Alan Ruttenberg Andrew Spear Pierre Grenon Holger Stenzhorn application/rdf+xml http://www.ifomis.org/bfo/1.1 en Institute for Formal Ontology and Medical Information Science (IFOMIS) http://creativecommons.org/licenses/by/3.0 Barry Smith and Pierre Grenon: "The Cornucopia of Formal Ontological Relations" Barry Smith: "Against Fantology" Barry Smith: "Basic Tools of Formal Ontology" Barry Smith: "Beyond Concepts: Ontology as Reality Representation" Pierre Grenon and Barry Smith: "SNAP and SPAN: Towards Geospatial Dynamics" Pierre Grenon, Barry Smith and Louis Goldberg: "Biodynamic Ontology: Applying BFO in the Biomedical Domain" Pierre Grenon: "BFO in a Nutshell: A Bi-categorial Axiomatization of BFO and Comparison with DOLCE" Pierre Grenon: "Nuts in BFO's Nutshell: Revisions to the Bi-categorial Axiomatization of BFO" Pierre Grenon: "Spatio-temporality in Basic Formal Ontology: SNAP and SPAN, Upper-Level Ontology, and Framework for Formalization" Basic Formal Ontology (BFO) 1.1.1 REL:0000027 A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in has_inherent has_inherer Comment in Relation Ontology (RO): Examples: red eye bearer_of redness bearer_of disposition_of REL:0000029 A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality</ has_quality REL:0000026 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. Comment in Relation Ontology (RO):This relation links qualities, functions, dispositions and other dependent continuants to their bearers. Examples: A particular shape that inheres in a lung; The redness that ineres in a Drosophila eye; Catalytic activity function inheres_in catalytic molecule. Note that inherence is a functional relation: if x inheres_in y at t and x inheres_in z at t, then y=z. We leave open the possibility of a relation multiply_inheres_in, such as between a gene sequence and the multiple chromosomes it multiply inheres in. The super-relation of both inheres_in and multiply_inheres_in would be depends_on inheres_in inheres_in_part_of bfo:Entity entity snap:Continuant 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. 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 Synonyms: endurant continuant snap:DependentContinuant 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. dependent_continuant snap:Disposition 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. 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. disposition snap:FiatObjectPart Definition: A material entity [snap:MaterialEntity] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities. 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 Synonyms: fiat substance part fiat_object_part snap:Function 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. 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 function snap:GenericallyDependentContinuant 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. Examples: a certain PDF file that exists in different and in several hard drives generically_dependent_continuant snap:IndependentContinuant 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. 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 Synonyms: substantial entity independent_continuant snap:MaterialEntity 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. Examples: collection of random bacteria, a chair, dorsal surface of the body material_entity snap:Object 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. Examples: an organism, a heart, a chair, a lung, an apple Synonyms: substance object snap:ObjectAggregate Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries. 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 Synonyms: substance aggregate object_aggregate snap:ObjectBoundary 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. 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 Synonyms: substance boundary object_boundary snap:OneDimensionalRegion Definition: A spatial region [snap:SpatialRegion] with one dimension. 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 one_dimensional_region snap:Quality Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property). 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 quality snap:RealizableEntity Comment: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized. 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. 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 realizable_entity snap:Role 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. 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 role snap:Site 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). 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. Examples: a particular room in a particular hospital, Maria's nostril or her intestines for a variety of bacteria. site 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. 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: 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. Examples: the sum total of all space in the universe, parts of the sum total of all space in the universe spatial_region snap:SpecificallyDependentContinuant 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. 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. Synonyms: property, trope, mode specifically_dependent_continuant snap:ThreeDimensionalRegion Definition: A spatial region [snap:SpatialRegion] with three dimensions. Examples: a cube-shaped part of space, a sphere-shaped part of space three_dimensional_region snap:TwoDimensionalRegion Definition: A spatial region [snap:SpatialRegion] with two dimensions. 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 two_dimensional_region snap:ZeroDimensionalRegion Definition: A spatial region [snap:SpatialRegion] with no dimensions. Examples: a point zero_dimensional_region span:ConnectedSpatiotemporalRegion 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]. Examples: the spatial and temporal location of an individual organism's life, the spatial and temporal location of the development of a fetus connected_spatiotemporal_region span:ConnectedTemporalRegion Definition: A temporal region [span:TemporalRegion] every point of which is mediately or immediately connected with every other point of which. Examples: the 1970s years, the time from the beginning to the end of a heart attack, the time taken up by cellular meiosis connected_temporal_region span:FiatProcessPart 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. 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 fiat_process_part span:Occurrent Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants. 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 Synonyms: perdurant occurrent span:Process Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities. Examples: the life of an organism, the process of sleeping, the process of cell-division process span:ProcessAggregate Definition: A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries. 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 process_aggregate span:ProcessBoundary Definition: A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary. 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 process_boundary span:ProcessualContext 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. 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. 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. processual_context span:ProcessualEntity Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. Examples: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird processual_entity span:ScatteredSpatiotemporalRegion 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. 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 scattered_spatiotemporal_region span:ScatteredTemporalRegion Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which. Examples: the time occupied by the individual games of the World Cup, the time occupied by the individual liaisons in a romantic affair scattered_temporal_region span:SpatiotemporalInstant Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] at a specific moment. Examples: the spatiotemporal region occupied by a single instantaneous temporal slice (part) of a process spatiotemporal_instant span:SpatiotemporalInterval Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] that endures for more than a single moment of time. Examples: the spatiotemporal region occupied by a process or by a fiat processual part spatiotemporal_interval span:SpatiotemporalRegion 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. 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. Definition: An occurrent [span:Occurrent] at or in which processual entity [span:ProcessualEntity] entities can be located. 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 spatiotemporal_region span:TemporalInstant Definition: A connected temporal region [span:ConnectedTemporalRegion] comprising a single moment of time. 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 temporal_instant span:TemporalInterval Definition: A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time. Examples: any continuous temporal duration during which a process occurs temporal_interval span:TemporalRegion 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: 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. 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]. 