format-version: 1.0
date: 08:10:2007 20:55
saved-by: Administrator
auto-generated-by: OBO-Edit 1.101
default-namespace: default_namespace

[Term]
id: GO:0000000
name: mode of transmission
is_a: ID:0000001 ! role

[Term]
id: GO:0000001
name: end reservoir
is_a: ID:0000059 ! reservoir

[Term]
id: GO:0000004
name: factor
comment: Role played by portion of physical substance in a biological process
is_a: ID:0000001 ! role

[Term]
id: GO:0000005
name: colonization
comment: the process by which a biotic entity establishes multiple copies of itself in a new environment (including an organismal environment).\n\nfix id\n"native" environment term
is_a: ID:0000000 ! process
relationship: part_of GO:0000021 ! infectious disease progression

[Term]
id: GO:0000006
name: biotic
is_a: ID:0000003 ! object

[Term]
id: GO:0000007
name: adhesin
is_obsolete: true

[Term]
id: GO:0000008
name: seroprevalence
comment: prevalence as measured by antibody
is_a: ID:0000019 ! prevalence

[Term]
id: GO:0000009
name: dormancy
comment: quality [state] of an organism that during its life cycle in which its growth. development, metabolism, etc is temporarily suspended \n\n\nsuspended state, non-replicative state, resting state
is_a: GO:0000011 ! quality of pathogen

[Term]
id: GO:0000010
name: quality of host
is_a: ID:0000002 ! quality

[Term]
id: GO:0000011
name: quality of pathogen
is_a: ID:0000002 ! quality

[Term]
id: GO:0000012
name: susceptibility
comment: can change depending on environment\n\nwhere should susceptibility factors go?
is_a: GO:0000010 ! quality of host

[Term]
id: GO:0000013
name: resistance
is_a: GO:0000010 ! quality of host

[Term]
id: GO:0000014
name: refractoriness
is_a: GO:0000010 ! quality of host

[Term]
id: GO:0000015
name: quality of host population
is_a: ID:0000002 ! quality

[Term]
id: GO:0000016
name: herd immunity
is_a: GO:0000015 ! quality of host population

[Term]
id: GO:0000017
name: quality of infectious disease
is_a: ID:0000002 ! quality

[Term]
id: GO:0000018
name: case of infectious disease
is_a: GO:0000010 ! quality of host

[Term]
id: GO:0000019
name: incubation period
comment: agent is incubated?\ndisease is incubated?
relationship: part_of GO:0000021 ! infectious disease progression

[Term]
id: GO:0000020
name: infectivity period
relationship: part_of GO:0000021 ! infectious disease progression

[Term]
id: GO:0000021
name: infectious disease progression
comment: the unfolding or course of infectious disease\n\nwhat do we say about infectious disease that always remain latent \nwhat about when a pathogen continues its progression \n\nwe need to think about whether we need a term called stage\nlife cycle?\nprogression?\ndevelopment?
is_a: ID:0000000 ! process

[Term]
id: GO:0000022
name: infectious disease course
is_a: ID:0000000 ! process

[Term]
id: GO:0000023
name: host recovery period
is_a: ID:0000000 ! process

[Term]
id: GO:0000024
name: intrinsic incubation period
is_a: GO:0000019 ! incubation period
is_a: ID:0000000 ! process

[Term]
id: GO:0000025
name: extrinsic incubation period
relationship: part_of GO:0000026 ! pathogen life cycle

[Term]
id: GO:0000026
name: pathogen life cycle
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?\n\ncan include phases in the existence of the entity before it becomes a pathogen
is_a: ID:0000000 ! process

[Term]
id: GO:0000027
name: dormancy period
comment: is a period a process?
is_a: ID:0000000 ! process

[Term]
id: GO:0000028
name: pathogen outbreak
is_a: ID:0000000 ! process

[Term]
id: GO:0000029
name: oral-fecal transmission
is_a: ID:0000083 ! transmission

[Term]
id: GO:0000030
name: vertical transmission
is_a: ID:0000083 ! transmission

[Term]
id: GO:0000031
name: horizontal transmission
is_a: ID:0000083 ! transmission

[Term]
id: GO:0000032
name: pathogen life cycle stage
is_obsolete: true

[Term]
id: GO:0000033
name: infectious disease progression stage
is_obsolete: true

[Term]
id: ID:0000000
name: process

[Term]
id: ID:0000001
name: role

[Term]
id: ID:0000002
name: quality

[Term]
id: ID:0000003
name: object

[Term]
id: ID:0000004
name: virulence
comment: the degree of pathogenicity\n\npathogenicity and virulence are used in some communities as synonyms.
is_a: GO:0000011 ! quality of pathogen

