2010-12-02 Albert Goldfain Barry Smith Bjoern Peters en Alan Ruttenberg The core Infectious Disease Ontology is an ontology of entities generally relevant to both the biomedical and clinical aspects of infectious diseases, including terms 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 cross-products of terms from Foundry ontologies to the extent possible. For more information, see http://www.infectiousdiseaseontology.org/Home.html. Lindsay Cowell 2010-12-02 http://www.infectiousdiseaseontology.org/Home.html Alexander Diehl immune response immune response Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. exotoxin Lindsay Cowell Alexander Diehl A molecular entity bearing an exotoxin disposition. Albert Goldfain _obsolete_resistance Alexander Diehl Lindsay Cowell A material entity with an antiviral disposition that is realized in a process of killing viruses. viricide DL needs 'process of killing viruses' Albert Goldfain An infection that has as part virus particles located in the blood. Alexander Diehl DL needs FMA term. Albert Goldfain Lindsay Cowell viremia Lindsay Cowell An immunity to infectious agent that inheres in an organism in virtue of components of its circulating body fluid. Albert Goldfain Alexander Diehl humoral immunity to infectious agent "Circulating body fluid" refers to blood, lymph, and hemolymph. The disposition is realized in a humoral immune response. _obsolete_symptomatic host A host exhibiting disease symptoms. Lindsay Cowell Alexander Diehl Albert Goldfain _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 Viruses Viruses _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_septicemia A bacteremia in which the baceteria are replicating. Alexander Diehl Albert Goldfain Lindsay Cowell microbicidal [entity] Lindsay Cowell Albert Goldfain DL needs 'process of killing microorganisms' microbicide Alexander Diehl A material entity with an antimicrobial disposition that is realized in a process of killing microorganisms. Albert Goldfain DL needs FMA term. An infection that has as part bacteria located in the blood. Alexander Diehl bacteremia Lindsay Cowell _obsolete_adaptive immunity to infectious agent Albert Goldfain An immunity to infectious agent realized in an adaptive immune response. Lindsay Cowell Alexander Diehl infectious agent transmissibility Alexander Diehl The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening. Lindsay Cowell Albert Goldfain A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process. _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 anatomical entity Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. anatomical entity _obsolete_quality of pathogen Albert Goldfain endotoxin Alexander Diehl IDO Error endotoxin role => endotoxin disposition Lindsay Cowell A molecular entity with a toxin disposition and that is a structural component of a pathogen and is released from the pathogen only upon cytolysis. infectious disease endemic level Alexander Diehl Infectious disease endemic level is relational to previous prevalences of the disease. Lindsay Cowell Albert Goldfain An infectious disease prevalence that is typical for an infectious disease in an organism population. virion Alexander Diehl Albert Goldfain Lindsay Cowell Melanie Courtot A virus that is in its assembled state consisting of genomic material (DNA or RNA) surrounded by coating molecules. antibiotic Lindsay Cowell Alexander Diehl Albert Goldfain A material entity bearing an antiviral disposition. _obsolete_end reservoir _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 Alexander Diehl pathogenic disposition pathogenicity Lindsay Cowell The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition. By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition. A disposition to initiate processes that result in a disorder. The disposition is realized in processes that create a disorder. Albert Goldfain A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. disease disease growth growth The increase in size or mass of an entire organism, a part of an organism or a cell. infected organism Lindsay Cowell Alexander Diehl Albert Goldfain An organism that has an infection in or on its extended organism. _obsolete_oral-fecal transmission _obsolete_quality of host enterotoxin Lindsay Cowell Albert Goldfain Alexander Diehl A molecular entity with an exotoxin disposition, the realization of which damages cells of the host intestinal mucosa. Lindsay Cowell Albert Goldfain antiparasitic A material entity bearing an antiparasitic disposition. Alexander Diehl organism population The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age. Alexander Diehl Albert Goldfain An aggregate of organisms of the same Species. Lindsay Cowell _obsolete_mode of transmission Lindsay Cowell Albert Goldfain invasive disposition A disposition borne by an infectious agent that is the disposition to penetrate the epithelial barriers of an organism of another Species. Alexander Diehl Albert Goldfain Alexander Diehl cell-mediated immunity to infectious agent Lindsay Cowell An immunity to infectious agent that inheres in an organism in virtue of its leukocytes. leukocyte-mediated immunity to infectious agent The disposition is realized in a leukocyte-mediated immune response. _obsolete_antibiotic resistance 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 A particular instance of infectious disease endemicity will depend on a type of infectious agent and a population. The population may be specified by temporal, geographic, or demographic constraints. Infectious diseases that are typical or common to a particular population are referred to as endemic. co-infected organism Lindsay Cowell Albert Goldfain Alexander Diehl An organism that has two infections with distinct Species of infectious agents. _obsolete_pathogen outbreak immunodeficient organism Alexander Diehl Lindsay Cowell Albert Goldfain An organism that has an immunodeficiency. immunocompromised organism _obsolete_quality of infectious disease infectious agent portal of exit Alexander Diehl Albert Goldfain Lindsay Cowell An anatomical entity bearing an infectious agent portal of exit role. zoonosis Lindsay Cowell Albert Goldfain Alexander Diehl An infectious disease that has as its physical basis an infectious disorder composed of infectious agents that have a zoonotic disposition. immunoglobulin complex A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. immunoglobulin complex Transmission Ontology: http://purl.org/obo/owl/TRANS A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. Suggested label: pathogen transmission process transmission process transmission process transmission process Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species. humoral immune response An immune response mediated through a body fluid. humoral immune response _obsolete_invasin Alexander Diehl Albert Goldfain Lindsay Cowell synonym of invasion factor 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 blood _obsolete_host recovery period _obsolete_herd immunity infectious agent portal of entry Alexander Diehl Albert Goldfain An anatomical entity bearing an infectious agent portal of entry role. Lindsay Cowell secondary infection Lindsay Cowell Alexander Diehl Albert Goldfain An infection bearing the secondary infection role. genetic resistance to infectious agent Albert Goldfain Alexander Diehl The resistance of individuals to HIV invasion oonferred by particular CCR5 alleles is an example. Resistance against malaria conferred by the sickle cell gene is another. Lindsay Cowell A resistance to infectious agent that inheres in an organism in virtue of a specific allele or combination of alleles in its genome. symptomatic host of infectious agent Alexander Diehl Albert Goldfain Lindsay Cowell An organism who is host to an infectious agent and has symptoms of the infectious disease associated with the infectious agent _obsolete_infectious disease course establishment of localization Gene Ontology: http://purl.org/obo/owl/GO establishment of localization establishment of localization The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location. Lindsay Cowell Alexander Diehl A material entity bearing an antiseptic role. antiseptic Albert Goldfain A cytokinesis process that involves a set of conserved proteins including FtsZ, and results in the formation of two similarly sized and shaped cells; the process by which prokaryotic cells divide. cytokinesis by binary fission cytokinesis by binary fission _obsolete_quality of host population intermediate host role Alexander Diehl Lindsay Cowell The role is realized in developmental processes of the host's partner in symbiosis. 