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]) An organism that has an immunodeficiency. Albert Goldfain Alexander Diehl Lindsay Cowell immunocompromised organism immunodeficient organism _obsolete_infectious disease course true A 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. Albert Goldfain Alexander Diehl Lindsay Cowell 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 A material entity bearing an antibacterial disposition. Albert Goldfain Alexander Diehl Lindsay Cowell antibiotic antibacterial http://www.ebi.ac.uk/efo/EFO A fungal infectious disease that is rare and may develop when people inhale a fungus called Blastomyces dermatitidis, a fungus that is found in moist soil, particularly where there is rotting vegetation. The fungus enters the body through the lungs, infecting them. The fungus then spreads to other areas of the body.The infection may affect the skin, bones and joints, and other areas. The disease usually affects people with weakened immune systems, such as those with HIV or who have had an organ transplant.[https://rarediseases.info.nih.gov/diseases/5931/blastomycosis ] Although blastomycosis is especially dangerous for those with weak immune systems, most people diagnosed with blastomycosis have healthy immune systems Source: doi:10.1016/j.ccm.2017.04.006 blastomycosis A pathologically immunosuppressed organism that is a human experiencing drug-based immunosuppression. Alex Diehl Lindsay Cowell NCI BBRB immunosuppressed human experiencing drug-based immunosuppression due to organ transplant http://www.ebi.ac.uk/efo/EFO A fungal infectious disease that is caused by Coccidioides immitis. Affected individuals usually have mild flu-like symptoms. However, pneumonia and systemic involvement with the formation of abscesses may develop as complications of the disease. [ NCIT : P378 ] San Joaquin Valley fever Valley fever desert rheumatism coccidioidomycosis An organism bearing an infectious agent host role. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent host A disposition to kill or inhibit the lifecycle of viruses. Albert Goldfain Alexander Diehl Lindsay Cowell antiviral disposition A disposition that inheres in a host of infectious agent and is a disposition to transmit infectious agents to organisms of the same Species through casual contact with a high likelihood of realization. Albert Goldfain Alexander Diehl Lindsay Cowell Highly contagious infections, those with a relatively high likelihood of spread, are referred to as contagious and are those for which spread is likely as a result of day-to-day activities of the host. The disposition is realized in a horizontal transmission process. contagiousness A pathologically immunosuppressed organism that is experiencing drug-based immunosuppression. Alex Diehl Lindsay Cowell immunosuppressed organism experiencing drug-based immunosuppression An immunity to infectious agent realized in an adaptive immune response. Albert Goldfain Alexander Diehl Lindsay Cowell _obsolete_adaptive immunity to infectious agent true 'can change depending on environmentnnwhere should susceptibility factors go?'-ID[O]:0000212: can change depending on environmentnnwhere should susceptibility factors go? id 'susceptibility'-ID[O]:0000212 from IDO 2007. May have replacement - TBD _obsolete_susceptibility true _obsolete_parasite true A role borne by an anatomical entity in virtue of the fact that it serves as the site through which an infectious agent enters a host. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in a process by which an infectious agent enters a host. infectious agent portal of entry role A material entity bearing an antiseptic role. Albert Goldfain Alexander Diehl Lindsay Cowell antiseptic A quality that inheres in an infection in virtue of the fact that the infection persists for an extended period of time. Albert Goldfain Alexander Diehl Lindsay Cowell persistent infection _obsolete_chronic quality of infection true 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 disposition to kill or inhibit the development or reproduction of microorganisms. Albert Goldfain Alexander Diehl Lindsay Cowell Some instances might be functions, depending on whether the bearer is something that exists and is used for the purpose (alcohol) or something that was designed for the purpose (pine sol). Entities that kill microorganisms are referred to as microbicidal; entities that inhibit the growth of microorganisms are referred to as microbistatic. The disposition is realized in the killing or inhibition of microorganisms. antimicrobial disposition (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] _obsolete_antibiotic resistance true 'holder and a carrier (actively transmits) and living: potentially make a cross product. every vector comes into contact with the target. (from one host to another?)'-ID[O]:0000063: holder and a carrier (actively transmits) and living: potentially make a cross product. every vector comes into contact with the target. (from one host to another?) id 'vector'-ID[O]:0000063 from IDO 2007. May have replacement - TBD _obsolete_vector true An immunity to infectious agent that inheres in an organism in virtue of its leukocytes. Albert Goldfain Alexander Diehl Lindsay Cowell cell-mediated immunity to infectious agent The disposition is realized in a leukocyte-mediated immune response. leukocyte-mediated immunity to infectious agent 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 expand assertion to A disposition borne by a biological macromolecule that is the disposition to participate in adherence to a host. Albert Goldfain Alexander Diehl Lindsay Cowell The disposition is realized in an adherence to host process. adhesion disposition A collective disposition the realization of which mitigates the damaging effects of some entity on members of the collection. Albert Goldfain Alexander Diehl Lindsay Cowell collective resistance disposition 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]) 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. per discussion with Barry Smith A resistance to infectious agent that inheres in an organism in virtue of immune system components in the extended organism. Albert Goldfain Alexander Diehl Lindsay Cowell protective immunity to infectious agent We don't specify that immunity results from prior exposure, because we want to include innate immunity. In addition, for adaptive immunity, there could be some low level immunity even in a primary immune response. immunity to infectious agent A susceptibility that is the degree to which an entity can be harmed or inhibited from surviving by a drug. Albert Goldfain Alexander Diehl Lindsay Cowell drug susceptibility An infectious agent whose infection incidence is increasing following its first introduction into a new host Species. Albert Goldfain Alexander Diehl Lindsay Cowell emerging pathogen s-region SpatialRegion 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 A disposition to initiate processes that result in a disorder. Albert Goldfain Alexander Diehl Lindsay Cowell pathogenicity A pathogenic disposition is realized in processes that create a disorder. The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition. By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition. pathogenic disposition 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) Chris Mungall GOC:mtg_berkeley_2013 results_in_formation_of results in formation of UNITE Community https://dx.doi.org/10.15156/BIO/TH031017 paracoccidioides _obsolete_transport by blood true A disposition borne by an infectious agent that is the disposition to penetrate the epithelial barriers of an organism of another Species. Albert Goldfain Alexander Diehl Lindsay Cowell invasive disposition A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population. Albert Goldfain Alexander Diehl Lindsay Cowell The organism corresponding to the extended organism is host to the infectious agents. By this definition, parts of the host can be considered part of the infection. infection A material entity bearing an antifungal disposition. Albert Goldfain Alexander Diehl Lindsay Cowell antifungal An infectious agent transporter role that is borne by an organism active in the transfer of an infectious agent to an organism of another Species and in which the agent is infectious. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in a transmission process. A bearer of a vector role is also a bearer of a host role. infectious agent vector role A disorder of an immune system component that results in defective functioning of the immune system. Albert Goldfain Alexander Diehl Lindsay Cowell immunodeficiency Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) _obsolete_mobile genetic element true Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. A material entity with a pathogenic disposition. Albert Goldfain Alexander Diehl Lindsay Cowell pathogen 'total number of cases of a particular disease at a given time in a particular population divided by the number of individuals in that particular populationnnthe burden of a disease in a population'-ID[O]:0000019: total number of cases of a particular disease at a given time in a particular population divided by the number of individuals in that particular populationnnthe burden of a disease in a population id 'prevalence'-ID[O]:0000019 from IDO 2007. May have replacement - TBD _obsolete_prevalence true An infectious disease that has as its physical basis an infectious disorder composed of infectious agents that have a zoonotic disposition. Albert Goldfain Alexander Diehl Lindsay Cowell zoonosis An organism population whose members each have an infectious disposition. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent population A role borne by an infectious agent when contained in a host in which its infectious disposition can be realized. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent role 'role played by a portion of substance to promote virulencennmagnitudendegree of pathogenesis'-ID[O]:0000040: role played by a portion of substance to promote virulencennmagnitudendegree of pathogenesis id 'virulence factor'-ID[O]:0000040 from IDO 2007. May have replacement - TBD _obsolete_virulence factor true A disposition to kill or inhibit the development or reproduction of fungal organisms. Albert Goldfain Alexander Diehl Lindsay Cowell antifungal disposition An organism bearing an infectious agent vector role. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent vector (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] http://www.orpha.net/ORDO/Orphanet Sporotrichosis is a fungal infectious disease that is caused by the dimorphic fungus Sporothrix schenckii, generally occurring by traumatic inoculation of fungus from contaminated soil, plants, and organic matter, that has a highly variable disease spectrum but that usually presents as a subcutaneous mycosis with a single sporotrichotic chancre that may ulcerate and can then progress to lymphocutaneous (most common form; sporotrichotic chancre at inoculation site and a string of similar nodules along the proximal lymphatics), fixed cutaneous (localized asymptomatic, erythematous, papules at the inoculation site), or multifocal or disseminated cutaneous (rare form, with 3 or more lesions involving 2 different anatomical sites) forms. Pulmonary sporotrichosis occurs following inhalation of fungus and manifests as chronic pneumonitis while extracutaneous or systemic sporotrichosis (with osteoarticular, pulmonary, and central nervous system/meningeal disease) has also been reported, usually occurring in the setting of immunosuppression. rose gardener’s disease can also be caused by sporothrix brasiliensis fungus sporotrichosis UNITE Community https://dx.doi.org/10.15156/BIO/TH030644 curvularia An infection that has as part organisms of the Genus Candida. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/IDO An infection that has as part organisms of the Genus Candida. moved original placement of candidiasis in IDO to reflect that candidiasis is the disease, with an infection as its material basis candidiasis An immunodeficiency that exists in an organism because of a genetic predisposition. Albert Goldfain Alex Diehl Lindsay Cowell congenital immunodeficiency primary immunodeficiency process Process 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) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process An organism bearing a host role. Albert Goldfain Alexander Diehl Lindsay Cowell host A life cycle temporal boundary that marks the end of the life cycle of the organism. life-death temporal boundary A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis utilizes the host to undergo a developmental stage transition, but the host is not required for continuation of the partner's life cycle. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in developmental processes of the host's partner in symbiosis. paratenic host role _obsolete_complement resistance true 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 participates in b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) An infectious disposition to become part of a disorder only in organisms whose defenses are compromised. Albert Goldfain Alexander Diehl Lindsay Cowell opportunitistic pathogenic disposition The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host. This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin). opportunistic infectious disposition curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. immune response 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) Person:Alan Ruttenberg has ID digit count 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 http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by _obsolete_primary pathogen true ic IndependentContinuant 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 (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] 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]) _obsolete_immunization true An infection resulting from a transmission process that unfolds in a nursing home. Albert Goldfain Alexander Diehl Lindsay Cowell nursing-home acquired infection 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 elucidation A role borne by an organism in symbiosis. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in symbiosis. symbiont role A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism. Albert Goldfain Alexander Diehl Lindsay Cowell host role An organism bearing the infectious agent carrier role. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent carrier _obsolete_engulfment by phagocyte true Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label A disposition to undergo a transmission process. Albert Goldfain Alex Diehl Lindsay Cowell The disposition is realized in a transmission process. transmissibility disposition http://purl.obolibrary.org/obo/NCIT A fungal infectious disease that is caused by Paracoccidioides brasiliensis that is most often seen in immunocompromised patients. It is typically a systemic mycosis. It affects the mucous membranes, lymph nodes, lungs and bones. [ NCI ] paracoccidioidomycosis st-region SpatiotemporalRegion the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region 'infection has occurred, but it might not have manifested itselfnquality of being in a non replicative statentime to manifest itself na pathogen when it is in a non replicative state'-ID[O]:0000009: infection has occurred, but it might not have manifested itselfnquality of being in a non replicative statentime to manifest itself na pathogen when it is in a non replicative state id 'latency'-ID[O]:0000009 from IDO 2007. May have replacement - TBD _obsolete_latency true Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process in which a virus is a participant. negative regulation of viral process An infectious organism population with a certain configuration quality (OGMS:0000039) (distributed across a spatial region (e.g., anatomical location in a host) in a particular way). Put e.g. In comments Albert Goldfain Alexander Diehl Lindsay Cowell _obsolete_configured infectious organism population true An organism bearing a paratenic host role. Albert Goldfain Alexander Diehl Lindsay Cowell paratenic host Sydney Cohen A fungus that has an infectious disposition fungal infectious agent 0d-s-region ZeroDimensionalSpatialRegion 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 sdc SpecificallyDependentContinuant 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 one-sided specifically dependent continuants: the mass of this tomato 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 role of being a doctor 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 &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) 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 doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region A role borne by an infectious disorder in virtue of the fact that (1) the host has at least two distinct infectious disorders, where neither arose from the other through metastasis, (2) at the time the infectious disorder was established in the host, the host had no infectious disorder, and (3) the infectious disorder increases the host's susceptibility to infectious disorders. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in a process by which the infectious disorder is established in the host. primary infection role Archaea _obsolete_role true http://purl.obolibrary.org/obo/NCIT A Cryptococcus that affects the membranes surrounding the brain and spinal column (meninges). It is a blood borne fungal infection caused by Cryptococcus, usually C. neoformans or C. gattii. It usually occurs in immunocompromised patients including persons with AIDS, transplant recipients, patients receiving cytotoxic chemotherapy, and patients with hematologic malignancies. [ NCI ] A cryptococcosis that is characterized by a blood borne fungal infection of the membranes surrounding the brain and spinal column (meninges). Caused by Cryptococcus, usually C. neoformans or C. gattii. It usually occurs in immunocompromised patients including persons with AIDS, transplant recipients, patients receiving cytotoxic chemotherapy, and patients with hematologic malignancies. [ NCI ] cryptococcal meningitis A production process in which a participant creates a copy of itself. Albert Goldfain Alexander Diehl Lindsay Cowell replication material MaterialEntity 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 UNITE Community https://dx.doi.org/10.15156/BIO/TH032704 fusarium Any process involved in the carrying out of an immune response by a leukocyte. leukocyte mediated immunity 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. Chris Mungall produces has output A disease course that is the realization of an infectious disease. Albert Goldfain Alexander Diehl Lindsay Cowell infectious disease course (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] 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]) _obsolete_therapeutic true _obsolete_co-infected true A generically dependent continuant that is the set of organism types whose instances have as one of their canonical dispositions, the disposition to bear the host role for a colony of a certain type. A quality that inheres in an infection and is the likelihood that infectious agents part of the infection will spread to other hosts. Albert Goldfain Alexander Diehl Lindsay Cowell _obsolete_contagiousness quality _obsolete_host range true UNITE Community https://dx.doi.org/10.15156/BIO/SH1192746.08FU scedosporium prolificans 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 occurs in Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) cf-boundary ContinuantFiatBoundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary A role borne by a material entity in virtue of the fact that it has an antimicrobial disposition and is applied to a non-living entity. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in the killing and/or growth inhibition of microorganisms on the non-living entity. disinfectant role _obsolete_temperature true A process by which a disorder comes into existence. Albert Goldfain Alexander Diehl Lindsay Cowell appearance of disorder An organism bearing a parasite host role. Albert Goldfain Alexander Diehl Lindsay Cowell parasite host (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] Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. Gene Ontology: http://purl.obolibrary.org/obo/go.owl establishment of localization A disposition borne by a biological macromolecule that is the disposition to facilitate breach of host epithelial barriers or entry into and survival in host cells. Albert Goldfain Alexander Diehl Lindsay Cowell A molecule with the invasion disposition is referred to as an invasion factor or invasin. invasion disposition A disease whose physical basis is an infectious disorder. Albert Goldfain Alexander Diehl Lindsay Cowell tranmissible disease The disposition is realized in an infectious disease course. infectious disease A disposition whose realization negatively regulates an immune response. Albert Goldfain Alexander Diehl Lindsay Cowell immunosuppressive disposition A process of infectious disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population. For a particular instance of infectious disease epidemic, signficance is determined based on the infectious disease incidence that is typical for an infectious disease for the particular population and time period. Albert Goldfain Alexander Diehl Lindsay Cowell infectious disease outbreak infectious disease epidemic A biological macromolecule that has an invasion disposition. Albert Goldfain Alexander Diehl Lindsay Cowell invasin invasion factor _obsolete_transport by lymph true _obsolete_fimbrial specific adherence true a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch 1d-s-region OneDimensionalSpatialRegion 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 An organism population in whose members an infectious disease is being realized. Albert Goldfain Alexander Diehl Lindsay Cowell diseased population this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function A role borne by a material entity in virtue of the fact that it contains a site from which an infectious agent is transmitted. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in a process that has as part a transmission process and a process by which the infectious agent or one of its offspring becomes part of a disorder in the host. source of infection role Sydney Cohen https://www.ncbi.nlm.nih.gov/books/NBK574511/ A fungal infectious disease that is caused by filamentous fungi and effects the skin and subcutaneous tissue. Characterized by deep granulomatous inflammation and the formation of grains which lead to the destruction of deep tissue, muscle, bone, joints, and tendons. The most common site of infection is the foot, followed by hands. Less frequently, other areas may be involved. eumycotic mycetoma Eumycetoma is a mycetoma caused by fungi (eumycotic) rather than a mycetoma caused by bacteria (actinomycotic) Mycetoma is a WHO-recognized neglected tropical disease with a significant disease burden. It primarily affects those in tropical and subtropical climates who are in direct contact with soil. non-exhaustive list of fungi that may cause the infection and disease. for more information, see https://doi.org/10.1111/jdv.13008 eumycetoma A resistance to drug that mitigates the damaging effects of an antibiotic. Albert Goldfain Alexander Diehl Lindsay Cowell antibiotic resistance Any process that modulates a measurable attribute of any biological process, quality or function. biological regulation http://purl.obolibrary.org/obo/NCIT An aspergillosis that is characterized by the presence of septate, acute, branching hyphae invading lung tissue. [ NCI ] Occurs when Aspergillus causes a serious infection, and usually affects people who have weakened immune systems, such as people who have had an organ transplant or a stem cell transplant. Invasive aspergillosis most commonly affects the lungs, but it can also spread to other parts of the body. invasive aspergillosis A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) _obsolete_prion true Sydney Cohen A mucormycosis that primarily affects the pulmonary system. It is most common type of mucormycosis in people with cancer and in people who have had an organ transplant or a stem cell transplant. Usually invasive and life-threatening lung mucormycosis there is no specific sign and symptoms, diagnostic criteria and specific antigen test for the diagnosis and management of PM. Any history of fever non-responding to antibiotics with pulmonary signs should also raise the suspicion of fungal infection like PM. More info: doi: 10.21037/jtd.2017.02.31 pulmonary mucormycosis Sydney Cohen https://www.cdc.gov/mucormycosis/hcp/clinical-overview/index.html A mucormycosis that spreads through the bloodstream to affect another part of the body. Disseminated mucormycosis most commonly affects the brain, but also can affect other organs such as the spleen, heart, and skin. disseminated mucormycosis process-profile ProcessProfile 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]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile UNITE Community https://dx.doi.org/10.15156/BIO/SH1160519.08FU aspergillus fumigatus 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 UNITE Community https://dx.doi.org/10.15156/BIO/TH030899 exophiala 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 Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates realizable RealizableEntity 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]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity An organism who is host to an infectious agent and has symptoms of the infectious disease associated with the infectious agent Albert Goldfain Alexander Diehl Lindsay Cowell symptomatic host of infectious agent UNITE Community https://dx.doi.org/10.15156/BIO/TH030905 phialophora http://www.ebi.ac.uk/efo/EFO A fungal infectious disease that can be caused by Cryptococcus neoformans. It can present as an acute, chronic, localized or disseminated infection. Sites of involvement include the lungs, central nervous system and meninges, skin, and visceral organs.--2004 [ NCIT : P378 ] A fungal infectious disease that is caused by the fungus Cryptococcus neoformansacute. Can be a chronic, localized or disseminated infection. Sites of involvement include the lungs, central nervous system and meninges, skin, and visceral organs.--2004 [ NCIT : P378 ] cryptococcosis (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] A molecular entity that has a toxin disposition. Albert Goldfain Alexander Diehl Lindsay Cowell toxin A colonization of human process in which the colonized site is the anterior nares. Albert Goldfain Alexander Diehl Lindsay Cowell colonization of human anterior nares 'agent is incubated?ndisease is incubated?'-ID[O]:0000219: agent is incubated?ndisease is incubated? id 'incubation period'-ID[O]:0000219 from IDO 2007. May have replacement - TBD _obsolete_incubation period true An organism population whose members have acquired immunity to an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell immune population A role borne by a material entity in virtue of the fact that an infectious agent is located in or on the entity and the entity has the capability to transfer (either actively or passively) the infectious agent from one location to another. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in a process that transfers an infectious organism from one location to another. infectious agent transporter role synonym of invasion factor Albert Goldfain Alexander Diehl Lindsay Cowell _obsolete_invasin true http://purl.obolibrary.org/obo/NCIT A candidiasis that is chracterized by infection of the oropharynx. This disease usually results from debilitation (as in immunosuppression and especially AIDS), physiologic change, prolonged administration of antibiotics, and iatrogenic and barrier breakage. SYN candidosis, moniliasis. [ NCI ] thrush Candida normally lives on the skin and inside the body, in places such as the mouth, throat, gut, and vagina, without causing any problems. Candida can multiply and cause an infection if the environment inside the mouth, throat, or esophagus changes in a way that encourages fungal growth. oropharyngeal candidiasis 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 PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w definition source 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 per discussion with Barry Smith An infection that is part of an asymptomatic host. Albert Goldfain Alexander Diehl Lindsay Cowell subclinical infection An immunity to infectious agent that inheres in an organism in virtue of antibodies not produced by that organism. Albert Goldfain Alexander Diehl Lindsay Cowell Passive immunity results from a passive immunization. The disposition is realized in a neutralizing process carried out by the antibodies. The protective antibodies are typically introduced by injection, breast feeding, or by passing from the placenta to the fetus. passive immunity to infectious agent A material entity that has a resistance disposition. Albert Goldfain Alexander Diehl Lindsay Cowell resistant entity An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host. Albert Goldfain Alexander Diehl Lindsay Cowell An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis. zoonotic disposition An aggregate of organisms of the same Species. Albert Goldfain Alexander Diehl Lindsay Cowell The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age. organism population UNITE Community https://dx.doi.org/10.15156/BIO/SH385070.07FU blastomyces dermatitidis A colonization of host process that results in a