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 temporal_region HPI:0000001 WEB: http://en.wikipedia.org/wiki/Organism OBI:0100026 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. Examples: fungus, animal, plant, virus organism HPI:0000002 ISBN: 92-5-104683-2 (Edition of the Glossary of Biotechnology and Genetic Engineering. FAO RESEARCH AND TECHNOLOGY PAPER 9.) NCBITaxon:131567 An individual living system, such as animal, plant or micro-organism, that is capable of reproduction, growth and maintenance. An organism, e.g. 'Homo sapiens'. cellular organisms HPI:0000003 Infectious Disease Ontology (IDO). GO:0018995 IDO:0000531 OBI:1110026 An organism bearing the host role. host organism Definition Wikipedia: http://en.wikipedia.org/wiki/Host_(biology) host HPI:0000004 Infectious Disease Ontology (IDO). IDO:0000528 A material entity with a pathogenic disposition. Natural Language Definition:A disease whose physical basis is an infectious disorder. pathogen HPI:0000005 ISBN: 92-5-104683-2 (Edition of the Glossary of Biotechnology and Genetic Engineering. FAO RESEARCH AND TECHNOLOGY PAPER 9. ) NCBITaxon:2 (pl.: bacteria) Unicellular prokaryotic organisms, without a distinct nucleus. Major distinctive groups are defined by Gram staining. Also classified on the basis of oxygen requirement (aerobic vs anaerobic) and shape (spherical = coccus; rodlike = bacillus; spiral = spirillum; comma-shaped = vibrio; corkscrew-shaped = spirochaete; filamentous). bacterium eubacteria monera not Bacteria Haeckel 1894 procaryotae prokaryota prokaryotae prokaryotes bacteria HPI:0000006 ISBN: 92-5-104683-2 (Edition of the Glossary of Biotechnology and Genetic Engineering. FAO RESEARCH AND TECHNOLOGY PAPER 9. ) NCBITaxon:590 A bacteria that is a a genus of rod-shaped, gram-negative bacteria that are a common cause of food poisoning. Nomenclature and taxonomy of the genus Salmonella (International Journal of Systematic and Evolutionary Microbiology (2005), 55, 521-524 (PMID: 15653930) salmonella HPI:0000007 NCBITaxon:54736 almonella enterica V almonella enterica subsp. V salmonella cholerae-suis subsp. Bongor salmonella choleraesuis subsp. Bongori salmonella enterica subsp. Bongori Nomenclature and taxonomy of the genus Salmonella (International Journal of Systematic and Evolutionary Microbiology (2005), 55, 521-524 (PMID: 15653930). salmonella bongori A subgenus of Salmonella containing several medically important serotypes. The habitat for the majority of strains is warm-blooded animals. HPI:0000008 Medical Subject Headings (MeSH: D019779). NCBITaxon:28901 s. choleraesuis s. enterica salmonella choleraesuis Nomenclature and taxonomy of the genus Salmonella (International Journal of Systematic and Evolutionary Microbiology (2005), 55, 521-524 (PMID: 15653930). salmonella enterica HPI:0000009 NCBITaxon:59203 The subspecies Arizonae of the species Salmonella Enterica. Salmonella enterica IIIa salmonella enterica serovar IIIa salmonella enterica subsp. IIIa Nomenclature and taxonomy of the genus Salmonella (International Journal of Systematic and Evolutionary Microbiology (2005), 55, 521-524 (PMID: 15653930). salmonella enterica subsp. arizonae HPI:0000010 NCBITaxon:59204 The subspecies Diarizonae of the species Salmonella Enterica. salmonella enterica IIIb salmonella enterica serovar IIIb salmonella enterica subsp. IIIb Nomenclature and taxonomy of the genus Salmonella (International Journal of Systematic and Evolutionary Microbiology (2005), 55, 521-524 (PMID: 15653930). salmonella enterica subsp. diarizonae HPI:0000011 NCBITaxon:59201 The subspecies Enterica of the species Salmonella Enterica. s. typhimurium;salmonella enterica I salmonella enterica I salmonella enterica subsp. I salmonella typhimurium Nomenclature and taxonomy of the genus Salmonella (International Journal of Systematic and Evolutionary Microbiology (2005), 55, 521-524 (PMID: 15653930). salmonella enterica subsp. enterica HPI:0000012 NCBITaxon:59205 The subspecies Houtenae of the species Salmonella Enterica. almonella enterica IV salmonella enterica subsp. IV Nomenclature and taxonomy of the genus Salmonella (International Journal of Systematic and Evolutionary Microbiology (2005), 55, 521-524 (PMID: 15653930). almonella enterica subsp. houtenae HPI:0000013 NCBITaxon:59207 The subspecies Indica of the species Salmonella Enterica. salmonella enterica VI salmonella enterica subsp. VI Nomenclature and taxonomy of the genus Salmonella (International Journal of Systematic and Evolutionary Microbiology (2005), 55, 521-524 (PMID: 15653930). salmonella enterica subsp. indica HPI:0000014 NCBITaxon:59202 The subspecies Salamaeof the species Salmonella Enterica. salmonella enterica II salmonella enterica serovar II salmonella enterica subsp. II Nomenclature and taxonomy of the genus Salmonella (International Journal of Systematic and Evolutionary Microbiology (2005), 55, 521-524 (PMID: 15653930). salmonella enterica subsp. salamae HPI:0000015 NCIThesaurus (C25796; http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Eukaryote) NCBITaxon:2759 Organism or cells with a nucleus separated from the cytoplasm by a two membrane nuclear envelope and compartmentalization of function into distinct cytoplasmic organelles. eucarya eucaryotae eucaryotes eukarya eukaryotae eukaryotes Common name: eukaryotes eukaryota HPI:0000016 NCIThesuarus (http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Mammal). NCBITaxon:40674 Any warm-blooded vertebrate having the skin more or less covered with hair; young are born alive except for the small subclass of monotremes and nourished with milk. mammal mammalian mammals mammalia HPI:0000017 Medical Subject Headings (MeSH: D034421). NCBITaxon:9823 A mammalian species that is a A species of SWINE, in the family Suidae, comprising a number of subspecies including the domestic pig Sus scrofa domestica. domestic pig domestic pigs pig pigs swine wild boar wild pig Common name: pig. sus scrofa HPI:0000018 IDO:0000509 A material enity of organisms of the same type that are members of the population because they meet a set of criteria, such as being present in a specified geographic region during a specified period of time. Natural Language Definition: A population of organisms. The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age. organism population HPI:0000019 HPI An organism population whose members are of type Sus scrofa. pig population Sus Scrofa population HPI:0000020 HPI A tract of land, as well as the group of buildings with and often surrounding a farmhouse, including barns, sheds, and other outbuildings, used for agricultural production of pigs. Definition partly from ENVO (00000078). pig farm HPI:0000021 HPI A Sus scrofa population whose members are inhabitants of pig farm x during a specified temporal interval. Sus Scrofa population of pig farm x HPI:0000022 Infectious Disease Ontology (IDO). IDO:0000586 OBI:1110021 A part of an extended organism that itself has as part an infectious agent or population of infectious agents and (1) which is clinically abnormal in virtue of the presence of the infectious agent(s), or (2) clinical abnormality is a likely consequence of transmission of the infectious agent, an offspring of the infectious agent, or a member of the infectious agent population to a canonical host. By this definition, parts of the host can be considered part of the infection. infection Infectious Disease Ontology (IDO). IDO:0000538 An organism bearing the host of pathogen role. pathogen host HPI:0000024 An host of pathogen bearing the host of salmonella role. salmonella host HPI:0000025 Infectious Disease Ontology (IDO). IDO:0000596 A pathogen whose pathogenic disposition is an infectious disposition. The term infectious agent refers to infectious organisms and prion proteins. infectious agent HPI:0000026 Ontology for General Medical Science (OGMS); http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf, http://code.google.com/p/ogms/issues/detail?id=34. DOID:4 OBI:1110055 OGMS:0000031 A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. disorder Examples: Epilepsy as a disease that disposes to the occurence of seizures (pathological process) due to an underlying abnormality in the neuronal circuitry of the brain (phyisical basis). disease HPI:0000027 IDO:0000436 OBI:1110040 A disease (OGMS:0000031) that has an infection (IDO:0000586) as its physical basis and is realized in an infectious disease course (IDO:0000495). tranmissible disease Axioms: The disposition is realized in a processual entity that is an infectious disease course (IDO:0000495). infectious disease A material entity that is matter in or on which organisms may live. HPI:0000028 Environment Ontology (ENVO). ENVO:00010483 Comment Environment Ontology (ENVO): Everything under this parent must be a mass noun. environmental matter HPI:0000029 Environment Ontology (ENVO). ENVO:00002005 A environmental matter that is the mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth. Xref in Environment Ontology (ENVO): http://en.wikipedia.org/wiki/Air. air HPI:0000030 ENVO:02000019 A environmental matter that is natural bodily fluid or secretion such as blood, semen, saliva, blood plasma, intracellular and interstitial fluids. body fluid Xref in Environment Ontology (ENVO): http://en.wikipedia.org/wiki/Bodily_fluid. Environment Ontology (ENVO). bodily fluid HPI:0000031 Environment