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 _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 primary infection Lindsay Cowell Alexander Diehl Albert Goldfain An infection bearing the primary infection role. _obsolete_extrinsic incubation period disorder A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. disorder infection Albert Goldfain 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 infectious agent population, or (2) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent popuation. The organism corresponding to the extended organism is host to the infectious agents. By this definition, parts of the host can be considered part of the infection. Lindsay Cowell Alexander Diehl innate immunity to infectious agent Albert Goldfain Lindsay Cowell Alexander Diehl The disposition is realized in an innate immune response. An immunity to infectious agent that inheres in an organism in virtue of germline encoded components that directly recognize components of potential pathogens. Lindsay Cowell A material entity bearing a disinfectant role. Albert Goldfain disinfectant Alexander Diehl Fungi/Metazoa group Fungi/Metazoa group _obsolete_transport by lymph paratenic host role The role is realized in developmental processes of the host's partner in symbiosis. 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 _obsolete_refractoriness _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 Lindsay Cowell Alexander Diehl DL needs 'process of inhibiting the growth of microorganisms' microbistatic A material entity with an antimicrobial disposition that is realized in a process of inhibiting the growth of microorganisms. Albert Goldfain _obsolete_intrinsic incubation period _obsolete_viral latency Alexander Diehl Lindsay Cowell Albert Goldfain Alexander Diehl A collective disposition to initiate processes that result in a disorder. collective pathogenic disposition The disposition is realized in processes that create a disorder. Lindsay Cowell Albert Goldfain host exposure to environment containing infectious agent A process in which a potential host of an infectious agent is exposed to an environment in which the infectious agent is present and physical contact between the two can occur, but such contact is not planned. Bjoern Peters infectious disease incidence rate Lindsay Cowell A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time. An instance of infectious disease incidence rate is measured by dividing a measure of an instance of the infectious disease incidence proportion by the length of the period of time over which the incidence was measured. Albert Goldfain Alexander Diehl infectious human pathogen Albert Goldfain Lindsay Cowell Alexander Diehl An infectious agent with a capability to infect human hosts. _obsolete_utilization of membranous cell gateway host role Albert Goldfain Lindsay Cowell A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism. Alexander Diehl colonization of human anterior nares Lindsay Cowell Alexander Diehl Albert Goldfain A colonization of human process in which the colonized site is the anterior nares. _obsolete_adhesin commensal role Alexander Diehl The role is realized in processes that result in the commensal's growth, survival, or fitness advantage. 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 immunization against infectious agent Lindsay Cowell Alexander Diehl Albert Goldfain A process by which an organism acquires immunity to an infectious agent. Lindsay Cowell Albert Goldfain antimicrobial Alexander Diehl A material entity with an antimicrobial disposition. DL needs nursing home (OGMS?) nursing-home acquired Albert Goldfain Alexander Diehl An infection resulting from a transmission process that unfolds in a nursing home. Lindsay Cowell 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 Albert Goldfain immunosuppressive disposition Alexander Diehl A disposition whose realization negatively regulates an immune response. Lindsay Cowell _obsolete_transport by blood cumulative incidence of infection infection incidence proportion An instance of infection incidence proportion is measured by dividing a measure of an instance of infection incidence by the number of members of the population not infected at the beginning of the specified period of time over which the incidence was measured. Albert Goldfain A quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time in whom the infectious disease begins during the specified period of time. Alexander Diehl Lindsay Cowell molecular entity molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. developmental process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. developmental process _obsolete_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 host living with infected household contact Lindsay Cowell Alexander Diehl Bjoern Peters 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 _obsolete_biotic parasite role In the medical community, the term 'parasite' is used with the narrower meaning of eukaryotic pathogen. The role is realized in processes that result in the parasite's growth, survival, or fitness advantage or in the other organism's growth, survival, or fitness reduction. 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 Lindsay Cowell Alexander Diehl long-term non-progressing 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 Alexander Diehl The partner in symbiosis bears the parasite role. The role is realized in processes that result in the parasite's growth, survival, or fitness advantage or in the host's growth, survival, or fitness reduction. A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis derives from the host a growth, survival, or fitness advantage while the host's growth, survival, or fitness is reduced. Albert Goldfain parasite host role Lindsay Cowell Lindsay Cowell adhesion factor A biological macromolecule that has an adhesion disposition. Albert Goldfain adhesion molecule Alexander Diehl adhesin _obsolete_prevention of infection Lindsay Cowell infectious disease incidence proportion An instance of infectious disease incidence proportion is measured by dividing a measure of an instance of infectious disease incidence by the number of members of the population in which the infectious disease course had not begun at the beginning of the specified period of time over which the incidence was measured. Alexander Diehl cumulative incidence of infectious disease Albert Goldfain A quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time in whom the infectious disease begins during the specified period of time. _obsolete_prion Bacteria Penetration by an organism into its host organism via active breaching of the physical barriers of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. entry into host through host barriers entry into host through host barriers 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 Lindsay Cowell Alexander Diehl Albert Goldfain Bjoern Peters _obsolete_contagious _obsolete_penetration via injury of epithelial barrier Lindsay Cowell mixed infection polymicrobial infection Alexander Diehl DL needs 'different species' An infection comprised of infectious organisms from different Species. Albert Goldfain complex infection appearance of disorder Albert Goldfain Alexander Diehl Lindsay Cowell A process by which a disorder comes into existence. Albert Goldfain A role borne by an organism in symbiosis. The role is realized in symbiosis. symbiont role Lindsay Cowell Alexander Diehl cell Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. cell _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 production A process in which an entity comes into being as a result of the process. Albert Goldfain Alexander Diehl Lindsay Cowell _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 vaccination against infectious agent Alexander Diehl Albert Goldfain An active immunization that begins with exposure of an organism to a vaccine. Lindsay Cowell _obsolete_engulfment by nonphagocyte _obsolete_immunization 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 By this definition, vectors and other organisms that may not be infected are bearers of the infectious agent host role. _obsolete_initiation of infection infection incidence Albert Goldfain Alexander Diehl A particular instance of infection incidence will depend on a type of infectious agent, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure. 