clinically abnormal colony. Albert Goldfain Alexander Diehl Lindsay Cowell establishment of a clinically abnormal colony http://purl.obolibrary.org/obo/NCIT A fungal infectious disease that is caused by Aspergillus. [ NCI ] A fungal infectious disease that occurs most often in the skin, ears, nasal sinuses, and lungs of people with suppressed immune systems. aspergillosis ## Elucidation This is used when the first-order logic form of the relation is binary, and takes no temporal argument. ## Example: Class: limb SubClassOf: develops_from some lateral-plate-mesoderm forall t, t2: forall x : instance_of(x,Limb,t) implies exists y : instance_of(y,LPM,t2) develops_from(x,y) relation has no temporal argument _obsolete_immunosuppressed true (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) An establishment of localization process in which a material entity reaches a site in an organism in which it can survive, grow, multiply, or mature. Requested addition of this term to the GO. Albert Goldfain Alexander Diehl Lindsay Cowell An organism begins bearing a particular host role as soon as the extended organism contains the relevant material entity, regardless of that entity's location in the extended organism. An establishment process is any process by which the entity reaches a location in the extended organism in which it can persist and continue its lifecycle. For example, an organism is host to a virus as soon as any part of the extended organism is occupied by virus particles. During an establishment process, virus particles enter host cells of the relevant type, and viral DNA is integrated into host DNA. establishment of localization in host An infectious disease prevalence that is typical for an infectious disease in an organism population. Albert Goldfain Alexander Diehl Lindsay Cowell Infectious disease endemic level is relational to previous prevalences of the disease. infectious disease endemic level An infectious disease course that unfolds over a long period of time. Albert Goldfain Alexander Diehl Lindsay Cowell persistent infectious disease course chronic infectious disease course Any 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. negative regulation of immune response A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process. Albert Goldfain Alexander Diehl Lindsay Cowell The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening. infectious agent transmissibility 'is this just the part of the life cycle of the biotic entity that has role pathogen for the period of time while it has role pathogen?nncan include phases in the existence of the entity before it becomes a pathogen'-ID[O]:0000226: is this just the part of the life cycle of the biotic entity that has role pathogen for the period of time while it has role pathogen?nncan include phases in the existence of the entity before it becomes a pathogen id 'pathogen life cycle'-ID[O]:0000226 from IDO 2007. May have replacement - TBD _obsolete_pathogen life cycle true _obsolete_progression rate true An infectious disease that has as its physical basis an infectious disorder composed of infectious agents that have a reverse zoonotic disposition. Albert Goldfain Alex Diehl Lindsay Cowell reverse zoonosis A organism bearing an intermediate host role. Albert Goldfain Alexander Diehl Lindsay Cowell secondary host intermediate host A process which is necessary for the survival of an organism. Alex Diehl Lindsay Cowell life-sustaining process UNITE Community https://dx.doi.org/10.15156/BIO/SH1213468.08FU Concern is rising over the emerging fungus Candida auris, which is rare in most areas of the United States but is a growing threat. Resistance rates for C. auris are much higher than for other Candida species, with: About 90% of U.S. C. auris samples being resistant to fluconazole, and Up to one-third are resistant to the antifungal drug amphotericin B source: doi: 10.1093/cid/ciw691 candida auris this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from derives from An infectious disposition to become part of a disorder in organisms that have intact defenses. Albert Goldfain Alexander Diehl Lindsay Cowell A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts. A quote from page 3 of Mandell's "Principles and Practice of Infectious Diseases" (Sixth edition): "It is useful to distinguish "principal" pathogens, which regularly cause disease in some proportion of susceptible individuals with apparently intact defense systems, from other potentially pathogenic microorganisms. ... even for most organisms classified as principal pathogens, for example, Staphylococcus aureus and the pneumococcus, some impairment or local breakdown in normal host defense mechanisms must occur for these bacteria to cause disease. ... Thus, it seems clear that the capacity of certain microorganisms to cause disease in seemingly uncompromised human hosts on a regular basis reflects some fundamental difference in their virulence capabilities from those of opportunists and the more numerous commensal species that rarely, if ever, cause disease." primary infectious disposition An infection established as a result of spread from another infection in a non-adjacent location in the extended organism of the host. Albert Goldfain Alexander Diehl Lindsay Cowell metatstatic infection r-quality RelationalQuality 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. a marriage bond, an instance of love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality Sydney Cohen A mycosis that results in infection located in skin or located in subcutaneous tissue, which penetrate the dermis or even deeper during or after a skin trauma. http://purl.obolibrary.org/obo/DOID_0050135 subcutaneous mycosis A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. disorder function Function 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. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function An establishment of localization in host process in which an organism establishes itself in a host. Establishment of one organism in the extended organism of another (the host) involves at least one of (1) movement of the organism to a location within the host in which the organism can persist, or (2) adherence or attachment of the organism to part of the host. Albert Goldfain Alexander Diehl Lindsay Cowell colonization of host A disposition that inheres in a collection of entities in virtue of the individual dispositions of the constituents of that collection. Albert Goldfain Alexander Diehl Lindsay Cowell "... in virtue of the individual dispositions of the contstituents" is intended to capture the fact that the collective disposition results from the combination of the individual dispositions. It is not necessary that every constituent of the aggregate have a relevant individual disposition. The disposition is realized in a process that has as part realizations of some of the individual dispositions. collective disposition Bacteria A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] An aspergillosis infection that is caused by one species of Aspergillus, A. fumigatus, that becomes resistant to certain medicines used to treat it. Patients with resistant infections might not get better with treatment Triazole antifungal drugs, commonly called azoles, are the primary treatment for aspergillosis. Azole-resistant A. fumigatus infections are difficult to treat, and these patients are up to 33% more likely to die than patients with infections that can be treated with azole (https://www.cdc.gov/fungal/diseases/aspergillosis/antifungal-resistant.html) azole-resistant aspergillus fumigatus 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]) 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]) mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO_0000053 some (RO_0000054 only ?Y) capable of http://purl.obolibrary.org/obo/NCIT A fungus that is multicellular and produces filaments and hyphae. A non-taxonomic grouping of fungi that grow in the form of mycelium of hyphae (vegetative filaments). mold (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] _obsolete_host true _obsolete_protective true UNITE Community https://dx.doi.org/10.15156/BIO/TH030957 aspergillus An immunization that begins with transfer to an organism of molecules not produced by that organism and that confer immunity against an infectious agent. Examples include the injection of antibodies and the transfer of maternal antibodies to the fetus. Albert Goldfain Alexander Diehl Lindsay Cowell passive immunization against infectious agent has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status A molecular entity bearing an exotoxin disposition. Albert Goldfain Alexander Diehl Lindsay Cowell exotoxin 'is a period a process?'-ID[O]:0000227: is a period a process? id 'dormancy period'-ID[O]:0000227 from IDO 2007. May have replacement - TBD _obsolete_dormancy period true An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects UNITE Community https://dx.doi.org/10.15156/BIO/TH035107 rhizopus (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) quality Quality 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]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith http://www.orpha.net/ORDO/Orphanet A fungal (or bacterial) eye infection that is characterized by inflammation involving the vitreous and/or aqueous humors, usually due to bacterial or fungal infection. It may arise endogenously from hematogenous spread of the infectious agent, or exogenously after direct inoculation, and can take an acute or chronic course. Clinical signs and symptoms include progressive vitritis, hypopyon, reduced or blurred vision, red eye, pain, and lid swelling. The condition may be complicated by panophthalmitis, corneal infiltration and perforation, affection of orbital structures, and phthisis bulbi. A fungal eye infection that is characterized by inflammation involving the vitreous and/or aqueous humors, usually due to bacterial or fungal infection. It is considered a rare ophthalmic disorder. It may arise endogenously from hematogenous spread of the infectious agent, or exogenously after direct inoculation, and can take an acute or chronic course. Clinical signs and symptoms include progressive vitritis, hypopyon, reduced or blurred vision, red eye, pain, and lid swelling. The condition may be complicated by panophthalmitis, corneal infiltration and perforation, affection of orbital structures, and phthisis bulbi. endophthalmitis An organism population whose members have an infection. Albert Goldfain Alexander Diehl Lindsay Cowell infected population An infectious agent vector bearing a mechanical vector of infectious agent role. Albert Goldfain Alexander Diehl Lindsay Cowell mechanical vector of infectious agent A material entity bearing an end reservoir of infectious agent role. Albert Goldfain Alexander Diehl Lindsay Cowell dead-end reservoir of infectious agent _obsolete_end reservoir of infectious agent true _obsolete_immunocompromised true b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission. Albert Goldfain Alexander Diehl Lindsay Cowell The disposition is realized in a direct, horizontal transmission process between members of the same Species. communicability x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y Chris Mungall negatively regulates (process to process) negatively regulates An infection bearing the primary infection role. Albert Goldfain Alexander Diehl Lindsay Cowell primary infection 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. organism _obsolete_outbreak true A quality that inheres in an organism population and is the infection incidence proportion per unit time. Albert Goldfain Alexander Diehl Lindsay Cowell 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 _obsolete_exogenous true 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]) A disposition to kill or inhibit the reproduction of bacteria. Albert Goldfain Alexander Diehl Lindsay Cowell antibiotic disposition antibacterial disposition A quality that inheres in an entity and is the degree to which it can be harmed by another entity. Albert Goldfain Alexander Diehl Lindsay Cowell Low susceptibility is often referred to as resistance. In this sense, resistance is a quality. susceptibility A disposition to colonize an organism and participate in mutualism or commensalism with that organism. Albert Goldfain Alexander Diehl Lindsay Cowell disposition to form a non-parasitic colony the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of 2D boundary of All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) _obsolete_live true A susceptibility that inheres in an organism and is the degree to which it can be harmed by an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell susceptibility to infectious agent An organism that has an infection in or on its extended organism. Albert Goldfain Alexander Diehl Lindsay Cowell infected organism 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 http://www.obofoundry.org/ro/#OBO_REL:part_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 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 located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in A resistance to infectious agent that inheres in an organism in virtue of a specific allele or combination of alleles in its genome. Albert Goldfain Alexander Diehl Lindsay Cowell 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 infectious agent An infection bearing the secondary infection role. Albert Goldfain Alexander Diehl Lindsay Cowell secondary infection A host role borne by an organism in virtue of the fact that its extended organism contains a pathogen. Albert Goldfain Alexander Diehl Lindsay Cowell Bearing the infectious agent host role implies bearing the pathogen host role, but the reverse is not true. See comment for infectious agent host role. pathogen host role A disposition that inheres in a material entity in virtue of the fact that the entity has a part (e.g. a gene product), which itself has a disposition to mitigate damage to the entity. Albert Goldfain Alexander Diehl Lindsay Cowell 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. The disposition is realized in a process that mitigates damage to the bearer and has the part as a participant. protective resistance An immunity to infectious agent 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. Albert Goldfain Alexander Diehl Lindsay Cowell adaptive immunity to infectious agent immune memory The disposition is realized in an immune response in which such antigen receptors participate. acquired immunity to infectious agent 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. 