Alan Ruttenberg Andrew Spear Birgit Kriener Erik De Schutter Fahim T. Imam INCF MultiScale Modeling Task Force Lars Schwabe Padraig Gleeson Pierre Grenon Sean Hill Stephen D. Larson Subhasis Ray Holger Stenzhorn Yann Le Franc 13/03/2012 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" An ontology to describe the field of Computational Neurosciences Basic Formal Ontology (BFO) Computational Neuroscience Ontology Dave Beckett Nikki Rogers Participants in W3C's Semantic Web Deployment Working Group. Alistair Miles Sean Bechhofer An RDF vocabulary for describing the basic structure and content of concept schemes such as thesauri, classification schemes, subject heading lists, taxonomies, 'folksonomies', other types of controlled vocabulary, and also concept schemes embedded in glossaries and terminologies. SKOS Vocabulary This ontology is used to add the Definition class of annotation as in NIF. The source of the definition can be defined with class from OBO-annotation This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. 1.1.1 version 0.5 editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term example A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source imported from Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. An entity responsible for making contributions to the content of the resource. Contributor Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges. The extent or scope of the content of the resource. Coverage Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. An entity primarily responsible for making the content of the resource. Creator Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). The physical or digital manifestation of the resource. Format Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN). An unambiguous reference to the resource within a given context. Resource Identifier Recommended best practice is to use RFC 3066 [RFC3066], which, in conjunction with ISO 639 [ISO639], defines two- and three-letter primary language tags with optional subtags. Examples include "en" or "eng" for English, "akk" for Akkadian, and "en-GB" for English used in the United Kingdom. A language of the intellectual content of the resource. Language Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity. An entity responsible for making the resource available Publisher Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a related resource. Relation Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource. Information about rights held in and over the resource. Rights Management The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. The topic of the content of the resource. Subject and Keywords Typically, a Title will be a name by which the resource is formally known. A name given to the resource. Title Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element. The nature or genre of the content of the resource. Resource Type has_obo_namespace has_related_synonym The range of skos:altLabel is the class of RDF plain literals. skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties. alternative label An alternative lexical label for a resource. Acronyms, abbreviations, spelling variants, and irregular plural/singular forms may be included among the alternative labels for a concept. Mis-spelled terms are normally included as hidden labels (see skos:hiddenLabel). change note A note about a modification to a concept. definition A statement or formal explanation of the meaning of a concept. editorial note A note for an editor, translator or maintainer of the vocabulary. example An example of the use of a concept. The range of skos:hiddenLabel is the class of RDF plain literals. skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties. hidden label A lexical label for a resource that should be hidden when generating visual displays of the resource, but should still be accessible to free text search operations. history note A note about the past state/use/meaning of a concept. note A general note, for any purpose. This property may be used directly, or as a super-property for more specific note types. A resource has no more than one value of skos:prefLabel per language tag, and no more than one value of skos:prefLabel without language tag. The range of skos:prefLabel is the class of RDF plain literals. skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties. preferred label The preferred lexical label for a resource, in a given language. scope note A note that helps to clarify the meaning and/or the use of a concept. This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about An information artifact IA mentions an entity E exactly when it has a component/part that denotes E 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition PERSON: Jonathan Rees Person: Alan Ruttenberg mentions A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later Alan Ruttenberg is quality measurement of relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of a relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. Person:Alan Ruttenberg Person:Bjoern Peters is quality specification of has broader match skos:broadMatch is used to state a hierarchical mapping link between two conceptual resources in different concept schemes. Broader concepts are typically rendered as parents in a concept hierarchy (tree). has broader Relates a concept to a concept that is more general in meaning. By convention, skos:broader is only used to assert an immediate (i.e. direct) hierarchical link between two conceptual resources. has broader transitive skos:broaderTransitive is a transitive superproperty of skos:broader. By convention, skos:broaderTransitive is not used to make assertions. Rather, the properties can be used to draw inferences about the transitive closure of the hierarchical relation, which is useful e.g. when implementing a simple query expansion algorithm in a search application. has close match skos:closeMatch is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, skos:closeMatch is not declared to be a transitive property. skos:exactMatch is disjoint with each of the properties skos:broadMatch and skos:relatedMatch. has exact match skos:exactMatch is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch. has top concept Relates, by convention, a concept scheme to a concept which is topmost in the broader/narrower concept hierarchies for that scheme, providing an entry point to these hierarchies. is in scheme Relates a resource (for example a concept) to a concept scheme in which it is included. A concept may be a member of more than one concept scheme. These concept mapping relations mirror semantic relations, and the data model defined below is similar (with the exception of skos:exactMatch) to the data model defined for semantic relations. A distinct vocabulary is provided for concept mapping relations, to provide a convenient way to differentiate links within a concept scheme from links between concept schemes. However, this pattern of usage is not a formal requirement of the SKOS data model, and relies on informal definitions of best practice. is in mapping relation with Relates two concepts coming, by convention, from different schemes, and that have comparable meanings has member Relates a collection to one of its members. For any resource, every item in the list given as the value of the skos:memberList property is also a value of the skos:member property. has member list Relates an ordered collection to the RDF list containing its members. has narrower match skos:narrowMatch is used to state a hierarchical mapping link between two conceptual resources in different concept schemes. Narrower concepts are typically rendered as children in a concept hierarchy (tree). has narrower Relates a concept to a concept that is more specific in meaning. By convention, skos:broader is only used to assert an immediate (i.e. direct) hierarchical link between two conceptual resources. has narrower transitive skos:narrowerTransitive is a transitive superproperty of skos:narrower. By convention, skos:narrowerTransitive is not used to make assertions. Rather, the properties can be used to draw inferences about the transitive closure of the hierarchical relation, which is useful e.g. when implementing a simple query expansion algorithm in a search application. skos:related is disjoint with skos:broaderTransitive has related Relates a concept to a concept with which there is an associative semantic relationship. has related match skos:relatedMatch is used to state an associative mapping link between two conceptual resources in different concept schemes. is in semantic relation with Links a concept to a concept related by meaning. This property should not be used directly, but as a super-property for all properties denoting a relationship of meaning between concepts. is top concept in scheme Relates a concept to the concept scheme that it is a top level concept of. name numerical value obo_annot:EnumerationClass IAO:0000030 