[Term]
id: ID:0000005
name: swollen
is_a: GO:0000010 ! quality of host

[Term]
id: ID:0000006
name: toxicity
is_a: ID:0000002 ! quality

[Term]
id: ID:0000007
name: active
is_a: ID:0000002 ! quality

[Term]
id: ID:0000008
name: contagious
is_a: GO:0000011 ! quality of pathogen

[Term]
id: ID:0000009
name: latency
comment: infection has occurred, but it might not have manifested itself\nquality of being in a non replicative state\ntime to manifest itself \na pathogen when it is in a non replicative state
is_a: GO:0000011 ! quality of pathogen

[Term]
id: ID:0000010
name: immunosuppressed
is_a: GO:0000010 ! quality of host

[Term]
id: ID:0000011
name: exogenous
is_a: GO:0000011 ! quality of pathogen

[Term]
id: ID:0000012
name: immunity
is_a: GO:0000010 ! quality of host

[Term]
id: ID:0000013
name: protective
is_a: ID:0000002 ! quality

[Term]
id: ID:0000015
name: temperature
is_a: GO:0000010 ! quality of host

[Term]
id: ID:0000016
name: inactivated
is_a: ID:0000002 ! quality

[Term]
id: ID:0000017
name: mortality
is_a: ID:0000002 ! quality

[Term]
id: ID:0000018
name: pandemic
is_a: ID:0000029 ! incidence

[Term]
id: ID:0000019
name: prevalence
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 population\n\nthe burden of a disease in a population
is_a: GO:0000015 ! quality of host population

[Term]
id: ID:0000020
name: epidemic
is_a: ID:0000029 ! incidence

[Term]
id: ID:0000021
name: infected
is_a: GO:0000010 ! quality of host

[Term]
id: ID:0000022
name: live
is_a: ID:0000002 ! quality

[Term]
id: ID:0000023
name: zoonotic
is_a: GO:0000011 ! quality of pathogen

[Term]
id: ID:0000024
name: immunocompromised
is_a: GO:0000010 ! quality of host

[Term]
id: ID:0000025
name: pathogenicity
comment: the ability of the biotic entity to cause disease in a host of a given type\n\ndo we need to say damage instead of disease?\n\npathogenicity and virulence are used as synonyms in some communities
is_a: GO:0000011 ! quality of pathogen

[Term]
id: ID:0000026
name: tropism
is_a: ID:0000002 ! quality

[Term]
id: ID:0000027
name: drug resistance
is_a: GO:0000011 ! quality of pathogen

[Term]
id: ID:0000028
name: antibiotic resistance
is_a: ID:0000027 ! drug resistance

[Term]
id: ID:0000029
name: incidence
comment: number of new cases in a given period of time
is_a: GO:0000017 ! quality of infectious disease

[Term]
id: ID:0000030
name: invasive
is_a: GO:0000011 ! quality of pathogen

[Term]
id: ID:0000031
name: endogenous
is_a: GO:0000011 ! quality of pathogen

[Term]
id: ID:0000032
name: attenuated
is_a: ID:0000002 ! quality

[Term]
id: ID:0000033
name: morbidity
is_a: ID:0000002 ! quality

[Term]
id: ID:0000034
name: endemic
is_a: GO:0000017 ! quality of infectious disease

[Term]
id: ID:0000035
name: fusion protein
is_a: ID:0000001 ! role

[Term]
id: ID:0000036
name: colonizer
is_a: ID:0000001 ! role

[Term]
id: ID:0000037
name: commensal
is_a: ID:0000036 ! colonizer

[Term]
id: ID:0000038
name: parasite
is_a: ID:0000036 ! colonizer

[Term]
id: ID:0000039
name: symbiant
is_a: ID:0000036 ! colonizer

[Term]
id: ID:0000040
name: virulence factor
comment: role played by a portion of substance to promote virulence\n\nmagnitude\ndegree of pathogenesis
is_a: GO:0000004 ! factor

[Term]
id: ID:0000041
name: route of entry
is_a: ID:0000001 ! role

[Term]
id: ID:0000042
name: invasin
is_a: ID:0000040 ! virulence factor

[Term]
id: ID:0000043
name: toxin
is_a: ID:0000040 ! virulence factor

[Term]
id: ID:0000044
name: endotoxin
is_a: ID:0000043 ! toxin

[Term]
id: ID:0000045
name: exotoxin
is_a: ID:0000043 ! toxin

[Term]
id: ID:0000046
name: sign
is_a: ID:0000001 ! role

[Term]
id: ID:0000047
name: treatment
is_a: ID:0000001 ! role

[Term]
id: ID:0000048
name: symptom
comment: look at mathias's ontology of cancer to get all the subterms...its under quality there
is_a: ID:0000001 ! role

