a: IAO:0000584
property_value: IAO:0000600 "A sequence of data points, where the position in the sequence of each data point corresponds to a specific time_step of the simulation." xsd:string
[Term]
id: APOLLO_SV:00000065
name: simulation identifier numeral
def: "A numeral that indexes a specific simulation." []
comment: Class was originally created to correspond with an element from Apollo XSD v3.1.0.
is_a: IAO:0000029
intersection_of: IAO:0000029
intersection_of: IAO:0000219 APOLLO_SV:00000005 ! simulating of process of type X
intersection_of: OBI:0000312 IAO:0020010 {all_only="true"}
relationship: IAO:0000219 APOLLO_SV:00000005 ! simulating of process of type X
property_value: IAO:0000600 "The run id indexes a run of a specific simulator version on a specific simulated population, disease(s), and optionally control measures. The simulator is responsible for generating a run id and ensuring its uniqueness." xsd:string
[Term]
id: APOLLO_SV:00000066
name: simulation of time step
def: "A purely intentional entity that simulates a temporal interval of pre-specified length." []
is_a: APOLLO_SV:00000070 ! simulation
property_value: APOLLO_SV:0000040 "simulation time step" xsd:string
property_value: IAO:0000600 "A purely intentional entity that simulates a temporal interval of pre-specified length." xsd:string
[Term]
id: APOLLO_SV:00000068
name: simulation time step action specification
def: "An action specification that specifies the length of the time steps interval assumed in a simulation." []
comment: simulation time step value\nsimulation time step unit\nsimulation run length\n\nThe time step value and unit are specified using a scalar value specification.
is_a: APOLLO_SV:00000793 ! epidemic simulator action specification
relationship: BFO:0000050 APOLLO_SV:00000007 ! simulation software application
relationship: IAO:0000136 APOLLO_SV:00000066 ! simulation of time step
relationship: OBI:0001938 OBI:0001931
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000600 "An action specification that specifies the length of the time steps interval assumed in a simulation." xsd:string
[Term]
id: APOLLO_SV:00000069
name: time step identifying numeral
def: "A numeral that indexes a specific time step of a simulation." []
is_a: IAO:0000029
intersection_of: IAO:0000029
intersection_of: IAO:0000219 APOLLO_SV:00000066 ! simulation of time step
intersection_of: OBI:0000312 IAO:0020010 {all_only="true"}
relationship: IAO:0000219 APOLLO_SV:00000066 ! simulation of time step
property_value: APOLLO_SV:0000040 "simulatorTime" xsd:string
property_value: IAO:0000600 "The time step number of a simulation." xsd:string
[Term]
id: APOLLO_SV:00000070
name: simulation
def: "A purely intentional entity that simulates an entity and its properties.\n\n" []
is_a: APOLLO_SV:00000000 ! purely intentional entity
intersection_of: APOLLO_SV:00000000 ! purely intentional entity
intersection_of: APOLLO_SV:00000067 BFO:0000001 ! simulates
relationship: APOLLO_SV:00000067 BFO:0000001 ! simulates
property_value: APOLLO_SV:0000040 "simulation" xsd:string
property_value: IAO:0000600 "A purely intentional entity that simulates an entity and its properties.\n\n" xsd:string
[Term]
id: APOLLO_SV:00000071
name: obsolete simulation of population location
def: "The simulation of geographical location in which a population is assumed to be located." []
is_a: ObsoleteClass
property_value: APOLLO_SV:0000040 "simulated population location" xsd:string
property_value: IAO:0000600 "An identifier referring to geographical location of a simulated population. Our intent is for the location identifiers to be INCITS codes." xsd:string
is_obsolete: true
[Term]
id: APOLLO_SV:00000072
name: simulation of susceptible organism
def: "A simulation of a susceptible organism in a simulated population." []
is_a: APOLLO_SV:00000034 ! simulation of organism
property_value: IAO:0000600 "A simulated organism in a simulated population that is capable of acquiring a particular simulated disease." xsd:string
[Term]
id: APOLLO_SV:00000073
name: simulation of symptomatic organism
def: "A simulation of a symptomatic infectious agent host." []
is_a: APOLLO_SV:00000034 ! simulation of organism
property_value: IAO:0000600 "A simulated organism in a simulated population that has at least one symptom caused by a particular simulated disease." xsd:string
[Term]
id: APOLLO_SV:00000074
name: simulation of asymptomatic organism
def: "A simulation of an asymptomatic infectious agent host." []