information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity PERSON: Chris Stoeckert OBI_0000142 information content entity OBI:0001617 PubMed ID A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information. Person: Chris Stoeckert, Jie Zheng PMID PubMed Identifier Website: http://en.wikipedia.org/wiki/Wikipedia:PMID PubMed ID Numerical parameter that quantifies the velocity of a chemical reaction. sbo reaction rate constant SBO:0000009 kinetic constant SBO:0000009 sbo SBO:0000016 unimolecular rate constant SBO:0000016 Numerical parameter that quantifies the velocity of a chemical reaction involving two reactants. sbo SBO:0000017 bimolecular rate constant SBO:0000017 sbo SBO:0000018 trimolecular rate constant SBO:0000018 sbo SBO:0000022 forward unimolecular rate constant SBO:0000022 Numerical parameter that quantifies the forward velocity of a chemical reaction involving two reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. sbo SBO:0000023 forward bimolecular rate constant SBO:0000023 sbo SBO:0000024 forward trimolecular rate constant SBO:0000024 Numerical parameter that quantifies the velocity of an enzymatic reaction. sbo kcat turnover number SBO:0000025 catalytic rate constant SBO:0000025 Numerical parameter that quantifies the reverse velocity of a chemical reaction involving only one product. This parameter encompasses all the contributions to the velocity except the quantity of the product. sbo SBO:0000032 reverse unimolecular rate constant SBO:0000032 Numerical parameter that quantifies the reverse velocity of a chemical reaction involving only one product. This parameter encompasses all the contributions to the velocity except the quantity of the product. sbo SBO:0000033 reverse bimolecular rate constant SBO:0000033 Numerical parameter that quantifies the reverse velocity of a chemical reaction involving three products. This parameter encompasses all the contributions to the velocity except the quantity of the products. sbo SBO:0000034 reverse trimolecular rate constant SBO:0000034 Numerical parameter that quantifies the forward velocity of a chemical reaction involving only one reactant. This parameter encompasses all the contributions to the velocity except the quantity of the reactant. It is to be used in a reaction modelled using a continuous framework. sbo SBO:0000035 forward unimolecular rate constant, continuous case SBO:0000035 Numerical parameter that quantifies the forward velocity of a chemical reaction involving two reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a continuous framework. sbo SBO:0000036 forward bimolecular rate constant, continuous case SBO:0000036 Numerical parameter that quantifies the forward velocity of a chemical reaction involving three reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a continuous framework. sbo SBO:0000037 forward trimolecular rate constant, continuous case SBO:0000037 Numerical parameter that quantifies the reverse velocity of a chemical reaction involving only one product. This parameter encompasses all the contributions to the velocity except the quantity of the product. It is to be used in a reaction modelled using a continuous framework. sbo SBO:0000038 reverse unimolecular rate constant, continuous case SBO:0000038 Numerical parameter that quantifies the reverse velocity of a chemical reaction involving only one product. This parameter encompasses all the contributions to the velocity except the quantity of the product. It is to be used in a reaction modelled using a continuous framework. sbo SBO:0000039 reverse bimolecular rate constant, continuous case SBO:0000039 Numerical parameter that quantifies the reverse velocity of a chemical reaction involving three products. This parameter encompasses all the contributions to the velocity except the quantity of the products. It is to be used in a reaction modelled using a continuous framework. sbo SBO:0000040 reverse trimolecular rate constant, continuous case SBO:0000040 Numerical parameter that quantifies the velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity. sbo SBO:0000046 zeroth order rate constant SBO:0000046 Numerical parameter that quantifies the forward velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity. It is to be used in a reaction modelled using a continuous framework. sbo SBO:0000048 forward zeroth order rate constant, continuous case SBO:0000048 Numerical parameter that quantifies the forward velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity. It is to be used in a reaction modelled using a discrete framework. sbo SBO:0000065 forward zeroth order rate constant, discrete case SBO:0000065 sbo SBO:0000066 forward unimolecular rate constant, discrete case SBO:0000066 Numerical parameter that quantifies the forward velocity of a chemical reaction involving two reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a discrete framework. sbo SBO:0000067 forward bimolecular rate constant, discrete case SBO:0000067 Numerical parameter that quantifies the forward velocity of a chemical reaction involving three reactants. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a discrete framework. sbo SBO:0000068 forward trimolecular rate constant, discrete case SBO:0000068 sbo SBO:0000148 temperature difference SBO:0000148 Numerical parameter that quantifies the forward velocity of a chemical reaction. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. sbo SBO:0000153 forward rate constant SBO:0000153 Numerical parameter that quantifies the forward velocity of a chemical reaction. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a continuous framework. sbo SBO:0000154 forward rate constant, continuous case SBO:0000154 Numerical parameter that quantifies the forward velocity of a chemical reaction. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a discrete framework. sbo SBO:0000155 forward rate constant, discrete case SBO:0000155 Numerical parameter that quantifies the forward velocity of a chemical reaction. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. sbo SBO:0000156 reverse rate constant SBO:0000156 Numerical parameter that quantifies the velocity of a chemical reaction where reactants have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. sbo SBO:0000159 non-integral order rate constant SBO:0000159 Numerical parameter that quantifies the forward velocity of a chemical reaction where reactants have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. sbo SBO:0000160 forward non-integral order rate constant SBO:0000160 Numerical parameter that quantifies the reverse velocity of a chemical reaction where products have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the products. sbo SBO:0000161 reverse non-integral order rate constant SBO:0000161 Numerical parameter that quantifies the forward velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity. sbo SBO:0000162 forward zeroth order rate constant SBO:0000162 sbo Vmax SBO:0000186 maximal velocity SBO:0000186 The amount of an entity per unit of volume. sbo [X] SBO:0000196 concentration of an entity pool SBO:0000196 Concentration of an object divided by the value of another parameter having the dimension of a concentration. sbo SBO:0000197 specific concentration of an entity SBO:0000197 SBO:0000225 Time during which some action is awaited. sbo SBO:0000225 delay SBO:0000225 A quantitative measure of an amount or property of an entity expressed in terms of another dimension, such as unit length, area or volume. sbo SBO:0000226 density of an entity pool SBO:0000226 The mass of an entity expressed with reference to another dimension, such as unit length, area or volume. sbo SBO:0000227 mass density of an entity SBO:0000227 Mass of an entity per unit volume. sbo SBO:0000228 volume density of an entity SBO:0000228 The mass of an entity per unit of surface area. sbo SBO:0000229 area density of an entity SBO:0000229 Mass of an entity per unit length. sbo SBO:0000230 linear density of an entity SBO:0000230 SBO:0000254 Measure of the degree to which an object opposes the passage of an electric current. The SI unit of electrical resistance is the ohm. sbo SBO:0000254 electrical resistance SBO:0000254 SBO:0000257 Measure of how easily electricity flows along a certain path through an electrical element. The SI derived unit of conductance is the Siemens. sbo SBO:0000257 conductance SBO:0000257 SBO:0000258 Measure of the amount of electric charge stored (or separated) for a given electric potential. The unit of capacitance is the Farad. sbo SBO:0000258 capacitance SBO:0000258 SBO:0000259 Difference of electrical potential between two points of an electrical network, expressed in volts. sbo electrical potential difference SBO:0000259 voltage SBO:0000259 sbo SBO:0000301 total catalytic efficiency SBO:0000301 sbo SBO:0000302 catalytic efficiency SBO:0000302 sbo kcatp SBO:0000320 product catalytic rate constant SBO:0000320 Numerical parameter that quantifies the velocity of substrate creation by a reversible enzymatic reaction. sbo