Ontology (ENVO). ENVO:02000022 GO:0007588 Excreta are bodily fluids consisting of waste matter, such as sweat or feces, discharged from the body. excretion Defintion of excretion in Gene Ontology: The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds. Xref in Environment Ontology (ENVO): http://en.wikipedia.org/wiki/Excreta. excreta HPI:0000032 ENVO:00002003 FMA:64183 Feces is an excreta consisting of waste products expelled from an animal's digestive tract through the anus (or cloaca) during defecation. droppings dung faeces fecal matter frass pellet stool Xref in Environment Ontology (ENVO): http://en.wikipedia.org/wiki/Feces. feces HPI:0000033 Environment Ontology (ENVO). ENVO:00001998 An environmental matter that is any material within 2 m from the Earth's surface that is in contact with the atmosphere, with the exclusion of living organisms, areas with continuous ice not covered by other material, and water bodies deeper than 2 m. Definition Wikipedia: Soil is a natural body consisting of layers (soil horizons) of mineral constituents of variable thicknesses, which differ from the parent materials in their morphological, physical, chemical, and mineralogical characteristics (definition from Birkeland, Peter W. Soils and Geomorphology, 3rd Edition. New York: Oxford University Press, 1999.) soil HPI:0000034 Environment Ontology (ENVO). CHEBI:15377 ENVO:00002006 An environmental matter that is the liquid form of dihydrogen monoxide. aqua dihydridooxygen dihydrogen oxide oxidane Xref in Environment Ontology (ENVO): http://en.wikipedia.org/wiki/Water. water HPI:0000035 Environment Ontology (ENVO). CHEBI:33290 ENVO:00002002 A material entity that is substance, usually composed primarily of carbohydrates, fats, water and/or proteins, that can be eaten or drunk by an animal or human being for nutrition or pleasure. Xref in Environment Ontology (ENVO): http://en.wikipedia.org/wiki/Food. food HPI:0000036 Foundational Model of Anatomy(FMA). FMA:63887 Anatomical structure which has as its parts one or more ordered aggregates of nucleotide, amino acid fatty acid or sugar molecules bonded to one another. Examples: collagen, DNA, neurotransmitter, troponin. Comment in Foundational Model of Anatomy(FMA): Biological macromolecule is an anatomical structure which is made up of molecules covalently linked. 1.30.02: OM- Biological macromolecule is an anatomical structure which consists of any of the following combinations of families of small molecules: sugars, fatty acids, nucleotides and amino acids. biological macromolecule HPI:0000037 Foundational Model of Anatomy(FMA). CARO:0000003 FMA:67135 Material anatomical entity which is generated by coordinated expression of the organism's own genes that guide its morphogenesis; has inherent 3D shape; its parts are connected and spatially related to one another in patterns determined by coordinated gene expression. Examples: heart, right ventricle, mitral valve, myocardium, endothelium, lymphocyte, fibroblast, thorax, cardiovascular system, hemoglobin, T cell receptor. biological structure Comment in Foundational Model of Anatomy(FMA): CR comments: 1. Inherent 3D shape implies that it is maximally connected; also there is no supertype "maximally connected material anatomical entity" in AT. 2. It is not sufficient to state that it is generated by the organism's own genome; tumors are also generated by the organism's own genome; different ones than the anatomical structures that bear them, or from which they are derived. Specifying morphogenesis constrains the genes that come into play. 3. Arrangement of parts is also important, because rouleaux etc have a shape. Old definition: Material anatomical entity which has inherent 3D shape; is generated by coordinated expression of the organism's own genome; its parts are spatially related to one another in patterns determined by coordinated gene expression. OM proposed definition: Material physical anatomical entity which has inherent 3D shape; the maximal aggregation of constitutional parts is generated by coordinated expression of the organism's own structural genes; consists of parts that are anatomical structures; spatially related to one another in patterns determined by coordinated gene expression. Examples: heart, right ventricle, mitral valve, myocardium, endothelium, lymphocyte, fibroblast, thorax, cardiovascular system, hemoglobin, T cell receptor, structural gene. anatomical structure HPI:0000038 Foundational Model of Anatomy(FMA). SO:0000704 Biological macromolecule which is a segment of a DNA molecule and which consists of sets of nucleotide pairs organized into regions of coding, noncoding and regulatory sequences. structural gene Comment in Foundational Model of Anatomy(FMA): The term "gene" is used in different contexts. In the FMA, we attempt to represent the gene as an anatomical structure and so we specify it as a "structural gene". Xref in Sequence types and features (SO): http://en.wikipedia.org/wiki/Gene. gene HPI:0000039 Uber anatomy ontology (UBERON). FMA:7199 Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. bowel intestines intestine HPI:0000040 Ontology for Biomedical Investigations (OBI). FMA:7197 OBI:0302743 Liver is an anatomical entity which constituent are mainly hepatocytes, which has a function of detoxification, hematopoietic center, glucose and fat metabolism management. liver is only found in animals , all Vertebrates and some families of invertebrates. liver HPI:0000041 Medical Subject Headings (MESH) (A.15.382.520.604.412). http://purl.bioontology.org/ontology/MSH/D008198. FMA:5034 An organ component that is an oval or bean shaped [body] (1 - 30 mm in diameter) located along the lymphatic system. lymph nodes lymph node HPI:0000042 NCI Thesaurus. FMA:7196 An organ that is part of the hematopoietic and immune systems. It is composed of the white pulp and the red pulp and is surrounded by a capsule. It is located in the left hypochondriac region. Its functions include lymphocyte production, blood cell storage, and blood cell destruction. spleen HPI:0000043 NCI Thesaurus. FMA:9609 A portion of naso-pharyngeal tissue that are the two organs situated in the throat on either side of the narrow passage from the mouth to the pharynx. They are composed of lymphoid tissues. palatine tonsil tonsils tonsil HPI:0000044 FMA:49184 Medical Subject Headings (MESH) (D009055). http://purl.bioontology.org/ontology/MSH/D009055. Slitlike space in the oral cavity, bounded externally by the lips andcheek, and internally by the gingiva and teeth. oral cavity oral part of face oral region mouth HPI:0000045 Foundational Model of Anatomy(FMA). FMA:46472 Subdivision of face which consists of the nasal skeleton, nasal septum and nasal cavity. nose HPI:0000046 Infectious Disease Ontology (IDO). IDO:0000437 A disposition borne by a biological macromolecule that is the disposition to participate in adherence to host. adhesion disposition HPI:0000047 Infectious Disease Ontology (IDO). IDO:0000439 A disposition to kill or inhibit the growth of microorganisms. antibiotic disposition Comment in Infectious Disease Ontology (IDO): Some instances might be functions, depending on whether the bearer is something that exists and is used for the purpose (alcohol) or something that was designed for the purpose (pine sol). Entities that kill microorganisms are referred to as microbicidal; entities that inhibit the growth of microorganisms are referred to as microbistatic. antimicrobial disposition HPI:0000048 Malaria Ontology (IDOMAL). A factor mediating colonization. Coment in IDOMAL: Role played by portion of physical substance which promotes colonization. colonization factor HPI:0000049 Infectious Disease Ontology (IDO). IDO:0000448 A host resistance to infectious agent that inheres in an organism in virtue of immune system components in the extended organism. protective immunity to infectious agent Comment in Infectious Disease Ontology (IDO): We don't specify that immunity results from prior exposure, because we want to include innate immunity. In addition, for adaptive immunity, there could be some low level immunity even in a primary immune response. immunity to infectious agent HPI:0000050 HPI. A host resistance to Salmonella that inheres in an organism in virtue of immune system components in the extended organism. immunity to salmonella HPI:0000051 Infectious Disease Ontology (IDO). IDO:0000438 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. Comment in Infectious Disease Ontology (IDO): A molecule with the invasion disposition is referred to as an invasion factor or invasin. invasion disposition HPI:0000052 Infectious Disease Ontology (IDO). IDO:0000444 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. Comment in Infectious Disease Ontology (IDO): This mitigation sometimes takes the form of protection. CCR5 mutations protect T cells from HIV invasion. If a patient's tumor is resistant to chemotherapy, then the patient is resistant to something beneficial, but the tumor is resistant to something damaging. In this case protective resistance inheres in the tumor's cells and in the tumor, but not in the patient. In some cases, the quality that confers the protective resistance will confer other dispositions that damage the entity, such as is the case with sickle cell trait. protective