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 Correlates a Chemopreventive Agent with the Pathways it affects. affectPathway Correlates the Chemopreventive agents that can cooperate to prevent a cancer type. coOperateWith A Published work can be commented in a Formum post as part of a discussion related to the specific Published work. commented in Correlates a Study with the Assays it contains containAssay Correlates a Source (e.g. Natural or Synthetic) with the Molecules it contains contain molecule Indicate the Studies contained into an Investigation. containStudy Relates an Organism with the Organs it contains. containsOrgan Correlates a Pathway with the Biological Targets (e.g. protein) it contains. containsTarget Correlates an Investigation with a Published work that describes the results of the Investigation. describedInPublication Correlates a Published work or a Forum Post with the Person that has written them. hasAuthor Indicate the Biological Mechanisms that has a Chemopreventive Agent. hasBiologicalMechanism Defines the input of an Assay. hasInput Correlates a Chemopreventive Agent with the sources where it is available or from where it originates. hasSource Correlates a Published work with the Expressions (i.e. scientific statements) it contains. hasStatement Indicate the target of biological mechanism in order to prevent cancer. hasTarget Indicates the concentration that is toxical. hasToxicalConcentration Indicates the Toxicity of a Chemopreventive Agent. hasToxicity has disease location Indicate the Chemopreventive Agents that have been identified during an Assay. identify Correlates a Chemopreventive Agent with the Biological Target it affects. induce prevent Correlates a Drug with the biological Targets it interacts with. interact with Correlates a Disease with the Chemopreventive Agent that can treat it. isTreatedBy Indicate the measurements made during a Study. measure Indicate whether a Source is Natural or Synthetic. naturalVsSynthetic Indicate the Study that a Bioassay is part of. part_of Correlates a Published work with other Published Work it references. referenceTo Correlated a Protocol or a Chemopreventive Agent with a Published work where the Protocol/Chemopriventive agent is described referredIntoPublication Correlates a Pathway with the Disease it is related related to disese topic Correlates an Protocol with the Experimental Factors used. use factor Correlates an In Silico Experiment with the Scientific Workflow used. use workflow Indicate the Chemopreventive Agents used by an Assay. used_cma Indicate the Organisms used by an experimental Protocol. used_organism Indicate the Protocol used by a Study. used_protocol uriLookupEndpoint type sameAs NAD(P)H:quinone reductase (quinone reductase, QR) activity cytochrome P450 (Cyp) 1A activity inchi InChl If you have an MDL Molfile for this component, insert it here MDLmolfile If you know the PDB Id of this component, insert it here. PDB_id If you have the SMILES notation for this agent, insert it here. SMILESnotation The access rights of a Study. accessRights What is the action mechanism of the component? actionMechanism The biological activity of a compound. activity affiliation Does this compound have antioxidative properties? antiOxidantActivity Indicate the cell type of the Toxicity cellType Indicate the chemoprevention mechanism of a compound. chemopreventionMechanism The common name of a Source, Natural or Synthetic. common name If you have a connection table for this chemical component, indicate it here. connectionTable A lexical definition of a concept. description If you have a link to an image with the 2D representation of this molecular, indicate its URL here diagram2D In this chemopreventative agent has been tested in vivo, what was the measured efficacy? efficacyInVivo The abstrac of a Published work. has abstract The cellular location where a Protein can be found. hasCellularLocation The citation of the Published work (e.g. the Journal and the year of publication). hasCitation The Claim of a Research Statement. hasClaim The comment of a forum post. hasComment The date the Forum post has been made. hasDate The chemical formula of the Molecule. hasFormula The Hypothesis of a Research Statement. hasHypothesis The procedure defined by the Protocol. has procedure The type of publication, e.g. journal, paper etc. hasPublicationType The sequence of ta Nucleid acid or Protein. hasSequence Indicate the status of a Published work hasStatus hashedFingerprint Indicates if a chemopreventive agents acts by inducing cell differentiation. induceDifferentiation input Indicates the level of toxicity. level The molecular weight of a Molecule. molecularWeight output Which metabolic pathways is this agent know to affect? pathwayAction The map (image