kcats SBO:0000321 substrate catalytic rate constant SBO:0000321 sbo Vmaxf SBO:0000324 forward maximal velocity SBO:0000324 sbo Vmaxr SBO:0000325 reverse maximal velocity SBO:0000325 Time interval over which a quantified entity is reduced to half its original value. sbo SBO:0000331 half-life SBO:0000331 sbo SBO:0000332 half-life of an exponential decay SBO:0000332 Rate with which a complex dissociates into its components. sbo kd SBO:0000338 dissociation rate constant SBO:0000338 Rate with which two components associate into a complex. sbo SBO:0000339 bimolecular association rate constant SBO:0000339 Rate with which three components associate into a complex. sbo SBO:0000340 trimolecular association rate constant SBO:0000340 Rate with which components associate into a complex. sbo SBO:0000341 association rate constant SBO:0000341 SBO:0000346 Fundamental quantity of the measuring system used to sequence events, to compare the durations of events and the intervals between them, and to quantify the motions or the transformation of entities. The SI base unit for time is the SI second. The second is the duration of 9,192,631,770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. sbo SBO:0000346 temporal measure SBO:0000346 SBO:0000347 Amount of time during which an event persists. sbo SBO:0000347 duration SBO:0000347 SBO:0000348 sbo mean lifetime SBO:0000348 exponential time constant SBO:0000348 sbo kinact SBO:0000349 inactivation rate constant SBO:0000349 The speed of an enzymatic reaction at a defined concentration of substrate(s) and enzyme. sbo SBO:0000350 forward reaction velocity SBO:0000350 Numerical parameter that quantifies the reverse velocity of a chemical reaction independant of the reactant quantities. This parameter encompasses all the contributions to the velocity. It is to be used in a reaction modelled using a continuous framework. sbo SBO:0000352 reverse zeroth order rate constant SBO:0000352 The speed of an enzymatic reaction at a defined concentration of substrate(s) and enzyme. sbo SBO:0000353 reverse reaction velocity SBO:0000353 sbo SBO:0000356 decay constant SBO:0000356 The enumeration of co-localised, identical biochemical entities of a specific state, which constitute a pool. The form of enumeration may be purely numerical, or may be given in relation to another dimension such as length or volume. sbo SBO:0000360 quantity of an entity pool SBO:0000360 sbo SBO:0000361 amount of an entity pool SBO:0000361 Numerical parameter that quantifies the forward velocity of a chemical reaction where reactants have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the reactants.It is to be used in a reaction modelled using a continuous framework. sbo SBO:0000365 forward non-integral order rate constant, continuous case SBO:0000365 Numerical parameter that quantifies the forward velocity of a chemical reaction where reactants have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the reactants. It is to be used in a reaction modelled using a discrete framework. sbo SBO:0000366 forward non-integral order rate constant, discrete case SBO:0000366 sbo SBO:0000367 reverse non-integral order rate constant, discrete case SBO:0000367 Numerical parameter that quantifies the reverse velocity of a chemical reaction where products have non-integral orders. This parameter encompasses all the contributions to the velocity except the quantity of the products. It is to be used in a reaction modelled using a continuous framework. sbo SBO:0000368 reverse non-integral order rate constant, continuous case SBO:0000368 number used as a multiplicative or exponential factor for quantities, expressions or functions sbo SBO:0000380 biochemical coefficient SBO:0000380 SBO:0000465 The measurable dimensions of an object which are minimally required to define the space that an object occupies. sbo SBO:0000465 spatial measure SBO:0000465 The length of an object is the longest measurable distance between its extremities. sbo SBO:0000466 length SBO:0000466 The area of an object is a quantity expressing its two-dimensional size, usually part or all of its surface. sbo SBO:0000467 area SBO:0000467 A quantity representing the three-dimensional space occupied by all or part of an object. sbo SBO:0000468 volume SBO:0000468 For a given substance, A, its mass fraction (x A) is defined as the ratio of its mass (m A) to the total mass (m total) in which it is present, where the sum of all mass fractions is equal to 1. This provides a means to express concentration in a dimensionless size. sbo SBO:0000470 mass fraction SBO:0000470 Molality denotes the number of moles of solute per kilogram of solvent (not solution). The term molal solution is used as a shorthand for a "one molal solution", i.e. a solution which contains one mole of the solute per kilogram of the solvent. The SI unit for molality is mol/kg. sbo SBO:0000471 molal concentration of an entity SBO:0000471 Molarity, or molar concentration, denotes the number of moles of a given substance per litre of solution. The unit of measure of molarity is mol/L, molar, or the capital letter M as an abbreviated form. sbo SBO:0000472 molar concentration of an entity SBO:0000472 The period is the duration of one cycle in a repeating event. [wikipedia] sbo SBO:0000476 period SBO:0000476 The measurable amount of time by which a periodic or cyclic is shifted or offset from defined reference point. sbo temporal offset SBO:0000477 phase shift SBO:0000477 sbo SBO:0000482 geometric mean rate constant SBO:0000482 The minimal velocity observed under defined conditions, which may or may not include the presence of an effector. For example in an inhibitory system, this would be the residual velocity observed under full inhibition. In non-essential activation, this would be the velocity in the absence of any activator. sbo SBO:0000485 basal rate constant SBO:0000485 A proportionality constant representing the amount of substance diffusing across a unit area through a unit concentration gradient in unit time. The higher the diffusion coefficient (of one substance with respect to another), the faster they diffuse into each other. This coefficient has an SI unit of m²/s (length²/time). sbo diffusivity SBO:0000491 diffusion coefficient SBO:0000491 Amplitude is the magnitude of change in the oscillating variable, with each oscillation, within an oscillating system. sbo SBO:0000492 amplitude SBO:0000492 The numerical quantification of an entity pool. This may be expressed as, for example, the number of molecules or the number of moles of identical entities of which an specific entity pool is comprised. sbo SBO:0000503 number of entity pool constituents SBO:0000503 The mass that comprises an entity pool. sbo SBO:0000504 mass of an entity pool SBO:0000504 Amount of enzyme present per unit of volume. The participant role 'enzymatic catalyst' is defined in SBO:0000460. sbo SBO:0000505 concentration of enzyme SBO:0000505 Amount, expressed as a mass, of an enzyme. The participant role 'enzymatic catalyst' is defined in SBO:0000460. sbo SBO:0000506 mass of enzyme SBO:0000506 Amount, expressed as a number, of a specific enzyme comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'enzymatic catalyst' is defined in SBO:0000460. sbo SBO:0000507 number of an enzyme SBO:0000507 The amount, expressed as a number, of a specific reactant comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'reactant' is defined in SBO:0000010. sbo SBO:0000508 number of a reactant SBO:0000508 sbo SBO:0000509 concentration of reactant SBO:0000509 The amount, expressed as a mass, of a specific reactant entity pool. The participant role 'reactant' is defined in SBO:0000010. sbo SBO:0000510 mass of reactant SBO:0000510 The amount, expressed as a number, of a specific product comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'product' is defined in SBO:0000011. sbo SBO:0000511 number of a product SBO:0000511 The amount of a specific entity pool product present per unit of volume. The participant role 'product' is defined in SBO:0000011. sbo SBO:0000512 concentration of product SBO:0000512 The amount, expressed as a mass, of a specific product entity pool. The participant role 'product' is defined in SBO:0000011. sbo SBO:0000513 mass of product SBO:0000513 The amount, expressed as a number, of a specific substrate comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'substrate' is defined in SBO:0000015. sbo SBO:0000514 number of a substrate SBO:0000514 The amount of a specific entity pool substrate present per unit of volume. The participant role 'substrate' is defined in SBO:0000015. sbo SBO:0000515 concentration of substrate SBO:0000515 The amount, expressed as a mass, of a specific substrate entity pool. The participant role 'substrate' is defined in SBO:0000015. sbo SBO:0000516 mass of substrate SBO:0000516 The amount, expressed as a number, of a specific modifier comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'modifier' is defined in SBO:0000019. sbo SBO:0000517 