]> 2010-05-26 Alan Ruttenberg 2010-05-26 Albert Goldfain en Alexander Diehl Barry Smith Lindsay Cowell The core Infectious Disease Ontology is an ontology of entities generally relevant to both the biomedical and clinical aspects of infectious diseases, such as 'pathogen', 'host', 'vector', and 'vaccine'. The structure of IDO adheres to the Basic Formal Ontology. Terms in IDO that are within the scope of other OBO Foundry ontologies, such as the Gene Ontology, are derived from those ontologies. Other terms are defined as much as possible as cross-products of terms from Foundry ontologies. For more information, see http://www.infectiousdiseaseontology.org/Home.html This ontology is in early development. Expect it to change. is_realized_by bearer_of occurs_in has_part _obsolete_process _obsolete_role _obsolete_quality _obsolete_object _obsolete_virulence 'the degree of pathogenicitynnpathogenicity and virulence are used in some communities as synonyms.'-ID[O]:0000004: the degree of pathogenicitynnpathogenicity and virulence are used in some communities as synonyms. id 'virulence'-ID[O]:0000004 from IDO 2007. May have replacement - TBD _obsolete_swollen _obsolete_toxicity _obsolete_active _obsolete_contagious _obsolete_latency 'infection has occurred, but it might not have manifested itselfnquality of being in a non replicative statentime to manifest itself na pathogen when it is in a non replicative state'-ID[O]:0000009: infection has occurred, but it might not have manifested itselfnquality of being in a non replicative statentime to manifest itself na pathogen when it is in a non replicative state id 'latency'-ID[O]:0000009 from IDO 2007. May have replacement - TBD _obsolete_immunosuppressed _obsolete_exogenous _obsolete_immunity _obsolete_protective _obsolete_temperature _obsolete_inactivated _obsolete_mortality _obsolete_pandemic _obsolete_prevalence 'total number of cases of a particular disease at a given time in a particular population divided by the number of individuals in that particular populationnnthe burden of a disease in a population'-ID[O]:0000019: total number of cases of a particular disease at a given time in a particular population divided by the number of individuals in that particular populationnnthe burden of a disease in a population id 'prevalence'-ID[O]:0000019 from IDO 2007. May have replacement - TBD _obsolete_epidemic _obsolete_infected _obsolete_live _obsolete_zoonotic _obsolete_immunocompromised _obsolete_pathogenicity 'the ability of the biotic entity to cause disease in a host of a given typenndo we need to say damage instead of disease?nnpathogenicity and virulence are used as synonyms in some communities'-ID[O]:0000025: the ability of the biotic entity to cause disease in a host of a given typenndo we need to say damage instead of disease?nnpathogenicity and virulence are used as synonyms in some communities id 'pathogenicity'-ID[O]:0000025 from IDO 2007. May have replacement - TBD _obsolete_tropism _obsolete_drug resistance _obsolete_antibiotic resistance _obsolete_incidence 'number of new cases in a given period of time'-ID[O]:0000029: number of new cases in a given period of time id 'incidence'-ID[O]:0000029 from IDO 2007. May have replacement - TBD _obsolete_invasive _obsolete_endogenous _obsolete_attenuated _obsolete_morbidity _obsolete_endemic _obsolete_fusion protein _obsolete_colonizer _obsolete_commensal _obsolete_parasite _obsolete_symbiant _obsolete_virulence factor 'role played by a portion of substance to promote virulencennmagnitudendegree of pathogenesis'-ID[O]:0000040: role played by a portion of substance to promote virulencennmagnitudendegree of pathogenesis id 'virulence factor'-ID[O]:0000040 from IDO 2007. May have replacement - TBD _obsolete_route of entry _obsolete_invasin _obsolete_toxin _obsolete_endotoxin _obsolete_exotoxin _obsolete_sign _obsolete_treatment _obsolete_symptom 'look at mathias's ontology of cancer to get all the subterms...its under quality there'-ID[O]:0000048: look at mathias's ontology of cancer to get all the subterms...its under quality there id 'symptom'-ID[O]:0000048 from IDO 2007. May have replacement - TBD _obsolete_antimicrobial _obsolete_medicine _obsolete_therapeutic _obsolete_vaccine _obsolete_antibiotic _obsolete_colonization factor 'role played by portion of physical substance which promotes colonization'-ID[O]:0000054: role played by portion of physical substance which promotes colonization id 'colonization factor'-ID[O]:0000054 from IDO 2007. May have replacement - TBD _obsolete_adhesion factor 'role played by portion of physical substance utilized by an organism in order to establish adherence to a surface in a host'-ID[O]:0000055: role played by portion of physical substance utilized by an organism in order to establish adherence to a surface in a host id 'adhesion factor'-ID[O]:0000055 from IDO 2007. May have replacement - TBD _obsolete_host _obsolete_carrier _obsolete_chronic carrier _obsolete_reservoir 'holding place for a potential pathogen...animate or inanimate'-ID[O]:0000059: holding place for a potential pathogen...animate or inanimate id 'reservoir'-ID[O]:0000059 from IDO 2007. May have replacement - TBD _obsolete_fomite 'inanimate holder, is water a fomite or only a reservoir?'-ID[O]:0000060: inanimate holder, is water a fomite or only a reservoir? id 'fomite'-ID[O]:0000060 from IDO 2007. May have replacement - TBD _obsolete_mobile genetic element _obsolete_pathogenicity island _obsolete_vector 'holder and a carrier (actively transmits) and living: potentially make a cross product. every vector comes into contact with the target. (from one host to another?)'-ID[O]:0000063: holder and a carrier (actively transmits) and living: potentially make a cross product. every vector comes into contact with the target. (from one host to another?) id 'vector'-ID[O]:0000063 from IDO 2007. May have replacement - TBD _obsolete_pathogen _obsolete_dependovirus _obsolete_infectious agent _obsolete_opportunistic pathogen _obsolete_emerging pathogen _obsolete_primary pathogen _obsolete_prion _obsolete_initiation of infection _obsolete_disruption of body surface _obsolete_disruption of normal microbioflora _obsolete_pathogen adherence to host cell 'create cross products for "host" and "pathogen" that will be part of this process.'-ID[O]:0000074: create cross products for "host" and "pathogen" that will be part of this process. id 'pathogen adherence to host cell'-ID[O]:0000074 from IDO 2007. May have replacement - TBD _obsolete_nonspecific adherence _obsolete_specific adherence _obsolete_afimbrial specific adherence _obsolete_fimbrial specific adherence _obsolete_penetration of epithelial barrier _obsolete_penetration via injury of epithelial barrier _obsolete_transcytosis _obsolete_utilization of membranous cell gateway _obsolete_transmission 'the process by which an infectious agent passes from one organism to another organism'-ID[O]:0000083: the process by which an infectious agent passes from one organism to another organism id 'transmission'-ID[O]:0000083 from IDO 2007. May have replacement - TBD _obsolete_pathogenesis 'GO:nthe specific processes that generate the ability of an organism to cause disease in anothernnnThis is defined in GO so import.'