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. Lindsay Cowell _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 DL needs 'extended period of time' chronic infection Alexander Diehl Lindsay Cowell Albert Goldfain An infection that persists for an extended period of time. persistent infection 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. _obsolete_transcytosis active immunization against infectious agent Albert Goldfain An immunization that begins with exposure of an organism to antigen and results in immunity against an infectious agent. Lindsay Cowell Alexander Diehl inoculation aymptomatic host of infectious agent Albert Goldfain Alexander Diehl An organism that is host to an infectious agent has no symptoms of the infectious disease associated with the infectious agent. Lindsay Cowell acute infection Alexander Diehl Albert Goldfain Lindsay Cowell An infectious disorder that is the physical basis for an unfolding acute infectious disease course. mutualist role A symbiont role borne by an organism in virtue of the fact that both symbionts derive a growth, survival, or fitness advantage from symbiosis. Alexander Diehl The role is realized in processes that result in the growth, survival, or fitness advantage of either organism. Albert Goldfain Lindsay Cowell B cell receptor complex B cell receptor complex An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. replication Alexander Diehl Lindsay Cowell A production process in which a participant creates a copy of itself. Albert Goldfain _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_case of infectious disease pathogen host role Albert Goldfain Bearing the infectious agent host role implies bearing the pathogen host role, but the reverse is not true. See comment for infectious agent host role. Alexander Diehl Lindsay Cowell A host role borne by an organism in virtue of the fact that its extended organism contains a pathogen. _obsolete_engulfment by phagocyte _obsolete_infection treatment process A material entity bearing an antiviral disposition. Albert Goldfain antiviral Alexander Diehl Lindsay Cowell symbiosis, encompassing mutualism through parasitism An interaction between two organisms living together in more or less intimate association. The term host is usually used for the larger (macro) of the two members of a symbiosis. The smaller (micro) member is called the symbiont organism. Microscopic symbionts are often referred to as endosymbionts. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. symbiosis, encompassing mutualism through parasitism _obsolete_toxicity 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. An infection for which the infectious agents that are part of the infection persist inside host cells. Alexander Diehl intracellular infection Lindsay Cowell Albert Goldfain infectious disease lifetime prevalence Albert Goldfain Lindsay Cowell 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 Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease lifetime prevalence will depend on a type of infectious disease and a population. Actual measures of prevalence are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. _obsolete_replicating biological material entity Albert Goldfain A biological material entity that is capable of replication. Alexander Diehl Lindsay Cowell _obsolete_inactivated _obsolete_infection 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. _obsolete_damaging host cells and tissues in subepithelial space infectious disease hyper-endemicity Albert Goldfain Lindsay Cowell Alexander Diehl An infectious disease endemicity that inheres in an organism population in virtue of the fact that the infectious disease endemic level for an infectious disease is persistently high in the population. Hyper-endemic infectious diseases may have high endemic levels only in certain seasons. A hyper-endemic disease affects all age groups equally. Albert Goldfain An infectious disposition to become part of a disorder only in organisms whose defenses are compromised. opportunistic infectious disposition Lindsay Cowell opportunitistic pathogenic disposition Alexander Diehl The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host. This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin). 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. _obsolete_active 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. symbiont host role The relevant environmental resources may include nutrient resources, warmth, or moisture. Alexander Diehl Albert Goldfain The role is realized in processes in which the host makes the relevant environmental resources available to its partner in symbiosis. A bearer of a symbiont host role is bearer also of a symbiont role. _obsolete_biological object colony Lindsay Cowell Albert Goldfain A biological object or group of biological objects in close spatial proximity. Alexander Diehl Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. negative regulation of immune response negative regulation of immune response 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 Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infection prevalence will depend on a type of infectious agent, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. colony Alexander Diehl Lindsay Cowell Albert Goldfain An organism population persisting in a site it has colonized. _obsolete_mortality _obsolete_outbreak _obsolete_induction of damaging host immune response 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. The role is realized in a process that transfers an infectious organism from one location to another. infectious agent transporter role Albert Goldfain Lindsay Cowell Alexander Diehl A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts. A quote from page 3 of Mandell's "Principles and Practice of Infectious Diseases" (Sixth edition): "It is useful to distinguish "principal" pathogens, which regularly cause disease in some proportion of susceptible individuals with apparently intact defense systems, from other potentially pathogenic microorganisms. ... even for most organisms classified as principal pathogens, for example, Staphylococcus aureus and the pneumococcus, some impairment or local breakdown in normal host defense mechanisms must occur for these bacteria to cause disease. ... Thus, it seems clear that the capacity of certain microorganisms to cause disease in seemingly uncompromised human hosts on a regular basis reflects some fundamental difference in their virulence capabilities from those of opportunists and the more numerous commensal species that rarely, if ever, cause disease." Alexander Diehl primary infectious disposition An infectious disposition to become part of a disorder in organisms that have intact defenses. Albert Goldfain Lindsay Cowell establishment of a clinically abnormal colony Albert Goldfain A colonization of host process that results in a clinically abnormal colony. Alexander Diehl Lindsay Cowell infectious disease endemic rate Lindsay Cowell Alexander Diehl Infectious disease endemic rate is relational to previous infectious disease incidence rates of the disease. Albert Goldfain An infectious disease incidence rate that is typical for an infectious disease in an organism population. macromolecular complex macromolecular complex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together. host exposure to substance that might have infectious agent Alexander Diehl Bjoern Peters 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 DL needs 'relatively small area' 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 _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_pandemic infectious disease prevalence Lindsay Cowell Alexander Diehl Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease prevalence will depend on a type of infectious disease, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. 