is_a: APOLLO_SV:00000034 ! simulation of organism
intersection_of: APOLLO_SV:00000067 APOLLO_SV:00000236 ! simulates asymptomatic host
intersection_of: RO:0000056 APOLLO_SV:00000005 ! simulating of process of type X
relationship: APOLLO_SV:00000067 APOLLO_SV:00000236 ! simulates asymptomatic host
property_value: IAO:0000600 "A simulated organism in a simulated population that has no symptoms caused by a particular simulated disease." xsd:string
[Term]
id: APOLLO_SV:00000075
name: infectious disease control objective specification
def: "An objective specification that is realized by processes that are able or likely to stop the spread of a disease in a population." []
comment: typically, the process endpoint is achievement of R0 < 1
is_a: IAO:0000005
property_value: IAO:0000600 "an objective of achieving satisfactory control of epidemic spread through a population" xsd:string
[Term]
id: APOLLO_SV:00000076
name: μ
is_a: ObsoleteClass
property_value: APOLLO_SV:0000040 "μ" xsd:string
property_value: IAO:0000600 "the mean or expectation of a distribution" xsd:string
is_obsolete: true
[Term]
id: APOLLO_SV:00000077
name: σ
is_a: ObsoleteClass
property_value: APOLLO_SV:0000040 "sigma" xsd:string
property_value: IAO:0000600 "standard deviation" xsd:string
is_obsolete: true
[Term]
id: APOLLO_SV:00000078
name: beta distribution
is_a: APOLLO_SV:00000251 ! continuous parametric probability distribution
property_value: APOLLO_SV:0000040 "beta distribution" xsd:string
property_value: IAO:0000600 "A continuous probability distribution whose characteristics and shape are determined by two parameters, alpha and beta." xsd:string
[Term]
id: APOLLO_SV:00000079
name: deprecated log normal distribution
is_a: ObsoleteClass
property_value: IAO:0000600 "a continuous probability distribution over variable X whose parameters denoted μ and σ are, respectively, the mean and standard deviation of the variable’s natural logarithm" xsd:string
is_obsolete: true
[Term]
id: APOLLO_SV:00000080
name: uniform distribution
is_a: APOLLO_SV:00000251 ! continuous parametric probability distribution
property_value: APOLLO_SV:0000040 "UniformDistribution" xsd:string
property_value: IAO:0000600 "A continous probability distribution whose parameters a and b, denote its minimum and maximum values" xsd:string
[Term]
id: APOLLO_SV:00000081
name: triangular distribution
is_a: APOLLO_SV:00000251 ! continuous parametric probability distribution
property_value: APOLLO_SV:0000040 "triangular distribution" xsd:string
property_value: IAO:0000600 "a continuous probability distribution with lower limit a, upper limit b and mode c, where a < b and a <= c <= b." xsd:string
[Term]
id: APOLLO_SV:00000082
name: Bayesian network
is_a: APOLLO_SV:00000246 ! joint probability distribution
property_value: APOLLO_SV:0000040 "BayesianNetwork" xsd:string
property_value: IAO:0000600 "a discrete probability distribution" xsd:string
[Term]
id: APOLLO_SV:00000083
name: temporal Bayesian network
is_a: APOLLO_SV:00001008 ! TODO
property_value: APOLLO_SV:0000040 "temporal Bayesian network" xsd:string
property_value: IAO:0000600 "a discrete probability distribution that conditions on time" xsd:string
[Term]
id: APOLLO_SV:00000084
name: control strategy dose schedule
def: "An action specification comprising the number of doses and their timing for administering a substance to an individual organism to prevent the negative effects of a specific infectious agent to that organism." []
is_a: APOLLO_SV:00000795 ! individual treatment control strategy action specification
relationship: BFO:0000050 APOLLO_SV:00000086 ! infectious disease control strategy
property_value: IAO:0000600 "A control strategy dose schedule specifies the intended timing of initial and subsequent doses of for example a vaccine or an antiviral for an individual organism. " xsd:string
[Term]
id: APOLLO_SV:00000085
name: age data in age brackets data set
def: "A data set consisting of measurements of age organized in age brackets." []
is_a: IAO:0000100
property_value: IAO:0000111 "age structure data set" xsd:string
property_value: IAO:0000600 "A data set consisting of measurements of age organized in age brackets." xsd:string
[Term]
id: APOLLO_SV:00000086
name: infectious disease control strategy
def: "A plan specification whose objective specification is an infectious disease control objective specification." []
comment: The essential goal of an infectious disease control strategy is to protect the susceptible organisms in a population.