-ID[O]:0000084: GO:nthe specific processes that generate the ability of an organism to cause disease in anothernnnThis is defined in GO so import. id 'pathogenesis'-ID[O]:0000084 from IDO 2007. May have replacement - TBD _obsolete_penetration of host cell _obsolete_engulfment _obsolete_fusion with host cell membrane _obsolete_membrane invagination _obsolete_passage through cell membrane _obsolete_engulfment by nonphagocyte _obsolete_engulfment by phagocyte _obsolete_damaging host cells and tissues in subepithelial space _obsolete_induction of damaging host immune response _obsolete_pathogen-induced apoptosis _obsolete_pathogen-induced necrosis _obsolete_virus-induced cytopathogenesis _obsolete_pathogen spread through host _obsolete_infectious disease 'comment about the instances:nncollections of etiologically connected cases of infectious disease in a given population'-ID[O]:0000098: comment about the instances:nncollections of etiologically connected cases of infectious disease in a given population id 'infectious disease'-ID[O]:0000098 from IDO 2007. May have replacement - TBD _obsolete_pathogen evasion of host immune response _obsolete_emergence 'the process by which an infectious disease establishes itself in a new population (or at a sufficiently higher rate? higher prevalence and/or higher incidence)'-ID[O]:0000101: the process by which an infectious disease establishes itself in a new population (or at a sufficiently higher rate? higher prevalence and/or higher incidence) id 'emergence'-ID[O]:0000101 from IDO 2007. May have replacement - TBD _obsolete_epidemiological spread of disease _obsolete_outbreak _obsolete_infection _obsolete_infection treatment process _obsolete_immunization _obsolete_prevention of infection _obsolete_transport by blood _obsolete_transport by lymph _obsolete_modulation of inflammatory response _obsolete_antigenic variation _obsolete_resist phagocytosis in subepithelial space _obsolete_serum resistance _obsolete_phase variation _obsolete_genetic diversification _obsolete_complement resistance _obsolete_epidemic spread of disease _obsolete_pandemic spread of disease _obsolete_vaccination _obsolete_mode of transmission _obsolete_end reservoir _obsolete_factor 'Role played by portion of physical substance in a biological process'-ID[O]:0000204: Role played by portion of physical substance in a biological process id 'factor'-ID[O]:0000204 from IDO 2007. May have replacement - TBD _obsolete_colonization 'the process by which a biotic entity establishes multiple copies of itself in a new environment (including an organismal environment).nnfix idn"native" environment term'-ID[O]:0000205: the process by which a biotic entity establishes multiple copies of itself in a new environment (including an organismal environment).nnfix idn"native" environment term id 'colonization'-ID[O]:0000205 from IDO 2007. May have replacement - TBD _obsolete_biotic _obsolete_adhesin _obsolete_seroprevalence 'prevalence as measured by antibody'-ID[O]:0000208: prevalence as measured by antibody id 'seroprevalence'-ID[O]:0000208 from IDO 2007. May have replacement - TBD _obsolete_dormancy 'quality [state] of an organism that during its life cycle in which its growth. development, metabolism, etc is temporarily suspended nnnsuspended state, non-replicative state, resting state'-ID[O]:0000209: quality [state] of an organism that during its life cycle in which its growth. development, metabolism, etc is temporarily suspended nnnsuspended state, non-replicative state, resting state id 'dormancy'-ID[O]:0000209 from IDO 2007. May have replacement - TBD _obsolete_quality of host _obsolete_quality of pathogen _obsolete_susceptibility 'can change depending on environmentnnwhere should susceptibility factors go?'-ID[O]:0000212: can change depending on environmentnnwhere should susceptibility factors go? id 'susceptibility'-ID[O]:0000212 from IDO 2007. May have replacement - TBD _obsolete_resistance _obsolete_refractoriness _obsolete_quality of host population _obsolete_herd immunity _obsolete_quality of infectious disease _obsolete_case of infectious disease _obsolete_incubation period 'agent is incubated?ndisease is incubated?'-ID[O]:0000219: agent is incubated?ndisease is incubated? id 'incubation period'-ID[O]:0000219 from IDO 2007. May have replacement - TBD _obsolete_infectivity period _obsolete_infectious disease progression 'the unfolding or course of infectious diseasennwhat do we say about infectious disease that always remain latent nwhat about when a pathogen continues its progression nnwe need to think about whether we need a term called stagenlife cycle?nprogression?ndevelopment?'-ID[O]:0000221: the unfolding or course of infectious diseasennwhat do we say about infectious disease that always remain latent nwhat about when a pathogen continues its progression nnwe need to think about whether we need a term called stagenlife cycle?nprogression?ndevelopment? id 'infectious disease progression'-ID[O]:0000221 from IDO 2007. May have replacement - TBD _obsolete_infectious disease course _obsolete_host recovery period _obsolete_intrinsic incubation period _obsolete_extrinsic incubation period _obsolete_pathogen life cycle 'is this just the part of the life cycle of the biotic entity that has role pathogen for the period of time while it has role pathogen?nncan include phases in the existence of the entity before it becomes a pathogen'-ID[O]:0000226: is this just the part of the life cycle of the biotic entity that has role pathogen for the period of time while it has role pathogen?nncan include phases in the existence of the entity before it becomes a pathogen id 'pathogen life cycle'-ID[O]:0000226 from IDO 2007. May have replacement - TBD _obsolete_dormancy period 'is a period a process?'-ID[O]:0000227: is a period a process? id 'dormancy period'-ID[O]:0000227 from IDO 2007. May have replacement - TBD _obsolete_pathogen outbreak _obsolete_oral-fecal transmission _obsolete_vertical transmission _obsolete_horizontal transmission _obsolete_pathogen life cycle stage _obsolete_infectious disease progression stage _obsolete_progression rate _obsolete_rapid progression _obsolete_long-term non-progression _obsolete_highly exposed persistently seronegative _obsolete_co-infected _obsolete_fitness 'is a quality relating to both bacteria and host'-ID[O]:0000306: is a quality relating to both bacteria and host id 'fitness'-ID[O]:0000306 from IDO 2007. May have replacement - TBD symbiont role Alexander Diehl Albert Goldfain A role borne by an organism in symbiosis. Lindsay Cowell mutualist role Alexander Diehl A symbiont role borne by an organism in virtue of the fact that both symbionts derive a growth, survival, or fitness advantage from symbiosis. Albert Goldfain Lindsay Cowell commensal role Alexander Diehl A symbiont role borne by an organism in virtue of the fact that it derives a growth, survival, or fitness advantage from symbiosis, but the other symbiont is neither advantaged nor disadvantaged. Albert Goldfain Lindsay Cowell parasite role A symbiont role borne by an organism in virtue of the fact that it derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent role A role borne by an infectious agent when contained in a host in which its infectious disposition can be realized. Albert Goldfain Lindsay Cowell Alexander Diehl pathogen role Lindsay Cowell A role borne by a material entity in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition. Albert Goldfain Alexander Diehl Formal definition: A role borne by an organism (x) by virtue of the fact that it has the pathogenic disposition relative to organisms of type Y, and 2) x, one of its parts, or one of its products and an organism (y) of type Y have spatiotemporal locations which allow processes resulting in disease or death of y to occur. The role is realized in y's disease course. opportunistic infectious disposition Albert Goldfain Lindsay Cowell Alexander Diehl An infectious disposition to become clinically abnormal only in organisms whose defenses are compromised. opportunitistic pathogenic disposition primary infectious disposition Alexander Diehl Lindsay Cowell Albert Goldfain An infectious disposition to become clinically abnormal in organisms that have intact defenses. symbiont host role Lindsay Cowell A host role borne by an organism in virtue of the fact that its extended organism contains a second organism and provides an environment supportive for the survival, growth, maturation, or reproduction of that organism. Albert Goldfain Alexander Diehl definitive host role Lindsay Cowell Alexander Diehl Albert Goldfain 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. primary host role intermediate host role Alexander Diehl Lindsay