Axiom
annotated source: generically dependent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

immunodeficient organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has part
    some values from: immunodeficiency
subclass of: organism
definition: An organism that has an immunodeficiency.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: immunocompromised organism

_obsolete_infectious disease course
type: Class
subclass of: Obsolete Class
deprecated: true

infectious disease lifetime prevalence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

antibacterial
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has disposition
    some values from: antibacterial disposition
subclass of: material entity
disjoint with: infection
disjoint with: disorder
definition: A material entity bearing an antibacterial disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: antibiotic

blastomycosis
type: Class
equivalent class: Class
  intersection of: fungal infectious disease
  intersection of: Restriction
    on property: has part
    some values from: blastomyces dermatitidis
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: systemic mycosis
subclass of: fungal infectious disease
imported from: http://www.ebi.ac.uk/efo/EFO
has definition: 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 ]
comment: 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

immunosuppressed human experiencing drug-based immunosuppression due to organ transplant
type: Class
subclass of: immunosuppressed organism experiencing drug-based immunosuppression
definition: A pathologically immunosuppressed organism that is a human experiencing drug-based immunosuppression.
term editor: Alex Diehl
term editor: Lindsay Cowell
ontology term requester: NCI BBRB

coccidioidomycosis
type: Class
equivalent class: Class
  intersection of: fungal infectious disease
  intersection of: Restriction
    on property: has part
    some values from: coccidioides
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: systemic mycosis
subclass of: fungal infectious disease
imported from: http://www.ebi.ac.uk/efo/EFO
has definition: 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 ]
has related synonym: San Joaquin Valley fever
has related synonym: Valley fever
has related synonym: desert rheumatism

infectious agent host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: infectious agent host role
subclass of: pathogen host
definition: An organism bearing an infectious agent host role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

antiviral disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: material entity
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Class
        union of: negative regulation of viral process
        union of: Restriction
disjoint with: antifungal disposition
disjoint with: antibacterial disposition
disjoint with: antiparasitic disposition
disjoint with: protective resistance
disjoint with: pathogenic disposition
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: A disposition to kill or inhibit the lifecycle of viruses.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

contagiousness
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: infectious agent host
  intersection of: Restriction
    on property: realized in
    all values from: horizontal pathogen transmission process
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.
comment: The disposition is realized in a horizontal transmission process.

immunosuppressed organism experiencing drug-based immunosuppression
type: Class
equivalent class: Class
  intersection of: pathologically immunosuppressed organism
  intersection of: Restriction
    on property: participates in
    some values from: drug-based immunosuppression
subclass of: pathologically immunosuppressed organism
definition: A pathologically immunosuppressed organism that is experiencing drug-based immunosuppression.
term editor: Alex Diehl
term editor: Lindsay Cowell

_obsolete_adaptive immunity to infectious agent
type: Class
subclass of: Obsolete Class
definition: An immunity to infectious agent realized in an adaptive immune response.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
deprecated: true

_obsolete_susceptibility
type: Class
subclass of: Obsolete Class
definition: 'can change depending on environmentnnwhere should susceptibility factors go?'-ID[O]:0000212: can change depending on environmentnnwhere should susceptibility factors go?
editor note: id 'susceptibility'-ID[O]:0000212 from IDO 2007. May have replacement - TBD
deprecated: true

_obsolete_parasite
type: Class
subclass of: Obsolete Class
deprecated: true

infectious agent portal of entry role
type: Class
subclass of: role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: anatomical entity
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: part of
        some values from: transmission process
disjoint with: infectious agent portal of exit role
disjoint with: disinfectant role
disjoint with: antiseptic role
disjoint with: primary infection role
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The role is realized in a process by which an infectious agent enters a host.

antiseptic
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: antiseptic role
subclass of: material entity
disjoint with: infection
disjoint with: organism
disjoint with: disorder
definition: A material entity bearing an antiseptic role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_chronic quality of infection
type: Class
subclass of: Obsolete Class
definition: A quality that inheres in an infection in virtue of the fact that the infection persists for an extended period of time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: persistent infection
deprecated: true

has role
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: 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.
alternative term: has_role

antimicrobial disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: material entity
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Class
        union of: Restriction
disjoint with: protective resistance
disjoint with: pathogenic disposition
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: A disposition to kill or inhibit the development or reproduction of microorganisms.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.
comment: The disposition is realized in the killing or inhibition of microorganisms.

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

_obsolete_antibiotic resistance
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_vector
type: Class
subclass of: Obsolete Class
definition: '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?)
editor note: id 'vector'-ID[O]:0000063 from IDO 2007. May have replacement - TBD
deprecated: true

leukocyte-mediated immunity to infectious agent
type: Class
equivalent class: Class
  intersection of: immunity to infectious agent
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: leukocyte
  intersection of: Restriction
    on property: realized in
    all values from: leukocyte mediated immunity
  intersection of: Restriction
    on property: has_material_basis_in
    all values from: leukocyte
subclass of: immunity to infectious agent
definition: An immunity to infectious agent that inheres in an organism in virtue of its leukocytes.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: cell-mediated immunity to infectious agent
comment: The disposition is realized in a leukocyte-mediated immune response.

expand assertion to
type: AnnotationProperty
editor preferred term: expand assertion to
example of usage: 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)"
definition: A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
term editor: Chris Mungall

adhesion disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: molecular entity
  intersection of: Restriction
    on property: realized in
    all values from: adhesion of symbiont to host
disjoint with: invasion disposition
disjoint with: antimicrobial disposition
disjoint with: antiviral disposition
disjoint with: antifungal disposition
disjoint with: antibacterial disposition
disjoint with: antiparasitic disposition
disjoint with: protective resistance
disjoint with: pathogenic disposition
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: A disposition borne by a biological macromolecule that is the disposition to participate in adherence to a host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The disposition is realized in an adherence to host process.

collective resistance disposition
type: Class
subclass of: collective disposition
definition: A collective disposition the realization of which mitigates the damaging effects of some entity on members of the collection.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

Axiom
annotated source: process boundary
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

Axiom
annotated source: spatial region
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000002
comment: per discussion with Barry Smith

immunity to infectious agent
type: Class
subclass of: resistance to infectious agent
definition: A resistance to infectious agent that inheres in an organism in virtue of immune system components in the extended organism.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: protective immunity to infectious agent
comment: 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.

drug susceptibility
type: Class
subclass of: susceptibility
definition: A susceptibility that is the degree to which an entity can be harmed or inhibited from surviving by a drug.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

emerging pathogen
type: Class
subclass of: infectious agent
definition: An infectious agent whose infection incidence is increasing following its first introduction into a new host Species.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

spatial region
type: Class
subclass of: immaterial entity
BFO OWL specification label: s-region
BFO CLIF specification label: SpatialRegion
editor note: BFO 2 Reference: Spatial regions do not participate in processes.
editor note: 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.
elucidation: 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])
has associated axiom(nl): All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has associated axiom(fol): (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has associated axiom(fol): (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]

pathogenic disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: material entity
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: results in formation of
        some values from: disorder
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: A disposition to initiate processes that result in a disorder.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: pathogenicity
comment: A pathogenic disposition is realized in processes that create a disorder.
comment: 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.

results in formation of
type: ObjectProperty
sub property of: results_in
example of usage: 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.
example of usage: every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
has curation status: IAO_0000125
term editor: Chris Mungall
definition source: GOC:mtg_berkeley_2013
shorthand: results_in_formation_of

paracoccidioides
type: Class
equivalent class: Class
  intersection of: dimorphic fungus
  intersection of: primary fungal pathogen
subclass of: dimorphic fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH031017

_obsolete_transport by blood
type: Class
subclass of: Obsolete Class
deprecated: true

invasive disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: infectious agent
  intersection of: Restriction
    on property: realized in
    all values from: entry into host through host barriers
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: A disposition borne by an infectious agent that is the disposition to penetrate the epithelial barriers of an organism of another Species.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infection
type: Class
subclass of: material entity
subclass of: Class
  intersection of: Restriction
    on property: part of
    some values from: extended organism
  intersection of: Restriction
    on property: has part
    some values from: infectious agent
disjoint with: immunodeficiency
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

antifungal
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has disposition
    some values from: antifungal disposition
subclass of: material entity
disjoint with: infection
disjoint with: disorder
definition: A material entity bearing an antifungal disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infectious agent vector role
type: Class
equivalent class: Class
  intersection of: infectious agent transporter role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: location of
        some values from: infectious agent
  intersection of: Restriction
    on property: realized in
    all values from: indirect
subclass of: infectious agent transporter role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The role is realized in a transmission process. A bearer of a vector role is also a bearer of a host role.

immunodeficiency
type: Class
subclass of: disorder
disjoint with: source of infection
definition: A disorder of an immune system component that results in defective functioning of the immune system.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

_obsolete_mobile genetic element
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: continuant fiat boundary
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000008

pathogen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has disposition
    some values from: pathogenic disposition
subclass of: material entity
disjoint with: disinfectant
disjoint with: antiseptic
disjoint with: immunodeficiency
definition: A material entity with a pathogenic disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_prevalence
type: Class
subclass of: Obsolete Class
definition: '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
editor note: id 'prevalence'-ID[O]:0000019 from IDO 2007. May have replacement - TBD
deprecated: true

zoonosis
type: Class
equivalent class: Class
  intersection of: infectious disease
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: Class
      intersection of: infectious disorder
      intersection of: Restriction
        on property: has part
        some values from: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
  intersection of: Restriction
    on property: has_material_basis_in
    all values from: Class
      intersection of: infectious disorder
      intersection of: Restriction
        on property: has part
        some values from: Class
  intersection of: Restriction
    on property: inheres in
    all values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
subclass of: infectious disease
disjoint with: reverse zoonosis
definition: An infectious disease that has as its physical basis an infectious disorder composed of infectious agents that have a zoonotic disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infectious agent population
type: Class
subclass of: organism population
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: infectious agent
  intersection of: Restriction
    on property: has part
    all values from: infectious agent
definition: An organism population whose members each have an infectious disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infectious agent role
type: Class
subclass of: pathogen role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: infectious agent
    intersection of: Restriction
      on property: located in
      some values from: host
definition: A role borne by an infectious agent when contained in a host in which its infectious disposition can be realized.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_virulence factor
type: Class
subclass of: Obsolete Class
definition: '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
editor note: id 'virulence factor'-ID[O]:0000040 from IDO 2007. May have replacement - TBD
deprecated: true

antifungal disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: material entity
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Class
        union of: Restriction
disjoint with: antibacterial disposition
disjoint with: antiparasitic disposition
disjoint with: protective resistance
disjoint with: pathogenic disposition
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: A disposition to kill or inhibit the development or reproduction of fungal organisms.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infectious agent vector
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: infectious agent vector role
subclass of: organism
definition: An organism bearing an infectious agent vector role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

Axiom
annotated source: zero-dimensional temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

sporotrichosis
type: Class
equivalent class: Class
  union of: Class
    intersection of: fungal infectious disease
    intersection of: Class
      union of: sporothrix schenckii
      union of: Restriction
        on property: has part
        some values from: sporothrix brasiliensis
    intersection of: Restriction
      on property: has_material_basis_in
      some values from: cutaneous mycosis
  union of: Restriction
    on property: has_material_basis_in
    some values from: systemic mycosis
  union of: Restriction
    on property: has_material_basis_in
    some values from: subcutaneous mycosis
subclass of: fungal infectious disease
imported from: http://www.orpha.net/ORDO/Orphanet
has definition: 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.
has related synonym: rose gardener’s disease
comment: can also be caused by sporothrix brasiliensis fungus

curvularia
type: Class
subclass of: dematiaceous fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH030644

candidiasis
type: Class
equivalent class: Class
  intersection of: fungal infectious disease
  intersection of: Restriction
    on property: has part
    some values from: candida
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: mycosis
subclass of: fungal infectious disease
definition: An infection that has as part organisms of the Genus Candida.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
imported from: http://purl.obolibrary.org/obo/IDO
has definition: An infection that has as part organisms of the Genus Candida.
comment: moved original placement of candidiasis in IDO to reflect that candidiasis is the disease, with an infection as its material basis

primary immunodeficiency
type: Class
subclass of: immunodeficiency
definition: An immunodeficiency that exists in an organism because of a genetic predisposition.
term editor: Albert Goldfain
term editor: Alex Diehl
term editor: Lindsay Cowell
alternative term: congenital immunodeficiency

process
type: Class
subclass of: occurrent
BFO OWL specification label: process
BFO CLIF specification label: Process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
definition: 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])
editor note: 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)
has associated axiom(fol): (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]

host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: host role
subclass of: organism
definition: An organism bearing a host role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

life-death temporal boundary
type: Class
subclass of: process
definition: A life cycle temporal boundary that marks the end of the life cycle of the organism.
imported from: uberon.owl

paratenic host role
type: Class
subclass of: symbiont host role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The role is realized in developmental processes of the host's partner in symbiosis.

_obsolete_complement resistance
type: Class
subclass of: Obsolete Class
deprecated: true

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
editor preferred term: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative term: participates_in

Axiom
annotated source: fiat object
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

opportunistic infectious disposition
type: Class
subclass of: infectious disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: has part
        some values from: establishment of localization in host
      intersection of: Restriction
        on property: has part
        some values from: transmission process
      intersection of: Restriction
        on property: has part
        some values from: Class
definition: An infectious disposition to become part of a disorder only in organisms whose defenses are compromised.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: opportunitistic pathogenic disposition
comment: The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host.
comment: This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin).

curator note
type: AnnotationProperty
editor preferred term: curator note
has curation status: IAO_0000122
definition: An administrative note of use for a curator but of no use for a user
term editor: PERSON:Alan Ruttenberg

immune response
type: Class
subclass of: biological_process
definition: Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
imported from: go.owl

has ID digit count
type: AnnotationProperty
example of usage: 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"
definition: 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)
term editor: Person:Alan Ruttenberg

preceded by
type: ObjectProperty
type: TransitiveProperty
inverse of: precedes
domain: occurrent
range: occurrent
editor preferred term: preceded by
editor note: 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.
alternative term: is preceded by
alternative term: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by

_obsolete_primary pathogen
type: Class
subclass of: Obsolete Class
deprecated: true

independent continuant
type: Class
subclass of: continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
definition: 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])
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (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]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

Axiom
annotated source: continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

Axiom
annotated source: quality
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

_obsolete_immunization
type: Class
subclass of: Obsolete Class
deprecated: true

nursing-home acquired infection
type: Class
subclass of: infection
definition: An infection resulting from a transmission process that unfolds in a nursing home.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

elucidation
type: AnnotationProperty
editor preferred term: elucidation
term editor: person:Alan Ruttenberg
definition source: Person:Barry Smith
elucidation: 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

symbiont role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: participates in
      some values from: symbiosis, encompassing mutualism through parasitism
disjoint with: pathogen role
disjoint with: infectious agent transporter role
disjoint with: infectious agent portal of entry role
disjoint with: infectious agent portal of exit role
disjoint with: disinfectant role
disjoint with: antiseptic role
disjoint with: primary infection role
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition: A role borne by an organism in symbiosis.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The role is realized in symbiosis.

host role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: part of
      some values from: Class
        intersection of: extended organism
        intersection of: Restriction
disjoint with: source of infection role
definition: A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infectious agent carrier
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: infectious agent carrier role
subclass of: infectious agent host
definition: An organism bearing the infectious agent carrier role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_engulfment by phagocyte
type: Class
subclass of: Obsolete Class
deprecated: true

BFO CLIF specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
definition source: Person:Alan Ruttenberg
curator note: Really of interest to developers only
sub property of: label

transmissibility disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: pathogen
  intersection of: Restriction
    on property: realized in
    all values from: transmission process
disjoint with: disease
definition: A disposition to undergo a transmission process.
term editor: Albert Goldfain
term editor: Alex Diehl
term editor: Lindsay Cowell
comment: The disposition is realized in a transmission process.

