Ontology of Genetic Susceptibility Factor (OGSF) is an application ontology to model/represent the notion of genetic susceptibility to a specific disease or an adverse event or a biological process. BFO 2 Reference: BFO does not claim to provide complete coverage of entities of all types. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning - coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation. BFO 2 Reference: BFO's treatment of continuants and occurrents - as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality - earlier called the 'SNAP' and 'SPAN' perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science. BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. 'Entity' is an example of a primitive term. Primitive terms in a highest-level ontology such as BFO are terms that are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms. 'Oliver' Yongqun He (YH) Alan Ruttenberg Albert Goldfain Barry Smith Bill Duncan Bjoern Peters Chris Mungall David Osumi-Sutherland Fabian Neuhaus Holger Stenzhorn James A. Overton Janna Hastings Jie Zheng Jonathan Bona Larry Hunter Leonard Jacuzzo Ludger Jansen Mark Ressler Mathias Brochhausen Mauricio Almeida Melanie Courtot Pierre Grenon Randall Dipert Ron Rudnicki Selja Seppälä Stefan Schulz Thomas Bittner Werner Ceusters Yongqun "Oliver" He 'Asiyah' Yu Lin (YL) 11-22-2014 New BSD license Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif. The BSD license on the BFO project site refers to code used to build BFO. This BFO 2.0 version represents a major update to BFO and is not strictly backwards compatible with BFO 1.1. The previous OWL version of BFO, version 1.1.1 will remain available at http://ifomis.org/bfo/1.1 and will no longer be updated. The BFO 2.0 OWL is a classes-only specification. The incorporation of core relations has been held over for a later version. 2.0 https://code.google.com/p/ogsf/ Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label 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 label editor preferred term 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 example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status definition definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 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 definition textual 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 editor note definition editor term editor Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people 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> definition_editor definition editor definition editor term editor 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 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 definition source definition source curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note curator note imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from elucidation has associated axiom(nl) has associated axiom(fol) has axiom label FLAG to record classes where we have issues or suggestions to feedback to an external ontology regarding a class imported into the home/current ontology (ie ReO). Most often used to address cases where imported term definitions are felt to be unclear, incomplete, erroneous, or inconsistent. reo_requires_feedback_to ReO alternative term has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym in_subset shorthand part_of is part of part of part_of inheres-in_at inheresInAt b inheres_in c at t =Def. b is a dependent continuant & c is an independent continuant that is not a spatial region & b s-depends_on c at t. (axiom label in BFO2 Reference: [051-002]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'inheres in at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'inheres in@en(x,y,t)'. BFO 2 Reference: Inherence is a subrelation of s-depends_on which holds between a dependent continuant and an independent continuant that is not a spatial region. Since dependent continuants cannot migrate from one independent continuant bearer to another, it follows that if b s-depends_on independent continuant c at some time, then b s-depends_on c at all times at which a exists. Inherence is in this sense redundantly time-indexed.For example, consider the particular instance of openness inhering in my mouth at t as I prepare to take a bite out of a donut, followed by a closedness at t+1 when I bite the donut and start chewing. The openness instance is then shortlived, and to say that it s-depends_on my mouth at all times at which this openness exists, means: at all times during this short life. Every time you make a fist, you make a new (instance of the universal) fist. (Every time your hand has the fist-shaped quality, there is created a new instance of the universal fist-shaped quality.) BFO2 Reference: independent continuant that is not a spatial region BFO2 Reference: specifically dependent continuant (iff (inheresInAt a b t) (and (DependentContinuant a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [051-002] inheres in inheres in at all times bearer-of_st bearerOfAt b bearer_of c at t =Def. c s-depends_on b at t & b is an independent continuant that is not a spatial region. (axiom label in BFO2 Reference: [053-004]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'bearer of at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'bearer of@en'(x,y,t) BFO2 Reference: independent continuant that is not a spatial region BFO2 Reference: specifically dependent continuant (iff (bearerOfAt a b t) (and (specificallyDependsOnAt b a t) (IndependentContinuant a) (not (SpatialRegion a)) (existsAt b t))) // axiom label in BFO2 CLIF: [053-004] bearer of at some time realizes realizes to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) (forall (x y t) (if (realizesAt x y t) (and (Process x) (or (Disposition y) (Role y)) (exists (z) (and (MaterialEntity z) (hasParticipantAt x z t) (bearerOfAt z y t)))))) // axiom label in BFO2 CLIF: [059-003] realizes participates-in_st participatesInAt [copied from inverse property 'has participant at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has participant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has participant@en'(x,y,t) [copied from inverse property 'has participant at some time'] BFO 2 Reference: Spatial regions do not participate in processes. [copied from inverse property 'has participant at some time'] BFO2 Reference: independent continuant that is not a spatial region, specifically dependent continuant, generically dependent continuant [copied from inverse property 'has participant at some time'] BFO2 Reference: process participates_in [copied from inverse property 'has participant at some time'] has_participant is an instance-level relation between a process, a continuant, and a temporal region at which the continuant participates in some way in the process. (axiom label in BFO2 Reference: [086-003]) participates in participates in at some time participates_in concretizes_st concretizesAt You may concretize a piece of software by installing it in your computer You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head. you may concretize a poem as a pattern of memory traces in your head Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t) b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002]) if b g-depends on c at some time t, then there is some d, such that d concretizes b at t and d s-depends_on c at t. (axiom label in BFO2 Reference: [076-001]) (forall (x y t) (if (concretizesAt x y t) (and (SpecificallyDependentContinuant x) (GenericallyDependentContinuant y) (exists (z) (and (IndependentContinuant z) (specificallyDependsOnAt x z t) (genericallyDependsOnAt y z t)))))) // axiom label in BFO2 CLIF: [075-002] (forall (x y t) (if (genericallyDependsOnAt x y t) (exists (z) (and (concretizesAt z x t) (specificallyDependsOnAt z y t))))) // axiom label in BFO2 CLIF: [076-001] concretizes concretizes at some time preceded by An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes precedes s-depends-on_at specificallyDependsOn A pain s-depends_on the organism that is experiencing the pain a gait s-depends_on the walking object. (All at some specific time.) a shape s-depends_on the shaped object one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs reciprocal s-dependence between occurrents: a process of buying and the associated process of selling reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball the one-sided dependence of an occurrent on an independent continuant: handwave on a hand the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45 the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45 the two-sided reciprocal s-dependence of the roles of husband and wife [20 Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'specifically depends on at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'specifically depends on@en(x,y,t)'. BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28 BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20 BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place. BFO2 Reference: specifically dependent continuant\; process; process boundary To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64 If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001]) If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001]) If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002]) an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002]) if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002]) (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002] (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002] (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001] (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002] (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] specifically depends on at all times has-f_st hasFunctionAt a has_function b at t =Def. b function_of a at t. (axiom label in BFO2 Reference: [070-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has function at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has function@en'(x,y,t) (iff (hasFunctionAt a b t) (functionOf b a t)) // axiom label in BFO2 CLIF: [070-001] has function at some time o-has-part hasOccurrentPart [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life [copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match. b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent [copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] has occurrent part o-has-ppart hasProperOccurrentPart [copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001]) b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001 has proper occurrent part has-t-part [copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life [copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life. [copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating [copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) [copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003]) has temporal part r-location-of_st [copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t) [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region [copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) has spatial occupant at some time has-s-dep_st [copied from inverse property 'specifically depends on at some time'] A pain s-depends_on the organism that is experiencing the pain [copied from inverse property 'specifically depends on at some time'] a gait s-depends_on the walking object. (All at some specific time.) [copied from inverse property 'specifically depends on at some time'] a shape s-depends_on the shaped object [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of buying and the associated process of selling [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces [copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball [copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: handwave on a hand [copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45 [copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45 [copied from inverse property 'specifically depends on at some time'] the two-sided reciprocal s-dependence of the roles of husband and wife [20 [copied from inverse property 'specifically depends on at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t) [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28 [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20 [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place. [copied from inverse property 'specifically depends on at some time'] BFO2 Reference: specifically dependent continuant\; process; process boundary [copied from inverse property 'specifically depends on at some time'] To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64 has specific dependent at some time occupied-by [copied from inverse property 'occupies spatiotemporal region'] BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region. [copied from inverse property 'occupies spatiotemporal region'] p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003]) has spatiotemporal occupant occupies occupiesSpatiotemporalRegion BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region. p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003]) occupies spatiotemporal region o-part-of occurrentPartOf Mary’s 5th birthday occurrent_part_of Mary’s life The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. the first set of the tennis match occurrent_part_of the tennis match. [copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. BFO2 Reference: occurrent b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001]) occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002]) occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001]) occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001]) occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001]) (forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001] (forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001] (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001] (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] part of occurrent t-part-of temporalPartOf the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life the process boundary which separates the 3rd and 4th years of your life. your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003]) if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002]) (forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002] (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001] (iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003] temporal part of s-projection-of-st_st spatial projection of spatiotemporal at some time t-projection-of-st temporal projection of spatiotemporal spans occupiesTemporalRegion p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) occupies temporal region span-of spanOf [copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) has temporal occupant during-which-exists [copied from inverse property 'exists at'] BFO2 Reference: entity [copied from inverse property 'exists at'] BFO2 Reference: temporal region [copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002]) during which exists c-part-of_st continuantPartOfAt Mary’s arm continuant_part_of Mary in the time of her life prior to her operation the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. [copied from inverse property 'has continuant part at some time'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t) BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. BFO2 Reference: continuant BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. [copied from inverse property 'has continuant part at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t) b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001]) continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002]) continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001]) continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001]) continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001]) if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002]) (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] (forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] part of continuant at some time c-part-of_at continuantPartOfAt Mary’s arm continuant_part_of Mary in the time of her life prior to her operation the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. [copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'. BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. BFO2 Reference: continuant BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. [copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times' b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001]) continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002]) continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001]) continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001]) continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001]) if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002]) (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] (forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] part of continuant at all times c-has-part_st hasContinuantPartAt [copied from inverse property 'part of continuant at some time'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation [copied from inverse property 'part of continuant at some time'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t) [copied from inverse property 'part of continuant at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t) [copied from inverse property 'part of continuant at some time'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) [copied from inverse property 'part of continuant at some time'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. [copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuant [copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. [copied from inverse property 'part of continuant at some time'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) (iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001] has continuant part at some time c-has-part-object_at [copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation [copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t) This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times' [copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'. [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. [copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) has continuant part at all times that part exists has_phase is_manufactured_by http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. Alan Ruttenberg Liju Fan has_make has_manufacturer is_manufactured_by <= Primitive instance level timing relation between events before_or_simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous_with t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) before Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during_which_ends di Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. encompasses X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends_after starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately_preceded_by Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during_which_starts starts_before ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately_precedes io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts_during d during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens_during o overlaps X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends_during x has participant y if and only if x realizes some active role that inheres in y has agent has active participant Allen A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to inverse of starts with Chris Mungall Allen starts Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. started by starts with inverse of ends with ends x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. finished by ends with bearer_of A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in http://purl.org/obo/owl/ro_proposed bearer_of inheres_in_part_of http://purl.org/obo/owl/ro_proposed inheres_in_part_of role_of A relation between a role R and an entity E. R role_of E iff: R inheres_in E and R is a role http://purl.org/obo/owl/ro_proposed role_of has_part member_of isAdjacentAfter(X,Y) : genetic interval X is adjacent the end part of genetic interval Y If genetic interval X is adjacent to the end part of genetic interval Y, then the start of X is after the start of Y and the end of X is after the end of Y, and the end of X is the same as the start of Y. isAdjacentAfter(X,Y) ↔ (hasStartPoint(x1,X) & hasStartPoint(y1,Y) & isLocatedAfter(x1,y1)) & (hasEndPoint(x2,X) & hasEndPoint(y2,Y) & isLocatedAfter(x2,y2)) & ((pointInterval(x2,X) == pointInterval(y1,X)) isAdjacentBefore(X,Y) : genetic interval X is adjacent to the start of genetic interval Y If genetic interval X is adjacent to the start of genetic interval Y, then the start of X is before the start of Y and the end of X is before the end of Y, and the end of X is identical with the start of Y. isAdjacentBefore(X,Y) ↔ (hasStartPoint(x1,X) & hasStartPoint(y1,Y) & isLocatedBefore(x1,y1)) & (hasEndPoint(x2,X) & hasEndPoint(y2,Y) & isLocatedBefore(x2,y2)) & ((pointInterval(x2,X) == pointInterval(y1,X)) isEndsWith(X,Y) : genetic interval X ends with genetic interval Y If genetic interval X ends with genetic interval Y, then the end of X and the end of Y are identical and the start of X is after the start of Y. isEndsWith(X,Y) ↔ ((hasEndPoint(x1,X) & hasEndPoint(x1,Y)) & (hasStartPoint(x2,X) & hasStartPoint(y,Y) & isLocatedAfter(x2,y)) isLocatedAfter(X,Y) : genetic interval X is located after genetic interval Y If genetic interval X is located after genetic interval Y, then the start of X is after the end of Y; or the end of Y is before the start of X. If isLocatedBefore(X,Y), then isLocatedAfter(Y,X) isLocatedAfter(X,Y) ↔ (hasStartPoint(x1,X) & hasEndPoint(y1,Y) & isLocatedAfter(x1,y1)) OR (hasEndPoint(x2,X) &. hasStartPoint(y2,Y) & isLocatedBefore(y2,x2)) isLocatedAfter(X,Y) == isLocatedBefore(Y,X) isLocatedBefore is both a Class-Class and an Instance-Instance relation. isLocatedBefore(X,Y): genetic interval X is located before genetic interval Y If genetic interval X is located before genetic interval Y, then the end of X is before the start of Y. isLocatedBefore(X,Y) ↔ hasEndPoint(x,X) & hasStartPoint(y,Y) & isLocatedBefore(x,y) is substituent group from hasSize hasOddsRatio hasPvalue BFO:0000001 entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) BFO:0000002 continuant Continuant continuant a heart a person a symphony orchestra the color of a tomato the disposition of blood to coagulate the lawn and atmosphere in front of our building the mass of a cloud An 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. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants endurant A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] BFO:0000003 occurrent Occurrent BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] BFO:0000004 ic IndependentContinuant independent continuant a chair a heart a leg a molecule a person a spatial region a symphony orchestra an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth the lawn and atmosphere in front of our building A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) substantial entity For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] true true BFO:0000006 s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] true true BFO:0000008 t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] BFO:0000009 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] true true BFO:0000011 st-region SpatiotemporalRegion the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] BFO:0000015 process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] BFO:0000016 disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocitosis and exocitosis the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type [89 BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] BFO:0000017 realizable RealizableEntity realizable entity the disposition of blood to coagulate the disposition of metal to conduct electricity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of the reproductive organs the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in 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. If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] BFO:0000018 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] BFO:0000019 quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] BFO:0000020 sdc SpecificallyDependentContinuant specifically dependent continuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the color of a tomato the disposition of fish to decay the disposition of this fish to decay the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc. the function of this heart: to pump blood the liquidity of blood the mass of a cloud the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of mozzarella the smell of this portion of mozzarella A 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. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. mode property trope (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] BFO:0000023 role Role role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a biological grandfather as legal guardian in the context of a system of laws the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target 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 person as a surgeon the role of a stone in marking a property boundary the role of a student in a university the role of a woman as a legal mother in the context of system of laws the role of ingested matter in digestion the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] BFO:0000024 fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] BFO:0000026 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] BFO:0000027 object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] BFO:0000028 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] BFO:0000029 site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] BFO:0000030 object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) BFO:0000031 gdc GenericallyDependentContinuant generically dependent continuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. a certain PDF file that exists in different and in several hard drives the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] BFO:0000034 function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] BFO:0000035 p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] BFO:0000038 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] BFO:0000040 material MaterialEntity material entity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. Examples: collection of random bacteria, a chair, dorsal surface of the body 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. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] BFO:0000140 cf-boundary ContinuantFiatBoundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] BFO:0000141 immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity BFO:0000142 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] BFO:0000144 process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] BFO:0000145 r-quality RelationalQuality John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. a marriage bond, an instance of requited love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] BFO:0000146 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] BFO:0000147 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] BFO:0000148 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] BFO:0000182 history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) The simplest aldehyde. CHEBI:14274 CHEBI:24077 CHEBI:337763 CHEBI:5142 Beilstein:1209228 ChEMBL:7381846 ChemIDplus:50-00-0 CiteXplore:18837732 Gmelin:445 KEGG COMPOUND:50-00-0 KEGG COMPOUND:C00067 NIST Chemistry WebBook:50-00-0 PDBeChem:FLH UM-BBD:c0122 Wikipedia:Formaldehyde FORMALDEHYDE Formaldehyde formaldehyde CH2O FORMALIN Formaldehyd Formalin InChI=1S/CH2O/c1-2/h1H2 InChIKey=WSFSSNUMVMOOMR-UHFFFAOYSA-N Methanal Methylene oxide Oxomethane Oxomethylene [H]C([H])=O CHEBI:16842 formaldehyde CHEBI:16842 Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity CHEBI:23367 A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. CHEBI:24431 chemical entity CHEBI:24431 When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue. amino-acid residue chebi_ontology amino acid residue amino-acid residues CHEBI:33708 amino-acid residue CHEBI:33708 chebi_ontology nucleotide residues CHEBI:50319 nucleotide residue CHEBI:50319 An organomercury compound (approximately 49% mercury by weight) used as an antiseptic and antifungal agent. Beilstein:8169555 ChemIDplus:54-64-8 CiteXplore:18837732 CiteXplore:21616561 Gmelin:1677155 KEGG COMPOUND:C08044 Thimerosal sodium [(2-carboxylatophenyl)sulfanyl](ethyl)mercurate(1-) sodium ethyl[2-(sulfanyl-kappaS)benzoato(2-)]mercurate(1-) C9H9HgNaO2S C9H9HgO2S.Na InChI=1S/C7H6O2S.C2H5.Hg.Na/c8-7(9)5-3-1-2-4-6(5)10;1-2;;/h1-4,10H,(H,8,9);1H2,2H3;;/q;;2*+1/p-2 InChIKey=RTKIYNMVFMVABJ-UHFFFAOYSA-L Merthiolate Thiomersal [(o-carboxyphenyl)thio]ethylmercury sodium salt [Na+].CC[Hg]Sc1ccccc1C([O-])=O ethyl(2-mercaptobenzoato-S)mercury sodium salt ethylmercurithiosalicylate sodium mercurothiolate o-(ethylmercurithio)benzoic acid sodium salt sodium ethylmercurithiosalicylate thiomersalate CHEBI:9546 thimerosal CHEBI:9546 ERO:0000016 A clinical trial to evaluate the efficacy of a new drug. An interventional study that contains a set of procedures in medical research and drug development that are conducted to allow safety (or more specifically, information about adverse drug reactions and adverse effects of other treatments) and efficacy data to be collected for health interventions (e.g., drugs, diagnostics, devices, therapy protocols) that is performed over phases. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Clinical_trial clinical trial ERO:0000019 genome wide association study A genome wide association study is an examination of genetic variation across a given genome, designed to identify genetic associations with observable traits. PERSON: Karen Corday GWAS http://en.wikipedia.org/wiki/Genome-wide_association_study genome wide association study ERO:0000348 case-only study Observational study whereby there is a single group of individuals with specific characteristics. This is a method that analyzes data from a case series and is used in case-crossover studies, in case-specular designs, and in molecular and genetic epidemiology to assess relationships between environmental exposures and genotypes. PERSON: Melissa Haendel A Dictionary of Epidemiology, Fifth Edition, Edited by Miquel Porta. p. 33. ISBN:978-0-19-531449-6 http://prsinfo.clinicaltrials.gov/definitions.html case-only study The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. GO:0008372 NIF_Subcellular:sao1337158144 cellular component cellular component unknown cellular_component GO:0005575 Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. cellular_component GO:0005575 A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus cellular_component GO:0005634 nucleus GO:0005634 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. Wikipedia:Chromosome interphase chromosome prophase chromosome cellular_component chromatid GO:0005694 chromosome GO:0005694 A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. NIF_Subcellular:sao1860313010 Wikipedia:Mitochondrion mitochondria cellular_component GO:0005739 mitochondrion GO:0005739 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. GO:0055133 Reactome:REACT_100559 Reactome:REACT_101280 Reactome:REACT_101497 Reactome:REACT_102679 Reactome:REACT_103614 Reactome:REACT_104547 Reactome:REACT_105292 Reactome:REACT_105467 Reactome:REACT_105835 Reactome:REACT_106018 Reactome:REACT_106104 Reactome:REACT_106382 Reactome:REACT_106434 Reactome:REACT_106732 Reactome:REACT_107075 Reactome:REACT_107423 Reactome:REACT_108461 Reactome:REACT_108634 Reactome:REACT_108739 Reactome:REACT_108768 Reactome:REACT_108929 Reactome:REACT_109137 Reactome:REACT_112472 Reactome:REACT_113703 Reactome:REACT_29423 Reactome:REACT_29444 Reactome:REACT_29691 Reactome:REACT_29764 Reactome:REACT_30149 Reactome:REACT_31024 Reactome:REACT_31919 Reactome:REACT_32546 Reactome:REACT_32932 Reactome:REACT_33572 Reactome:REACT_33874 Reactome:REACT_50018 Reactome:REACT_53588 Reactome:REACT_6729 Reactome:REACT_6738 Reactome:REACT_6750 Reactome:REACT_6769 Reactome:REACT_6798 Reactome:REACT_6869 Reactome:REACT_6936 Reactome:REACT_6939 Reactome:REACT_77532 Reactome:REACT_79188 Reactome:REACT_79450 Reactome:REACT_80432 Reactome:REACT_80571 Reactome:REACT_80896 Reactome:REACT_80988 Reactome:REACT_81803 Reactome:REACT_83095 Reactome:REACT_84829 Reactome:REACT_85561 Reactome:REACT_86410 Reactome:REACT_86739 Reactome:REACT_87233 Reactome:REACT_87449 Reactome:REACT_87590 Reactome:REACT_88085 Reactome:REACT_88384 Reactome:REACT_88529 Reactome:REACT_89355 Reactome:REACT_89439 Reactome:REACT_89725 Reactome:REACT_90512 Reactome:REACT_90809 Reactome:REACT_90838 Reactome:REACT_91184 Reactome:REACT_91302 Reactome:REACT_92527 Reactome:REACT_92644 Reactome:REACT_92706 Reactome:REACT_94983 Reactome:REACT_95253 Reactome:REACT_95329 Reactome:REACT_96115 Reactome:REACT_96804 Reactome:REACT_96998 Reactome:REACT_97204 Reactome:REACT_97726 Reactome:REACT_99948 Wikipedia:DNA_replication biological_process GO:0006260 See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'. DNA replication GO:0006260 The cellular synthesis of RNA on a template of DNA. GO:0006350 GO:0061018 GO:0061022 cellular transcription transcription Wikipedia:Transcription_(genetics) DNA-dependent transcription cellular transcription, DNA-dependent biological_process transcription regulator activity GO:0006351 transcription, DNA-dependent GO:0006351 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. GO:0006416 GO:0006453 GO:0043037 Reactome:REACT_100338 Reactome:REACT_100851 Reactome:REACT_101045 Reactome:REACT_101324 Reactome:REACT_1014 Reactome:REACT_103420 Reactome:REACT_105544 Reactome:REACT_29980 Reactome:REACT_33559 Reactome:REACT_77710 Reactome:REACT_79784 Reactome:REACT_81734 Reactome:REACT_81833 Reactome:REACT_82171 Reactome:REACT_83429 Reactome:REACT_83530 Reactome:REACT_86996 Reactome:REACT_95535 Reactome:REACT_96394 Wikipedia:Translation_(genetics) protein anabolism protein biosynthesis protein biosynthetic process protein formation protein synthesis protein translation biological_process GO:0006412 translation GO:0006412 Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. GO:0000004 GO:0007582 Wikipedia:Biological_process biological process physiological process biological process unknown biological_process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. biological_process GO:0008150 The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. Reactome:REACT_100537 Reactome:REACT_101147 Reactome:REACT_101952 Reactome:REACT_105649 Reactome:REACT_108313 Reactome:REACT_29068 Reactome:REACT_34240 Reactome:REACT_71 Reactome:REACT_78136 Reactome:REACT_78959 Reactome:REACT_79662 Reactome:REACT_85241 Reactome:REACT_85359 Reactome:REACT_86357 Reactome:REACT_89816 Reactome:REACT_91657 Reactome:REACT_91965 Reactome:REACT_93586 Reactome:REACT_93968 Reactome:REACT_94814 Reactome:REACT_98256 Wikipedia:Gene_expression biological_process GO:0010467 gene expression GO:0010467 Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. NIF_Subcellular:sao1539965131 Wikipedia:Organelle cellular_component GO:0043226 organelle GO:0043226 IAO:0000005 objective specification purpose of a study; support of hypothesis, discovery of new information a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification IAO:0000027 data item Data items include counts of things, analyte concentrations, and statistical summaries. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item 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 IAO:0000033 An information content entity whose concretizations indicate to their bearer how to realize them in a process. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity IAO:0000078 curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification IAO:0000102 data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part IAO:0000144 conclusion textual entity that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/23 Alan Ruttenberg: We need to work on the definition still Person:Alan Ruttenberg conclusion textual entity IAO:0000300 textual entity Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. PERSON: Lawrence Hunter text textual entity IAO:0000310 document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document IAO:0000311 publication A journal article or book A document that has been accepted by a publisher PERSON: Lawrence Hunter publication IAO:0000312 publication about an investigation Most scientific journal articles A publication that is about an investigation PERSON: Lawrence Hunter scientific publication publication about an investigation IAO:0000442 author role A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. PERSON: Alan Ruttenberg PERSON: Melanie Courtot author role NCBITaxon:10239 Viruses Viruses NCBITaxon:10241 Chordopoxvirinae Chordopoxvirinae NCBITaxon:10255 Variola virus Variola virus NCBITaxon:11308 Orthomyxoviridae Orthomyxoviridae NCBITaxon:11309 unidentified influenza virus unidentified influenza virus NCBITaxon:11320 Influenza A virus Influenza A virus NCBITaxon:114727 H1N1 subtype H1N1 subtype NCBITaxon:117571 Euteleostomi Euteleostomi NCBITaxon:197911 Influenzavirus A Influenzavirus A NCBITaxon:197912 Influenzavirus B Influenzavirus B NCBITaxon:197913 Influenzavirus C Influenzavirus C NCBITaxon:2759 Eukaryota Eukaryota NCBITaxon:314146 Euarchontoglires Euarchontoglires NCBITaxon:314293 Simiiformes Simiiformes NCBITaxon:32524 Amniota Amniota NCBITaxon:33154 Opisthokonta Opisthokonta NCBITaxon:33213 Bilateria Bilateria NCBITaxon:35237 dsDNA viruses, no RNA stage dsDNA viruses, no RNA stage NCBITaxon:35301 ssRNA negative-strand viruses ssRNA negative-strand viruses NCBITaxon:35324 unclassified Orthomyxoviridae unclassified Orthomyxoviridae NCBITaxon:40674 Mammalia Mammalia NCBITaxon:439488 ssRNA viruses ssRNA viruses NCBITaxon:89593 Craniata Craniata NCBITaxon:9347 Eutheria Eutheria NCBITaxon:9606 Homo sapiens Homo sapiens OAE:0000001 a pathological bodily process that occurs after a medical intervention. Mélanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'. YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device. YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention. YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events. YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'. YH AE adverse reaction WEB: http://en.wikipedia.org/wiki/Adverse_event WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm The OAE official website is: http://www.oae-ontology.org/. adverse event OAE:0000004 an adverse event that is induced by vaccination. YH vaccine adverse event OAE:0000053 a respiratory system AE which has an outcome of wheezing SS, YH wheezing AE MedDRA ID: 10047924 OAE:0000063 an adverse event that occurs systematically in a patient's body. YH systematic adverse event OAE:0000361 an abnormal body temperature AE which has an outcome of fever YH, SS body temperature increased AE febrile response pyrexia AE WEB: http://en.wikipedia.org/wiki/Pyrexia Fever is a frequent medical sign that describes an increase in internal body temperature to levels above normal. Fever is characterized as a temporary elevation in the body's thermoregulatory set-point, usually by about 1-2 °F). fever AE MedDRA: 10005911 MedDRA: 10037660 OAE:0000429 a nervous system AE that has the symptom of GBS. Guillain-Barre syndrome (GBS) is a disorder in which the body's immune system attacks part of the peripheral nervous system. The first symptoms of this disorder include varying degrees of weakness or tingling sensations in the legs. In many instances, the weakness and abnormal sensations spread to the arms and upper body. These symptoms can increase in intensity until the muscles cannot be used at all and the patient is almost totally paralyzed. In these cases, the disorder is life-threatening and is considered a medical emergency. Usually Guillain-Barre occurs a few days or weeks after the patient has had symptoms of a respiratory or gastrointestinal viral infection. Occasionally, surgery or vaccinations will trigger the syndrome. Reference: http://www.ninds.nih.gov/disorders/gbs/gbs.htm. YH, SS GBS AE WEB: http://www.ncbi.nlm.nih.gov/pubmed/23299621 Guillain-Barre syndrome AE MedDRA ID: 10018767 MedDRA: 10018767 OAE:0000481 multiple sclerosis AE is an immune system disorder AE, or an autoimmune condition in which the immune system attacks the central nervous system, leading to demyelination. YH MS disseminated sclerosis encephalomyelitis disseminata multiple sclerosis AE MedDRA ID: 10028245 OBI:0000011 planned process Injecting mice with a vaccine in order to test its efficacy A processual entity that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process OBI:0000016 regulation-assigned role Approval letter Regulation-assigned role is a regulatory role defined by legislation or governmental orders Person: Jennifer Fostel regulation-assigned role OBI:0000017 regulatory role Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008 a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. GROUP: Role branch OBI, CDISC govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent regulatory role OBI:0000047 processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material OBI:0000066 investigation Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived Could add specific objective specification investigation OBI:0000097 study subject role study subject role inheres in an entity and realized through the execution of a study design in which the entity participates by being that which the results are about. GROUP: Role Branch OBI study subject role OBI:0000174 study group role The group of randomized participants that are assigned to a treatment arm of the trial a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol Jennifer Fostel study group population study group role OBI:0000175 p-value A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. May be outside the scope of OBI long term, is needed so is retained PERSON:Chris Stoeckert WEB: http://en.wikipedia.org/wiki/P-value p-value OBI:0000181 population PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area PERSON: Philippe Rocca-Serra adapted from Oxford English Dictionnary rem1: collection somehow always involve a selection process population OBI:0000245 organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization OBI:0000319 material to be added role drug added to a buffer contained in a tube; substance injected into an animal; material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process Role Branch OBI 9 March 09 from discussion with PA branch material to be added role OBI:0000444 target of material addition role peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application. target of material addition role is a role realized by an entity into which a material is added in a material addition process From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role. GROUP: Role Branch OBI target of material addition role OBI:0000725 host role In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09 host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition GROUP: Role Branch 30 Mar09 submitted by vaccine community OBI http://en.wikipedia.org/wiki/Host_(biology) host role OBI:0000811 primary structure of DNA macromolecule a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. placeholder for SO BP et al primary structure of DNA macromolecule OBI:0000845 primary structure of RNA molecule The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together Person:Bjoern Peters primary structure of RNA molecule OBI:0000885 secondary structure of sequence macromolecule 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO Person: Philippe Rocca-Serra Wikipedia secondary structure of sequence macromolecule OBI:0000896 secondary structure of RNA molecule PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA. 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO Person: Philippe Rocca-Serra secondary structure of RNA molecule OBI:0001225 genetic population background information genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information a genetic characteristics information which is a part of genotype information that identifies the population of organisms proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genetic population background information OBI:0001294 wild type organism genotype information C57BL/6J wild type a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms. proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group wild type organism genotype information OBI:0001305 genotype information Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc. discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genotype information OBI:0001352 allele information genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition. discussed on San Diego OBI workshop, March 2011 Person: Chris Stoeckert, Jie Zheng MO_58 Allele allele information OBI:0001364 genetic alteration information a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc. proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genetic alteration information OBI:0001369 wild type allele information an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism. discussed on San Diego OBI workshop, March 2011 Person: Chris Stoeckert, Jie Zheng MO_605 genotype wild type allele information OBI:0001404 genetic characteristics information a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes. Person: Chris Stoeckert, Jie Zheng MO_66 IndividualGeneticCharacteristics genetic characteristics information OBI:0100026 organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism OBI:0200000 data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A data transformation is a process which produces output data from input data Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors data transformation OBI:0600007 administering substance in vivo Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally A process by which a substance is intentionally given to an organism 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178 Different routes and means of administration should go as children underneath this needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor. Bjoern Peters Person:Bjoern Peters IEDB administering substance in vivo OGI.owl:0000014 three dimention structure of biological interval 1 1 OGI:0000001 the spatial continuous physical entity which contains ordered biological sets (DNA segments, Genetic Markers, Nucleic Acid Base Residues, RNA segments, Protein segments) between two boundaries: start boundary and end boundary on a chromosome, RNA or protein. biological material interval