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. 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. infectious agent colony Albert Goldfain Alexander Diehl Lindsay Cowell A colony whose members are infectious agents. infectious agent vector role Alexander Diehl 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. The role is realized in a transmission process. A bearer of a vector role is also a bearer of a host role. Lindsay Cowell Albert Goldfain _obsolete_pathogen-induced apoptosis immunodeficiency Albert Goldfain A disorder of an immune system component that results in defective functioning of the immune system. Alexander Diehl DL needs immune system component (FMA?) and defective functioning (OGMS?) Lindsay Cowell Eukaryota 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?). infectious disease course A disease course that is the realization of an infectious disease. Alexander Diehl Albert Goldfain Lindsay Cowell _obsolete_epidemiological spread of disease 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 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 DL needs 'distributed throughout' 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. _obsolete_swollen Any process involved in the carrying out of an immune response by a leukocyte. leukocyte mediated immunity leukocyte mediated immunity innate immune response Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. innate immune response infection incidence rate Lindsay Cowell An instance of infection incidence rate is measured by dividing a measure of an instance of infection incidence proportion by the length of the period of time over which the incidence was measured. A quality that inheres in an organism population and is the infection incidence proportion per unit time. Albert Goldfain Alexander Diehl _obsolete_pathogen-induced necrosis _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 Lindsay Cowell Alexander Diehl Albert Goldfain immunocompetence A disposition that is the ability to mount a normal immune response. The disposition inheres in a bearer in virtue of the fact that the bearer has all canonical immune system components and none are disordered. The disposition is realized in a successful immune response. _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 infectious disease sporadicity Lindsay Cowell Albert Goldfain A quality that inheres in an organism population by virtue of the fact that realizations of an infectious disease occur in the population with a fluctuating prevalence. Sporadic quality of infectious disease is relational to previous prevalence of the disease. Alexander Diehl Alexander Diehl pathogen role Clostridium botulinum is an example of an entity with the capability to bear the pathogen role but that does not have the capability to bear the infectious agent role or the parasite role. The influenza viruses are examples of organisms that can bear both the infectious agent and pathogen roles. Albert Goldfain Lindsay Cowell A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition. acquired immunodeficiency Causes of acquired immunodeficiences include infection and drug treatments (e.g. chemotherapy). Albert Goldfain An immunodeficiency that is not caused by a genetic predisposition. Lindsay Cowell Alexander Diehl _obsolete_antigenic variation infectious agent reservoir Albert Goldfain Lindsay Cowell A material entity bearing an infectious agent reservoir role. Alexander Diehl _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 Lindsay Cowell A disposition borne by a biological macromolecule produced by a pathogen that is a disposition to undergo processes that increase the pathogen's virulence. virulence factor disposition Alexander Diehl The virulence factor disposition is typically realized in processes that improve survival of the pathogen in a host, increase the likelihood of transmission to a host, or cause pathological processes in a host. Albert Goldfain The disposition is realized in an immune response in which such antigen receptors participate. Albert Goldfain Lindsay Cowell An immunity to infectious agent that inheres in an organism in virtue of antigen receptors encoded by somatically diversified genes in the organism's genome and expressed by cells that have undergone selection during a primary immune response in that organism. immune memory Alexander Diehl adaptive immunity to infectious agent acquired immunity to infectious agent _obsolete_genetic diversification _obsolete_afimbrial specific adherence DL needs 'health care facility' community-acquired infection Albert Goldfain Lindsay Cowell Alexander Diehl An infection resulting from a transmission process that did not unfold in a health care facility. _obsolete_pathogen dead-end host Albert Goldfain Alexander Diehl incidental host Lindsay Cowell An organism bearing a dead-end host role. Albert Goldfain Some instances might be functions, depending on whether the bearer is something that exists and is used for the purpose (alcohol) or something that was designed for the purpose (pine sol). Entities that kill microorganisms are referred to as microbicidal; entities that inhibit the growth of microorganisms are referred to as microbistatic. Lindsay Cowell The disposition is realized in the killing or growth inhibition of microorganisms. Alexander Diehl A disposition to kill or inhibit the development or reproduction of microorganisms. antimicrobial disposition colonization of human Alexander Diehl A colonization of host process in which the host is of Species Homo sapiens. Albert Goldfain Lindsay Cowell 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 normal resident microflora population physiologic immunosuppression Alexander Diehl Lindsay Cowell Albert Goldfain An immunosuppression which unfolds as part of the natural self-regulation of an immune response. _obsolete_pathogen spread through host _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 infectivity Lindsay Cowell Alexander Diehl This quality is measured by the proportion of exposed who become infected. 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 _obsolete_temperature adhesion to host The attachment of an organism to its host via adhesion molecules, general stickiness etc., either directly or indirectly. The host is defined as the larger of the organisms involved in a symbiotic interaction. adhesion to host host coming into contact with vector of infectious agent Lindsay Cowell Albert Goldfain Alexander Diehl Bjoern Peters A host exposure to environment with infectious agent where the environment contains an infectious agent vector. Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern commensal Albert Goldfain Alexander Diehl An organism bearing a commensal role. Lindsay Cowell _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_resist phagocytosis in subepithelial space DL needs 'end reservoir of infectious agent role' _obsolete_end reservoir of infectious agent A material entity bearing an end reservoir of infectious agent role. Albert Goldfain Alexander Diehl Lindsay Cowell dead-end reservoir of infectious agent _obsolete_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 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 reservoir of infectious agent role The role is realized in a process that has as part life and multiplication processes of an infectious agent and a transmission process. Alexander Diehl Lindsay Cowell If the material entity bearing the reservoir role is an organism, then this organism also bears the host role. The organism may also bear the vector role. Albert Goldfain DL needs 'hospital' (OGMS?) hospital-acquired infection nosocomial infection Alexander Diehl Lindsay Cowell An infection resulting from a transmission process that unfolds in a hospital. _obsolete_complement resistance _obsolete_dependovirus parasite host Albert Goldfain An organism bearing a parasite host role. Lindsay Cowell Alexander Diehl _obsolete_specific adherence A molecule with the invasion disposition is referred to as an invasion factor or invasin. 