paracoccidioidomycosis
type: Class
equivalent class: Class
  intersection of: fungal infectious disease
  intersection of: Restriction
    on property: has part
    some values from: paracoccidioides
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: systemic mycosis
subclass of: fungal infectious disease
imported from: http://purl.obolibrary.org/obo/NCIT
has definition: 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 ]

spatiotemporal region
type: Class
subclass of: occurrent
BFO OWL specification label: st-region
BFO CLIF specification label: SpatiotemporalRegion
example of usage: the spatiotemporal region occupied by a human life
example of usage: the spatiotemporal region occupied by a process of cellular meiosis.
example of usage: the spatiotemporal region occupied by the development of a cancer tumor
elucidation: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has associated axiom(nl): All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has associated axiom(nl): Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has associated axiom(nl): Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has associated axiom(nl): Every spatiotemporal region occupies_spatiotemporal_region itself.
has associated axiom(nl): Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has associated axiom(fol): (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has associated axiom(fol): (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has associated axiom(fol): (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]

_obsolete_latency
type: Class
subclass of: Obsolete Class
definition: '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
editor note: id 'latency'-ID[O]:0000009 from IDO 2007. May have replacement - TBD
deprecated: true

negative regulation of viral process
type: Class
subclass of: biological regulation
definition: Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process in which a virus is a participant.
imported from: go.owl

_obsolete_configured infectious organism population
type: Class
subclass of: Obsolete Class
definition: 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
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
deprecated: true

paratenic host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: paratenic host role
subclass of: host
definition: An organism bearing a paratenic host role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

fungal infectious agent
type: Class
equivalent class: Class
  intersection of: fungus
  intersection of: Restriction
    on property: has disposition
    some values from: pathogenic disposition
subclass of: pathogen
term editor: Sydney Cohen
has definition: A fungus that has an infectious disposition

zero-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 0d-s-region
BFO CLIF specification label: ZeroDimensionalSpatialRegion
elucidation: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]

specifically dependent continuant
type: Class
subclass of: continuant
disjoint with: generically dependent continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
example of usage: 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
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: 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.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: 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.
definition: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
definition: 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])
editor note: 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.
has associated axiom(fol): (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]
has associated axiom(fol): (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]

temporal region
type: Class
subclass of: occurrent
BFO OWL specification label: t-region
BFO CLIF specification label: TemporalRegion
editor note: 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
elucidation: 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])
has associated axiom(nl): All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has associated axiom(fol): (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has associated axiom(fol): (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has associated axiom(fol): (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]

primary infection role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: infectious disorder
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The role is realized in a process by which the infectious disorder is established in the host.

Archaea
type: Class
subclass of: organism
imported from: ncbitaxon.owl

_obsolete_role
type: Class
subclass of: Obsolete Class
deprecated: true

cryptococcal meningitis
type: Class
subclass of: cryptococcus gattii cryptococcosis
subclass of: cryptococcosis
imported from: http://purl.obolibrary.org/obo/NCIT
has definition: 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 ]
has definition: 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 ]

replication
type: Class
subclass of: production
definition: A production process in which a participant creates a copy of itself.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: 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
editor note: 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.
editor note: 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.
elucidation: 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])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (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]
has associated axiom(fol): (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]

fusarium
type: Class
equivalent class: Class
  union of: primary fungal pathogen
  union of: Class
    intersection of: mold
    intersection of: opportunistic fungal pathogen
subclass of: mold
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH032704

leukocyte mediated immunity
type: Class
subclass of: immune response
definition: Any process involved in the carrying out of an immune response by a leukocyte.
imported from: go.owl

has output
type: ObjectProperty
sub property of: has participant
has curation status: IAO_0000125
definition: 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.
term editor: Chris Mungall
alternative term: produces

infectious disease course
type: Class
equivalent class: Class
  intersection of: disease course
  intersection of: Restriction
    on property: realizes
    some values from: infectious disease
subclass of: disease course
definition: A disease course that is the realization of an infectious disease.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

_obsolete_therapeutic
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_co-infected
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_contagiousness quality
type: Class
subclass of: Obsolete Class
definition: 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.
definition: A quality that inheres in an infection and is the likelihood that infectious agents part of the infection will spread to other hosts.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
label: _obsolete_host range
deprecated: true

scedosporium prolificans
type: Class
subclass of: scedosporium
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1192746.08FU

occurs in
type: ObjectProperty
inverse of: contains process
domain: occurrent
range: independent continuant
property chain axiom: part of
property chain axiom: occurs in
editor preferred term: occurs in
definition: 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
alternative term: occurs_in
alternative term: unfolds in
alternative term: unfolds_in
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

continuant fiat boundary
type: Class
subclass of: immaterial entity
BFO OWL specification label: cf-boundary
BFO CLIF specification label: ContinuantFiatBoundary
definition: 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])
editor note: 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.
editor note: 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
editor note: 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.
has associated axiom(nl): Every continuant fiat boundary is located at some spatial region at every time at which it exists
has associated axiom(fol): (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]

disinfectant role
type: Class
subclass of: role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has disposition
        some values from: antimicrobial disposition
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Class
        union of: Restriction
disjoint with: antiseptic role
disjoint with: primary infection role
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The role is realized in the killing and/or growth inhibition of microorganisms on the non-living entity.

_obsolete_temperature
type: Class
subclass of: Obsolete Class
deprecated: true

appearance of disorder
type: Class
equivalent class: Restriction
  on property: results in formation of
  some values from: disorder
subclass of: process
definition: A process by which a disorder comes into existence.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

parasite host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: parasite host role
subclass of: host
definition: An organism bearing a parasite host role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

establishment of localization
type: Class
subclass of: biological_process
definition: Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
imported from: go.owl
imported from: Gene Ontology: http://purl.obolibrary.org/obo/go.owl

invasion disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: molecular entity
  intersection of: Restriction
    on property: realized in
    all values from: Restriction
      on property: positively regulates
      some values from: entry into host through host barriers
disjoint with: antimicrobial disposition
disjoint with: antiviral disposition
disjoint with: antifungal disposition
disjoint with: antibacterial disposition
disjoint with: antiparasitic disposition
disjoint with: protective resistance
disjoint with: pathogenic disposition
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: A molecule with the invasion disposition is referred to as an invasion factor or invasin.

infectious disease
type: Class
equivalent class: Class
  intersection of: disease
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: infectious disorder
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
  intersection of: Restriction
    on property: realized in
    all values from: infectious disease course
  intersection of: Restriction
    on property: has_material_basis_in
    all values from: infectious disorder
  intersection of: Restriction
    on property: inheres in
    all values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
subclass of: disease
definition: A disease whose physical basis is an infectious disorder.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: tranmissible disease
comment: The disposition is realized in an infectious disease course.

immunosuppressive disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: material entity
  intersection of: Restriction
    on property: realized in
    all values from: immunosuppression
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: A disposition whose realization negatively regulates an immune response.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infectious disease epidemic
type: Class
subclass of: process
definition: A process of infectious disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population.
editor note: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: infectious disease outbreak

invasion factor
type: Class
equivalent class: Class
  intersection of: molecular entity
  intersection of: Restriction
    on property: has disposition
    some values from: invasion disposition
subclass of: molecular entity
definition: A biological macromolecule that has an invasion disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: invasin

_obsolete_transport by lymph
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_fimbrial specific adherence
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

in branch
type: AnnotationProperty
editor preferred term: in branch
definition: An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
term editor: GROUP:OBI
definition source: OBI_0000277

one-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 1d-s-region
BFO CLIF specification label: OneDimensionalSpatialRegion
example of usage: an edge of a cube-shaped portion of space.
elucidation: 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])
has associated axiom(fol): (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]

diseased population
type: Class
subclass of: organism population
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: participates in
        some values from: infectious disease course
  intersection of: Restriction
    on property: has part
    all values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: participates in
        some values from: infectious disease course
definition: An organism population in whose members an infectious disease is being realized.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

has function
type: ObjectProperty
sub property of: bearer of
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: 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.
alternative term: has_function

source of infection role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
definition: A role borne by a material entity in virtue of the fact that it contains a site from which an infectious agent is transmitted.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

eumycetoma
type: Class
equivalent class: Class
  intersection of: fungal infectious disease
  intersection of: Class
    union of: cutaneous mycosis
    union of: systemic mycosis
    union of: Restriction
      on property: has_material_basis_in
      some values from: subcutaneous mycosis
  intersection of: Restriction
    on property: has part
    some values from: dematiaceous fungus
subclass of: fungal infectious disease
term editor: Sydney Cohen
definition source: https://www.ncbi.nlm.nih.gov/books/NBK574511/
has definition: 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.
has exact synonym: eumycotic mycetoma
comment: Eumycetoma is a mycetoma caused by fungi (eumycotic) rather than a mycetoma caused by bacteria (actinomycotic)
comment: 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.
comment: non-exhaustive list of fungi that may cause the infection and disease. for more information, see https://doi.org/10.1111/jdv.13008

antibiotic resistance
type: Class
subclass of: resistance to drug
definition: A resistance to drug that mitigates the damaging effects of an antibiotic.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

biological regulation
type: Class
subclass of: process
definition: Any process that modulates a measurable attribute of any biological process, quality or function.
imported from: go.owl

invasive aspergillosis
type: Class
equivalent class: Class
  intersection of: aspergillosis
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: systemic mycosis
subclass of: aspergillosis
imported from: http://purl.obolibrary.org/obo/NCIT
has definition: An aspergillosis that is characterized by the presence of septate, acute, branching hyphae invading lung tissue. [ NCI ]
comment: 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.

Axiom
annotated source: function
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

_obsolete_prion
type: Class
subclass of: Obsolete Class
deprecated: true

pulmonary mucormycosis
type: Class
equivalent class: Class
  intersection of: mucormycosis
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: systemic mycosis
subclass of: mucormycosis
term editor: Sydney Cohen
has definition: 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
has related synonym: lung mucormycosis
comment: 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

disseminated mucormycosis
type: Class
equivalent class: Class
  union of: Class
    intersection of: mucormycosis
    intersection of: Restriction
      on property: has_material_basis_in
      some values from: systemic mycosis
  union of: Restriction
    on property: has_material_basis_in
    some values from: cutaneous mycosis
  union of: Restriction
    on property: has_material_basis_in
    some values from: subcutaneous mycosis
subclass of: mucormycosis
term editor: Sydney Cohen
definition source: https://www.cdc.gov/mucormycosis/hcp/clinical-overview/index.html
has definition: 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.

process profile
type: Class
subclass of: process
disjoint with: history
BFO OWL specification label: process-profile
BFO CLIF specification label: ProcessProfile
example of usage: 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
example of usage: 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.
example of usage: 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.
definition: 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])
elucidation: 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])
has associated axiom(fol): (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]
has associated axiom(fol): (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]

aspergillus fumigatus
type: Class
equivalent class: Restriction
  on property: has disposition
  some values from: antifungal resistance
subclass of: aspergillus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1160519.08FU

Axiom
annotated source: continuant
annotated property: editor note
annotated target: 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
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000007

exophiala
type: Class
subclass of: dematiaceous fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH030899

regulates
type: ObjectProperty
type: TransitiveProperty
domain: process
range: process
has curation status: IAO_0000125
definition: 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
editor note: 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
term editor: Chris Mungall
term editor: David Hill
term editor: Tanya Berardini
definition source: causal-relations
definition source: GO
curator note: Regulation precludes parthood; the regulatory process may not be within the regulated process.
OBO foundry unique label: regulates (processual)
elucidation: false

realizable entity
type: Class
subclass of: specifically dependent continuant
disjoint with: quality
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: 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.
elucidation: 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])
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (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]
has associated axiom(fol): (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]

symptomatic host of infectious agent
type: Class
subclass of: infectious agent host
subclass of: Restriction
  on property: has role
  some values from: infectious agent host role
definition: An organism who is host to an infectious agent and has symptoms of the infectious disease associated with the infectious agent
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

phialophora
type: Class
subclass of: dematiaceous fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH030905

cryptococcosis
type: Class
equivalent class: Class
  intersection of: fungal infectious disease
  intersection of: Class
    union of: Restriction
      on property: has_material_basis_in
      some values from: cutaneous mycosis
    union of: Restriction
      on property: has_material_basis_in
      some values from: systemic mycosis
  intersection of: Restriction
    on property: has part
    some values from: cryptococcus neoformans
subclass of: fungal infectious disease
imported from: http://www.ebi.ac.uk/efo/EFO
has definition: 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 ]
has definition: 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 ]

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

toxin
type: Class
equivalent class: Class
  intersection of: molecular entity
  intersection of: Restriction
    on property: has disposition
    some values from: toxin disposition
subclass of: molecular entity
definition: A molecular entity that has a toxin disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

colonization of human anterior nares
type: Class
subclass of: colonization of human
definition: A colonization of human process in which the colonized site is the anterior nares.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_incubation period
type: Class
subclass of: Obsolete Class
definition: 'agent is incubated?ndisease is incubated?'-ID[O]:0000219: agent is incubated?ndisease is incubated?
editor note: id 'incubation period'-ID[O]:0000219 from IDO 2007. May have replacement - TBD
deprecated: true

immune population
type: Class
subclass of: organism population
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: has disposition
        some values from: acquired immunity to infectious agent
  intersection of: Restriction
    on property: has part
    all values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: has disposition
        some values from: acquired immunity to infectious agent
definition: An organism population whose members have acquired immunity to an infectious agent.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infectious agent transporter role
type: Class
subclass of: role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: location of
        some values from: infectious agent
  intersection of: Restriction
    on property: realized in
    all values from: indirect
disjoint with: infectious agent portal of entry role
disjoint with: infectious agent portal of exit role
disjoint with: disinfectant role
disjoint with: antiseptic role
disjoint with: primary infection role
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The role is realized in a process that transfers an infectious organism from one location to another.

_obsolete_invasin
type: Class
subclass of: Obsolete Class
definition: synonym of invasion factor
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
deprecated: true

oropharyngeal candidiasis
type: Class
subclass of: candidiasis
imported from: http://purl.obolibrary.org/obo/NCIT
has definition: 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 ]
has exact synonym: thrush
comment: 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.

definition source
type: AnnotationProperty
editor preferred term: definition source
has curation status: IAO_0000122
definition: 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
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w

Axiom
annotated source: entity
annotated property: editor note
annotated target: 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
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith

subclinical infection
type: Class
subclass of: infection
definition: An infection that is part of an asymptomatic host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

passive immunity to infectious agent
type: Class
subclass of: immunity to infectious agent
definition: An immunity to infectious agent that inheres in an organism in virtue of antibodies not produced by that organism.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: Passive immunity results from a passive immunization.
comment: The disposition is realized in a neutralizing process carried out by the antibodies.
comment: The protective antibodies are typically introduced by injection, breast feeding, or by passing from the placenta to the fetus.

resistant entity
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has disposition
    some values from: protective resistance
subclass of: material entity
disjoint with: immunodeficiency
definition: A material entity that has a resistance disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

zoonotic disposition
type: Class
subclass of: infectious disposition
definition: An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis.

organism population
type: Class
subclass of: object aggregate
definition: An aggregate of organisms of the same Species.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age.

blastomyces dermatitidis
type: Class
equivalent class: Class
  intersection of: dimorphic fungus
  intersection of: opportunistic fungal pathogen
  intersection of: primary fungal pathogen
subclass of: dimorphic fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH385070.07FU

establishment of a clinically abnormal colony
type: Class
subclass of: colonization of host
definition: A colonization of host process that results in a clinically abnormal colony.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

aspergillosis
type: Class
equivalent class: Class
  intersection of: fungal infectious disease
  intersection of: Class
    union of: Restriction
      on property: has_material_basis_in
      some values from: cutaneous mycosis
    union of: Restriction
      on property: has_material_basis_in
      some values from: systemic mycosis
    union of: Restriction
      on property: has_material_basis_in
      some values from: subcutaneous mycosis
  intersection of: Restriction
    on property: has part
    some values from: aspergillus
subclass of: fungal infectious disease
imported from: http://purl.obolibrary.org/obo/NCIT
has definition: A fungal infectious disease that is caused by Aspergillus. [ NCI ]
comment: A fungal infectious disease that occurs most often in the skin, ears, nasal sinuses, and lungs of people with suppressed immune systems.

relation has no temporal argument
type: NamedIndividual
definition: ## 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)

_obsolete_immunosuppressed
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001

establishment of localization in host
type: Class
equivalent class: Restriction
  on property: occurs in
  some values from: host
subclass of: establishment of localization
definition: 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.
editor note: Requested addition of this term to the GO.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

infectious disease endemic level
type: Class
subclass of: infectious disease prevalence
definition: An infectious disease prevalence that is typical for an infectious disease in an organism population.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: Infectious disease endemic level is relational to previous prevalences of the disease.

chronic infectious disease course
type: Class
subclass of: infectious disease course
definition: An infectious disease course that unfolds over a long period of time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: persistent infectious disease course

negative regulation of immune response
type: Class
subclass of: biological regulation
definition: 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.
imported from: go.owl

infectious agent transmissibility
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: infectious agent
definition: A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening.