representation) of a Pathway. pathwayMap The order of action in a Pathway. pathwayOrder The value of the percentage percentageValue publication How many times has this compound been cited in the literature? publicationNumber Has this been component been published before? Answer yes or no. published The size of a Molecule. size If this compound is normally found in a natural substatnce, indicate which in the domain source ?? species structuralKey Indicate whether there is a known target orgain for this chemopreventative agent targetOrgan The title of concept. title If toxic, at which concentration has it been deemed toxic? toxicConcentration false toxicity Anti-metastatic_Anti-agiogenic Metastasis is a complex series of steps in which cancer cells leave the original tumor site and migrate to other parts of the body via the bloodstream or the lymphatic system. Malignant cells break away from the primary tumor and attach to and degrade proteins that make up the surrounding extracellular matrix (ECM). By degrading these proteins, cancer cells are able to breach the ECM and escape. The body resists metastasis by a variety of mechanisms through the actions of a class of proteins known as metastasis suppressors. One of the critical events required is the growth of new blood vessels from pre-existing vessels growth of a new network of blood vessels (Angiogenesis). Anti-metastatic Anti-agiogenic Antiinflammatory Anti-inflammatory refers to the property of a substance or treatment that reduces inflammation. Antiinflammatory Antioxidant Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage. Antioxidant Antiproliferative Antiproliferative agents work to block the proliferative phase of acute cellular rejection. Antiproliferative Apoptotic Apoptosis is programmed cell death, a normal component of the development and health of multicellular organisms. Cells die in response to a variety of stimuli and during apoptosis they do so in a controlled, regulated fashion. This makes apoptosis distinct from another form of cell death called necrosis in which uncontrolled cell death leads to lysis of cells, inflammatory responses and, potentially, to serious health problems. Upon receiving specific signals instructing the cells to undergo apoptosis a number of distinctive changes occur in the cell. A family of proteins known as caspases are typically activated in the early stages of apoptosis. These proteins breakdown or cleave key cellular components that are required for normal cellular function including structural proteins in the cytoskeleton and nuclear proteins such as DNA repair enzymes. The caspases can also activate other degradative enzymes such as DNases, which begin to cleave the DNA in the nucleus. Apoptotic Assay Test performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements (data). Assay BioMaterial A biomaterial is any matter, surface, or construct that interacts with biological systems BioMaterial BiologicalTarget A biological target is a biopolymer such as a protein or nucleic acid whose activity can be modified by an external stimulus. A Chemopreventive agent has a Biological target in order to "hit" it and change its behavior in order to prevent a disease. Biological Target CD Concentration required to double the specific activity of quinone reductase CD COX1IC50 Cox-1 inhibition IC50 [µM] COX1IC50 Cancer A disease characterized by abnormal and uncontrolled cell division Cancer CancerType Cancer has many cancer types modeled by this class CancerType Cell_line A cell line is a cell factor which describes a population of cells cultured in vitro that are descended through one or more generations (and possible sub-cultures) from a single primary culture which was originally derived from part of an organism. The cells of such a population share common characteristics. Cell line ChemopreventiveAgent A Chemopreventive agent is a Molecule that has shown some evidence that it may be able to prevent or delay the development of a specific Disease (e.g. cancer) by interfering with a Biological target. For example - cancer chemopreventive agents are used to inhibit, delay, or reverse carcinogenesis. A Chemopreventive agent can be tested into an Experiment and can be contained into a Natural source or a Drug. References to a Chemopreventive agent can be found into a Publication. ChemopreventiveAgent ClinicalTrial A Clinical trial is a research study that prospectively assigns human participants or groups of humans to one or more health-related interventions to evaluate the effects on health outcomes. Interventions include but are not restricted to drugs, cells and other biological products, surgical procedures, radiologic procedures, devices, behavioral treatments, process-of-care changes, and preventive care. Clinical trial Concentration In chemistry, concentration is defined as the abundance of a constituent divided by the total volume of a mixture. Concentration Cyp1AIC50 IC50 of Cyp1A Cyp1AIC50 DPPHSC50 Numbers in parentheses indicate the percentage of scavenging or inhibition at the indicated concentrations. 