Cowell Albert Goldfain 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. secondary host role paratenic host role Alexander Diehl Lindsay Cowell A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis utilizes the host to undergo a developmental stage transition, but the host is not required for continuation of the partner's life cycle. Albert Goldfain dead-end host role 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. Lindsay Cowell Alexander Diehl Albert Goldfain incidental host role parasite host role Albert Goldfain Alexander Diehl 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. Lindsay Cowell infectious agent host role A pathogen host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell pathogen host role Albert Goldfain Alexander Diehl Lindsay Cowell A host role borne by an organism in virtue of the fact that its extended organism contains a pathogen. Formal definition: A host role borne by an organism (x) by virtue of the fact that it is participating in a process of symbiosis (GO:0044403) with an organism (y) that has the pathogenic disposition to organisms of type Z; x may be of type Z or another type. In the symbiosis process, y is bearer of the pathogen role. The role is realized in the processes that result in disease or death of an organism of type Z. infectious agent carrier role Alexander Diehl Lindsay Cowell Albert Goldfain 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. infectious agent transporter role A role borne by a material entity in virtue of the fact that an infectious agent is located in or on the entity and the entity has the capability to transfer (either actively or passively) the infectious agent from one location to another. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent vector role Alexander Diehl Lindsay Cowell Albert Goldfain 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. Formal definition: A transporter of infectious organism role borne by an organism (x) by virtue of the fact that 1) it is active in the transmission of an infectious organism (y) to a host organism (z) while carrying out a process that is part of its normal life history (e.g. moving from place to place), 2) y has the infectious disposition relative to organisms of type Z, 3) x is not an organism of type Z, 4) z is an organism of type Z, 5) and x does not itself cause an infectious disease caused by Y in Z. The role is realized in the transmission process (TRANS:0000000). mechanical vector of infectious agent role Alexander Diehl Lindsay Cowell Albert Goldfain 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. biological vector of infectious agent role Alexander Diehl Lindsay Cowell Albert Goldfain An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent multiplies in or on the vector. infectious agent vehicle role Albert Goldfain Lindsay Cowell Alexander Diehl An infectious agent transporter role borne by an entity in virtue of the fact that the entity is not a complete organism. biological vehicle of infectious agent role Albert Goldfain 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. Lindsay Cowell Alexander Diehl fomite role Albert Goldfain Alexander Diehl An infectious agent vehicle role borne by an entity in virtue of the fact that the entity is not alive. Lindsay Cowell reservoir of infectious agent role A role borne by a material entity in virtue of the fact that it is a habitat in which infectious agents can persist and multiply and from which they can be transmitted in virtue of prevailing practices of potential hosts. Albert Goldfain Alexander Diehl Lindsay Cowell virulence factor disposition Alexander Diehl Lindsay Cowell Albert Goldfain A disposition borne by a biological macromolecule produced by a pathogen that is the disposition to improve survival of the pathogen in a host, improve transmission of the pathogen to a host, or cause pathological processes in a host. toxin disposition Alexander Diehl Lindsay Cowell A virulence factor disposition to cause I) malfunction of cells, ii) damage to extracellular matrix, or iii) damage of cells to a degree that can result in cell death. Albert Goldfain exotoxin disposition Albert Goldfain A toxin disposition to damage cells or extracellular matrix by a direct enzymatic process. Alexander Diehl Lindsay Cowell enterotoxin disposition Lindsay Cowell Alexander Diehl Albert Goldfain An exotoxin disposition to damage cells of the host intestinal mucosa. endotoxin disposition Albert Goldfain Lindsay Cowell A toxin disposition that inheres in a protein or protein complex that is released from a pathogen only upon cytolysis. Alexander Diehl infectious agent portal of entry role 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. Lindsay Cowell Alexander Diehl Albert Goldfain Formal definition: A role borne by an anatomical entity (CARO:0000000) by virtue of the fact that 1) the anatomical entity is part of an organism (x) of type X, 2) x is participating in a process of establishing an infection in x, and 3) the anatomical entity serves as the site through which infectious organism enters x. The role is realized in the process by which the infectious organism enters x. infectious agent portal of exit role Lindsay Cowell Alexander Diehl Albert Goldfain 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. Formal definition: A role borne by an anatomical entity (CARO:0000000) by virtue of the fact that 1) the anatomical entity is part of an organism (x) of type X, 2) x is participating in a process of transmitting x, and 3) the anatomical entity serves as the site through which infectious organism exits x. The role is realized in the process by which the infectious organism exits x. disinfectant role Alexander Diehl A role borne by a material entity in virtue of the fact that it has an antimicrobial disposition and is applied to a non-living entity. Albert Goldfain Lindsay Cowell antiseptic role 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. Alexander Diehl Lindsay Cowell Albert Goldfain primary infection role Alexander Diehl Lindsay Cowell Albert Goldfain 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. secondary infection role Alexander Diehl 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. Lindsay Cowell Albert Goldfain infectious disease Albert Goldfain Alexander Diehl A disease whose physical basis is an infectious disorder. Formal definition: A disease (OGMS:0000031) that has an infection (IDO:0000586) as its physical basis and is realized in an infectious disease course (IDO:0000495). Lindsay Cowell tranmissible disease adhesion disposition Albert Goldfain Lindsay Cowell Alexander Diehl A disposition borne by a biological macromolecule that is the disposition to participate in adherence to host. invasion disposition Albert Goldfain 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. Alexander Diehl Lindsay Cowell antimicrobial disposition Alexander Diehl Lindsay Cowell A disposition to kill or inhibit the growth of microorganisms. Albert Goldfain antibiotic disposition antiviral disposition Alexander Diehl Lindsay Cowell Albert Goldfain An antimicrobial disposition to kill or inhibit the growth of viruses. antifungal disposition Lindsay Cowell Albert Goldfain Alexander Diehl An antimicrobial disposition to kill or inhibit the growth of fungal organisms. antibacterial disposition Lindsay Cowell Albert Goldfain Alexander Diehl An antimicrobial disposition to kill or inhibit the growth of bacteria. antiparasitic disposition Albert Goldfain Lindsay Cowell A disposition to kill or inhibit the growth of eukaryotic parasites. Alexander Diehl protective resistance Lindsay Cowell Alexander Diehl A disposition that inheres in a material entity in virtue of the fact that the entity has a part (e.g. a gene product), which itself has a disposition to mitigate damage to the entity. Albert Goldfain resistance to drug Albert Goldfain Lindsay Cowell A protective resistance that mitigates the damaging effects of a drug. Alexander Diehl drug