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 imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from A 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. Albert Goldfain Alexander Diehl Lindsay Cowell 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 _obsolete_disruption of body surface true An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects _obsolete_specific adherence true Eukaryota An immune response mediated through a body fluid. humoral immune response An infection comprised of infectious organisms from different Species. Albert Goldfain Alexander Diehl Lindsay Cowell mixed infection polymicrobial infection complex infection A material entity bearing a source of infection role. Albert Goldfain Alex Diehl Lindsay Cowell source of infection en Sydney Cohen This is an extension of the Infectious Disease Ontology. MIDO's purpose is to provide standardized human- and computer-interpretable annotation and representation of various fungal infectious diseases. Its development follows the OBO Foundry Principles. https://github.com/SydCo99/MIDO.git 2022-12-04 _obsolete_engulfment true A biological macromolecule produced by a pathogen and that has a virulence factor disposition. Albert Goldfain Alexander Diehl Lindsay Cowell virulence factor (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] A drug-based immunosuppression process that results from chronic systemic steroid use. Alex Diehl Lindsay Cowell chronic systemic steroid use-based immunosuppression Sydney Cohen World Health Organization: https://www.who.int/india/home/emergencies/coronavirus-disease-(covid-19)/mucormycosis Mucormycosis is a fungal infectious disease that is caused by a group of fungi called mucormycetes(previously called zygomycosis). It is a rare but serious angio-invasive infection. Clinical presentation is classified according to the organ involvement. It can be rhino-orbital cerebral, pulmonary, cutaneous, gastrointestinal, or disseminated. zygomycosis (previous name) didn't import EFO:0007380, which also refers to mucormycosis, since that defintion mentions Zygomycota, a phylum of fungi that no longer exists mucormycosis An immunosuppressed organism that is a human experiencing HIV-based immunosuppression. Alex Diehl Lindsay Cowell NCI BBRB immunosuppressed human experiencing HIV-based immunosuppression A quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time. Albert Goldfain Alexander Diehl Lindsay Cowell 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 ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation axiom holds for all times _obsolete_invasin true Sydney Cohen https://www.cdc.gov/mucormycosis/hcp/clinical-overview/index.html A mucormycosis that is in the sinuses and that can spread to the brain. This is most common in people with uncontrolled diabetes and in people who have had a kidney transplant. sinus and brain mucormycosis rhinocerebral mucormycosis A colonization of human process in which the colonized site is a perineum. Albert Goldfain Alex Diehl Lindsay Cowell colonization of human perineum An infectious agent that is an organism. Albert Goldfain Alexander Diehl Lindsay Cowell _obsolete_infectious organism true Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. biological_process Sydney Cohen https://doi.org/10.1590/abd1806-4841.20176614 A mucormycosis that is cutaneous (affecting skin, hair, eyes, nails, or potentially deeper levels of epidermis). It is an emerging fungal disease. It is usually acquired by direct inoculation through trauma. The clinical presentation is nonspecific, but an indurated plaque that rapidly evolves to necrosis is a common finding. cutaneous mucormycosis _obsolete_phase variation true An infectious agent 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. Albert Goldfain Alexander Diehl Lindsay Cowell Examples include blood, serum, tissue, or fresh produce. biological vehicle of infectious agent role _obsolete_mode of transmission true A disposition to kill or inhibit the development or reproduction of eukaryotic parasites. Albert Goldfain Alexander Diehl Lindsay Cowell In the term name, we are using parasite in the medical sense of eukaryotic organisms that are parasitic in humans. antiparasitic disposition All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) A part of a multicellular 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 multicellular organism with granularity above the level of a protein complex. anatomical entity (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] _obsolete_morbidity true A serious form of candidiasis that can affect the blood, heart, brain, eyes, bones, and other parts of the body. Candidemia Candidemia, a bloodstream infection with Candida, is a common infection in hospitalized patients. invasive candidiasis immaterial ImmaterialEntity 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 An infection for which the infectious agents that are part of the infection persist inside host cells. Albert Goldfain Alexander Diehl Lindsay Cowell intracellular infection antisymmetric property part_of antisymmetric property xsd:true use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis derives from the host a growth, survival, or fitness advantage while the host's growth, survival, or fitness is reduced. Albert Goldfain Alexander Diehl Lindsay Cowell The partner in symbiosis bears the parasite role. The role is realized in processes that result in the parasite's growth, survival, or fitness advantage or in the host's growth, survival, or fitness reduction. parasite host role _obsolete_infected true site Site Manhattan Canyon) 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 the trunk of your car the interior of your bedroom 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]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site An infectious disposition to be transmitted directly from one human host to another. Albert Goldfain Alexander Diehl Lindsay Cowell _obsolete_communicable disposition true An organism that has two infections with distinct Species of infectious agents. Albert Goldfain Alexander Diehl Lindsay Cowell co-infected organism A cryptococcosis that is caused by a C. gatti infection that may cause pulmonary cryptococcosis, basal meningitis and cerebral cryptococcomas. It is also associated with skin, soft tissue, lymph node, bone, and joint infections. A fungal infectious disease that can result from C. gatti infection, that may cause pulmonary cryptococcosis, basal meningitis and cerebral cryptococcomas. It is also associated with skin, soft tissue, lymph node, bone, and joint infections. C. gatti cryptococcosis In humans, C. gattii causes predominantly meningoencephalitis and other CNS and pulmonary diseases and is associated with substantial morbidity. It also poses a concern for veterinarians, and some animal infections, in particular those in feline and canine companion animals and Australian native koalas, represent sentinels for human exposure. more info: https://doi.org/10.1128/CMR.00126-13 cryptococcus gattii cryptococcosis UNITE Community https://dx.doi.org/10.15156/BIO/TH033417 candida A process in which a potential host of an infectious agent is exposed to an environment in which the infectious agent is present and physical contact between the two can occur, but such contact is not planned. Bjoern Peters host exposure to environment containing infectious agent An organism that has an infectious disposition. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent A disposition that is the ability to mount a normal immune response. Albert Goldfain Alexander Diehl Lindsay Cowell The disposition inheres in a bearer in virtue of the fact that the bearer has all canonical immune system components and none are disordered. The disposition is realized in a successful immune response. immunocompetence The increase in size or mass of an entire organism, a part of an organism or a cell. growth A 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. Albert Goldfain Alexander Diehl Lindsay Cowell 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 Any process that stops, prevents, or reduces the frequency, rate or extent of a life-sustaining process. Alex Diehl Lindsay Cowell negative regulation of life-sustaining process A 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. Albert Goldfain Alexander Diehl Lindsay Cowell Sporadic quality of infectious disease is relational to previous prevalence of the disease. infectious disease sporadicity UNITE Community https://dx.doi.org/10.15156/BIO/SH1178418.08FU paracoccidioides brasiliensis A toxin disposition to damage cells or extracellular matrix by a direct enzymatic process. Albert Goldfain Alexander Diehl Lindsay Cowell The disposition is realized in a direct enzymatic process that damages host cells or extracellular matrix. exotoxin disposition (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] UNITE Community https://dx.doi.org/10.15156/BIO/SH1178417.08FU histoplasma capsulatum _obsolete_exotoxin true UNITE Community https://dx.doi.org/10.15156/BIO/SH1150522.08FU used to be called penicillium marneffei talaromyces marneffei _obsolete_quality of host true An infection resulting from a transmission process that unfolds in a hospital. Albert Goldfain Alexander Diehl Lindsay Cowell nosocomial infection hospital-acquired infection An infectious agent with a capability to infect human hosts. Albert Goldfain Alexander Diehl Lindsay Cowell infectious human pathogen fiat-object FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object _obsolete_serum resistance true disposition of Sydney Cohen https://doi.org/10.3390/genes9090461 Polyenes are a group of antifungals that directly bind to and remove the ergosterol present in the fungal cell membrane. This results in the loss of membrane permeability, subsequent membrane leakage, and eventually cell death. Structurally, polyenes are characterized by the presense of poly-unsaturated organic compounds that contain at least three alternating double and single carbon–carbon bonds. Four models of the polyene mode of antifungal action have been proposed: the pore forming model, the surface adsorption model, the sterol sponge model and the oxidative damage model. More info: https://doi.org/10.3390/jof6040321 polyene A continuous temporal interval during which an infectious agent host bears a contagiousness disposition. Albert Goldfain Alexander Diehl Lindsay Cowell communicability period this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of quality of Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] An infectious agent transporter role borne by an entity in virtue of the fact that the entity is not a complete organism. Albert Goldfain Alexander Diehl Lindsay Cowell Drinking water bears the infectious agent vehicle role, but does not bear either of the subtype roles. infectious agent vehicle role _obsolete_epidemic spread of disease true _obsolete_pandemic spread of disease true A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. disease Sydney Cohen https://www.hopkinsmedicine.org/health/conditions-and-diseases/allergic-pulmonary-aspergillosis An aspergillosis that is chracterized by an allergic reaction to a fungus called aspergillus, which may cause inflammation of the airways and air sacs of the lungs. allergic aspergillosis 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 realized in An interaction between two organisms living together in more or less intimate association. Microscopic symbionts are often referred to as endosymbionts. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. symbiosis, encompassing mutualism through parasitism 'is a quality relating to both bacteria and host'-ID[O]:0000306: is a quality relating to both bacteria and host id 'fitness'-ID[O]:0000306 from IDO 2007. May have replacement - TBD _obsolete_fitness true 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary 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 http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant occurrent Occurrent 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 doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent An organism population whose members are not infected with an infectious agent and who lack immunity to the infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell at-risk population susceptible population Sydney Cohen Talaromycosis is a fungal infectious disease that is caused by the fungus Talaromyces marneffei. Talaromycosis only affects people who live in or visit Southeast Asia, southern China, or eastern India. Most people who get talaromycosis have a medical condition that weakens their immune system, such as HIV/AIDS, or another condition that lowers the body’s ability to fight germs and sickness. Bumps on the skin are a common symptom. These bumps are usually small and painless. The bumps usually appear on the face and neck but can also appear in other places on the body. talaromycosis A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition. Albert Goldfain Alexander Diehl Lindsay Cowell Clostridium botulinum is an example of an entity with the capability to bear the pathogen role but that does not have the capability to bear the infectious agent role or the parasite role. The influenza viruses are examples of organisms that can bear both the infectious agent and pathogen roles. pathogen role continuant Continuant 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 _obsolete_quality of host population true _obsolete_infectivity period true A biological object or group of biological objects in close spatial proximity. Albert Goldfain Alexander Diehl Lindsay Cowell _obsolete_biological object colony true A collective resistance disposition that inheres in an organism population in virtue of the fact that the proportion of the population with immunity to an infectious agent is high resulting in a low number of transmissions from hosts in the population to susceptible individuals in the population and thereby mitigating the damaging effects of the infectious agent on the population. Albert Goldfain Alexander Diehl Lindsay Cowell herd immunity to infectious organism An immunosuppression which unfolds as part of the natural self-regulation of an immune response. Albert Goldfain Alexander Diehl Lindsay Cowell physiologic immunosuppression (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into role Role 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]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role An organism bearing a dead-end host role. Albert Goldfain Alexander Diehl Lindsay Cowell incidental host dead-end host An organism bearing a mutualist role. Albert Goldfain Alexander Diehl Lindsay Cowell mutualist A 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. Albert Goldfain Alexander Diehl Lindsay Cowell toxin disposition Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. innate immune response 'role played by portion of physical substance which promotes colonization'-ID[O]:0000054: role played by portion of physical substance which promotes colonization id 'colonization factor'-ID[O]:0000054 from IDO 2007. May have replacement - TBD _obsolete_colonization