_obsolete_pathogen life cycle
type: Class
subclass of: Obsolete Class
definition: '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
editor note: id 'pathogen life cycle'-ID[O]:0000226 from IDO 2007. May have replacement - TBD
deprecated: true

_obsolete_progression rate
type: Class
subclass of: Obsolete Class
deprecated: true

reverse zoonosis
type: Class
equivalent class: Class
  intersection of: infectious disease
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: Class
      intersection of: infectious disorder
      intersection of: Restriction
        on property: has part
        some values from: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
  intersection of: Restriction
    on property: has_material_basis_in
    all values from: Class
      intersection of: infectious disorder
      intersection of: Restriction
        on property: has part
        some values from: Class
  intersection of: Restriction
    on property: inheres in
    all values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: part of
        some values from: Class
subclass of: infectious disease
definition: An infectious disease that has as its physical basis an infectious disorder composed of infectious agents that have a reverse zoonotic disposition.
term editor: Albert Goldfain
term editor: Alex Diehl
term editor: Lindsay Cowell

intermediate host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: intermediate host role
subclass of: host
definition: A organism bearing an intermediate host role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: secondary host

life-sustaining process
type: Class
subclass of: biological_process
definition: A process which is necessary for the survival of an organism.
term editor: Alex Diehl
term editor: Lindsay Cowell

candida auris
type: Class
subclass of: candida
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1213468.08FU
comment: 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

derives from
type: ObjectProperty
inverse of: derives into
example of usage: this cell derives from this parent cell (cell division)
example of usage: this nucleus derives from this parent nucleus (nuclear division)
has curation status: IAO_0000125
definition: 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
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
alternative term: derives_from

primary infectious disposition
type: Class
equivalent class: Class
  intersection of: infectious disposition
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: has part
        some values from: establishment of localization in host
      intersection of: Restriction
        on property: has part
        some values from: transmission process
      intersection of: Restriction
        on property: has part
        some values from: Class
subclass of: infectious disposition
definition: An infectious disposition to become part of a disorder in organisms that have intact defenses.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts.
comment: 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."

metatstatic infection
type: Class
subclass of: infection
definition: An infection established as a result of spread from another infection in a non-adjacent location in the extended organism of the host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

relational quality
type: Class
subclass of: quality
BFO OWL specification label: r-quality
BFO CLIF specification label: RelationalQuality
example of usage: 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.
example of usage: a marriage bond, an instance of love, an obligation between one person and another.
definition: 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])
has associated axiom(fol): (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]

subcutaneous mycosis
type: Class
subclass of: mycosis
term editor: Sydney Cohen
has definition: 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.
has related synonym: http://purl.obolibrary.org/obo/DOID_0050135

disorder
type: Class
subclass of: material entity
definition: A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
imported from: ogms.owl

function
type: Class
subclass of: disposition
BFO OWL specification label: function
BFO CLIF specification label: Function
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
editor note: 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.
elucidation: 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])
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

colonization of host
type: Class
equivalent class: Class
  intersection of: establishment of localization in host
  intersection of: Restriction
    on property: has output
    some values from: colony
subclass of: establishment of localization in host
definition: An establishment of localization in host process in which an organism establishes itself in a host.
editor note: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

collective disposition
type: Class
subclass of: disposition
subclass of: Restriction
  on property: inheres in
  some values from: object aggregate
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: A disposition that inheres in a collection of entities in virtue of the individual dispositions of the constituents of that collection.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: "... 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.
comment: The disposition is realized in a process that has as part realizations of some of the individual dispositions.

Bacteria
type: Class
subclass of: organism
imported from: ncbitaxon.owl

concretizes
type: ObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
example of usage: 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).
example of usage: 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).
definition: 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.

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001

azole-resistant aspergillus fumigatus
type: Class
equivalent class: Class
  intersection of: aspergillosis
  intersection of: Restriction
    on property: has part
    some values from: aspergillus fumigatus
equivalent class: Restriction
  on property: has disposition
  some values from: antifungal resistance
subclass of: aspergillosis
has definition: 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
comment: 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)

Axiom
annotated source: BFO_0000134
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/080-003

Axiom
annotated source: independent continuant
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

capable of
type: ObjectProperty
domain: independent continuant
range: process
example of usage: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
example of usage: osteoclast SubClassOf 'capable of' some 'bone resorption'
has curation status: IAO_0000125
definition: 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.
term editor: Chris Mungall
alternative term: has function realized in
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20123131
definition source: http://www.ncbi.nlm.nih.gov/pubmed/21208450
curator note: 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)".
expand expression to: RO_0000053 some (RO_0000054 only ?Y)

mold
type: Class
subclass of: fungus
imported from: http://purl.obolibrary.org/obo/NCIT
has definition: A fungus that is multicellular and produces filaments and hyphae.
comment: A non-taxonomic grouping of fungi that grow in the form of mycelium of hyphae (vegetative filaments).

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

_obsolete_host
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_protective
type: Class
subclass of: Obsolete Class
deprecated: true

aspergillus
type: Class
equivalent class: Class
  intersection of: mold
  intersection of: opportunistic fungal pathogen
subclass of: mold
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH030957

passive immunization against infectious agent
type: Class
subclass of: immunization against infectious agent
definition: An immunization that begins with transfer to an organism of molecules not produced by that organism and that confer immunity against an infectious agent.
editor note: Examples include the injection of antibodies and the transfer of maternal antibodies to the fetus.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

has curation status
type: AnnotationProperty
editor preferred term: has curation status
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bill Bug
term editor: PERSON:Melanie Courtot
definition source: OBI_0000281

exotoxin
type: Class
equivalent class: Class
  intersection of: molecular entity
  intersection of: Restriction
    on property: has disposition
    some values from: exotoxin disposition
subclass of: toxin
definition: A molecular entity bearing an exotoxin disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_dormancy period
type: Class
subclass of: Obsolete Class
definition: 'is a period a process?'-ID[O]:0000227: is a period a process?
editor note: id 'dormancy period'-ID[O]:0000227 from IDO 2007. May have replacement - TBD
deprecated: true

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000011

rhizopus
type: Class
subclass of: mold
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH035107

Axiom
annotated source: function
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

Axiom
annotated source: zero-dimensional temporal region
annotated property: elucidation
annotated target: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

quality
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: quality
BFO CLIF specification label: Quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
elucidation: 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])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (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]

Axiom
annotated source: specifically dependent continuant
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith

endophthalmitis
type: Class
subclass of: fungal eye infection
imported from: http://www.orpha.net/ORDO/Orphanet
has definition: 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.
has definition: 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.

infected population
type: Class
subclass of: organism population
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: infected organism
  intersection of: Restriction
    on property: has part
    all values from: infected organism
definition: An organism population whose members have an infection.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

mechanical vector of infectious agent
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: mechanical vector of infectious agent role
subclass of: infectious agent vector
definition: An infectious agent vector bearing a mechanical vector of infectious agent role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_end reservoir of infectious agent
type: Class
subclass of: Obsolete Class
definition: A material entity bearing an end reservoir of infectious agent role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: dead-end reservoir of infectious agent
deprecated: true

_obsolete_immunocompromised
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: continuant fiat boundary
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

communicability
type: Class
equivalent class: Class
  intersection of: infectious disposition
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: has part
        some values from: establishment of localization in host
      intersection of: Restriction
        on property: has part
        some values from: appearance of disorder
      intersection of: Restriction
        on property: has part
        some values from: horizontal pathogen transmission process
subclass of: infectious disposition
definition: An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The disposition is realized in a direct, horizontal transmission process between members of the same Species.

negatively regulates
type: ObjectProperty
sub property of: regulates
has curation status: IAO_0000125
definition: x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y
term editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: negatively regulates (process to process)

primary infection
type: Class
equivalent class: Class
  intersection of: infectious disorder
  intersection of: Restriction
    on property: has role
    some values from: primary infection role
subclass of: infectious disorder
disjoint with: secondary infection
definition: An infection bearing the primary infection role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: material entity
disjoint with: disorder
definition: 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.
imported from: obi.owl

_obsolete_outbreak
type: Class
subclass of: Obsolete Class
deprecated: true

infection incidence rate
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: A quality that inheres in an organism population and is the infection incidence proportion per unit time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

_obsolete_exogenous
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: role
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

antibacterial disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: material entity
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Class
        union of: Restriction
disjoint with: antiparasitic disposition
disjoint with: protective resistance
disjoint with: pathogenic disposition
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: A disposition to kill or inhibit the reproduction of bacteria.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: antibiotic disposition

susceptibility
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: material entity
definition: A quality that inheres in an entity and is the degree to which it can be harmed by another entity.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: Low susceptibility is often referred to as resistance. In this sense, resistance is a quality.

disposition to form a non-parasitic colony
type: Class
subclass of: disposition
disjoint with: transmissibility disposition
disjoint with: disease
definition: A disposition to colonize an organism and participate in mutualism or commensalism with that organism.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

2D boundary of
type: ObjectProperty
inverse of: has 2D boundary
example of usage: the surface of my skin is a 2D boundary of my body
definition: a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative term: 2D_boundary_of
alternative term: boundary of
alternative term: is 2D boundary of
alternative term: is boundary of
temporal interpretation: axiom holds for all times

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

_obsolete_live
type: Class
subclass of: Obsolete Class
deprecated: true

susceptibility to infectious agent
type: Class
subclass of: susceptibility
subclass of: Restriction
  on property: inheres in
  some values from: organism
disjoint with: drug susceptibility
definition: A susceptibility that inheres in an organism and is the degree to which it can be harmed by an infectious agent.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infected organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: extended organism
      intersection of: Restriction
        on property: has part
        some values from: infection
subclass of: organism
definition: An organism that has an infection in or on its extended organism.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

part of
type: ObjectProperty
type: TransitiveProperty
inverse of: has part
editor preferred term: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: 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.
editor note: 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
editor note: 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'.
alternative term: part_of
temporal interpretation: axiom holds for all times

located in
type: ObjectProperty
type: TransitiveProperty
editor preferred term: located in
example of usage: my brain is located in my head
example of usage: this rat is located in this cage
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
editor note: 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
editor note: 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
alternative term: located_in
temporal interpretation: axiom holds for all times
source: http://www.obofoundry.org/ro/#OBO_REL:located_in

genetic resistance to infectious agent
type: Class
subclass of: resistance to infectious agent
definition: A resistance to infectious agent that inheres in an organism in virtue of a specific allele or combination of alleles in its genome.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

secondary infection
type: Class
equivalent class: Class
  intersection of: infectious disorder
  intersection of: Restriction
    on property: has role
    some values from: secondary infection role
subclass of: infectious disorder
definition: An infection bearing the secondary infection role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

pathogen host role
type: Class
subclass of: host role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: part of
      some values from: Class
        intersection of: extended organism
        intersection of: Restriction
definition: A host role borne by an organism in virtue of the fact that its extended organism contains a pathogen.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

protective resistance
type: Class
subclass of: disposition
subclass of: Restriction
  on property: inheres in
  some values from: material entity
disjoint with: pathogenic disposition
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.
comment: The disposition is realized in a process that mitigates damage to the bearer and has the part as a participant.

acquired immunity to infectious agent
type: Class
equivalent class: Class
  intersection of: immunity to infectious agent
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: Class
      union of: immunoglobulin complex
      union of: B cell receptor complex
      union of: T cell receptor complex
  intersection of: Restriction
    on property: realized in
    all values from: adaptive immune response
  intersection of: Restriction
    on property: has_material_basis_in
    all values from: Class
      union of: immunoglobulin complex
      union of: B cell receptor complex
      union of: T cell receptor complex
subclass of: immunity to infectious agent
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: adaptive immunity to infectious agent
alternative term: immune memory
comment: The disposition is realized in an immune response in which such antigen receptors participate.

zero-dimensional temporal region
type: Class
subclass of: temporal region
BFO OWL specification label: 0d-t-region
BFO CLIF specification label: ZeroDimensionalTemporalRegion
example of usage: a temporal region that is occupied by a process boundary
example of usage: right now
example of usage: the moment at which a child is born
example of usage: the moment at which a finger is detached in an industrial accident
example of usage: the moment of death.
alternative term: temporal instant.
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]

imported from
type: AnnotationProperty
editor preferred term: imported from
has curation status: IAO_0000125
definition: For external terms/classes, the ontology from which the term was imported
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

infectious disease mortality rate
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

_obsolete_disruption of body surface
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000301

_obsolete_specific adherence
type: Class
subclass of: Obsolete Class
deprecated: true

Eukaryota
type: Class
subclass of: organism
imported from: ncbitaxon.owl

humoral immune response
type: Class
subclass of: immune response
definition: An immune response mediated through a body fluid.
imported from: go.owl

complex infection
type: Class
subclass of: infection
definition: An infection comprised of infectious organisms from different Species.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: mixed infection
alternative term: polymicrobial infection

source of infection
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: source of infection role
subclass of: material entity
definition: A material entity bearing a source of infection role.
term editor: Albert Goldfain
term editor: Alex Diehl
term editor: Lindsay Cowell

mido.owl
type: Ontology
default language: en
creator: Sydney Cohen
license: http://creativecommons.org/licenses/by/3.0/
comment: 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.
version info: 2022-12-04

_obsolete_engulfment
type: Class
subclass of: Obsolete Class
deprecated: true

virulence factor
type: Class
equivalent class: Class
  intersection of: molecular entity
  intersection of: Restriction
    on property: has disposition
    some values from: virulence factor disposition
subclass of: molecular entity
definition: A biological macromolecule produced by a pathogen and that has a virulence factor disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

Axiom
annotated source: zero-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

chronic systemic steroid use-based immunosuppression
type: Class
subclass of: drug-based immunosuppression
definition: A drug-based immunosuppression process that results from chronic systemic steroid use.
term editor: Alex Diehl
term editor: Lindsay Cowell

mucormycosis
type: Class
equivalent class: Class
  union of: Class
    intersection of: fungal infectious disease
    intersection of: Class
      union of: rhizopus
      union of: mucor
      union of: syncephalastrum
      union of: apophysomyces
      union of: lichtheimia
      union of: Restriction
        on property: has part
        some values from: rhizomucor
    intersection of: Restriction
      on property: has_material_basis_in
      some values from: cutaneous mycosis
  union of: Restriction
    on property: has_material_basis_in
    some values from: systemic mycosis
  union of: Restriction
    on property: has_material_basis_in
    some values from: subcutaneous mycosis
subclass of: fungal infectious disease
term editor: Sydney Cohen
definition source: World Health Organization: https://www.who.int/india/home/emergencies/coronavirus-disease-(covid-19)/mucormycosis
has definition: 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.
has related synonym: zygomycosis (previous name)
comment: didn't import EFO:0007380, which also refers to mucormycosis, since that defintion mentions Zygomycota, a phylum of fungi that no longer exists

immunosuppressed human experiencing HIV-based immunosuppression
type: Class
subclass of: immunosuppressed organism experiencing HIV-based immunosuppression
definition: An immunosuppressed organism that is a human experiencing HIV-based immunosuppression.
term editor: Alex Diehl
term editor: Lindsay Cowell
ontology term requester: NCI BBRB

infectious disease prevalence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

axiom holds for all times
type: NamedIndividual
definition: ## 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

_obsolete_invasin
type: Class
subclass of: Obsolete Class
deprecated: true

rhinocerebral mucormycosis
type: Class
equivalent class: Class
  intersection of: mucormycosis
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: systemic mycosis
subclass of: mucormycosis
term editor: Sydney Cohen
definition source: https://www.cdc.gov/mucormycosis/hcp/clinical-overview/index.html
has definition: 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.
has related synonym: sinus and brain mucormycosis

colonization of human perineum
type: Class
subclass of: colonization of human
definition: A colonization of human process in which the colonized site is a perineum.
term editor: Albert Goldfain
term editor: Alex Diehl
term editor: Lindsay Cowell

_obsolete_infectious organism
type: Class
subclass of: Obsolete Class
definition: An infectious agent that is an organism.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
deprecated: true

biological_process
type: Class
subclass of: process
definition: 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.
imported from: go.owl

cutaneous mucormycosis
type: Class
equivalent class: Class
  union of: Class
    intersection of: mucormycosis
    intersection of: Restriction
      on property: has_material_basis_in
      some values from: cutaneous mycosis
  union of: Restriction
    on property: has_material_basis_in
    some values from: subcutaneous mycosis
subclass of: mucormycosis
term editor: Sydney Cohen
definition source: https://doi.org/10.1590/abd1806-4841.20176614
has definition: 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.