resistance host resistance to infectious agent Albert Goldfain Alexander Diehl A protective resistance that inheres in an organism and mitigates the damaging effects on that organism of an infectious agent. Lindsay Cowell herd immunity to infectious organism Alexander Diehl Albert Goldfain 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 a host to a susceptible individual and thereby mitigating the damaging effects of the infectious agent on the population. Lindsay Cowell immunity to infectious agent Alexander Diehl Lindsay Cowell Albert Goldfain A host resistance to infectious agent that inheres in an organism in virtue of immune system components in the extended organism. protective immunity to infectious agent sterilizing immunity to infectious agent Alexander Diehl Lindsay Cowell Albert Goldfain An immunity to infectious agent that results in elimination of the infectious agent from the host. pathogenic disposition Alexander Diehl Formal definition: A disposition that inheres in an object (x) relative to an organism of type Y by virtue of the fact that x has the capability to initiate processes that result in the presence of a disorder (OGMS:0000045) in organisms of type Y. If x is an organism, x is not of type Y. The disposition is realized in the processes that create the disorder. Lindsay Cowell A disposition to initiate processes that result in a disorder. Albert Goldfain pathogenicity invasive disposition A disposition borne by an infectious agent that is the disposition to penetrate the epithelial barriers of an organism of another species. Lindsay Cowell Albert Goldfain Alexander Diehl infectious disposition A pathogenic disposition that inheres in a material entity and is the disposition for that entity (1) to be transmitted to a host, (2) to establish itself in the host, and (3) to become part of a disorder in the host. Lindsay Cowell Albert Goldfain Alexander Diehl Formal definition: A pathogenic disposition (IDO:0000450) that inheres in an object (x) relative to an organism of type Y by virtue of the fact that x has the capability 1) to be transmitted (TRANS:0000000), either directly or indirectly, to organisms of type Y and 2) to establish a clinically abnormal colony in any organism of type Y (IDO:0000606). If x is an organism, x is not of type Y. zoonotic disposition Albert Goldfain Lindsay Cowell Alexander Diehl An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host. reverse zoonotic disposition Albert Goldfain An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host. Lindsay Cowell Alexander Diehl collective disposition Lindsay Cowell A disposition that inheres in a collection of entities in virtue of the individual dispositions of the constituents of that collection. Albert Goldfain Alexander Diehl immunosuppressed organism Albert Goldfain Alexander Diehl An organism that is experiencing pregnancy-induced or pathologic immunosuppression. Formal definition: A quality that inheres in an organism with an immune system by virtue of the fact that the organism's immunocompetence is reduced as a result of substances, such as drugs, or infections that interfere with one or more immune system processes (GO:0002376). Lindsay Cowell immunocompetent host Alexander Diehl Albert Goldfain An organism that has immunocompetence. Lindsay Cowell contagiousness 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. Alexander Diehl Albert Goldfain Formal definition: A quality inhering in a bearer of the host of infectious agent role by virtue of the fact that the host's infectious disease is at a stage during which the infectious organism causing the disease is easily transmitted from one host to another. 'Easily' refers to the fact that transimission is likely as a result of pathological processes, like coughing and sneezing, that are a manifestation of the disease during a particular stage. Lindsay Cowell colonized host Albert Goldfain Lindsay Cowell A host that contains a colony in or on its extended organism. Alexander Diehl infected host Lindsay Cowell Alexander Diehl Albert Goldfain A host that has an infection in or on its extended organism. Formal definition: A quality inhering in an organism by virtue of the fact that the organism is the bearer of the host of infectious parasite role in a symbiosis process (GO:0044403) with an organism that has the infectious disposition and that has established an infection in the host. co-infected host Lindsay Cowell Albert Goldfain Alexander Diehl An infected host that has two infections with different species of infectious agents as part. Formal definition: A quality inhering in an organism by virtue of the fact that the organism is the bearer of the host of infectious parasite role in a symbiosis process (GO:0044403) with organisms of at least two different types that have the infectious disposition and that have established an infection in the host. symptomatic host A host exhibiting disease symptoms. Lindsay Cowell Alexander Diehl Albert Goldfain infectious agent transmissibility Alexander Diehl Lindsay Cowell A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process. Albert Goldfain infectivity Lindsay Cowell Alexander Diehl A quality that inheres in an infectious agent and is the liklihood that the infectious disposition will be realized upon exposure of a susceptible organism. Albert Goldfain Formal definition: A quality inhering in an organism that has the infectious disposition relative to organisms of type Y and is the likelihood that organisms of type Y that are exposed to the infectious organism become infected. virulence Alexander Diehl 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. Formal definition: A quality inhering in an organism that has the pathogenic disposition and is the degree to which realizations of the disease caused by the organism become severe or fatal. Lindsay Cowell Albert Goldfain susceptibility A quality that inheres in an entity and is the degree to which it can be harmed by another entity. Lindsay Cowell Albert Goldfain Alexander Diehl Formal definition: A quality inhering in a material entity (x) that is the degree to which another material entity can harm x. susceptibility to infectious agent Albert Goldfain Lindsay Cowell Alexander Diehl A susceptibility that inheres in an organism and is the degree to which it can be harmed by an infectious agent. Formal definition: A susceptibility that inheres in an organism (x) of type X relative to an organism of type Y 1) by virtue of the fact that Y have the infectious disposition relative to X, and X have the capability to bear the host of infectious agent role in symbiosis with some Y, and is 2) the likelihood that x will participate in a symbiosis process (GO:0044403) with some Y in which it plays the host of infectious agent role, or 3) the degree to which x can be harmed by participation in the symbiosis process or by pathoglocial processes that are the realization of an infectious disease caused by Y. drug susceptibility Albert Goldfain A susceptibility that is the degree to which an entity can be harmed or inhibited from surviving by a drug. Lindsay Cowell Alexander Diehl drug susceptibility of infectious agent Lindsay Cowell Alexander Diehl Albert Goldfain 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. complex infection Alexander Diehl Albert Goldfain An infection comprised of infectious organisms from different species. Lindsay Cowell mixed infection polymicrobial infection extracellular infection Alexander Diehl Lindsay Cowell Albert Goldfain An infection for which the infectious agents that are part of the infection persist in the extracellular space of the host. intracellular infection Lindsay Cowell Albert Goldfain Alexander Diehl An infection for which the infectious agents that are part of the infection persist inside host cells. systemic infection Lindsay Cowell Albert Goldfain Alexander Diehl An infection for which the infectious agents that are part of the infection are distributed throughout