factor true A host exhibiting disease symptoms. Albert Goldfain Alexander Diehl Lindsay Cowell _obsolete_symptomatic host true http://purl.obolibrary.org/obo/NCIT A fungal infectious disease that is caused by the fungus Histoplasma capsulatum. It primarily affects the lungs but can also occur as a disseminated disease that affects additional organs. The acute respiratory disease has symptoms similar to those of a cold or flu and it usually resolves without treatment in healthy individuals. The disseminated form is generally fatal if untreated. [ NCI ] More info: https://doi.org/10.1007/82_2018_114 histoplasmosis _obsolete_penetration of host cell true _obsolete_inactivated true UNITE Community https://dx.doi.org/10.15156/BIO/SH1160224.08FU fonsecaea pedrosoi 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor 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]) 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary precedes precedes _obsolete_mortality true A pathologic immunosuppression process which arises as the result of treatment with a drug that attenuates immune responses. Alex Diehl Lindsay Cowell drug-based immunosuppression An organism that can only reach developmental maturity, replicate, or persist in symbiosis. Albert Goldfain Alexander Diehl Lindsay Cowell obligatory symbiont 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 bearer of Sydney Cohen A fungal infectious agent that usually has an opportunistic infectious disposition. may include fungi that exist normally in healthy human flora, that have the capacity to cause infection opportunistic fungal pathogen A cytokinesis process that involves a set of conserved proteins including FtsZ, and results in the formation of two similarly sized and shaped cells. FtsZ-dependent cytokinesis A continuous temporal interval during which a transmission process occurs. Albert Goldfain Alexander Diehl Lindsay Cowell transmission period An infection comprised of infectious organisms all of the same Species. Albert Goldfain Alexander Diehl Lindsay Cowell simple infection UNITE Community https://dx.doi.org/10.15156/BIO/TH035111 syncephalastrum An organism that contains a colony in or on its extended organism. Albert Goldfain Alexander Diehl Lindsay Cowell colonized host 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]) Indirect transmission is a transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by intermediary vehicles, vectors or as airborne dust particles. Suggested label: indirect pathogen transmission process indirect (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of function 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 inheres in A material entity bearing an infectious agent vehicle role. Albert Goldfain Alexander Diehl Lindsay Cowell vehicle of infectious agent A molecular entity with a toxin disposition, the realization of which damages or interferes with the function of nerve tissue. Albert Goldfain Alexander Diehl Lindsay Cowell neurotoxin An organism population whose members are participating in non-parasitic symbiosis with a particular host. Albert Goldfain Alexander Diehl Lindsay Cowell normal resident microflora population normal resident microbiota population Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. entry into host A role borne by an infectious disorder in virtue of the fact that (1) the host has at least two distinct infectious disorders, where neither arose from the other through metastasis, (2) at the time the infectious disorder was established in the host, the host had a primary infectious disorder, and (3) establishment of the infectious disorder occurs because of increased susceptibility to infectious disorders conferred by the primary infectious disorder. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in a process by which the infectious disorder is established in the host. secondary infection role _obsolete_transcytosis true (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] _obsolete_pathogen-induced apoptosis true A virus that is in its assembled state consisting of genomic material (DNA or RNA) surrounded by coating molecules. Albert Goldfain Alexander Diehl Lindsay Cowell virion _obsolete_symbiant true Sydney Cohen https://doi.org/10.1155/2020/8876125 A mucormycosis that is characterized by the invasion of Mucorales into the gastric mucosa. It is rare but potentially lethal form of mucormycosis. It may result in high mortality due to increased risk of complications in immunocompromised patients. more common among young children than adults. Premature and low-birth-weight infants less than 1 month of age are at risk if they have had antibiotics, surgery, or medications that lower the body’s ability to fight germs and sickness. gastrointestinal mucormycosis Sydney Cohen https://www.cdc.gov/fungal/diseases/fungal-eye-infections/definition.html An endophthalmitis that is caused by a bloodstream infection (for example, candidemia) spreads to one or both eyes An endophthalmitis that occurs when a bloodstream infection (for example, candidemia) spreads to one or both eyes endogenous fungal endophthalmitis A molecular entity with an exotoxin disposition, the realization of which damages cells of the host intestinal mucosa. Albert Goldfain Alexander Diehl Lindsay Cowell enterotoxin If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] A collective disposition to initiate processes that result in a disorder. Albert Goldfain Alexander Diehl Lindsay Cowell The disposition is realized in processes that create a disorder. collective pathogenic disposition An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent multiplies in the vector. Albert Goldfain Alexander Diehl Lindsay Cowell biological vector of infectious agent role b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) 'prevalence as measured by antibody'-ID[O]:0000208: prevalence as measured by antibody id 'seroprevalence'-ID[O]:0000208 from IDO 2007. May have replacement - TBD _obsolete_seroprevalence true A protective resistance that mitigates the damaging effects of a drug. Albert Goldfain Alexander Diehl Lindsay Cowell drug resistance resistance to drug A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) _obsolete_resistance true A role borne by an anatomical entity in virtue of the fact that it serves as the site through which an infectious agent exits a host. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in a process by which an infectious agent exists a host. infectious agent portal of exit role (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] 'look at mathias's ontology of cancer to get all the subterms...its under quality there'-ID[O]:0000048: look at mathias's ontology of cancer to get all the subterms...its under quality there id 'symptom'-ID[O]:0000048 from IDO 2007. May have replacement - TBD _obsolete_symptom true (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] A symbiont role borne by an organism in virtue of the fact that both symbionts derive a growth, survival, or fitness advantage from symbiosis. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in processes that result in the growth, survival, or fitness advantage of either organism. mutualist role A disposition borne by a biological macromolecule produced by a pathogen that is a disposition to undergo processes that increase the pathogen's virulence. Albert Goldfain Alexander Diehl Lindsay Cowell 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 UNITE Community https://dx.doi.org/10.15156/BIO/TH033035 madurella 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. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason A pathogenic disposition that inheres in an organism and is a disposition for that organism (1) to be transmitted to a host, (2) to establish itself in the host, (3) to initiate processes that result in a disorder in the host, and (4) to become part of that disorder. Albert Goldfain Alexander Diehl Lindsay Cowell The disposition is realized in a process that has as part a transmission process, an establishment in host process, a process that results in a disorder, and a process in which the bearer of the disposition becomes part of that disorder. The infectious disposition has a complementary disposition that inheres in an organism and is the capability to be host to an organism with an infectious disposition and to undergo processes initiated by that infectious organism that result in a disorder. infectious disposition An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent does not multiply in or on the vector. Albert Goldfain Alexander Diehl Lindsay Cowell mechanical vector of infectious agent role An anatomical entity bearing an infectious agent portal of entry role. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent portal of entry site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis reaches developmental maturity or reproduces sexually in the host. Albert Goldfain Alexander Diehl Lindsay Cowell primary host role The role is realized in developmental and reproduction processes of the host's partner in symbiosis. definitive host role object-aggregate ObjectAggregate 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). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate _obsolete_infection treatment process true An organism experiencing a long-term non-progressing infectious disease course. Albert Goldfain Alexander Diehl Lindsay Cowell long-term non-progressor A pathologically immunosuppressed organism that is experiencing HIV-based immunosuppression. These individuals may also be immunodeficient due to depletion of CD4+ T cells and other effects of HIV. Alex Diehl Lindsay Cowell immunosuppressed organism experiencing HIV-based immunosuppression An organism bearing a definitive host role. Albert Goldfain Alexander Diehl Lindsay Cowell primary host definitive host A material entity bearing a disinfectant role. Albert Goldfain Alexander Diehl Lindsay Cowell disinfectant An active immunization that begins with exposure of an organism to a vaccine. Albert Goldfain Alexander Diehl Lindsay Cowell vaccination against infectious agent An infection for which the infectious agents that are part of the infection are limited to a relatively small area of the host's body. Albert Goldfain Alexander Diehl Lindsay Cowell local infection An immunodeficiency that is not caused by a genetic predisposition. Albert Goldfain Alexander Diehl Lindsay Cowell Causes of acquired immunodeficiences include infection and drug treatments (e.g. chemotherapy). acquired immunodeficiency UNITE Community https://dx.doi.org/10.15156/BIO/SH396686.07FU source for primary fungal pathogen classification: https://www.ncbi.nlm.nih.gov/books/NBK431060/ cryptococcus gatti 'inanimate holder, is water a fomite or only a reservoir?'-ID[O]:0000060: inanimate holder, is water a fomite or only a reservoir? id 'fomite'-ID[O]:0000060 from IDO 2007. May have replacement - TBD _obsolete_fomite true 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]) 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage 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') Alan Ruttenberg is denotator type (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] _obsolete_epidemic true A protective resistance that inheres in an organism and mitigates the damaging effects on that organism of an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell resistance to infectious agent UNITE Community https://dx.doi.org/10.15156/BIO/SH1507445.08FU neoscytalidium dimidiatum _obsolete_penetration of epithelial barrier true zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot 'number of new cases in a given period of time'-ID[O]:0000029: number of new cases in a given period of time id 'incidence'-ID[O]:0000029 from IDO 2007. May have replacement - TBD _obsolete_incidence true Homo sapiens A 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. macromolecular complex http://purl.obolibrary.org/obo/MONDO A fungal infectious disease that affects the eyes. It can be caused by a variety of fungi, usually through four possible mechanisms: superficial infection producing conjunctivitis, keratitis, or lacrimal obstruction; extension of infection from neighboring structures - skin, paranasal sinuses, nasopharynx; direct introduction during surgery or accidental penetrating trauma; or via the blood or lymphatic routes in patients with underlying mycoses. [ MESH : D015821 ] fungal eye infection A 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. Albert Goldfain Alexander Diehl Lindsay Cowell drug susceptibility of infectious agent Sydney Cohen https://www.cdc.gov/fungal/diseases/sporotrichosis/index.html A sporotrichosisoccurs that most commonly affects the skin on the hands or arms. Can occur when the fungus enters the skin through a small cut or scrape, usually after someone touches contaminated plant matter. most common form of the infection. It usually occurs on a person’s hand or the arm after touching contaminated plant matter. cutaneous sporotrichosis A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis has the infectious disposition but cannot be transmitted from the host to the partner's definitive host. Albert Goldfain Alexander Diehl Lindsay Cowell incidental host role dead-end host role A symbiont role borne by an organism in virtue of the fact that it derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced. Albert Goldfain Alexander Diehl Lindsay Cowell In the medical community, the term 'parasite' is used with the narrower meaning of eukaryotic pathogen. The role is realized in processes that result in the parasite's growth, survival, or fitness advantage or in the other organism's growth, survival, or fitness reduction. parasite 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 _obsolete_utilization of membranous cell gateway true An anatomical entity bearing an infectious agent portal of exit role. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent portal of exit An active immunization that begins with exposure to smallpox in the form of a scab from a pustule and results in immunity against smallpox. Albert Goldfain Alexander Diehl Lindsay Cowell variolation 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition 2d-s-region TwoDimensionalSpatialRegion 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 _obsolete_vaccination true A material entity with an antimicrobial disposition. Albert Goldfain Alexander Diehl Lindsay Cowell antimicrobial A host exposure to environment with infectious agent where the environment is an area in which an infectious agent is endemic Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern host living in endemic area A process that is a systemic inflammatory response to infection. Albert Goldfain Alexander Diehl Lindsay Cowell sepsis A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species. Suggested label: pathogen transmission process Transmission Ontology: http://purl.obolibrary.org/obo/trans.owl transmission process An immunosuppression induced by progesterone and other factors upregulated in pregnant women. Albert Goldfain Alexander Diehl Lindsay Cowell pregnancy-induced immunosuppression An 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). adaptive immune response A process by which an organism acquires immunity to an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell immunization against infectious agent An infection that persists for an extended period of time. Albert Goldfain Alexander Diehl Lindsay Cowell persistent infection chronic infection A 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. T cell receptor complex (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. developmental process _obsolete_antigenic variation true An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. leukocyte 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. 