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 invasion disposition Albert Goldfain primary immunodeficiency Albert Goldfain Lindsay Cowell An immunodeficiency that exists in an organism because of a genetic predisposition. congenital immunodeficiency Alex Diehl _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 immunosuppression Alexander Diehl A process that attenuates an immune response. Lindsay Cowell Albert Goldfain _obsolete_virus-induced cytopathogenesis infectious disease incidence Alexander Diehl Albert Goldfain A particular instance of infectious disease incidence will depend on a type of infectious disease, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure. 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. _obsolete_immunocompromised release of infectious human pathogen in laboratory Alexander Diehl Lindsay Cowell Albert Goldfain Bjoern Peters A host exposure to environment with infectious agent where the exposure is accidental; the environment is a laboratory, and the infectious agent is infectious in humans. Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern parasite A organism bearing a parasite role. Albert Goldfain Lindsay Cowell Alexander Diehl _obsolete_passage through cell membrane _obsolete_vaccine DL: Needs 'product of' relation. It is a product of this process: production and has_participant some (has_role some pathogen and has_disposition some 'virulence factor disposition') virulence factor Albert Goldfain A biological macromolecule produced by a pathogen and that has a virulence factor disposition. Lindsay Cowell Alexander Diehl _obsolete_serum resistance exotoxin disposition Albert Goldfain The disposition is realized in a direct enzymatic process that damages host cells or extracellular matrix. A toxin disposition to damage cells or extracellular matrix by a direct enzymatic process. Alexander Diehl Lindsay Cowell Alexander Diehl Lindsay Cowell intermediate host Albert Goldfain A organism bearing an intermediate host role. secondary host Albert Goldfain adhesion disposition Lindsay Cowell A disposition borne by a biological macromolecule that is the disposition to participate in adherence to host. Alexander Diehl The disposition is realized in an adherence to host process. colonization of human perineum Albert Goldfain Alex Diehl A colonization of human process in which the colonized site is a perineum. Lindsay Cowell _obsolete_infectious agent DL needs 'another infection in a non-adjacent location' 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. _obsolete_penetration of epithelial barrier virulence This quality is measured by the proportion of clinically apparent cases that are severe or fatal. 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. Lindsay Cowell Albert Goldfain infectious agent population Albert Goldfain Lindsay Cowell Alexander Diehl An organism population whose members each have an infectious disposition. 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. _obsolete_biological object Albert Goldfain Alexander Diehl Lindsay Cowell primitive _obsolete_drug resistance _obsolete_protective _obsolete_infectious organism Albert Goldfain Alexander Diehl An infectious agent that is an organism. Lindsay Cowell The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism. reproduction reproduction _obsolete_antibiotic invasion factor Lindsay Cowell Alexander Diehl A biological macromolecule that has an invasion disposition. Albert Goldfain invasin _obsolete_membrane invagination reverse zoonosis Albert Goldfain An infectious disease that has as its physical basis an infectious disorder composed of infectious agents that have a reverse zoonotic disposition. Alex Diehl Lindsay Cowell _obsolete_modulation of inflammatory response Alexander Diehl A disposition to cause I) malfunction of cells, ii) damage to extracellular matrix, or iii) damage of cells to a degree that can result in cell death. Lindsay Cowell toxin disposition Albert Goldfain paratenic host Lindsay Cowell Alexander Diehl Albert Goldfain An organism bearing a paratenic host role. _obsolete_opportunistic pathogen _obsolete_pathogen evasion of host immune response infectious disease tranmissible disease The disposition is realized in an infectious disease course. Albert Goldfain Alexander Diehl A disease whose physical basis is an infectious disorder. Lindsay Cowell neurotoxin Albert Goldfain Alexander Diehl Lindsay Cowell A molecular entity with a toxin disposition, the realization of which damages or interferes with the function of nerve tissue. _obsolete_phase variation _obsolete_fimbrial specific adherence _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 susceptibility Low susceptibility is often referred to as resistance. In this sense, resistance is a quality. 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 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 pathologic immunosuppression Alexander Diehl Lindsay Cowell Albert Goldfain An immunosuppression process which arises as the result of a disorder. Disorders that result in immunosuppression include those that result from infection, stress, malnutrition, and treatments such as chemotherapy or calcineurin inhibition. _obsolete_tropism _obsolete_immunity Albert Goldfain Lindsay Cowell Alexander Diehl pathogen A material entity with a pathogenic disposition. definitive host role Lindsay Cowell Albert Goldfain Alexander Diehl 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. The role is realized in developmental and reproduction processes of the host's partner in symbiosis. primary host role 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. infectious agent carrier Albert Goldfain Lindsay Cowell Alexander Diehl An organism bearing the infectious agent carrier role. _obsolete_vaccination infectious agent seroprevalence Albert Goldfain Alexander Diehl Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious agent seroprevalence will depend on a type of infectious agent and a population. Actual measures of seroprevalence are based only on tested individuals and usually specify a geographic location. Other constraints may include population demographics. 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. _obsolete_disruption of normal microbioflora source of infection role A role borne by a material entity in virtue of the fact that it contains a site from which an infectious agent is transmitted. The role is realized in a process that has as part a transmission process and a process by which the infectious agent or one of its offspring becomes part of a disorder in the host. Albert Goldfain Lindsay Cowell Alexander Diehl leukocyte An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. leukocyte Lindsay Cowell Albert Goldfain 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. Alexander Diehl establishment of localization in host An establishment of localization process in which a material entity reaches a site in an organism in which it can survive, grow, multiply, or mature. Requested addition of this term to the GO. _obsolete_fusion with host cell membrane _obsolete_endotoxin disposition Albert Goldfain Lindsay Cowell A toxin disposition that inheres in a protein or protein complex that is a structural component of a pathogen and is released from the pathogen only upon cytolysis. Alexander Diehl _obsolete_role toxin Albert Goldfain Lindsay Cowell Alexander Diehl A molecular entity that has a toxin disposition. 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. Sterilizing immunity is typically conferred by neutralizing antibodies. _obsolete_medicine _obsolete_infected _obsolete_invasive _obsolete_exogenous _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_long-term non-progression infected population Lindsay Cowell Albert Goldfain Alexander Diehl An organism population whose members have an infection. 