the host. Formal definition: A quality that inheres in an infection by virtue of the fact that the organisms comprising the infection are distributed throughout the host, including multiple host organs and/or systems (e.g. circulatory system). local infection Albert Goldfain Alexander Diehl 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. Lindsay Cowell focal infection Lindsay Cowell Albert Goldfain Alexander Diehl A local infection for which symptoms are observed in parts of the host's extended organism that are distant from the infection. acute infectious disease course Albert Goldfain Lindsay Cowell Alexander Diehl An infectious disease course that begins soon after infection is established and progresses rapidly to severe stages. _obsolete_chronic quality of infection Albert Goldfain Lindsay Cowell A quality that inheres in an infection in virtue of the fact that the infection persists for an extended period of time. Alexander Diehl persistent infection infectious disease incidence Alexander Diehl Albert Goldfain Formal definition: A quality that 1) inheres in a pre-speciified organism population whose members have the capability to play the host of infectious agent role in symbiosis with organisms of the type that cause infectious disease X and 2) is the number of realizations of the infectious disease for which the infectious disease course (the realization of the disease) begins during a specified period of time. Lindsay Cowell 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. infection incidence Albert Goldfain Alexander Diehl 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. Formal definition: A quality that 1) inheres in a pre-speciified organism population whose members have the capability to play the host of infectious agent role for organisms of type X and 2) is the number of organisms in the population that begin bearing the host role for the infectious organism during a specified period of time. Lindsay Cowell infectious disease incidence proportion A quality that inheres in an organism population and is the infectious disease incidence divided 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. Alexander Diehl Albert Goldfain Lindsay Cowell cumulative incidence of infectious disease infection incidence proportion A quality that inheres in an organism population and is the infection incidence divided by the number of members of the population that are not infected at the beginning of the specified period of time. Alexander Diehl Albert Goldfain Lindsay Cowell cumulative incidence of infection infectious disease incidence rate A quality that inheres in an organism population and is the infectious disease incidence proportion divided by the period of time over which the incidence was measured. Lindsay Cowell Albert Goldfain Alexander Diehl infection incidence rate Lindsay Cowell Albert Goldfain A quality that inheres in an organism population and is the incidence proportion of infection divided by the period of time over which the incidence was measured. Alexander Diehl infectious disease prevalence Lindsay Cowell Alexander Diehl Albert Goldfain 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. infection prevalence Lindsay Cowell 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. Alexander Diehl Albert Goldfain infectious disease lifetime prevalence Lindsay Cowell Albert Goldfain 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. Alexander Diehl infectious agent seroprevalence Albert Goldfain Alexander Diehl Lindsay Cowell 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. infectious disease mortality rate Alexander Diehl A quality that inheres in an organism population and is the proportion of deaths in the population resulting from an infectious disease over a specified period of time. Lindsay Cowell Albert Goldfain infectious disease endemicity Alexander Diehl Lindsay Cowell A quality that inheres in an organism population in virtue of the fact that infections of the type that causes an infectious disease are maintained in the population via intra-population transmission or by transmission from a local reservoir. Albert Goldfain Formal definition: A quality that 1) inheres in a pre-speciified organism population whose members have the capability to play the host of infectious agent role in symbiosis with organisms of the type that cause infectious disease X, 2) by virtue of the fact that infections of the organism type that causes infectious disease X are maintained in the population without the need for transmission into the population from hosts that are not members of the population. Infectious diseases that are typical or common to a particular population are referred to as endemic. infectious disease endemic level Alexander Diehl Lindsay Cowell Albert Goldfain A quality that inheres in an organism population and is the infectious disease prevalence that is typical for an infectious disease in that organism population. infectious disease endemic rate Lindsay Cowell Alexander Diehl A quality that inheres in an organism population and is the infectious disease incidence rate that is typical for an infectious disease in that organism population. Albert Goldfain infectious disease hyper-endemicity Albert Goldfain Lindsay Cowell Alexander Diehl An infectious disease endemicity quality 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. infectious disease sporadicicity A quality that inheres in an organism population by virtue of the fact that infections of the infectious agent that causes a certain type of infectious disease occur in the population with a fluctuating prevalence. Lindsay Cowell Albert Goldfain Alexander Diehl infectious disease course A disease course that is the realization of an infectious disease. Alexander Diehl Albert Goldfain Formal definition: A disease course (OGMS:0000063) that is the total process of realization of an infectious disease (IDO:0000436), beginning with the manifestation of pathological processes caused by an infection (IDO:0000586) and ending with 1) clearance of the infection, 2) long-term control of the infection by the host's immune response accompanied by the resolution of symptoms, or 3) death of the host. Lindsay Cowell long-term nonprogressing infectious disease course A chronic infectious disease course that does not progress to severe stages for a long period of time. Alexander Diehl Lindsay Cowell Albert Goldfain immunization against infectious agent Lindsay Cowell Alexander Diehl Albert Goldfain A process by which an organism acquires immunity to an infectious agent. active immunization against infectious agent Albert Goldfain An immunization process that begins with exposure of an organism to antigen and results in immunity against an infectious agent. Lindsay Cowell Alexander Diehl inoculation vaccination against infectious agent Alexander Diehl Albert Goldfain An active immunization process that begins with exposure of an organism to a vaccine and results in immunity against an infectious agent. Lindsay Cowell variolation Alexander Diehl Albert Goldfain An active immunization process that begins with exposure to smallpox in the form of a scab from a pustule and results in immunity against smallpox. Lindsay Cowell passive immunization against infectious agent Alexander Diehl Albert Goldfain An immunization process that begins with transfer to an organism of molecules not produced by that organism and that confer immunity against an infectious agent. Examples include the injection of antibodies and the transfer of maternal antibodies to the fetus. Lindsay Cowell infectious disease epidemic Albert Goldfain Lindsay Cowell Alexander Diehl A process of infectious disease realizations and for which there is a significant increase in the infectious disease incidence of a population. For a particular instance of infectious disease epidemic, signficance is determined based on the infectious disease incidence that is typical for an infectious disease for the particular