part_of
type: ObjectProperty
has OBO namespace: default_namespace

has_participant
type: ObjectProperty
has OBO namespace: default_namespace

has_quality
type: ObjectProperty
has OBO namespace: default_namespace

has_role
type: ObjectProperty
has OBO namespace: default_namespace

preceded_by
type: ObjectProperty
has OBO namespace: default_namespace

mode of transmission
type: Class
subclass of: role
has OBO namespace: default_namespace

end reservoir
type: Class
subclass of: reservoir
has OBO namespace: default_namespace

factor
type: Class
subclass of: role
comment: Role played by portion of physical substance in a biological process
has OBO namespace: default_namespace

colonization
type: Class
subclass of: process
subclass of: Restriction
  on property: part_of
  some values from: infectious disease progression
comment: 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
has OBO namespace: default_namespace

biotic
type: Class
subclass of: object
has OBO namespace: default_namespace

adhesin
type: Class
subclass of: ObsoleteClass
has OBO namespace: default_namespace

seroprevalence
type: Class
subclass of: prevalence
comment: prevalence as measured by antibody
has OBO namespace: default_namespace

dormancy
type: Class
subclass of: quality of pathogen
comment: 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
has OBO namespace: default_namespace

quality of host
type: Class
subclass of: quality
has OBO namespace: default_namespace

quality of pathogen
type: Class
subclass of: quality
has OBO namespace: default_namespace

susceptibility
type: Class
subclass of: quality of host
comment: can change depending on environmentnnwhere should susceptibility factors go?
has OBO namespace: default_namespace

resistance
type: Class
subclass of: quality of host
has OBO namespace: default_namespace

refractoriness
type: Class
subclass of: quality of host
has OBO namespace: default_namespace

quality of host population
type: Class
subclass of: quality
has OBO namespace: default_namespace

herd immunity
type: Class
subclass of: quality of host population
has OBO namespace: default_namespace

quality of infectious disease
type: Class
subclass of: quality
has OBO namespace: default_namespace

case of infectious disease
type: Class
subclass of: quality of host
has OBO namespace: default_namespace

incubation period
type: Class
subclass of: Restriction
  on property: part_of
  some values from: infectious disease progression
comment: agent is incubated?ndisease is incubated?
has OBO namespace: default_namespace

infectivity period
type: Class
subclass of: Restriction
  on property: part_of
  some values from: infectious disease progression
has OBO namespace: default_namespace

infectious disease progression
type: Class
subclass of: process
comment: 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?
has OBO namespace: default_namespace

infectious disease course
type: Class
subclass of: process
has OBO namespace: default_namespace

host recovery period
type: Class
subclass of: process
has OBO namespace: default_namespace

intrinsic incubation period
type: Class
subclass of: incubation period
subclass of: process
has OBO namespace: default_namespace

extrinsic incubation period
type: Class
subclass of: Restriction
  on property: part_of
  some values from: pathogen life cycle
has OBO namespace: default_namespace

pathogen life cycle
type: Class
subclass of: process
comment: 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
has OBO namespace: default_namespace

dormancy period
type: Class
subclass of: process
comment: is a period a process?
has OBO namespace: default_namespace

pathogen outbreak
type: Class
subclass of: process
has OBO namespace: default_namespace

oral-fecal transmission
type: Class
subclass of: transmission
has OBO namespace: default_namespace

vertical transmission
type: Class
subclass of: transmission
has OBO namespace: default_namespace

horizontal transmission
type: Class
subclass of: transmission
has OBO namespace: default_namespace

pathogen life cycle stage
type: Class
subclass of: ObsoleteClass
has OBO namespace: default_namespace

infectious disease progression stage
type: Class
subclass of: ObsoleteClass
has OBO namespace: default_namespace

process
type: Class
has OBO namespace: default_namespace

role
type: Class
has OBO namespace: default_namespace

quality
type: Class
has OBO namespace: default_namespace

object
type: Class
has OBO namespace: default_namespace

virulence
type: Class
subclass of: quality of pathogen
comment: the degree of pathogenicitynnpathogenicity and virulence are used in some communities as synonyms.
has OBO namespace: default_namespace