resistance HPI:0000053 Infectious Disease Ontology (IDO). IDO:0000447 A collective resistance disposition that inheres in an organism population in virtue of the fact that the proportion of the population with immunity to an infectious agent is high resulting in a low number of transmissions from a host to a susceptible individual and thereby mitigating the damaging effects of the infectious agent on the population. herd immunity to infectious organism HPI:0000054 Infectious Disease Ontology (IDO). IDO:0000455 A disposition that inheres in a collection of entities in virtue of the individual dispositions of the constituents of that collection. Axioms in Infectious Disease Ontology (IDO): The disposition is realized in a processual entity that has as part realizations of some of the individual dispositions. Comment in Infectious Disease Ontology (IDO): "... that does not itself inhere in any subaggregate" is intended to capture the fact that the aggregate has a capability that the individuals don't have. "... in virtue of the individual dispositions of the contstituents" is intended to capture the fact that the collective disposition results from the combination of the individual dispositions. It is not necessary that every constituent of the aggregate have a relevant individual disposition. collective disposition HPI:0000055 Infectious Disease Ontology (IDO). IDO:0000588 A collective disposition the realization of which mitigates the damaging effects of some entity on members of the collection. collective resistance disposition HPI:0000056 partly from Infectious Disease Ontology (IDO). A herd immunity to infectious organism that inheres in an organism population in virtue of the fact that the proportion of the population with immunity to Salmonella is high resulting in a low number of transmissions from a host to a susceptible individual and thereby mitigating the damaging effects of Salmonella on the population. herd immunity to salmonella HPI:0000057 Infectious Disease Ontology (IDO). IDO:0000445 A protective resistance that mitigates the damaging effects of a drug. drug resistance resistance to drug HPI:0000058 Infectious Disease Ontology (IDO). IDO:0000581 A resistance to drug that mitigates the damaging effects of an antibiotic. antibiotic resistance HPI:0000059 Gene Ontology (GO): [source: http://www.copewithcytokines.de/cope.cgi?key=Cytokines]. GO:0008009 The function of a family of chemotactic pro-inflammatory activation-inducible cytokines acting primarily upon hemopoietic cells in immunoregulatory processes; all chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Comment in Gene Ontology See also the molecular function term 'cytokine activity ; GO:0005125'. chemokine activity HPI:0000060 Gene Ontology (GO): [source: ISBN:0198599471] . GO:0005125 Functions to control the survival, growth, differentiation and effector function of tissues and cells. cytokine activity HPI:0000061 Infectious Disease Ontology (IDO). IDO:0000629 OBI:0000725 A role borne by an organism in virtue of the fact that it's extended organism contains a material entity. Definition Ontology for Biomedical Investigations (OBI): host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role host role HPI:0000062 Infectious Disease Ontology (IDO). IDO:0000415 A host role borne by an organism in virtue of the fact that its extended organism contains a pathogen. Formal definition Infectious Disease Ontology (IDO): A host role borne by an organism (x) by virtue of the fact that it is participating in a process of symbiosis (GO:0044403) with an organism (y) that has the pathogenic disposition to organisms of type Z; x may be of type Z or another type. In the symbiosis process, y is bearer of the pathogen role. The role is realized in the processes that result in disease or death of an organism of type Z. pathogen host role HPI:0000063 IDO:0000414 A pathogen host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent. infectious agent host role HPI:0000064 IDO:0000405 OBI:0000718 A role borne by a material entity in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition. Definition Ontology for Biomedical Investigations (OBI): pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role Formal definition Infectious Disease Ontology (IDO): A role borne by an organism (x) by virtue of the fact that it has the pathogenic disposition relative to organisms of type Y, and 2) x, one of its parts, or one of its products and an organism (y) of type Y have spatiotemporal locations which allow processes resulting in disease or death of y to occur. The role is realized in y's disease course. pathogen role HPI:0000065 IDO:0000416 An infectious agent host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent, the infectious agent has the infectious disposition towards the host, and the host has no symptoms of the infectious disease caused by the infectious agent. infectious agent carrier role HPI:0000066 An infectious agent carrier host role borne by an organism in virtue of the fact that its extended organism contains salmonella, salmonellat has the infectious disposition towards the host, and the host has no symptoms of the infectious disease caused by salmonella. salmonella carrier role HPI:0000067 Sequence types and features (SO). SO:0000773 Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species. pathogenicity island Comment in Sequence types and features (SO): Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker. pathogenic island HPI:0000068 SPI-1 SPI1 salmonella pathogenicity island 1 salmonella pathogenicity island-1 HPI:0000069 SPI-2 SPI2 salmonella pathogenicity island 2 salmonella pathogenicity island-2 HPI:0000070 SPI-3 SPI3 salmonella pathogenicity island 3 salmonella pathogenicity island-3 HPI:0000071 SPI-4 SPI4 salmonella pathogenicity island 4 salmonella pathogenicity island-4 HPI:0000072 SPI-5 SPI5 salmonella pathogenicity island 5 salmonella pathogenicity island-5 HPI:0000073 Infectious Disease Ontology (IDO). IDO:0000430 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. Formal definition in Infectious Disease Ontology (IDO): A role borne by an anatomical entity (CARO:0000000) by virtue of the fact that 1) the anatomical entity is part of an organism (x) of type X, 2) x is participating in a process of establishing an infection in x, and 3) the anatomical entity serves as the site through which infectious organism enters x. The role is realized in the process by which the infectious organism enters x. infectious agent portal of entry role HPI:0000074 Infectious Disease Ontology (IDO). IDO:0000553 An anatomical entity bearing the infectious agent portal of entry role. infectious agent portal of entry HPI:0000075 Common Anatomy Reference Ontology (CARO) CARO:0000000 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. anatomical entity HPI:0000076 Infectious Disease Ontology (IDO). IDO:0000554 An anatomical entity bearing the infectious agent portal of exit role. infectious agent portal of exit HPI:0000077 Infectious Disease Ontology (IDO). IDO:0000431 A role borne by an anatomical entity in virtue of the fact that it serves as the site through which an infectious agent exits a host. Formal definition Infectious Disease Ontology (IDO): A role borne by an anatomical entity (CARO:0000000) by virtue of the fact that 1) the anatomical entity is part of an organism (x) of type X, 2) x is participating in a process of transmitting x, and 3) the anatomical entity serves as the site through which infectious organism exits x. The role is realized in the process by which the infectious organism exits x. infectious agent portal of exit role HPI:0000078 A infectious agent portal of entry role borne by an anatomical entity in virtue of the fact that it serves as the site through which Salmonella enters a host. Formal definition: A infectious agent portal of role borne by an anatomical entity (CARO:0000000) by virtue of the fact that 1) the anatomical entity is part of an organism (x) of type X, 2) x is participating in a process of establishing an infection in x, and 3) the anatomical entity serves as the site through whichSalmonella enters x. The role is realized in the process by which the Salmonella enters x. salmonella portal of entry role HPI:0000079 A salmonella portal of entry role borne by an anatomical entity in virtue of the fact that it serves as the site through which Salmonella enters Sus scrofa. salmonella portal of entry into pig role salmonella portal of entry into pigs role Formal definition: A infectious agent portal of role borne by an anatomical entity (CARO:0000000) by virtue of the fact that 1) the anatomical entity is part of an organism (x) of type Sus scrofa, 2) x is participating in a process of establishing an infection in x, and 3) the anatomical entity serves as the site through whichSalmonella enters x. The role is realized in the process by which the Salmonella enters x. salmonella portal of entry into sus scrofa role HPI:0000080 A infectious agent portal of exit role borne by an anatomical entity in virtue of the fact that it serves as the site through which Salmonella exits a host. Formal definition: A role borne by an anatomical entity (CARO:0000000) by virtue of the fact that 1) the anatomical entity is part of an organism (x) of type X, 2) x is participating in a process