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. _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 transition to clinical abnormality A process by which a part of an organism or something contained in an organism becomes clinically abnormal. infectious disease mortality rate Alexander Diehl Lindsay Cowell Albert Goldfain A particular instance of infectious disease mortality rate will depend on a type of infectious disease and a population. Actual measures of mortality rate are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. Mortality rate is typically expressed in units of deaths per 1000 individuals per year. A quality that inheres in an organism population and is the per capita number of deaths in the population resulting from an infectious disease over a specified period of time. _obsolete_engulfment _obsolete_enterotoxin disposition Lindsay Cowell Alexander Diehl Albert Goldfain An exotoxin disposition to damage cells of the host intestinal mucosa. _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. Albert Goldfain A quality that inheres in an infection and is the likelihood that infectious agents part of the infection will spread to other hosts. _obsolete_therapeutic _obsolete_process _obsolete_epidemic symbiont Lindsay Cowell Albert Goldfain Alexander Diehl An organism bearing a symbiont role. immunity to infectious agent A resistance to infectious agent that inheres in an organism in virtue of immune system components in the extended organism. Alexander Diehl Lindsay Cowell We don't specify that immunity results from prior exposure, because we want to include innate immunity. In addition, for adaptive immunity, there could be some low level immunity even in a primary immune response. Albert Goldfain protective immunity to infectious agent _obsolete_endogenous _obsolete_rapid progression _obsolete_disruption of body surface _obsolete_route of entry _obsolete_immunosuppressed drug susceptibility Albert Goldfain Lindsay Cowell A susceptibility that is the degree to which an entity can be harmed or inhibited from surviving by a drug. Alexander Diehl _obsolete_mobile genetic element source of infection A material entity bearing a source of infection role. Alex Diehl Albert Goldfain Lindsay Cowell diseased population Lindsay Cowell Alexander Diehl Albert Goldfain An organism population in whose members an infectious disease is being realized. severe sepsis Albert Goldfain A sepsis that results in organ dysfunction, hypotension, or hypofusion of at least one organ. Alexander Diehl Lindsay Cowell _obsolete_nonspecific adherence _obsolete_pathogenicity island infectious agent host Lindsay Cowell Alexander Diehl Albert Goldfain An organism bearing an infectious agent host role. _obsolete_epidemic spread of disease communicability Alexander Diehl The disposition is realized in a direct, horizontal transmission process between members of the same Species. Albert Goldfain An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission. Lindsay Cowell extended organism An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. extended organism _obsolete_object _obsolete_penetration of host cell _obsolete_zoonotic _obsolete_progression rate life-sustaining process Lindsay Cowell Alex Diehl A process which is necessary for the survival of an organism. obligatory symbiont Lindsay Cowell Albert Goldfain Alexander Diehl An organism that can only reach developmental maturity, replicate, or persist in symbiosis. _obsolete_invasin sepsis A process that is a systemic inflammatory response to infection. Lindsay Cowell Alexander Diehl Albert Goldfain _obsolete_pandemic spread of disease _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 pathogen host Alexander Diehl Lindsay Cowell Albert Goldfain An organism bearing a pathogen host role. OBI organism 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. A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. _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_quality disposition to form a non-parasitic colony Lindsay Cowell Albert Goldfain A disposition to colonize an organism and participate in mutualism or commensalism with that organism. Alexander Diehl _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_live mutualist Albert Goldfain An organism bearing a mutualist role. Lindsay Cowell Alexander Diehl negative regulation of life-sustaining process Lindsay Cowell Alex Diehl Any process that stops, prevents, or reduces the frequency, rate or extent of a life-sustaining process. _obsolete_toxin entry into host Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. entry into host potential host of infectious agent Alexander Diehl An organism that has the capability to bear a host of infectious agent role. Lindsay Cowell Albert Goldfain _obsolete_vertical transmission symptom A quality of a patient that is observed by the patient and is hypothesized by the patient to be a realization of a disease. symptom _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 colonized host Albert Goldfain Lindsay Cowell Alexander Diehl An organism that contains a colony in or on its extended organism. _obsolete_endotoxin antibiotic resistance A resistance to drug that mitigates the damaging effects of an antibiotic. Lindsay Cowell Albert Goldfain Alexander Diehl _obsolete_endemic resistance to drug Albert Goldfain A protective resistance that mitigates the damaging effects of a drug. Lindsay Cowell Alexander Diehl drug resistance host exposure to infectious agent Bjoern Peters A process in which a potential host of an infectious agent is exposed to an infectious agent. 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. Lindsay Cowell Alexander Diehl Albert Goldfain infectious agent portal of exit role The role is realized in a process by which an infectious agent exists a host. DL needs NCBI taxonomy term. Shigellosis Lindsay Cowell Albert Goldfain Alexander Diehl An infection located in the bowel and that has as part organisms of the Genus Shigella. adaptive immune response An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory). adaptive immune response Alexander Diehl 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. Lindsay Cowell The disposition is realized in a horizontal transmission process. contagiousness Albert Goldfain Highly contagious infections, those with a relatively high likelihood of spread, are referred to as contagious and are those for which spread is likely as a result of data-to-day activities of the host. An organism that has an infectious disposition. infectious agent Lindsay Cowell Alexander Diehl Albert Goldfain Any process that stops, prevents, or reduces the frequency, rate or extent of the viral life cycle, the set of processes by which a virus reproduces and spreads among hosts. negative regulation of viral reproduction negative regulation of viral reproduction _obsolete_exotoxin _obsolete_horizontal transmission _obsolete_co-infected long-term non-progressor Lindsay Cowell Alexander Diehl Albert Goldfain An organism experiencing a long-term non-progressing infectious disease course. _obsolete_fusion protein Alexander Diehl Lindsay Cowell The disposition is realized in a process that mitigates damage to the bearer and has the part as a participant. protective resistance Albert Goldfain 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. This mitigation sometimes takes the form of protection. CCR5 mutations protect T cells from HIV invasion. If a patient's tumor is resistant to chemotherapy, then the patient is resistant to something beneficial, but the tumor is resistant to something damaging. In this case protective resistance inheres in the tumor's cells and in the tumor, but not in the patient. In some cases, the quality that confers the protective resistance will confer other dispositions that damage the entity, such as is the case with sickle cell trait. susceptible organism Alex Diehl Lindsay Cowell An organism that is not infected with an infectious agent and lacks protective immunity to the infectious agent. Alexander Diehl Albert Goldfain Lindsay Cowell The role is realized in a process by which an infectious agent enters a host. 