number of a modifier SBO:0000517 The amount of a specific modifier entity pool present per unit of volume. The participant role 'modifier' is defined in SBO:0000019. sbo SBO:0000518 concentration of modifier SBO:0000518 The amount, expressed as a mass, of a specific modifier entity pool. The participant role 'modifier' is defined in SBO:0000019. sbo SBO:0000519 mass of modifier SBO:0000519 The amount, expressed as a number, of a specific inhibitor comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'inhibitor' is defined in SBO:0000020. sbo SBO:0000520 number of an inhibitor SBO:0000520 sbo SBO:0000521 concentration of inhibitor SBO:0000521 The amount, expressed as a mass, of a specific inhibitor entity pool. The participant role 'inhibitor' is defined in SBO:0000020. sbo SBO:0000522 mass of inhibitor SBO:0000522 The amount, expressed as a number, of a specific activator comprising an entity pool. This may be expressed, for example, as the number of molecules, or the number of moles. The participant role 'activator' is defined in SBO:0000459. sbo SBO:0000523 number of an activator SBO:0000523 The amount of a specific activator entity pool present per unit of volume. The participant role 'activator' is defined in SBO:0000459. sbo SBO:0000524 concentration of activator SBO:0000524 The amount, expressed as a mass, of a specific activator entity pool. The participant role 'activator' is defined in SBO:0000459. sbo SBO:0000525 mass of activator SBO:0000525 A parameter that represents the permeability of an ion channel with respect to a particular ion. sbo membrane permeability SBO:0000538 ionic permeability SBO:0000538 A quantitative parameter that represents a probability value, assigned to a specific event. sbo SBO:0000539 probabilistic parameter SBO:0000539 A ratio that represents the quantity of a defined constituent entity over the total number of all constituent entities present. sbo SBO:0000540 fraction of an entity pool SBO:0000540 The number of moles of a constituent entity, divided by the total number of all constituent entities present in a system. sbo SBO:0000541 mole fraction SBO:0000541 The permeability of an ion through a channel or membrane expressed in relation to the reference ion, which is given the value 1. For example, if a membrane is most permeable to K+, then that is assigned the reference permeability value of 1, and the value for Na+ may be 0.05. sbo SBO:0000566 relative permeability SBO:0000566 A physical constant featured in many fundamental equations in the physical sciences. It is equivalent to the Boltzmann constant, but expressed in units of energy per temperature increment per mole (rather than energy per temperature increment per particle). It has the value 8.314 J.K-1.mol-1 and is denoted by the symbol R. sbo gas constant ideal gas constant molar gas constant SBO:0000567 universal gas constant SBO:0000567 Named after Michael Faraday, it is the magnitude of electric charge per mole of electrons. It has the value 96,485.3365 C/mol (Coulombs per Mole), and the symbol F. sbo SBO:0000568 Faraday constant SBO:0000568 A duration of time after which a phase shift occurs. sbo SBO:0000584 temporal offset SBO:0000584 The total length of time over which a model is simulated, where the time scale is indicated within the model simulation. sbo SBO:0000585 simulation duration SBO:0000585 A conceptualisation of time which is intrinsic to a mathematical model, and which can be used to describe other variables or parameters of the model. sbo SBO:0000586 model time SBO:0000586 A discrete value attributed to an entity pool. sbo SBO:0000592 discrete amount of an entity pool SBO:0000592 A defined entity pool state which can be modified by a petri net transition [SBO:0000591]. sbo SBO:0000593 petri net place SBO:0000593 cno_0000001 This general class includes the most common types of models classified based on the level of description of the nervous system. definition based on the following NCI thesaurus entry: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Type_of_Event defined model type defined type of model a generically_dependent_continuant that is a category of models regarded as sharing particular characteristics, qualities, and/or defined similarities. cno_0000002 This class is based on the assumption that models can represented as particular assemblies of components that can be either specific to the different level of description (cellular, synaptic and network) or generic. definition based on element from NCI Thesaurus: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Element_Part model component model element a generically dependent continuant that is a constituent part of a model cno_0000003 parameter elementary model component role that defines an elementary model component as constant value determining the characteristics or behaviour of the model cno_0000004 reset potential value of the membrane potential at which the model is maintained after the emission of a spike. cno_0000005 cno_alpha:cno_0000005 SBO:0000565 http://en.wikipedia.org/wiki/Physical_constant physical constant A physical constant that is required in the calculation of a system parameter cno_0000007 http://www.scholarpedia.org/article/Models_of_synaptic_plasticity http://www.scholarpedia.org/article/Models_of_synaptic_plasticity phenomenological plasticity model long term plasticity model that is based on an input-output relationship between neuronal activity and synaptic plasticity. This type of model does not explicitly account for the biochemistry and physiology leading to synaptic plasticity. cno_0000008 The distinction between the different subclasses is based on the different "spiking mechanisms". cellular model a defined type of model that represent the biological activities of a cell. cno_0000009 synapse model a defined type of model that represents the biological processes involved in synaptic transmission cno_0000010 network model a defined type of model that represents biological neural networks. cno_0000011 plasticity model a defined type of model that describes the mechanisms underlying the plasticity of the nervous system. cno_0000012 This class can be further subdivided into binary neuron, McCullogh neurons and all variants of the artificial neuron models. artificial neuron model a cellular model that represents the electrical activity of a nerve cell with simplified function cno_0000013 point process model a cellular model that reproduce particular features of real neuron spiking patterns with statistical point process models. cno_0000014 spiking model a cellular model that describes the mechanism of action potential emission in biological nerve cell. cno_0000015 PMID: 10809012 balanced random network defined model that corresponds to a network of sparsely connected excitatory and inhibitory neurons which can switch between firing states depending on the balance between excitation and inhibition. cno_0000016 http://en.wikipedia.org/wiki/Hopfield_network Hopfield network defined model that is a form of recurrent artificial neural network invented by John Hopfield. cno_0000017 biophysical spiking model a spiking model that describe the interactions between the ionic conductances that participates to the generation of an action potential cno_0000018 threshold-based spiking model a spiking model that represents the spiking mechanism as the result of a threshold crossing. cno_0000019 This class could become a superclass called dynamical models or dynamical system models in contrast with biophysical and threshold based models. It should contain models like Fitzhugh-Nagumo, Morris-Lecar models. reduced model biophysical model that is obtained by dimensionality reduction of a detailed model. cno_0000020 detailed model biophysical model that describes in detail the conductance variations of the ionic currents responsible of the generation of an action potential cno_0000021 conductance-based model This classe refers to detailed integrate-and-fire models as described in Destexhe A. (1997, PMID: 9097470) and Hill S. and Tononi G. (2005, PMID: 15537811) pulse-based model a threshold based spiking neuron model that is an hybrid between Hodgkin and Huxley and integrate-and-fire models. The model describes the impact of fast sodium and delayed rectifier potassium conductances on the subthreshold membrane voltage dynamic and considers action potentials as pulses during which the sodium and potassium conductances are set to particular values representing their participation to the generation and repolarization of the action potential. cno_0000022 one variable model a threshold-based model that uses only one variable to describe the nerve cells behavior. cno_0000023 two variable model a threshold-based model that uses two variables to describe the nerve cells behavior. cno_0000024 three variable model a threshold-based model that uses three variables to describe the nerve cells behavior cno_0000025 spike response model a threshold-based model that correspond