is_a: IAO:0000104
intersection_of: IAO:0000104
intersection_of: BFO:0000051 APOLLO_SV:00000075 ! infectious disease control objective specification
relationship: BFO:0000051 APOLLO_SV:00000075 ! infectious disease control objective specification
property_value: APOLLO_SV:0000040 "InfectiousDiseaseControlMeasure" xsd:string
property_value: IAO:0000600 "A plan with the goal of preventing or mitigating the effects of infections in a population due to one or more pathogens." xsd:string
[Term]
id: APOLLO_SV:00000087
name: count of susceptible population
def: "The count of individuals in a susceptible population (empirical or virtual)." []
is_a: APOLLO_SV:00000617 ! population count
property_value: IAO:0000600 "The count of individuals in a susceptible population (empirical or virtual)." xsd:string
[Term]
id: APOLLO_SV:00000088
name: count of contacted population
def: "The count of individuals in an exposed population (empirical or virtual)." []
is_a: APOLLO_SV:00000617 ! population count
property_value: IAO:0000600 "The count of individuals in an exposed population (empirical or virtual)." xsd:string
[Term]
id: APOLLO_SV:00000089
name: measured vaccination efficacy
def: "A measurement datum that is about a vaccination efficacy and is the specified output of a vaccination efficacy study." []
comment: 1. Apollo-SV does not distinguish between ‘vaccine efficacy’ and ‘vaccine effectiveness.’\n\n2. Apollo-SV also considers the use of ‘vaccine’ in both terms a misnomer.\n
is_a: IAO:0000109
property_value: APOLLO_SV:0000040 "VaccinationEfficacyMeasured" xsd:string
property_value: IAO:0000600 "A vaccination efficacy that results from a vaccination efficacy study." xsd:string
[Term]
id: APOLLO_SV:00000090
name: vaccination efficacy study design execution
def: "a study design execution that has as its specified output one or more measured vaccination efficacy data items" []
is_a: OBI:0000471
intersection_of: OBI:0000471
intersection_of: BFO:0000051 APOLLO_SV:00000142 ! vaccination
intersection_of: OBI:0000299 APOLLO_SV:00000089 ! measured vaccination efficacy
relationship: BFO:0000051 APOLLO_SV:00000142 ! vaccination
relationship: OBI:0000299 APOLLO_SV:00000089 ! measured vaccination efficacy
property_value: APOLLO_SV:0000040 "VaccinationEfficacyStudy" xsd:string
property_value: IAO:0000600 "an experiment that measures vaccination efficacy from a sample of vaccinated and possibly unvaccinated individuals" xsd:string
[Term]
id: APOLLO_SV:00000091
name: obsolete immune
is_a: ObsoleteClass
property_value: APOLLO_SV:0000040 "immune" xsd:string
property_value: IAO:0000600 "an organism that has the property of being immune to a specific disease agent" xsd:string
is_obsolete: true
[Term]
id: APOLLO_SV:00000092
name: 95% confidence interval
is_a: APOLLO_SV:00001008 ! TODO
property_value: APOLLO_SV:0000040 "95% confidence interval" xsd:string
property_value: IAO:0000600 "a type of interval estimate of a population parameter used to indicate the reliability of an estimate. How frequently the observed interval contains the parameter is determined by the confidence level or confidence coefficient, in this type the confidence level is 95%" xsd:string
[Term]
id: APOLLO_SV:00000093
name: Bayesian credible interval
is_a: APOLLO_SV:00001008 ! TODO
property_value: APOLLO_SV:0000040 "Baysesian credible interval" xsd:string
property_value: IAO:0000600 "a type of interval estimate of a population parameter that has the property that the true value of the estimated populatin parameter has a (specified) particular probability of being in the confidence interval given the data on which the estimate is derived." xsd:string
[Term]
id: APOLLO_SV:00000094
name: community
def: "Two or more distinct populations that are part of the same biotic ecosystem." []
is_a: BFO:0000027
property_value: APOLLO_SV:0000040 "community" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "William R. Hogan" xsd:string
property_value: IAO:0000600 "Two or more distinct populations that are part of the same biotic ecosystem." xsd:string
[Term]
id: APOLLO_SV:00000095