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 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 has part http://purl.obolibrary.org/obo/NCIT A spectrum of disorders associated with long-term Aspergillosis of the lung that may be characterized by pulmonary fibrosis or cavitation. Usually occurs in immunocompetent individuals with underlying respiratory disorders. [ NCI ] Occurs when Aspergillus infection causes cavities in the lungs, and can be a long-term (3 months or more) condition. One or more fungal balls (aspergillomas) may also be present in the lungs chronic pulmonary aspergillosis 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 _obsolete_initiation of infection true _obsolete_passage through cell membrane true An exotoxin disposition to damage cells of the host intestinal mucosa. Albert Goldfain Alexander Diehl Lindsay Cowell _obsolete_enterotoxin disposition enterotoxin disposition true A process in which multiple infectious disease epidemics of the same type of infectious disease unfold over overlapping periods of time and affect organism populations located in different geographic regions, including different countries and continents. Albert Goldfain Alexander Diehl Lindsay Cowell infectious disease pandemic entity Entity 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 _obsolete_pathogen true An infectious agent vector bearing a biological vector of infectious agent role. Albert Goldfain Alexander Diehl Lindsay Cowell biological vector of infectious agent An immunity to infectious agent that results in elimination of the infectious agent from the host. Albert Goldfain Alexander Diehl Lindsay Cowell Sterilizing immunity is typically conferred by neutralizing antibodies. sterilizing immunity to infectious agent UNITE Community https://dx.doi.org/10.15156/BIO/SH1165051.08FU aspergillus flavus A continuous temporal interval beginning with the extablishment of an infectious agent colony and ending with the onset of symptoms (or infectious disease course?). Albert Goldfain Alexander Diehl Lindsay Cowell incubation period An immunity to infectious agent that inheres in an organism in virtue of germline encoded components that directly recognize components of potential pathogens. Albert Goldfain Alexander Diehl Lindsay Cowell The disposition is realized in an innate immune response. innate immunity to infectious agent UNITE Community https://dx.doi.org/10.15156/BIO/SH349490.07FU formerly known as Pseudallescheria boydii scedosporium boydii Albert Goldfain Alexander Diehl Lindsay Cowell _obsolete_viral latency true this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality 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]) An immunity to infectious agent that inheres in an organism in virtue of components of its circulating body fluid. Albert Goldfain Alexander Diehl Lindsay Cowell "Circulating body fluid" refers to blood, lymph, and hemolymph. The disposition is realized in a humoral immune response. humoral immunity to infectious agent disposition Disposition 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]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host. Albert Goldfain Alexander Diehl Lindsay Cowell An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis. reverse zoonotic disposition An organism that is not infected with an infectious agent and lacks protective immunity to the infectious agent. Alex Diehl Lindsay Cowell susceptible organism An organism bearing a pathogen host role. Albert Goldfain Alexander Diehl Lindsay Cowell pathogen host A fungal infectious disease that tends to cause finger-nails or toe-nails to thicken, discolor, disfigure, and split. [ HPO : probinson ] onychomycosis _obsolete_oral-fecal transmission true http://purl.obolibrary.org/obo/MONDO A candidiasis that results in esophagitis. [ NCIT : P378 ] esophageal candidiasis (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] An organism that has the capability to bear a host of infectious agent role. Albert Goldfain Alexander Diehl Lindsay Cowell potential host of infectious agent _obsolete_prevention of infection true A host exposure to environment with infectious agent where the exposure is accidental; the environment is a laboratory, and the infectious agent is infectious in humans. Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern release of infectious human pathogen in laboratory 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 Chris Mungall expand expression to A sepsis that results in organ dysfunction, hypotension, or hypofusion of at least one organ. Albert Goldfain Alexander Diehl Lindsay Cowell severe sepsis (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) A pathogen host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell By this definition, vectors and other organisms that may not be infected are bearers of the infectious agent host role. infectious agent host role 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]) A host exposure to environment with infectious agent where the environment contains a material entity that has been assessed to confer a risk of infection. Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern host exposure to substance that might have infectious agent 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]) A process that attenuates an immune response. Albert Goldfain Alexander Diehl Lindsay Cowell immunosuppression (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] _obsolete_biotic true An immunosuppressed organism that is a human experiencing chronic systemic steroid use-based immunosuppression. Alex Diehl Lindsay Cowell NCI BBRB immunosuppressed human experiencing chronic systemic steroid use-based immunosuppression An organism that has immunocompetence. Albert Goldfain Alexander Diehl Lindsay Cowell immunocompetent organism A quality that inheres in an organism population and is the number of organisms in the population infected with an infectious agent at a specified time. Albert Goldfain Alexander Diehl Lindsay Cowell 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 p-boundary ProcessBoundary 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]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary A chronic infectious disease course that does not progress to severe stages for a long period of time. Albert Goldfain Alexander Diehl Lindsay Cowell long-term non-progressing infectious disease course _obsolete_process true An infectious disease course that begins soon after infection is established and progresses rapidly to severe stages. Albert Goldfain Alexander Diehl Lindsay Cowell acute infectious disease course A organism bearing a parasite role. Albert Goldfain Alexander Diehl Lindsay Cowell parasite Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) shorthand An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of A molecular entity with a toxin disposition and that is a structural component of a pathogen and is released from the pathogen only upon cytolysis. Albert Goldfain Alexander Diehl Lindsay Cowell endotoxin has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg 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 A role borne by a material entity in virtue of the fact that it has an antimicrobial disposition and is applied to an anatomical entity of a living organism. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in the killing and/or growth inhibition of microorganisms on the anatomical entity. antiseptic role _obsolete_object true A material entity with an antimicrobial disposition that is realized in a process of killing microorganisms. Albert Goldfain Alexander Diehl Lindsay Cowell microbicidal [entity] microbicide https://doi.org/10.3390/genes9090461 Echinocandins are a group of antifungals that inhibit the biosynthesis of an essential component of the fungal cell wall, the 1,3-ß-glucan. Echinocandins are amphiphilic lipopeptides, and products of cyclopentamine. echinocandin An immunization that begins with exposure of an organism to antigen and results in immunity against an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell inoculation active immunization against infectious agent _obsolete_afimbrial specific adherence true http://purl.obolibrary.org/obo/DOID A fungal infectious disease (specifically, dermatophytosis) that results_in contagious fungal infection located_in scalp, located_in hair of head, located_in eyebrow or located_in eyelash, has_material_basis_in Ascomycota fungi that belong to a group called dermatophytes and has_symptom itching of the scalp, has_symptom pus filled lesions on the scalp, and has_symptom patches of hair loss, sometimes with a 'black dot' pattern. dermatophytosis tinea tinea capitis ringworm A symbiont role borne by an organism in virtue of the fact that it derives a growth, survival, or fitness advantage from symbiosis, but the other symbiont is neither advantaged nor disadvantaged. Albert Goldfain Alexander Diehl Lindsay Cowell The role is realized in processes that result in the commensal's growth, survival, or fitness advantage. commensal role 'holding place for a potential pathogen...animate or inanimate'-ID[O]:0000059: holding place for a potential pathogen...animate or inanimate id 'reservoir'-ID[O]:0000059 from IDO 2007. May have replacement - TBD _obsolete_reservoir true An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) 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:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label A symbiont host role borne by an organism in virtue of the fact that its 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. Albert Goldfain Alexander Diehl Lindsay Cowell secondary host role The role is realized in developmental processes of the host's partner in symbiosis. intermediate host role _obsolete_damaging host cells and tissues in subepithelial space true http://purl.obolibrary.org/obo/NCIT An allergic aspergillus that primarily affects patients suffering from asthma or cystic fibrosis. [ NCI ] Occurs when Aspergillus causes inflammation in the lungs and allergy symptoms such as coughing and wheezing, but doesn’t necessarily cause an infection allergic bronchopulmonary aspergillosis https://doi.org/10.3390/genes9090461 Azoles are group of antifungals that function by targeting the cytochrome P450 enzyme-lanosterol 14α-demethylase, that converts lanosterol to ergosterol. Ergosterol is the main membrane sterol in most fungal species, holding an important role in controlling membrane fluidity. Effective azoles decrease membrane fluidity enough to inhibit cell growth. Azoles are heterocyclic compounds containing at least one nitrogen atom as part of the ring. excessive use of azoles for treatment and in agriculture is a contributor to increased antifungal resistance azole A process in which a potential host of an infectious agent comes into direct physical contact with the infectious agent. Bjoern Peters direct host exposure to infectious agent _obsolete_quality of pathogen true A 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. Lindsay Cowell horizontal pathogen transmission process A material entity with an antimicrobial disposition that is realized in a process of inhibiting the growth of microorganisms. Albert Goldfain Alexander Diehl Lindsay Cowell microbistatic 'the process by which an infectious agent passes from one organism to another organism'-ID[O]:0000083: the process by which an infectious agent passes from one organism to another organism id 'transmission'-ID[O]:0000083 from IDO 2007. May have replacement - TBD _obsolete_transmission true 'GO:nthe specific processes that generate the ability of an organism to cause disease in anothernnnThis is defined in GO so import.'-ID[O]:0000084: GO:nthe specific processes that generate the ability of an organism to cause disease in anothernnnThis is defined in GO so import. id 'pathogenesis'-ID[O]:0000084 from IDO 2007. May have replacement - TBD _obsolete_pathogenesis true _obsolete_drug resistance true _obsolete_adhesin true _obsolete_tropism true A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. 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). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region An infectious disorder that is the physical basis for an unfolding acute infectious disease course. Albert Goldfain Alexander Diehl Lindsay Cowell acute infection A host role borne by an organism in virtue of the fact that its extended organism contains a second organism and provides an environment supportive for the survival, growth, maturation, or reproduction of that organism. Albert Goldfain Alexander Diehl Lindsay Cowell The relevant environmental resources may include nutrient resources, warmth, or moisture. The role is realized in processes in which the host makes the relevant environmental resources available to its partner in symbiosis. A bearer of a symbiont host role is bearer also of a symbiont role. symbiont host role 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. cell cell 'the unfolding or course of infectious diseasennwhat do we say about infectious disease that always remain latent nwhat about when a pathogen continues its progression nnwe need to think about whether we need a term called stagenlife cycle?nprogression?ndevelopment?'-ID[O]:0000221: the unfolding or course of infectious diseasennwhat do we say about infectious disease that always remain latent nwhat about when a pathogen continues its progression nnwe need to think about whether we need a term called stagenlife cycle?nprogression?ndevelopment? id 'infectious disease progression'-ID[O]:0000221 from IDO 2007. May have replacement - TBD _obsolete_infectious disease progression true ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) gdc GenericallyDependentContinuant 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. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. 