to a generalization of the leaky integrate-and-fire model and give a simple description of action potential generation in neurons cno_0000026 current-based model a model of chemical synapse that consider the impact of the chemical release as a current source in the post-synaptic model with the postsynaptic membrane voltage considered to be constant. cno_0000027 conductance-based model a model of chemical synapse that consider the impact of the chemical release as a modification of conductance in the post-synaptic model with the post-synaptic potential varying over time. cno_0000028 rate model network model composed of rate-based neuron models cno_0000029 corresponds to Kohonen maps, Multiple Layer perceptron, ... artificial neural network model network model composed of artificial neuron models. cno_0000030 spiking network model network model that is composed of spiking neuron models. cno_0000031 chemical synapse model a synapse model that describes the impact of chemical compounds released by the synapse cno_0000032 electrical synapse model a synapse model that describe synapses transmitting directly ionic currents. cno_0000033 This class would contains models that describes the link between potassium channels and NMDA activation as described in hippocampus for instance. cellular plasticity model plasticity model that describes the variations of the cellular intrinsic excitability due to regulation of ionic conductances depending on the network activity. cno_0000034 synaptic plasticity model synaptic plasticity rule model of plasticity that represents the mechanisms underlying changes in synaptic transmission, depending on the network or cellular activity. cno_0000035 short term facilitation model a model of short term synaptic plasticity that represents the increase of the synaptic efficacy for a short period of time. cno_0000036 cellular model component aggregated model composed that is used to build cellular models cno_0000037 synapse model component aggregated model component that is used to build synaptic models. cno_0000038 resting membrane potential value of the neuronal membrane potential at rest cno_0000039 This is a general term that encompass the refractory period usually defined with a time constant and the resetting of the membrane potential during the refractory period. refractory mechanism a cellular model component that represents the mechanism by which the model is kept unresponsive to any stimulus after the emission of an action potential. cno_0000040 model quality quality that represents a qualitative feature of the model that can be either independent of the model specification or a property resulting of the particular model specification cno_0000041 spiking mechanism a cellular model component that represents the mechanisms generating action potential in a cellular model type. cno_0000042 morphology a cellular model component that represents the morphology of the model cno_0000043 intracellular dynamic a cellular model component that represents a chemical signaling occuring inside the nerve cell cno_0000044 stimulation current current model that represents input currents provided to the model via an electrode (intracellular or extracellular). cno_0000045 generic model component cno_0000046 probabilistic component a generic model component that represents the probabilistic variations of any model component. cno_0000047 ionic current model a current model that describes the flow of ions through cellular membrane. cno_0000048 synaptic current current model that represents the flow of ions triggered by the activation of a chemical or electrical synapse model. cno_0000049 abstract current model a current model that is an abtraction of complex current interactions and which is used to reproduce a particular cellular behavior such as rebound or adaptation. cno_0000050 continuous a spiking mechanism that considers the action potential initiation as a continuous process often based on the non linearity of the conductance changes supporting the initiation of an action potential. This mechanism is the opposite of a threshold-based mechanisms. cno_0000051 threshold-based a spiking mechanism that considers the action potential initiation as a result of a thresholding operation. cno_0000052 point a morphology that is used to represents the models without specified geometry. cno_0000053 single compartment a morphology that consider the cellular morphology as a unique compartment cno_0000054 multiple compartment a morphology that represents the modeled cell with multiple compartments. This morphology spans the models called the Ball-and-stick model and the models based on reconstructed morphologies. cno_0000055 reconstructed morphological quality that represents model morphologies build upon the reconstruction of a real nerve cell morphology using imaging techniques such as camera lucida or two-photon imaging. cno_0000056 calcium dynamic an intracellular dynamic model component that represents the variation of the intracellular calcium concentration over time. cno_0000057 NOTE: Shouldn't be separated from calcium dynamic as calcium is also a molecular participant. One possible solution would be to change into: reduced calcium dynamic to represent the simplification of buffering and detailed biochemical reactions that details the calcium buffering!!! biochemical dynamic an intracellular dynamic model component that represents the dynamic of the intracellular biochemical reactions and molecular participant concentrations over time. cno_0000058 network model component a model component that is used to build network model types. cno_0000059 non linear spike generation current abstract current model that represents an additional non-linear current ψ which leads to a divergence of the potential toward infinity in a finite time during the emission of an action potential. cno_0000060 defined model a generically_dependent_continuant that represent the set of models commonly used to build other models. cno_0000061 http://en.wikipedia.org/wiki/Biological_neuron_model#Integrate-and-fire integrate-and-fire a defined model that represent the evolution of voltage as the derivative of the law of capacitance. The action potential is emitted when the value of the voltage reaches a threshold and is considered as Dirac function. After the emission the voltage is resetted to the resting potential value. cno_0000062 http://www.scholarpedia.org/article/Adaptive_exponential_integrate-and-fire_model AdEx adaptive exponential integrate-and-fire a defined model that is a spiking neuron model with two variables. The first equation describes the dynamics of the membrane potential and includes an activation ter with an exponential voltage dependence. Voltage is coupled to a second equation which describes adaptation. Both variables are reset if an action potential has been triggered. This model has been introduced by Brette and Gerstner in 2005. cno_0000063 http://en.wikipedia.org/wiki/Variable_(mathematics) independent variable variable regarded as inputs to a system and may take on different values freely cno_0000064 http://en.wikipedia.org/wiki/Variable_(mathematics) dependent variable variable regarded as values that change as a consequence of changes in other values in the system. cno_0000065 w.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1001056 EIF exponential integrate-and-fire a defined model that is an integrate-and-fire model in which the action potentials are generated by an exponential current instead of a fixed threshold. The exponential integrate-and-fire model is defined in Fourcaud-Trocme and al. 2003 cno_0000066 http://en.wikipedia.org/wiki/Biological_neuron_model#Leaky_integrate-and-fire LIF, Lapicque's model leaky integrate-and-fire a defined model that is an integrate-and-fire model with a leak component added to the membrane potential, reflecting the diffusion of ions that occurs through the membrane when some equilibrium is not reached in the cell. cno_0000067 QIF quadratic integrate-and-fire a defined model that is an integrate-and-fire model in which the action potentials are generated by a quadratic current instead of a fixed threshold. The quadratic integrate-and-fire model is defined in Latham and al. 2000. This model is identical to the Theta neuron proposed by Ermentrout and Kopell (1986) with a variable change. cno_0000068 http://en.wikipedia.org/wiki/Theta_model theta neuron model a defined model that is well suited to describe the processes involving rapid changes in membrane potential, known as bursts. The theta model describes parabolic bursting and has been defined in Ermentrout and Kopell, SIAM journal of Applied Mathematics 1986. cno_0000069 ALIF adaptive integrate-and-fire a defined model that is a two-variable integrate-and-fire model. The second variable accounts for the currents involved in spike frequency adaptation. This variable increase transiently during action potentials and decay between action potential. cno_0000070 PMID: 