name: deprecated discrete probability distribution
is_a: ObsoleteClass
property_value: APOLLO_SV:0000040 "discrete probability distribution" xsd:string
property_value: IAO:0000600 "a probability distribution over a discrete random variable" xsd:string
is_obsolete: true
[Term]
id: APOLLO_SV:00000096
name: obsolete unit of measure
property_value: IAO:0000600 "The increments of measurement for a measurable thing" xsd:string
is_obsolete: true
[Term]
id: APOLLO_SV:00000097
name: ecosystem
def: "The sum of all biotic and abiotic entities in a geographical region. " []
is_a: BFO:0000040
property_value: APOLLO_SV:0000040 "Ecosystem" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "William R. Hogan" xsd:string
property_value: IAO:0000600 "The sum of all biotic and abiotic entities in a geographical region. " xsd:string
[Term]
id: APOLLO_SV:00000098
name: count of contagious population
def: "The count of individuals in a contagious population (empirical or virtual)." []
is_a: APOLLO_SV:00000617 ! population count
property_value: IAO:0000600 "The count of individuals in a contagious population (empirical or virtual)." xsd:string
[Term]
id: APOLLO_SV:00000099
name: count of resistant population
def: "The count of individuals in a resistant population (empirical or virtual)." []
is_a: APOLLO_SV:00000617 ! population count
property_value: IAO:0000600 "The count of individuals in a resistant population (empirical or virtual)." xsd:string
[Term]
id: APOLLO_SV:00000100
name: abiotic ecosystem
def: "The abiotic ecosystem is the sum total of all continuants in a geographical region that are not organisms, parts of organisms, or dependent continuants that inhere in organisms." []
is_a: BFO:0000040
property_value: APOLLO_SV:0000040 "AbioticEcosystem" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "William R. Hogan" xsd:string
property_value: IAO:0000600 "The abiotic ecosystem is the sum total of all continuants in a geographical region that are not organisms, parts of organisms, or dependent continuants that inhere in organisms." xsd:string
[Term]
id: APOLLO_SV:00000101
name: fixed control strategy start time specification
def: "An action specification that is part of a simulation software and specifies the time step numeral identifying the time step after which a simulation of a control strategy starts." []
is_a: APOLLO_SV:00000794 ! infectious disease control strategy action specification
property_value: APOLLO_SV:0000040 "FixedStartTime" xsd:string
property_value: IAO:0000600 "The number of time steps after which a control strategy starts in a simulator." xsd:string
[Term]
id: APOLLO_SV:00000103
name: control strategy reactive endpoint fraction
def: "A rule that is part of an infectious disease control strategy specification and specifies at which fraction of a population a control strategy is to be discontinued." []
is_a: IAO:0000055
relationship: BFO:0000050 APOLLO_SV:00000086 ! infectious disease control strategy
property_value: APOLLO_SV:0000040 "controlStrategyReactiveEndpointFraction" xsd:string
property_value: IAO:0000600 "A fraction of a population that is targeted for treatment at which the control strategy is discontinued.\n\nThe concept derives from the epidemiological notion of ‘herd immunity,’ which is a level of immunity in a population at which there are not enough susceptible individuals for a contagious disease to maintain the chain reaction. Technically, it is when the effective reproduction rate <= 1, which means that infectious individuals at most infect one person during the course of their illness." xsd:string
[Term]
id: APOLLO_SV:00000104
name: biotic ecosystem
def: "The biotic ecosystem is the sum total of all organism populations in a particular geographical region." []
is_a: BFO:0000040
property_value: APOLLO_SV:0000040 "BioticEcosystem" xsd:string
property_value: http://purl.org/dc/elements/1.1/creator "William R. Hogan" xsd:string
property_value: IAO:0000600 "The biotic ecosystem is the sum total of all organism populations in a particular geographical region." xsd:string
[Term]
id: APOLLO_SV:00000105
name: software developer identifier