population and time period. infectious disease outbreak infectious disease pandemic Albert Goldfain 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. Lindsay Cowell Alexander Diehl infectious disorder Alexander Diehl Albert Goldfain Lindsay Cowell An infection that is clinically abnormal. viremia Lindsay Cowell Albert Goldfain Alexander Diehl An infection that has as part virus particles located in the blood. Formal definition: An infection defined by the presence of virions in the blood. bacteremia Lindsay Cowell Alexander Diehl Albert Goldfain An infection that has as part bacteria located in the blood. Formal definition: An infection defined by the presence of bacteria in the blood. _obsolete_septicemia A bacteremia in which the baceteria are replicating. Alexander Diehl Albert Goldfain Lindsay Cowell virion Alexander Diehl Albert Goldfain Lindsay Cowell A virus that is in its assembled state consisting of genomic material (DNA or RNA) surrounded by coating molecules. organism population Alexander Diehl A population of organisms. Albert Goldfain Lindsay Cowell infected population Lindsay Cowell Albert Goldfain Alexander Diehl An organism population whose members have an infection. diseased population Lindsay Cowell Alexander Diehl Albert Goldfain An infected population in whose members the infectious disease caused by the infectious agent is being realized. infectious organism population Albert Goldfain Lindsay Cowell Alexander Diehl An organism population whose members each have an infectious disposition. susceptible population Alexander Diehl Albert Goldfain Lindsay Cowell An organism population whose members are not infected with an infectious agent and who lack immunity to the infectious agent. at-risk population normal resident microbiota population Alexander Diehl Albert Goldfain An organism population whose members are particpating in non-parasitic symbiosis with a particular host. Lindsay Cowell Formal definition: An infectious organism population (IDO:0000513) (1) that is not part of any infection (IDO:0000586), (2) whose members are participating in a process of symbiosis (GO:0044403) with the same host, and (3) whose members are organisms of types among the normal resident microbiota for the type of host organism. normal resident microflora population _obsolete_configured infectious organism population Alexander Diehl Albert Goldfain 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 Lindsay Cowell incubation period Albert Goldfain Lindsay Cowell Alexander Diehl A continuous temporal interval beginning with the extablishment of an infectious agent colony and ending with the onset of symptoms (or infectious disease course?). communicability period A continuous temporal interval during which contagiousness inhering in the bearer of a host role. Lindsay Cowell Alexander Diehl Albert Goldfain symbiont Lindsay Cowell Albert Goldfain Alexander Diehl An organism bearing the symbiont role. obligatory symbiont Lindsay Cowell Albert Goldfain Alexander Diehl An organism that can only reach developmental maturity, replicate, or persist in symbiosis. mutualist Albert Goldfain A symbiont bearing the mutualist role. Lindsay Cowell Alexander Diehl commensal Albert Goldfain Alexander Diehl Lindsay Cowell A symbiont bearing the commensal role. parasite A symbiont bearing the parasite role. Albert Goldfain Lindsay Cowell Alexander Diehl infectious organism Albert Goldfain Alexander Diehl An infectious agent that is an organism. Lindsay Cowell pathogen Lindsay Cowell Alexander Diehl A material entity with a pathogenic disposition. Albert Goldfain primary pathogen Alexander Diehl Albert Goldfain An infectious agent with the primary infectious disposition. Lindsay Cowell host Albert Goldfain An organism bearing the host role. Lindsay Cowell Alexander Diehl definitive host A host bearing the definitive host role. Lindsay Cowell Albert Goldfain Alexander Diehl primary host intermediate host A host bearing the intermediate host role. Alexander Diehl Lindsay Cowell Albert Goldfain secondary host paratenic host Lindsay Cowell Alexander Diehl Albert Goldfain A host bearing the paratenic host role. dead-end host Lindsay Cowell Alexander Diehl Albert Goldfain A host bearing the dead-end host role. incidental host parasite host A host bearing the parasite host role. Albert Goldfain Lindsay Cowell Alexander Diehl infectious agent host A host bearing the infectious agent host role. Albert Goldfain Lindsay Cowell Alexander Diehl pathogen host Alexander Diehl Lindsay Cowell A host bearing the pathogen host role. Albert Goldfain infectious agent carrier Albert Goldfain Lindsay Cowell Alexander Diehl An infectious agent host bearing the infectious agent carrier role. infectious agent vector Alexander Diehl Lindsay Cowell Albert Goldfain An organism bearing the infectious agent vector role. mechanical vector of infectious agent Albert Goldfain Alexander Diehl An infectious agent vector bearing the mechanical vector of infectious agent role. Lindsay Cowell biological vector of infectious agent Albert Goldfain Alexander Diehl An infectious agent vector bearing the biological vector of infectious agent role. Lindsay Cowell vehicle of infectious agent Alexander Diehl A material entity bearing the infectious agent vehicle role. Lindsay Cowell Albert Goldfain fomite Alexander Diehl Lindsay Cowell Albert Goldfain An material entity bearing the fomite role. infectious agent reservoir Albert Goldfain A material entity bearing the infectious agent reservoir role. Lindsay Cowell Alexander Diehl end reservoir of infectious agent Albert Goldfain A material entity bearing the end reservoir of infectious agent role. Alexander Diehl Lindsay Cowell dead-end reservoir of infectious agent virulence factor Albert Goldfain Lindsay Cowell A biological macromolecule produced by a pathogen and that has the virulence factor disposition. Alexander Diehl invasion factor Lindsay Cowell Alexander Diehl A biological macromolecule that has the invasion disposition. Albert Goldfain invasin toxin Albert Goldfain Alexander Diehl Lindsay Cowell A biological macromolecule bearing the toxin disposition. exotoxin Lindsay Cowell Alexander Diehl A biological macromolecule bearing the exotoxin disposition. Albert Goldfain enterotoxin Lindsay Cowell Albert Goldfain Alexander Diehl A biological macromolecule bearing the enterotoxin disposition. endotoxin Lindsay Cowell Albert Goldfain Alexander Diehl A biological macromolecule bearing the endotoxin role. infectious agent portal of entry Alexander Diehl Albert Goldfain Lindsay Cowell An anatomical entity bearing the infectious agent portal of entry role. infectious agent portal of exit Alexander Diehl Albert Goldfain Lindsay Cowell An anatomical entity bearing the infectious agent portal of exit role. disinfectant Albert Goldfain A material entity bearing the disinfectant role. Alexander Diehl Lindsay Cowell antiseptic Albert Goldfain A material entity bearing the antiseptic role. Lindsay Cowell Alexander Diehl adhesion factor Alexander Diehl A biological macromolecule that has the adhesion disposition. Lindsay Cowell Albert Goldfain adhesin adhesion molecule antimicrobial Lindsay Cowell Alexander Diehl A material entity with the antimicrobial disposition. Albert Goldfain antiviral Lindsay Cowell Alexander Diehl Albert Goldfain An antimicrobial bearing the antiviral disposition. antifungal Lindsay Cowell Albert Goldfain Alexander Diehl An antimicrobial bearing the antifungal disposition. antiparasitic Lindsay Cowell Albert Goldfain Alexander Diehl An antimicrobial bearing the antiparasitic disposition. antibiotic Albert Goldfain Alexander Diehl Lindsay Cowell An antimicrobial bearing the antibiotic disposition. microbicide Lindsay Cowell Albert Goldfain Alexander Diehl An antimicrobial whose antimicrobial disposition is realized in a process of killing microorganisms. microbicidal [entity] viricide Lindsay Cowell Albert Goldfain Alexander Diehl An antiviral whose