12611957 GIF generalized integrate-and-fire a defined model that is a two variable integrate-and-fire model with a threshold for spike generation and a reset as in the leaky integrate-and-fire model. The two variables represent subthreshold resonance behavior and result from the linearization of the Hodgkin and Huxley equation around a subthreshold holding potential. This model is similar to the resonate-and-fire model proposed by Izhikevich (2001) cno_0000071 IFB integrate-and-fire-or-burst a defined model that is a two-variable integrate-and-fire model. The second variable is a slow variable that represents the inactivation of the low-threshold calcium current. This model reproduces the features of the bursting behavior of thalamo-cortical relay neurons and has been proposed by Smith and al., 2000 cno_0000072 PMID: 18244602 Izhikevich model a defined model that is a minimal two-variable integrate-and-fire model that reproduces different features depending on the value of 4 parameters. The second variable represents the adaptation. This model has been proposed in Izhikevich, 2003. cno_0000073 PMID: 11665779 resonate-and-fire a defined model that is a two variable integrate-and-fire model proposed by Izhikevich in Izhikevich, 2001. cno_0000074 PMID: 6144106 http://en.wikipedia.org/wiki/Hindmarsh%E2%80%93Rose_model HindMarch and Rose model a defined model that is a three-variable model: the membrane potential written in dimensionless unit, the spiking variable that represent the fast transport of sodium and potassium ions and the bursting variable that represent the slow transport of other ions. This model aims to study the spiking-bursting behavior of the membrane potential observed in experiments. cno_0000075 PMID: 16927211 Rotstein model a defined model that is three variable reduced model defined in Rotstein and al. 2006 in J. Comp. Neurosci. cno_0000076 PMID: 20478693 Shinomoto model a defined model that is a multi-timescale adaptive threshold model of neuronal spiking incorporated into the stochastic framework of the linear-nonlinear Poisson model in the form of a generalized linear model. cno_0000077 doi:10.1162/neco.1997.9.5.1015 http://icwww.epfl.ch/~gerstner/SPNM/node27.html http://www.scholarpedia.org/article/Spike-response_model spike response model a defined model that is a generalization of the leaky integrate-and-fire model. As in the leaky integrate-and-fire model, action potentials are generated when the voltage passes a threshold. Leaky integrate-and-fire models are formulated using differential equations for the voltage, whereas the Spike Response Model is formulated using filters. cno_0000078 PMID: 16633938 http://icwww.epfl.ch/~gerstner/SPNM/node27.html#SECTION02323000000000000000 http://www.scholarpedia.org/article/Spike-response_model#Spike_Response_Model_SRM.5C.28_0.5C.29 spike response model SRM0 a defined model that is a simplified version of the Spike Response Model and does not include a dependence of the response kernel κ upon the time since the last spike. cno_0000079 PMID: 8888612 http://www.scholarpedia.org/article/Spike-response_model#Cumulative_Spike_Response_Model:_bursting_and_adaptation cumulative spike response model a defined model that is a spike response model where refractoriness and adaptation were modeled by the combined effects of the spike after potentials of several previous spikes, rather than only the most recent spike. cno_0000080 http://www.scholarpedia.org/article/Spike-response_model#Spike_Response_Model_with_a_cumulative_dynamic_threshold spike response model with cumulative dynamic threshold a defined model that is a spike response model in which the value of the threshold depends on all previous spikes not only the most recent one. cno_0000081 dynamic threshold a threshold-based spiking mechanism that represent the variation of the spiking threshold over time based on particular criterions. cno_0000082 fixed threshold a threshold-based spiking mechanism that considers the threshold as constant over time. cno_0000083 http://www.scholarpedia.org/article/Spike-response_model#Mathematical_formulation spike shape kernel a cellular model component that is used to build spike response model and which describes the form of the action potential and its spike after-potential. This kernel is a function of the time since the last action potential. It can describe a depolarizing, hyperpolarizing or resonating spike after-potential. cno_0000084 http://www.scholarpedia.org/article/Spike-response_model#Mathematical_formulation linear filter of the membrane responsiveness kernel a cellular model component that is used to build spike response model and which describes the linear response to an incoming short pulse. The responsiveness kernel to an input pulse depends on the time since the last spike. cno_0000085 adaptation current an abstract current model that represents the mechanism of spiking frequency adaptation. cno_0000086 rebound current abstract current model that represents the mechanisms of rebound. cno_0000087 http://en.wikipedia.org/wiki/Hindmarsh%E2%80%93Rose_model spiking variable, y spiking current abstract current model that represents the mechanisms involved in the action potential and which is used to build HindMarch and Rose models cno_0000088 http://en.wikipedia.org/wiki/Hindmarsh%E2%80%93Rose_model bursting variable, z bursting current abstract current model that represents the mechanisms of bursting and used to build HindMarch and Rose models. cno_0000089 PMID: 18244602 membrane recovery variable abstract current model which accounts for the activation of potassium ionic currents and inactivation of sodium ionic currents and provides negative feedback to the membrane voltage cno_0000090 PMID: 5575343 http://www.scholarpedia.org/article/Conductance-based_models#Examples_and_Variants Connor-Stevens model a defined model that is an extended action potential generating model using gastropod somas. This model is similar to the Hodgkin and Huxley model and contains a sodium, potassium and leak current with faster dynamics for the sodium and potassium currents. In addition, a transient potassium current, called, A-current, has been included. cno_0000091 PMID: 8815919 Wang-Buzsaki model a defined model that is a network model composed of single compartment models, derived from the original Hodgkin-Huxley model. This network model represents a network of hippocampal interneurons. cno_0000092 PMID: 19431309 http://www.scholarpedia.org/article/FitzHugh-Nagumo_model Bonhoeffer-van der Pol model Fitzhugh-Nagumo model a defined model that is a two-dimensional simplification of the Hodgkin-Huxley model of spike generation in squid giant axons. The model consist of a voltage-like variable having cubic nonlinearity that allows regenerative self-excitation via positive feedback and a recovery variable having a linear dynamics that provides a slower negative feedback. cno_0000093 PMID: 7260316 http://www.scholarpedia.org/article/Morris-Lecar_model Morris-Lecar model a defined model that is a two-dimensional reduced excitation model applicable to systems having two non-inactivating voltage-sensitive conductances. The original form of the model employed an instantaneously responding voltage-sensitive calcium conductance for excitation and a delayed voltage-dependent potassium conductance for recovery. cno_0000094 synaptic action a synapse model component that describes the impact of synaptic model on the post-synaptic model. cno_0000095 connection element a synapse model component that describe how the synapse is connected between two neuron models cno_0000096 http://en.wikipedia.org/wiki/Synaptic_weight synaptic weight a synapse model component that refers to the strength or amplitude of a connection between two nodes, corresponding in biology to the amount of influence the firing of one neuron has on another. cno_0000097 plasticity mechanism a synapse model component that relates to plasticity models. cno_0000098 synaptic conductance dynamic a synaptic model component that describes the dynamic of the synaptic conductance in the post-synaptic model cno_0000099 synaptic delay delay between the activation of the synapse and its impact on the post-synaptic model. cno_0000100 voltage dependent receptor activation a synapse model component that describes the voltage dependent activation of receptor such as NMDA receptor that will participate in the total synaptic current. cno_0000101 release mechanism a synapse model component that describes the neurotrasmitter release. cno_0000102 neurotransmittor diffusion a synapse model component that describes the diffusion of neurotransmitter in the extracellular space. cno_0000103 post-synaptic element a connection element which points to the model elements of the post-synaptic model that are used in the equations of the synapse model. cno_0000104 pre-synaptic element a connection element which points to the model elements of the pre-synaptic model that are used in the equations