_obsolete_phase variation
type: Class
subclass of: Obsolete Class
deprecated: true

biological vehicle of infectious agent role
type: Class
subclass of: infectious agent vehicle role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: Examples include blood, serum, tissue, or fresh produce.

_obsolete_mode of transmission
type: Class
subclass of: Obsolete Class
deprecated: true

antiparasitic disposition
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: material entity
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Class
        union of: Restriction
disjoint with: protective resistance
disjoint with: pathogenic disposition
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: A disposition to kill or inhibit the development or reproduction of eukaryotic parasites.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: In the term name, we are using parasite in the medical sense of eukaryotic organisms that are parasitic in humans.

Axiom
annotated source: spatial region
annotated property: has associated axiom(nl)
annotated target: All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

anatomical entity
type: Class
subclass of: material entity
disjoint with: infectious disorder
disjoint with: pathogen
disjoint with: disinfectant
disjoint with: antiseptic
disjoint with: antimicrobial
disjoint with: antiviral
disjoint with: antifungal
disjoint with: antibacterial
disjoint with: infection
disjoint with: immunodeficiency
definition: 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.
imported from: caro.owl

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

_obsolete_morbidity
type: Class
subclass of: Obsolete Class
deprecated: true

invasive candidiasis
type: Class
equivalent class: Class
  intersection of: candidiasis
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: systemic mycosis
subclass of: candidiasis
has definition: A serious form of candidiasis that can affect the blood, heart, brain, eyes, bones, and other parts of the body.
has related synonym: Candidemia
comment: Candidemia, a bloodstream infection with Candida, is a common infection in hospitalized patients.

immaterial entity
type: Class
subclass of: independent continuant
BFO OWL specification label: immaterial
BFO CLIF specification label: ImmaterialEntity
editor note: 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

intracellular infection
type: Class
equivalent class: Class
  intersection of: infection
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: infectious agent
      intersection of: Restriction
        on property: located in
        some values from: cell
subclass of: infection
definition: An infection for which the infectious agents that are part of the infection persist inside host cells.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

antisymmetric property
type: AnnotationProperty
editor preferred term: antisymmetric property
example of usage: part_of antisymmetric property xsd:true
definition: use boolean value xsd:true to indicate that the property is an antisymmetric property
term editor: Alan Ruttenberg

parasite host role
type: Class
subclass of: symbiont host role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: part of
      some values from: Class
        intersection of: extended organism
        intersection of: Restriction
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The partner in symbiosis bears the parasite role.
comment: 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.

_obsolete_infected
type: Class
subclass of: Obsolete Class
deprecated: true

site
type: Class
subclass of: immaterial entity
BFO OWL specification label: site
BFO CLIF specification label: Site
example of usage: Manhattan Canyon)
example of usage: a hole in the interior of a portion of cheese
example of usage: a rabbit hole
example of usage: an air traffic control region defined in the airspace above an airport
example of usage: the Grand Canyon
example of usage: the Piazza San Marco
example of usage: the cockpit of an aircraft
example of usage: the hold of a ship
example of usage: the interior of a kangaroo pouch
example of usage: the interior of the trunk of your car
example of usage: the interior of your bedroom
example of usage: the interior of your office
example of usage: the interior of your refrigerator
example of usage: the lumen of your gut
example of usage: your left nostril (a fiat part – the opening – of your left nasal cavity)
elucidation: 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])
has associated axiom(fol): (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]

_obsolete_communicable disposition
type: Class
subclass of: Obsolete Class
definition: An infectious disposition to be transmitted directly from one human host to another.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
deprecated: true

co-infected organism
type: Class
subclass of: infected organism
definition: An organism that has two infections with distinct Species of infectious agents.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

cryptococcus gattii cryptococcosis
type: Class
equivalent class: Class
  intersection of: fungal infectious disease
  intersection of: Class
    union of: Restriction
      on property: has_material_basis_in
      some values from: cutaneous mycosis
    union of: Restriction
      on property: has_material_basis_in
      some values from: systemic mycosis
  intersection of: Restriction
    on property: has part
    some values from: cryptococcus gatti
subclass of: fungal infectious disease
subclass of: cryptococcosis
has definition: 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.
has definition: 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.
has exact synonym: C. gatti cryptococcosis
comment: 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.
comment: more info: https://doi.org/10.1128/CMR.00126-13

candida
type: Class
equivalent class: Class
  intersection of: dimorphic fungus
  intersection of: opportunistic fungal pathogen
subclass of: dimorphic fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH033417

host exposure to environment containing infectious agent
type: Class
subclass of: host exposure to infectious agent
definition: 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.
term editor: Bjoern Peters

infectious agent
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has disposition
    some values from: infectious disposition
subclass of: pathogen
subclass of: organism
definition: An organism that has an infectious disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

immunocompetence
type: Class
subclass of: disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: realized in
    all values from: immune response
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: A disposition that is the ability to mount a normal immune response.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

growth
type: Class
subclass of: biological_process
definition: The increase in size or mass of an entire organism, a part of an organism or a cell.
imported from: go.owl

infectious disease incidence proportion
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: cumulative incidence of infectious disease
comment: 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.

negative regulation of life-sustaining process
type: Class
equivalent class: Restriction
  on property: negatively regulates
  some values from: life-sustaining process
subclass of: biological regulation
definition: Any process that stops, prevents, or reduces the frequency, rate or extent of a life-sustaining process.
term editor: Alex Diehl
term editor: Lindsay Cowell

infectious disease sporadicity
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: Sporadic quality of infectious disease is relational to previous prevalence of the disease.

paracoccidioides brasiliensis
type: Class
subclass of: paracoccidioides
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1178418.08FU

exotoxin disposition
type: Class
subclass of: toxin disposition
definition: A toxin disposition to damage cells or extracellular matrix by a direct enzymatic process.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The disposition is realized in a direct enzymatic process that damages host cells or extracellular matrix.

Axiom
annotated source: role
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

histoplasma capsulatum
type: Class
equivalent class: Class
  union of: primary fungal pathogen
  union of: Class
    intersection of: dimorphic fungus
    intersection of: opportunistic fungal pathogen
subclass of: dimorphic fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1178417.08FU

_obsolete_exotoxin
type: Class
subclass of: Obsolete Class
deprecated: true

talaromyces marneffei
type: Class
equivalent class: Class
  intersection of: dimorphic fungus
  intersection of: opportunistic fungal pathogen
subclass of: dimorphic fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1150522.08FU
has related synonym: used to be called penicillium marneffei

_obsolete_quality of host
type: Class
subclass of: Obsolete Class
deprecated: true

hospital-acquired infection
type: Class
subclass of: infection
disjoint with: community-acquired infection
definition: An infection resulting from a transmission process that unfolds in a hospital.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: nosocomial infection

infectious human pathogen
type: Class
subclass of: infectious agent
definition: An infectious agent with a capability to infect human hosts.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

fiat object
type: Class
subclass of: material entity
BFO OWL specification label: fiat-object
BFO CLIF specification label: FiatObjectPart
example of usage: 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
example of usage: the FMA:regional parts of an intact human body.
example of usage: the Western hemisphere of the Earth
example of usage: the division of the brain into regions
example of usage: the division of the planet into hemispheres
example of usage: the dorsal and ventral surfaces of the body
example of usage: the upper and lower lobes of the left lung
editor note: BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
elucidation: 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])
has associated axiom(fol): (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]

_obsolete_serum resistance
type: Class
subclass of: Obsolete Class
deprecated: true

disposition of
type: ObjectProperty
sub property of: inheres in

polyene
type: Class
subclass of: antifungal
term editor: Sydney Cohen
definition source: https://doi.org/10.3390/genes9090461
has definition: 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.
comment: 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

communicability period
type: Class
subclass of: one-dimensional temporal region
definition: A continuous temporal interval during which an infectious agent host bears a contagiousness disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

quality of
type: ObjectProperty
sub property of: inheres in
inverse of: has quality
example of usage: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
alternative term: is quality of
alternative term: quality_of

molecular entity
type: Class
subclass of: material entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
imported from: chebi.owl

Axiom
annotated source: fiat object
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

infectious agent vehicle role
type: Class
equivalent class: Class
  intersection of: infectious agent transporter role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: material entity
      intersection of: Class
        complement of: organism
      intersection of: Restriction
        on property: location of
        some values from: infectious agent
  intersection of: Restriction
    on property: realized in
    all values from: indirect
subclass of: infectious agent transporter role
definition: An infectious agent transporter role borne by an entity in virtue of the fact that the entity is not a complete organism.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: Drinking water bears the infectious agent vehicle role, but does not bear either of the subtype roles.

_obsolete_epidemic spread of disease
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_pandemic spread of disease
type: Class
subclass of: Obsolete Class
deprecated: true

disease
type: Class
subclass of: disposition
definition: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
imported from: ogms.owl

allergic aspergillosis
type: Class
equivalent class: Class
  intersection of: aspergillosis
  intersection of: Restriction
    on property: participates in
    some values from: immune response
subclass of: aspergillosis
term editor: Sydney Cohen
definition source: https://www.hopkinsmedicine.org/health/conditions-and-diseases/allergic-pulmonary-aspergillosis
has definition: 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.

realized in
type: ObjectProperty
inverse of: realizes
domain: realizable entity
range: process
editor preferred term: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative term: is realized by
alternative term: realized_in
elucidation: [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])
comment: 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

symbiosis, encompassing mutualism through parasitism
type: Class
subclass of: multi-organism process
definition: 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.
imported from: go.owl

_obsolete_fitness
type: Class
subclass of: Obsolete Class
definition: 'is a quality relating to both bacteria and host'-ID[O]:0000306: is a quality relating to both bacteria and host
editor note: id 'fitness'-ID[O]:0000306 from IDO 2007. May have replacement - TBD
deprecated: true

one-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 1d-cf-boundary
BFO CLIF specification label: OneDimensionalContinuantFiatBoundary
example of usage: The Equator
example of usage: all geopolitical boundaries
example of usage: all lines of latitude and longitude
example of usage: the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
example of usage: the median sulcus of your tongue
elucidation: 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])
has associated axiom(fol): (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]

has participant
type: ObjectProperty
domain: occurrent
range: continuant
editor preferred term: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: 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.
alternative term: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

occurrent
type: Class
subclass of: entity
disjoint with: Restriction
  on property: part of
  some values from: continuant
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
editor note: 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
editor note: 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.
editor note: 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.
editor note: 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.
elucidation: 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])
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

susceptible population
type: Class
subclass of: organism population
definition: An organism population whose members are not infected with an infectious agent and who lack immunity to the infectious agent.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: at-risk population

talaromycosis
type: Class
equivalent class: Class
  intersection of: fungal infectious disease
  intersection of: Restriction
    on property: has part
    some values from: talaromyces marneffei
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: systemic mycosis
subclass of: fungal infectious disease
term editor: Sydney Cohen
has definition: 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.

pathogen role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: pathogen
disjoint with: infectious agent transporter role
disjoint with: infectious agent portal of entry role
disjoint with: infectious agent portal of exit role
disjoint with: disinfectant role
disjoint with: antiseptic role
disjoint with: primary infection role
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

continuant
type: Class
subclass of: entity
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
definition: 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.
editor note: 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
editor note: 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
elucidation: 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])
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(nl): 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])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

_obsolete_quality of host population
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_infectivity period
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_biological object colony
type: Class
subclass of: Obsolete Class
definition: A biological object or group of biological objects in close spatial proximity.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
deprecated: true

herd immunity to infectious organism
type: Class
equivalent class: Class
  intersection of: collective resistance disposition
  intersection of: Restriction
    on property: inheres in
    some values from: organism population
  intersection of: Restriction
    on property: realized in
    all values from: Restriction
      on property: realizes
      some values from: immunity to infectious agent
subclass of: collective resistance disposition
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

physiologic immunosuppression
type: Class
subclass of: immunosuppression
definition: An immunosuppression which unfolds as part of the natural self-regulation of an immune response.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

derives into
type: ObjectProperty
example of usage: this parent cell derives into this cell (cell division)
example of usage: this parent nucleus derives into this nucleus (nuclear division)
has curation status: IAO_0000125
definition: 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
editor note: 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'.
alternative term: derives_into

role
type: Class
subclass of: realizable entity
BFO OWL specification label: role
BFO CLIF specification label: Role
example of usage: 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.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
definition: 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.
editor note: 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.
elucidation: 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])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

dead-end host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: dead-end host role
subclass of: host
definition: An organism bearing a dead-end host role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: incidental host

mutualist
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: mutualist role
subclass of: symbiont
definition: An organism bearing a mutualist role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

toxin disposition
type: Class
subclass of: disposition
subclass of: Restriction
  on property: inheres in
  some values from: molecular entity
disjoint with: adhesion disposition
disjoint with: invasion disposition
disjoint with: antimicrobial disposition
disjoint with: antiviral disposition
disjoint with: antifungal disposition
disjoint with: antibacterial disposition
disjoint with: antiparasitic disposition
disjoint with: protective resistance
disjoint with: pathogenic disposition
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

innate immune response
type: Class
subclass of: immune response
definition: Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
imported from: go.owl

_obsolete_colonization factor
type: Class
subclass of: Obsolete Class
definition: 'role played by portion of physical substance which promotes colonization'-ID[O]:0000054: role played by portion of physical substance which promotes colonization
editor note: id 'colonization factor'-ID[O]:0000054 from IDO 2007. May have replacement - TBD
deprecated: true