of transmitting x, and 3) the anatomical entity serves as the site through which Salmonella exits x. The role is realized in the process by which the Salmonella exits x. salmonella portal of exit role HPI:0000081 A infectious agent portal of exit role borne by an anatomical entity in virtue of the fact that it serves as the site through which Salmonella exits Sus scrofa salmonella portal of exit from pig role salmonella portal of exit from pigs role Formal definition: A role borne by an anatomical entity (CARO:0000000) by virtue of the fact that 1) the anatomical entity is part of an organism (x) of type Sus Ssrofa, 2) x is participating in a process of transmitting x, and 3) the anatomical entity serves as the site through which Salmonella exits x. The role is realized in the process by which the Salmonella exits x. salmonella portal of exit from sus scrofa role HPI:0000082 An infectious agent portal of entry bearing the Salmonella portal of entry role. salmonella portal of entry HPI:0000083 An Salmonella portal of entry bearing the Salmonella portal of entry into Sus scrofa role. salmonella portal of entry into pig salmonella portal of entry into pigs salmonella portal of entry into sus scrofa HPI:0000084 An infectious agent portal of exit bearing the Salmonella portal of exit role. salmonella portal of exit HPI:0000085 An Salmonella portal of exit bearing the Salmonella portal of exit from Sus scrofa role. salmonella portal of exit from pig salmonella portal of exit from pigs salmonella portal of exit from sus scrofa HPI:0000086 Infectious Disease Ontology (IDO). IDO:0000424 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. reservoir of infectious agent role HPI:0000087 A reservoir of infectious agent role borne by a material entity in virtue of the fact that it is a habitat in which Salmonella can persist and multiply and from which they can be transmitted in virtue of prevailing practices of potential hosts. reservoir of salmonella role HPI:0000088 Infectious Disease Ontology (IDO). IDO:0000417 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. infectious agent transporter role HPI:0000089 An infectious agent transporter role borne by a material entity in virtue of the fact that Salmonella is located in or on the entity and the entity has the capability to transfer (either actively or passively) Salmonella from one location to another. Salmonella transporter role HPI:0000090 Ontology for General Medical Science (OGMS). http://code.google.com/p/ogms/issues/detail?id=35 OGMS:0000090 A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder. therapy treatment HPI:0000091 IDO:0000450 A disposition to initiate processes that result in a disorder. pathogenicity Formal definition infectious disease ontology (IDO): A disposition that inheres in an object (x) relative to an organism of type Y by virtue of the fact that x has the capability to initiate processes that result in the presence of a disorder (OGMS:0000045) in organisms of type Y. If x is an organism, x is not of type Y. The disposition is realized in the processes that create the disorder. pathogenic disposition HPI:0000092 Infectious Disease Ontology (IDO). IDO:0000425 A disposition borne by a biological macromolecule produced by a pathogen that is the disposition to improve survival of the pathogen in a host, improve transmission of the pathogen to a host, or cause pathological processes in a host. virulence factor disposition HPI:0000093 Infectious Disease Ontology (IDO). IDO:0000426 A virulence factor disposition to cause I) malfunction of cells, ii) damage to extracellular matrix, or iii) damage of cells to a degree that can result in cell death. toxin disposition HPI:0000094 Infectious Disease Ontology (IDO). IDO:0000427 A toxin disposition to damage cells or extracellular matrix by a direct enzymatic process. exotoxin disposition HPI:0000095 Infectious Disease Ontology (IDO). IDO:0000428 An exotoxin disposition to damage cells of the host intestinal mucosa. enterotoxin disposition HPI:0000096 Infectious Disease Ontology (IDO). IDO:0000584 An exotoxin disposition that is the disposition to damage host cells. cytotoxin disposition HPI:0000097 Infectious Disease Ontology (IDO). IDO:0000429 A toxin disposition that inheres in a protein or protein complex that is released from a pathogen only upon cytolysis. endotoxin disposition HPI:0000098 Phenotypic quality (PATO). PATO:0001241 A quality which inheres in a continuant. quality of a continuant quality of an object quality of continuant physical object quality HPI:0000099 Phenotypic quality (PATO). PATO:0001237 A physical object quality which inheres in a single-bearer. monadic quality of a continuant monadic quality of a physical entity monadic quality of an object monadic quality of continuant single bearer quality of a physical entity singly inhering of a physical entity quality of a single physical entity HPI:0000100 Phenotypic quality (PATO). PATO:0001018 A quality of a single physical entity that exists through action of continuants at the physical level of organisation. physical quality HPI:0000101 Phenotypic quality (PATO). PATO:0000165 A quality in which events occur in sequence. time HPI:0000102 Phenotypic quality (PATO). http://wordnet.princeton.edu/ PATO:0000011 A time quality inhering in a bearer by virtue of how long the bearer has existed. age HPI:0000103 Infectious Disease Ontology (IDO). IDO:0000459 A host that contains a colony in or on its extended organism. colonized host HPI:0000104 The number of crypts per villus V/C ratio crypt :villus ratio crypt to villous ratio crypt-to-villus ratio crypt/villous ratio crypt/villus ratio HPI:0000105 Phenotypic quality (PATO). PATO:0001238 A physical entity quality which exists in relation towards some other entity. multiple bearer quality of a physical entity multiply inhering quality of a physical entity relational quality of a continuant relational quality of an object relational quality of continuant Comment in Phenotypic quality (PATO): Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles quality of related physical entities HPI:0000106 Ontology for Biomedical Investigations (OBI). OBI:0000577 A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity. molecular concentration HPI:0000107 A molecular concentration that inheres in a material entity and is the number of cytokine molecules contained in the entity divided by the volume of the material entity. cytokine concentration HPI:0000108 A cytokine concentration that inheres in a material entity and is the number of interleukin molecules contained in the entity divided by the volume of the material entity. interleukin concentration HPI:0000109 A cytokine concentration that inheres in a material entity and is the number of tumor necrosis factor molecules contained in the entity divided by the volume of the material entity. TNF concentration TNFA concentration cachectin concentration tumor necrosis factor alpha concentration tumor necrosis factor concentration ISBN:0-683-40008-8 "Stedman's Medical Dictionary, 27th edition", PMID:9744866. Mammalian phenotype (MP). DOID:3400 MP:0001429 SYMP:0000020 Excessive water loss from the body or from an organ or bodily part. body water dehydration deficient fluid volume dehydration HPI:0000111 Animal Trait Ontology (ATO). ATO:0000340 The amount of feed needed to produce a given amount of product. feed utilisation eed utilization efficiency feed consumption index feed conversion efficiency feed efficiency feed utilisation efficiency feed utilization feed conversion HPI:0000112 Animal Trait Ontology (ATO). ATO:0000296 Weight of consumed food per live weight gain in the fattening period. feed conversion ratio HPI:0000113 GO:0001660 SYMP:0000613 Wikipedia:Fever A quality that inheres in an organism by virtue of the fact that the organism's body temperature (PATO:0000146) is above normal for that organism as the result of a fever process (GO:0001660). pyrexia fever HPI:0000114 Infectious Disease Ontology (IDO). IDO:0000480 A quality that inheres in an organism population and is the number of organisms in the population that become infected with an infectious agent during a specified period of time. Formal definition Infectious Disease Ontology (IDO): A quality that 1) inheres in a pre-speciified organism population whose members have the capability to play the host of infectious agent role for organisms of type X and 2) is the number of organisms in the population that begin bearing the host role for the infectious organism during a specified period of time. infection incidence HPI:0000115 An infectious incidence that inheres in an organism population and is the number of organisms in the population that become infected with salmonella during a specified period of time. salmonella infection incidence HPI:0000116 An Salmonella incidence that inheres in Sus scrofa population and is the number of organisms in the Sus scrofa population that become infected with salmonella during a specified period of time. salmonella incidence in pig salmonella incidence in pigs salmonella infection incidence in sus scrofa HPI:0000117 Infectious Disease Ontology (IDO). IDO:0000479 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. Formal definition Infectious Disease Ontology (IDO): A quality that 1) inheres in a pre-speciified organism