def: "An identifier that refers to the legal person that creates and maintains software." []
is_a: IAO:0020000
property_value: APOLLO_SV:0000040 "softwareDeveloper" xsd:string
property_value: IAO:0000600 "An identifier that refers to the legal person that creates and maintains software." xsd:string
[Term]
id: APOLLO_SV:00000106
name: complete software identifier
def: "An identifier that refers to a specific piece of software." []
is_a: IAO:0020000
intersection_of: IAO:0020000
intersection_of: IAO:0000219 IAO:0000594 {cardinality="1"}
relationship: IAO:0000219 IAO:0000594
property_value: APOLLO_SV:0000040 "SoftwareIdentification" xsd:string
property_value: IAO:0000600 "An identifier that refers to a specific piece of software." xsd:string
[Term]
id: APOLLO_SV:00000107
name: atmosphere
def: "a fiat object part that is in gaseous phase and that is the outer layer of an object in space and is held to the object by gravitational force" []
comment: atmosphere of Earth, Earth's moon, Saturn, Titan, etc.
comment: outer, gaseous layers of exoplanets are called extraterrestrial atmosphere.
is_a: BFO:0000024
property_value: http://purl.org/dc/elements/1.1/creator "William R. Hogan" xsd:string
property_value: IAO:0000600 "a fiat object part that is in gaseous phase and that is the outer layer of an object in space and is held to the object by gravitational force" xsd:string
[Term]
id: APOLLO_SV:00000108
name: software version identifier
def: "An identifier that, as part of a complete software identifier, refers to one specific version of the software." []
is_a: IAO:0020000
relationship: BFO:0000050 APOLLO_SV:00000106 ! complete software identifier
property_value: APOLLO_SV:0000040 "softwareVersion" xsd:string
property_value: IAO:0000600 "An identifier that, as part of a complete software identifier, refers to one specific version of the software." xsd:string
[Term]
id: APOLLO_SV:00000109
name: software identifier
def: "An identifier that refers to all version of a specific software." []
is_a: IAO:0020000
intersection_of: IAO:0020000
intersection_of: IAO:0000219 IAO:0000010
relationship: BFO:0000050 APOLLO_SV:00000106 ! complete software identifier
relationship: IAO:0000219 IAO:0000010
property_value: APOLLO_SV:0000040 "softwareName" xsd:string
property_value: IAO:0000600 "An identifier that refers to all version of a specific software." xsd:string
[Term]
id: APOLLO_SV:00000110
name: atmosphere of geographical region
is_a: GEO:000000371
[Term]
id: APOLLO_SV:00000111
name: obsolete educational institution
def: "An educational institution is an place organization which provides the necessary system for people of different ages gain an education. It includes (among others) preschools, childcare, elementary schools, and universities." []
is_a: ObsoleteClass
property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Types_of_educational_institutions (amended)" xsd:string
property_value: IAO:0000600 "An educational institution is an place organization which provides the necessary system for people of different ages gain an education. It includes (among others) preschools, childcare, elementary schools, and universities." xsd:string
is_obsolete: true
[Term]
id: APOLLO_SV:00000112
name: school closure target facilities
def: "An information content entity about educational institutions that is part of the action sepcification of a school closure control measure." []
is_a: IAO:0000030
property_value: IAO:0000600 "The specification of which facilities to target in a school closure control measure." xsd:string
[Term]
id: APOLLO_SV:00000114
name: infection
def: "A reproduction of a pathogen organism of a particular biological taxon in a tissue of a host organism from another taxon." []
comment: infection is reproduction of a pathogen inside some tissue of a host. By associating infection with the classes latent period and infectious period, which are associated with specific pathogen species and host species, Apollo-SV defines infection further as reproduction of a particular pathogen taxon inside some tissue of a particular host taxon.