_obsolete_symptomatic host
type: Class
subclass of: Obsolete Class
definition: A host exhibiting disease symptoms.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
deprecated: true

histoplasmosis
type: Class
equivalent class: Class
  intersection of: fungal infectious disease
  intersection of: Restriction
    on property: has part
    some values from: histoplasma capsulatum
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: systemic mycosis
subclass of: fungal infectious disease
imported from: http://purl.obolibrary.org/obo/NCIT
has definition: 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 ]
comment: More info: https://doi.org/10.1007/82_2018_114

_obsolete_penetration of host cell
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_inactivated
type: Class
subclass of: Obsolete Class
deprecated: true

fonsecaea pedrosoi
type: Class
subclass of: dematiaceous fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1160224.08FU

term editor
type: AnnotationProperty
editor preferred term: term editor
has curation status: IAO_0000122
definition: 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
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

Axiom
annotated source: process
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

two-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 2d-cf-boundary
BFO CLIF specification label: TwoDimensionalContinuantFiatBoundary
elucidation: 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])
has associated axiom(fol): (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]

precedes
type: ObjectProperty
type: TransitiveProperty
domain: occurrent
range: occurrent
editor preferred term: precedes

_obsolete_mortality
type: Class
subclass of: Obsolete Class
deprecated: true

drug-based immunosuppression
type: Class
subclass of: pathologic immunosuppression
definition: A pathologic immunosuppression process which arises as the result of treatment with a drug that attenuates immune responses.
term editor: Alex Diehl
term editor: Lindsay Cowell

obligatory symbiont
type: Class
subclass of: symbiont
subclass of: Restriction
  on property: has role
  some values from: symbiont role
definition: An organism that can only reach developmental maturity, replicate, or persist in symbiosis.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

bearer of
type: ObjectProperty
range: specifically dependent continuant
editor preferred term: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: 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
editor note: 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.
alternative term: bearer_of
alternative term: is bearer of
temporal interpretation: axiom holds for all times

opportunistic fungal pathogen
type: Class
equivalent class: Class
  intersection of: fungal infectious agent
  intersection of: Restriction
    on property: has disposition
    some values from: opportunistic infectious disposition
subclass of: fungal infectious agent
term editor: Sydney Cohen
has definition: A fungal infectious agent that usually has an opportunistic infectious disposition.
comment: may include fungi that exist normally in healthy human flora, that have the capacity to cause infection

FtsZ-dependent cytokinesis
type: Class
subclass of: reproduction
definition: A cytokinesis process that involves a set of conserved proteins including FtsZ, and results in the formation of two similarly sized and shaped cells.
imported from: go.owl

transmission period
type: Class
subclass of: one-dimensional temporal region
definition: A continuous temporal interval during which a transmission process occurs.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

simple infection
type: Class
subclass of: infection
definition: An infection comprised of infectious organisms all of the same Species.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

syncephalastrum
type: Class
subclass of: mold
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH035111

colonized host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: part of
    some values from: Class
      intersection of: extended organism
      intersection of: Restriction
        on property: has part
        some values from: colony
subclass of: organism
definition: An organism that contains a colony in or on its extended organism.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

indirect
type: Class
subclass of: transmission process
definition: 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.
editor note: Suggested label: indirect pathogen transmission process
imported from: trans.owl

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

function of
type: ObjectProperty
sub property of: inheres in
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: 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.
alternative term: function_of
alternative term: is function of

inheres in
type: ObjectProperty
inverse of: bearer of
editor preferred term: inheres in
example of usage: this fragility inheres in this vase
example of usage: this red color inheres in this apple
definition: 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
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
alternative term: inheres_in
temporal interpretation: axiom holds for all times

vehicle of infectious agent
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: infectious agent vehicle role
subclass of: material entity
disjoint with: immunodeficiency
definition: A material entity bearing an infectious agent vehicle role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

neurotoxin
type: Class
subclass of: toxin
subclass of: Restriction
  on property: has disposition
  some values from: toxin disposition
definition: A molecular entity with a toxin disposition, the realization of which damages or interferes with the function of nerve tissue.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

normal resident microbiota population
type: Class
subclass of: organism population
definition: An organism population whose members are participating in non-parasitic symbiosis with a particular host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: normal resident microflora population

entry into host
type: Class
subclass of: multi-organism process
definition: 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.
imported from: go.owl

secondary infection role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: infectious disorder
disjoint with: host role
disjoint with: source of infection role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The role is realized in a process by which the infectious disorder is established in the host.

_obsolete_transcytosis
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

_obsolete_pathogen-induced apoptosis
type: Class
subclass of: Obsolete Class
deprecated: true

virion
type: Class
subclass of: Viruses
definition: A virus that is in its assembled state consisting of genomic material (DNA or RNA) surrounded by coating molecules.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_symbiant
type: Class
subclass of: Obsolete Class
deprecated: true

gastrointestinal mucormycosis
type: Class
equivalent class: Class
  intersection of: mucormycosis
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: systemic mycosis
subclass of: mucormycosis
term editor: Sydney Cohen
definition source: https://doi.org/10.1155/2020/8876125
has definition: 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.
comment: 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.

endogenous fungal endophthalmitis
type: Class
subclass of: endophthalmitis
term editor: Sydney Cohen
definition source: https://www.cdc.gov/fungal/diseases/fungal-eye-infections/definition.html
has definition: An endophthalmitis that is caused by a bloodstream infection (for example, candidemia) spreads to one or both eyes
has definition: An endophthalmitis that occurs when a bloodstream infection (for example, candidemia) spreads to one or both eyes

enterotoxin
type: Class
subclass of: exotoxin
subclass of: Restriction
  on property: has disposition
  some values from: exotoxin disposition
definition: A molecular entity with an exotoxin disposition, the realization of which damages cells of the host intestinal mucosa.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

Axiom
annotated source: disposition
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

collective pathogenic disposition
type: Class
equivalent class: Class
  intersection of: collective disposition
  intersection of: Restriction
    on property: inheres in
    some values from: object aggregate
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: results in formation of
        some values from: disorder
subclass of: collective disposition
disjoint with: collective resistance disposition
definition: A collective disposition to initiate processes that result in a disorder.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The disposition is realized in processes that create a disorder.

biological vector of infectious agent role
type: Class
subclass of: infectious agent vector role
subclass of: Class
  intersection of: infectious agent vector role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: location of
        some values from: Class
  intersection of: Restriction
    on property: realized in
    all values from: indirect
definition: An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent multiplies in the vector.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

Axiom
annotated source: process profile
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

_obsolete_seroprevalence
type: Class
subclass of: Obsolete Class
definition: 'prevalence as measured by antibody'-ID[O]:0000208: prevalence as measured by antibody
editor note: id 'seroprevalence'-ID[O]:0000208 from IDO 2007. May have replacement - TBD
deprecated: true

resistance to drug
type: Class
subclass of: protective resistance
disjoint with: resistance to infectious agent
definition: A protective resistance that mitigates the damaging effects of a drug.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: drug resistance

Axiom
annotated source: temporal region
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

_obsolete_resistance
type: Class
subclass of: Obsolete Class
deprecated: true

infectious agent portal of exit role
type: Class
subclass of: role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: anatomical entity
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: part of
        some values from: transmission process
disjoint with: disinfectant role
disjoint with: antiseptic role
disjoint with: primary infection role
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The role is realized in a process by which an infectious agent exists a host.

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

Axiom
annotated source: relational quality
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

_obsolete_symptom
type: Class
subclass of: Obsolete Class
definition: '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
editor note: id 'symptom'-ID[O]:0000048 from IDO 2007. May have replacement - TBD
deprecated: true

Axiom
annotated source: one-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

mutualist role
type: Class
subclass of: symbiont role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: participates in
      some values from: mutualism
definition: A symbiont role borne by an organism in virtue of the fact that both symbionts derive a growth, survival, or fitness advantage from symbiosis.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The role is realized in processes that result in the growth, survival, or fitness advantage of either organism.

virulence factor disposition
type: Class
subclass of: disposition
subclass of: Restriction
  on property: inheres in
  some values from: molecular entity
disjoint with: toxin disposition
disjoint with: adhesion disposition
disjoint with: invasion disposition
disjoint with: antimicrobial disposition
disjoint with: antiviral disposition
disjoint with: antifungal disposition
disjoint with: antibacterial disposition
disjoint with: antiparasitic disposition
disjoint with: protective resistance
disjoint with: pathogenic disposition
disjoint with: invasive disposition
disjoint with: collective disposition
disjoint with: contagiousness
disjoint with: immunocompetence
disjoint with: immunosuppressive disposition
disjoint with: disposition to form a non-parasitic colony
disjoint with: transmissibility disposition
disjoint with: disease
definition: A disposition borne by a biological macromolecule produced by a pathogen that is a disposition to undergo processes that increase the pathogen's virulence.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

madurella
type: Class
subclass of: dematiaceous fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH033035

has obsolescence reason
type: AnnotationProperty
editor preferred term: has obsolescence reason
definition: 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.
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot

infectious disposition
type: Class
subclass of: pathogenic disposition
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Restriction
        on property: has part
        some values from: establishment of localization in host
      intersection of: Restriction
        on property: has part
        some values from: appearance of disorder
      intersection of: Restriction
        on property: has part
        some values from: transmission process
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

mechanical vector of infectious agent role
type: Class
subclass of: infectious agent vector role
subclass of: Class
  intersection of: infectious agent vector role
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: organism
      intersection of: Restriction
        on property: location of
        some values from: Class
  intersection of: Restriction
    on property: realized in
    all values from: indirect
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infectious agent portal of entry
type: Class
equivalent class: Class
  intersection of: anatomical entity
  intersection of: Restriction
    on property: has role
    some values from: infectious agent portal of entry role
subclass of: anatomical entity
definition: An anatomical entity bearing an infectious agent portal of entry role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

contains process
type: ObjectProperty
editor preferred term: site of
definition: [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
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

definitive host role
type: Class
subclass of: symbiont host role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: primary host role
comment: The role is realized in developmental and reproduction processes of the host's partner in symbiosis.

object aggregate
type: Class
subclass of: material entity
BFO OWL specification label: object-aggregate
BFO CLIF specification label: ObjectAggregate
example of usage: a collection of cells in a blood biobank.
example of usage: a swarm of bees is an aggregate of members who are linked together through natural bonds
example of usage: a symphony orchestra
example of usage: 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)
example of usage: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
example of usage: defined via attributive delimitations such as: the patients in this hospital
example of usage: the aggregate of bearings in a constant velocity axle joint
example of usage: the aggregate of blood cells in your body
example of usage: the nitrogen atoms in the atmosphere
example of usage: the restaurants in Palo Alto
example of usage: your collection of Meissen ceramic plates.
editor note: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
editor note: 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).
definition source: 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.
elucidation: 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])
has associated axiom(fol): (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]

_obsolete_infection treatment process
type: Class
subclass of: Obsolete Class
deprecated: true

long-term non-progressor
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property:
      inverse of: occurs in
    some values from: long-term non-progressing infectious disease course
subclass of: organism
definition: An organism experiencing a long-term non-progressing infectious disease course.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

immunosuppressed organism experiencing HIV-based immunosuppression
type: Class
subclass of: immunosuppressed organism experiencing infection-based immunosuppression
definition: A pathologically immunosuppressed organism that is experiencing HIV-based immunosuppression.
editor note: These individuals may also be immunodeficient due to depletion of CD4+ T cells and other effects of HIV.
term editor: Alex Diehl
term editor: Lindsay Cowell

definitive host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: definitive host role
subclass of: host
definition: An organism bearing a definitive host role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: primary host

disinfectant
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: disinfectant role
subclass of: material entity
disjoint with: infection
disjoint with: organism
disjoint with: disorder
definition: A material entity bearing a disinfectant role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

vaccination against infectious agent
type: Class
subclass of: active immunization against infectious agent
definition: An active immunization that begins with exposure of an organism to a vaccine.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

local infection
type: Class
subclass of: infection
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

acquired immunodeficiency
type: Class
subclass of: immunodeficiency
disjoint with: primary immunodeficiency
definition: An immunodeficiency that is not caused by a genetic predisposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: Causes of acquired immunodeficiences include infection and drug treatments (e.g. chemotherapy).

cryptococcus gatti
type: Class
equivalent class: Class
  intersection of: primary fungal pathogen
  intersection of: cryptococcus
subclass of: cryptococcus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH396686.07FU
comment: source for primary fungal pathogen classification: https://www.ncbi.nlm.nih.gov/books/NBK431060/

_obsolete_fomite
type: Class
subclass of: Obsolete Class
definition: 'inanimate holder, is water a fomite or only a reservoir?'-ID[O]:0000060: inanimate holder, is water a fomite or only a reservoir?
editor note: id 'fomite'-ID[O]:0000060 from IDO 2007. May have replacement - TBD
deprecated: true

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

example of usage
type: AnnotationProperty
editor preferred term: example
has curation status: IAO_0000122
definition: 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.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

is denotator type
type: AnnotationProperty
editor preferred term: is denotator type
definition: relates an class defined in an ontology, to the type of it's denotator
editor note: In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
term editor: Alan Ruttenberg

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

_obsolete_epidemic
type: Class
subclass of: Obsolete Class
deprecated: true

resistance to infectious agent
type: Class
subclass of: protective resistance
subclass of: Restriction
  on property: inheres in
  some values from: organism
definition: A protective resistance that inheres in an organism and mitigates the damaging effects on that organism of an infectious agent.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

neoscytalidium dimidiatum
type: Class
subclass of: dematiaceous fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1507445.08FU

_obsolete_penetration of epithelial barrier
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000001
comment: requested by Melanie Courtot

_obsolete_incidence
type: Class
subclass of: Obsolete Class
definition: 'number of new cases in a given period of time'-ID[O]:0000029: number of new cases in a given period of time
editor note: id 'incidence'-ID[O]:0000029 from IDO 2007. May have replacement - TBD
deprecated: true

Homo sapiens
type: Class
subclass of: Eukaryota
imported from: ncbitaxon.owl

macromolecular complex
type: Class
subclass of: material entity
definition: 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.
imported from: go.owl

fungal eye infection
type: Class
equivalent class: Class
  intersection of: fungal infectious disease
  intersection of: Class
    union of: Restriction
      on property: has_material_basis_in
      some values from: cutaneous mycosis
    union of: Restriction
      on property: has_material_basis_in
      some values from: systemic mycosis
    union of: Restriction
      on property: has_material_basis_in
      some values from: superficial mycosis
    union of: Restriction
      on property: has_material_basis_in
      some values from: subcutaneous mycosis
subclass of: fungal infectious disease
imported from: http://purl.obolibrary.org/obo/MONDO
has definition: 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 ]

drug susceptibility of infectious agent
type: Class
subclass of: drug susceptibility
subclass of: Restriction
  on property: inheres in
  some values from: infectious agent
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

cutaneous sporotrichosis
type: Class
equivalent class: Class
  union of: Class
    intersection of: sporotrichosis
    intersection of: Restriction
      on property: has_material_basis_in
      some values from: cutaneous mycosis
  union of: Restriction
    on property: has_material_basis_in
    some values from: subcutaneous mycosis
subclass of: sporotrichosis
term editor: Sydney Cohen
definition source: https://www.cdc.gov/fungal/diseases/sporotrichosis/index.html
has definition: 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.
comment: most common form of the infection. It usually occurs on a person’s hand or the arm after touching contaminated plant matter.

dead-end host role
type: Class
subclass of: symbiont host role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: incidental host role

parasite role
type: Class
subclass of: symbiont role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: In the medical community, the term 'parasite' is used with the narrower meaning of eukaryotic pathogen.
comment: 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.

has disposition
type: ObjectProperty
sub property of: bearer of
inverse of: disposition of
domain: independent continuant
range: disposition
definition: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