1,1-diphenyl-2 picrylhydrazyl SC50 Databases Links Databases related to CanCO e.g. kegg, chebi, pubmed, pubchem etc. Databases Disease A Disease is any abnormal condition of the body or mind that causes discomfort, dysfunction, or distress to the person affected or those in contact with the person. The term is often used broadly to include injuries, disabilities, syndromes, symptoms, deviant behaviors, and atypical variations of structure and function. Disease Drug A Drug is any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances. A Chemopreventive agent may be contained into a drug. Drug Estrogenic_Activity Compounds having similar structure with steroid hormones, like estrogens, can bind to and activate estrogen receptors (ER) which in turn modulate the expression of many genes. Estrogenic Activity ExperimentalFactor Experimental factors are the variable aspect of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. Experimental factor ForumPost A Forum Post is related to a Published Work and contains comments about this specific Publication. It allows the discussion and the exchange of ideas related to the Published Work. Forum post HL60IC50 Inhibition of 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced superoxide anion radical generation in differentiated HL-60 cells (HL-60 assay). Numbers in parentheses indicate the percentage of scavenging or inhibition at the indicated concentrations. HL60IC50. IC Maximum Inhibitory concentration IC IC50 half-maximal inhibitory concentration IC50 Investigation High-level concept to link related studies Investigation Lipid A class of hydrocarbon-containing organic compounds. Lipids are insoluble in water but soluble in nonpolar solvents and play important roles in living organisms: these roles include functioning as energy storage molecules, serving as structural components of cell membranes, and constituting important signaling molecules. Lipids can be subdivided into 2 groups: fatty acids and glycerides. Lipid Macromolecule Macromolecules are molecules made of many smaller molecules Macromolecule Measurement Measured values and units. Measurement Molecule The smallest particle of a substance that has all of the physical and chemical properties of that substance. Molecules are made up of one or more atoms. If they contain more than one atom, the atoms can be the same (an oxygen molecule has two oxygen atoms) or different (a water molecule has two hydrogen atoms and one oxygen atom). Biological molecules, such as proteins and DNA, can be made up of many thousands of atoms. Molecule NaturalSource A Natural Source is a substance found in nature that usually has a pharmacological or biological activity. A Chemopreventive agent may be contained into a Natural Source. Natural source NucleicAcid Nucleic Acid are a family of macromolecules, composed of various moieties: purines, pyrimidines, phosphoric acid, and a pentose, either d-ribose or d-deoxyribose. Nucleic acids as DNA or RNA is found in the chromosomes, nucleoli, mitochondria, and cytoplasm of all cells, and in viruses. Nucleic acids are the major players in controlling cellular function and heredity. NucleicAcid OCDIC50 Inhibition of ODC induction IC50 [µM] OCDIC50 ORAC Measurement of oxygen radical absorbance capacity. One ORAC unit equals the net protection produced by 1 µM Trolox. ORAC ORACOH A measurement, subclass of ORAC. ORACOH ORACROO A measurement, subclass of ORAC. ORACROO Organ A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region. Representative examples include the heart, lung, liver, spleen, and uterus. Organ Organism A living entity. Organism Pathway A Pathways is a set or series of interactions, often forming a network, which biologists have found useful to group together for organizational, historic, biophysical, or other reasons. The Chemopreventive agent affects a Biological target in order to brake the series of interactions that leads to a Disease (i.e. cancer). Instances can come from any of the pathway databases. Instances should be indexed with those URI. Pathway Person Person Protein A Protein is a group of complex organic macromolecules composed of one or more chains (linear polymers) of alpha-L-amino acids linked by peptide bonds and ranging in size from a few thousand to over 1 million Daltons. Proteins are fundamental genetically encoded components of living cells with specific structures and functions dictated by amino acid sequence. Protein Protocol A protocol is an information entity which