antiviral disposition is realized in a process of killing viruses. microbistatic Albert Goldfain Lindsay Cowell Alexander Diehl An antimicrobial whose antimicrobial disposition is realized in a process of inhibiting the growth of microorganisms. primary infection Lindsay Cowell Alexander Diehl Albert Goldfain An infection bearing the primary infection role. secondary infection Lindsay Cowell Alexander Diehl Albert Goldfain An infection bearing the secondary infection role. zoonosis Lindsay Cowell Alexander Diehl Albert Goldfain An infectious disease that has as its physical basis an infection composed of infectious agents that have the zoonotic disposition. aymptomatic host of infectious agent Albert Goldfain Alexander Diehl An infectious agent host who has no symptoms of the infectious disease associated with the infectious agent. Lindsay Cowell subclinical infection Alexander Diehl Albert Goldfain An infection that is part of an asymptomatic host. Lindsay Cowell resistant entity Albert Goldfain A material entity that has the resistance disposition. Alexander Diehl Lindsay Cowell chronic carrier of infectious agent Albert Goldfain Alexander Diehl An infectious agent carrier who has been bearer of the infectious agent carrier role for an extended period of time. Lindsay Cowell symptomatic host of infectious agent Alexander Diehl Albert Goldfain Lindsay Cowell An infectious agent host who has symptoms of the infectious disease associated with the infectious agent _obsolete_invasin Alexander Diehl Albert Goldfain Lindsay Cowell synonym of invasion factor _obsolete_viral latency Alexander Diehl Lindsay Cowell Albert Goldfain innate immunity to infectious agent Albert Goldfain Lindsay Cowell Alexander Diehl An immunity to infectious agent realized in an innate immune response. adaptive immunity to infectious agent Albert Goldfain An immunity to infectious agent realized in an adaptive immune response. Lindsay Cowell Alexander Diehl humoral immunity to infectious agent Albert Goldfain Alexander Diehl An immunity to infectious agent realized in a humoral immune response. Lindsay Cowell cell-mediated immunity to infectious agent Lindsay Cowell Albert Goldfain Alexander Diehl An immunity to infectious agent realized in an immune response whose participants are T cells or other cells of the immune system. _obsolete_passive immunity to infectious agent passive immunity to infectious agent Albert Goldfain Alexander Diehl An immunity to infectious agent that inheres in an organism in virtue of antibodies not produced by that organism. An immunity to infectious organism that results from a passive immunization (IDO:0000066). Lindsay Cowell antibiotic resistance A resistance to drug that mitigates the damaging effects of an antibiotic. Lindsay Cowell Albert Goldfain Alexander Diehl long-term non-progressor Lindsay Cowell Alexander Diehl Albert Goldfain An organism experiencing a long-term non-progressing infectious disease course. emerging pathogen Lindsay Cowell Alexander Diehl Albert Goldfain An infectious agent whose infection incidence is increasing following its first introduction into a new host population. Formal definition: An infectious agent whose incidence is increasing following its first introduction into a new host population. cytotoxin disposition Alexander Diehl Albert Goldfain An exotoxin disposition that is the disposition to damage host cells. Lindsay Cowell collective pathogenic disposition Alexander Diehl A collective disposition to initiate processes that result in a disorder. Lindsay Cowell Albert Goldfain infection Alexander Diehl Albert Goldfain Lindsay Cowell A part of an extended organism that itself has as part a population of one or more infectious agents and that is (1) clinically abnormal in virtue of the presence of this population, or (2) such that clinical abnormality is a likely consequence of transmission of the infectious agent, an offspring of the infectious agent, or a member of the infectious agent population to a canonical host. host genetic resistance to infectious agent Albert Goldfain Alexander Diehl A host resistance to infectious agent that inheres in an organism in virtue of its genetic or epigenetic qualities. Lindsay Cowell collective resistance disposition A collective disposition the realization of which mitigates the damaging effects of some entity on members of the collection. Albert Goldfain Alexander Diehl Lindsay Cowell immunodeficient host Alexander Diehl Lindsay Cowell A host that has an immunodeficiency. Albert Goldfain immunocompromised host chronic infectious disease course Albert Goldfain Alexander Diehl An infectious disease course that unfolds over a long period of time. Lindsay Cowell persistent infectious disease course _obsolete_communicable disposition Alexander Diehl An infectious disposition to be transmitted directly from one human host to another. Lindsay Cowell Albert Goldfain immune population Lindsay Cowell Albert Goldfain Alexander Diehl An organism population whose members have acquired immunity to an infectious agent. transmission period Lindsay Cowell Albert Goldfain Alexander Diehl A continuous temporal interval during which a transmission process occurs. host exposure to infectious agent Alexander Diehl A process in which an infectious agent comes into physical contact with a potential host of the infectious agent. Albert Goldfain Lindsay Cowell potential host of infectious agent Alexander Diehl An organism that has the capability to bear the host of infectious agent role. Lindsay Cowell Albert Goldfain infectious agent Lindsay Cowell A pathogen whose pathogenic disposition is an infectious disposition. Albert Goldfain Alexander Diehl host exposure to environment with infectious agent Lindsay Cowell 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. Alexander Diehl Albert Goldfain host living with infected household contact Lindsay Cowell Alexander Diehl A host exposure to environment with infectious agent where the environment is a household that also has an infected host Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern Albert Goldfain host living in endemic area A host exposure to environment with infectious agent where the environment is an area in which an infectious agent is endemic Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern Alexander Diehl Lindsay Cowell Albert Goldfain release of infectious human pathogen in laboratory Alexander Diehl Lindsay Cowell Albert Goldfain A host exposure to environment with infectious agent where the exposure is accidental and the environment is a laboratory and where the infectious agent has infectious to human disposition. Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern host coming into contact with vector of infectious agent Albert Goldfain Lindsay Cowell Alexander Diehl A host exposure to environment with infectious agent where the environment contains a infectious agent vector. Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern host exposure to substance that might have infectious agent Alexander Diehl 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. Lindsay Cowell Albert Goldfain Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern process of establishing an infection A process by which an infectious agent, established in a host, becomes part of an infection in the host. Albert Goldfain Lindsay Cowell Alexander Diehl colonization of host Alexander Diehl Lindsay Cowell Albert Goldfain An establishment in host process in which an organism establishes itself in a host. Establishment of one organism in the extended organism of another (the host) involves at least one of (1) movement of the organism to a location within the host in which the organism can persist, or (2) adherence or attachment of the organism to part of the host. _obsolete_biological object colony Lindsay Cowell Albert Goldfain A biological object or group of biological objects in close spatial proximity. Alexander Diehl process of establishing a clinically abnormal colony A colonization of host process that results in a clinically abnormal colony. Albert Goldfain Alexander Diehl Lindsay Cowell production A process in which an entity comes into being as a result of the process. Albert Goldfain Alexander Diehl Lindsay Cowell replication Lindsay Cowell Alexander Diehl A production process in which a participant creates a copy of itself. Albert Goldfain colonization of human anterior nares colonization of human perineum Alexander Diehl Lindsay Cowell Albert Goldfain A colonization of human process in which the colonized site is the anterior nares. A colonization of human process in which the colonized site is the perineum. immunosuppression Alexander Diehl Lindsay Cowell A process that attenuates an immune response. Albert Goldfain physiologic immunosuppression Alexander Diehl Lindsay Cowell Albert Goldfain An immunosuppression process which unfolds as part of the natural self-regulation of an immune response. pathologic immunosuppression Alexander Diehl Lindsay Cowell Albert Goldfain An immunosuppression process which arises as the result of a disorder. Immunosuppressive disorders include those that result from infection, stress, malnutrition, and treatments such as chemotherapy or calcineurin inhibition. _obsolete_biological object Albert Goldfain Alexander Diehl Lindsay Cowell primitive _obsolete_replicating biological material entity Albert Goldfain A biological material entity that is capable of replication. Alexander Diehl Lindsay Cowell colony Alexander Diehl Lindsay Cowell Albert Goldfain An organism population persisting in a site it has colonized. infectious agent colony A colony that is an infectious agent or a population of infectious agents. Albert Goldfain Alexander Diehl Lindsay Cowell immunodeficiency A disorder of an immune system component that results in defective functioning of the immune system. Lindsay Cowell Alexander Diehl Albert Goldfain immunocompetence Lindsay Cowell Alexander Diehl A disposition that is the ability to mount a normal immune response. Albert Goldfain immunosuppressive disposition Lindsay Cowell Alexander Diehl Albert Goldfain A disposition whose realization negatively regulates an immune response. acquired immunity to infectious agent Albert Goldfain An immunity to infectious agent that inheres in an organism in virtue of lymphocytes and lymphocyte receptors that came into being as a result of a primary immune response in that organism. Lindsay Cowell Alexander Diehl adaptive immunity immune memory disposition to form a non-parasitic colony Albert Goldfain Lindsay Cowell A disposition to colonize an organism and participate in mutualism or commensalism with that organism. Alexander Diehl communicability normal resident microbiota Alexander Diehl A generically dependent continuant that is the set of organism types whose instances have as one of their canonical dispositions, the disposition to form a non-parasitic colony in organisms of a particular type. Albert Goldfain An infectious disposition to be transmitted directly from one organism to another of the same species by horizontal transmission. Lindsay Cowell normal resident microflora _obsolete_contagiousness quality host range Lindsay Cowell Alexander Diehl A generically dependent continuant that is the set of organism types whose instances have as one of their canonical dispositions, the disposition to bear the host role for a colony of a certain type. A quality that inheres in an infection and is the likelihood that infectious agents part of the infection will spread to other hosts. Albert Goldfain establishment in host Lindsay Cowell Alexander Diehl Albert Goldfain A process starting when a material entity is in a host and during which it reaches a site in the host in which it can survive, grow, multiply, or mature. 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. appearance of disorder Albert Goldfain Alexander Diehl Lindsay Cowell A process by which a disorder comes into existence. acute infection Alexander Diehl Albert Goldfain Lindsay Cowell An infectious disorder that is the physical basis for an unfolding acute infectious disease course. chronic infection Alexander Diehl Lindsay Cowell Albert Goldfain An infection that persists for an extended period of time. persistent infection host role A role borne by an organism in virtue of the fact that it's extended organism contains a material entity. Albert Goldfain Lindsay Cowell Alexander Diehl hospital-acquired infection Albert Goldfain Alexander Diehl An infection resulting from a transmission process that unfolds in a hospital. Lindsay Cowell nosocomial infection community-acquired infection Albert Goldfain Lindsay Cowell Alexander Diehl An infection resulting from a transmission process that does not unfold in a health care facility. neurotoxin Albert Goldfain Alexander Diehl Lindsay Cowell A toxin disposition that is the disposition to interfere with the function of host nerve cells. metatstatic infection Lindsay Cowell Albert Goldfain Alexander Diehl An infection established as a result of spread from another infection in a non-adjacent location in the extended organism of the host. source of infection A role borne by a material entity in virtue of the fact that it contains a site from which an infectious agent is transmitted. Lindsay Cowell Albert Goldfain Alexander Diehl sepsis A process that is a systemic inflammatory response to infection. Alexander Diehl Lindsay Cowell Albert Goldfain severe sepsis Albert Goldfain A sepsis that results in organ dysfunction, hypotension, or hypofusion of at least one organ. Alexander Diehl Lindsay Cowell nursing-home acquired Alexander Diehl Albert Goldfain An infection resulting from a transmission process that unfolds in a nursing home. Lindsay Cowell infectious human pathogen primary immunodeficiency Albert Goldfain Lindsay Cowell Alexander Diehl An immunodeficiency that exists in an organism because of a genetic predisposition. An infectious agent with a capability to infect human hosts. congenital immunodeficiency acquired immunodeficiency Albert Goldfain An immunodeficiency that is not caused by a genetic predisposition. Lindsay Cowell Alexander Diehl simple infection Lindsay Cowell Alexander Diehl Albert Goldfain An infection comprised of infectious organism all of the same species. re-emerging pathogen Lindsay Cowell Alexander Diehl Albert Goldfain 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. Formal definition: An infectious agent whose incidence is increasing in a host population as a result of changes in its underlying epidemiology. pregnancy-induced immunosuppression Alexander Diehl An immunosuppression induced by progesterone and other factors upregulated in pregnant women. Lindsay Cowell Albert Goldfain candidiasis Albert Goldfain Alexander Diehl An infection that has as part organisms of the Genus Candida. Lindsay Cowell trichomoniasis Albert Goldfain Alexander Diehl An infection that has as part organisms of the Species Trichomonas vaginalis. Lindsay Cowell leptospirosis Albert Goldfain An infection that has as part organisms of the Genus Leptospira. Lindsay Cowell Alexander Diehl Shigellosis Albert Goldfain Lindsay Cowell Alexander Diehl An acute infection located in the bowel and that has as part organisms of the Genus Shigella. bacillary dysentery amebiasis Albert Goldfain Alexander Diehl Lindsay Cowell An infection located in the colon and that has as part organisms of the Species Entamoeba histolytica colonization of human Alexander Diehl A colonization of host process in which the host is of Species Homo sapiens. Albert Goldfain Lindsay Cowell transition to clinical abnormality A process by which a disorder comes into existence. a biological object becomes clinically abnormal. organism An organism is 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. anatomical entity molecular entity cellular component extracellular space establishment of localization Viruses transmission process