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]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] _obsolete_resist phagocytosis in subepithelial space true A quality that inheres in an infectious agent and is the degree to which realizations of the infectious disease caused by the infectious agent become severe or fatal. Albert Goldfain Alexander Diehl Lindsay Cowell This quality is measured by the proportion of clinically apparent cases that are severe or fatal. virulence (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] A host exposure to environment with infectious agent where the environment contains an infectious agent vector. Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern host coming into contact with vector of infectious agent _obsolete_carrier true http://purl.obolibrary.org/obo/MONDO A mycosis that involves the integument and its appendages, including hair and nails. Infection may involve the stratum corneum or deeper layers of the epidermis. [ https://www.ncbi.nlm.nih.gov/books/NBK7902 ] dermatomycosis dermatophyte infections tinea cutaneous mycosis history History 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 _obsolete_induction of damaging host immune response true changed label to lowercase per best practice http://purl.obolibrary.org/obo/NCBITaxon opisthokonta 'the process by which an infectious disease establishes itself in a new population (or at a sufficiently higher rate? higher prevalence and/or higher incidence)'-ID[O]:0000101: the process by which an infectious disease establishes itself in a new population (or at a sufficiently higher rate? higher prevalence and/or higher incidence) id 'emergence'-ID[O]:0000101 from IDO 2007. May have replacement - TBD _obsolete_emergence true 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]) UNITE Community https://dx.doi.org/10.15156/BIO/TH032948 scedosporium my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary has 2D boundary 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 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term Obsolete Class 3d-s-region ThreeDimensionalSpatialRegion 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 _obsolete_endotoxin true (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] https://doi.org/10.3390/genes9090461 Pyrimidine analogs are a group of antifungals that are nucleosides, that mimic the structure of natural pyrimidines. Some pyrimidine analogs have the potential to convert into 5-fluorouracyl and further to 5-fluorodeoxyuridine inside the fungal cell. Subsequently, 5-fluorodeoxyuridine interferes with DNA, RNA, and protein synthesis. The transformation of flucytosine into 5-fluorouracyl is catalyzed by the action of the fungal enzyme cytosine deaminase (encoded by the yeast gene FCY1), which is not present in humans. The only pyrimidine analog with antimycotic properties currently in use for human treatment is flucytosine. Although it is one of the more effective and safest antimycotic in the health system, it is not used in monotherapy due to the rapid development of resistance towards this drug pyrimidine analog 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 A 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 _obsolete_infectious disease progression stage true An infectious agent with an opportunistic infectious disposition. Albert Goldfain Alex Diehl Lindsay Cowell opportunist opportunistic pathogen An infectious agent vehicle role borne by an entity in virtue of the fact that the entity is not alive. Albert Goldfain Alexander Diehl Lindsay Cowell fomite role Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] An interaction between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected. commensalism A quality of a patient that is observed by the patient or a processual entity experienced by the patient, either of which is hypothesized by the patient to be a realization of a disease. symptom https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4531547/ doi: 10.3904/kjim.2004.19.1.38 An aspergillosis that involves a ball of Aspergillus growing in the lungs or sinuses, but it usually does not spread to other parts of the body. Aspergilloma is also called a “fungus ball.” pulmonary aspergilloma usually develops in the patients with underlying lung diseases aspergilloma A biological macromolecule that has an adhesion disposition. Albert Goldfain Alexander Diehl Lindsay Cowell adhesin adhesion molecule adhesion factor (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] UNITE Community https://dx.doi.org/10.15156/BIO/TH030639 alternaria A process by which an infectious agent, established in a host, becomes part of an infection in the host. Albert Goldfain Alexander Diehl Lindsay Cowell process of establishing an infection A fluid that is composed of blood plasma and erythrocytes. blood 'role played by portion of physical substance utilized by an organism in order to establish adherence to a surface in a host'-ID[O]:0000055: role played by portion of physical substance utilized by an organism in order to establish adherence to a surface in a host id 'adhesion factor'-ID[O]:0000055 from IDO 2007. May have replacement - TBD _obsolete_adhesion factor true _obsolete_pathogen spread through host true (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y Chris Mungall positively regulates (process to process) positively regulates An organism that is experiencing pregnancy-induced or pathologic immunosuppression. Albert Goldfain Alexander Diehl Lindsay Cowell immunosuppressed organism The attachment of a symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly. The host is defined as the larger of the organisms involved in a symbiotic interaction. adhesion of symbiont to host _obsolete_genetic diversification true A 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. Albert Goldfain Alexander Diehl Lindsay Cowell 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 _obsolete_pathogen evasion of host immune response true term tracker item 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 Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) _obsolete_disruption of normal microbioflora true UNITE Community https://dx.doi.org/10.15156/BIO/TH034644 predominantly found as a yeast, though some researchers believe it important to understant cryptococcus as a dimorphic fungi, as it does switch from yeast growth to hyphal growth during its sexual cycle source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3318972/ cryptococcus _obsolete_chronic carrier true If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) Sydney Cohen A sporotrichosis that follows inhalation of fungus and manifests as chronic pneumonitis while extracutaneous or systemic sporotrichosis (with osteoarticular, pulmonary, and central nervous system/meningeal disease), usually occurring in the setting of immunosuppression. adding specificity to orphanet parent term is rare but can happen after someone breathes in fungal spores from the environment. pulmonary sporotrichosis _obsolete_invasive true UNITE Community https://dx.doi.org/10.15156/BIO/SH1178825.08FU source for opportunistic fungal pathogen classification: https://www.ncbi.nlm.nih.gov/books/NBK431060/ cryptococcus neoformans 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]) http://purl.obolibrary.org/obo/NCIT A fungus that is single celled and has little to no mycelium development. Any of various single-celled ascomycetes, basidiomycetes and imperfect fungi with little or no mycelium development that asexually reproduce by budding. They ferment sugars to produce alcohol and carbon dioxide. A non-taxonomic grouping of fungi that are single-celled. Alt defintion: Various single-celled members of the fungal families, ascomycetes, basidiomycetes and imperfect fungi that tend to be unicellular for the greater part of their life cycle. [ from On-line Medical Dictionary NCI ] yeast A local infection for which symptoms are observed in parts of the host's extended organism that are distant from the infection. Albert Goldfain Alexander Diehl Lindsay Cowell focal infection _obsolete_toxin true term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg term replaced by alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) 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 _obsolete_medicine true A toxin disposition that inheres in a protein or protein complex that is a structural component of a pathogen and is released from the pathogen only upon cytolysis. A toxin disposition that inheres in a protein or protein complex that is released from a pathogen only upon cytolysis. Albert Goldfain Alexander Diehl Lindsay Cowell _obsolete_endotoxin disposition endotoxin disposition true _obsolete_commensal true A molecular entity with a toxin disposition, the realization of which damages host cells. Albert Goldfain Alexander Diehl Lindsay Cowell cytotoxin _obsolete_refractoriness true (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] Sydney Cohen https://doi.org/10.1016/0190-9622(90)70288-s https://www.merckvetmanual.com/pharmacology/antifungal-agents/allylamines-for-use-in-animals Allylamines are a group of antifungals that inhibit ergosterol synthesis at the level of squalene epoxidase. Their mechanism is competitive inhibition of squalene epoxidase, blocking conversion of squalene to lanosterol, leading to squaline accumulation and ergosterol depletion in the cell membrane. These agents are highly selective for the fungal enzyme and have a minimal effect on mammalian cholesterol synthesis. allylamines _obsolete_fusion protein true A heterogenous grouping of fungus (mostly mold, a few yeasts) that is chracterized by the presence of melanin in their cell walls that can cause a wide range of diseases including phaeohyphomycosis, chromoblastomycosis, and eumycotic mycetoma. These organisms are widespread in the environment, being found in soil, wood, and decomposing plant debris. Cutaneous, subcutaneous, and corneal infections with dematiaceous fungi occur worldwide, but are more common in tropical and subtropical climates. Infection results from traumatic implantation. Most cases occur in immunocompetent individuals. Dematiaceous moulds are also important causes of invasive sinusitis and allergic fungal sinusitis. Infection is thought to follow inhalation. dematiaceous fungi more info: https://doi.org/10.1179/joc.2003.15.Supplement-2.36 dematiaceous fungus _obsolete_antimicrobial true (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) http://purl.obolibrary.org/obo/MONDO A mycosis that involves the lungs, abdominal viscera, bones and or central nervous system. [ https://www.ncbi.nlm.nih.gov/books/NBK7902 ] deep mycosis Usually follow inhalation (or via or gastrointestinal tract or blood vessels) and may be subsequent to primary pulmonary infections systemic mycosis 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 Person:Alan Ruttenberg has ID range allocated to first order logic expression PERSON:Alan Ruttenberg first order logic expression (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] _obsolete_immunity true 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary 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 The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. reproduction changed label to singular dimorphic fungus per best practices http://purl.obolibrary.org/obo/NCIT A fungus that grows as either a yeast or a mold. [ NCI ] dimorphic fungi dimorphic fungus results_in UNITE Community https://dx.doi.org/10.15156/BIO/SH1331956.08FU madurella mycetomatis 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 realizes A quality that inheres in an organism population and is the number of organisms in the population that become infected with an infectious agent during a specified period of time. Albert Goldfain Alexander Diehl Lindsay Cowell 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 _obsolete_pathogenicity island true A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time. Albert Goldfain Alexander Diehl Lindsay Cowell 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 Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith An infectious disease endemicity that inheres in an organism population in virtue of the fact that the infectious disease endemic level for an infectious disease is persistently high in the population. Albert Goldfain Alexander Diehl Lindsay Cowell Hyper-endemic infectious diseases may have high endemic levels only in certain seasons. A hyper-endemic disease affects all age groups equally. infectious disease hyper-endemicity changed fungi to fungus per best practice http://purl.obolibrary.org/obo/NCBITaxon fungi mycota fungus A disposition to participate in a process of symbiosis in which the bearer derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced. parasitic disposition UNITE Community https://dx.doi.org/10.15156/BIO/TH035093 mucor A process in which a potential host of an infectious agent is exposed to an infectious agent. Bjoern Peters host exposure to infectious agent A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as An infection resulting from a transmission process that did not unfold in a health care facility. Albert Goldfain Alexander Diehl Lindsay Cowell community-acquired infection A bacteremia in which the baceteria are replicating. Albert Goldfain Alexander Diehl Lindsay Cowell _obsolete_septicemia true UNITE Community https://dx.doi.org/10.15156/BIO/SH1821630.08FU sporothrix schenckii A pathologically immunosuppressed organism that is experiencing infection-based immunosuppression. Alex Diehl Lindsay Cowell immunosuppressed organism experiencing infection-based immunosuppression Sydney Cohen https://www.cdc.gov/fungal/diseases/fungal-eye-infections/definition.html An endophthalmitis that is caused by fungal spores entering the eye from an external source An endophthalmitis that occurs after fungal spores enter the eye from an external source exogenous fungal endophthalmitis _obsolete_attenuated true A quality that inheres in an infectious agent and is the liklihood that the infectious disposition will be realized upon exposure of a susceptible organism. Albert Goldfain Alexander Diehl Lindsay Cowell This quality is measured by the proportion of exposed who become infected. infectivity An organism bearing a symbiont role. Albert Goldfain Alexander Diehl Lindsay Cowell symbiont A quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for an infectious agent in their serum at a specified time. Albert Goldfain Alexander Diehl Lindsay Cowell 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. infectious agent seroprevalence _obsolete_toxicity true primitive Albert Goldfain Alexander Diehl Lindsay Cowell _obsolete_biological object true UNITE Community https://dx.doi.org/10.15156/BIO/TH035079 rhizomucor _obsolete_swollen true A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. obsolete dependent continuant true An immunosuppressed organism that is experiencing pathologic immunosuppression. Alex Diehl Lindsay Cowell pathologically immunosuppressed