format-version: 1.2 date: 05:12:2010 18:08 saved-by: generate-ido-obo auto-generated-by: http://purl.obolibrary.org/obo/infectious-disease-ontology/repository/trunk/src/tools/generate-obo.lisp default-namespace: IDO idspace: RO http://www.obofoundry.org/ro/ro.owl# "OBO Relation ontology official home on OBO Foundry" idspace: ROP http://purl.org/obo/owl/OBO_REL# "Relation ontology proposed terms" idspace: PATO http://purl.org/obo/owl/PATO# "Phenotype Ontology" idspace: snap http://www.ifomis.org/bfo/1.1/snap# "BFO SNAP ontology (continuants)" idspace: span http://www.ifomis.org/bfo/1.1/span# "BFO SPAN ontology (occurrents)" idspace: OBI http://purl.obolibrary.org/obo/OBI_ "Ontology for Biomedical Investigations" idspace: CHEBI http://purl.org/obo/owl/CHEBI# "Chemical Entities of Biological Interest" idspace: CL http://purl.org/obo/owl/CL# "Cell Ontology" idspace: NCBITaxon http://purl.org/obo/owl/NCBITaxon# "NCBI Taxonomy" idspace: birn_anat http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl# "NIF Standard Anatomy" idspace: IAO http://purl.obolibrary.org/obo/IAO "Information Artifact Ontology" idspace: BFO http://www.ifomis.org/bfo/1.1/ "Basic Formal Ontology" idspace: GO http://purl.org/obo/owl/GO# "Gene Ontology" idspace: FMA http://purl.org/obo/owl/FMA# "Foundational Model of Anatomy" idspace: PRO http://purl.org/obo/owl/PRO# "Protein Ontology" idspace: UO http://purl.org/obo/owl/UO# "Unit Ontology" idspace: ENVO http://purl.org/obo/owl/ENVO# "Environment Ontology" idspace: VO http://purl.obolibrary.org/obo/VO "Vaccine Ontology" idspace: SO http://purl.org/obo/owl/SO# "Sequence Ontology" idspace: HPO http://purl.org/obo/owl/HP# "Human Phenotype Ontology" idspace: UBERON http://purl.org/obo/owl/UBERON# "Multi-species anatomy" remark: This file is a subset of IDO adequate for indexing using the OLS service. It does not include all logical assertions present in the OWL file, which can be obtained at http://purl.obolibrary.org/obo/ido/2010-12-02/ido-base.owl remark: creators: Linsday Cowell, Albert Goldfain, Alexander Diehl, Barry Smith, Bjoern Peters, Alan Ruttenberg remark: 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. remark: version of 2010-12-02 remark: available from http://purl.obolibrary.org/obo/ido/2010-12-02/ido.obo [Term] id: span:ConnectedTemporalRegion name: connected_temporal_region def:"Examples: the 1970s years\, the time from the beginning to the end of a heart attack\, the time taken up by cellular meiosis; Definition: A temporal region [span:TemporalRegion] every point of which is mediately or immediately connected with every other point of which." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: span:TemporalRegion ! temporal_region [Term] id: GO:0008150 name: biological_process def:"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." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: span:ProcessualEntity ! processual_entity [Term] id: snap:MaterialEntity name: material_entity def:"Examples: collection of random bacteria\, a chair\, dorsal surface of the body; Definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object]\, fiat object part [snap:FiatObjectPart]\, and object aggregate [snap:ObjectAggregate]\, which assume a three level theory of granularity\, which is inadequate for some domains\, such as biology." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:IndependentContinuant ! independent_continuant [Term] id: OGMS:0000063 name: disease course def:"The totality of all processes through which a given disease instance is realized." [OBO:imported "http://purl.obolibrary.org/obo/ogms.owl"] is_a: span:ProcessualEntity ! processual_entity [Term] id: IDO:0000000 name: _obsolete_process is_obsolete: true [Term] id: IDO:0000001 name: _obsolete_role is_obsolete: true [Term] id: IDO:0000002 name: _obsolete_quality is_obsolete: true [Term] id: IDO:0000003 name: _obsolete_object is_obsolete: true [Term] id: IAO:0000102 name: data about an ontology part def:"data about an ontology part is a data item about a part of an ontology\, for example a term" [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"] is_a: IAO:0000027 ! data item [Term] id: IDO:0000004 name: _obsolete_virulence def:"'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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000005 name: _obsolete_swollen is_obsolete: true [Term] id: IDO:0000006 name: _obsolete_toxicity is_obsolete: true [Term] id: IDO:0000007 name: _obsolete_active is_obsolete: true [Term] id: IDO:0000008 name: _obsolete_contagious is_obsolete: true [Term] id: IDO:0000009 name: _obsolete_latency def:"'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" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: CARO:0000000 name: anatomical entity def:"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." [OBO:imported "http://purl.org/obo/owl/CARO"] is_a: snap:MaterialEntity ! material_entity [Term] id: GO:0032502 name: developmental process def:"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." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0008150 ! biological_process [Term] id: TRANS:0000000 name: Suggested label: pathogen transmission process def:"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 definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species." [OBO:imported "http://purl.org/obo/owl/TRANS"] is_a: span:ProcessualEntity ! processual_entity [Term] id: TRANS:0000002 name: indirect def:"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." [OBO:imported "http://purl.org/obo/owl/TRANS"] is_a: TRANS:0000000 ! Suggested label: pathogen transmission process [Term] id: IDO:0000011 name: _obsolete_exogenous is_obsolete: true [Term] id: IDO:0000012 name: _obsolete_immunity is_obsolete: true [Term] id: span:TemporalInterval name: temporal_interval def:"Examples: any continuous temporal duration during which a process occurs; Definition: A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: span:ConnectedTemporalRegion ! connected_temporal_region [Term] id: IDO:0000010 name: _obsolete_immunosuppressed is_obsolete: true [Term] id: snap:Continuant name: continuant def:"Synonyms: endurant; Examples: a heart\, a person\, the color of a tomato\, the mass of a cloud\, a symphony orchestra\, the disposition of blood to coagulate\, the lawn and atmosphere in front of our building; Definition: An entity [bfo:Entity] that exists in full at any time in which it exists at all\, persists through time while maintaining its identity and has no temporal parts." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: BFO:Entity ! entity [Term] id: IDO:0000019 name: _obsolete_prevalence def:"'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" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000017 name: _obsolete_mortality is_obsolete: true [Term] id: IDO:0000018 name: _obsolete_pandemic is_obsolete: true [Term] id: IDO:0000015 name: _obsolete_temperature is_obsolete: true [Term] id: IDO:0000016 name: _obsolete_inactivated is_obsolete: true [Term] id: IDO:0000013 name: _obsolete_protective is_obsolete: true [Term] id: snap:Role name: role def:"Examples: the role of a person as a surgeon\, the role of a chemical compound in an experiment\, the role of a patient relative as defined by a hospital administrative form\, the role of a woman as a legal mother in the context of system of laws\, the role of a biological grandfather as legal guardian in the context of a system of laws\, the role of ingested matter in digestion\, the role of a student in a university; Definition: A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural\, social or institutional contexts." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:RealizableEntity ! realizable_entity [Term] id: IDO:0000020 name: _obsolete_epidemic is_obsolete: true [Term] id: IDO:0000021 name: _obsolete_infected is_obsolete: true [Term] id: IDO:0000022 name: _obsolete_live is_obsolete: true [Term] id: IDO:0000023 name: _obsolete_zoonotic is_obsolete: true [Term] id: IDO:0000028 name: _obsolete_antibiotic resistance is_obsolete: true [Term] id: IDO:0000029 name: _obsolete_incidence def:"'number of new cases in a given period of time'-ID[O]:0000029: number of new cases in a given period of time" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000024 name: _obsolete_immunocompromised is_obsolete: true [Term] id: IDO:0000025 name: _obsolete_pathogenicity def:"'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" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000026 name: _obsolete_tropism is_obsolete: true [Term] id: IDO:0000027 name: _obsolete_drug resistance is_obsolete: true [Term] id: snap:GenericallyDependentContinuant name: generically_dependent_continuant def:"Examples: a certain PDF file that exists in different and in several hard drives; Definition: A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:DependentContinuant ! dependent_continuant [Term] id: OGMS:0000045 name: disorder def:"A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease." [OBO:imported "http://purl.obolibrary.org/obo/ogms.owl"] is_a: snap:MaterialEntity ! material_entity [Term] id: NCBITaxon:2 name: Bacteria is_a: OBI:0100026 ! organism [Term] id: GO:0085030 name: mutualism def:"An interaction between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0044403 ! symbiosis, encompassing mutualism through parasitism [Term] id: GO:0002443 name: leukocyte mediated immunity def:"Any process involved in the carrying out of an immune response by a leukocyte." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0006955 ! immune response [Term] id: GO:0085031 name: commensalism def:"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." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0044403 ! symbiosis, encompassing mutualism through parasitism [Term] id: span:ScatteredTemporalRegion name: scattered_temporal_region def:"Examples: the time occupied by the individual games of the World Cup\, the time occupied by the individual liaisons in a romantic affair; Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: span:TemporalRegion ! temporal_region [Term] id: OBI:0100026 name: organism def:"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.; 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." [OBO:imported "http://purl.obolibrary.org/obo/obi.owl"] is_a: snap:MaterialEntity ! material_entity [Term] id: IAO:0000030 name: information content entity is_a: snap:GenericallyDependentContinuant ! generically_dependent_continuant [Term] id: GO:0019815 name: B cell receptor complex def:"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." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0032991 ! macromolecular complex [Term] id: GO:0019814 name: immunoglobulin complex def:"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." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0032991 ! macromolecular complex [Term] id: span:ProcessualEntity name: processual_entity def:"Examples: the life of an organism\, the process of meiosis\, the course of a disease\, the flight of a bird; Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening\, has temporal parts and always involves and depends on some entity." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: span:Occurrent ! occurrent [Term] id: NCBITaxon:33154 name: Fungi/Metazoa group is_a: NCBITaxon:2759 ! Eukaryota [Term] id: snap:SpecificallyDependentContinuant name: specifically_dependent_continuant def:"Synonyms: property\, trope\, mode; Examples: the mass of a cloud\, the smell of mozzarella\, the liquidity of blood\, the color of a tomato\, the disposition of fish to decay\, the role of being a doctor\, the function of the heart in the body: to pump blood\, to receive de-oxygenated and oxygenated blood\, etc.; Definition: A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:DependentContinuant ! dependent_continuant [Term] id: IAO:0000027 name: data item is_a: IAO:0000030 ! information content entity [Term] id: OGMS:0000087 name: extended organism def:"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." [OBO:imported "http://purl.obolibrary.org/obo/ogms.owl"] is_a: snap:ObjectAggregate ! object_aggregate [Term] id: BFO:Entity name: entity [Term] id: snap:Object name: object def:"Synonyms: substance; Examples: an organism\, a heart\, a chair\, a lung\, an apple; Definition: A material entity [snap:MaterialEntity] that is spatially extended\, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:MaterialEntity ! material_entity [Term] id: NCBITaxon:10239 name: Viruses is_a: OBI:0100026 ! organism [Term] id: IDO:0000593 name: transmission period def:"A continuous temporal interval during which a transmission process occurs." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: span:TemporalInterval ! temporal_interval [Term] id: IDO:0000592 name: immune population def:"An organism population whose members have acquired immunity to an infectious agent." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000509 ! organism population [Term] id: IDO:0000595 name: potential host of infectious agent def:"An organism that has the capability to bear a host of infectious agent role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: OBI:0100026 ! organism [Term] id: IDO:0000481 name: infectious disease incidence proportion def:"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. " [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: CL:0000738 name: leukocyte def:"An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement\, found in blood or other tissue." [OBO:imported "http://purl.org/obo/owl/CL"] is_a: CL:0000000 ! cell [Term] id: IDO:0000480 name: infection incidence def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: IDO:0000594 name: direct host exposure to infectious agent def:"A process in which a potential host of an infectious agent comes into direct physical contact with the infectious agent." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000658 ! host exposure to infectious agent [Term] id: IDO:0000483 name: infectious disease incidence rate def:"A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: IDO:0000109 name: _obsolete_transport by lymph is_obsolete: true [Term] id: IDO:0000482 name: infection incidence proportion def:"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. " [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: IDO:0000485 name: infectious disease prevalence def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: IDO:0000591 name: _obsolete_communicable disposition def:"An infectious disposition to be transmitted directly from one human host to another." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000484 name: infection incidence rate def:"A quality that inheres in an organism population and is the infection incidence proportion per unit time." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: IDO:0000590 name: chronic infectious disease course def:"An infectious disease course that unfolds over a long period of time." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000495 ! infectious disease course [Term] id: IDO:0000209 name: _obsolete_dormancy def:"'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" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000487 name: infectious disease lifetime prevalence def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: IDO:0000486 name: infection prevalence def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: IDO:0000208 name: _obsolete_seroprevalence def:"'prevalence as measured by antibody'-ID[O]:0000208: prevalence as measured by antibody" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000489 name: infectious disease mortality rate def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: IDO:0000488 name: infectious agent seroprevalence def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: IDO:0000597 name: host exposure to environment containing infectious agent def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000658 ! host exposure to infectious agent [Term] id: IDO:0000596 name: infectious agent def:"An organism that has an infectious disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000528 ! pathogen is_a: OBI:0100026 ! organism [Term] id: IDO:0000081 name: _obsolete_transcytosis is_obsolete: true [Term] id: IDO:0000599 name: host living in endemic area def:"A host exposure to environment with infectious agent where the environment is an area in which an infectious agent is endemic" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000597 ! host exposure to environment containing infectious agent [Term] id: IDO:0000080 name: _obsolete_penetration via injury of epithelial barrier is_obsolete: true [Term] id: IDO:0000598 name: host living with infected household contact def:"A host exposure to environment with infectious agent where the environment is a household that also has an infected host" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000597 ! host exposure to environment containing infectious agent [Term] id: IDO:0000200 name: _obsolete_mode of transmission is_obsolete: true [Term] id: IDO:0000071 name: _obsolete_initiation of infection is_obsolete: true [Term] id: IDO:0000201 name: _obsolete_end reservoir is_obsolete: true [Term] id: IDO:0000072 name: _obsolete_disruption of body surface is_obsolete: true [Term] id: IDO:0000073 name: _obsolete_disruption of normal microbioflora is_obsolete: true [Term] id: IDO:0000100 name: _obsolete_pathogen evasion of host immune response is_obsolete: true [Term] id: IDO:0000074 name: _obsolete_pathogen adherence to host cell def:"'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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000204 name: _obsolete_factor def:"'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" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000075 name: _obsolete_nonspecific adherence is_obsolete: true [Term] id: IDO:0000076 name: _obsolete_specific adherence is_obsolete: true [Term] id: IDO:0000205 name: _obsolete_colonization def:"'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" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000077 name: _obsolete_afimbrial specific adherence is_obsolete: true [Term] id: IDO:0000206 name: _obsolete_biotic is_obsolete: true [Term] id: IDO:0000207 name: _obsolete_adhesin is_obsolete: true [Term] id: IDO:0000078 name: _obsolete_fimbrial specific adherence is_obsolete: true [Term] id: IDO:0000079 name: _obsolete_penetration of epithelial barrier is_obsolete: true [Term] id: IDO:0000105 name: _obsolete_infection treatment process is_obsolete: true [Term] id: IDO:0000106 name: _obsolete_immunization is_obsolete: true [Term] id: IDO:0000107 name: _obsolete_prevention of infection is_obsolete: true [Term] id: IDO:0000108 name: _obsolete_transport by blood is_obsolete: true [Term] id: IDO:0000101 name: _obsolete_emergence def:"'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)" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000102 name: _obsolete_epidemiological spread of disease is_obsolete: true [Term] id: IDO:0000103 name: _obsolete_outbreak is_obsolete: true [Term] id: span:TemporalRegion name: temporal_region def:"Comment: All instances of occurrent [span:Occurrent] are temporal entities\, that is\, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case\, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way\, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant].; Comment: Time and temporal region [span:TemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called "absolutist" or "the container view" in analogy to what is traditionally the case with space (see spatial region [snap:SpatialRegion].; Comment: An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe\, a designated individual\, which is thus a temporal region itself.; Definition: An occurrent [span:Occurrent] that is part of time.; Examples: the time it takes to run a marathon\, the duration of a surgical procedure\, the moment of death" [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: span:Occurrent ! occurrent [Term] id: IDO:0000104 name: _obsolete_infection is_obsolete: true [Term] id: IDO:0000470 name: drug susceptibility of infectious agent def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000469 ! drug susceptibility [Term] id: IDO:0000474 name: systemic infection def:"An infection for which the infectious agents that are part of the infection are distributed throughout the host." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: IDO:0000473 name: intracellular infection def:"An infection for which the infectious agents that are part of the infection persist inside host cells." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: IDO:0000472 name: extracellular infection def:"An infection for which the infectious agents that are part of the infection persist in the extracellular space of the host." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: IDO:0000471 name: complex infection def:"An infection comprised of infectious organisms from different Species." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: snap:Disposition name: disposition def:"Examples: the disposition of vegetables to decay when not refrigerated\, the disposition of a vase to brake if dropped\, the disposition of blood to coagulate\, the disposition of a patient with a weakened immune system to contract disease\, the disposition of metal to conduct electricity.; Definition: A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres\, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform\, initiate a process) R under conditions C." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:RealizableEntity ! realizable_entity [Term] id: IDO:0000478 name: _obsolete_chronic quality of infection def:"A quality that inheres in an infection in virtue of the fact that the infection persists for an extended period of time." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000477 name: acute infectious disease course def:"An infectious disease course that begins soon after infection is established and progresses rapidly to severe stages." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000495 ! infectious disease course [Term] id: IDO:0000476 name: focal infection def:"A local infection for which symptoms are observed in parts of the host's extended organism that are distant from the infection." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000475 ! local infection [Term] id: IDO:0000475 name: local infection def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: IDO:0000092 name: _obsolete_damaging host cells and tissues in subepithelial space is_obsolete: true [Term] id: IDO:0000091 name: _obsolete_engulfment by phagocyte is_obsolete: true [Term] id: IDO:0000090 name: _obsolete_engulfment by nonphagocyte is_obsolete: true [Term] id: IDO:0000479 name: infectious disease incidence def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: IDO:0000084 name: _obsolete_pathogenesis def:"'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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000085 name: _obsolete_penetration of host cell is_obsolete: true [Term] id: IDO:0000082 name: _obsolete_utilization of membranous cell gateway is_obsolete: true [Term] id: IDO:0000083 name: _obsolete_transmission def:"'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" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000088 name: _obsolete_membrane invagination is_obsolete: true [Term] id: IDO:0000089 name: _obsolete_passage through cell membrane is_obsolete: true [Term] id: IDO:0000086 name: _obsolete_engulfment is_obsolete: true [Term] id: IDO:0000087 name: _obsolete_fusion with host cell membrane is_obsolete: true [Term] id: IDO:0000097 name: _obsolete_pathogen spread through host is_obsolete: true [Term] id: IDO:0000226 name: _obsolete_pathogen life cycle def:"'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" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000227 name: _obsolete_dormancy period def:"'is a period a process?'-ID[O]:0000227: is a period a process?" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000098 name: _obsolete_infectious disease def:"'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" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000228 name: _obsolete_pathogen outbreak is_obsolete: true [Term] id: IDO:0000229 name: _obsolete_oral-fecal transmission is_obsolete: true [Term] id: IDO:0000222 name: _obsolete_infectious disease course is_obsolete: true [Term] id: IDO:0000093 name: _obsolete_induction of damaging host immune response is_obsolete: true [Term] id: IDO:0000094 name: _obsolete_pathogen-induced apoptosis is_obsolete: true [Term] id: IDO:0000223 name: _obsolete_host recovery period is_obsolete: true [Term] id: IDO:0000224 name: _obsolete_intrinsic incubation period is_obsolete: true [Term] id: IDO:0000095 name: _obsolete_pathogen-induced necrosis is_obsolete: true [Term] id: IDO:0000225 name: _obsolete_extrinsic incubation period is_obsolete: true [Term] id: IDO:0000096 name: _obsolete_virus-induced cytopathogenesis is_obsolete: true [Term] id: IDO:0000220 name: _obsolete_infectivity period is_obsolete: true [Term] id: IDO:0000221 name: _obsolete_infectious disease progression def:"'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?" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000496 name: long-term non-progressing infectious disease course def:"A chronic infectious disease course that does not progress to severe stages for a long period of time." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000590 ! chronic infectious disease course [Term] id: IDO:0000495 name: infectious disease course def:"A disease course that is the realization of an infectious disease." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: OGMS:0000063 ! disease course [Term] id: IDO:0000494 name: infectious disease sporadicity def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: IDO:0000493 name: infectious disease hyper-endemicity def:"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. " [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000490 ! infectious disease endemicity [Term] id: IDO:0000492 name: infectious disease endemic rate def:"An infectious disease incidence rate that is typical for an infectious disease in an organism population. " [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000483 ! infectious disease incidence rate [Term] id: CL:0000000 name: cell def:"Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [OBO:imported "http://purl.org/obo/owl/CL"] is_a: CARO:0000000 ! anatomical entity [Term] id: IDO:0000491 name: infectious disease endemic level def:"An infectious disease prevalence that is typical for an infectious disease in an organism population. " [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000485 ! infectious disease prevalence [Term] id: IDO:0000490 name: infectious disease endemicity def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: GO:0051234 name: establishment of localization def:"The directed movement of a cell\, substance or cellular entity\, such as a protein complex or organelle\, to a specific location." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0008150 ! biological_process [Term] id: IDO:0000499 name: vaccination against infectious agent def:"An active immunization that begins with exposure of an organism to a vaccine." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000498 ! active immunization against infectious agent [Term] id: IDO:0000498 name: active immunization against infectious agent def:"An immunization that begins with exposure of an organism to antigen and results in immunity against an infectious agent." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000497 ! immunization against infectious agent [Term] id: IDO:0000219 name: _obsolete_incubation period def:"'agent is incubated?ndisease is incubated?'-ID[O]:0000219: agent is incubated?ndisease is incubated?" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000497 name: immunization against infectious agent def:"A process by which an organism acquires immunity to an infectious agent." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: span:ProcessualEntity ! processual_entity [Term] id: IDO:0000217 name: _obsolete_quality of infectious disease is_obsolete: true [Term] id: IDO:0000218 name: _obsolete_case of infectious disease is_obsolete: true [Term] id: IDO:0000215 name: _obsolete_quality of host population is_obsolete: true [Term] id: IDO:0000216 name: _obsolete_herd immunity is_obsolete: true [Term] id: IDO:0000213 name: _obsolete_resistance is_obsolete: true [Term] id: IDO:0000214 name: _obsolete_refractoriness is_obsolete: true [Term] id: IDO:0000211 name: _obsolete_quality of pathogen is_obsolete: true [Term] id: IDO:0000212 name: _obsolete_susceptibility def:"'can change depending on environmentnnwhere should susceptibility factors go?'-ID[O]:0000212: can change depending on environmentnnwhere should susceptibility factors go?" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000210 name: _obsolete_quality of host is_obsolete: true [Term] id: GO:0032991 name: macromolecular complex def:"A stable assembly of two or more macromolecules\, i.e. proteins\, nucleic acids\, carbohydrates or lipids\, in which the constituent parts function together." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: snap:MaterialEntity ! material_entity [Term] id: IDO:0000442 name: antibacterial disposition def:"A disposition to kill or inhibit the reproduction of bacteria." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000556 name: antiseptic def:"A material entity bearing an antiseptic role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000558 ! antimicrobial [Term] id: IDO:0000443 name: antiparasitic disposition def:"A disposition to kill or inhibit the development or reproduction of eukaryotic parasites." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000557 name: adhesion factor def:"A biological macromolecule that has an adhesion disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: CHEBI:23367 ! molecular entity [Term] id: IDO:0000444 name: protective resistance def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000558 name: antimicrobial def:"A material entity with an antimicrobial disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:MaterialEntity ! material_entity [Term] id: IDO:0000559 name: antiviral def:"A material entity bearing an antiviral disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:MaterialEntity ! material_entity [Term] id: IDO:0000445 name: resistance to drug def:"A protective resistance that mitigates the damaging effects of a drug." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000444 ! protective resistance [Term] id: IDO:0000446 name: resistance to infectious agent def:"A protective resistance that inheres in an organism and mitigates the damaging effects on that organism of an infectious agent." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000444 ! protective resistance [Term] id: IDO:0000552 name: endotoxin def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000549 ! toxin [Term] id: IDO:0000447 name: herd immunity to infectious organism def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000588 ! collective resistance disposition [Term] id: IDO:0000553 name: infectious agent portal of entry def:"An anatomical entity bearing an infectious agent portal of entry role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: CARO:0000000 ! anatomical entity [Term] id: IDO:0000554 name: infectious agent portal of exit def:"An anatomical entity bearing an infectious agent portal of exit role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: CARO:0000000 ! anatomical entity [Term] id: IDO:0000448 name: immunity to infectious agent def:"A resistance to infectious agent that inheres in an organism in virtue of immune system components in the extended organism." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000446 ! resistance to infectious agent [Term] id: IDO:0000449 name: sterilizing immunity to infectious agent def:"An immunity to infectious agent that results in elimination of the infectious agent from the host." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000448 ! immunity to infectious agent [Term] id: IDO:0000555 name: disinfectant def:"A material entity bearing a disinfectant role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000558 ! antimicrobial [Term] id: CHEBI:23367 name: molecular entity def:"Any constitutionally or isotopically distinct atom\, molecule\, ion\, ion pair\, radical\, radical ion\, complex\, conformer etc.\, identifiable as a separately distinguishable entity." [OBO:imported "http://purl.org/obo/owl/CHEBI"] is_a: snap:MaterialEntity ! material_entity [Term] id: IDO:0000550 name: exotoxin def:"A molecular entity bearing an exotoxin disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000549 ! toxin [Term] id: IDO:0000551 name: enterotoxin def:"A molecular entity with an exotoxin disposition\, the realization of which damages cells of the host intestinal mucosa." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000550 ! exotoxin [Term] id: IDO:0000440 name: antiviral disposition def:"A disposition to kill or inhibit the lifecycle of viruses." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000441 name: antifungal disposition def:"A disposition to kill or inhibit the development or reproduction of fungal organisms." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000036 name: _obsolete_colonizer is_obsolete: true [Term] id: IDO:0000035 name: _obsolete_fusion protein is_obsolete: true [Term] id: IDO:0000038 name: _obsolete_parasite is_obsolete: true [Term] id: IDO:0000037 name: _obsolete_commensal is_obsolete: true [Term] id: IDO:0000039 name: _obsolete_symbiant is_obsolete: true [Term] id: IDO:0000030 name: _obsolete_invasive is_obsolete: true [Term] id: IDO:0000032 name: _obsolete_attenuated is_obsolete: true [Term] id: IDO:0000031 name: _obsolete_endogenous is_obsolete: true [Term] id: IDO:0000034 name: _obsolete_endemic is_obsolete: true [Term] id: GO:0051704 name: multi-organism process def:"Any process by which an organism has an effect on another organism of the same or different species." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0008150 ! biological_process [Term] id: IDO:0000033 name: _obsolete_morbidity is_obsolete: true [Term] id: IDO:0000433 name: antiseptic role def:"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. " [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Role ! role [Term] id: IDO:0000569 name: aymptomatic host of infectious agent def:"An organism that is host to an infectious agent has no symptoms of the infectious disease associated with the infectious agent." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000537 ! infectious agent host [Term] id: snap:ObjectAggregate name: object_aggregate def:"Synonyms: substance aggregate; Examples: a heap of stones\, a group of commuters on the subway\, a collection of random bacteria\, a flock of geese\, the patients in a hospital; Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:MaterialEntity ! material_entity [Term] id: IDO:0000434 name: primary infection role def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Role ! role [Term] id: IDO:0000567 name: secondary infection def:"An infection bearing the secondary infection role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000504 ! infectious disorder [Term] id: IDO:0000431 name: infectious agent portal of exit role def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Role ! role [Term] id: IDO:0000432 name: disinfectant role def:"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. " [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Role ! role [Term] id: IDO:0000568 name: zoonosis def:"An infectious disease that has as its physical basis an infectious disorder composed of infectious agents that have a zoonotic disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000436 ! infectious disease [Term] id: IDO:0000565 name: microbistatic def:"A material entity with an antimicrobial disposition that is realized in a process of inhibiting the growth of microorganisms." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000558 ! antimicrobial [Term] id: IDO:0000437 name: adhesion disposition def:"A disposition borne by a biological macromolecule that is the disposition to participate in adherence to host." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000438 name: invasion disposition def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000566 name: primary infection def:"An infection bearing the primary infection role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000504 ! infectious disorder [Term] id: IDO:0000435 name: secondary infection role def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Role ! role [Term] id: IDO:0000563 name: microbicide def:"A material entity with an antimicrobial disposition that is realized in a process of killing microorganisms." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000558 ! antimicrobial [Term] id: IDO:0000564 name: viricide def:"A material entity with an antiviral disposition that is realized in a process of killing viruses." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000559 ! antiviral [Term] id: IDO:0000436 name: infectious disease def:"A disease whose physical basis is an infectious disorder." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: OGMS:0000031 ! disease [Term] id: IDO:0000561 name: antiparasitic def:"A material entity bearing an antiparasitic disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:MaterialEntity ! material_entity [Term] id: IDO:0000562 name: antibiotic def:"A material entity bearing an antiviral disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:MaterialEntity ! material_entity [Term] id: IDO:0000560 name: antifungal def:"A material entity bearing an antifungal disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:MaterialEntity ! material_entity [Term] id: IDO:0000430 name: infectious agent portal of entry role def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Role ! role [Term] id: IDO:0000049 name: _obsolete_antimicrobial is_obsolete: true [Term] id: IDO:0000048 name: _obsolete_symptom def:"'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" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000047 name: _obsolete_treatment is_obsolete: true [Term] id: GO:0044409 name: entry into host def:"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." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0051704 ! multi-organism process [Term] id: IDO:0000046 name: _obsolete_sign is_obsolete: true [Term] id: IDO:0000232 name: _obsolete_pathogen life cycle stage is_obsolete: true [Term] id: IDO:0000231 name: _obsolete_horizontal transmission is_obsolete: true [Term] id: IDO:0000230 name: _obsolete_vertical transmission is_obsolete: true [Term] id: GO:0044406 name: adhesion to host def:"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." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0008150 ! biological_process [Term] id: IDO:0000041 name: _obsolete_route of entry is_obsolete: true [Term] id: IDO:0000040 name: _obsolete_virulence factor def:"'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" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: GO:0044403 name: symbiosis, encompassing mutualism through parasitism def:"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." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0051704 ! multi-organism process [Term] id: IDO:0000233 name: _obsolete_infectious disease progression stage is_obsolete: true [Term] id: IDO:0000439 name: antimicrobial disposition def:"A disposition to kill or inhibit the development or reproduction of microorganisms." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000045 name: _obsolete_exotoxin is_obsolete: true [Term] id: IDO:0000044 name: _obsolete_endotoxin is_obsolete: true [Term] id: IDO:0000043 name: _obsolete_toxin is_obsolete: true [Term] id: IDO:0000042 name: _obsolete_invasin is_obsolete: true [Term] id: IDO:0000574 name: _obsolete_invasin def:"synonym of invasion factor" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000468 name: susceptibility to infectious agent def:"A susceptibility that inheres in an organism and is the degree to which it can be harmed by an infectious agent." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000467 ! susceptibility [Term] id: IDO:0000469 name: drug susceptibility def:"A susceptibility that is the degree to which an entity can be harmed or inhibited from surviving by a drug." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000467 ! susceptibility [Term] id: IDO:0000575 name: _obsolete_viral latency is_obsolete: true [Term] id: IDO:0000576 name: innate immunity to infectious agent def:"An immunity to infectious agent that inheres in an organism in virtue of germline encoded components that directly recognize components of potential pathogens." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000448 ! immunity to infectious agent [Term] id: IDO:0000577 name: _obsolete_adaptive immunity to infectious agent def:"An immunity to infectious agent realized in an adaptive immune response." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000464 name: infectivity def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: IDO:0000578 name: humoral immunity to infectious agent def:"An immunity to infectious agent that inheres in an organism in virtue of components of its circulating body fluid." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000448 ! immunity to infectious agent [Term] id: IDO:0000579 name: leukocyte-mediated immunity to infectious agent def:"An immunity to infectious agent that inheres in an organism in virtue of its leukocytes." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000448 ! immunity to infectious agent [Term] id: IDO:0000466 name: virulence def:"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. " [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: snap:TwoDimensionalRegion name: two_dimensional_region def:"Examples: the surface of a cube-shaped part of space\, the surface of a sphere-shaped part of space\, the surface of a rectilinear planar figure-shaped part of space; Definition: A spatial region [snap:SpatialRegion] with two dimensions." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:SpatialRegion ! spatial_region [Term] id: IDO:0000467 name: susceptibility def:"A quality that inheres in an entity and is the degree to which it can be harmed by another entity." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: IDO:0000460 name: infected organism def:"An organism that has an infection in or on its extended organism." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: OBI:0100026 ! organism [Term] id: IDO:0000461 name: co-infected organism def:"An organism that has two infections with distinct Species of infectious agents." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000460 ! infected organism [Term] id: IDO:0000462 name: _obsolete_symptomatic host def:"A host exhibiting disease symptoms." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000463 name: infectious agent transmissibility def:"A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Quality ! quality [Term] id: IDO:0000570 name: subclinical infection def:"An infection that is part of an asymptomatic host." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: IDO:0000571 name: resistant entity def:"A material entity that has a resistance disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:MaterialEntity ! material_entity [Term] id: IDO:0000572 name: chronic carrier of infectious agent def:"An organism who has been bearer of the infectious agent carrier role for an extended period of time." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000539 ! infectious agent carrier [Term] id: IDO:0000573 name: symptomatic host of infectious agent def:"An organism who is host to an infectious agent and has symptoms of the infectious disease associated with the infectious agent" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000537 ! infectious agent host [Term] id: span:SpatiotemporalInstant name: spatiotemporal_instant def:"Examples: the spatiotemporal region occupied by a single instantaneous temporal slice (part) of a process; Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] at a specific moment." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: span:ConnectedSpatiotemporalRegion ! connected_spatiotemporal_region [Term] id: IDO:0000058 name: _obsolete_chronic carrier is_obsolete: true [Term] id: IDO:0000057 name: _obsolete_carrier is_obsolete: true [Term] id: IDO:0000059 name: _obsolete_reservoir def:"'holding place for a potential pathogen...animate or inanimate'-ID[O]:0000059: holding place for a potential pathogen...animate or inanimate" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000054 name: _obsolete_colonization factor def:"'role played by portion of physical substance which promotes colonization'-ID[O]:0000054: role played by portion of physical substance which promotes colonization" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000053 name: _obsolete_antibiotic is_obsolete: true [Term] id: IDO:0000056 name: _obsolete_host is_obsolete: true [Term] id: GO:0044411 name: entry into host through host barriers def:"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." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0044409 ! entry into host [Term] id: IDO:0000055 name: _obsolete_adhesion factor def:"'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" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000050 name: _obsolete_medicine is_obsolete: true [Term] id: IDO:0000052 name: _obsolete_vaccine is_obsolete: true [Term] id: GO:0016265 name: death def:"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." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0008150 ! biological_process [Term] id: IDO:0000051 name: _obsolete_therapeutic is_obsolete: true [Term] id: IDO:0000459 name: colonized host def:"An organism that contains a colony in or on its extended organism." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: OBI:0100026 ! organism [Term] id: IDO:0000587 name: genetic resistance to infectious agent def:"A resistance to infectious agent that inheres in an organism in virtue of a specific allele or combination of alleles in its genome." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000446 ! resistance to infectious agent [Term] id: IDO:0000070 name: _obsolete_prion is_obsolete: true [Term] id: IDO:0000588 name: collective resistance disposition def:"A collective disposition the realization of which mitigates the damaging effects of some entity on members of the collection." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000455 ! collective disposition [Term] id: IDO:0000457 name: immunocompetent organism def:"An organism that has immunocompetence." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: OBI:0100026 ! organism [Term] id: IDO:0000585 name: collective pathogenic disposition def:"A collective disposition to initiate processes that result in a disorder." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000455 ! collective disposition [Term] id: IDO:0000458 name: contagiousness def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000586 name: infection def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:MaterialEntity ! material_entity [Term] id: IDO:0000455 name: collective disposition def:"A disposition that inheres in a collection of entities in virtue of the individual dispositions of the constituents of that collection. " [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000456 name: immunosuppressed organism def:"An organism that is experiencing pregnancy-induced or pathologic immunosuppression." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: OBI:0100026 ! organism [Term] id: IDO:0000589 name: immunodeficient organism def:"An organism that has an immunodeficiency." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: OBI:0100026 ! organism [Term] id: IDO:0000453 name: zoonotic disposition def:"An infectious disposition that is the disposition to be transmitted from an infected\, non-human host to a human host." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000452 ! infectious disposition [Term] id: snap:ObjectBoundary name: object_boundary def:"Definition: An independent continuant [snap:IndependentContinuant] that is a lower dimensional part of a spatial entity\, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [snap:Object] entities that exist at exactly the point where the object [snap:Object] is separated off from the rest of the existing entities in the world.; Examples: the surface of the skin\, the surface of the earth\, the surface of the interior of the stomach\, the outer surface of a cell or cell wall; Comment: Boundaries are theoretically difficult entities to account for\, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.; Synonyms: substance boundary" [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:IndependentContinuant ! independent_continuant [Term] id: IDO:0000454 name: reverse zoonotic disposition def:"An infectious disposition that is the disposition to be transmitted from an infected\, human host to a non-human host." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000452 ! infectious disposition [Term] id: IDO:0000451 name: invasive disposition def:"A disposition borne by an infectious agent that is the disposition to penetrate the epithelial barriers of an organism of another Species." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000580 name: passive immunity to infectious agent def:"An immunity to infectious agent that inheres in an organism in virtue of antibodies not produced by that organism." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000448 ! immunity to infectious agent [Term] id: IDO:0000452 name: infectious disposition def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000450 ! pathogenic disposition [Term] id: IDO:0000450 name: pathogenic disposition def:"A disposition to initiate processes that result in a disorder." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000583 name: emerging pathogen def:"An infectious agent whose infection incidence is increasing following its first introduction into a new host Species." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000596 ! infectious agent [Term] id: IDO:0000584 name: cytotoxin def:"A molecular entity with a toxin disposition\, the realization of which damages host cells." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000549 ! toxin [Term] id: IDO:0000581 name: antibiotic resistance def:"A resistance to drug that mitigates the damaging effects of an antibiotic." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000445 ! resistance to drug [Term] id: IDO:0000582 name: long-term non-progressor def:"An organism experiencing a long-term non-progressing infectious disease course." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: OBI:0100026 ! organism [Term] id: span:Occurrent name: occurrent def:"Synonyms: perdurant; Examples: the life of an organism\, a surgical operation as processual context for a nosocomical infection\, the spatiotemporal context occupied by a process of cellular meiosis\, the most interesting part of Van Gogh's life\, the spatiotemporal region occupied by the development of a cancer tumor; Definition: An entity [bfo:Entity] that has temporal parts and that happens\, unfolds or develops through time. Sometimes also called perdurants." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: BFO:Entity ! entity [Term] id: IDO:0000115 name: _obsolete_genetic diversification is_obsolete: true [Term] id: IDO:0000114 name: _obsolete_phase variation is_obsolete: true [Term] id: IDO:0000113 name: _obsolete_serum resistance is_obsolete: true [Term] id: IDO:0000112 name: _obsolete_resist phagocytosis in subepithelial space is_obsolete: true [Term] id: IDO:0000119 name: _obsolete_vaccination is_obsolete: true [Term] id: IDO:0000118 name: _obsolete_pandemic spread of disease is_obsolete: true [Term] id: IDO:0000117 name: _obsolete_epidemic spread of disease is_obsolete: true [Term] id: IDO:0000069 name: _obsolete_primary pathogen is_obsolete: true [Term] id: IDO:0000068 name: _obsolete_emerging pathogen is_obsolete: true [Term] id: IDO:0000116 name: _obsolete_complement resistance is_obsolete: true [Term] id: IDO:0000067 name: _obsolete_opportunistic pathogen is_obsolete: true [Term] id: IDO:0000066 name: _obsolete_infectious agent is_obsolete: true [Term] id: IDO:0000065 name: _obsolete_dependovirus is_obsolete: true [Term] id: IDO:0000064 name: _obsolete_pathogen is_obsolete: true [Term] id: IDO:0000111 name: _obsolete_antigenic variation is_obsolete: true [Term] id: IDO:0000063 name: _obsolete_vector def:"'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?)" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000110 name: _obsolete_modulation of inflammatory response is_obsolete: true [Term] id: IDO:0000062 name: _obsolete_pathogenicity island is_obsolete: true [Term] id: IDO:0000061 name: _obsolete_mobile genetic element is_obsolete: true [Term] id: IDO:0000060 name: _obsolete_fomite def:"'inanimate holder\, is water a fomite or only a reservoir?'-ID[O]:0000060: inanimate holder\, is water a fomite or only a reservoir?" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000648 name: Shigellosis def:"An infection located in the bowel and that has as part organisms of the Genus Shigella." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: IDO:0000649 name: amebiasis def:"An infection located in the colon and that has as part organisms of the Species Entamoeba histolytica" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: IDO:0000516 name: _obsolete_configured infectious organism population def:"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" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000519 name: incubation period def:"A continuous temporal interval beginning with the extablishment of an infectious agent colony and ending with the onset of symptoms (or infectious disease course?)." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: span:TemporalInterval ! temporal_interval [Term] id: IDO:0000417 name: infectious agent transporter role def:"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. " [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Role ! role [Term] id: IDO:0000418 name: infectious agent vector role def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000417 ! infectious agent transporter role [Term] id: IDO:0000419 name: mechanical vector of infectious agent role def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000418 ! infectious agent vector role [Term] id: IDO:0000410 name: intermediate host role def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000408 ! symbiont host role [Term] id: IDO:0000412 name: dead-end host role def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000408 ! symbiont host role [Term] id: IDO:0000411 name: paratenic host role def:"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. " [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000408 ! symbiont host role [Term] id: IDO:0000414 name: infectious agent host role def:"A pathogen host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000415 ! pathogen host role [Term] id: IDO:0000413 name: parasite host role def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000408 ! symbiont host role [Term] id: IDO:0000416 name: infectious agent carrier role def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000414 ! infectious agent host role [Term] id: IDO:0000415 name: pathogen host role def:"A host role borne by an organism in virtue of the fact that its extended organism contains a pathogen." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000629 ! host role [Term] id: IDO:0000513 name: infectious agent population def:"An organism population whose members each have an infectious disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000509 ! organism population [Term] id: IDO:0000512 name: diseased population def:"An organism population in whose members an infectious disease is being realized." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000509 ! organism population [Term] id: IDO:0000640 name: acquired immunodeficiency def:"An immunodeficiency that is not caused by a genetic predisposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000617 ! immunodeficiency [Term] id: IDO:0000515 name: normal resident microbiota population def:"An organism population whose members are particpating in non-parasitic symbiosis with a particular host." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000509 ! organism population [Term] id: IDO:0000643 name: re-emerging pathogen def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000596 ! infectious agent [Term] id: IDO:0000642 name: simple infection def:"An infection comprised of infectious organisms all of the same Species." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: IDO:0000514 name: susceptible population def:"An organism population whose members are not infected with an infectious agent and who lack immunity to the infectious agent." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000509 ! organism population [Term] id: IDO:0000645 name: candidiasis def:"An infection that has as part organisms of the Genus Candida." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: IDO:0000644 name: pregnancy-induced immunosuppression def:"An immunosuppression induced by progesterone and other factors upregulated in pregnant women." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000610 ! immunosuppression [Term] id: IDO:0000511 name: infected population def:"An organism population whose members have an infection." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000509 ! organism population [Term] id: IDO:0000647 name: leptospirosis def:"An infection that has as part organisms of the Genus Leptospira." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: IDO:0000646 name: trichomoniasis def:"An infection that has as part organisms of the Species Trichomonas vaginalis." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: IDO:0000639 name: infectious human pathogen def:"An infectious agent with a capability to infect human hosts." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000596 ! infectious agent [Term] id: IDO:0000637 name: severe sepsis def:"A sepsis that results in organ dysfunction\, hypotension\, or hypofusion of at least one organ." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000636 ! sepsis [Term] id: IDO:0000638 name: nursing-home acquired def:"An infection resulting from a transmission process that unfolds in a nursing home." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: IDO:0000527 name: _obsolete_infectious organism def:"An infectious agent that is an organism." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000528 name: pathogen def:"A material entity with a pathogenic disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:MaterialEntity ! material_entity [Term] id: IDO:0000428 name: _obsolete_enterotoxin disposition def:"An exotoxin disposition to damage cells of the host intestinal mucosa." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000429 name: _obsolete_endotoxin disposition def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000423 name: fomite role def:"An infectious agent vehicle role borne by an entity in virtue of the fact that the entity is not alive." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000421 ! infectious agent vehicle role [Term] id: IDO:0000422 name: biological vehicle of infectious agent role def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000421 ! infectious agent vehicle role [Term] id: IDO:0000421 name: infectious agent vehicle role def:"An infectious agent transporter role borne by an entity in virtue of the fact that the entity is not a complete organism." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000417 ! infectious agent transporter role [Term] id: IDO:0000420 name: biological vector of infectious agent role def:"An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent multiplies in or on the vector." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000418 ! infectious agent vector role [Term] id: IDO:0000427 name: exotoxin disposition def:"A toxin disposition to damage cells or extracellular matrix by a direct enzymatic process." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000426 ! toxin disposition [Term] id: IDO:0000426 name: toxin disposition def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000425 name: virulence factor disposition def:"A disposition borne by a biological macromolecule produced by a pathogen that is a disposition to undergo processes that increase the pathogen's virulence." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000424 name: reservoir of infectious agent role def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Role ! role [Term] id: IDO:0000632 name: neurotoxin def:"A molecular entity with a toxin disposition\, the realization of which damages or interferes with the function of nerve tissue." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000549 ! toxin [Term] id: IDO:0000526 name: parasite def:"A organism bearing a parasite role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000522 ! symbiont [Term] id: IDO:0000631 name: community-acquired infection def:"An infection resulting from a transmission process that did not unfold in a health care facility." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: IDO:0000525 name: commensal def:"An organism bearing a commensal role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000522 ! symbiont [Term] id: IDO:0000630 name: hospital-acquired infection def:"An infection resulting from a transmission process that unfolds in a hospital." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: IDO:0000524 name: mutualist def:"An organism bearing a mutualist role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000522 ! symbiont [Term] id: IDO:0000523 name: obligatory symbiont def:"An organism that can only reach developmental maturity\, replicate\, or persist in symbiosis." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000522 ! symbiont [Term] id: IDO:0000522 name: symbiont def:"An organism bearing a symbiont role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: OBI:0100026 ! organism [Term] id: IDO:0000636 name: sepsis def:"A process that is a systemic inflammatory response to infection." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: span:ProcessualEntity ! processual_entity [Term] id: IDO:0000635 name: source of infection role def:"A role borne by a material entity in virtue of the fact that it contains a site from which an infectious agent is transmitted." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Role ! role [Term] id: IDO:0000520 name: communicability period def:"A continuous temporal interval during which contagiousness inhering in the bearer of a host role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: span:TemporalInterval ! temporal_interval [Term] id: IDO:0000633 name: metatstatic infection def:"An infection established as a result of spread from another infection in a non-adjacent location in the extended organism of the host." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: IDO:0000538 name: pathogen host def:"An organism bearing a pathogen host role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000531 ! host [Term] id: IDO:0000539 name: infectious agent carrier def:"An organism bearing the infectious agent carrier role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000537 ! infectious agent host [Term] id: IAO:0000409 name: denotator type def:"A denotator type indicates how a term should be interpreted from an ontological perspective." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"] is_a: IAO:0000102 ! data about an ontology part [Term] id: GO:0042101 name: T cell receptor complex def:"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." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0032991 ! macromolecular complex [Term] id: IDO:0000531 name: host def:"An organism bearing a host role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: OBI:0100026 ! organism [Term] id: IDO:0000530 name: primary pathogen def:"An infectious agent with a primary infectious disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000596 ! infectious agent [Term] id: IDO:0000533 name: intermediate host def:"A organism bearing an intermediate host role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000531 ! host [Term] id: GO:0006955 name: immune response def:"Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0008150 ! biological_process [Term] id: IDO:0000532 name: definitive host def:"An organism bearing a definitive host role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000531 ! host [Term] id: IDO:0000535 name: dead-end host def:"An organism bearing a dead-end host role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000531 ! host [Term] id: IDO:0000663 name: negative regulation of life-sustaining process def:"Any process that stops\, prevents\, or reduces the frequency\, rate or extent of a life-sustaining process." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: GO:0065007 ! biological regulation [Term] id: IDO:0000662 name: life-sustaining process def:"A process which is necessary for the survival of an organism." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: GO:0008150 ! biological_process [Term] id: IDO:0000534 name: paratenic host def:"An organism bearing a paratenic host role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000531 ! host [Term] id: IDO:0000537 name: infectious agent host def:"An organism bearing an infectious agent host role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000538 ! pathogen host [Term] id: IDO:0000665 name: source of infection def:"A material entity bearing a source of infection role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:MaterialEntity ! material_entity [Term] id: GO:0006959 name: humoral immune response def:"An immune response mediated through a body fluid." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0006955 ! immune response [Term] id: IDO:0000536 name: parasite host def:"An organism bearing a parasite host role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000531 ! host [Term] id: IDO:0001002 name: transition to clinical abnormality def:"A process by which a part of an organism or something contained in an organism becomes clinically abnormal." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: span:ProcessualEntity ! processual_entity [Term] id: IDO:0000549 name: toxin def:"A molecular entity that has a toxin disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: CHEBI:23367 ! molecular entity [Term] id: NCBITaxon:2759 name: Eukaryota is_a: OBI:0100026 ! organism [Term] id: IDO:0000659 name: susceptible organism def:"An organism that is not infected with an infectious agent and lacks protective immunity to the infectious agent." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: OBI:0100026 ! organism [Term] id: span:SpatiotemporalRegion name: spatiotemporal_region def:"Examples: the spatiotemporal region occupied by a human life\, the spatiotemporal region occupied by the development of a cancer tumor\, the spatiotemporal context occupied by a process of cellular meiosis; Comment: All instances of occurrent [span:Occurrent] are spatiotemporal entities\, that is\, they enter in the relation of (spatiotemporal) location with spatiotemporal region [span:SpatiotemporalRegion] entities. As a particular case\, the exact spatiotemporal location of a spatiotemporal region [span:SpatiotemporalRegion] is this region itself.; Definition: An occurrent [span:Occurrent] at or in which processual entity [span:ProcessualEntity] entities can be located.; Comment: An instance of the spatiotemporal region [span:SpatiotemporalRegion] is a part of spacetime. All parts of spacetime are spatiotemporal region [span:SpatiotemporalRegion] entities and only spatiotemporal region [span:SpatiotemporalRegion] entities are parts of spacetime. In particular\, neither spatial region [snap:SpatialRegion] entities nor temporal region [span:TemporalRegion] entities are in BFO parts of spacetime. Spacetime is the entire extent of the spatiotemporal universe\, a designated individual\, which is thus itself a spatiotemporal region [span:SpatiotemporalRegion]. Spacetime is among occurrents the analogous of space among continuant [snap:Continuant] entities.; Comment: Spacetime and spatiotemporal region [span:SpatiotemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of spacetime can be called "absolutist" or "the container view". In BFO\, the class processual context [span:ProcessualContext] allows for a so-called relational view of spacetime\, that is to say\, a view according to which spatiotemporality is a matter of relative location between entities and not a matter of being tied to spacetime. In BFO\, the bridge between these two views is secured through the fact that instances of processual context [span:ProcessualContext] are too spatiotemporal entities." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: span:Occurrent ! occurrent [Term] id: UBERON:0000178 name: blood is_a: CARO:0000000 ! anatomical entity [Term] id: snap:Site name: site def:"Comment: An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities\, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which\, then\, are site [snap:Site] entities) through a relation of "occupation". That relation is connected to\, but distinct from\, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO\, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class).; Examples: a particular room in a particular hospital\, Maria's nostril or her intestines for a variety of bacteria.; Definition: An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [snap:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [snap:Site] entities are entities that can be occupied by other continuant [snap:Continuant] entities." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:IndependentContinuant ! independent_continuant [Term] id: IDO:0000408 name: symbiont host role def:"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. " [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000629 ! host role [Term] id: IDO:0000409 name: definitive host role def:"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. " [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000408 ! symbiont host role [Term] id: IDO:0000406 name: opportunistic infectious disposition def:"An infectious disposition to become part of a disorder only in organisms whose defenses are compromised." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000452 ! infectious disposition [Term] id: IDO:0000407 name: primary infectious disposition def:"An infectious disposition to become part of a disorder in organisms that have intact defenses." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000452 ! infectious disposition [Term] id: IDO:0000405 name: pathogen role def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Role ! role [Term] id: snap:DependentContinuant name: dependent_continuant def:"Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:Continuant ! continuant [Term] id: snap:IndependentContinuant name: independent_continuant def:"Synonyms: substantial entity; Examples: an organism\, a heart\, a leg\, a person\, a symphony orchestra\, a chair\, the bottom right portion of a human torso\, the lawn and atmosphere in front of our building; Definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities\, in which other entities inhere and which itself cannot inhere in anything." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:Continuant ! continuant [Term] id: IDO:0000650 name: colonization of human def:"A colonization of host process in which the host is of Species Homo sapiens." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000604 ! colonization of host [Term] id: IDO:0000404 name: infectious agent role def:"A role borne by an infectious agent when contained in a host in which its infectious disposition can be realized." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000405 ! pathogen role [Term] id: IDO:0000403 name: parasite role def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000400 ! symbiont role [Term] id: span:ProcessBoundary name: process_boundary def:"Examples: birth\, death\, the forming of a synapse\, the onset of REM sleep\, the detaching of a finger in an industrial accident\, the final separation of two cells at the end of cell-division\, the incision at the beginning of a surgery; Definition: A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: span:ProcessualEntity ! processual_entity [Term] id: IDO:0000402 name: commensal role def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000400 ! symbiont role [Term] id: IDO:0000401 name: mutualist role def:"A symbiont role borne by an organism in virtue of the fact that both symbionts derive a growth\, survival\, or fitness advantage from symbiosis." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000400 ! symbiont role [Term] id: IDO:0000540 name: infectious agent vector def:"An organism bearing an infectious agent vector role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: OBI:0100026 ! organism [Term] id: IDO:0000400 name: symbiont role def:"A role borne by an organism in symbiosis." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Role ! role [Term] id: IDO:0000658 name: host exposure to infectious agent def:"A process in which a potential host of an infectious agent is exposed to an infectious agent." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: span:ProcessualEntity ! processual_entity [Term] id: IDO:0000544 name: fomite def:"A material entity bearing a fomite role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000543 ! vehicle of infectious agent [Term] id: IDO:0000543 name: vehicle of infectious agent def:"A material entity bearing an infectious agent vehicle role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:MaterialEntity ! material_entity [Term] id: IDO:0000657 name: process that results in death def:"A process that results in death." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: span:ProcessualEntity ! processual_entity [Term] id: IDO:0000656 name: horizontal pathogen transmission process def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: TRANS:0000000 ! Suggested label: pathogen transmission process [Term] id: IDO:0000542 name: biological vector of infectious agent def:"An infectious agent vector bearing a biological vector of infectious agent role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000540 ! infectious agent vector [Term] id: GO:0000003 name: reproduction def:"The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0008150 ! biological_process [Term] id: IDO:0000541 name: mechanical vector of infectious agent def:"An infectious agent vector bearing a mechanical vector of infectious agent role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000540 ! infectious agent vector [Term] id: IDO:0000655 name: transmissibility disposition def:"A disposition to undergo a transmission process." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000548 name: invasion factor def:"A biological macromolecule that has an invasion disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: CHEBI:23367 ! molecular entity [Term] id: IDO:0000654 name: opportunistic pathogen def:"An infectious agent with an opportunistic infectious disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000596 ! infectious agent [Term] id: IDO:0000547 name: virulence factor def:"A biological macromolecule produced by a pathogen and that has a virulence factor disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: CHEBI:23367 ! molecular entity [Term] id: IDO:0000653 name: reverse zoonosis def:"An infectious disease that has as its physical basis an infectious disorder composed of infectious agents that have a reverse zoonotic disposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000436 ! infectious disease [Term] id: IDO:0000546 name: _obsolete_end reservoir of infectious agent def:"A material entity bearing an end reservoir of infectious agent role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000652 name: colonization of human perineum def:"A colonization of human process in which the colonized site is a perineum." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000650 ! colonization of human [Term] id: IDO:0000651 name: primary immunodeficiency def:"An immunodeficiency that exists in an organism because of a genetic predisposition." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000617 ! immunodeficiency [Term] id: IDO:0000545 name: infectious agent reservoir def:"A material entity bearing an infectious agent reservoir role." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:MaterialEntity ! material_entity [Term] id: IDO:0000605 name: _obsolete_biological object colony def:"A biological object or group of biological objects in close spatial proximity." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000604 name: colonization of host def:"An establishment in host process in which an organism establishes itself in a host." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000625 ! establishment of localization in host [Term] id: IDO:0000607 name: production def:"A process in which an entity comes into being as a result of the process." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: span:Process ! process [Term] id: IDO:0000606 name: establishment of a clinically abnormal colony def:"A colonization of host process that results in a clinically abnormal colony." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000604 ! colonization of host [Term] id: IDO:0000609 name: colonization of human anterior nares def:"A colonization of human process in which the colonized site is the anterior nares." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000650 ! colonization of human [Term] id: IDO:0000608 name: replication def:"A production process in which a participant creates a copy of itself." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000607 ! production [Term] id: IDO:0000600 name: release of infectious human pathogen in laboratory def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000597 ! host exposure to environment containing infectious agent [Term] id: IDO:0000601 name: host coming into contact with vector of infectious agent def:"A host exposure to environment with infectious agent where the environment contains an infectious agent vector." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000597 ! host exposure to environment containing infectious agent [Term] id: IDO:0000602 name: host exposure to substance that might have infectious agent def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000597 ! host exposure to environment containing infectious agent [Term] id: IDO:0000603 name: process of establishing an infection def:"A process by which an infectious agent\, established in a host\, becomes part of an infection in the host." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: span:ProcessualEntity ! processual_entity [Term] id: span:FiatProcessPart name: fiat_process_part def:"Examples: chewing during a meal\, the middle part of a rainstorm\, the worst part of a heart-attack\, the most interesting part of Van Gogh's life; Definition: A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: span:ProcessualEntity ! processual_entity [Term] id: GO:0050777 name: negative regulation of immune response def:"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." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0065007 ! biological regulation [Term] id: GO:0045087 name: innate immune response def:"Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0006955 ! immune response [Term] id: snap:SpatialRegion name: spatial_region def:"Comment: An instance of spatial region [snap:SpatialRegion] is a part of space. All parts of space are spatial region [snap:SpatialRegion] entities and only spatial region [snap:SpatialRegion] entities are parts of space. Space is the entire extent of the spatial universe\, a designated individual\, which is thus itself a spatial region [snap:SpatialRegion].; Comment: All instances of continuant [snap:Continuant] are spatial entities\, that is\, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case\, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself.; Examples: the sum total of all space in the universe\, parts of the sum total of all space in the universe; Comment: Space and spatial region [snap:SpatialRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called "absolutist" or "the container view". In BFO\, the class site [snap:Site] allows for a so-called relational view of space\, that is to say\, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site [snap:Site] are not spatial region [snap:SpatialRegion] entities\, they are nevertheless spatial entities.; Definition: A continuant [snap:Continuant] that is neither bearer of quality [snap:Quality] entities nor inheres in any other entities." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:Continuant ! continuant [Term] id: GO:0043093 name: cytokinesis by binary fission def:"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." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0000003 ! reproduction [Term] id: IDO:0000627 name: acute infection def:"An infectious disorder that is the physical basis for an unfolding acute infectious disease course." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000504 ! infectious disorder [Term] id: IDO:0000626 name: appearance of disorder def:"A process by which a disorder comes into existence." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: span:ProcessualEntity ! processual_entity [Term] id: IDO:0000629 name: host role def:"A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Role ! role [Term] id: IDO:0000628 name: chronic infection def:"An infection that persists for an extended period of time." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000586 ! infection [Term] id: IDO:0000622 name: disposition to form a non-parasitic colony def:"A disposition to colonize an organism and participate in mutualism or commensalism with that organism." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000623 name: communicability def:"An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000452 ! infectious disposition [Term] id: IDO:0000624 name: obsolete_host range def:"A quality that inheres in an infection and is the likelihood that infectious agents part of the infection will spread to other hosts.; 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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000625 name: establishment of localization in host def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: GO:0051234 ! establishment of localization [Term] id: IDO:0000621 name: acquired immunity to infectious agent def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000448 ! immunity to infectious agent [Term] id: span:ScatteredSpatiotemporalRegion name: scattered_spatiotemporal_region def:"Examples: the space and time occupied by the individual games of the World Cup\, the space and time occupied by the individual liaisons in a romantic affair; Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has spatial and temporal dimensions and every spatial and temporal point of which is not connected with every other spatial and temporal point of which." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: span:SpatiotemporalRegion ! spatiotemporal_region [Term] id: span:ConnectedSpatiotemporalRegion name: connected_spatiotemporal_region def:"Examples: the spatial and temporal location of an individual organism's life\, the spatial and temporal location of the development of a fetus; Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has temporal and spatial dimensions such that all points within the spatiotemporal region are mediately or immediately connected to all other points within the same spatiotemporal region [span:SpatiotemporalRegion]." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: span:SpatiotemporalRegion ! spatiotemporal_region [Term] id: IDO:0000508 name: virion def:"A virus that is in its assembled state consisting of genomic material (DNA or RNA) surrounded by coating molecules." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: NCBITaxon:10239 ! Viruses [Term] id: IDO:0000302 name: _obsolete_long-term non-progression is_obsolete: true [Term] id: IDO:0000507 name: _obsolete_septicemia def:"A bacteremia in which the baceteria are replicating." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000301 name: _obsolete_rapid progression is_obsolete: true [Term] id: IDO:0000300 name: _obsolete_progression rate is_obsolete: true [Term] id: IDO:0000506 name: bacteremia def:"An infection that has as part bacteria located in the blood." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000472 ! extracellular infection [Term] id: IDO:0000505 name: viremia def:"An infection that has as part virus particles located in the blood." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000472 ! extracellular infection [Term] id: IDO:0000619 name: immunosuppressive disposition def:"A disposition whose realization negatively regulates an immune response." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000306 name: _obsolete_fitness def:"'is a quality relating to both bacteria and host'-ID[O]:0000306: is a quality relating to both bacteria and host" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000618 name: immunocompetence def:"A disposition that is the ability to mount a normal immune response." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:Disposition ! disposition [Term] id: IDO:0000617 name: immunodeficiency def:"A disorder of an immune system component that results in defective functioning of the immune system." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: OGMS:0000045 ! disorder [Term] id: IDO:0000305 name: _obsolete_co-infected is_obsolete: true [Term] id: IDO:0000616 name: infectious agent colony def:"A colony whose members are infectious agents." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000615 ! colony [Term] id: span:Process name: process def:"Examples: the life of an organism\, the process of sleeping\, the process of cell-division; Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: span:ProcessualEntity ! processual_entity [Term] id: IDO:0000303 name: _obsolete_highly exposed persistently seronegative is_obsolete: true [Term] id: IDO:0000615 name: colony def:"An organism population persisting in a site it has colonized." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000509 ! organism population [Term] id: IDO:0000509 name: organism population def:"An aggregate of organisms of the same Species." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: snap:ObjectAggregate ! object_aggregate [Term] id: IDO:0000613 name: _obsolete_biological object def:"primitive" [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000500 name: variolation def:"An active immunization that begins with exposure to smallpox in the form of a scab from a pustule and results in immunity against smallpox." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000498 ! active immunization against infectious agent [Term] id: IDO:0000614 name: _obsolete_replicating biological material entity def:"A biological material entity that is capable of replication." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_obsolete: true [Term] id: IDO:0000611 name: physiologic immunosuppression def:"An immunosuppression which unfolds as part of the natural self-regulation of an immune response." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000610 ! immunosuppression [Term] id: IDO:0000612 name: pathologic immunosuppression def:"An immunosuppression process which arises as the result of a disorder." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000610 ! immunosuppression [Term] id: IDO:0000503 name: infectious disease pandemic def:"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." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: span:ProcessualEntity ! processual_entity [Term] id: IDO:0000610 name: immunosuppression def:"A process that attenuates an immune response." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: span:ProcessualEntity ! processual_entity [Term] id: IDO:0000504 name: infectious disorder def:"An infection that is clinically abnormal." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: OGMS:0000045 ! disorder is_a: IDO:0000586 ! infection [Term] id: IDO:0000501 name: passive immunization against infectious agent def:"An immunization that begins with transfer to an organism of molecules not produced by that organism and that confer immunity against an infectious agent." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: IDO:0000497 ! immunization against infectious agent [Term] id: IDO:0000502 name: infectious disease epidemic def:"A process of infectious disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population." [OBO:sourced "IDO consortium http://www.infectiousdiseaseontology.org"] is_a: span:ProcessualEntity ! processual_entity [Term] id: span:ProcessualContext name: processual_context def:"Comment: An instance of a processual context [span:ProcessualContext] is a mixture of processual entity [span:ProcessualEntity] which stand as surrounding environments for other processual entity [span:ProcessualEntity] entities. The class processual context [span:ProcessualContext] is the analogous among occurrent [span:Occurrent] entities to the class site [snap:Site] among continuant [snap:Continuant] entities.; Examples: The processual context for a given manipulation occurring as part of an experiment is made of processual entities which occur in parallel\, are not necessarily all parts of the experiment themselves and may involve continuant [snap:Continuant] entities which are in the spatial vicinity of the participants in the experiment.; Definition: An occurrent [span:Occurrent] consisting of a characteristic spatial shape inhering in some arrangement of other occurrent [span:Occurrent] entities. Processual context [span:ProcessualContext] entities are characteristically entities at or in which other occurrent [span:Occurrent] entities can be located or occur." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: span:ProcessualEntity ! processual_entity [Term] id: span:ProcessAggregate name: process_aggregate def:"Examples: the beating of the hearts of each of seven individuals in the room\, the playing of each of the members of an orchestra\, a process of digestion and a process of thinking taken together; Definition: A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: span:ProcessualEntity ! processual_entity [Term] id: GO:0051093 name: negative regulation of developmental process def:"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)." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0065007 ! biological regulation [Term] id: ENVO:00002036 name: habitat def:"A spatial region having environmental qualities which may sustain an organism or a community of organisms." [OBO:imported "http://purl.org/obo/owl/ENVO"] is_a: snap:Site ! site [Term] id: snap:Quality name: quality def:"Examples: the color of a tomato\, the ambient temperature of air\, the circumference of a waist\, the shape of a nose\, the mass of a piece of gold\, the weight of a chimpanzee; Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property)." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:SpecificallyDependentContinuant ! specifically_dependent_continuant [Term] id: snap:ZeroDimensionalRegion name: zero_dimensional_region def:"Examples: a point; Definition: A spatial region [snap:SpatialRegion] with no dimensions." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:SpatialRegion ! spatial_region [Term] id: snap:Function name: function def:"Examples: the function of a birth canal to enable transport\, the function of the heart in the body: to pump blood\, to receive de-oxygenated and oxygenated blood\, etc.\, the function of reproduction in the transmission of genetic material\, the digestive function of the stomach to nutriate the body\, the function of a hammer to drive in nails\, the function of a computer program to compute mathematical equations\, the function of an automobile to provide transportation\, the function of a judge in a court of law; Definition: A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:RealizableEntity ! realizable_entity [Term] id: snap:RealizableEntity name: realizable_entity def:"Comment: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant]\, this does not imply that it is actually realized.; Examples: the role of being a doctor\, the function of the reproductive organs\, the disposition of blood to coagulate\, the disposition of metal to conduct electricity; Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap:Continuant] entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation\, functioning or process that occurs under certain circumstances." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:SpecificallyDependentContinuant ! specifically_dependent_continuant [Term] id: NCBITaxon:2157 name: Archaea is_a: OBI:0100026 ! organism [Term] id: span:SpatiotemporalInterval name: spatiotemporal_interval def:"Examples: the spatiotemporal region occupied by a process or by a fiat processual part; Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] that endures for more than a single moment of time." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: span:ConnectedSpatiotemporalRegion ! connected_spatiotemporal_region [Term] id: IAO:0000078 name: curation status specification def:"The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"] is_a: IAO:0000102 ! data about an ontology part [Term] id: snap:ThreeDimensionalRegion name: three_dimensional_region def:"Examples: a cube-shaped part of space\, a sphere-shaped part of space; Definition: A spatial region [snap:SpatialRegion] with three dimensions." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:SpatialRegion ! spatial_region [Term] id: snap:FiatObjectPart name: fiat_object_part def:"Synonyms: fiat substance part; Examples: upper and lower lobes of the left lung\, the dorsal and ventral surfaces of the body\, the east side of Saarbruecken\, the lower right portion of a human torso; Definition: A material entity [snap:MaterialEntity] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:MaterialEntity ! material_entity [Term] id: GO:0065007 name: biological regulation def:"Any process that modulates the frequency\, rate or extent of any biological process\, quality or function." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: span:ProcessualEntity ! processual_entity [Term] id: GO:0048525 name: negative regulation of viral reproduction def:"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." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0065007 ! biological regulation [Term] id: IAO:0000225 name: obsolescence reason specification def:"The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [OBO:imported "http://purl.obolibrary.org/obo/iao.owl"] is_obsolete: true [Term] id: OGMS:0000020 name: symptom def:"A quality of a patient that is observed by the patient and is hypothesized by the patient to be a realization of a disease." [OBO:imported "http://purl.obolibrary.org/obo/ogms.owl"] is_a: snap:Quality ! quality [Term] id: span:TemporalInstant name: temporal_instant def:"Examples: right now\, the moment at which a finger is detached in an industrial accident\, the moment at which a child is born\, the moment of death; Definition: A connected temporal region [span:ConnectedTemporalRegion] comprising a single moment of time." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: span:ConnectedTemporalRegion ! connected_temporal_region [Term] id: OGMS:0000031 name: disease def:"A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." [OBO:imported "http://purl.obolibrary.org/obo/ogms.owl"] is_a: snap:Disposition ! disposition [Term] id: GO:0040007 name: growth def:"The increase in size or mass of an entire organism\, a part of an organism or a cell." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0008150 ! biological_process [Term] id: snap:OneDimensionalRegion name: one_dimensional_region def:"Examples: the part of space that is a line stretching from one end of absolute space to the other\, an edge of a cube-shaped part of space; Definition: A spatial region [snap:SpatialRegion] with one dimension." [OBO:imported "http://www.ifomis.org/bfo/1.1/"] is_a: snap:SpatialRegion ! spatial_region [Term] id: GO:0002250 name: adaptive immune response def:"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)." [OBO:imported "http://purl.org/obo/owl/GO"] is_a: GO:0006955 ! immune response [Typedef] id: RO:part_of name: part_of def:"For continuants: C part_of C' if and only if: given any c that instantiates C at a time t\, there is some c' such that c' instantiates C' at time t\, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t\, there is some p' such that p' instantiates P' at time t\, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)" [OBO:imported "http://www.obofoundry.org/ro/ro.owl"] inverse_of: RO:has_part ! has_part is_a: RO:improper_part_of ! improper_part_of is_a: RO:proper_part_of ! proper_part_of is_a: RO:integral_part_of ! integral_part_of [Typedef] id: ROP:has_output name: has_output def:"C has_output C'" [OBO:imported "http://purl.org/obo/owl/OBO_REL"] [Typedef] id: RO:location_of name: location_of inverse_of: RO:located_in ! located_in [Typedef] id: RO:participates_in name: participates_in inverse_of: RO:has_participant ! has_participant is_a: RO:agent_in ! agent_in [Typedef] id: RO:has_participant name: has_participant def:"P has_participant C if and only if: given any process p that instantiates P there is some continuant c\, and some time t\, such that: c instantiates C at t and c participates in p at t" [OBO:imported "http://www.obofoundry.org/ro/ro.owl"] inverse_of: RO:participates_in ! participates_in is_a: RO:has_agent ! has_agent [Typedef] id: RO:has_integral_part name: has_integral_part inverse_of: RO:integral_part_of ! integral_part_of [Typedef] id: ROP:realized_by name: realized_by def:"Relation between a realizable and a process. Reciprocal relation of realizes; Relation between a realizable and a process. Reciprocal relation of realizes" [OBO:imported "http://purl.org/obo/owl/OBO_REL"] [Typedef] id: ROP:positively_regulates name: positively_regulates def:"A regulation relation in which the unfolding of the regulating process *increases* the frequency\, rate or extent of the regulated process" [OBO:imported "http://purl.org/obo/owl/OBO_REL"] [Typedef] id: IDO:0000664 name: has_material_basis_in [Typedef] id: RO:agent_in name: agent_in inverse_of: RO:has_agent ! has_agent [Typedef] id: RO:has_improper_part name: has_improper_part def:"See reasons for obsoletion of improper_part_of" [OBO:imported "http://www.obofoundry.org/ro/ro.owl"] inverse_of: RO:improper_part_of ! improper_part_of [Typedef] id: RO:derived_into name: derived_into inverse_of: RO:derives_from ! derives_from [Typedef] id: RO:improper_part_of name: improper_part_of def:"As for part_of\, with the additional constraint that subject and object may be identical" [OBO:imported "http://www.obofoundry.org/ro/ro.owl"] inverse_of: RO:has_improper_part ! has_improper_part [Typedef] id: RO:proper_part_of name: proper_part_of def:"As for part_of\, with the additional constraint that subject and object are distinct" [OBO:imported "http://www.obofoundry.org/ro/ro.owl"] inverse_of: RO:has_proper_part ! has_proper_part [Typedef] id: RO:has_part name: has_part inverse_of: RO:part_of ! part_of is_a: RO:has_improper_part ! has_improper_part is_a: RO:has_proper_part ! has_proper_part is_a: RO:has_integral_part ! has_integral_part [Typedef] id: ROP:has_function name: has_function def:"Relation between an independent continuant and a function." [OBO:imported "http://purl.org/obo/owl/OBO_REL"] [Typedef] id: ROP:regulates name: regulates def:"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" [OBO:imported "http://purl.org/obo/owl/OBO_REL"] is_a: ROP:positively_regulates ! positively_regulates is_a: ROP:negatively_regulates ! negatively_regulates [Typedef] id: ROP:has_disposition name: has_disposition [Typedef] id: RO:derives_from name: derives_from def:"Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t\, if c instantiates C at time t\, then there is some c' and some t'\, such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'." [OBO:imported "http://www.obofoundry.org/ro/ro.owl"] inverse_of: RO:derived_into ! derived_into [Typedef] id: RO:relationship name: relationship def:"A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances." [OBO:imported "http://www.obofoundry.org/ro/ro.owl"] [Typedef] id: ROP:bearer_of name: bearer_of def:"A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in" [OBO:imported "http://purl.org/obo/owl/OBO_REL"] is_a: ROP:has_role ! has_role [Typedef] id: RO:preceded_by name: preceded_by def:"P preceded_by P' if and only if: given any process p that instantiates P at a time t\, there is some process p' such that p' instantiates P' at time t'\, and t' is earlier than t. " [OBO:imported "http://www.obofoundry.org/ro/ro.owl"] inverse_of: RO:precedes ! precedes [Typedef] id: ROP:inheres_in name: inheres_in def:"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." [OBO:imported "http://purl.org/obo/owl/OBO_REL"] [Typedef] id: RO:integral_part_of name: integral_part_of def:"C integral_part_of C' if and only if: C part_of C' AND C' has_part C" [OBO:imported "http://www.obofoundry.org/ro/ro.owl"] inverse_of: RO:has_integral_part ! has_integral_part [Typedef] id: RO:located_in name: located_in def:"C located_in C' if and only if: given any c that instantiates C at a time t\, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)" [OBO:imported "http://www.obofoundry.org/ro/ro.owl"] inverse_of: RO:location_of ! location_of [Typedef] id: ROP:results_in_formation_of name: results_in_formation_of def:"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" [OBO:imported "http://purl.org/obo/owl/OBO_REL"] [Typedef] id: ROP:unfolds_in name: unfolds_in def:"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" [OBO:imported "http://purl.org/obo/owl/OBO_REL"] [Typedef] id: RO:contained_in name: contained_in def:"C contained_in C' if and only if: given any instance c that instantiates C at a time t\, there is some c' such that: c' instantiates C' at time t and c located_in c' at t\, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.)" [OBO:imported "http://www.obofoundry.org/ro/ro.owl"] inverse_of: RO:contains ! contains [Typedef] id: RO:adjacent_to name: adjacent_to def:"C adjacent to C' if and only if: given any instance c that instantiates C at a time t\, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity" [OBO:imported "http://www.obofoundry.org/ro/ro.owl"] [Typedef] id: RO:has_agent name: has_agent def:"As for has_participant\, but with the additional condition that the component instance is causally active in the relevant process" [OBO:imported "http://www.obofoundry.org/ro/ro.owl"] inverse_of: RO:agent_in ! agent_in [Typedef] id: RO:precedes name: precedes inverse_of: RO:preceded_by ! preceded_by [Typedef] id: RO:contains name: contains inverse_of: RO:contained_in ! contained_in [Typedef] id: ROP:negatively_regulates name: negatively_regulates def:"A regulation relation in which the unfolding of the regulating process *decreases* the frequency\, rate or extent of the regulated process" [OBO:imported "http://purl.org/obo/owl/OBO_REL"] [Typedef] id: RO:transformation_of name: transformation_of def:"Relation between two classes\, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t\, if c instantiates C at time t\, then for some t'\, c instantiates C' at t' and t' earlier t\, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2." [OBO:imported "http://www.obofoundry.org/ro/ro.owl"] [Typedef] id: ROP:has_role name: has_role def:"A relation between a continuant C and a role R. The reciprocal relation of role_of." [OBO:imported "http://purl.org/obo/owl/OBO_REL"] [Typedef] id: RO:has_proper_part name: has_proper_part inverse_of: RO:proper_part_of ! proper_part_of [Typedef] id: ROP:realizes name: realizes def:"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" [OBO:imported "http://purl.org/obo/owl/OBO_REL"]