swollen
type: Class
subclass of: quality of host
has OBO namespace: default_namespace

toxicity
type: Class
subclass of: quality
has OBO namespace: default_namespace

active
type: Class
subclass of: quality
has OBO namespace: default_namespace

contagious
type: Class
subclass of: quality of pathogen
has OBO namespace: default_namespace

latency
type: Class
subclass of: quality of pathogen
comment: 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
has OBO namespace: default_namespace

immunosuppressed
type: Class
subclass of: quality of host
has OBO namespace: default_namespace

exogenous
type: Class
subclass of: quality of pathogen
has OBO namespace: default_namespace

immunity
type: Class
subclass of: quality of host
has OBO namespace: default_namespace

protective
type: Class
subclass of: quality
has OBO namespace: default_namespace

temperature
type: Class
subclass of: quality of host
has OBO namespace: default_namespace

inactivated
type: Class
subclass of: quality
has OBO namespace: default_namespace

mortality
type: Class
subclass of: quality
has OBO namespace: default_namespace

pandemic
type: Class
subclass of: incidence
has OBO namespace: default_namespace

prevalence
type: Class
subclass of: quality of host population
comment: 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
has OBO namespace: default_namespace

epidemic
type: Class
subclass of: incidence
has OBO namespace: default_namespace

infected
type: Class
subclass of: quality of host
has OBO namespace: default_namespace

live
type: Class
subclass of: quality
has OBO namespace: default_namespace

zoonotic
type: Class
subclass of: quality of pathogen
has OBO namespace: default_namespace

immunocompromised
type: Class
subclass of: quality of host
has OBO namespace: default_namespace

pathogenicity
type: Class
subclass of: quality of pathogen
comment: 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
has OBO namespace: default_namespace

tropism
type: Class
subclass of: quality
has OBO namespace: default_namespace

drug resistance
type: Class
subclass of: quality of pathogen
has OBO namespace: default_namespace

antibiotic resistance
type: Class
subclass of: drug resistance
has OBO namespace: default_namespace

incidence
type: Class
subclass of: quality of infectious disease
comment: number of new cases in a given period of time
has OBO namespace: default_namespace

invasive
type: Class
subclass of: quality of pathogen
has OBO namespace: default_namespace

endogenous
type: Class
subclass of: quality of pathogen
has OBO namespace: default_namespace

attenuated
type: Class
subclass of: quality
has OBO namespace: default_namespace

morbidity
type: Class
subclass of: quality
has OBO namespace: default_namespace

endemic
type: Class
subclass of: quality of infectious disease
has OBO namespace: default_namespace

fusion protein
type: Class
subclass of: role
has OBO namespace: default_namespace

colonizer
type: Class
subclass of: role
has OBO namespace: default_namespace

commensal
type: Class
subclass of: colonizer
has OBO namespace: default_namespace

parasite
type: Class
subclass of: colonizer
has OBO namespace: default_namespace

symbiant
type: Class
subclass of: colonizer
has OBO namespace: default_namespace

virulence factor
type: Class
subclass of: factor
comment: role played by a portion of substance to promote virulencennmagnitudendegree of pathogenesis
has OBO namespace: default_namespace

route of entry
type: Class
subclass of: role
has OBO namespace: default_namespace

invasin
type: Class
subclass of: virulence factor
has OBO namespace: default_namespace

toxin
type: Class
subclass of: virulence factor
has OBO namespace: default_namespace

endotoxin
type: Class
subclass of: toxin
has OBO namespace: default_namespace

exotoxin
type: Class
subclass of: toxin
has OBO namespace: default_namespace

sign
type: Class
subclass of: role
has OBO namespace: default_namespace

treatment
type: Class
subclass of: role
has OBO namespace: default_namespace

symptom
type: Class
subclass of: role
comment: look at mathias's ontology of cancer to get all the subterms...its under quality there
has OBO namespace: default_namespace

antimicrobial
type: Class
subclass of: treatment
has OBO namespace: default_namespace

medicine
type: Class
subclass of: treatment
has OBO namespace: default_namespace

therapeutic
type: Class
subclass of: treatment
has OBO namespace: default_namespace