is_a: GO:0000003
relationship: RO:0002087 APOLLO_SV:00000115 ! infection acquisition
property_value: http://purl.org/dc/elements/1.1/creator "M. Brochhausen" xsd:string
property_value: IAO:0000117 "William R. Hogan" xsd:string
property_value: IAO:0000118 "infection process" xsd:string
property_value: IAO:0000118 "process of infection" xsd:string
property_value: IAO:0000600 "A process of reproduction of a particular pathogen species inside some tissue of a particular host species." xsd:string
[Term]
id: APOLLO_SV:00000115
name: infection acquisition
def: "The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources" []
comment: Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use. The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things.\nThe likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient. \nAn infection is acquired from an infectious organism or a contaminated thing. \n
comment: Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing
is_a: GO:0044409
relationship: RO:0002411 APOLLO_SV:00000114 ! infection
property_value: APOLLO_SV:0000040 "InfectionAcquisition" xsd:string
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
property_value: IAO:0000600 "A process where a susceptible organism from a particular species becomes infected by a particular pathogen. The infection is acquired from an infected organism of a particular species or from a contaminated thing. \n\nNote that the susceptible and infectious organisms can be of different species.\n\n" xsd:string
[Term]
id: APOLLO_SV:00000117
name: vaccine identifier
def: "An identifier that refers to a type of vaccine, i.e., one of a class of manufactured vaccines that public health would consider interchangable." []
is_a: IAO:0020000
relationship: IAO:0000219 BFO:0000040
property_value: APOLLO_SV:0000040 "vaccineOntologyId" xsd:string
property_value: IAO:0000600 "A unique identifier for a vaccine." xsd:string
[Term]
id: APOLLO_SV:00000118
name: latent period
is_a: BFO:0000015
relationship: BFO:0000139 APOLLO_SV:00000114 ! infection
property_value: IAO:0000117 "Mathias Brochhausen" xsd:string
[Term]
id: APOLLO_SV:00000119
name: vaccination identifier
def: "a unique identifier that refers to a protocol for vaccinating one person" []
is_a: IAO:0020000
relationship: IAO:0000219 IAO:0000033
property_value: IAO:0000600 "A unique identifier for a vaccination protocol (the process of vaccinating one person)" xsd:string
[Term]
id: APOLLO_SV:00000120
name: vaccination course
is_a: APOLLO_SV:00000795 ! individual treatment control strategy action specification
property_value: IAO:0000600 "the number of doses of vaccine that are recommended to achieve immunity" xsd:string
[Term]
id: APOLLO_SV:00000121
name: species
is_a: APOLLO_SV:00001008 ! TODO
property_value: APOLLO_SV:0000040 "species" xsd:string
property_value: IAO:0000600 "an interbreeding population" xsd:string
[Term]
id: APOLLO_SV:00000122
name: antiviral identifier
def: "a unique identifier that refers to an antiviral drug product" []
is_a: IAO:0020000
relationship: IAO:0000219 BFO:0000040
property_value: APOLLO_SV:0000040 "antiviralId" xsd:string
property_value: IAO:0000600 "A unique identifier for an antiviral drug" xsd:string
[Term]
id: APOLLO_SV:00000123
name: school closure control strategy
def: "A place closure control strategy whose action specification is realized in a school closure process." []
is_a: APOLLO_SV:00000229 ! place closure control strategy