_obsolete_utilization of membranous cell gateway
type: Class
subclass of: Obsolete Class
deprecated: true

infectious agent portal of exit
type: Class
equivalent class: Class
  intersection of: anatomical entity
  intersection of: Restriction
    on property: has role
    some values from: infectious agent portal of exit role
subclass of: anatomical entity
definition: An anatomical entity bearing an infectious agent portal of exit role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

variolation
type: Class
subclass of: active immunization against infectious agent
definition: An active immunization that begins with exposure to smallpox in the form of a scab from a pustule and results in immunity against smallpox.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

definition
type: AnnotationProperty
editor preferred term: definition
has curation status: IAO_0000122
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.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 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.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: textual definition

two-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 2d-s-region
BFO CLIF specification label: TwoDimensionalSpatialRegion
example of usage: an infinitely thin plane in space.
example of usage: the surface of a sphere-shaped part of space
elucidation: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has associated axiom(fol): (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]

_obsolete_vaccination
type: Class
subclass of: Obsolete Class
deprecated: true

antimicrobial
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has disposition
    some values from: antimicrobial disposition
subclass of: material entity
disjoint with: infection
disjoint with: disorder
definition: A material entity with an antimicrobial disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

host living in endemic area
type: Class
subclass of: host exposure to environment containing infectious agent
definition: A host exposure to environment with infectious agent where the environment is an area in which an infectious agent is endemic
editor note: Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern

sepsis
type: Class
subclass of: process
definition: A process that is a systemic inflammatory response to infection.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

transmission process
type: Class
subclass of: process
definition: 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.
editor note: Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species.
editor note: Suggested label: pathogen transmission process
imported from: trans.owl
imported from: Transmission Ontology: http://purl.obolibrary.org/obo/trans.owl

pregnancy-induced immunosuppression
type: Class
subclass of: immunosuppression
definition: An immunosuppression induced by progesterone and other factors upregulated in pregnant women.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

adaptive immune response
type: Class
subclass of: immune response
definition: 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).
imported from: go.owl

immunization against infectious agent
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: has output
    some values from: Restriction
      on property:
        inverse of: has_material_basis_in
      some values from: immunity to infectious agent
subclass of: process
definition: A process by which an organism acquires immunity to an infectious agent.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

chronic infection
type: Class
subclass of: infection
definition: An infection that persists for an extended period of time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: persistent infection

T cell receptor complex
type: Class
subclass of: macromolecular complex
definition: 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.
imported from: go.owl

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002

developmental process
type: Class
subclass of: biological_process
definition: 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.
imported from: go.owl

_obsolete_antigenic variation
type: Class
subclass of: Obsolete Class
deprecated: true

leukocyte
type: Class
subclass of: cell
definition: An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
imported from: cl.owl

has part
type: ObjectProperty
type: TransitiveProperty
sub property of: topObjectProperty
editor preferred term: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: 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.
editor note: 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
editor note: 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'.
alternative term: has_part
temporal interpretation: axiom holds for all times

chronic pulmonary aspergillosis
type: Class
equivalent class: Class
  intersection of: chronic infection
  intersection of: Class
    intersection of: aspergillosis
    intersection of: Restriction
      on property: has_material_basis_in
      some values from: systemic mycosis
  intersection of: Restriction
    on property: has part
    some values from: aspergilloma
subclass of: aspergillosis
imported from: http://purl.obolibrary.org/obo/NCIT
has definition: 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 ]
comment: 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

negative regulation of developmental process
type: Class
subclass of: biological regulation
definition: 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).
imported from: go.owl

_obsolete_initiation of infection
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_passage through cell membrane
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_enterotoxin disposition
type: Class
subclass of: exotoxin disposition
subclass of: Obsolete Class
definition: An exotoxin disposition to damage cells of the host intestinal mucosa.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
label: enterotoxin disposition
deprecated: true

infectious disease pandemic
type: Class
subclass of: process
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

entity
type: Class
subclass of: Thing
BFO OWL specification label: entity
BFO CLIF specification label: Entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
editor note: 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
editor note: 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
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

_obsolete_pathogen
type: Class
subclass of: Obsolete Class
deprecated: true

biological vector of infectious agent
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: biological vector of infectious agent role
subclass of: infectious agent vector
definition: An infectious agent vector bearing a biological vector of infectious agent role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

sterilizing immunity to infectious agent
type: Class
subclass of: immunity to infectious agent
definition: An immunity to infectious agent that results in elimination of the infectious agent from the host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: Sterilizing immunity is typically conferred by neutralizing antibodies.

aspergillus flavus
type: Class
subclass of: aspergillus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1165051.08FU

incubation period
type: Class
subclass of: one-dimensional temporal region
definition: A continuous temporal interval beginning with the extablishment of an infectious agent colony and ending with the onset of symptoms (or infectious disease course?).
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

innate immunity to infectious agent
type: Class
subclass of: immunity to infectious agent
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: realized in
    all values from: innate immune response
definition: An immunity to infectious agent that inheres in an organism in virtue of germline encoded components that directly recognize components of potential pathogens.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The disposition is realized in an innate immune response.

scedosporium boydii
type: Class
equivalent class: Class
  intersection of: mold
  intersection of: opportunistic fungal pathogen
subclass of: mold
subclass of: scedosporium
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH349490.07FU
has related synonym: formerly known as Pseudallescheria boydii

_obsolete_viral latency
type: Class
subclass of: Obsolete Class
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
deprecated: true

has quality
type: ObjectProperty
sub property of: bearer of
range: quality
example of usage: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: 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.
alternative term: has_quality

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

humoral immunity to infectious agent
type: Class
subclass of: immunity to infectious agent
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: organism
  intersection of: Restriction
    on property: realized in
    all values from: humoral immune response
definition: An immunity to infectious agent that inheres in an organism in virtue of components of its circulating body fluid.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: "Circulating body fluid" refers to blood, lymph, and hemolymph.
comment: The disposition is realized in a humoral immune response.

disposition
type: Class
subclass of: realizable entity
disjoint with: role
BFO OWL specification label: disposition
BFO CLIF specification label: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: 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.
elucidation: 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])
has associated axiom(nl): 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])
has associated axiom(fol): (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]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

reverse zoonotic disposition
type: Class
subclass of: infectious disposition
definition: An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis.

susceptible organism
type: Class
subclass of: organism
definition: An organism that is not infected with an infectious agent and lacks protective immunity to the infectious agent.
term editor: Alex Diehl
term editor: Lindsay Cowell

pathogen host
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: pathogen host role
subclass of: host
definition: An organism bearing a pathogen host role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

onychomycosis
type: Class
equivalent class: Class
  intersection of: fungal infectious disease
  intersection of: Class
    union of: Restriction
      on property: has_material_basis_in
      some values from: cutaneous mycosis
    union of: Restriction
      on property: has_material_basis_in
      some values from: subcutaneous mycosis
  intersection of: Restriction
    on property: has part
    some values from: fungus
subclass of: fungal infectious disease
has definition: A fungal infectious disease that tends to cause finger-nails or toe-nails to thicken, discolor, disfigure, and split. [ HPO : probinson ]

_obsolete_oral-fecal transmission
type: Class
subclass of: Obsolete Class
deprecated: true

esophageal candidiasis
type: Class
subclass of: candidiasis
imported from: http://purl.obolibrary.org/obo/MONDO
has definition: A candidiasis that results in esophagitis. [ NCIT : P378 ]

Axiom
annotated source: generically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

potential host of infectious agent
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has disposition
    some values from: Restriction
      on property: realized in
      some values from: Restriction
        on property: realizes
        some values from: infectious agent host role
subclass of: organism
definition: An organism that has the capability to bear a host of infectious agent role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_prevention of infection
type: Class
subclass of: Obsolete Class
deprecated: true

release of infectious human pathogen in laboratory
type: Class
subclass of: host exposure to environment containing infectious agent
definition: 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.
editor note: Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern

expand expression to
type: AnnotationProperty
editor preferred term: expand expression to
example of usage: 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)"
definition: 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
term editor: Chris Mungall

severe sepsis
type: Class
subclass of: sepsis
definition: A sepsis that results in organ dysfunction, hypotension, or hypofusion of at least one organ.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

infectious agent host role
type: Class
subclass of: pathogen host role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: part of
      some values from: Class
        intersection of: extended organism
        intersection of: Restriction
definition: A pathogen host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: By this definition, vectors and other organisms that may not be infected are bearers of the infectious agent host role.

Axiom
annotated source: disposition
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

host exposure to substance that might have infectious agent
type: Class
subclass of: host exposure to environment containing infectious agent
definition: 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.
editor note: Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern

Axiom
annotated source: process profile
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

immunosuppression
type: Class
equivalent class: Class
  intersection of: process
  intersection of: Restriction
    on property: negatively regulates
    some values from: immune response
subclass of: process
definition: A process that attenuates an immune response.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

_obsolete_biotic
type: Class
subclass of: Obsolete Class
deprecated: true

immunosuppressed human experiencing chronic systemic steroid use-based immunosuppression
type: Class
subclass of: immunosuppressed organism experiencing chronic systemic steroid use-based immunosuppression
definition: An immunosuppressed organism that is a human experiencing chronic systemic steroid use-based immunosuppression.
term editor: Alex Diehl
term editor: Lindsay Cowell
ontology term requester: NCI BBRB

immunocompetent organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has disposition
    some values from: immunocompetence
subclass of: organism
disjoint with: immunodeficient organism
definition: An organism that has immunocompetence.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infection prevalence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

process boundary
type: Class
subclass of: occurrent
BFO OWL specification label: p-boundary
BFO CLIF specification label: ProcessBoundary
example of usage: the boundary between the 2nd and 3rd year of your life.
definition: 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])
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has associated axiom(fol): (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
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]

long-term non-progressing infectious disease course
type: Class
subclass of: chronic infectious disease course
definition: A chronic infectious disease course that does not progress to severe stages for a long period of time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_process
type: Class
subclass of: Obsolete Class
deprecated: true

acute infectious disease course
type: Class
subclass of: infectious disease course
definition: An infectious disease course that begins soon after infection is established and progresses rapidly to severe stages.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

parasite
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: parasite role
subclass of: symbiont
definition: A organism bearing a parasite role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

shorthand
type: AnnotationProperty

member of
type: ObjectProperty
sub property of: part of
inverse of: has member
example of usage: An organism that is a member of a population of organisms
definition: is member of is a mereological relation between a item and a collection.
alternative term: is member of
alternative term: member part of
definition source: SIO
temporal interpretation: axiom holds for all times

endotoxin
type: Class
subclass of: toxin
subclass of: Restriction
  on property: has disposition
  some values from: toxin disposition
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

has axiom label
type: AnnotationProperty
editor preferred term: has axiom id
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: 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

antiseptic role
type: Class
subclass of: role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: Class
      intersection of: material entity
      intersection of: Restriction
        on property: has disposition
        some values from: antimicrobial disposition
  intersection of: Restriction
    on property: realized in
    all values from: Class
      intersection of: process
      intersection of: Class
        union of: Restriction
disjoint with: primary infection role
disjoint with: secondary infection role
disjoint with: host role
disjoint with: source of infection role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The role is realized in the killing and/or growth inhibition of microorganisms on the anatomical entity.

_obsolete_object
type: Class
subclass of: Obsolete Class
deprecated: true

microbicide
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has disposition
    some values from: Class
      intersection of: antimicrobial disposition
      intersection of: Restriction
        on property: realized in
        all values from: Restriction
subclass of: antimicrobial
definition: A material entity with an antimicrobial disposition that is realized in a process of killing microorganisms.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: microbicidal [entity]

echinocandin
type: Class
subclass of: antifungal
definition source: https://doi.org/10.3390/genes9090461
has definition: 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.

active immunization against infectious agent
type: Class
subclass of: immunization against infectious agent
definition: An immunization that begins with exposure of an organism to antigen and results in immunity against an infectious agent.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: inoculation

_obsolete_afimbrial specific adherence
type: Class
subclass of: Obsolete Class
deprecated: true

ringworm
type: Class
equivalent class: Class
  intersection of: fungal infectious disease
  intersection of: Restriction
    on property: has part
    some values from: fungus
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: cutaneous mycosis
subclass of: fungal infectious disease
imported from: http://purl.obolibrary.org/obo/DOID
has definition: 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.
has related synonym: dermatophytosis
has related synonym: tinea
has related synonym: tinea capitis

commensal role
type: Class
subclass of: symbiont role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: participates in
      some values from: commensalism
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The role is realized in processes that result in the commensal's growth, survival, or fitness advantage.

_obsolete_reservoir
type: Class
subclass of: Obsolete Class
definition: 'holding place for a potential pathogen...animate or inanimate'-ID[O]:0000059: holding place for a potential pathogen...animate or inanimate
editor note: id 'reservoir'-ID[O]:0000059 from IDO 2007. May have replacement - TBD
deprecated: true

Axiom
annotated source: entity
annotated property: elucidation
annotated target: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/001-001

OBO foundry unique label
type: AnnotationProperty
editor preferred term: OBO foundry unique label
has curation status: IAO_0000125
definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: 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 .
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

intermediate host role
type: Class
subclass of: symbiont host role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: secondary host role
comment: The role is realized in developmental processes of the host's partner in symbiosis.

_obsolete_damaging host cells and tissues in subepithelial space
type: Class
subclass of: Obsolete Class
deprecated: true

allergic bronchopulmonary aspergillosis
type: Class
subclass of: allergic aspergillosis
imported from: http://purl.obolibrary.org/obo/NCIT
has definition: An allergic aspergillus that primarily affects patients suffering from asthma or cystic fibrosis. [ NCI ]
comment: Occurs when Aspergillus causes inflammation in the lungs and allergy symptoms such as coughing and wheezing, but doesn’t necessarily cause an infection

azole
type: Class
subclass of: antifungal
definition source: https://doi.org/10.3390/genes9090461
has definition: 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.
comment: excessive use of azoles for treatment and in agriculture is a contributor to increased antifungal resistance

direct host exposure to infectious agent
type: Class
subclass of: host exposure to infectious agent
definition: A process in which a potential host of an infectious agent comes into direct physical contact with the infectious agent.
term editor: Bjoern Peters

_obsolete_quality of pathogen
type: Class
subclass of: Obsolete Class
deprecated: true

horizontal pathogen transmission process
type: Class
subclass of: transmission process
definition: 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.
term editor: Lindsay Cowell

microbistatic
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has disposition
    some values from: Class
      intersection of: antimicrobial disposition
      intersection of: Restriction
        on property: realized in
        all values from: Class
subclass of: antimicrobial
definition: A material entity with an antimicrobial disposition that is realized in a process of inhibiting the growth of microorganisms.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_transmission
type: Class
subclass of: Obsolete Class
definition: '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
editor note: id 'transmission'-ID[O]:0000083 from IDO 2007. May have replacement - TBD
deprecated: true

_obsolete_pathogenesis
type: Class
subclass of: Obsolete Class
definition: '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.
editor note: id 'pathogenesis'-ID[O]:0000084 from IDO 2007. May have replacement - TBD
deprecated: true

_obsolete_drug resistance
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_adhesin
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_tropism
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: three-dimensional spatial region
annotated property: elucidation
annotated target: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000012

one-dimensional temporal region
type: Class
subclass of: temporal region
disjoint with: zero-dimensional temporal region
BFO OWL specification label: 1d-t-region
BFO CLIF specification label: OneDimensionalTemporalRegion
example of usage: the temporal region during which a process occurs.
editor note: 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).
elucidation: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]

acute infection
type: Class
equivalent class: Class
  intersection of: infectious disorder
  intersection of: Restriction
    on property:
      inverse of: has_material_basis_in
    some values from: Restriction
      on property: realized in
      some values from: acute infectious disease course
subclass of: infectious disorder
definition: An infectious disorder that is the physical basis for an unfolding acute infectious disease course.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

symbiont host role
type: Class
subclass of: host role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: organism
    intersection of: Restriction
      on property: part of
      some values from: Class
        intersection of: extended organism
        intersection of: Restriction
disjoint with: pathogen host role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: The relevant environmental resources may include nutrient resources, warmth, or moisture.
comment: 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.

cell
type: Class
subclass of: anatomical entity
definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
imported from: cl.owl

_obsolete_infectious disease progression
type: Class
subclass of: Obsolete Class
definition: '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?
editor note: id 'infectious disease progression'-ID[O]:0000221 from IDO 2007. May have replacement - TBD
deprecated: true

Axiom
annotated source: object aggregate
annotated property: definition source
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000300

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

generically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
example of usage: 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.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: 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.
definition: 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])
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

_obsolete_resist phagocytosis in subepithelial space
type: Class
subclass of: Obsolete Class
deprecated: true

virulence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: infectious agent
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: This quality is measured by the proportion of clinically apparent cases that are severe or fatal.