vaccine
type: Class
subclass of: treatment
has OBO namespace: default_namespace

antibiotic
type: Class
subclass of: antimicrobial
has OBO namespace: default_namespace

colonization factor
type: Class
subclass of: factor
comment: role played by portion of physical substance which promotes colonization
has OBO namespace: default_namespace
has related synonym: <new synonym>

adhesion factor
type: Class
subclass of: factor
comment: role played by portion of physical substance utilized by an organism in order to establish adherence to a surface in a host
has OBO namespace: default_namespace
has related synonym: adhesin factor
has related synonym: adhesin

host
type: Class
subclass of: role
has OBO namespace: default_namespace

carrier
type: Class
subclass of: host
has OBO namespace: default_namespace

chronic carrier
type: Class
subclass of: carrier
has OBO namespace: default_namespace

reservoir
type: Class
subclass of: role
comment: holding place for a potential pathogen...animate or inanimate
has OBO namespace: default_namespace

fomite
type: Class
subclass of: reservoir
comment: inanimate holder, is water a fomite or only a reservoir?
has OBO namespace: default_namespace

mobile genetic element
type: Class
subclass of: role
has OBO namespace: default_namespace

pathogenicity island
type: Class
subclass of: role
has OBO namespace: default_namespace

vector
type: Class
subclass of: role
comment: 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?)
has OBO namespace: default_namespace

pathogen
type: Class
subclass of: role
has OBO namespace: default_namespace

dependovirus
type: Class
subclass of: pathogen
has OBO namespace: default_namespace

infectious agent
type: Class
subclass of: pathogen
has OBO namespace: default_namespace

opportunistic pathogen
type: Class
subclass of: pathogen
has OBO namespace: default_namespace

emerging pathogen
type: Class
subclass of: infectious agent
has OBO namespace: default_namespace

primary pathogen
type: Class
subclass of: infectious agent
has OBO namespace: default_namespace

prion
type: Class
subclass of: infectious agent
has OBO namespace: default_namespace

initiation of infection
type: Class
subclass of: process
has OBO namespace: default_namespace

disruption of body surface
type: Class
subclass of: initiation of infection
has OBO namespace: default_namespace

disruption of normal microbioflora
type: Class
subclass of: initiation of infection
has OBO namespace: default_namespace

pathogen adherence to host cell
type: Class
subclass of: process
subclass of: Restriction
  on property: part_of
  some values from: infectious disease progression
comment: create cross products for "host" and "pathogen" that will be part of this process.
has OBO namespace: default_namespace

nonspecific adherence
type: Class
subclass of: pathogen adherence to host cell
has OBO namespace: default_namespace

specific adherence
type: Class
subclass of: pathogen adherence to host cell
has OBO namespace: default_namespace

afimbrial specific adherence
type: Class
subclass of: specific adherence
has OBO namespace: default_namespace

fimbrial specific adherence
type: Class
subclass of: specific adherence
has OBO namespace: default_namespace

penetration of epithelial barrier
type: Class
subclass of: process
has OBO namespace: default_namespace

penetration via injury of epithelial barrier
type: Class
subclass of: penetration of epithelial barrier
has OBO namespace: default_namespace

transcytosis
type: Class
subclass of: penetration of epithelial barrier
has OBO namespace: default_namespace

utilization of membranous cell gateway
type: Class
subclass of: penetration of epithelial barrier
has OBO namespace: default_namespace

transmission
type: Class
subclass of: process
subclass of: Restriction
  on property: part_of
  some values from: infectious disease progression
comment: the process by which an infectious agent passes from one organism to another organism
has OBO namespace: default_namespace

pathogenesis
type: Class
subclass of: process
comment: GO:nthe specific processes that generate the ability of an organism to cause disease in anothernnnThis is defined in GO so import.
has OBO namespace: default_namespace

penetration of host cell
type: Class
subclass of: process
has OBO namespace: default_namespace

engulfment
type: Class
subclass of: penetration of host cell
has OBO namespace: default_namespace

fusion with host cell membrane
type: Class
subclass of: penetration of host cell
has OBO namespace: default_namespace