of the synapse model. cno_0000105 voltage-dependent current model an ionic current model that represents the current flowing through ionic channel triggered by the change in voltage. cno_0000106 voltage and ionic dependent current model an ionic current model that represents the current flowing through ionic channel triggered by the change of voltage and the binding of a particular ion. cno_0000107 http://en.wikipedia.org/wiki/Supervised_learning supervised learning learning rule that produces an infered function to predict correct output value for any valid input object, based on an error function estimated through the training period with the presentation of input/output pairs. cno_0000108 ionic dependent current model a biochemically activated current model that represents the current flowing through ionic channel triggered by the binding of a particular ion. cno_0000109 biochemically activated current an ionic current model that represents the current flowing through ionic channels triggered by action of biochemical components. cno_0000110 unsupervised learning learning rule that produces an infered function based on unlabeled data without any feedback to evaluate the potential solution. cno_0000111 excitatory action a synaptic action that increases the post-synaptic model activity and/or voltage cno_0000112 inhibitory action a synaptic action that decreases the post-synaptic activity and/or voltage cno_0000113 shunting action a synaptic action that modifies the global conductance of the post-synaptic model cno_0000114 instantaneous rise and monexponential decay a synaptic conductance dynamic which assumes an instanteanous rise of the conductance followed by an exponential decay with a time constant. cno_0000115 difference of two exponentials a synaptic conductance dynamic that is described as the difference of two exponential functions which represent the rising and the decay phase with two distinct time constants. cno_0000116 alpha function a synaptic conductance dynamic describing a conductance that has a rising phase with a certain rise time. As it has just a single time constant, the time course of the rise and decay are correlated. cno_0000117 cellular elements a network model component that refers to the cellular model type used to build the network model cno_0000118 synaptic element a network model component that refers to the synapse model type used to build the network model cno_0000119 connectivity pattern a model component quality that represents a connectivity pattern obtained with specific connectivity rule cno_0000120 rate function a cellular model component that describes the dynamic of the cellular model firing rate. cno_0000121 http://en.wikipedia.org/wiki/Recurrent_neural_network#Fully_recurrent_network recurrent a connectivity pattern in which connections between units form a directed cycle. cno_0000122 http://en.wikipedia.org/wiki/Feedforward_neural_networks feedforward a connectivity pattern in which connections between units do not form a directed cycle. cno_0000123 http://en.wikipedia.org/wiki/Small-world_network small world a connectivity pattern in which most nodes are not neighbors of one another, but most node can be reached from every other by a small number of hops or steps. cno_0000124 functional grouping cellular grouping quality that represents cellular grouping defined by common functional criterons. cno_0000125 anatomical grouping cellular grouping quality that represents cellular grouping based on anatomical information cno_0000126 current model a cellular model component that represents the different types of modeled currents that can influence the trajectory of the membrane voltage cno_0000127 current localization current model quality that represents the location of the current source on a neuronal model (somatic, primary dendrite, ...) cno_0000128 current distribution current model quality that represents the spatial distribution of current sources (ionic channels, synaptic channels, stimulation electrode) on a compartment cno_0000129 connectivity rule a network layout component that describe the rules used to establish connections between the cellular elements of the network model cno_0000130 http://www.ebi.ac.uk/sbo/main/SBO:0000259 voltage cno_0000131 capacitance cno_0000132 current cno_0000133 diameter cno_0000134 length cno_0000135 synaptic plasticity element cno_0000136 frequency cno_0000137 maximal conductance cno_0000138 random cellular grouping quality that represents probabilistic grouping of cellular models within network models. cno_0000139 spike time cno_0000140 time constant cno_0000141 volume cno_0000142 indices cno_0000143 cellular grouping quality a model component quality that represent the properties of cellular grouping in network models cno_0000144 rate-based neuron model a cellular model that describe the firing activity of neuron using a rate function. cno_0000145 refractory period a duration that represent the duration during which the model cannot emit a subsequent spike following an initial spike. cno_0000146 spiking threshold voltage above which the model emits a spike cno_0000147 elementary model component role role played by the model elements cno_0000148 cellular grouping a network layout component that defines the common attribute or property used to create arbitrary groups of cellular model type. cno_0000149 Models can be defined without any mention of space. The model can be enriched with particular spatial embedding. spatial embedding a generic model component that add spatial information to the model cno_0000150 relates to http://neurolex.org/wiki/Category:Two_dimensional_region two dimensional layout cno_0000151 http://neurolex.org/wiki/Category:Three_dimensional_region three dimensional layout cno_0000152 spatial coordinates cno_0000153 2D coordinates cno_0000154 3D coordinates cno_0000155 polar coordinates cno_0000156 This term should be transformed into a datatype. pre-synaptic indice a pre-synaptic element that specifies the indices of the pre-synaptic neuron model cno_0000157 is a quality user-defined cellular distribution quality that represents the distribution of cellular models in network models arranged based on user-defined criterions that are not based on anatomical information. cno_0000158 abstract morphology a morphological quality that describe abstract representation of the morphology. Often cellular compartment are represented as iso-potential cylindrical compartments. cno_0000159 is a quality uniform cellular distribution quality that represents a cellular distribution in network models where cellular models are uniformly distributed in the abstract space. cno_0000160 pre-synaptic variable elementary model component that specifies the variable of the neuronal model used into the equations of the synapse model. cno_0000161 developmental plasticity model model of network plasticity based on developmental rules that will change the structure of the network. cno_0000162 PMID: 12991237 http://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model Hodgkin and Huxley model defined model that describes how action potentials in neurons are initiated and propagated in squid giant axon. cno_0000163 post-synaptic indice a post-synaptic element that specifies the indices of the post-synaptic neuron model cno_0000164 is a quality anatomically defined cellular distribution quality that represents the cellular distribution in the network model based on criterions derived from anatomical information cno_0000165 Similar to sao1057800815 morphological quality a model component quality that described the kind of morphology used in the neuron models. cno_0000166 Example: oscillatory, bursting, synchronization, ... functional quality a model quality that describes the intrinsic functional quality of the models cno_0000167 post-synaptic variable elementary model component that specifies the variable of the neuronal model used into the equations of the synapse model. cno_0000168 uniform a current distribution where current models are uniformly distributed. cno_0000169 http://en.wikipedia.org/wiki/Learning_rule learning rule network model component that is a method which improves the neural network's performance. It is done by updating the weights and bias level of a network after a network is stimulated in an environment. cno_0000170 random a current distribution where current models are distributed according to a particular probability distribution. cno_0000171 non-linear a current distribution where current models are distributed according to a non-linear function of space. cno_0000172 linear a current distribution where current models are distributed according to a linear function of space. cno_0000173 concentration cno_0000174 current model quality model component quality that represent specific properties attached to current models cno_0000175 cno_alpha:cno_0000175 model description an information content entity that represents the differents types of formats which can