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. DL needs NCBI taxonomy term. amebiasis Albert Goldfain Alexander Diehl Lindsay Cowell An infection located in the colon and that has as part organisms of the Species Entamoeba histolytica _obsolete_sign transmission period Lindsay Cowell Albert Goldfain Alexander Diehl A continuous temporal interval during which a transmission process occurs. _obsolete_pathogen life cycle stage immunocompetent organism Alexander Diehl Albert Goldfain An organism that has immunocompetence. Lindsay Cowell variolation Alexander Diehl Albert Goldfain An active immunization that begins with exposure to smallpox in the form of a scab from a pustule and results in immunity against smallpox. Lindsay Cowell _obsolete_attenuated herd immunity to infectious organism Alexander Diehl Albert Goldfain Lindsay Cowell A collective resistance disposition that inheres in an organism population in virtue of the fact that the proportion of the population with immunity to an infectious agent is high resulting in a low number of transmissions from hosts in the population to susceptible individuals in the population and thereby mitigating the damaging effects of the infectious agent on the population. emerging pathogen Lindsay Cowell Alexander Diehl Albert Goldfain An infectious agent whose infection incidence is increasing following its first introduction into a new host Species. DL needs NCBI taxonomy terms. trichomoniasis Albert Goldfain Alexander Diehl An infection that has as part organisms of the Species Trichomonas vaginalis. Lindsay Cowell _obsolete_infectious disease progression stage _obsolete_treatment communicability period A continuous temporal interval during which contagiousness inhering in the bearer of a host role. Lindsay Cowell Alexander Diehl Albert Goldfain _obsolete_highly exposed persistently seronegative immunosuppressed organism Albert Goldfain Alexander Diehl An organism that is experiencing pregnancy-induced or pathologic immunosuppression. Lindsay Cowell direct host exposure to infectious agent Bjoern Peters A process in which a potential host of an infectious agent comes into direct physical contact with the infectious agent. cytotoxin Alexander Diehl A molecular entity with a toxin disposition, the realization of which damages host cells. Albert Goldfain Lindsay Cowell Any process that modulates the frequency, rate or extent of any biological process, quality or function. biological regulation biological regulation 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 _obsolete_morbidity infectious agent vector Alexander Diehl Lindsay Cowell Albert Goldfain An organism bearing an infectious agent vector role. DL needs NCBI Taxonomy term. leptospirosis Albert Goldfain An infection that has as part organisms of the Genus Leptospira. Lindsay Cowell Alexander Diehl The totality of all processes through which a given disease instance is realized. disease course disease course _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 T cell receptor complex T cell receptor complex A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. infectious disease epidemic Albert Goldfain Lindsay Cowell A process of infectious disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population. Alexander Diehl 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 Alexander Diehl antifungal disposition Albert Goldfain A disposition to kill or inhibit the development or reproduction of fungal organisms. Lindsay Cowell A disposition that inheres in a collection of entities in virtue of the individual dispositions of the constituents of that collection. Lindsay Cowell Alexander Diehl collective disposition "... in virtue of the individual dispositions of the contstituents" is intended to capture the fact that the collective disposition results from the combination of the individual dispositions. It is not necessary that every constituent of the aggregate have a relevant individual disposition. Albert Goldfain The disposition is realized in a process that has as part realizations of some of the individual dispositions. An interaction between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected. commensalism commensalism _obsolete_parasite _obsolete_communicable disposition Alexander Diehl An infectious disposition to be transmitted directly from one human host to another. Lindsay Cowell Albert Goldfain The role is realized in a process by which the infectious disorder is established in the host. 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 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 secondary infection role Alexander Diehl infectious agent vehicle role Albert Goldfain Drinking water bears the infectious agent vehicle role, but does not bear either of the subtype roles. 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. resistant entity Albert Goldfain A material entity that has a resistance disposition. Alexander Diehl Lindsay Cowell mechanical vector of infectious agent Albert Goldfain Alexander Diehl An infectious agent vector bearing a mechanical vector of infectious agent role. Lindsay Cowell _obsolete_emerging pathogen pregnancy-induced immunosuppression Alexander Diehl An immunosuppression induced by progesterone and other factors upregulated in pregnant women. Lindsay Cowell Albert Goldfain _obsolete_infectivity period opportunistic pathogen An infectious agent with an opportunistic infectious disposition. Lindsay Cowell Albert Goldfain Alex Diehl opportunist _obsolete_chronic carrier host Albert Goldfain Alexander Diehl An organism bearing a host role. Lindsay Cowell negative regulation of developmental process Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). negative regulation of developmental process _obsolete_antimicrobial Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. biological_process biological_process Suggested label: indirect pathogen transmission process indirect indirect Indirect transmission is a transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by intermediary vehicles, vectors or as airborne dust particles. reverse zoonotic disposition Albert Goldfain Lindsay Cowell An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis. Alexander Diehl An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host. Alexander Diehl antiviral disposition A disposition to kill or inhibit the lifecycle of viruses. Lindsay Cowell Albert Goldfain passive immunization against infectious agent Alexander Diehl Albert Goldfain An immunization that begins with transfer to an organism of molecules not produced by that organism and that confer immunity against an infectious agent. Examples include the injection of antibodies and the transfer of maternal antibodies to the fetus. Lindsay Cowell mutualism mutualism An interaction between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other. immune population Lindsay Cowell Albert Goldfain Alexander Diehl An organism population whose members have acquired immunity to an infectious agent. _obsolete_symbiant chronic carrier of infectious agent Albert Goldfain Alexander Diehl An organism who has been bearer of the infectious agent carrier role for an extended period of time. Lindsay Cowell 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. primary infection role The role is realized in a process by which the infectious disorder is established in the host. Alexander Diehl 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. _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 Lindsay Cowell Albert Goldfain definitive host Alexander Diehl An organism bearing a definitive host role. primary host DL needs NCBI taxonomy term. candidiasis Albert Goldfain Alexander Diehl An infection that has as part organisms of the Genus Candida. Lindsay Cowell biological vector of infectious agent Albert Goldfain Alexander Diehl An infectious agent vector bearing a biological vector of infectious agent role. Lindsay Cowell _obsolete_primary pathogen transmissibility disposition Alex Diehl Lindsay Cowell A disposition to undergo a transmission process. Albert Goldfain The disposition is realized in a transmission process. _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 zoonotic disposition Albert Goldfain An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis. Lindsay Cowell Alexander Diehl An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host. Any process by which an organism has an effect on another organism of the same or different species. multi-organism process multi-organism process _obsolete_colonizer Lindsay Cowell Albert Goldfain Alexander Diehl infectious disorder An infection that is clinically abnormal. A spatial region having environmental qualities which may sustain an organism or a community of organisms. habitat habitat A disposition to kill or inhibit the development or reproduction of eukaryotic parasites. Lindsay Cowell In the term name, we are using parasite in the medical sense of eukaryotic organisms that are parasitic in humans. Alexander Diehl Albert Goldfain antiparasitic disposition Archaea needs 'species' simple infection Lindsay Cowell Albert Goldfain Alexander Diehl An infection comprised of infectious organisms all of the same Species. Albert Goldfain Lindsay Cowell Alexander Diehl The role is realized in the killing and/or growth inhibition of microorganisms on the anatomical entity. 