population whose members have the capability to play the host of infectious agent role in symbiosis with organisms of the type that cause infectious disease X and 2) is the number of realizations of the infectious disease for which the infectious disease course (the realization of the disease) begins during a specified period of time. infectious disease incidence HPI:0000118 A infectious disease incidence that inheres in an organism population and is the number of realizations of salmonellosis for which salmonellosis course begins during a specified period of time. salmonellosis incidence HPI:0000119 A salmonellosis incidence that inheres in Sus scrofa population and is the number of realizations of salmonellosis for which salmonellosis course begins during a specified period of time. salmonellosis incidence in pigs salmonellosis incidence in sus scrofa HPI:0000120 Infectious Disease Ontology (IDO). IDO:0000481 A quality that inheres in an organism population and is the infectious disease incidence divided by the number of members of the population in which the infectious disease course had not begun at the beginning of the specified period of time. cumulative incidence of infectious disease infectious disease incidence proportion HPI:0000121 A infectious disease incidence proportion that inheres in an organism population and is salmonellosis incidence divided by the number of members of the population in which salmonellosis course had not begun at the beginning of the specified period of time. cumulative incidence of salmonellosis salmonellosis incidence proportion HPI:0000122 A infectious disease incidence proportion that inheres in Sus scrofa population and is salmonellosis incidence divided by the number of members of the population in which salmonellosis course had not begun at the beginning of the specified period of time. cumulative incidence of salmonellosis in pigs cumulative incidence of salmonellosis in sus scrofa salmonellosis incidence proportion in pigs salmonellosis incidence proportion in sus scrofa HPI:0000123 Infectious Disease Ontology (IDO). IDO:0000482 A quality that inheres in an organism population and is the infection incidence divided by the number of members of the population that are not infected at the beginning of the specified period of time. cumulative incidence of infection infection incidence proportion HPI:0000124 A infectious disease incidence proportion that inheres in an organism population and is the salmonella incidence divided by the number of members of the population that are not infected at the beginning of the specified period of time. cumulative incidence of salmonella salmonella infection incidence proportion HPI:0000125 A Salmonella incidence proportion that inheres in Sus scrofa population and is the salmonella incidence divided by the number of members of the Sus scrofa population that are not infected at the beginning of the specified period of time. cumulative incidence of salmonella in pigs cumulative incidence of salmonella in sus scrofa salmonella incidence proportion in pigs salmonella infection incidence proportion in sus scrofa HPI:0000126 Infectious Disease Ontology (IDO). IDO:0000484 A quality that inheres in an organism population and is the incidence proportion of infection divided by the period of time over which the incidence was measured. infection incidence rate HPI:0000127 A infection incidence rate that inheres in an organism population and is the incidence proportion of Salmonella infection divided by the period of time over which the incidence was measured. salmonella infection incidence rate HPI:0000128 A salmonella infection incidence rate that inheres in Sus scrofa population and is the incidence proportion of Salmonella infection divided by the period of time over which the incidence was measured. salmonella infection incidence rate in pigs salmonella infection incidence rate in sus scrofa HPI:0000129 Infectious Disease Ontology (IDO). IDO:0000483 A quality that inheres in an organism population and is the infectious disease incidence rate divided by the period of time over which the incidence was measured. infectious disease incidence rate HPI:0000130 A infectious disease incidence rate that inheres in an organism population and is he salmonelllosis incidence rate divided by the period of time over which the incidence was measured. salmonellosis incidence rate A salmonellosie incidence rate that inheres in sus scrofa population and is he salmonelllosis incidence rate divided by the period of time over which the incidence was measured HPI:0000131 salmonellosis incidence rate in sus scrofa HPI:0000132 A quality that inheres in an organism population and is the proportion of members that are ill in the population resulting from an infectious disease over a specified period of time. infectious disease morbidity rate HPI:0000133 A infectious disease morbidity rate that inheres in an organism population and is the proportion of members that are ill in the population resulting from salmonellosis over a specified period of time. salmonellosis morbidity rate HPI:0000134 A salmonellosis morbidity rate that inheres in Sus scrofa population and is the proportion of members that are ill in the population resulting from salmonellosis over a specified period of time. salmonellosis morbidity rate in pigs salmonellosis morbidity rate in sus scrofa HPI:0000135 Infectious Disease Ontology (IDO). IDO:0000489 A quality that inheres in an organism population and is the proportion of deaths in the population resulting from an infectious disease over a specified period of time. infectious disease mortality rate HPI:0000136 A infectious disease mortality rate that inheres in an organism population and is the proportion of deaths in the population resulting from salmonellosis over a specified period of time. salmonellosis mortality rate HPI:0000137 A salmonellosis mortality rate that inheres in Sus scrofa population and is the proportion of deaths in the population resulting from salmonellosis over a specified period of time. salmonellosis mortality rate in sus scrofa HPI:0000138 A quality that inheres in a material entity and is the number of pathogenic organisms associated an organism. bacterial load Formal definition: A quality that inheres in a single material entity or aggregate of material entities and is the number of pathogenic organisms contained in the entity or aggregate divided by i) the volume of the entity, if the entity is a portion of some material entity, or ii) the number of entities if the entities have bona fide boundaries. pathogen load HPI:0000139 A pathogen load that inheres in a material entity and is the number of salmonella associated an organism. Formal definition: A pathogen load that inheres in a material entity or aggregate of material entities and is the number of Salmonella organisms contained in the entity or aggregate divided by i) the volume of the entity, if the entity is a portion of some material entity, or ii) the number of entities if the entities have bona fide boundaries. salmonella load HPI:0000140 A quality inheres in a material entity by virtue of the fact that the organism contains Salmonella organisms. presence of salmonella HPI:0000141 A presence of Salmonella inheres in a material entity derived from a Sus scrofa organism by virtue of the fact that the entity contains Salmonella organisms. presence of salmonella in sus scrofa HPI:0000142 Infectious Disease Ontology (IDO). IDO:0000486 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. infection prevalence HPI:0000143 A infection prevalence that inheres in an organism population and is the number of organisms in the population infected with Salmonella at a specified time. salmonelle infection prevalence HPI:0000144 A infection prevalence that inheres in Sus scrofa population and is the number of organisms in the population infected with Salmonella at a specified time. salmonella infection prevalence in pigs salmonella infection prevalence in sus scrofa HPI:0000145 Infectious Disease Ontology (IDO). IDO:0000485 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. infectious disease prevalence HPI:0000146 A infectious disease prevalence that inheres in an organism population and is the number of realizations of salmonellosis in the population at a specified time. salmonellosis prevalence HPI:0000147 salmonellosis prevalence in pigs salmonellosis prevalence in sus scrofa HPI:0000148 Infectious Disease Ontology (IDO). IDO:0000488 A quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for an infectious agent in their serum at a specified time. infectious agent seroprevalence HPI:0000149 A infectious agent seroprevalence that inheres in an organism population and is the number of organisms in the population that have antibody specific for Salmonella in their serum at a specified time. salmonella seroprevalence HPI:0000150 A infectious agent seroprevalence that inheres in Sus scrofa population and is the number of organisms in the population that have antibody specific for Salmonella in their serum at a specified time. salmonella seroprevalence in pigs salmonella seroprevalence in sus scrofa HPI:0000151 MESH (D012480): Infections with bacteria of the genus SALMONELLA. An infectious disease that has as its physical basis (an infectious disorder whose etiology includes the presence of Salmonella). salmonella infection An infection composed of organisms of the type Salmonella. salmonellosis HPI:0000152 A host exhibiting salmonellosis symptoms. symptomaitc salmonellosis host HPI:0000153 Phenotypic quality (PATO). PATO:0000146 A physical quality of the thermal energy of a system. temperature HPI:0000154 Phenotypic quality (PATO). http://en.wikipedia.org/wiki/Weight PATO:0000128 weight HPI:0000155 A quality that refers to all aspects of the health of individuals or populations health level health levels level of health health status Gene Ontology (GO). GO:0006955 Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. HPI:0000156 immune response HPI:0000157 Gene Ontology (GO). GO:0002250 An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory). adaptive immune response SYMP:0000184 A processual entity inheres in an organism which results in a change in an organism's skin color Skin discolouration discoloration of skin discolouration of skin skin discoloration When the change in skin color is from a color normal for the organism type to some abnormal color, the change may be considered a symptom of disease. HPI:0000158 changes in skin color HPI:0000159 Gene Ontology (GO). GO:0008150 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. physiological process biological process HPI:0000160 GOC:add, ISBN:0781735149 'Fundamental Immunolog' Gene Ontology (GO). GO:0001816 The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. cytokine production HPI:0000161 Gene Ontology (GO). GO:0020012 Any process, either active or passive, by which an organism avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction. evasion or tolerance of host immune response Gene Ontology (GO). HPI:0000162 GO:0050896 A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. physiological response to stimulus response to stimulus HPI:0000163 Ontology for General Medical Science (OGMS). OGMS:0000063 The totality of all processes through which a given disease instance is realized. disease course HPI:0000164 Infectious Disease Ontology (IDO). IDO:0000495 A disease course that is the realization of an infectious disease. Formal definition Infectious Disease Ontology (IDO): A disease course (OGMS:0000063) that is the total process of realization of an infectious disease (IDO:0000436), beginning with the manifestation of pathological processes caused by an infection (IDO:0000586) and ending with 1) clearance of the infection, 2) long-term control of the infection by the host's immune response accompanied by the resolution of symptoms, or 3) death of the host. infectious disease course HPI:0000165 A infectious disease course that is the realization of salmonellosis. salmonellosis disease course HPI:0000166 A salmonellosis disease course that is the realization of salmonellosis in Sus scrofa. salmonellosis disease course in pigs salmonellosis disease course in sus scrofa HPI:0000167 GOC:mtg_15nov05, GO_REF:0000022, ISBN:0198506732 'Oxford Dictionary of Biochemistry and Molecular Biology' Gene Ontology (GO). GO:0006954 The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. inflammatory response HPI:0000168 GOC:add, GOC:ebc, GOC:mtg_15nov05, GOC:mtg_sensu, GO_REF:0000022 Gene Ontology (GO). GO:0045087 Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. nonspecific immune response innate immune response HPI:0000169 GOC:jal, GOC:mtg_15nov05, GO_REF:0000022, ISBN:0781735149 Gene Ontology (GO). GO:0002385 An immune response taking place in mucosal tissues, including those of the intestinal tract, nasal and upper respiratory tract, and genital tract. mucosal immune response HPI:0000170 Medical Subject Headings (MESH). The abnormal mechanisms and forms involved in the dysfunctions of tissues and organs. pathologic process Pathological process HPI:0000171 NCIThesaurus (C37935; http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cough) SYMP:614 A pathological process that is a sudden, often repetitive, spasmodic contraction of the thoracic cavity, resulting in violent release of air from the lungs, and usually accompanied by a distinctive sound. cough HPI:0000172 ISBN:0-683-40008-8 'Stedman's Medical Dictionary, 27th edition' Mammalian phenotype (MP). MP:0001575 SYMP:537 A pathological process that results in a dark bluish or purple skin discoloration resulting from deficient oxygenation of the blood. cyanotic cyanosis HPI:0000173 A pathological process that results in cessation of metabolic activity and loss of capability for that to restart. death process HPI:0000174 NCIThesaurus (C2987; http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Diarrhea). SYMP:570 A pathological process that is the condition of frequent and watery bowel movements. diarrhoea diarrhea HPI:0000175 SYMP:0000738 A diarrhea that has the color yellowish green. yellowish green diarrhoea yellowish green diarrhea HPI:0000176 SYMP:0019153 breathing difficulty breathlessness difficulty breathing labored respiration shortness of breath dyspnea HPI:0000177 NCIThesuarus (C2982; http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Depression). SYMP:0000022 A pathological process of disordered brain function that results in a melancholy feeling of sadness and despair. episode of depression HPI:0000178 Gene Ontology (GO). A rise in body temperature above the normal, often as a response to infection. fever process HPI:0000179 NCIThesaurus (C3445; http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Weight_Loss) SYMP:0000178 A pathological process resulting in a reduction in overall body mass. loss of weight weight losses weight reductions weight loss HPI:0000180 GOC:cc, http://www.free-definition.com Gene Ontology (GO). GO:0044403 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. host-pathogen interaction symbiosis symbiotic interaction symbiotic interaction between host and organism symbiotic interaction between organisms symbiotic interaction between species symbiotic interaction with other non-host organism Comment in Gene Ontology (GO): Note that this term encompasses all symbiotic relationships between species along a continuum from mutualism through to parasitism, as outlined in the definition. symbiosis, encompassing mutualism through parasitism HPI:0000181 GOC:add; ISBN:0781735149 'Fundamental Immunology' Gene Ontology (GO). GO:0042088 An immune response which is associated with resistance to intracellular bacteria, fungi, and protozoa, and pathological conditions such as arthritis, and which is typically orchestrated by the production of particular cytokines by T-helper 1 cells, most notably interferon-gamma, IL-2, and lymphotoxin. Th1 immune response T-helper 1 type immune response HPI:0000182 Pathogen transmission (TRANS). http://www2a.cdc.gov/phtn/catalog/pdf-file/Epi_Course.pdf TRANS:0000000 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. transmission process HPI:0000183 Pathogen transmission (TRANS). http://www2a.cdc.gov/phtn/catalog/pdf-file/Epi_Course.pdf TRANS:0000001 Direct transmission is a transmission process that is the means during which the pathogen is transmitted immediately from a reservoir, source or host to another host. direct transmission process HPI:0000184 Pathogen transmission (TRANS). TRANS:0000007 Contact transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by kissing, skin-to-skin contact, sexual intercourse, or by contact with soil or vegetation containing the pathogen. contact transmission process HPI:0000185 Pathogen transmission (TRANS). TRANS:0000008 Droplet spread transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by spray of aerosols over a short distance, spray from sneezing, coughing or talking. droplet spread transmission process HPI:0000186 Pathogen transmission (TRANS). http://www2a.cdc.gov/phtn/catalog/pdf-file/Epi_Course.pdf TRANS:0000002 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. indirect transmission process HPI:0000187 Pathogen transmission (TRANS). TRANS:0000009 Airborne transmission is an indirect transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host while suspended in the air as dust. AirborneTransmissionProcess HPI:0000188 Pathogen transmission (TRANS). http://www2a.cdc.gov/phtn/catalog/pdf-file/Epi_Course.pdf TRANS:0000010 Vehicle-borne transmission is an indirect transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by inanimate intermediary vehicle objects. vehicle-borne transmission process HPI:0000189 Pathogen transmission (TRANS). TRANS:0000012 Vehicle-borne ingestion transmission is an indirect vehicle-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by ingestion of fluids or foods or food products including: food, water, milk, or meat products. vehicle-borne ingestion transmission process HPI:0000190 Pathogen transmission (TRANS). TRANS:0000011 Vehicle-borne fomite transmission is an indirect vehicle-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by inanimate objects including: medical instruments, cloth, fur, metal or plastic utensils. vehicle-borne fomite transmission process HPI:0000191 ISBN:0-683-40008-8 'Stedman's Medical Dictionary, 27th edition' Mammalian phenotype (MP). MP:0005202 SYMP:0000075 Mild impairment of consciousness resulting in reduced alertness and awareness; ultimately due to generalized brain dysfunction. Formal definition: A disposition