organism _obsolete_endemic true _obsolete_penetration via injury of epithelial barrier true (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] A material entity bearing an antiviral disposition. Albert Goldfain Alexander Diehl Lindsay Cowell antiviral The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester has member is a mereological relation between a collection and an item. SIO has member (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] 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]) An infectious agent 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. Albert Goldfain Alexander Diehl Lindsay Cowell re-emerging pathogen An infection that is clinically abnormal. Albert Goldfain Alexander Diehl Lindsay Cowell infectious disorder _obsolete_extrinsic incubation period true A biological material entity that is capable of replication. Albert Goldfain Alexander Diehl Lindsay Cowell _obsolete_replicating biological material entity true _obsolete_herd immunity true 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" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for _obsolete_horizontal transmission true _obsolete_fusion with host cell membrane true _obsolete_vertical transmission true UNITE Community https://dx.doi.org/10.15156/BIO/SH1412585.08FU paracoccidioides lutzii A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) An organism that is host to an infectious agent and has no symptoms of the infectious disease associated with the infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell asymptomatic host of infectious agent _obsolete_pandemic true A process by which a part of an organism or something contained in an organism becomes clinically abnormal. transition to clinical abnormality 'the ability of the biotic entity to cause disease in a host of a given typenndo we need to say damage instead of disease?nnpathogenicity and virulence are used as synonyms in some communities'-ID[O]:0000025: the ability of the biotic entity to cause disease in a host of a given typenndo we need to say damage instead of disease?nnpathogenicity and virulence are used as synonyms in some communities id 'pathogenicity'-ID[O]:0000025 from IDO 2007. May have replacement - TBD _obsolete_pathogenicity true https://www.ncbi.nlm.nih.gov/pmc/articles/PMC105285/ An aspergillosis that is caused by Aspergillus entering the body through a break in the skin (for example, after surgery or a burn wound) and causes infection, usually in people who have weakened immune systems. Cutaneous aspergillosis can also occur if invasive aspergillosis spreads to the skin from somewhere else in the body, such as the lungs cutaneous aspergillosis An infectious agent with a primary infectious disposition. Albert Goldfain Alexander Diehl Lindsay Cowell principal pathogen primary pathogen An infectious disease incidence rate that is typical for an infectious disease in an organism population. Albert Goldfain Alexander Diehl Lindsay Cowell Infectious disease endemic rate is relational to previous infectious disease incidence rates of the disease. infectious disease endemic rate A colonization of host process in which the host is of Species Homo sapiens. Albert Goldfain Alexander Diehl Lindsay Cowell colonization of human A disposition to initiate processes that result in a disorder in a human organism. human pathogenicity disposition A biological process which involves another organism of the same or different species. multi-organism process _obsolete_antibiotic true Penetration by an organism into its host organism via active breaching of the physical barriers of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. entry into host through host barriers A process in which an entity comes into being as a result of the process. Albert Goldfain Alexander Diehl Lindsay Cowell production UNITE Community https://dx.doi.org/10.15156/BIO/SH1160231.08FU cladophialophora bantiana (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] _obsolete_highly exposed persistently seronegative true 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]) UNITE Community https://dx.doi.org/10.15156/BIO/TH035085 apophysomyces 'comment about the instances:nncollections of etiologically connected cases of infectious disease in a given population'-ID[O]:0000098: comment about the instances:nncollections of etiologically connected cases of infectious disease in a given population id 'infectious disease'-ID[O]:0000098 from IDO 2007. May have replacement - TBD _obsolete_infectious disease true _obsolete_engulfment by nonphagocyte true this term deviated from similarly labeled DOID:1564 in order to better fit the IDO structures of disease and infection Sydney Cohen An infectious disease that has material basis in some mycosis, which pass the resistance barriers of the body. fungal infectious disease _obsolete_pathogen life cycle stage true An organism bearing a commensal role. Albert Goldfain Alexander Diehl Lindsay Cowell commensal _obsolete_rapid progression true 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]) UNITE Community https://dx.doi.org/10.15156/BIO/TH030641 bipolaris All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] _obsolete_membrane invagination true 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]) An infection-based immunosuppression process which arises as the result of an HIV infection. Alex Diehl Lindsay Cowell HIV-based immunosuppression b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) http://www.ebi.ac.uk/efo/EFO A candidiasis that involves fungal infection of the vaginal mucous membranes in women caused by Candida albicans. The symptoms can include intense vulval pruritus, burning, erythema and dyspareunia associated with a creamy white, curd-like discharge. vaginal candidiasis 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" PERSON:Alan Ruttenberg is allocated id range _obsolete_quality true An organism who has been bearer of the infectious agent carrier role for an extended period of time. Albert Goldfain Alexander Diehl Lindsay Cowell chronic carrier of infectious agent 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]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) 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]) _obsolete_pathogen-induced necrosis true 'the degree of pathogenicitynnpathogenicity and virulence are used in some communities as synonyms.'-ID[O]:0000004: the degree of pathogenicitynnpathogenicity and virulence are used in some communities as synonyms. id 'virulence'-ID[O]:0000004 from IDO 2007. May have replacement - TBD _obsolete_virulence true _obsolete_contagious true _obsolete_endogenous true Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) A 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. Albert Goldfain Alexander Diehl Lindsay Cowell 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 _obsolete_pathogen outbreak true _obsolete_infectious agent true _obsolete_vaccine true _obsolete_intrinsic incubation period true A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) 'create cross products for "host" and "pathogen" that will be part of this process.'-ID[O]:0000074: create cross products for "host" and "pathogen" that will be part of this process. id 'pathogen adherence to host cell'-ID[O]:0000074 from IDO 2007. May have replacement - TBD _obsolete_pathogen adherence to host cell true (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] label Sydney Cohen https://www.cdc.gov/fungal/diseases/sporotrichosis/index.html A sporotrichosis that has spread to another part of the body, such as bones, joints, or central nervous system. This form of sporotrichosis usually affects people with health problems or who take medicines that lower the body’s ability to fight germs and sickness, such as people living with HIV disseminated sporotrichosis A pathologic immunosuppression process which arises as the result of an infection and is initiated or dysregulated by the infectious agent population. The definition should perhaps read "as the result of an infectious disorder". Alex Diehl Lindsay Cowell infection-based immunosuppression Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) Sydney Cohen A fungal infectious agent that usually has a primary infectious disposition. may cause infection in both immunocompromised and immunocompetent people primary fungal pathogen http://purl.obolibrary.org/obo/MONDO A mycosis that is limited to the stratum corneum and essentially elicits no inflammation. [ https://www.ncbi.nlm.nih.gov/books/NBK7902/ ] superficial mycosis _obsolete_emerging pathogen true 'the process by which a biotic entity establishes multiple copies of itself in a new environment (including an organismal environment).nnfix idn"native" environment term'-ID[O]:0000205: the process by which a biotic entity establishes multiple copies of itself in a new environment (including an organismal environment).nnfix idn"native" environment term id 'colonization'-ID[O]:0000205 from IDO 2007. May have replacement - TBD _obsolete_colonization true _obsolete_end reservoir true https://www.cdc.gov/fungal/antifungal-resistance.html A resistance to antifungal drugs that mitigates the damaging effects of antifungal treatments. Occurs when fungi develop the ability to defeat the drugs designed to kill them. These antifungal resistant fungi no longer respond to antifungal drugs. antifungal resistance An interaction between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other. mutualism (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] UNITE Community https://dx.doi.org/10.15156/BIO/TH035078 lichtheimia The totality of all processes through which a given disease instance is realized. disease course (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] An immunoglobulin complex that is 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. B cell receptor complex UNITE Community https://dx.doi.org/10.15156/BIO/SH1159131.08FU pneumocystis jirovecii has_material_basis_in 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> editor note http://purl.obolibrary.org/obo/NCIT An infection that is caused by a fungus. [ NCI ] fungal infection mycosis _obsolete_opportunistic pathogen true UNITE Community https://dx.doi.org/10.15156/BIO/TH031014 coccidioides _obsolete_zoonotic true An infectious agent host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent, the infectious agent has the infectious disposition towards the host, and the host has no symptoms of the infectious disease caused by the infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent carrier role An immunosuppression process which arises as the result of a disorder. Disorders that result in immunosuppression include those that result from infection, stress, malnutrition, and treatments such as chemotherapy or calcineurin inhibition. Albert Goldfain Alexander Diehl Lindsay Cowell pathologic immunosuppression 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]) UNITE Community https://dx.doi.org/10.15156/BIO/SH1225764.08FU sporothrix brasiliensis An organism population persisting in a site it has colonized. Albert Goldfain Alexander Diehl Lindsay Cowell colony A colony whose members are infectious agents. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent colony has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] A 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. Albert Goldfain Alexander Diehl Lindsay Cowell 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 Viruses Sydney Cohen An allergic aspergillosis that may cause inflammation in the sinuses and symptoms of a sinus infection (drainage, stuffiness, headache) but doesn’t necessarily cause an infection allergic aspergillus sinusitis An 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. extended organism 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]) _obsolete_quality of infectious disease true _obsolete_dependovirus true _obsolete_epidemiological spread of disease true _obsolete_modulation of inflammatory response true has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] a pathologically immunosuppressed organism that is experiencing chronic systemic steroid use-based immunosuppression. Alex Diehl Lindsay Cowell immunosuppressed organism experiencing chronic systemic steroid use-based immunosuppression 'Role played by portion of physical substance in a biological process'-ID[O]:0000204: Role played by portion of physical substance in a biological process id 'factor'-ID[O]:0000204 from IDO 2007. May have replacement - TBD _obsolete_factor true _obsolete_active true _obsolete_infection true Person:Alan Ruttenberg _obsolete_case of infectious disease true _obsolete_colonizer true http://purl.obolibrary.org/obo/NCIT Pneumocystis Pneumonia is a fungal infectious disease that appears as a pneumonia resulting from infection with Pneumocystis jirovecii, frequently seen in the immunologically compromised, such as persons with AIDS, or steroid-treated individuals, the elderly, or premature or debilitated babies during their first three months. Patients may be only slightly febrile (or even afebrile), but are likely to be extremely weak, dyspneic, and cyanotic. This is a major cause of morbidity among patients with AIDS. pneumocystis pneumonia _obsolete_nonspecific adherence true _obsolete_virus-induced cytopathogenesis true _obsolete_route of entry true _obsolete_long-term non-progression true 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 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. Person:Alan Ruttenberg has ID prefix _obsolete_treatment true temporal interpretation https://github.com/oborel/obo-relations/wiki/ROAndTime A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) http://www.ebi.ac.uk/efo/EFO A fungal eye infection is characterized by inflammation of the cornea. [ NCIT : C26805 ] A fungal eye infection that is characterized by inflammation of the cornea. [ NCIT : C26805 ] keratitis _obsolete_sign true UNITE Community https://dx.doi.org/10.15156/BIO/SH1189319.08FU candida albicans (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] _obsolete_host recovery period true 'quality [state] of an organism that during its life cycle in which its growth. development, metabolism, etc is temporarily suspended nnnsuspended state, non-replicative state, resting state'-ID[O]:0000209: quality [state] of an organism that during its life cycle in which its growth. development, metabolism, etc is temporarily suspended nnnsuspended state, non-replicative state, resting state id 'dormancy'-ID[O]:0000209 from IDO 2007. May have replacement - TBD _obsolete_dormancy true (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] A host exposure to environment with infectious agent where the environment is a household that also has an infected host Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern host living with infected household contact (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]