is a set of instructions that describe how an Study is done. Protocol PublishedWork A printed or electronic work offered for distribution. PublishedWork QRIC50 IC50 of Quinone Reductase QRIC50 ReactiveOxygenSpecies Reactive oxygen species are organic or inorganic chemicals that contain an oxygen atom with an unpaired electron. This unstable electron configuration causes these chemicals to be highly reactive with other molecules. Reactive oxygen species ResearchStatement A Research Statement is a declarative sentence supported by a specific Publication. ResearchStatement Resources Links for resources related to the model. Resources SC50 half-maximal scavenging concentration SC50 ScientificWorkflow The Scientific workflow is a pipeline of connected components (in-silico tools, models) to perform an in silico experiment. ScientificWorkflow Source The source of a Chemopreventive agent can be either Natural (e.g. pomegranate) or Synthetic (e.g. a drug) Source Study A study is a collection of bioassays sharing a protocol Study Sugar Any member of a class of edible, crystalline carbohydrates (mainly sucrose, lactose and fructose) characterised by a sweet flavour; a loose term applied to monosaccharides, disaccharides, trisaccharides and oligosaccharides, in contrast to complex carbohydrates such as polysaccharides. Sugar SyntheticSource A Synthetic Source is constructed and has a pharmacological or biological activity. A Chemopreventive agent may be contained into a Synthetic Source. Synthetic source Toxicity Toxicity is a quality of a chemical substance which indicates the capacity to cause injury to an organism in a dose dependent manner. Toxicity VirtualScreening Virtual Screening refers to the technique of performing a Biomedical experiment entirely in a computer via computer simulation. Virtual screening XXOSC50 Numbers in parentheses indicate the percentage of scavenging or inhibition at the indicated concentrations. xanthine oxidase SC50 biologicalMechanism The way a Chemopreventive Agent acts on a Target in order to prevent disease (e.g Cancer) biological Mechanism carcinogenActivating e.g. Inhibition of cytochrome P450 (Cyp) 1A activity carcinogenActivating chebiURI The URI of chebi chebiURI http://chebi.bio2rdf.org/sparql chemSpiderURL The URL of chemspider chemSpiderURL chemopreventionStudy A Study related to Cancer Chemoprevention. chemopreventionStudy dbpediaURI The URI of dppedia dbpediaURI drugbankURI The URI of drug bank drugbankURI enzymeInduction e.g. NAD(P)H:quinone reductase (quinone reductase, QR) activity enzymeInduction epigeneticsStudy A Study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence. epigeneticsStudy fractionation_guided An in-vivo bioassay the uses fractionation. fractionation_guided goURI The Gene Ontology URI goURI iNOSIC50 Inhibition of iNOS induction A-IC50. iNOSIC50 iNOSTIC50 Inhibition of iNOS induction A-IC50 [µM]a T-IC50 [µM]b iNOSTIC50 inVitroBioAssay A Bioassay is a laboratory test or analysis of the biological activity of a substance (e.g. Chemopreventive agent) performed by studying its effect on an organism or in a test tube under controlled conditions. A Bioassay is part of an experiment that includes also other bioassays. in vitro bio assay inVivoBioassay A Bioassay is a laboratory test or analysis of the biological activity of a substance (e.g. Chemopreventive agent) performed by studying its effect on an organism or in a test tube under controlled conditions. A Bioassay is part of an experiment that includes also other bioassays. Bioassay in_silico_assay An In silico assay is performed on computer or via computer simulation. in_silico_assay in_vitro_assay An in vitro (Latin for within the glass) assay refers to the technique of performing an assay in a controlled environment outside of a living organism. in_vitro_assay in_vivo_assay An In vivo (Latin for "within the living") refers to experimentation using a whole, living organism as opposed to a partial or dead organism. in_vivo_assay keggURI The Kegg URI keggURI max_percent_inhibition mechanism_based An in vivo bioassay based on mechanosms. mechanism_based percent_inhibition percent_inhibition pubchemURI The pubchem URI pubchemURI pubmedURI The pubmed URI pubmedURI pubmedURL The pubmed URL pubmedURL toxicityStudy A Study related to the toxicity of e.g. a Chemopreventive Agent. toxicityStudy user_assay A user defined assay. user_assay void2:Dataset The URLs of SPARQL endpoints. Dataset 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 owl:Thing chebi sparql endpoint drugbank dbpedia sparql endpoint go sparql endpoint kegg spaql endpoint linked life data sparql endpoint drugbank sparql endpoint Indicate the cell lines used by an experimental Protocol. used_cellLine 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