Axiom
annotated source: two-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

host coming into contact with vector of infectious agent
type: Class
subclass of: host exposure to environment containing infectious agent
definition: A host exposure to environment with infectious agent where the environment contains an infectious agent vector.
editor note: Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern

_obsolete_carrier
type: Class
subclass of: Obsolete Class
deprecated: true

cutaneous mycosis
type: Class
subclass of: mycosis
imported from: http://purl.obolibrary.org/obo/MONDO
has definition: 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 ]
has related synonym: dermatomycosis
has related synonym: dermatophyte infections
has related synonym: tinea

history
type: Class
subclass of: process
BFO OWL specification label: history
BFO CLIF specification label: History
elucidation: 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])

_obsolete_induction of damaging host immune response
type: Class
subclass of: Obsolete Class
deprecated: true

opisthokonta
type: Class
subclass of: Eukaryota
editor note: changed label to lowercase per best practice
imported from: http://purl.obolibrary.org/obo/NCBITaxon

_obsolete_emergence
type: Class
subclass of: Obsolete Class
definition: '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)
editor note: id 'emergence'-ID[O]:0000101 from IDO 2007. May have replacement - TBD
deprecated: true

Axiom
annotated source: BFO_0000134
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/081-003

scedosporium
type: Class
subclass of: dematiaceous fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH032948

has 2D boundary
type: ObjectProperty
domain: material entity
range: immaterial entity
example of usage: my body has 2D boundary the surface of my skin
definition: a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
editor note: A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
editor note: Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
alternative term: has boundary
alternative term: has_2D_boundary
temporal interpretation: axiom holds for all times

editor preferred term
type: AnnotationProperty
editor preferred term: editor preferred term
has curation status: IAO_0000122
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

Obsolete Class
type: Class
subclass of: Thing

three-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 3d-s-region
BFO CLIF specification label: ThreeDimensionalSpatialRegion
example of usage: a cube-shaped region of space
example of usage: a sphere-shaped region of space,
elucidation: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has associated axiom(fol): (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]

_obsolete_endotoxin
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

pyrimidine analog
type: Class
subclass of: antifungal
definition source: https://doi.org/10.3390/genes9090461
has definition: 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.
comment: 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

BFO OWL specification label
type: AnnotationProperty
definition: 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.
curator note: Really of interest to developers only
sub property of: label

immunoglobulin complex
type: Class
subclass of: macromolecular complex
definition: 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.
imported from: go.owl

_obsolete_infectious disease progression stage
type: Class
subclass of: Obsolete Class
deprecated: true

opportunistic pathogen
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has disposition
    some values from: opportunistic infectious disposition
subclass of: infectious agent
definition: An infectious agent with an opportunistic infectious disposition.
term editor: Albert Goldfain
term editor: Alex Diehl
term editor: Lindsay Cowell
alternative term: opportunist

fomite role
type: Class
subclass of: infectious agent vehicle role
definition: An infectious agent vehicle role borne by an entity in virtue of the fact that the entity is not alive.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: object aggregate
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

commensalism
type: Class
subclass of: symbiosis, encompassing mutualism through parasitism
definition: 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.
imported from: go.owl

symptom
type: Class
subclass of: entity
definition: 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.
imported from: ogms.owl

aspergilloma
type: Class
equivalent class: Class
  union of: opportunistic fungal pathogen
  union of: Restriction
    on property: has disposition
    some values from: primary fungal pathogen
subclass of: aspergillosis
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4531547/ doi: 10.3904/kjim.2004.19.1.38
has definition: 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.”
has exact synonym: pulmonary aspergilloma
comment: usually develops in the patients with underlying lung diseases

adhesion factor
type: Class
equivalent class: Class
  intersection of: molecular entity
  intersection of: Restriction
    on property: has disposition
    some values from: adhesion disposition
subclass of: molecular entity
definition: A biological macromolecule that has an adhesion disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: adhesin
alternative term: adhesion molecule

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: object aggregate
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: 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.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

alternaria
type: Class
subclass of: dematiaceous fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH030639

process of establishing an infection
type: Class
subclass of: process
definition: A process by which an infectious agent, established in a host, becomes part of an infection in the host.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

blood
type: Class
subclass of: anatomical entity
definition: A fluid that is composed of blood plasma and erythrocytes.
imported from: uberon.owl

_obsolete_adhesion factor
type: Class
subclass of: Obsolete Class
definition: '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
editor note: id 'adhesion factor'-ID[O]:0000055 from IDO 2007. May have replacement - TBD
deprecated: true

_obsolete_pathogen spread through host
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: process
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

positively regulates
type: ObjectProperty
sub property of: regulates
definition: x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y
term editor: Chris Mungall
definition source: causal-relations
OBO foundry unique label: positively regulates (process to process)

immunosuppressed organism
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: participates in
    some values from: Class
      union of: pathologic immunosuppression
      union of: pregnancy-induced immunosuppression
subclass of: organism
disjoint with: immunocompetent organism
definition: An organism that is experiencing pregnancy-induced or pathologic immunosuppression.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

adhesion of symbiont to host
type: Class
subclass of: biological_process
definition: 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.
imported from: go.owl

_obsolete_genetic diversification
type: Class
subclass of: Obsolete Class
deprecated: true

infection incidence proportion
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: cumulative incidence of infection
comment: 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.

_obsolete_pathogen evasion of host immune response
type: Class
subclass of: Obsolete Class
deprecated: true

term tracker item
type: AnnotationProperty
editor preferred term: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
has curation status: IAO_0000125
definition: An IRI or similar locator for a request or discussion of an ontology term.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.

Axiom
annotated source: two-dimensional spatial region
annotated property: elucidation
annotated target: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

_obsolete_disruption of normal microbioflora
type: Class
subclass of: Obsolete Class
deprecated: true

cryptococcus
type: Class
equivalent class: Class
  intersection of: dimorphic fungus
  intersection of: yeast
subclass of: yeast
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH034644
comment: 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/

_obsolete_chronic carrier
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: quality
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

pulmonary sporotrichosis
type: Class
equivalent class: Class
  intersection of: sporotrichosis
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: systemic mycosis
subclass of: sporotrichosis
term editor: Sydney Cohen
has definition: 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.
comment: adding specificity to orphanet parent term
comment: is rare but can happen after someone breathes in fungal spores from the environment.

_obsolete_invasive
type: Class
subclass of: Obsolete Class
deprecated: true

cryptococcus neoformans
type: Class
equivalent class: Class
  intersection of: opportunistic fungal pathogen
  intersection of: cryptococcus
subclass of: cryptococcus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1178825.08FU
comment: source for opportunistic fungal pathogen classification: https://www.ncbi.nlm.nih.gov/books/NBK431060/

Axiom
annotated source: site
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002

yeast
type: Class
subclass of: fungus
imported from: http://purl.obolibrary.org/obo/NCIT
has definition: 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.
comment: A non-taxonomic grouping of fungi that are single-celled.
comment: 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 ]

focal infection
type: Class
subclass of: local infection
definition: A local infection for which symptoms are observed in parts of the host's extended organism that are distant from the infection.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_toxin
type: Class
subclass of: Obsolete Class
deprecated: true

term replaced by
type: AnnotationProperty
editor preferred term: term replaced by
has curation status: IAO_0000125
definition: Add as annotation triples in the granting ontology
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg

alternative term
type: AnnotationProperty
editor preferred term: alternative term
has curation status: IAO_0000125
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

Axiom
annotated source: occurrent
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/077-002

role of
type: ObjectProperty
sub property of: inheres in
inverse of: has role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: 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.
alternative term: is role of
alternative term: role_of

_obsolete_medicine
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_endotoxin disposition
type: Class
subclass of: toxin disposition
subclass of: Obsolete Class
definition: 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.
definition: A toxin disposition that inheres in a protein or protein complex that is released from a pathogen only upon cytolysis.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
label: endotoxin disposition
deprecated: true

_obsolete_commensal
type: Class
subclass of: Obsolete Class
deprecated: true

cytotoxin
type: Class
subclass of: toxin
subclass of: Restriction
  on property: has disposition
  some values from: toxin disposition
definition: A molecular entity with a toxin disposition, the realization of which damages host cells.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_refractoriness
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: one-dimensional temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

allylamines
type: Class
subclass of: antifungal
term editor: Sydney Cohen
definition source: https://doi.org/10.1016/0190-9622(90)70288-s
definition source: https://www.merckvetmanual.com/pharmacology/antifungal-agents/allylamines-for-use-in-animals
has definition: 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.
comment: These agents are highly selective for the fungal enzyme and have a minimal effect on mammalian cholesterol synthesis.

_obsolete_fusion protein
type: Class
subclass of: Obsolete Class
deprecated: true

dematiaceous fungus
type: Class
equivalent class: Class
  intersection of: fungus
  intersection of: fungal infectious agent
equivalent class: Class
  union of: opportunistic fungal pathogen
  union of: primary fungal pathogen
subclass of: fungus
has definition: 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.
has related synonym: dematiaceous fungi
comment: more info: https://doi.org/10.1179/joc.2003.15.Supplement-2.36

_obsolete_antimicrobial
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

Axiom
annotated source: relational quality
annotated property: definition
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

systemic mycosis
type: Class
subclass of: mycosis
imported from: http://purl.obolibrary.org/obo/MONDO
has definition: A mycosis that involves the lungs, abdominal viscera, bones and or central nervous system. [ https://www.ncbi.nlm.nih.gov/books/NBK7902 ]
has exact synonym: deep mycosis
comment: Usually follow inhalation (or via or gastrointestinal tract or blood vessels) and may be subsequent to primary pulmonary infections

has ID range allocated to
type: AnnotationProperty
example of usage: Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300]
definition: 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
term editor: Person:Alan Ruttenberg

first order logic expression
type: AnnotationProperty
editor preferred term: first order logic expression
term editor: PERSON:Alan Ruttenberg

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

_obsolete_immunity
type: Class
subclass of: Obsolete Class
deprecated: true

zero-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 0d-cf-boundary
BFO CLIF specification label: ZeroDimensionalContinuantFiatBoundary
example of usage: the geographic North Pole
example of usage: the point of origin of some spatial coordinate system.
example of usage: the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
editor note: 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.
elucidation: 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])
has associated axiom(fol): (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]

location of
type: ObjectProperty
type: TransitiveProperty
inverse of: located in
editor preferred term: is location of
example of usage: my head is the location of my brain
example of usage: this cage is the location of this rat
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
editor note: 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
alternative term: location_of
temporal interpretation: axiom holds for all times

reproduction
type: Class
subclass of: biological_process
definition: The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
imported from: go.owl

dimorphic fungus
type: Class
subclass of: fungus
editor note: changed label to singular dimorphic fungus per best practices
imported from: http://purl.obolibrary.org/obo/NCIT
has definition: A fungus that grows as either a yeast or a mold. [ NCI ]
has related synonym: dimorphic fungi

results_in
type: ObjectProperty

madurella mycetomatis
type: Class
equivalent class: Class
  intersection of: mold
  intersection of: primary fungal pathogen
subclass of: mold
subclass of: madurella
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1331956.08FU

realizes
type: ObjectProperty
domain: process
range: realizable entity
editor preferred term: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
elucidation: 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])
comment: 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

infection incidence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

_obsolete_pathogenicity island
type: Class
subclass of: Obsolete Class
deprecated: true

infectious disease incidence rate
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

Axiom
annotated source: temporal region
annotated property: editor note
annotated target: 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
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000003
comment: per discussion with Barry Smith

infectious disease hyper-endemicity
type: Class
subclass of: infectious disease endemicity
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: Hyper-endemic infectious diseases may have high endemic levels only in certain seasons. A hyper-endemic disease affects all age groups equally.

fungus
type: Class
subclass of: opisthokonta
editor note: changed fungi to fungus per best practice
imported from: http://purl.obolibrary.org/obo/NCBITaxon
has related synonym: fungi
has related synonym: mycota

parasitic disposition
type: Class
subclass of: disposition
definition: 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.

mucor
type: Class
subclass of: mold
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH035093

host exposure to infectious agent
type: Class
subclass of: process
definition: A process in which a potential host of an infectious agent is exposed to an infectious agent.
term editor: Bjoern Peters

is concretized as
type: ObjectProperty
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
example of usage: 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).
example of usage: 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).
definition: 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.

community-acquired infection
type: Class
subclass of: infection
disjoint with: nursing-home acquired infection
definition: An infection resulting from a transmission process that did not unfold in a health care facility.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_septicemia
type: Class
subclass of: Obsolete Class
definition: A bacteremia in which the baceteria are replicating.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
deprecated: true

sporothrix schenckii
type: Class
equivalent class: Class
  union of: Class
    intersection of: dimorphic fungus
    intersection of: opportunistic fungal pathogen
  union of: Class
    intersection of: dimorphic fungus
    intersection of: primary fungal pathogen
subclass of: dimorphic fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1821630.08FU

immunosuppressed organism experiencing infection-based immunosuppression
type: Class
equivalent class: Class
  intersection of: pathologically immunosuppressed organism
  intersection of: Restriction
    on property: participates in
    some values from: infection-based immunosuppression
subclass of: pathologically immunosuppressed organism
definition: A pathologically immunosuppressed organism that is experiencing infection-based immunosuppression.
term editor: Alex Diehl
term editor: Lindsay Cowell

exogenous fungal endophthalmitis
type: Class
subclass of: endophthalmitis
term editor: Sydney Cohen
definition source: https://www.cdc.gov/fungal/diseases/fungal-eye-infections/definition.html
has definition: An endophthalmitis that is caused by fungal spores entering the eye from an external source
has definition: An endophthalmitis that occurs after fungal spores enter the eye from an external source

_obsolete_attenuated
type: Class
subclass of: Obsolete Class
deprecated: true

infectivity
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: This quality is measured by the proportion of exposed who become infected.

symbiont
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: symbiont role
subclass of: organism
definition: An organism bearing a symbiont role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infectious agent seroprevalence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

_obsolete_toxicity
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_biological object
type: Class
subclass of: Obsolete Class
definition: primitive
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
deprecated: true

rhizomucor
type: Class
equivalent class: Class
  intersection of: mold
  intersection of: opportunistic fungal pathogen
subclass of: mold
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH035079

_obsolete_swollen
type: Class
subclass of: Obsolete Class
deprecated: true

obsolete dependent continuant
type: Class
subclass of: Obsolete Class
definition: A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
deprecated: true

pathologically immunosuppressed organism
type: Class
equivalent class: Class
  intersection of: immunosuppressed organism
  intersection of: Restriction
    on property: participates in
    some values from: pathologic immunosuppression
subclass of: immunosuppressed organism
definition: An immunosuppressed organism that is experiencing pathologic immunosuppression.
term editor: Alex Diehl
term editor: Lindsay Cowell

_obsolete_endemic
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_penetration via injury of epithelial barrier
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: three-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

antiviral
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has disposition
    some values from: antiviral disposition
subclass of: material entity
disjoint with: infection
disjoint with: disorder
definition: A material entity bearing an antiviral disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

ontology term requester
type: AnnotationProperty
has curation status: IAO_0000125
definition: The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'term requester' can credit the person, organization or project who request the ontology term.

has member
type: ObjectProperty
type: IrreflexiveProperty
sub property of: has part
definition: has member is a mereological relation between a collection and an item.
definition source: SIO
temporal interpretation: axiom holds for all times

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

Axiom
annotated source: one-dimensional spatial region
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

re-emerging pathogen
type: Class
subclass of: infectious agent
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infectious disorder
type: Class
equivalent class: Class
  intersection of: infection
  intersection of: disorder
subclass of: infection
subclass of: disorder
disjoint with: immunodeficiency
definition: An infection that is clinically abnormal.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_extrinsic incubation period
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_replicating biological material entity
type: Class
subclass of: Obsolete Class
definition: A biological material entity that is capable of replication.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
deprecated: true

_obsolete_herd immunity
type: Class
subclass of: Obsolete Class
deprecated: true

has ID policy for
type: AnnotationProperty
example of usage: 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"
definition: Relating an ontology used to record id policy to the ontology namespace whose policy it manages
term editor: Person:Alan Ruttenberg

_obsolete_horizontal transmission
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_fusion with host cell membrane
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_vertical transmission
type: Class
subclass of: Obsolete Class
deprecated: true

paracoccidioides lutzii
type: Class
subclass of: paracoccidioides
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1412585.08FU

Axiom
annotated source: zero-dimensional spatial region
annotated property: elucidation
annotated target: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

asymptomatic host of infectious agent
type: Class
subclass of: infectious agent host
subclass of: Restriction
  on property: has role
  some values from: infectious agent host role
definition: An organism that is host to an infectious agent and has no symptoms of the infectious disease associated with the infectious agent.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_pandemic
type: Class
subclass of: Obsolete Class
deprecated: true

transition to clinical abnormality
type: Class
subclass of: process
definition: A process by which a part of an organism or something contained in an organism becomes clinically abnormal.