[Term]
id: ID:0000049
name: antimicrobial
is_a: ID:0000047 ! treatment

[Term]
id: ID:0000050
name: medicine
is_a: ID:0000047 ! treatment

[Term]
id: ID:0000051
name: therapeutic
is_a: ID:0000047 ! treatment

[Term]
id: ID:0000052
name: vaccine
is_a: ID:0000047 ! treatment

[Term]
id: ID:0000053
name: antibiotic
is_a: ID:0000049 ! antimicrobial

[Term]
id: ID:0000054
name: colonization factor
comment: role played by portion of physical substance which promotes colonization
related_synonym: "<new synonym>" []
is_a: GO:0000004 ! factor

[Term]
id: ID:0000055
name: adhesion factor
comment: role played by portion of physical substance utilized by an organism in order to establish adherence to a surface in a host
related_synonym: "adhesin" []
related_synonym: "adhesin factor" []
is_a: GO:0000004 ! factor

[Term]
id: ID:0000056
name: host
is_a: ID:0000001 ! role

[Term]
id: ID:0000057
name: carrier
is_a: ID:0000056 ! host

[Term]
id: ID:0000058
name: chronic carrier
is_a: ID:0000057 ! carrier

[Term]
id: ID:0000059
name: reservoir
comment: holding place for a potential pathogen...animate or inanimate
is_a: ID:0000001 ! role

[Term]
id: ID:0000060
name: fomite
comment: inanimate holder, is water a fomite or only a reservoir?
is_a: ID:0000059 ! reservoir

[Term]
id: ID:0000061
name: mobile genetic element
is_a: ID:0000001 ! role

[Term]
id: ID:0000062
name: pathogenicity island
is_a: ID:0000001 ! role

[Term]
id: ID:0000063
name: vector
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?)
is_a: ID:0000001 ! role

[Term]
id: ID:0000064
name: pathogen
is_a: ID:0000001 ! role

[Term]
id: ID:0000065
name: dependovirus
is_a: ID:0000064 ! pathogen

[Term]
id: ID:0000066
name: infectious agent
is_a: ID:0000064 ! pathogen

[Term]
id: ID:0000067
name: opportunistic pathogen
is_a: ID:0000064 ! pathogen

[Term]
id: ID:0000068
name: emerging pathogen
is_a: ID:0000066 ! infectious agent

[Term]
id: ID:0000069
name: primary pathogen
is_a: ID:0000066 ! infectious agent

[Term]
id: ID:0000070
name: prion
is_a: ID:0000066 ! infectious agent

[Term]
id: ID:0000071
name: initiation of infection
is_a: ID:0000000 ! process

[Term]
id: ID:0000072
name: disruption of body surface
is_a: ID:0000071 ! initiation of infection

[Term]
id: ID:0000073
name: disruption of normal microbioflora
is_a: ID:0000071 ! initiation of infection

[Term]
id: ID:0000074
name: pathogen adherence to host cell
comment: create cross products for "host" and "pathogen" that will be part of this process.
is_a: ID:0000000 ! process
relationship: part_of GO:0000021 ! infectious disease progression

[Term]
id: ID:0000075
name: nonspecific adherence
is_a: ID:0000074 ! pathogen adherence to host cell

[Term]
id: ID:0000076
name: specific adherence
is_a: ID:0000074 ! pathogen adherence to host cell

[Term]
id: ID:0000077
name: afimbrial specific adherence
is_a: ID:0000076 ! specific adherence

[Term]
id: ID:0000078
name: fimbrial specific adherence
is_a: ID:0000076 ! specific adherence

[Term]
id: ID:0000079
name: penetration of epithelial barrier
is_a: ID:0000000 ! process

[Term]
id: ID:0000080
name: penetration via injury of epithelial barrier
is_a: ID:0000079 ! penetration of epithelial barrier

[Term]
id: ID:0000081
name: transcytosis
is_a: ID:0000079 ! penetration of epithelial barrier

[Term]
id: ID:0000082
name: utilization of membranous cell gateway
is_a: ID:0000079 ! penetration of epithelial barrier

[Term]
id: ID:0000083
name: transmission
comment: the process by which an infectious agent passes from one organism to another organism
is_a: ID:0000000 ! process
relationship: part_of GO:0000021 ! infectious disease progression

[Term]
id: ID:0000084
name: pathogenesis
comment: GO:\nthe specific processes that generate the ability of an organism to cause disease in another\n\n\nThis is defined in GO so import.
is_a: ID:0000000 ! process

[Term]
id: ID:0000085
name: penetration of host cell
is_a: ID:0000000 ! process

[Term]
id: ID:0000086
name: engulfment
is_a: ID:0000085 ! penetration of host cell

[Term]
id: ID:0000087
name: fusion with host cell membrane
is_a: ID:0000085 ! penetration of host cell