OGI:0000002 the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points(Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture. genetic material interval genomic material interval Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology) It is genomic, so that protein is not the child of this class. it is continuous, so that neither genome(colletive of chormosomes), nor genotype diploid(collective alleles comes from different chromosomes), nor gene family(collective of genes of same homolog located to different chromosomes) are genomic interval. Whereas gene cluster which are juxtapositioned genes can be subclass of genomic interval. By length, the longest Genomic Interval is the interval with same start point and end point with chromosome, and smallest is when one start point and end point are equal( one residue of DNA or RNA). Interval holds property interval relation. genetic interval OGI:0000003 DNA interval OGI:0000004 a genertically dependent continuant that correspond to one or more DNA sequences that carry the coding information required to produce a specific protein, and that protein in turn carries out a particular function within te cell. Miko, I. & LeJeune, L., eds. Essentials of Genetics. Cambridge, MA: NPG Education, 2009 in RNA virus, there will be RNA interval codes for protein. gene OGI:0000005 RNA interval OGI:0000006 naturally material segment of DNA molecule located in a chromosome DNA segment OGI:0000007 a sepcific gene sequence stored in a EntrezGene database the textual sequencial sets of 'A,T,C,G' or 'A,U,C,G' represent the primary structure of a genetic interval. The textual sequence refects the order of the nucleotide residue within a gene or a choromsome or any genetic interval. The chromosome includes not only the nucelotide residues interwined into DNA helix but also proteins such as Histone, so we make a distinction that the textual sequence of genetic interval only reflects the primary structure of a genetic interval. textual sequence of genetic interval OGI:0000008 Mutually exclusive alternative forms of the same genetic interval occupying the same locus on homologous chromosomes, differing in DNA sequence and governing the same biochemical and developmental process. http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C16277 One of two or more DNA sequences occurring at a particular gene locus. Typically one allele (normal DNA sequence) is common, and other alleles (mutations) are rare. allele OGI:0000009 genetic interval base residue OGI:0000010 The biological material interval that is a protein, which is made of amino acid chain. protein interval OGI:0000011 biological interval structure OGI:0000012 Genetic variationis a variation in alleles of genes, occurs both within and among populations. http://en.wikipedia.org/wiki/Genetic_variation The genetic variation is the differences of the genetic intervals, such as DNA gene or RNA gene, that occupies the same location along the chromosome within or among a population. The genetic variation is counted at the population level, at the individual level, only the maxim two different forms of the sequencial sets of nucleotide exists, which is called allele. We assert it as quality because it must be beared by an independent entity, such as a genetic interval. needs to align with SO: seuqeunce variant (SO_0001060) genetic variation OGI:0000013 primary structure of biological interval OGI:0000014 the liner sequence of simple repeating units composes DNA molecule, RNA molecule or Protein. biological sequence OGI:0000015 two dimention structure of biological interval OGI:0000016 circular OGI:0000017 linear OGI:0000018 genetic marker role OGI:0000019 genetic interval aggregate OGI:0000020 genomic site OGI:0000021 location on map OGI:0000022 a unique chromosomal location defining the position of an individual gene or DNA sequence. locus OGI:0000023 gene locus OGI:0000024 linked loci OGI:0000025 amino acid sequence OGI:0000026 a genomic site that is occupied by alleles of polymorphism this seems similar with SO's sequence feature. polymorphic site OGI:0000027 any unique piece of DNA for which a specific PCR assay has been designed, so that any DNA sample can be easily tested for its presence or absense. STS sequence tagged site OGI:0000028 location on cytogenetic map OGI:0000029 ensembl cytogenetic band OGI:0000030 entrez gene cytogenetic band OGI:0000031 HGNC cytogenetic band OGI:0000032 location on genetic physical map OGI:0000033 allele of SNP that designated by smaller allele frequency in a population than a more common allele's frequency. alternative allele of SNP OGI:0000034 location on linkage map OGI:0000035 allele that is a set of alternative forms of the same gene occupying the same gene locus. allele of gene OGI:0000036 allele of phenotype OGI:0000037 allele that is set of alternative form of the polymorphic region that occupy the same locus on chromosomes. allele of polymorphism OGI:0000038 allele shared by sibs OGI:0000039 CDS OGI:0000040 chromosome part OGI:0000041 exon OGI:0000042 gene regulatory element 2 OGI:0000043 haplotype OGI:0000044 The DNA segment between genes. intergenic region OGI:0000045 intron OGI:0000046 LD block need a definition. Also consider the place for 'linkage disequilibrium' linkage disequilibrium block OGI:0000047 definition and term 'linkage' linkage interval OGI:0000048 mutant OGI:0000049 part of exon OGI:0000050 part of intron OGI:0000051 A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites. http://en.wikipedia.org/wiki/Genetic_marker genetic marker sounds as a role genetic marker OGI:0000052 DNA marker OGI:0000053 protein marker OGI:0000054 polymorphic DNA marker OGI:0000055 STS marker OGI:0000056 microsatellite marker OGI:0000057 non STS microsatellite marker OGI:0000058 STS microsatellite marker OGI:0000059 SNP marker OGI:0000060 allel of repeat sequnce polymorphism OGI:0000061 allele of copy number polymorphism OGI:0000062 The two alternative forms of SNP that occupying the same SNP site on the chromosome. allele of SNP OGI:0000063 allele of microsatellite OGI:0000064 a fragment of DNA of variable length (usually 100-1000 bases long), which is used to detect in DNA or RNA samples the presence of nucleotide sequences (the DNA target) that are complementary to the sequence in the probe. probe OGI:0000065 genetic marker probe OGI:0000066 RNA segment OGI:0000067 adenine residue OGI:0000068 cytosine residue OGI:0000069 guanine residue OGI:0000070 thymine residue OGI:0000071 nucleotide sequence OGI:0000072 RNA sequence OGI:0000073 DNA sequence OGI:0000074 "A map represents order and distance among markers along a chromosome."(GDB description of its object Map) we can think genetic map as a marker sequence modeling same with DNA seuqence. genetics map OGI:0000075 A map based on the co-occurrence of markers in a panel of radiation hybrid cell lines, resulting in an ordering of markers along a chromosome backbone. RH map http://binfo.ym.edu.tw/binfo/lectures/jou1/tsld008.htm radiation hybrid map OGI:0000076 A map based upon frequency of recombination between genomic segments, resulting in the ordering of markers along a chromosome backbone, usually measured in centiMorgans (cM). linkage map OGI:0000077 An ordered set of genomic DNA clones demarcated with restriction endonuclease recognition or sequence tagged sites. The distance between sites is mesured in base pair. genetic physical map OGI:0000078 a map of a chromosome based on its banding pattern. cytogenetic map OGI:0000079 High resolution physical maps indicating nucleotide-level features of the genome such as exons, introns, regulatory regions, etc. sequence feature map OGI:0000080 contig OGI:0000081 gene family OGI:0000082 collective of allele which comes from different homologus chromosomes respecitvely. genotype diploid genotype OGI:0000083 genome that is located in mitochondria. mitochondiral genome OGI:0000084 set of 24 different chromosomal DNA molecules located in nucleus nuclear genome OGI:0000085 a genetic interval that bears the SNP quality and has only one nucleotide residue single nucleotide polymorphism interval SNP interval OGI:0000086 A chromosome anomaly, abnormality or aberration reflects an atypical number of chromosomes or a structural abnormality in one or more chromosomes. http://en.wikipedia.org/wiki/Chromosome_abnormality chromosome abnormality OGI:0000087 genomic aberration OGI:0000088 In genetics, a mutation is a change of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element. http://en.wikipedia.org/wiki/Mutation Mutation may align to SO: sequence alternation And it may be a process that leads to the existence of genetic polymorphism mutation OGI:0000089 strictly, the existense of two or more variants(alleles, phenotypes, sequence variants, chromosomal structural variants) at significant frequencies (i.e. more than 1%) in the population. Looser usages among molecular genetics include (1) any sequence variant present at a frequency >1% in a population (2) any non-pathogenic sequence variant, regardless of frequency. genetic polymorohism OGI:0000090 SNP OGI:0000091 copy number polymorphism OGI:0000092 deletion polymorphism OGI:0000093 insertion polymorphism OGI:0000094 repeat sequence polymorphism OGI:0000095 RFLPs restriction fragment length polymorphism OGI:0000096 SSCP single-strand conformatinal polymorphism OGI:0000097 microsatellite polymorphism OGI:0000098 VNTR minisatellite polymorphism OGI:0000099 satellite polymorphism OGI:0000100 point mutation OGI:0000101 segmental Mutation OGI:0000102 interactive gene group OGI:0000103 is equal to anscestor allele in dbSNP. allele of HLA gene ancestrol allele of SNP OGI:0000104 is the ratio of chromosomes in the population carrying the less common variant to those with the more common variant. minor allele frequency OGI:1000001 biomolecule boundary is the surface of a biomolecule ,which is a lower dimensional part of a molecule. biomolecule bounday can separate a biological molecule from the rest of the existing entities in the world.(for example, DNA molecule is separate from rest part in the cell nucleus by DNA molecule boundary) different with DNA segment, which is part of DNA molecule, and is surrounding by other DNA segment. biomolecule boundary OGI:1000002 The starts and ends of biological interval, which associate to a location on a genetic or physical map. boundary point of interval OGI:1000003 end point of interval OGI:1000004 start point of interval OGMS:0000033 A predisposition to disease of type X whose physical basis is a constitutional abnormality in an organism's genome. This abnormality is the physical basis for the increased risk of acquiring the disease X. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:23:07Z The incorrect usage of 'constitutional abnormalty' was discussed through OGMS-discussion group. A suggestion is to replace 'abnormality' with 'variant'. See: https://groups.google.com/forum/?fromgroups=#!topic/ogms-discuss/7SYug0AWAcE (commented by YL, Feb.13 2013) genetic predisposition to disease of type X OGMS:0000061 A bodily process that is clinically abnormal. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:54:29Z pathological bodily process OGSF:0000000 a disposition that is physically based on some genetic material, such as one or more gene mutations or variant, such that if the genome of an organism has the genetic material as its part, the organism may have an increased likelihood or chance to develop: 1) a particular disease; 2) a peculiar biological/bodily process. genetic predisposition YL,YH genetic susceptibility OGSF:0000001 a genetic susceptibility that lead to the increased possibilities to initiate a patholoical bodily process in the organism, whose genome has related genetic susceptibility factor (he physical basis of this genetic susceptibility) as its part. genetic susceptibility to pathological bodily process OGSF:0000002 a genetic susceptibility that lead to the increased possibilities to initiate a biological process in an organism, whose genome has related genetic susceptibility factor (he physical basis of this genetic susceptibility) as its part. genetic susceptibility to biological process OGSF:0000003 a genetic susceptibility that lead to the increased possibilities to initiate adverse event in an organism, whose genome has related genetic susceptibility factor (he physical basis of this genetic susceptibility) as its part. genetic susceptibility to adverse event OGSF:0000004 a genetic material that is the material base of genetic susceptibility Many types of genetic material can be called a genetic susceptibility factor, such as a gene, a haplotype, a microsatellite, a genotype and so on. The notion of the genetic susceptibility factor based on the output of a scientific investigation that aims to elucidate the association between a phenotype and genotype. The statistical methods, study population and geographical characteristic of the population often has an impact on the assessment of the 'genetic susceptibility'. The more replicate result among different study groups the stronger evidence can be used to determine the 'genetic susceptibility factor'. (YL. Feb. 13, 2013) YL, YH genetic susceptibility factor OGSF:0000005 genetic susceptibility factor that is a gene susceptibility gene 2 OGSF:0000006 genetic susceptibility factor that is a haplotype susceptibility haplotype OGSF:0000007 genetic susceptibility factor that is a Simple Nucleotide Polymorphism (SNP). The susceptibility allele of SNP is usually the minor allele of SNP susceptibility allele of SNP OGSF:0000008 genetic susceptibility factor that is a genotype YL, YH susceptibility genotype OGSF:0000009 genetic susceptibility factor that is an allele Usually the susceptibility allele is the minor allele. We may set up rules here. susceptibility allele OGSF:0000010 a genetic susceptibility to adverse event that is proceded by a vaccination process. genetic susceptibility to vaccine adverse event OGSF:0000011 susceptibility gene OGSF:0000012 textual conclusion of genetic association textual conclusion of genetic susceptibility OGSF:0000014 susceptibility interactive gene group OGSF:0000015 a genetic susceptibility to adverse event that is proceded by a drug administration genetic susceptibility to drug adverse event OGSF:0000016 investigation that aims to test whether single-locus alleles or genotype frequencies (or more generally, multilocus haplotype frequencies) differ between two groups of individuals (usually diseased subjects and healthy controls). Genetic association studies are based on the principle that genotypes can be compared "directly", i.e. with the sequences of the actual genomes. http://en.wikipedia.org/wiki/Genetic_association Genetic association can be between phenotypes, such as visible characteristics such as flower colour or height, between a phenotype and a genetic polymorphism, such as a single nucleotide polymorphism (SNP), or between two genetic polymorphisms. Association between genetic polymorphisms occurs when there is non-random association of their alleles as a result of their proximity on the same chromosome; this is known as genetic linkage. Linkage disequilibrium (LD) is a term used in the study of population genetics for the non-random association of alleles at two or more loci, not necessarily on the same chromosome. It is not the same as linkage, which is the phenomenon whereby two or more loci on a chromosome have reduced recombination between them because of their physical proximity to each other. LD describes a situation in which some combinations of alleles or genetic markers occur more or less frequently in a population than would be expected from a random formation of haplotypes from alleles based on their frequencies. Genetic association studies are performed to determine whether a genetic variant is associated with a disease or trait: if association is present, a particular allele, genotype or haplotype of a polymorphism or polymorphisms will be seen more often than expected by chance in an individual carrying the trait. Thus, a person carrying one or two copies of a high-risk variant is at increased risk of developing the associated disease or having the associated trait. genetic association investigation OGSF:0000017 Genetic association investigation that use to observe the non-random differences of a genetic factor's frequency between case group and control group. The case group and control group are differed by their phenotyp outcome measurement, for example, the case group is a group of people that has disease A, but control group has no disease A. Usually other characteristics of the control and case group are carefully matched (e.g. by age, sex, enviroment) to avoid other variables's co-effets on the variable that is under investigation. case control genetic association study OGSF:0000018 The first Genome Wide Association Study that conducted in a population to observe the genetic association with a phenotype or trait. initial GWAS study OGSF:0000019 the GWAS study that intend to repeat initial GWAS study's observation over a different population using a different design and methods by different investigation teams. Tthe repeated observation of associations between covariates by different investigative teams, in different populations, using different designs and methods is typically taken as evidence that the association is not an artifact. ref: Replication in Genome-Wide Association Studies [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865141/] replicate GWAS study OGSF:0000020 human study subject OGSF:0000021 human study subject group OGSF:0000022 human case group OGSF:0000023 human control group OGSF:0000025 human study subject group size OGSF:0000026 odds ratio measurement OGSF:0000027 logistic regression measurement OGSF:0000028 odds ratio OGSF:0000030 human gene OGSF:0000031 The textual conclusion from the paper that mentioned the genetic susceptibility of the genetic susceptibility factors that is statistically meaningful (statistically supported). positive conclusion of genetic susceptibility OGSF:0000032 The textual conclusion from the paper that mentioned the genetic susceptibility of a genetic susceptibility factors that is denied by statistical calculation. negative conclusion of genetic susceptibility OGSF:0000033 The textual conclusion from the paper that mentioned the genetic susceptibility of a genetic susceptibility factors is neither deny nor support by statistical calculation. neutral conclusion of genetic susceptibility OGSF:0000034 susceptibility SNP OGSF:0000035 in this kind of study, the vaccination related adverse event is well controlled by selecting healthy or vaccinia naive individuals for enrollment to clinical trial. To analyze the genetic association with AE, the vaccinees experiencing AE will be used for case group, and others will be used fror control group. genetic association with adverse event clinical trail OGSF:0000103 two dimentional structure of genetic interval OGSF:0000104 three dimention structure of genetic interval OGSF:0001000 multiple sclerosis AE patient OGSF:0001004 HLA DBR1 gene OGSF:0001007 pandemrix vaccination OGSF:0001013 T allele of rs2070874 SNP OGSF:0001014 C allele of rs2243268 SNP OGSF:0001015 A allele of rs2243290 SNP OGSF:0001016 MTHFR gene OGSF:0001017 IRF1 gene OGSF:0001018 IL4 gene OGSF:0001021 human vaccinee OGSF:0001022 human vaccinee experiencing systematic adverse event OGSF:0001039 a genetic susceptibility to adverse event that is proceded by a vaccination process. genetic susceptibility to adverse event following Pandemix vaccination OGSF:0001040 a genetic susceptibility to adverse event that is proceded by a vaccination process. genetic susceptibility to multiple scelorosis AE following Pandemix vaccination OGSF:0001041 smallpox vaccination OGSF:0001042 wheezing AE after influenza vaccination OGSF:0001043 influenza vaccination PATO:0000169 viability An organismal quality inhering in a bearer or a population by virtue of the bearer's ability or inability to survive and develop normally or the number of surviving individuals in a given population. viability PATO:0000719 viable A viability quality inhering in a bearer or a population by virtue of the bearer's ability to survive and develop normally or the long term survival ability of a given population. live viable PATO:0001237 quality of a single physical entity A physical object quality which inheres in a single-bearer. quality of a single physical entity PATO:0001241 physical object quality A quality which inheres in a continuant. physical object quality PATO:0001995 organismal quality A quality that inheres in an entire organism or part of an organism. organismal quality PATO:0002146 virulence A quality inhering in a bearer by virtue of the bearer's pathogenicity. virulence REO:0000826 A nucleic acid macromolecule or submolecule that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny. genetic nucleic acid genomic material genomic nucleic acid adapted from 'genetic material' class definition in OBI ExpDesign.owl OBI - The concept of 'genetic material' was discussed in 2011 among OBI members, but a final definition or implementation was nver reached. There is a definition in OBO ExpDesign sandbox version, which was used to inform our definition and usage here. Further discussions with OBI will be required, however. genetic material SO:0000001 A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. sequence SO:0000001 SOFA This term is asserted as Quality in OBI, and OBI uses OBI's preferrable label: ' primary structure of sequence macromolecule'. In REO, this term is asserted as a 'generically dependent continuant'. region SO:0000704 A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. SO:gene SO:0000704 SOFA http://en.wikipedia.org/wiki/Gene This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance. SO:gene SO:0001023 An allele is one of a set of coexisting sequence variants of a gene. SO:allele allelomorph SO:0001023 http://en.wikipedia.org/wiki/Allele SO:allele SO:0001026 A genome is the sum of genetic material within a cell or virion. SO:0001026 http://en.wikipedia.org/wiki/Genome genome SO:0001411 A region defined by its disposition to be involved in a biological process. biological region SO:0001411 SOFA biological_region VO:0000001 A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine. Many vaccines are developed to protect against infectious pathogens. Many vaccines are also being developed against some diseases such as cancer and autoimmune diseases. Vaccine is developed against a disease. Allergy. YH, BP, BS, MC, LC, XZ, RS vaccine MeSH: D014612 VO:0000002 a process of administering substance in vivo that involves in adding a vaccine into a host (e.g., human) in vivo with the intent to invoke a protective or therapeutic adaptive immune response. YH, BP vaccine administration vaccination VO:0000093 a vaccine adjuvant that is formed as a mineral salt. SGS, YH mineral salt vaccine adjuvant CVX: 119 VO:0000137 A role that inheres in a material entity that helps or enhances the effect of other agents, such as a drug or vaccine. YH,YL adjuvant role VO:0000147 an adjuvant role that inheres in a material entity which is added as part of a vaccine and induces enhanced adaptive immune response to the vaccine antigen. YH vaccine adjuvant role VO:0000173 YH attenuated VO:0000179 a processed material that is output of the vaccine preparation and part of a vaccine. YH cardinal part of vaccine vaccine ingredient vaccine component VO:0000278 