inhering in an organism 1) by virtue of the fact that the organism has some generalized brain dysfunction and 2) that is realzed in impairment of consciousness resulting in reduced alertness and awareness. lethargy HPI:0000192 Gene Ontology (GO): [source: ISBN:0395448956; GOC:ems; Wikipedia:Behavior]. GO:0007610 The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions. behavior behavioral response to stimulus behavioural response to stimulus behaviour HPI:0000193 Gene Ontology (GO): [source: GOC:jl ; ISBN:01928006X]. GO:0042755 The specific actions or reactions of an organism relating to the intake of food, any substance (usually solid) that can be metabolized by an organism to give energy and build tissue. eating behavior eating behaviour HPI:0000194 A eating behaviour that result in a decreased intake of food. reduction of food intake HPI:0000195 Infectious Disease Ontology (IDO). IDO:0000628 An infection that persists for an extended period of time. persistent infection chronic infection HPI:0000196 Infectious Disease Ontology (IDO). IDO:0000627 An infectious disorder that is the physical basis for an unfolding acute infectious disease course. acute infection HPI:0000197 Infectious Disease Ontology (IDO). IDO:0000474 An infection for which the infectious agents that are part of the infection are distributed throughout the host. Formal definition in Infectious Disease Ontology (IDO): A quality that inheres in an infection by virtue of the fact that the organisms comprising the infection are distributed throughout the host, including multiple host organs and/or systems (e.g. circulatory system). systemic infection HPI:0000198 An infection of the intestinal tract. intestinal infection enteric infection HPI:0000199 Infectious Disease Ontology (IDO). IDO:0000537 A host bearing the infectious agent host role. infectious agent host HPI:0000200 Infectious Disease Ontology (IDO). IDO:0000539 An infectious agent host bearing the infectious agent carrier role. infectious agent carrier HPI:0000201 An infectious agent carrier bearing the salmonella carrier role. salmonella carrier HPI:0000202 Infectious Disease Ontology (IDO). IDO:0000543 A material entity bearing the infectious agent vehicle role. vehicle of infectious agent HPI:0000203 Infectious Disease Ontology (IDO). IDO:0000544 An material entity bearing the fomite role. fomite HPI:0000204 Infectious Disease Ontology (IDO). IDO:0000421 An infectious agent transporter role borne by an entity in virtue of the fact that the entity is not a complete organism. infectious agent vehicle role HPI:0000205 Infectious Disease Ontology (IDO). IDO:0000423 An infectious agent vehicle role borne by an entity in virtue of the fact that the entity is not alive. fomite role HPI:0000206 Infectious Disease Ontology (IDO). IDO:0000545 A material entity bearing the infectious agent reservoir role. infectious agent reservoir HPI:0000207 A infectious agent reservoir bearing the reservoir of salmonella role . salmonella reservoir HPI:0000208 Chemical entities of biological interest (CHEBI). CHEBI:23367 Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. entidad molecular entidades moleculares entite moleculaire molecular entities molecular entity molekulare Entitaet molecular entity HPI:0000209 Infectious Disease Ontology (IDO). IDO:0000547 A biological macromolecule produced by a pathogen and that has the virulence factor disposition. virulence factor HPI:0000210 Infectious Disease Ontology (IDO). IDO:0000548 A biological macromolecule that has the invasion disposition. invasion factor HPI:0000211 Infectious Disease Ontology (IDO). IDO:0000549 A biological macromolecule bearing the toxin disposition. toxin HPI:0000212 Infectious Disease Ontology (IDO). IDO:0000552 A biological macromolecule bearing the endotoxin role. endotoxin HPI:0000213 Infectious Disease Ontology (IDO). IDO:0000550 A biological macromolecule bearing the exotoxin disposition. exotoxin HPI:0000214 Infectious Disease Ontology (IDO). IDO:0000551 A biological macromolecule bearing the enterotoxin disposition. enterotoxin HPI:0000215 Atlas of Immunology by Julius M. Cruse and Robert E. Lewis. ISBN:0-8493-1567-0. Cytokines serve as chemical communicators from one cell to another as well as being biological response modifiers. cytokine HPI:0000216 Infectious Disease Ontology (IDO). IDO:0000557 A biological macromolecule that has the adhesion disposition. adhesin adhesion molecule adhesion factor HPI:0000217 Infectious Disease Ontology (IDO). IDO:0000569 An infectious agent host who has no symptoms of the infectious disease associated with the infectious agent. asymptomatic host of infectious agent HPI:0000218 Infectious Disease Ontology (IDO). IDO:0000570 An infection that is part of an asymptomatic host. subclinical infection HPI:0000219 Infectious Disease Ontology (IDO). IDO:0000573 An infectious agent host who has symptoms of the infectious disease associated with the infectious agent symptomatic host of infectious agent HPI:0000220 Infectious Disease Ontology (IDO). IDO:0000446 A protective resistance that inheres in an organism and mitigates the damaging effects on that organism of an infectious agent. host resistance to infectious agent HPI:0000221 Infectious Disease Ontology (IDO). IDO:0000576 An immunity to infectious agent realized in an innate immune response. innate immunity to infectious agent An innate immunity to Salmonella realized in an innate immune response. HPI:0000222 innate immunity to salmonella HPI:0000223 Infectious Disease Ontology (IDO). IDO:0000577 An immunity to infectious agent realized in an adaptive immune response. adaptive immunity to infectious agent HPI:0000224 An immunity to Salmonella realized in an adaptive immune response. adaptive immunity to salmonella HPI:0000225 Infectious Disease Ontology (IDO). An immunity to infectious agent realized in a humoral immune response. IDO:0000578 humoral immunity to infectious agent HPI:0000226 An humoral immunity to Salmonella realized in a humoral immune response. humoral immunity to salmonella Infectious Disease Ontology (IDO). IDO:0000579 An immunity to infectious agent realized in an immune response whose participants are T cells or other cells of the immune system. HPI:0000227 cell-mediated immunity to infectious agent HPI:0000228 An cell-mediated immunity to Salmonella realized in an immune response whose participants are T cells or other cells of the immune system. cell-mediated immunity to salmonella HPI:0000229 MGI:cwg "Carroll-Ann W. Goldsmith, Mouse Genome Informatics Curator" ISBN:0-8153-1691-7 "Immunobiology, The Immune System in Health and Disease" Mammalian phenotype (MP). MP:0001861 Local accumulation of fluid, plasma proteins, and leukocytes in the lung. lung inflammation pulmonary inflammation pneumonia HPI:0000230 NCIThesuarus (C2982; http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Depression). A melancholy feeling of sadness and despair. depression HPI:0000231 Infectious Disease Ontology (IDO). IDO:0000460 A host that has an infection in or on its extended organism. Formal definition Infectious Disease Ontology (IDO): A quality inhering in an organism by virtue of the fact that the organism is the bearer of the host of infectious parasite role in a symbiosis process (GO:0044403) with an organism that has the infectious disposition and that has established an infection in the host. infected host HPI:0000232 Chemical entities of biological interest (CHEBI). CHEBI:37577 A molecular entity consisting of two or more chemical elements. heteroatomic molecular entity chemical compound CHEBI:27902 HPI:0000233 A broad-spectrum polyketide antibiotic produced by the Streptomyces genus of actinobacteria. Chemical entities of biological interest (CHEBI). tetracycline antibiotic tetracycline antibiotics tetracycline HPI:00000234 Infectious Disease Ontology (IDO). CHEBI:33281 IDO:0000558 A material entity with the antimicrobial disposition. antimicrobials antimicrobial agent antimicrobial HPI:0000235 Infectious Disease Ontology (IDO). CHEBI:22582 IDO:0000562 An antimicrobial bearing the antibiotic disposition. antibiotic agent antibiotic agents antibiotics antibiotika antibiotikum antibiotique antibiotic HPI:0000236 Infectious Disease Ontology (IDO). DO:0000462 A host exhibiting disease symptoms. symptomatic host Alan Ruttenberg Andrew Spear Pierre Grenon Holger Stenzhorn application/rdf+xml http://www.ifomis.org/bfo/1.1 en Institute for Formal Ontology and Medical Information Science (IFOMIS) http://creativecommons.org/licenses/by/3.0 Barry Smith and Pierre Grenon: "The Cornucopia of Formal Ontological Relations" Barry Smith: "Against Fantology" Barry Smith: "Basic Tools of Formal Ontology" Barry Smith: "Beyond Concepts: Ontology as Reality Representation" Pierre Grenon and Barry Smith: "SNAP and SPAN: Towards Geospatial Dynamics" Pierre Grenon, Barry Smith and Louis Goldberg: "Biodynamic Ontology: Applying BFO in the Biomedical Domain" Pierre Grenon: "BFO in a Nutshell: A Bi-categorial Axiomatization of BFO and Comparison with DOLCE" Pierre Grenon: "Nuts in BFO's Nutshell: Revisions to the Bi-categorial Axiomatization of BFO" Pierre Grenon: "Spatio-temporality in Basic Formal Ontology: SNAP and SPAN, Upper-Level Ontology, and Framework for Formalization" Basic Formal Ontology (BFO) 1.1.1 HPI:0000057