membrane invagination
type: Class
subclass of: penetration of host cell
has OBO namespace: default_namespace

passage through cell membrane
type: Class
subclass of: penetration of host cell
has OBO namespace: default_namespace

engulfment by nonphagocyte
type: Class
subclass of: engulfment
has OBO namespace: default_namespace

engulfment by phagocyte
type: Class
subclass of: engulfment
has OBO namespace: default_namespace

damaging host cells and tissues in subepithelial space
type: Class
subclass of: process
subclass of: Restriction
  on property: part_of
  some values from: infectious disease progression
has OBO namespace: default_namespace

induction of damaging host immune response
type: Class
subclass of: damaging host cells and tissues in subepithelial space
has OBO namespace: default_namespace

pathogen-induced apoptosis
type: Class
subclass of: damaging host cells and tissues in subepithelial space
has OBO namespace: default_namespace

pathogen-induced necrosis
type: Class
subclass of: damaging host cells and tissues in subepithelial space
has OBO namespace: default_namespace

virus-induced cytopathogenesis
type: Class
subclass of: damaging host cells and tissues in subepithelial space
has OBO namespace: default_namespace

pathogen spread through host
type: Class
subclass of: process
subclass of: Restriction
  on property: part_of
  some values from: infectious disease progression
has OBO namespace: default_namespace

infectious disease
type: Class
subclass of: quality of host population
comment: comment about the instances:nncollections of etiologically connected cases of infectious disease in a given population
has OBO namespace: default_namespace

pathogen evasion of host immune response
type: Class
subclass of: process
subclass of: Restriction
  on property: part_of
  some values from: infectious disease progression
has OBO namespace: default_namespace

emergence
type: Class
subclass of: process
comment: 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)
has OBO namespace: default_namespace

epidemiological spread of disease
type: Class
subclass of: process
has OBO namespace: default_namespace

outbreak
type: Class
subclass of: process
has OBO namespace: default_namespace

infection
type: Class
subclass of: process
has OBO namespace: default_namespace

infection treatment process
type: Class
subclass of: process
has OBO namespace: default_namespace

immunization
type: Class
subclass of: process
has OBO namespace: default_namespace

prevention of infection
type: Class
subclass of: process
has OBO namespace: default_namespace

transport by blood
type: Class
subclass of: pathogen spread through host
has OBO namespace: default_namespace

transport by lymph
type: Class
subclass of: pathogen spread through host
has OBO namespace: default_namespace

modulation of inflammatory response
type: Class
subclass of: ObsoleteClass
has OBO namespace: default_namespace

antigenic variation
type: Class
subclass of: pathogen evasion of host immune response
has OBO namespace: default_namespace

resist phagocytosis in subepithelial space
type: Class
subclass of: pathogen evasion of host immune response
has OBO namespace: default_namespace

serum resistance
type: Class
subclass of: pathogen evasion of host immune response
has OBO namespace: default_namespace

phase variation
type: Class
subclass of: antigenic variation
has OBO namespace: default_namespace

genetic diversification
type: Class
subclass of: antigenic variation
has OBO namespace: default_namespace

complement resistance
type: Class
subclass of: serum resistance
has OBO namespace: default_namespace

epidemic spread of disease
type: Class
subclass of: epidemiological spread of disease
has OBO namespace: default_namespace

pandemic spread of disease
type: Class
subclass of: epidemiological spread of disease
has OBO namespace: default_namespace

vaccination
type: Class
subclass of: immunization
has OBO namespace: default_namespace

progression rate
type: Class
subclass of: quality
has OBO namespace: default_namespace

rapid progression
type: Class
subclass of: progression rate
has OBO namespace: default_namespace

long-term non-progression
type: Class
subclass of: progression rate
has OBO namespace: default_namespace

highly exposed persistently seronegative
type: Class
subclass of: progression rate
has OBO namespace: default_namespace

<new term>
type: Class
subclass of: ObsoleteClass
has OBO namespace: default_namespace

co-infected
type: Class
subclass of: quality of host
has OBO namespace: default_namespace

fitness
type: Class
subclass of: quality
comment: is a quality relating to both bacteria and host
has OBO namespace: default_namespace