vaccine function is a function that inheres in a vaccine that induces protective immune response against a disease. It is realized in the immunization process in the host. PERSPN: Oliver He: There has been hot discussion about whether we use 'vaccine function' or 'vaccine role'. Vaccine role may not be the good term to use. Vaccine is designed to be 'vaccine', so it should be vaccine function. One special case is cowpox virus. The cowpox virus can be mixed with some liquid like water and used as a smallpox vaccine. In this case, people often say: the cowpox virus has a 'vaccine role'. However, the cowpox virus vaccine is a processed material of a mix of the virus with water. The virus is a virus, it is not a vaccine per se. Therefore, vaccine role may not be an accurate term. YH, MC, XZ, and AR vaccine function VO:0000299 YH company VO:0000363 A vaccine that is licensed for commercial use. YH licensed vaccine VO:0000410 Pandemrix is an influenza vaccine for influenza pandemics, such as the H1N1 2009 flu pandemic colloquially called the swine flu. The vaccine was developed by GlaxoSmithKline and patented in September 2006. Pandemrix H1N1 http://en.wikipedia.org/wiki/Pandemrix TODO: the component 'egg protein' and 'sodium deoxycholate' is not added yet. YL ATC code J07BB02 Pandemrix VO:0000415 YL,YH Page 73, Chapter 6, Vaccine, 5th Edition. EXPERT CONSULT by Plotkin SA., et. al. 2008 a role inheres in a material entity, that has been added into a vaccine's formulation by the manufacture for a specific purpose. For example: adjuvant to enhance the effect of immunogen, perservatives, stablizers and those materials added for affecting PH and isotonicity. vaccine additive role VO:0000420 a vaccine component that originates from an organism such as a pathogen or a modified organism. YH pathogen organism component in vaccine VO:0000452 preventive vaccine function is a vaccine function realized by the process of vaccination and leading to induction of an adaptive immune response to the antigens in a vaccine, which protects against a specific disorder. YH prophylactic vaccine function preventive vaccine function VO:0000490 immunization is a processual entity that primes or modifies an adaptivie immune response to some antigens. YH, XZ, BP WEB: http://en.wikipedia.org/wiki/Immunization immunization VO:0000491 Active immunization is an immunization process that entails the introduction of a foreign molecule into the body, which causes the body itself to generate adaptive immunity against the target. YH, XZ WEB: http://en.wikipedia.org/wiki/Immunization active immunization VO:0000494 artificial active immunization is an active immunization that occurs when a person or animal is vaccinated with a specific vaccine. YH, XZ artificial active immunization WEB: http://en.wikipedia.org/wiki/Immunization vaccine immunization VO:0000495 induction of adaptive immune response to antigen is an active immunization process that results in induction of adaptive immune response to some antigens, for example, in a vaccine. YH, XZ induction of adaptive immune response to antigen VO:0000496 disorder prevention is a processual entity that prevents a disorder that is the physical basis of a disease. YH, XZ disorder prevention VO:0000497 disorder treatment is a processual entity that leads to treat a disorder that is the physical basis of a disease. YH, XZ disorder treatment VO:0000498 modification of adaptive immune response to antigen is an active immunization process that results in modification of an adaptive immune response to some antigens, for example, in a therapeutic vaccine. YH, XZ modification of adaptive immune response to antigen VO:0000562 The therapeutic vaccine function is a function realized by the process of vaccination and leading to induction of an adaptive immune response to the antigens in a vaccine, which ameliorates a specific disorder. YH therapeutic vaccine function VO:0000576 vaccine preservative that has thimerosal as part. YH thimerosal vaccine preservative VO:0000580 a vaccine component that is chemical substance added to vaccine and enhance and direct immune response to protective antigen. Many of vaccine adjuvants cause a range of serious side-effects. YH vaccine adjuvant VO:0000585 immunization objective is the specification of an objective to achieve immunization. YH, XZ WEB: http://en.wikipedia.org/wiki/Immunization immunization objective VO:0000590 vaccine preparation is a manufacturing process to produce a vaccine. YH, BP vaccine generation vaccine production vaccine preparation VO:0000609 A vaccine that protects against some viral disease. YH viral vaccine MeSH: D014765 VO:0000624 YH whole organism in vaccine is a organism component in vaccine that includes the whole organism such as a whole live attenuated organism. whole pathogen organism as vaccine component VO:0000630 licensed vaccine role is a regulation-assigned role that indicates that a vaccine obtains official approval for commercial production and selling on the market. YH licensed vaccine role VO:0000642 A viral vaccine that protects against infection with influenza virus. YH Influenza vaccine Influenza virus vaccine MeSH: D007252 VO:0000651 A viral vaccine that protects against infection with Smallpox virus. YH Smallpox virus vaccine MeSH: D012900 VO:0000771 BCG Vaccine is a Mycobacterium tuberculosis vaccine that is a live attenuated strain of Mycobacterium bovis (Bacillus Calmette Guerin; BCG). YH Bacillus Calmette Guerin BCG vaccine CVX: 19 VO:0000850 a vaccine component that is added to the immunogen by the vaccine manufacturer for a specific purpose. Additives include adjuvants, preservatives and stablizers, as well as materials that are added to affect pH and isotonicity. YH Finn TM and Egan W, in Vaccines fifth edition, 2008. Page 73. vaccine additive VO:0000851 YH antimicrobial agent in vaccine vaccine preservative VO:0000853 a vaccine additive that helps to protect the vaccine from adverse conditions such as the freeze-drying process (for those vaccines that are freeze-dried) or heat. YH Finn TM and Egan W, in Vaccines fifth edition, 2008. Page 75. vaccine stabilizer VO:0000884 a mineral salt vaccine adjuvant that is composed of aluminum salt. Aluminum vaccine adjuvant is a vaccine adjuvant that is composed of some aluminum compound. YH aluminum vaccine adjuvant VO:0000885 a role inhers in a vaccine component that when added into a vccine formmulation, it can prevent the growth of bacteria or fungi that inadvertently may be introduced into the vaccine during administrating process or the manufacturing process. YH,YL P73 Chapter 6, Vaccine 5th edition by Plotkin, S. et al. The CFR requires that, with certain defined exceptions, preservatives must be added to mulitdose vials of vaccine. (P73 Chapter 6, Vaccine 5th edition by Plotkin, S. et al.) vaccine preservative role VO:0001274 a role of host that contains vaccine. It is a role that inheres in an organism that is the target of a vaccine administration (vaccination process). YH, ZX vaccine host role VO:0001275 YH, ZX a role that represents a target (i.e., some disorder) of immunization. immunization target role VO:0001346 a vaccine preservative that contains formaldehyde. YH, SGS WEB: http://www.mja.com.au/public/issues/184_04_200206/eld10500_fm.pdf formaldehyde vaccine preservative VO:0001374 an organism that is vaccinated with a vaccine Vaccinee YH, YL, MC vaccinated organism VO:0001375 a vaccinated organism that is vaccinated with a licensed vaccine YH, YL, MC vaccinee organism vaccinated with a licensed vaccine VO:0001479 The objective that intends to produce vaccine via the vaccine preparation process. YH vaccine target specification VO:0003026 a role inheres in vaccine component when added into vaccine's formulation, it tends to inhibit the reaction between two or more other vaccine substances in the final vaccine formulation; it also helps to protect the vaccine from adverse conditions such as the freeze-drying process or heat. YL vaccine stabilizer role VO:0003034 a vaccine stabilizer that is specifically made by a sugar. YH, YL sugar vaccine stabilizer VO:0003036 a vaccine stabilizer that is specifically made by a sucrose. YH, YL sucrose vaccine stabilizer OGI:Author a human being that bears an author role. author OGI:Biological_Macromolecule biological macromolecule OGI:Biological_Molecule biological molecule OGI:Biological_Small_Molecule biological small molecule OGI:Book book OGI:Coding_RNA_Molecule coding RNA molecule OGI:CpG_Island CpG islands are commonly defined as regions of DNA of at least 200 bp in length and that have a G+C content above 50% and a ratio of observed vs. expected CpGs close to or above 0.6. ( Ref. Gardiner-Garden and Fromer (1987) ). Sets of CG repeat elements, usually found upstream of transcribed regions of the genome. CpG Island OGI:DNA_Molecule Dexyribonuleic acid molecule OGI:Enhancer a set of short sequence elements which stimulate transcription of a gene and whose function is not critically dependent on their precise position or orientation. An enhancer is a short region of DNA that can be bound with proteins (namely, the trans-acting factors, much like a set of transcription factors) to enhance transcription levels of genes (hence the name) in a gene cluster. While enhancers are usually cis-acting, an enhancer does not need to be particularly close to the genes it acts on, and sometimes need not be located on the same chromosome. (http://en.wikipedia.org/wiki/Enhancer_(genetics)) enhancer OGI:Genomic_DNA also gDNA genomic DNA OGI:Histone histone OGI:Non_Coding_RNA_Molecule non codling RNA molecule OGI:Nucleic_Acid nucleic acid OGI:Polymer polymer OGI:Polypeptide polypeptide OGI:Polypeptide_Encoding_Gene polypeptide coding gene OGI:Primary_Transcript primary transcript OGI:Promoter a combination of short sequence elements, normally just upstream of a gene, to which RNA polymerase binds in order to initiate transcription of the gene. In genetics, a promoter is a region of DNA that initiates transcription of a particular gene. Promoters are located near the genes they transcribe, on the same strand and upstream on the DNA (towards the 3' region of the anti-sense strand, also called template strand and non-coding strand). Promoters can be about 100–1000 base pairs long. (http://en.wikipedia.org/wiki/Promoter_(genetics)) promoter OGI:Protein protein OGI:Pseudogene pseudogene OGI:RNA_Gene RNA gene OGI:RNA_Molecule RNA molecule OGI:STS_Non_Polymorphic_Marker STS non polymorphic marker OGI:Transcript An RNA synthesized on a DNA or RNA template by an RNA polymerase. transcript OGI:cDNA In genetics, complementary DNA (cDNA) is DNA synthesized from a mature mRNA template in a reaction catalyzed by the enzyme reverse transcriptase.(wikipedia) complementary DNA OGI:mRNA messenger RNA OGI:miRNA short(22nt) RNA molecules encoded within normal genomes that have a role in regulation of gene expression and maybe also of chromatin structure. Sometimes called small temporal RNA(stRNA). Micro RNAs OGI:msDNA multicopy single-stranded DNA OGI:mtDNA Mitochondrial DNA OGI:rRNA ribosomal RNA OGI:tRNA transfer RNA owl:Nothing owl:Thing example to be eventually removed metadata complete organizational term ready for release metadata incomplete uncurated pending final vetting to be replaced with external ontology term requires discussion publication_PMID_22841884 The HLA DRB1*15:01 allele is responsible for genetic susceptibility to positive conclusion of genetic susceptibility_1 genetic association invesitgation 1 publication_PMID_18454680 genetic adverse event association clinical trial 1 genetic adverse event association clinical trial 2 4.1 0.01 positive conclusion 1 of genetic susceptibility_trial2 2.3 0.03 positive conclusion 1 of genetic susceptibility_trial1 3.2 0.03 positive conclusion 2 of genetic susceptibility_trial1 3.0 0.03 positive conclusion 2 of genetic susceptibility_trial2 3.2 0.03 positive conclusion 3 of genetic susceptibility_trial1 3.0 0.03 positive conclusion 3 of genetic susceptibility_trial2 3.2 0.03 positive conclusion 4 of genetic susceptibility_trial1 3.0 0.03 positive conclusion 4 of genetic susceptibility_trial2 2.4 0.05 positive conclusion 5 of genetic susceptibility_trial1 3.8 0.06 positive conclusion 5 of genetic susceptibility_trial2 YH http://www.gsk-bio.com/english/index.html GlaxoSmithKline Biologicals 2 2 2 2.0 has_part has part realized-in realizedIn [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) if a realizable entity b is realized in a process p, then p stands in the has_participant relation to the bearer of b. (axiom label in BFO2 Reference: [106-002]) (forall (x y z t) (if (and (RealizableEntity x) (Process y) (realizesAt y x t) (bearerOfAt z x t)) (hasParticipantAt y z t))) // axiom label in BFO2 CLIF: [106-002] is realized by realized in has-participant_st hasParticipantAt has participant Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has participant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has participant@en'(x,y,t) BFO 2 Reference: Spatial regions do not participate in processes. BFO2 Reference: independent continuant that is not a spatial region, specifically dependent continuant, generically dependent continuant BFO2 Reference: process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant has_participant is an instance-level relation between a process, a continuant, and a temporal region at which the continuant participates in some way in the process. (axiom label in BFO2 Reference: [086-003]) if b has_participant c at t & c is a generically dependent continuant, then there is some independent continuant that is not a spatial region d, and which is such that c g-depends on d at t & b s-depends_on d at t. (axiom label in BFO2 Reference: [091-003]) if b has_participant c at t & c is a specifically dependent continuant, then there is some independent continuant that is not a spatial region d, c s-depends_on d at t & b s-depends_on d at t. (axiom label in BFO2 Reference: [090-003]) if b has_participant c at t then b is an occurrent. (axiom label in BFO2 Reference: [087-001]) if b has_participant c at t then c exists at t. (axiom label in BFO2 Reference: [089-001]) if b has_participant c at t then c is a continuant. (axiom label in BFO2 Reference: [088-001]) (forall (x y t) (if (and (hasParticipantAt x y t) (GenericallyDependentContinuant y)) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (genericallyDependsOn y z t) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [091-003] (forall (x y t) (if (and (hasParticipantAt x y t) (SpecificallyDependentContinuant y)) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t) (specificallyDependsOnAt y z t))))) // axiom label in BFO2 CLIF: [090-003] (forall (x y t) (if (hasParticipantAt x y t) (Continuant y))) // axiom label in BFO2 CLIF: [088-001] (forall (x y t) (if (hasParticipantAt x y t) (Occurrent x))) // axiom label in BFO2 CLIF: [087-001] (forall (x y t) (if (hasParticipantAt x y t) (existsAt y t))) // axiom label in BFO2 CLIF: [089-001] http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant has participant at some time concretized-by_st [copied from inverse property 'concretizes at some time'] You may concretize a piece of software by installing it in your computer [copied from inverse property 'concretizes at some time'] You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head. [copied from inverse property 'concretizes at some time'] you may concretize a poem as a pattern of memory traces in your head [copied from inverse property 'concretizes at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t) [copied from inverse property 'concretizes at some time'] b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002]) concretized by at some time is concretization of preceded by preceded_by is preceded by located-at-r_st occupiesSpatialRegionAt Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t) BFO2 Reference: independent continuant BFO2 Reference: spatial region b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002]) if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001]) (forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002] (forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002] (forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001] occupies spatial region at some time has-q_st has quality at some time has-r_st hasRoleAt a has_role b at t =Def. b role_of a at t. (axiom label in BFO2 Reference: [068-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has role at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has role@en'(x,y,t) (iff (hasRoleAt a b t) (roleOfAt b a t)) // axiom label in BFO2 CLIF: [068-001] has role at some time exists-at existsAt BFO2 Reference: entity BFO2 Reference: temporal region b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002]) exists at c-has-part_at hasContinuantPartAt [copied from inverse property 'part of continuant at all times that whole exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t) b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'. [copied from inverse property 'part of continuant at all times that whole exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times' (iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001] has continuant part at all times st-projects-onto-s_st projects onto spatial region at some time st-projects-onto-t projects onto temporal region s-depends-on_st specificallyDependsOn A pain s-depends_on the organism that is experiencing the pain a gait s-depends_on the walking object. (All at some specific time.) a shape s-depends_on the shaped object one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs reciprocal s-dependence between occurrents: a process of buying and the associated process of selling reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball the one-sided dependence of an occurrent on an independent continuant: handwave on a hand the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45 the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45 the two-sided reciprocal s-dependence of the roles of husband and wife [20 Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t) BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28 BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20 BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place. BFO2 Reference: specifically dependent continuant\; process; process boundary To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64 If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001]) If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001]) If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002]) an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002]) if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002]) (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002] (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002] (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001] (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002] (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] specifically depends on at some time c-part-of-object_at [copied from inverse property 'has continuant part at all times'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t) This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times' [copied from inverse property 'has continuant part at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part part of continuant at all times that whole exists 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 has_specified_input see is_input_of example_of_usage A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input has_specified_output A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective allele of is a relation to link an allele with its original form is_allele_of_gene OGSF:0001003 DRB1*15:01 OGSF:0001006 multiple sclerosis AE after Pandemrix vaccination is positive supporting statistical evidence of is negative statistical evidence of OGSF:0001010 T allele of rs1801133 SNP OGSF:0001011 G allele of rs9282763 SNP OGSF:0001012 A allele of rs839 SNP OGSF:0001019 haplotype 1 in IRF1 gene OGSF:0001020 haplotype 2 in IL4 gene OGSF:0001028 systematic adverse event after smallpox vaccination x actively participates in y if and only if x participates in y and x realizes some active role agent in actively participates in YL Yongqun He vaccine immunization for host Yongqun He vaccine immunization against microbe BFO 2 Reference: BFO does not claim to provide complete coverage of entities of all types. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning - coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation. BFO 2 Reference: BFO's treatment of continuants and occurrents - as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality - earlier called the 'SNAP' and 'SPAN' perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science. BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. 'Entity' is an example of a primitive term. Primitive terms in a highest-level ontology such as BFO are terms that are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms. Alan Ruttenberg Albert Goldfain Barry Smith Bill Duncan Bjoern Peters Chris Mungall David Osumi-Sutherland Fabian Neuhaus Holger Stenzhorn James A. Overton Janna Hastings Jie Zheng Jonathan Bona Larry Hunter Leonard Jacuzzo Ludger Jansen Mark Ressler Mathias Brochhausen Mauricio Almeida Melanie Courtot Pierre Grenon Randall Dipert Ron Rudnicki Selja Seppälä Stefan Schulz Thomas Bittner Werner Ceusters Yongqun "Oliver" He Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif. The BSD license on the BFO project site refers to code used to build BFO. This BFO 2.0 version represents a major update to BFO and is not strictly backwards compatible with BFO 1.1. The previous OWL version of BFO, version 1.1.1 will remain available at http://ifomis.org/bfo/1.1 and will no longer be updated. The BFO 2.0 OWL is a classes-only specification. The incorporation of core relations has been held over for a later version. inheres_in A relation between a dependent continuant D and an entity E. D inheres_in E iff: given any d that instantiates D at t, there exists some e that instantiates E at t and d *inheres_in* e at t. Here *inheres_in* is the primitive instance level relation. http://purl.org/obo/owl/ro_proposed inheres_in Ontology of Genetic Susceptibility Factor (OGSF) is an application ontology to model/represent the notion of genetic susceptibility to a specific disease or an adverse event or a biological process. 'Oliver' Yongqun He (YH) 'Asiyah' Yu Lin (YL) 11-22-2014 New BSD license 2.0 https://code.google.com/p/ogsf/ variant_of This is OGI specific relation. We extended the allen caculus relation from temporal domain to material interval domain. Reference: Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology) isContainedIn(X,Y) genetic interval X is contained inside genetic interval Y If genetic interval X is contained in genetic interval Y, then start of X is after the start of Y and the end of X is before the end of Y and the start of X is unique with thestart of Y, the end of X is unique with the end of Y. isContainedIn(X,Y) ↔ (hasStartPoint(x1,X) & hasStartPoint(y1,Y) & isLocatedAfter(x1,y1)) & (hasEndPoint(x2,X) & hasEndPoint(y2,Y) & isLocatedBefore(x2,y2)) & ((pointInterval(x1,X) & pointInterval(y1,X)) & ((pointInterval(x2,X) & pointInterval(y2,X)) unsolved problem, Is isContainedIn a transitive relation? is short relation for author 'participate in' some ('writing book process' and ( 'has specific output of' some book))