_obsolete_pathogenicity
type: Class
subclass of: Obsolete Class
definition: '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
editor note: id 'pathogenicity'-ID[O]:0000025 from IDO 2007. May have replacement - TBD
deprecated: true

cutaneous aspergillosis
type: Class
equivalent class: Class
  union of: Class
    intersection of: aspergillosis
    intersection of: Class
      union of: subcutaneous mycosis
      union of: Restriction
        on property: has_material_basis_in
        some values from: cutaneous mycosis
  union of: Restriction
    on property: preceded by
    some values from: systemic mycosis
equivalent class: Class
  union of: Class
    intersection of: aspergillosis
    intersection of: Class
      union of: Restriction
        on property: has_material_basis_in
        some values from: cutaneous mycosis
      union of: Restriction
        on property: has_material_basis_in
        some values from: subcutaneous mycosis
  union of: Restriction
    on property: preceded by
    some values from: systemic mycosis
subclass of: aspergillosis
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC105285/
has definition: 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

primary pathogen
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has disposition
    some values from: primary infectious disposition
subclass of: infectious agent
definition: An infectious agent with a primary infectious disposition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
alternative term: principal pathogen

infectious disease endemic rate
type: Class
subclass of: infectious disease incidence rate
definition: An infectious disease incidence rate that is typical for an infectious disease in an organism population.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: Infectious disease endemic rate is relational to previous infectious disease incidence rates of the disease.

colonization of human
type: Class
subclass of: colonization of host
definition: A colonization of host process in which the host is of Species Homo sapiens.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

human pathogenicity disposition
type: Class
subclass of: pathogenic disposition
definition: A disposition to initiate processes that result in a disorder in a human organism.

multi-organism process
type: Class
subclass of: biological_process
definition: A biological process which involves another organism of the same or different species.
imported from: go.owl

_obsolete_antibiotic
type: Class
subclass of: Obsolete Class
deprecated: true

entry into host through host barriers
type: Class
subclass of: entry into host
definition: 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.
imported from: go.owl

production
type: Class
subclass of: process
definition: A process in which an entity comes into being as a result of the process.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

cladophialophora bantiana
type: Class
subclass of: dematiaceous fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1160231.08FU

Axiom
annotated source: site
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002

_obsolete_highly exposed persistently seronegative
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: realizable entity
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

apophysomyces
type: Class
subclass of: mold
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH035085

_obsolete_infectious disease
type: Class
subclass of: Obsolete Class
definition: '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
editor note: id 'infectious disease'-ID[O]:0000098 from IDO 2007. May have replacement - TBD
deprecated: true

_obsolete_engulfment by nonphagocyte
type: Class
subclass of: Obsolete Class
deprecated: true

fungal infectious disease
type: Class
equivalent class: Class
  intersection of: infectious disease
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: mycosis
subclass of: infectious disease
editor note: this term deviated from similarly labeled DOID:1564 in order to better fit the IDO structures of disease and infection
term editor: Sydney Cohen
has definition: An infectious disease that has material basis in some mycosis, which pass the resistance barriers of the body.

_obsolete_pathogen life cycle stage
type: Class
subclass of: Obsolete Class
deprecated: true

commensal
type: Class
equivalent class: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: commensal role
subclass of: symbiont
definition: An organism bearing a commensal role.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

_obsolete_rapid progression
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

bipolaris
type: Class
subclass of: dematiaceous fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH030641

Axiom
annotated source: realizable entity
annotated property: has associated axiom(nl)
annotated target: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: spatiotemporal region
annotated property: elucidation
annotated target: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

_obsolete_membrane invagination
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: material entity
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

HIV-based immunosuppression
type: Class
subclass of: infection-based immunosuppression
definition: An infection-based immunosuppression process which arises as the result of an HIV infection.
term editor: Alex Diehl
term editor: Lindsay Cowell

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

vaginal candidiasis
type: Class
equivalent class: Class
  intersection of: candidiasis
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: cutaneous mycosis
subclass of: candidiasis
imported from: http://www.ebi.ac.uk/efo/EFO
has definition: 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.

is allocated id range
type: AnnotationProperty
editor preferred term: is allocated id range
definition: Add as annotation triples in the granting ontology
definition: 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"
term editor: PERSON:Alan Ruttenberg

_obsolete_quality
type: Class
subclass of: Obsolete Class
deprecated: true

chronic carrier of infectious agent
type: Class
subclass of: infectious agent carrier
subclass of: Class
  intersection of: organism
  intersection of: Restriction
    on property: has role
    some values from: infectious agent carrier role
definition: An organism who has been bearer of the infectious agent carrier role for an extended period of time.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

Axiom
annotated source: continuant
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/131-004

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

_obsolete_pathogen-induced necrosis
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_virulence
type: Class
subclass of: Obsolete Class
definition: '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.
editor note: id 'virulence'-ID[O]:0000004 from IDO 2007. May have replacement - TBD
deprecated: true

_obsolete_contagious
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_endogenous
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

infectious disease endemicity
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

_obsolete_pathogen outbreak
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_infectious agent
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_vaccine
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_intrinsic incubation period
type: Class
subclass of: Obsolete Class
deprecated: true

Axiom
annotated source: one-dimensional temporal region
annotated property: elucidation
annotated target: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

_obsolete_pathogen adherence to host cell
type: Class
subclass of: Obsolete Class
definition: '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.
editor note: id 'pathogen adherence to host cell'-ID[O]:0000074 from IDO 2007. May have replacement - TBD
deprecated: true

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

label
type: AnnotationProperty

disseminated sporotrichosis
type: Class
equivalent class: Class
  union of: Class
    intersection of: sporotrichosis
    intersection of: Restriction
      on property: has_material_basis_in
      some values from: systemic mycosis
  union of: Restriction
    on property: has_material_basis_in
    some values from: cutaneous mycosis
  union of: Restriction
    on property: has_material_basis_in
    some values from: subcutaneous mycosis
subclass of: sporotrichosis
term editor: Sydney Cohen
definition source: https://www.cdc.gov/fungal/diseases/sporotrichosis/index.html
has definition: 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

infection-based immunosuppression
type: Class
subclass of: pathologic immunosuppression
definition: A pathologic immunosuppression process which arises as the result of an infection and is initiated or dysregulated by the infectious agent population.
editor note: The definition should perhaps read "as the result of an infectious disorder".
term editor: Alex Diehl
term editor: Lindsay Cowell

Axiom
annotated source: process boundary
annotated property: has associated axiom(nl)
annotated target: Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

primary fungal pathogen
type: Class
equivalent class: Class
  intersection of: fungal infectious agent
  intersection of: Restriction
    on property: has disposition
    some values from: primary infectious disposition
subclass of: primary pathogen
subclass of: fungal infectious agent
term editor: Sydney Cohen
has definition: A fungal infectious agent that usually has a primary infectious disposition.
comment: may cause infection in both immunocompromised and immunocompetent people

superficial mycosis
type: Class
subclass of: mycosis
imported from: http://purl.obolibrary.org/obo/MONDO
has definition: A mycosis that is limited to the stratum corneum and essentially elicits no inflammation. [ https://www.ncbi.nlm.nih.gov/books/NBK7902/ ]

_obsolete_emerging pathogen
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_colonization
type: Class
subclass of: Obsolete Class
definition: '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
editor note: id 'colonization'-ID[O]:0000205 from IDO 2007. May have replacement - TBD
deprecated: true

_obsolete_end reservoir
type: Class
subclass of: Obsolete Class
deprecated: true

antifungal resistance
type: Class
subclass of: resistance to drug
definition source: https://www.cdc.gov/fungal/antifungal-resistance.html
has definition: A resistance to antifungal drugs that mitigates the damaging effects of antifungal treatments.
comment: Occurs when fungi develop the ability to defeat the drugs designed to kill them. These antifungal resistant fungi no longer respond to antifungal drugs.

mutualism
type: Class
subclass of: symbiosis, encompassing mutualism through parasitism
definition: An interaction between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other.
imported from: go.owl

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

lichtheimia
type: Class
subclass of: mold
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH035078

disease course
type: Class
subclass of: process
definition: The totality of all processes through which a given disease instance is realized.
imported from: ogms.owl

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

B cell receptor complex
type: Class
subclass of: macromolecular complex
definition: 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.
imported from: go.owl

pneumocystis jirovecii
type: Class
equivalent class: Class
  intersection of: yeast
  intersection of: opportunistic fungal pathogen
subclass of: yeast
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1159131.08FU

has_material_basis_in
type: ObjectProperty
range: material entity

editor note
type: AnnotationProperty
editor preferred term: editor note
has curation status: IAO_0000122
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>

mycosis
type: Class
equivalent class: Class
  intersection of: infection
  intersection of: Restriction
    on property: has part
    some values from: fungal infectious agent
subclass of: infection
imported from: http://purl.obolibrary.org/obo/NCIT
has definition: An infection that is caused by a fungus. [ NCI ]
has exact synonym: fungal infection

_obsolete_opportunistic pathogen
type: Class
subclass of: Obsolete Class
deprecated: true

coccidioides
type: Class
equivalent class: Class
  intersection of: dimorphic fungus
  intersection of: opportunistic fungal pathogen
  intersection of: primary fungal pathogen
subclass of: dimorphic fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/TH031014

_obsolete_zoonotic
type: Class
subclass of: Obsolete Class
deprecated: true

infectious agent carrier role
type: Class
subclass of: infectious agent host role
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

pathologic immunosuppression
type: Class
subclass of: immunosuppression
definition: An immunosuppression process which arises as the result of a disorder.
editor note: Disorders that result in immunosuppression include those that result from infection, stress, malnutrition, and treatments such as chemotherapy or calcineurin inhibition.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

Axiom
annotated source: history
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/138-001

sporothrix brasiliensis
type: Class
subclass of: dimorphic fungus
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1225764.08FU

colony
type: Class
subclass of: organism population
definition: An organism population persisting in a site it has colonized.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

infectious agent colony
type: Class
equivalent class: Class
  intersection of: colony
  intersection of: Restriction
    on property: has part
    some values from: infectious agent
  intersection of: Restriction
    on property: has part
    all values from: infectious agent
subclass of: colony
definition: A colony whose members are infectious agents.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell

has associated axiom(fol)
type: AnnotationProperty
editor preferred term: has associated axiom(fol)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom expressed in first order logic using CLIF syntax

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

infectious disease incidence
type: Class
subclass of: quality
subclass of: Restriction
  on property: inheres in
  some values from: organism population
definition: 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.
term editor: Albert Goldfain
term editor: Alexander Diehl
term editor: Lindsay Cowell
comment: 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.

Viruses
type: Class
subclass of: organism
imported from: ncbitaxon.owl

allergic aspergillus sinusitis
type: Class
subclass of: allergic aspergillosis
term editor: Sydney Cohen
has definition: 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

extended organism
type: Class
subclass of: object aggregate
definition: 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.
imported from: ogms.owl

BFO_0000134
elucidation: 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])
elucidation: 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
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_dependovirus
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_epidemiological spread of disease
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_modulation of inflammatory response
type: Class
subclass of: Obsolete Class
deprecated: true

has associated axiom(nl)
type: AnnotationProperty
editor preferred term: has associated axiom(nl)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom associated with a term expressed using natural language

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

immunosuppressed organism experiencing chronic systemic steroid use-based immunosuppression
type: Class
subclass of: immunosuppressed organism experiencing drug-based immunosuppression
definition: a pathologically immunosuppressed organism that is experiencing chronic systemic steroid use-based immunosuppression.
term editor: Alex Diehl
term editor: Lindsay Cowell

_obsolete_factor
type: Class
subclass of: Obsolete Class
definition: '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
editor note: id 'factor'-ID[O]:0000204 from IDO 2007. May have replacement - TBD
deprecated: true

_obsolete_active
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_infection
type: Class
subclass of: Obsolete Class
deprecated: true

bfo-spec-label
definition source: Person:Alan Ruttenberg

_obsolete_case of infectious disease
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_colonizer
type: Class
subclass of: Obsolete Class
deprecated: true

pneumocystis pneumonia
type: Class
equivalent class: Class
  intersection of: fungal infectious disease
  intersection of: Restriction
    on property: has part
    some values from: pneumocystis jirovecii
  intersection of: Restriction
    on property: has_material_basis_in
    some values from: systemic mycosis
subclass of: fungal infectious disease
imported from: http://purl.obolibrary.org/obo/NCIT
has definition: 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.

_obsolete_nonspecific adherence
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_virus-induced cytopathogenesis
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_route of entry
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_long-term non-progression
type: Class
subclass of: Obsolete Class
deprecated: true

has ID prefix
type: AnnotationProperty
example of usage: 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"
definition: 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.
term editor: Person:Alan Ruttenberg

_obsolete_treatment
type: Class
subclass of: Obsolete Class
deprecated: true

temporal interpretation
type: AnnotationProperty

Axiom
annotated source: spatial region
annotated property: elucidation
annotated target: 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])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

keratitis
type: Class
subclass of: fungal eye infection
imported from: http://www.ebi.ac.uk/efo/EFO
has definition: A fungal eye infection is characterized by inflammation of the cornea. [ NCIT : C26805 ]
has definition: A fungal eye infection that is characterized by inflammation of the cornea. [ NCIT : C26805 ]

_obsolete_sign
type: Class
subclass of: Obsolete Class
deprecated: true

candida albicans
type: Class
subclass of: candida
imported from: UNITE Community https://dx.doi.org/10.15156/BIO/SH1189319.08FU

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

_obsolete_host recovery period
type: Class
subclass of: Obsolete Class
deprecated: true

_obsolete_dormancy
type: Class
subclass of: Obsolete Class
definition: '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
editor note: id 'dormancy'-ID[O]:0000209 from IDO 2007. May have replacement - TBD
deprecated: true

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (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]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

host living with infected household contact
type: Class
subclass of: host exposure to environment containing infectious agent
definition: A host exposure to environment with infectious agent where the environment is a household that also has an infected host
editor note: Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001