[Term]
id: ID:0000088
name: membrane invagination
is_a: ID:0000085 ! penetration of host cell

[Term]
id: ID:0000089
name: passage through cell membrane
is_a: ID:0000085 ! penetration of host cell

[Term]
id: ID:0000090
name: engulfment by nonphagocyte
is_a: ID:0000086 ! engulfment

[Term]
id: ID:0000091
name: engulfment by phagocyte
is_a: ID:0000086 ! engulfment

[Term]
id: ID:0000092
name: damaging host cells and tissues in subepithelial space
is_a: ID:0000000 ! process
relationship: part_of GO:0000021 ! infectious disease progression

[Term]
id: ID:0000093
name: induction of damaging host immune response
is_a: ID:0000092 ! damaging host cells and tissues in subepithelial space

[Term]
id: ID:0000094
name: pathogen-induced apoptosis
is_a: ID:0000092 ! damaging host cells and tissues in subepithelial space

[Term]
id: ID:0000095
name: pathogen-induced necrosis
is_a: ID:0000092 ! damaging host cells and tissues in subepithelial space

[Term]
id: ID:0000096
name: virus-induced cytopathogenesis
is_a: ID:0000092 ! damaging host cells and tissues in subepithelial space

[Term]
id: ID:0000097
name: pathogen spread through host
is_a: ID:0000000 ! process
relationship: part_of GO:0000021 ! infectious disease progression

[Term]
id: ID:0000098
name: infectious disease
comment: comment about the instances:\n\ncollections of etiologically connected cases of infectious disease in a given population
is_a: GO:0000015 ! quality of host population

[Term]
id: ID:0000100
name: pathogen evasion of host immune response
is_a: ID:0000000 ! process
relationship: part_of GO:0000021 ! infectious disease progression

[Term]
id: ID:0000101
name: emergence
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)
is_a: ID:0000000 ! process

[Term]
id: ID:0000102
name: epidemiological spread of disease
is_a: ID:0000000 ! process

[Term]
id: ID:0000103
name: outbreak
is_a: ID:0000000 ! process

[Term]
id: ID:0000104
name: infection
is_a: ID:0000000 ! process

[Term]
id: ID:0000105
name: infection treatment process
is_a: ID:0000000 ! process

[Term]
id: ID:0000106
name: immunization
is_a: ID:0000000 ! process

[Term]
id: ID:0000107
name: prevention of infection
is_a: ID:0000000 ! process

[Term]
id: ID:0000108
name: transport by blood
is_a: ID:0000097 ! pathogen spread through host

[Term]
id: ID:0000109
name: transport by lymph
is_a: ID:0000097 ! pathogen spread through host

[Term]
id: ID:0000110
name: modulation of inflammatory response
is_obsolete: true

[Term]
id: ID:0000111
name: antigenic variation
is_a: ID:0000100 ! pathogen evasion of host immune response

[Term]
id: ID:0000112
name: resist phagocytosis in subepithelial space
is_a: ID:0000100 ! pathogen evasion of host immune response

[Term]
id: ID:0000113
name: serum resistance
is_a: ID:0000100 ! pathogen evasion of host immune response

[Term]
id: ID:0000114
name: phase variation
is_a: ID:0000111 ! antigenic variation

[Term]
id: ID:0000115
name: genetic diversification
is_a: ID:0000111 ! antigenic variation

[Term]
id: ID:0000116
name: complement resistance
is_a: ID:0000113 ! serum resistance

[Term]
id: ID:0000117
name: epidemic spread of disease
is_a: ID:0000102 ! epidemiological spread of disease

[Term]
id: ID:0000118
name: pandemic spread of disease
is_a: ID:0000102 ! epidemiological spread of disease

[Term]
id: ID:0000119
name: vaccination
is_a: ID:0000106 ! immunization

[Term]
id: TB:0000000
name: progression rate
is_a: ID:0000002 ! quality

[Term]
id: TB:0000001
name: rapid progression
is_a: TB:0000000 ! progression rate

[Term]
id: TB:0000002
name: long-term non-progression
is_a: TB:0000000 ! progression rate

[Term]
id: TB:0000003
name: highly exposed persistently seronegative
is_a: TB:0000000 ! progression rate

[Term]
id: TB:0000004
name: <new term>
is_obsolete: true

[Term]
id: TB:0000005
name: co-infected
is_a: GO:0000010 ! quality of host

[Term]
id: TB:0000006
name: fitness
comment: is a quality relating to both bacteria and host
is_a: ID:0000002 ! quality

[Typedef]
id: has_participant
name: has_participant

[Typedef]
id: has_quality
name: has_quality

[Typedef]
id: has_role
name: has_role

[Typedef]
id: part_of
name: part_of

[Typedef]
id: preceded_by
name: preceded_by