exist for describing a model (scientific paper, database entry, XML format, ...) cno_0000176 link to SBO, Kisao, Teddy mathematical concept a thing that represents the differents mathematical concepts used to represent models. cno_0000177 network layout component a network model component that describe the different level of organization of the network model cno_0000178 cellular distribution a network layout component that represents the distribution of the cellular model type in euclidian or non euclidean space. cno_0000179 related to definition in NIF: http://neurolex.org/wiki/Category:One_dimensional_region one dimensional layout cno_0000180 model a generically_dependent_continuant that is a placeholder for any model cno_0000181 cno_alpha:cno_0000181 http://www.thefreedictionary.com/elementary elementary model component an elementary model component is the smallest model component on which aggregated component are built. These elements can have either the role of parameter or the role of variable. cno_0000182 short term plasticity model short term plasticity rule model of synaptic plasticity that describes the short term changes in the synaptic activity. cno_0000183 long term plasticity model long term plasticity rule model of synaptic plasticity that describes the long term changes in the synaptic activity. cno_0000184 rate-based plasticity model a phenomenological model of long term synaptic plasticity that represent the variation of synaptic impact depending on the firing rate of the models. cno_0000185 spike timing dependent plasticity model a phenomenological model of long term synaptic plasticity that represent the variation of synaptic efficacy depending on the relative spike timing of the pre- and post-synaptic models. cno_0000186 biophysical model a model of long term synaptic plasticity that represents the biophysical mechanisms involved in the changes of synaptic efficacy. cno_0000187 http://en.wikipedia.org/wiki/Homeostatic_plasticity homeostatic plasticity model homeostatic plasticity rule synaptic plasticity model that account for the capacity of neurons to regulate their own excitability relative to network activity. cno_0000188 PMID: 9012851 Markram and Tsodyks model defined model that describes the impact of neurotransmitter release and synaptic depression. cno_0000189 PMID: 10966623 http://www.scholarpedia.org/article/Models_of_synaptic_plasticity#Spike_timing_based_models Song and Abbott model defined model that is a phenomenological model of spike timing dependent plasticity cno_0000190 relates to http://neurolex.org/wiki/Category:Zero_dimensional_region zero dimensional layout cno_0000191 http://www.ebi.ac.uk/sbo/main/SBO:0000254 resistance cno_0000192 time cno_0000194 rate cno_0000195 developmental learning learning rule based on the mechanisms taking place during the development of the nervous system. cno_0000196 http://www.scholarpedia.org/article/Reinforcement_learning reward-based learning reinforcement learning a learning rule that allow to learn by interacting with an environment through a trial and error process during which the reward is maximized. cno_0000197 synaptic plasticity model component a component of plasticity models that describes the rules governing the changes in synaptic efficacy. cno_0000198 pair-based rule timing dependency that modifies the synaptic weight depending on the time difference between pairs of action potentials. cno_0000199 triplet-based rule timing dependency that modifies the synaptic weight depending on the time difference between triplets of action potentials. cno_0000200 reference the model from Froemke and Dan, 2002 described in Morrisson, 2008 suppression model timing dependency that accounts for the suppression of NMDA receptor during spike timing dependent long term depression cno_0000201 short term depression model a model of short term synaptic plasticity that represent the decrease of the synaptic efficacy for a short period of time cno_0000202 model component quality quality exhibited by model components cno_0000203 cellular distribution quality model component quality that describes the distribution of cellular model in abstract space cno_0000205 ModelDB accession number A CRID symbol that is sufficient to look up a model from ModelDB cno_0000206 mixed grouping cellular grouping quality that represents the grouping of cellular model based on two criterions: anatomical and functional cno_0000207 http://www.ebi.ac.uk/sbo/main/SBO:0000225 delay cno_0000208 http://www.ebi.ac.uk/sbo/main/SBO:0000347 duration cno_0000209 obsolete cno_0000210 plasticity model component a model component that is used to build a plasticity model type cno_0000211 timing dependency a component of a synaptic plasticity rule that describes the dependency of synaptic changes on the relative spike timing in the pre- and post-synaptic models cno_0000212 weight update component a component of a synaptic plasticity rule that describes the changes in synaptic weight. cno_0000213 voltage dependency a component of a synaptic plasticity rule that describes the relation between the post-synaptic voltage and the change in synaptic efficacy. cno_0000214 weight independent additive a weight update component that updates the weight with additive increment cno_0000215 http://www.scholarpedia.org/article/Spike-timing_dependent_plasticity#Weight_dependence:_hard_bounds_and_soft_bounds weight dependent weight update component that updates the weight within bounded range by multiplying the changes by constants called soft bounds or multiplicative weight dependence. cno_0000216 learning rate elementary model component that set the amount by which synaptic weight are updated cno_0000217 http://www.scholarpedia.org/article/Conductance-based_models leakage current abstract current model that approximates the passive properties of biological neurons. cno_0000218 aggregated model component a model component that results from the aggregation of parameters and/or variable and/or mathematical operators cno_0000219 http://en.wikipedia.org/wiki/Variable_(mathematics) variable elementary model component role that defines an elementary model component as a value that may change within the scope of a given problem or set of operations. cno_0000220 membrane capacitance Measure of the amount of electric charge stored (or separated) by the cellular membrane for a given electric potential. The unit of capacitance is the Farad. cno_0000221 membrane resistance Measure of the degree to which the cellular membrane opposes the passage of an electric current. The SI unit of electrical resistance is the ohm. cno_0000222 membrane time constante 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 rdf:List core:Collection skos:Collection Collection A meaningful collection of concepts. Labelled collections can be used where you would like a set of concepts to be displayed under a 'node label' in the hierarchy. core:Concept skos:Concept Concept An idea or notion; a unit of thought. core:ConceptScheme skos:ConceptScheme Concept Scheme A set of concepts, optionally including statements about semantic relationships between those concepts. Thesauri, classification schemes, subject heading lists, taxonomies, 'folksonomies', and other types of controlled vocabulary are all examples of concept schemes. Concept schemes are also embedded in glossaries and terminologies. A concept scheme may be defined to include concepts from different sources. skos:OrderedCollection Ordered Collection An ordered collection of concepts, where both the grouping and the ordering are meaningful. Ordered collections can be used where you would like a set of concepts to be displayed in a specific order, and optionally under a 'node label'. version 0.5 Birgit Kriener Erik De Schutter Fahim T. Imam INCF MultiScale Modeling Task Force Lars Schwabe Padraig Gleeson Sean Hill Stephen D. Larson Subhasis Ray Yann Le Franc 13/03/2012 An ontology to describe the field of Computational Neurosciences Computational Neuroscience Ontology This ontology is used to add the Definition class of annotation as in NIF. The source of the definition can be defined with class from OBO-annotation This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. version 0.5 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 Dave Beckett Nikki Rogers Participants in W3C's Semantic Web Deployment Working Group. Alistair Miles Sean Bechhofer An RDF vocabulary for describing the basic structure and content of concept schemes such as thesauri, classification schemes, subject heading lists, taxonomies, 'folksonomies', other types of controlled vocabulary, and also concept schemes embedded in glossaries and terminologies. SKOS Vocabulary notation A notation, also known as classification code, is a string of characters such as "T58.5" or "303.4833" used to uniquely identify a concept within the scope of a given concept scheme. By convention, skos:notation is used with a typed literal in the object position of the triple.