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. 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 vehicle of infectious agent Alexander Diehl A material entity bearing an infectious agent vehicle role. Lindsay Cowell Albert Goldfain horizontal pathogen transmission process Lindsay Cowell A pathogen transmission process in which a pathogen is transmitted from one host to another of the same Species, and the two hosts are not in a parent-child relationship. _obsolete_host infectious disposition A pathogenic disposition that inheres in an organism and is the disposition for that organism (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 The disposition is realized in a process that has as part a transmission process, an establishment in host process, and a process in which an entity becomes part of a disorder. The infectious disposition has a complementary disposition that inheres in an organism and is the capability to be host to an entity with an infectious disposition and to undergo processes intiated by that entity that result in a disorder. Albert Goldfain Alexander Diehl The disposition is realized in a neutralizing process carried out by the antibodies. Lindsay Cowell Albert Goldfain Alexander Diehl Passive immunity results from a passive immunization. passive immunity to infectious agent The protective antibodies are typically introduced by injection, breast feeding, or by passing from the placenta to the fetus. An immunity to infectious agent that inheres in an organism in virtue of antibodies not produced by that organism. 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 infectious disease pandemic A process in which multiple infectious disease epidemics of the same type of infectious disease unfold over overlapping periods of time and affect organism populations located in different geographic regions, including different countries and continents. Albert Goldfain Lindsay Cowell Alexander Diehl _obsolete_commensal death A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism. death antibacterial disposition Alexander Diehl antibiotic disposition A disposition to kill or inhibit the reproduction of bacteria. Lindsay Cowell Albert Goldfain 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. subclinical infection Alexander Diehl Albert Goldfain An infection that is part of an asymptomatic host. Lindsay Cowell biological vehicle of infectious agent role Albert Goldfain Examples include blood, serum, tissue, or fresh produce. Alexander Diehl 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 process that results in death A process that results in death. Lindsay Cowell Alex Diehl Alexander Diehl Albert Goldfain 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. Lindsay Cowell disinfectant role The role is realized in the killing and/or growth inhibition of microorganisms on the non-living entity. Alexander Diehl A material entity bearing a fomite role. Albert Goldfain fomite Lindsay Cowell _obsolete_carrier primary pathogen Alexander Diehl principal pathogen Albert Goldfain An infectious agent with a primary infectious disposition. Lindsay Cowell Alexander Diehl A material entity bearing an antifungal disposition. antifungal Lindsay Cowell Albert Goldfain negatively_regulates A regulation relation in which the unfolding of the regulating process *decreases* the frequency, rate or extent of the regulated process relationship regulates A relation between a process and a process or quality. A regulates B if the unfolding of A affects the frequency, rate or extent of B. A is called the regulating process, B the regulates process relationship has_role A relation between a continuant C and a role R. The reciprocal relation of role_of. GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship OBO_REL:0000033 has_output Examples: secretory cells. Should this be has_function (export of ...) C has_output C' GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship results_in_formation_of Example: autophagic vacuole formation results_in_formation_of autophagic vacuole. macromolecular complex assembly results_in_formation_of a macromolecule. Note: essentially the same as biosynthesis, although in biosynthesis the assembly is via chemical reactions P results_in_formation_of C : any instance of P gives rise to a C from the parts of C. Formally: forall pP, exists some c such that c instantiates C at end-of p, and c has some parts c1, c2, ... such that the parts are connected at the end-of p and disconected at the start-of p GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm results_in_creation_of results_in_assembly_of relationship has_function heart has_function to-pump-blood Relation between an independent continuant and a function. GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship OBO_REL:0000031 positively_regulates A regulation relation in which the unfolding of the regulating process *increases* the frequency, rate or extent of the regulated process relationship inheres_in This relation links qualities, functions, dispositions and other dependent continuants to their bearers. Examples: A particular shape that inheres in a lung; The redness that ineres in a Drosophila eye; Catalytic activity function inheres_in catalytic molecule. Note that inherence is a functional relation: if x inheres_in y at t and x inheres_in z at t, then y=z. We leave open the possibility of a relation multiply_inheres_in, such as between a gene sequence and the multiple chromosomes it multiply inheres in. The super-relation of both inheres_in and multiply_inheres_in would be depends_on A relation between a dependent continuant D and an entity E. D inheres_in E iff: given any d that instantiates D at t, there exists some e that instantiates E at t and d *inheres_in* e at t. Here *inheres_in* is the primitive instance level relation. GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm has_bearer relationship OBO_REL:0000026 has_part Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm realizes is_realization_of involves_execution_of The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes. NOTE: there appears to be some consistency in usage as to whether processes or continuants realize executes has_function_part OBO_REL:0000034 relationship has_inherent has_inherer Examples: red eye bearer_of redness OBO_REL:0000027 relationship A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm bearer_of unfolds_in Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte P unfolds_in C : the execution of P is spatially contained by C. forall pP, forall c' partipates_in p, c' located_in C at t, for some t in P GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship capable_of has_disposition relationship results_in has_material_basis_in OBO_REL:0000035 executed_during OBO_REL:realized_as NOTE: there appears to be some consistency in usage as to whether processes or continuants realize has_realization realized_by relationship Relation between a realizable and a process. Reciprocal relation of realizes GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm has_realization executed_during Relation between a realizable and a process. Reciprocal relation of realizes GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm