]> Yongqun "Oliver" He (YH) Jie Zheng (JZ) Asiyah Yu Lin (YL) The vaccination informed consent Ontology (VICO) is an ontology in the domain of vaccination/immunization informed consent. 2016-01-30 Arbor version; 1.0.52 BFO OWL specification label BFO OWL specification label BFO OWL specification label Really of interest to developers only 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. BFO CLIF specification label BFO CLIF specification label Person:Alan Ruttenberg BFO CLIF specification label Really of interest to developers only Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 editor preferred term editor preferred term~editor preferred label editor preferred label editor preferred term editor preferred term~editor preferred label GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) editor preferred term example of usage example of usage 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 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober example example of usage has curation status has curation status OBI_0000281 PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition textual definition definition definition definition GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober 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. definition editor note editor note editor note 1 IAO:0000116 editor_note editor_note uberon 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. GROUP:OBI:<http://purl.obfoundry.org/obo/obi> PERSON:Daniel Schober editor note term editor definition editor definition editor term editor 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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 PERSON:Daniel Schober definition editor term editor alternative term alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober alternative term definition source definition source Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober 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 curator notes curator note curator note 1 IAO:0000232 curator_notes curator_notes uberon An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note imported from imported from For external terms/classes, the ontology from which the term was imported GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Alan Ruttenberg PERSON:Melanie Courtot imported from elucidation elucidation Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which 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 elucidation person:Alan Ruttenberg has associated axiom(nl) has associated axiom(nl) An axiom associated with a term expressed using natural language Person:Alan Ruttenberg Person:Alan Ruttenberg has associated axiom(nl) has associated axiom(fol) has associated axiom(fol) An axiom expressed in first order logic using CLIF syntax Person:Alan Ruttenberg Person:Alan Ruttenberg has associated axiom(fol) term_mapping_to_UMLS term_mapping_to_NCIT term_mapping_to_HL7v3 has_specified_input has_specified_input 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: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input 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. PERSON: Alan Ruttenberg has_specified_input see is_input_of example_of_usage has_specified_output has_specified_output PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot 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 has_specified_output ISA alternative term ISA tools project (http://isa-tools.org) Person: Philippe Rocca-Serra ISA alternative term Person: Alejandra Gonzalez-Beltran An alternative term used by the ISA tools project (http://isa-tools.org). organism NCBITaxon ID The NCBITaxon ontology ID of an organism. Oliver He, Yue Liu temporal interpretation temporal interpretation https://code.google.com/p/obo-relations/wiki/ROAndTime https://github.com/oborel/obo-relations/wiki/ROAndTime An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation logical macro assertion https://github.com/oborel/obo-relations/wiki/ShortcutRelations An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion on a property A logical macro assertion whose domain is an IRI for a property logical macro assertion on an object property has_rank has_rank A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy eco subset Creator creator Creator Source Source subset_property has_alternative_id has_alternative_id has_broad_synonym has_broad_synonym database_cross_reference database_cross_reference has_exact_synonym has_exact_synonym has_obo_namespace has_obo_namespace has_related_synonym has_related_synonym in_subset in_subset shorthand shorthand label part of Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. http://www.obofoundry.org/ro/#OBO_REL:part_of Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell. http://www.obofoundry.org/ro/#OBO_REL:part_of Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime a core relation that holds between a part and its whole my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) part of part_of this day is part of this year (occurrent parthood) has part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime a core relation that holds between a whole and its part has part has_part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) inheres in at all times inheresInAt BFO2 Reference: independent continuant that is not a spatial region inheres-in_at BFO2 Reference: specifically dependent continuant 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)'. (iff (inheresInAt a b t) (and (DependentContinuant a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [051-002] 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.) 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]) bearer of 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 '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 bearerOfAt (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] 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]) bearer-of_st BFO2 Reference: specifically dependent continuant realized in [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]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process (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] [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]) realizedIn realized-in 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]) is realized by realized in realized_in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation realizes realizes Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes (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 this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility 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]) participates_in participates in participates in at some time participates-in_st [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'] 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'] BFO2 Reference: process participatesInAt [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'] 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 has participant has participant at some time (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) (Occurrent x))) // axiom label in BFO2 CLIF: [087-001] (forall (x y t) (if (hasParticipantAt x y t) (Continuant y))) // axiom label in BFO2 CLIF: [088-001] hasParticipantAt (forall (x y t) (if (hasParticipantAt x y t) (existsAt y t))) // axiom label in BFO2 CLIF: [089-001] BFO2 Reference: process has-participant_st (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] 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 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]) concretized by at some time [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. 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'] 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]) [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) 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) concretizes_st (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] concretizesAt (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] 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. 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]) you may concretize a poem as a pattern of memory traces in your head preceded_by preceded by specifically depends on at all times (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] BFO2 Reference: specifically dependent continuant\; process; process boundary s-depends-on_at (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 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] A pain s-depends_on the organism that is experiencing the pain 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 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]) a gait s-depends_on the walking object. (All at some specific time.) 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]) 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 reciprocal s-dependence between occurrents: a process of buying and the associated process of selling specificallyDependsOn (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] 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)'. (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] 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. 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]) 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 a shape s-depends_on the shaped object 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]) 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 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 located in at all times locatedInAt BFO2 Reference: independent continuant (forall (x y z t) (if (and (IndependentContinuant x) (IndependentContinuant y) (IndependentContinuant z) (locatedInAt x y t) (continuantPartOfAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [049-001] (iff (locatedInAt a b t) (and (IndependentContinuant a) (IndependentContinuant b) (exists (r_1 r_2) (and (occupiesSpatialRegionAt a r_1 t) (occupiesSpatialRegionAt b r_2 t) (continuantPartOfAt r_1 r_2 t))))) // axiom label in BFO2 CLIF: [045-001] located-in_at (forall (x y z t) (if (and (locatedInAt x y t) (locatedInAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [046-001] (forall (x y z t) (if (and (IndependentContinuant x) (IndependentContinuant y) (IndependentContinuant z) (continuantPartOfAt x y t) (locatedInAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [048-001] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'located in at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'located in@en(x,y,t)'. Located_in is transitive. (axiom label in BFO2 Reference: [046-001]) Mary located_in Salzburg b located_in c at t = Def. b and c are independent continuants, and the region at which b is located at t is a (proper or improper) continuant_part_of the region at which c is located at t. (axiom label in BFO2 Reference: [045-001]) for all independent continuants b, c, and d: if b continuant_part_of c at t & c located_in d at t, then b located_in d at t. (axiom label in BFO2 Reference: [048-001]) for all independent continuants b, c, and d: if b located_in c at t & c continuant_part_of d at t, then b located_in d at t. (axiom label in BFO2 Reference: [049-001]) the Empire State Building located_in New York. this portion of cocaine located_in this portion of blood this stem cell located_in this portion of bone marrow your arm located_in your body occupies spatial region at some time located-at-r_st (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] BFO2 Reference: independent continuant 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) (forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002] BFO2 Reference: spatial region (forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002] 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]) occupiesSpatialRegionAt has function at some time has-f_st (iff (hasFunctionAt a b t) (functionOf b a t)) // axiom label in BFO2 CLIF: [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) a has_function b at t =Def. b function_of a at t. (axiom label in BFO2 Reference: [070-001]) hasFunctionAt has quality at some time has-q_st has role at some time hasRoleAt has-r_st 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] a has_role b at t =Def. b role_of a at t. (axiom label in BFO2 Reference: [068-001]) exists at BFO2 Reference: entity b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002]) existsAt BFO2 Reference: temporal region exists-at has continuant part at all times (iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001] [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' [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) 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)'. hasContinuantPartAt b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) c-has-part_at has occurrent part [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'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) [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. b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) o-has-part (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent hasOccurrentPart [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match. has proper 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 temporal 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'] 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]) [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 has-t-part has spatial occupant at some time r-location-of_st [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]) [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant [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: spatial region has location at some time [copied from inverse property 'located in at some time'] Mary located_in Salzburg [copied from inverse property 'located in at some time'] the Empire State Building located_in New York. [copied from inverse property 'located in at some time'] b located_in c at t = Def. b and c are independent continuants, and the region at which b is located at t is a (proper or improper) continuant_part_of the region at which c is located at t. (axiom label in BFO2 Reference: [045-001]) [copied from inverse property 'located in 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 'located in at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'located in@en'(x,y,t) [copied from inverse property 'located in at some time'] your arm located_in your body [copied from inverse property 'located in at some time'] this portion of cocaine located_in this portion of blood has-location_st [copied from inverse property 'located in at some time'] BFO2 Reference: independent continuant [copied from inverse property 'located in at some time'] this stem cell located_in this portion of bone marrow has specific dependent at some time [copied from inverse property 'specifically depends on at some time'] a shape s-depends_on the shaped object has-s-dep_st [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 [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'] 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'] a gait s-depends_on the walking object. (All at some specific time.) [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'] 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'] the two-sided reciprocal s-dependence of the roles of husband and wife [20 [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'] 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'] 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'] 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'] 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'] BFO2 Reference: specifically dependent continuant\; process; process boundary [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'] 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'] 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'] 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'] 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 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 a process on something: a process of cell death s-depends_on a cell [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: 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'] 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 one occurrent on another: a process of answering a question is dependent on a prior process of asking a question has spatiotemporal occupant [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. occupied-by [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]) occupies spatiotemporal region 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. occupies 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]) part of occurrent BFO2 Reference: occurrent occurrentPartOf o-part-of (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] [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]) (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] (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] 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. 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. 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]) the first set of the tennis match occurrent_part_of the tennis match. temporal part of (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001] (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] 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]) temporalPartOf t-part-of (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] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) 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]) 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 projects onto spatial region at some time st-projects-onto-s_st spatial projection of spatiotemporal at some time s-projection-of-st_st projects onto temporal region st-projects-onto-t temporal projection of spatiotemporal t-projection-of-st occupies temporal region 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]) has temporal occupant [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]) span-of spanOf during which exists [copied from inverse property 'exists at'] BFO2 Reference: entity during-which-exists [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]) bearer of at all times (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] bearerOfAt BFO2 Reference: independent continuant that is not a spatial region bearer-of_at 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 all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'bearer of@en(x,y,t)'. BFO2 Reference: specifically dependent continuant 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]) has quality at all times has-q_at has role at all times hasRoleAt 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 all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has role@en(x,y,t)'. has-r_at (iff (hasRoleAt a b t) (roleOfAt b a t)) // axiom label in BFO2 CLIF: [068-001] a has_role b at t =Def. b role_of a at t. (axiom label in BFO2 Reference: [068-001]) has participant 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 participant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has participant@en(x,y,t)'. has-participant_at (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] BFO2 Reference: independent continuant that is not a spatial region, specifically dependent continuant, generically dependent continuant (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) (Continuant y))) // axiom label in BFO2 CLIF: [088-001] BFO2 Reference: process hasParticipantAt (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) (existsAt y t))) // axiom label in BFO2 CLIF: [089-001] BFO 2 Reference: Spatial regions do not participate in processes. 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]) has specific dependent at all times has-s-dep_at specifically depends on at some time s-depends-on_st BFO2 Reference: specifically dependent continuant\; process; process boundary (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] (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] 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. 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]) 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 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 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: 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 specificallyDependsOn 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) (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 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 z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002] A pain s-depends_on the organism that is experiencing the pain 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 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]) a gait s-depends_on the walking object. (All at some specific time.) a shape s-depends_on the shaped object 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]) 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 multiple independent continuants: a relational process of hitting a ball with a cricket bat 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 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 located in at some time (iff (locatedInAt a b t) (and (IndependentContinuant a) (IndependentContinuant b) (exists (r_1 r_2) (and (occupiesSpatialRegionAt a r_1 t) (occupiesSpatialRegionAt b r_2 t) (continuantPartOfAt r_1 r_2 t))))) // axiom label in BFO2 CLIF: [045-001] locatedInAt BFO2 Reference: independent continuant (forall (x y z t) (if (and (IndependentContinuant x) (IndependentContinuant y) (IndependentContinuant z) (continuantPartOfAt x y t) (locatedInAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [048-001] located-in_st (forall (x y z t) (if (and (IndependentContinuant x) (IndependentContinuant y) (IndependentContinuant z) (locatedInAt x y t) (continuantPartOfAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [049-001] (forall (x y z t) (if (and (locatedInAt x y t) (locatedInAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [046-001] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'located in at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'located in@en'(x,y,t) Located_in is transitive. (axiom label in BFO2 Reference: [046-001]) Mary located_in Salzburg b located_in c at t = Def. b and c are independent continuants, and the region at which b is located at t is a (proper or improper) continuant_part_of the region at which c is located at t. (axiom label in BFO2 Reference: [045-001]) for all independent continuants b, c, and d: if b continuant_part_of c at t & c located_in d at t, then b located_in d at t. (axiom label in BFO2 Reference: [048-001]) for all independent continuants b, c, and d: if b located_in c at t & c continuant_part_of d at t, then b located_in d at t. (axiom label in BFO2 Reference: [049-001]) the Empire State Building located_in New York. this portion of cocaine located_in this portion of blood this stem cell located_in this portion of bone marrow your arm located_in your body part of continuant at some time (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] [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) 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'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) (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] (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] (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) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] (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] 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]) c-part-of_st 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 (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] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation continuantPartOfAt 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) 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]) the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. part of continuant at all times (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] BFO2 Reference: continuant (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] continuantPartOfAt (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] [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) c-part-of_at BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] 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)'. (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 t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] 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. Mary’s arm continuant_part_of Mary in the time of her life prior to her operation [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]) the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. has continuant part at some time [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'] 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]) [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 (iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001] c-has-part_st 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'] BFO2 Reference: continuant [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: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. hasContinuantPartAt [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. [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]) b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) part of continuant at all times that whole exists [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@en(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' forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t) [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]) c-part-of-object_at has continuant part at all times that part exists [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant [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. c-has-part-object_at forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t) [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]) [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 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'] 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'] 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'] 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: 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. is about Smith, Ceusters, Ruttenberg, 2000 years of philosophy This document is about information artifacts and their representations is about is_about is a (currently) primitive relation that relates an information artifact to an entity. person:Alan Ruttenberg is associated with review board approval number EE, YH, YL, AK, MH a relation that links an informed consent form to an associated IRB number is assigned by organization an object perperty that represents a relation between a unique identifier (ID) and an organization that assigns the ID. YH, EE, YL, AK, MH has participant quality adverse event occurs in is_supported_by_data Philly 2011 workshop The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. is_supported_by_data OBI OBI has_specified_input has_specified_input 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: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input 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. PERSON: Alan Ruttenberg has_specified_input see is_input_of example_of_usage is_specified_input_of PERSON:Bjoern Peters is_specified_input_of 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. Alan Ruttenberg is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay has_specified_output has_specified_output PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot 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 has_specified_output is_manufactured_by Alan Ruttenberg Liju Fan 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. has_make has_manufacturer 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) is_manufactured_by is_specified_output_of PERSON:Bjoern Peters 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 is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' BP, AR, PPPB branch PPPB branch derived 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. achieves_planned_objective modified according to email thread from 1/23/09 in accordince with DT and PPPB branch objective_achieved_by This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. objective_achieved_by OBI OBI is genome of organism a 'part of continuant at some time' relation that incides a genome belongs to a organism. Yongqun He, Bin Zhao is gene of organism Oliver He, Yue Liu a relation between a gene and the organism where this gene belongs to the organism in nature. It does not include a foreign gene that is transferred to an organism by a genetic engineering method. inheres in A dependent inheres in its bearer at all times for which the dependent exists. a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence inheres in inheres_in this fragility inheres in this vase this red color inheres in this apple bearer of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence bearer of bearer_of is bearer of this apple is bearer of this red color this vase is bearer of this fragility participates in a relation between a continuant and a process, in which the continuant is somehow involved in the process participates in participates_in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation has participant 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. a relation between a process and a continuant, in which the continuant is somehow involved in the process has participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has_participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) concretizes A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). concretizes has quality A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence has_quality this apple has quality this red color has role A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence has role has_role this person has role this investigator role (more colloquially: this person has this role of investigator) located_in located_in (type level) located in RO:0001025 file:/Users/michaelashburner/Desktop/gaz/gaz.obo located_in located_in http://www.obofoundry.org/ro/#OBO_REL:located_in Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime a relation between two independent continuants, the target and the location, in which the target is entirely within the location located in located_in my brain is located in my head this rat is located in this cage has component For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. is about vaccination procedure a relation between a question or a questionnaire that is specifically designed for a certain vaccination procedure. It is not clear if all questionnaires use the same question for a certain vaccination. If it is true, this relation is class level relation. If not, it is instance level relation. However, in a questionnaire and vaccination procedure, this is always true. asking vaccination patient documented by YH,YL, JZ an object property that represents a relation between a document and an entity that writes, maintains and releases the document. screening questionnaire is filled by used in geographic location has gender has vaccine contraindication This relation may be replaced by has_vaccine_allergen. We need to determine if any vaccine contraindicator is not a vaccine allergen. YH has_vaccine_contraindication is a relation that specifies contraindication of a vaccine. has vaccine allergen a object property that specifies a relation between a vaccine and a vaccine allergen YH vaccinated in route an object property that specifies a relation between a vaccine and a vaccinate route is_distributed_by is_distributed_by is a relation that specifies a company that distributes a product (e.g., vaccine). The company is very likely not the manufacturer of the product. YH, ZX vaccine immunization against disase Oliver He Asiyah Yu Lin vaccine immunization for host Yongqun He YL vaccine immunization against microbe Yongqun He bearer_of http://purl.org/obo/owl/ro_proposed A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in bearer_of inheres_in http://purl.org/obo/owl/ro_proposed 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. inheres_in inheres_in_part_of http://purl.org/obo/owl/ro_proposed inheres_in_part_of role_of http://purl.org/obo/owl/ro_proposed A relation between a role R and an entity E. R role_of E iff: R inheres_in E and R is a role role_of unfolds_in http://purl.org/obo/owl/ro_proposed P unfolds_in C : the execution of P is spatially contained by C. forall pP, forall c' partipates_in p, c' located_in C at t, for some t in P unfolds_in hasAge entity entity entity 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 An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) 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 Julius Caesar Verdi’s Requiem entity the Second World War your body mass index continuant continuant Continuant (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] (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] 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]) continuant 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. 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 a heart a person a symphony orchestra continuant endurant 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]) 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 occurrent (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] 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. (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] An entity that has temporal parts and that happens, unfolds or develops through time. 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]) 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 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. occurrent 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]) occurrent independent continuant IndependentContinuant (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] (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. a leg ic A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. 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]) a chair a heart a molecule a person a spatial region a symphony orchestra an atom an orchestra. an organism 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]) independent continuant substantial entity the bottom right portion of a human torso the interior of your mouth the lawn and atmosphere in front of our building spatial region true true (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] s-region BFO 2 Reference: Spatial regions do not participate in processes. SpatialRegion (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] 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]) 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. temporal region true true (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) 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 TemporalRegion t-region (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] 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]) spatiotemporal region true true st-region (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. SpatiotemporalRegion (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] 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 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]) 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 process (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] An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process Process 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) a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping 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]) process the course of a disease the flight of a bird the life of an organism your process of aging. disposition (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 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. Disposition (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] 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 disposition 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]) an atom of element X has the disposition to decay to an atom of element Y 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]) 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 realizable entity 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. All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) RealizableEntity realizable (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] (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] 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]) 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 quality (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] quality Quality (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] 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]) 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]) 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 specifically dependent continuant (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] (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] SpecificallyDependentContinuant 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. 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. 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]) 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. sdc 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. 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 mode property specifically dependent continuant 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 trope role Role role (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] 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. 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. 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]) role 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 three-dimensional spatial region ThreeDimensionalSpatialRegion 3d-s-region (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) a cube-shaped region of space a sphere-shaped region of space, site site Site (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] 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 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]) 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) generically dependent continuant gdc (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] GenericallyDependentContinuant 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. 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. 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 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]) generically dependent continuant 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. process boundary (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] Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) p-boundary ProcessBoundary 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]) the boundary between the 2nd and 3rd year of your life. material entity material (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 y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] (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] 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]) An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. MaterialEntity 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. Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) 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 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 every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) material entity the undetached arm of a human being immaterial entity 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 ImmaterialEntity zero-dimensional temporal region (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] ZeroDimensionalTemporalRegion 0d-t-region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) a temporal region that is occupied by a process boundary right now temporal instant. the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. gross anatomical part Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. gross anatomical part urea A carbonyl group with two C-bound amine groups. Beilstein:635724 CH4N2O CHEBI:15292 CHEBI:16199 CHEBI:27218 CHEBI:46379 CHEBI:9888 Carbamide ChemIDplus:57-13-6 CiteXplore:22770225 DrugBank:DB03904 E927b Gmelin:1378 H2NC(O)NH2 HMDB:HMDB00294 Harnstoff InChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4) InChIKey=XSQUKJJJFZCRTK-UHFFFAOYSA-N KEGG COMPOUND:57-13-6 KEGG COMPOUND:C00086 KEGG DRUG:D00023 Karbamid MetaCyc:UREA NC(N)=O NIST Chemistry WebBook:57-13-6 PDBeChem:URE Reaxys:635724 UM-BBD:c0165 UREA Urea Wikipedia:Urea carbamide carbonyldiamide chebi_ontology ur urea uree formaldehyde Beilstein:1209228 CH2O CHEBI:14274 CHEBI:16842 CHEBI:24077 CHEBI:337763 CHEBI:5142 ChEMBL:7381846 ChemIDplus:50-00-0 CiteXplore:18837732 DrugBank:DB03843 FORMALDEHYDE FORMALIN Formaldehyd Formaldehyde Formalin Gmelin:445 InChI=1S/CH2O/c1-2/h1H2 InChIKey=WSFSSNUMVMOOMR-UHFFFAOYSA-N KEGG COMPOUND:50-00-0 KEGG COMPOUND:C00067 Methanal Methylene oxide NIST Chemistry WebBook:50-00-0 Oxomethane Oxomethylene PDBeChem:FLH The simplest aldehyde. UM-BBD:c0122 Wikipedia:Formaldehyde [H]C([H])=O chebi_ontology formaldehyde streptomycin 2,4-Diguanidino-3,5,6-trihydroxycyclohexyl 5-deoxy-2-O-(2-deoxy-2-methylamino-alpha-L-glucopyranosyl)-3-C-formyl-beta-L-lyxopentanofuranoside A amino cyclitol glycoside that consists of streptidine having a disaccharyl moiety attached at the 4-position. The parent of the streptomycin class Beilstein:74498 C21H39N7O12 CHEBI:15119 CHEBI:17076 CHEBI:26784 CHEBI:45745 CHEBI:9284 CN[C@H]1[C@H](O)[C@@H](O)[C@H](CO)O[C@H]1O[C@H]1[C@@H](O[C@@H](C)[C@]1(O)C=O)O[C@H]1[C@H](O)[C@@H](O)[C@H](NC(N)=N)[C@@H](O)[C@@H]1NC(N)=N ChemIDplus:57-92-1 CiteXplore:11228320 CiteXplore:11905029 CiteXplore:12118520 CiteXplore:13030054 CiteXplore:13116094 CiteXplore:13136149 CiteXplore:13596285 CiteXplore:13691614 CiteXplore:13985260 CiteXplore:13990247 CiteXplore:14623118 CiteXplore:14828344 CiteXplore:14852338 CiteXplore:14939639 CiteXplore:15081082 CiteXplore:15137533 CiteXplore:15207172 CiteXplore:15686853 CiteXplore:15736038 CiteXplore:16904706 CiteXplore:17105735 CiteXplore:17238915 CiteXplore:17429930 CiteXplore:18173084 CiteXplore:18916143 CiteXplore:19052412 CiteXplore:19335957 CiteXplore:21350946 CiteXplore:21362244 CiteXplore:21593257 CiteXplore:21937264 DrugBank:DB01082 InChI=1S/C21H39N7O12/c1-5-21(36,4-30)16(40-17-9(26-2)13(34)10(31)6(3-29)38-17)18(37-5)39-15-8(28-20(24)25)11(32)7(27-19(22)23)12(33)14(15)35/h4-18,26,29,31-36H,3H2,1-2H3,(H4,22,23,27)(H4,24,25,28)/t5-,6-,7+,8-,9-,10-,11+,12-,13-,14+,15+,16-,17-,18-,21+/m0/s1 InChIKey=UCSJYZPVAKXKNQ-HZYVHMACSA-N KEGG COMPOUND:57-92-1 KEGG COMPOUND:C00413 KEGG DRUG:D08531 Kantrex N,N'''-[(1R,2R,3S,4R,5R,6S)-4-{5-deoxy-2-O-[2-deoxy-2-(methylamino)-alpha-L-glucopyranosyl]-3-C-formyl-alpha-L-lyxofuranosyloxy}-2,5,6-trihydroxycyclohexane-1,3-diyl]diguanidine PDBeChem:SRY Reaxys:74498 SM STREPTOMYCIN Wikipedia:Streptomycin [2-deoxy-2-(dimethylamino)-alpha-L-glucopyranosyl]-(1->2)-[5-deoxy-3-C-formyl-alpha-L-lyxofuranosyl]-(1->4)-{N',N'''-[(1,3,5/2,4,6)-2,4,5,6-tetrahydroxycyclohexane-1,3-diyl]diguanidine} chebi_ontology streptomycin lactose (+)-lactose (Gal)1 (Glc)1 1-beta-D-Galactopyranosyl-4-D-glucopyranose 4-(beta-D-galactosido)-D-glucose 4-O-beta-D-galactopyranosyl-D-glucose A disaccharide, found most notably in milk, that consists of D-galactose and D-glucose fragments bonded through a beta-1->4 glycosidic linkage. The glucose fragment can be in either the alpha- or beta-pyranose form, whereas the galactose fragment can only have the beta-pyranose form. Beilstein:1292745 C12H22O11 CHEBI:10296 CHEBI:10380 CHEBI:14497 CHEBI:17716 CHEBI:22460 CHEBI:22760 CHEBI:25005 CHEBI:27755 CHEBI:613009 ChEMBL:19053747 ChemIDplus:63-42-3 CiteXplore:1292745 CiteXplore:17329833 CiteXplore:18300214 CiteXplore:19846069 CiteXplore:19913595 CiteXplore:20094999 CiteXplore:20503067 CiteXplore:20699559 CiteXplore:20873837 CiteXplore:20961532 CiteXplore:21403918 CiteXplore:2432147 CiteXplore:2456994 CiteXplore:6194884 CiteXplore:7574700 D-lactose Galbeta1-4-Glc Gmelin:882872 InChI=1S/C12H22O11/c13-1-3-5(15)6(16)9(19)12(22-3)23-10-4(2-14)21-11(20)8(18)7(10)17/h3-20H,1-2H2/t3-,4-,5+,6+,7-,8-,9-,10-,11?,12+/m1/s1 InChIKey=GUBGYTABKSRVRQ-QKKXKWKRSA-N KEGG COMPOUND:C00243 KEGG GLYCAN:G10504 Lac Laktobiose Laktose Milchzucker NIST Chemistry WebBook:63-42-3 OC[C@H]1O[C@@H](O[C@@H]2[C@@H](CO)OC(O)[C@H](O)[C@H]2O)[C@H](O)[C@@H](O)[C@H]1O Reaxys:1292745 beta-D-Gal-(1->4)-D-Glc beta-D-Galp-(1->4)-D-Glcp beta-D-galactopyranosyl-(1->4)-D-glucopyranose beta-Gal1,4-Glc chebi_ontology lactobiose lactose milk sugar gentamycin 4,6-diamino-3-[3-deoxy-4-C-methyl-3-(methylamino)pentopyranosyloxy]-2-hydroxycyclohexyl 2-amino-2,3,4,6,7-pentadeoxy-6-(methylamino)heptopyranoside Any of a group of aminoglycoside antibiotics produced by fermentation of some Micromonospora spp. CHEBI:14293 CHEBI:17833 CHEBI:24206 CHEBI:24212 CHEBI:5306 DrugBank:DB00798 Gentamicin KEGG COMPOUND:1403-66-3 KEGG COMPOUND:C00505 chebi_ontology gentamicin gentamycins sucrose 1-alpha-D-Glucopyranosyl-2-beta-D-fructofuranoside Beilstein:90825 C12H22O11 CHEBI:15128 CHEBI:17992 CHEBI:26812 CHEBI:45795 CHEBI:9314 Cane sugar ChemIDplus:57-50-1 CiteXplore:11021636 CiteXplore:11093712 CiteXplore:11111003 CiteXplore:12065720 CiteXplore:12706980 CiteXplore:13508893 CiteXplore:15291457 CiteXplore:15660210 CiteXplore:15792978 CiteXplore:15845855 CiteXplore:16228482 CiteXplore:16304615 CiteXplore:16313996 CiteXplore:16525719 CiteXplore:16660545 CiteXplore:16663947 CiteXplore:16665852 CiteXplore:17233733 CiteXplore:17439666 CiteXplore:17597061 CiteXplore:18625236 CiteXplore:19199566 CiteXplore:19726178 CiteXplore:21703290 CiteXplore:21972845 CiteXplore:22085755 CiteXplore:22311778 CiteXplore:22404833 CiteXplore:22751876 DrugBank:DB02772 Gmelin:97695 HMDB:HMDB00258 InChI=1S/C12H22O11/c13-1-4-6(16)8(18)9(19)11(21-4)23-12(3-15)10(20)7(17)5(2-14)22-12/h4-11,13-20H,1-3H2/t4-,5-,6-,7-,8+,9-,10+,11-,12+/m1/s1 InChIKey=CZMRCDWAGMRECN-UGDNZRGBSA-N KEGG COMPOUND:57-50-1 KEGG COMPOUND:C00089 KEGG DRUG:D00025 KEGG GLYCAN:G00370 MetaCyc:SUCROSE NIST Chemistry WebBook:57-50-1 OC[C@H]1O[C@H](O[C@]2(CO)O[C@H](CO)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H](O)[C@@H]1O PDBeChem:SUC Reaxys:1435311 Reaxys:90825 SUCROSE Saccharose Sacharose Sucrose Sucrose is a disaccharide formed by glucose and fructose units joined by an acetal oxygen bridge from hemiacetal of glucose to the hemiketal of the fructose. White sugar Wikipedia:Sucrose beta-D-Fruf-(2<->1)-alpha-D-Glcp beta-D-fructofuranosyl alpha-D-glucopyranoside chebi_ontology sacarosa table sugar molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. CHEBI:23367 chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molecular entity molekulare Entitaet aspartame 1-methyl N-L-alpha-aspartyl-L-phenylalanate 3-Amino-N-(alpha-carboxyphenethyl)succinamic acid N-methyl ester 3-Amino-N-(alpha-methoxycarbonylphenethyl) succinamic acid A dipeptide that has formula C14H18N2O5. Asp-phe-ome Aspartame Aspartylphenylalanine methyl ester Beilstein:2223850 C14H18N2O5 CHEBI:2877 COC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](N)CC(O)=O ChemIDplus:22839-47-0 DrugBank:DB00168 InChI=1S/C14H18N2O5/c1-21-14(20)11(7-9-5-3-2-4-6-9)16-13(19)10(15)8-12(17)18/h2-6,10-11H,7-8,15H2,1H3,(H,16,19)(H,17,18)/t10-,11-/m0/s1 InChIKey=IAOZJIPTCAWIRG-QWRGUYRKSA-N KEGG COMPOUND:C11045 KEGG DRUG:D02381 L-Aspartyl-L-phenylalanine methyl ester aspartam aspartame aspartamo aspartamum chebi_ontology methyl L-alpha-aspartyl-L-phenylalaninate glucitol Beilstein:1721909 C6H14O6 CHEBI:15093 CHEBI:26724 CHEBI:26726 CHEBI:30911 CHEBI:33795 CHEBI:33796 CHEBI:9201 Gmelin:83165 Sorbitol chebi_ontology glucitol gulitol rel-(2R,3R,4R,5S)-hexane-1,2,3,4,5,6-hexol sorbitol dextran (C12H20O10)n A (1->6)-alpha-D-glucan which has extra branching consisting of (1->2), (1->3) or (1->4) linkages. CHEBI:52071 ChemIDplus:9004-54-0 CiteXplore:8154046 Dextran 40 Dextran 70 KEGG DRUG:D00060 chebi_ontology dextran dextrano dextrans dextranum monosodium glutamate An organic sodium salt that is the monosodium salt of glutamic acid. C5H8NNaO4 CHEBI:64220 CiteXplore:22293291 InChI=1S/C5H9NO4.Na/c6-3(5(9)10)1-2-4(7)8;/h3H,1-2,6H2,(H,7,8)(H,9,10);/q;+1/p-1 InChIKey=LPUQAYUQRXPFSQ-UHFFFAOYSA-M MSG Reaxys:17003240 [Na+].[NH3+]C(CCC([O-])=O)C([O-])=O chebi_ontology sodium 2-ammoniopentanedioate sodium 2-azaniumylpentanedioate sodium glutamate neomycin A broad-spectrum highly toxic antibiotic or mixture of antibiotics produced by a streptomyces (Streptomyces fradiae) and used medically especially to treat local infections. CHEBI:7507 DrugBank:DB00994 KEGG COMPOUND:C00384 Neomycin chebi_ontology thimerosal An organomercury compound (approximately 49% mercury by weight) used as an antiseptic and antifungal agent. Beilstein:8169555 C9H9HgNaO2S C9H9HgO2S.Na CHEBI:9546 ChemIDplus:54-64-8 CiteXplore:18837732 CiteXplore:21616561 Gmelin:1677155 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 KEGG COMPOUND:C08044 Merthiolate Thimerosal Thiomersal [(o-carboxyphenyl)thio]ethylmercury sodium salt [Na+].CC[Hg]Sc1ccccc1C([O-])=O chebi_ontology ethyl(2-mercaptobenzoato-S)mercury sodium salt ethylmercurithiosalicylate sodium mercurothiolate o-(ethylmercurithio)benzoic acid sodium salt sodium [(2-carboxylatophenyl)sulfanyl](ethyl)mercurate(1-) sodium ethyl[2-(sulfanyl-kappaS)benzoato(2-)]mercurate(1-) sodium ethylmercurithiosalicylate thiomersalate cardiomyopathy 2012-01-03T02:54:11Z A heart disease and a myopathy that is characterized by deterioration of the function of the heart muscle. Cardiomyopathies DOID:0050700 ICD10CM:I42 ICD10CM:I42.9 ICD10CM:I51.5 ICD9CM:425 ICD9CM:425.9 MSH:D009202 MSH:D009202 added from NeuroDevNet [WAK]. NCI:C34830 NCI:C53654 SNOMEDCT_US_2015_03_01:155351008 SNOMEDCT_US_2015_03_01:155353006 SNOMEDCT_US_2015_03_01:195035002 SNOMEDCT_US_2015_03_01:195037005 SNOMEDCT_US_2015_03_01:20072003 SNOMEDCT_US_2015_03_01:266244008 SNOMEDCT_US_2015_03_01:266301006 SNOMEDCT_US_2015_03_01:57809008 SNOMEDCT_US_2015_03_01:85898001 SNOMEDCT_US_2015_03_01:89461002 SNOMEDCT_US_2015_03_01:89600009 UMLS_CUI:C0033141 UMLS_CUI:C0036529 UMLS_CUI:C0878544 disease_ontology lschriml lymphoma A hematologic cancer that affects lymphocytes that reside in the lymphatic system and in blood-forming organs. DOID:0060058 DOID:1033 DOID:353 ICD10CM:C85.9 MSH:D008223 NCI:C3208 NCI:C7065 SNOMEDCT_US_2015_03_01:115244002 SNOMEDCT_US_2015_03_01:118600007 SNOMEDCT_US_2015_03_01:134218000 SNOMEDCT_US_2015_03_01:188676008 SNOMEDCT_US_2015_03_01:188694002 SNOMEDCT_US_2015_03_01:188695001 SNOMEDCT_US_2015_03_01:188704004 SNOMEDCT_US_2015_03_01:189959002 SNOMEDCT_US_2015_03_01:189965002 SNOMEDCT_US_2015_03_01:21964009 SNOMEDCT_US_2015_03_01:269627002 SNOMEDCT_US_2015_03_01:414628006 UMLS_CUI:C0024299 UMLS_CUI:C0598798 disease_ontology lymphoid cancer heart disease A cardiovascular system disease that involves the heart. DOID:114 ICD10CM:I51.9 ICD9CM:429.9 MSH:D006331 NCI:C3079 SNOMEDCT_US_2015_03_01:155263000 SNOMEDCT_US_2015_03_01:194707003 SNOMEDCT_US_2015_03_01:195152001 SNOMEDCT_US_2015_03_01:266275004 SNOMEDCT_US_2015_03_01:266311004 SNOMEDCT_US_2015_03_01:56265001 UMLS_CUI:C0018799 disease_ontology hypersensitivity reaction type I disease An immune system disease that is an exaggerated immune response to allergens, such as insect venom, dust mites, pollen, pet dander, drugs or some foods. DOID:1205 ICD10CM:T78.40 MSH:D006967 NCI:C3114 SNOMEDCT_US_2015_03_01:106190000 SNOMEDCT_US_2015_03_01:127072000 SNOMEDCT_US_2015_03_01:157754004 SNOMEDCT_US_2015_03_01:157758001 SNOMEDCT_US_2015_03_01:212998004 SNOMEDCT_US_2015_03_01:212999007 SNOMEDCT_US_2015_03_01:21957007 SNOMEDCT_US_2015_03_01:257550005 SNOMEDCT_US_2015_03_01:269284003 SNOMEDCT_US_2015_03_01:269432007 SNOMEDCT_US_2015_03_01:274211000 SNOMEDCT_US_2015_03_01:282092005 SNOMEDCT_US_2015_03_01:418168000 SNOMEDCT_US_2015_03_01:418634005 SNOMEDCT_US_2015_03_01:418925002 SNOMEDCT_US_2015_03_01:421668005 SNOMEDCT_US_2015_03_01:421961002 SNOMEDCT_US_2015_03_01:91232002 UMLS_CUI:C0020517 allergy disease_ontology hypersensitivity leukemia A cancer that affects the blood or bone marrow characterized by an abnormal proliferation of blood cells. DOID:1240 DOID:9145 ICD10CM:C95 ICD10CM:C95.9 ICD10CM:C95.90 ICD9CM:208 ICD9CM:208.9 MSH:D007938 NCI:C3161 SNOMEDCT_US_2015_03_01:154598008 SNOMEDCT_US_2015_03_01:188762002 SNOMEDCT_US_2015_03_01:188767008 SNOMEDCT_US_2015_03_01:190024009 SNOMEDCT_US_2015_03_01:190025005 SNOMEDCT_US_2015_03_01:190029004 SNOMEDCT_US_2015_03_01:190071003 SNOMEDCT_US_2015_03_01:255049003 SNOMEDCT_US_2015_03_01:87163000 SNOMEDCT_US_2015_03_01:93143009 UMLS_CUI:C0023418 disease_ontology Guillain-Barre syndrome An autoimmune disease of peripheral nervous system that causes body's immune system to attack part of the peripheral nervous system. DOID:12842 Guillain-Barre syndrome (disorder) ICD10CM:G61.0 ICD9CM:357.0 Infectious neuronitis (disorder) MSH:D020275 NCI:C26790 OMIM mapping confirmed by DO. [SN]. OMIM:139393 Post-infectious polyneuritis (disorder) Postinfectious polyneuritis SNOMEDCT_US_2015_03_01:128085000 SNOMEDCT_US_2015_03_01:129131007 SNOMEDCT_US_2015_03_01:155082001 SNOMEDCT_US_2015_03_01:193173004 SNOMEDCT_US_2015_03_01:193174005 SNOMEDCT_US_2015_03_01:193176007 SNOMEDCT_US_2015_03_01:267707000 SNOMEDCT_US_2015_03_01:40956001 UMLS_CUI:C0018378 acute Infective Polyneuritis acute inf. polyneuritis acute infective polyneuritis acute infective polyneuritis (disorder) acute infective polyneuritis NOS (disorder) acute postinfectious polyneuropathy disease_ontology diarrhea A gastrointestinal system disease described as the condition of having frequent loose or liquid bowel movements. Acute diarrhea is a common cause of death in developing countries and the second most common cause of infant deaths worldwide. The loss of fluids through diarrhea can cause severe dehydration which is one cause of death in diarrhea sufferers. Along with water, sufferers also lose dangerous amounts of important salts, electrolytes, and other nutrients. There are at least four types of diarrhea: secretory diarrhea, osmotic diarrhea, motility-related diarrhea, and inflammatory diarrhea. DOID:0050006 DOID:13250 ICD9CM:009.2 MSH:D004403 SNOMEDCT_US_2015_03_01:111939009 SNOMEDCT_US_2015_03_01:154268000 SNOMEDCT_US_2015_03_01:154279005 SNOMEDCT_US_2015_03_01:186165000 SNOMEDCT_US_2015_03_01:186167008 SNOMEDCT_US_2015_03_01:19213003 SNOMEDCT_US_2015_03_01:236076004 SNOMEDCT_US_2015_03_01:266173000 SNOMEDCT_US_2015_03_01:266180003 UMLS_CUI:C0013369 diarrhea of presumed infectious origin diarrhoea disease_ontology thrombocytopenia A blood platelet disease characterized by low a platelet count in the blood. DOID:1588 ICD10CM:D69.6 ICD9CM:287.5 MSH:D013921 NCI:C3408 OMIM:188000 OMIM:273900 OMIM:300367 OMIM:313900 OMIM:612004 ORDO:852 SNOMEDCT_US_2015_03_01:142969008 SNOMEDCT_US_2015_03_01:154827000 SNOMEDCT_US_2015_03_01:165556002 SNOMEDCT_US_2015_03_01:191326009 SNOMEDCT_US_2015_03_01:302215000 SNOMEDCT_US_2015_03_01:415116008 SNOMEDCT_US_2015_03_01:70786006 UMLS_CUI:C0040034 Xref MGI. disease_ontology cancer A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. DOID:162 ICD10CM:C80 ICD10CM:C80.1 ICD9CM:199 ICD9CM:239.4 MSH:D009369 NCI:C9305 SNOMEDCT_2010_1_31:189535002 SNOMEDCT_US_2015_03_01:154432008 SNOMEDCT_US_2015_03_01:154433003 SNOMEDCT_US_2015_03_01:154577008 SNOMEDCT_US_2015_03_01:187597000 SNOMEDCT_US_2015_03_01:188475001 SNOMEDCT_US_2015_03_01:188482002 SNOMEDCT_US_2015_03_01:190150006 SNOMEDCT_US_2015_03_01:269513004 SNOMEDCT_US_2015_03_01:269623003 SNOMEDCT_US_2015_03_01:269626006 SNOMEDCT_US_2015_03_01:269634000 SNOMEDCT_US_2015_03_01:363346000 SNOMEDCT_US_2015_03_01:38807002 UMLS_CUI:C0006826 UMLS_CUI:C0027639 Updating out dated UMLS CUI. disease_ontology malignant neoplasm malignant tumor primary cancer transient cerebral ischemia DOID:224 DOID:2315 ICD10CM:G45.9 ICD9CM:435.8 MSH:D002546 NCI:C50781 SNOMEDCT_US_2015_03_01:155404005 SNOMEDCT_US_2015_03_01:195196001 SNOMEDCT_US_2015_03_01:195207009 SNOMEDCT_US_2015_03_01:266257000 SNOMEDCT_US_2015_03_01:266314007 SNOMEDCT_US_2015_03_01:313242003 SNOMEDCT_US_2015_03_01:38609002 TIA TIA - Transient ischaemic attack TRANSIENT ISCHEMIC ATTACK Transient cerebral ischaemia Transient cerebral ischaemia NOS Transient cerebral ischemia (disorder) [Ambiguous] Transient ischemic attacks (disorder) UMLS_CUI:C0007787 UMLS_CUI:C0155728 disease_ontology transient ischemic attack anemia A hematopoietic system disease that is characterized by a decrease in the normal number of red blood cells. DOID:2355 EFO:0004272 ICD10CM:D64.9 ICD9CM:285.9 MSH:D000740 NCI:C2869 PRISM. SNOMEDCT_US_2015_03_01:154786001 SNOMEDCT_US_2015_03_01:154812000 SNOMEDCT_US_2015_03_01:191277004 SNOMEDCT_US_2015_03_01:267531008 SNOMEDCT_US_2015_03_01:271737000 SNOMEDCT_US_2015_03_01:64593003 UMLS_CUI:C0002871 anaemia disease_ontology agammaglobulinemia A B cell deficiency that is caused by a reduction in all types of gamma globulins. DOID:2583 DOID:618 ICD10CM:D80.1 ICD9CM:279.00 IGHM MSH:D000361 NCI:C26931 OMIM mapping confirmed by DO. [SN]. OMIM:601495 OMIM:612692 OMIM:613500 OMIM:613501 OMIM:613502 OMIM:613506 OMIM:615214 SNOMEDCT_US_2015_03_01:119249001 SNOMEDCT_US_2015_03_01:119250001 SNOMEDCT_US_2015_03_01:190977001 SNOMEDCT_US_2015_03_01:190978006 SNOMEDCT_US_2015_03_01:267512002 SNOMEDCT_US_2015_03_01:81282009 UMLS_CUI:C0001768 UMLS_CUI:C0086438 disease_ontology hypogammaglobulinemia mu heavy chain deficiency dermatitis A skin disease characterized by itchy, erythematous, vesicular, weeping and crusting patches of skin. DOID:2723 DOID:8614 DOID:8917 ICD10CM:L30.9 MSH:D003872 NCI:C2983 SNOMEDCT_US_2015_03_01:156358005 SNOMEDCT_US_2015_03_01:156388001 SNOMEDCT_US_2015_03_01:182782007 SNOMEDCT_US_2015_03_01:200884006 SNOMEDCT_US_2015_03_01:238538009 SNOMEDCT_US_2015_03_01:267847004 SNOMEDCT_US_2015_03_01:267856007 SNOMEDCT_US_2015_03_01:43116000 SNOMEDCT_US_2015_03_01:4979002 UMLS_CUI:C0011603 disease_ontology eczema skin inflammation keratosis follicularis DARIER-WHITE DISEASE DOID:2734 Darier's disease ICD10CM:E50.8 Keratosis follicularis (disorder) MSH:D007644 NCI:C84665 OMIM mapping confirmed by DO. [SN]. OMIM:124200 SNOMEDCT_US_2015_03_01:157017000 SNOMEDCT_US_2015_03_01:205582000 SNOMEDCT_US_2015_03_01:240633005 SNOMEDCT_US_2015_03_01:268355000 SNOMEDCT_US_2015_03_01:48611009 UMLS_CUI:C0022595 disease_ontology asthma A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors. The disease has_symptom recurring periods of wheezing (a whistling sound while breathing), has_symptom chest tightness, has_symptom shortness of breath, has_symptom mucus production and has_symptom coughing. The symptoms appear due to a variety of triggers such as allergens, irritants, respiratory infections, weather changes, exercise, stress, reflux disease, medications, foods and emotional anxiety. DOID:12703 DOID:13829 DOID:13830 DOID:2840 DOID:2841 DOID:5783 EFO:0000270 Exercise induced asthma ICD10CM:J45 ICD10CM:J45.90 ICD10CM:J45.909 ICD9CM:493 ICD9CM:493.9 KEGG:05310 MSH:D001249 NCI:C28397 OMIM:600807 SNOMEDCT_US_2015_03_01:155574008 SNOMEDCT_US_2015_03_01:155579003 SNOMEDCT_US_2015_03_01:187687003 SNOMEDCT_US_2015_03_01:195967001 SNOMEDCT_US_2015_03_01:195979001 SNOMEDCT_US_2015_03_01:195983001 SNOMEDCT_US_2015_03_01:21341004 SNOMEDCT_US_2015_03_01:266365004 SNOMEDCT_US_2015_03_01:266398009 SNOMEDCT_US_2015_03_01:278517007 UMLS_CUI:C0004096 Xref MGI. bronchial hyperreactivity chronic obstructive asthma chronic obstructive asthma with acute exacerbation chronic obstructive asthma with status asthmaticus disease_ontology exercise-induced asthma food allergy A hypersensitivity reaction type I disease that is an abnormal response to a food, triggered by the body's immune system. DOID:3044 MSH:D005512 SNOMEDCT_US_2015_03_01:157801005 SNOMEDCT_US_2015_03_01:213018006 SNOMEDCT_US_2015_03_01:414285001 SNOMEDCT_US_2015_03_01:52332009 UMLS_CUI:C0016470 disease_ontology food hypersensitivity chronic obstructive pulmonary disease COLD (chronic obstructive lung disease) COPD DOID:11500 DOID:3083 DOID:6144 EFO:0000341 ICD10CM:J44.9 MSH:D029424 NCI:C3199 SNOMEDCT_US_2015_03_01:10169006 SNOMEDCT_US_2015_03_01:13645005 SNOMEDCT_US_2015_03_01:155565006 SNOMEDCT_US_2015_03_01:155569000 SNOMEDCT_US_2015_03_01:155585005 SNOMEDCT_US_2015_03_01:155617000 SNOMEDCT_US_2015_03_01:195935004 SNOMEDCT_US_2015_03_01:195948000 SNOMEDCT_US_2015_03_01:196003006 SNOMEDCT_US_2015_03_01:413846005 UMLS_CUI:C0024117 chronic obstructive airway disease chronic obstructive lung disease disease_ontology thymoma A thymus cancer that derives_from epithelial cells located_in the thymus. The tumor cells in a thymoma look similar to the normal cells of the thymus, grow slowly, and rarely spread beyond the thymus. DOID:3275 MSH:D013945 NCI:C3411 SNOMEDCT_US_2015_03_01:128856005 SNOMEDCT_US_2015_03_01:189721001 SNOMEDCT_US_2015_03_01:444231005 UMLS_CUI:C0040100 disease_ontology disease A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. DOID:4 MSH:D004194 NCI:C2991 SNOMEDCT_US_2015_03_01:64572001 UMLS_CUI:C0012634 disease_ontology liver disease DOID:2164 DOID:2165 DOID:409 DOID:46 ICD10CM:K70-K77 ICD10CM:K76.9 ICD9CM:573.9 MSH:D008107 NCI:C3196 SNOMEDCT_US_2015_03_01:155807008 SNOMEDCT_US_2015_03_01:155817003 SNOMEDCT_US_2015_03_01:155822003 SNOMEDCT_US_2015_03_01:197375001 SNOMEDCT_US_2015_03_01:197551000 SNOMEDCT_US_2015_03_01:235856003 SNOMEDCT_US_2015_03_01:266535008 SNOMEDCT_US_2015_03_01:62857009 UMLS_CUI:C0023895 disease_ontology disorder of liver (disorder) hepatic disorder hypersensitivity reaction type II disease An immune system disease that is an overactive immune response of the body against substances and tissues normally present in the body resulting from an abnormal functioning of the immune system that results in the production of antibodies or T cell directed against the host tissues. DOID:417 ICD9CM:720 UMLS_CUI:C0003089 Xref MGI. autoimmune disease disease_ontology egg allergy A food allergy that is an allergy or hypersensitivity to dietary substances from the yolk or whites of eggs, causing an overreaction of the immune system which may lead to severe physical symptoms. Allergy to eggs (disorder) DOID:4377 Egg allergy MSH:D021181 SNOMEDCT_US_2015_03_01:157802003 SNOMEDCT_US_2015_03_01:213019003 SNOMEDCT_US_2015_03_01:91930004 UMLS_CUI:C0559469 disease_ontology thymus gland disease DOID:11024 DOID:533 ICD10CM:E32 ICD10CM:E32.9 ICD9CM:254 ICD9CM:254.9 NCI:C26962 SNOMEDCT_US_2015_03_01:154703006 SNOMEDCT_US_2015_03_01:190500009 SNOMEDCT_US_2015_03_01:20673009 SNOMEDCT_US_2015_03_01:267482009 UMLS_CUI:C0154199 disease of thymus gland disease_ontology kidney disease A urinary system disease that is located_in the kidney. DOID:557 EFO:0003086 ICD10CM:N08 ICD10CM:N28.9 MSH:D007674 NCI:C3149 NCI:C34843 SNOMEDCT_US_2015_03_01:155871008 SNOMEDCT_US_2015_03_01:266612003 SNOMEDCT_US_2015_03_01:266624005 SNOMEDCT_US_2015_03_01:266627003 SNOMEDCT_US_2015_03_01:274108006 SNOMEDCT_US_2015_03_01:90708001 UMLS_CUI:C0022658 disease_ontology nephropathy myocardial infarction A coronary artery disease characterized by myocardial cell death (myocardial necrosis) due to prolonged ischaemia. DOID:5844 EFO:0000612 ICD10CM:I21 ICD10CM:I22 MSH:D009203 Myocardial infarct NCI:C27996 OMIM:608446 OMIM:608557 SNOMEDCT_US_2015_03_01:155304006 SNOMEDCT_US_2015_03_01:194796000 SNOMEDCT_US_2015_03_01:22298006 SNOMEDCT_US_2015_03_01:233824008 SNOMEDCT_US_2015_03_01:266288001 SNOMEDCT_US_2015_03_01:66514008 UMLS_CUI:C0027051 Xref MGI. disease_ontology heart attack congestive heart failure A heart disease that is characterized by any structural or functional cardiac disorder that impairs the ability of the heart to fill with or pump a sufficient amount of blood throughout the body. CHF Cardiac Failure Congestive Congestive heart disease DOID:395 DOID:6000 ICD10CM:I50 ICD10CM:I50.9 ICD9CM:428 ICD9CM:428.0 ICD9CM:428.9 MSH:D006333 NCI:C3080 NCI:C50577 SNOMEDCT_US_2015_03_01:155374007 SNOMEDCT_US_2015_03_01:155375008 SNOMEDCT_US_2015_03_01:155377000 SNOMEDCT_US_2015_03_01:195108009 SNOMEDCT_US_2015_03_01:195117009 SNOMEDCT_US_2015_03_01:266248006 SNOMEDCT_US_2015_03_01:266308000 SNOMEDCT_US_2015_03_01:42343007 SNOMEDCT_US_2015_03_01:84114007 UMLS_CUI:C0018801 UMLS_CUI:C0018802 Weak heart disease_ontology acquired immunodeficiency syndrome A Human immunodeficiency virus infectious disease that results_in reduction in the numbers of CD4-bearing helper T cells below 200 per µL of blood or 14% of all lymphocytes thereby rendering the subject highly vulnerable to life-threatening infections and cancers, has_material_basis_in Human immunodeficiency virus 1 or has_material_basis_in Human immunodeficiency virus 2, which are transmitted_by sexual contact, transmitted_by transfer of blood, semen, vaginal fluid, pre-ejaculate, or breast milk, transmitted_by congenital method, and transmitted_by contaminated needles. Opportunistic infections are common in people with AIDS. AIDS DOID:635 EFO:0000765 ICD10CM:B20 MSH:D000163 NCI:C2851 OMIM:609423 SNOMEDCT_US_2015_03_01:186705005 SNOMEDCT_US_2015_03_01:186715004 SNOMEDCT_US_2015_03_01:234644008 SNOMEDCT_US_2015_03_01:266201009 SNOMEDCT_US_2015_03_01:62479008 UMLS_CUI:C0001175 acquired Immune deficiency acquired immune deficiency syndrome disease_ontology acne A sebaceous gland disease characterized by areas of blackheads, whiteheads, pimples, greasy skin, and possibly scarring. Acne varioliformis DOID:6543 DOID:9906 ICD10CM:L70 ICD10CM:L70.2 ICD10CM:L70.9 ICD9CM:706.0 MTH:217 NCI:C27195 OMIM:604324 SNOMEDCT_US_2015_03_01:11381005 SNOMEDCT_US_2015_03_01:201210008 SNOMEDCT_US_2015_03_01:201211007 SNOMEDCT_US_2015_03_01:201212000 SNOMEDCT_US_2015_03_01:201229002 SNOMEDCT_US_2015_03_01:201408008 SNOMEDCT_US_2015_03_01:23894009 SNOMEDCT_US_2015_03_01:267815009 UMLS_CUI:C0152249 UMLS_CUI:C0702166 acne vulgaris disease_ontology frontalis acne cerebrovascular disease An artery disease that is characterized by dysfunction of the blood vessels supplying the brain. CVA (cerebral vascular accident) Cerebrovascular accident (disorder) DOID:12214 DOID:3455 DOID:6713 DOID:8231 EFO:0000712 ICD10CM:I60-I69 ICD10CM:I63.9 ICD10CM:I67.9 ICD9CM:430-438.99 ICD9CM:437.9 MSH:D002561 MSH:D020521 NCI:C2938 NCI:C3390 OMIM mapping confirmed by DO. [SN]. OMIM:601367 SNOMEDCT_US_2015_03_01:155388006 SNOMEDCT_US_2015_03_01:155405006 SNOMEDCT_US_2015_03_01:155412002 SNOMEDCT_US_2015_03_01:195208004 SNOMEDCT_US_2015_03_01:195249004 SNOMEDCT_US_2015_03_01:195595007 SNOMEDCT_US_2015_03_01:230690007 SNOMEDCT_US_2015_03_01:266312006 SNOMEDCT_US_2015_03_01:266315008 SNOMEDCT_US_2015_03_01:270883006 SNOMEDCT_US_2015_03_01:313267000 SNOMEDCT_US_2015_03_01:62914000 SNOMEDCT_US_2015_03_01:82797006 UMLS_CUI:C0007820 UMLS_CUI:C0038454 cerebrovascular accident cerebrovascular disorder disease_ontology stroke ankylosing spondylitis A bone inflammation disease that results_in inflammation in the joints of the spine and pelvis. The disease has_symptom pain, has_symptom stiffness in the spine, has_symptom stiffness in the neck, has_symptom stiffness in the hips, has_symptom stiffness in the jaw and has_symptom stiffness in the rib cage. Bekhterev syndrome Bekhterev's disease DOID:7147 EFO:0003898 ICD10CM:M45 ICD9CM:720.0 MSH:D013167 Marie-Strumpell disease NCI:C84564 ORDO:825 SNOMEDCT_US_2015_03_01:156619005 SNOMEDCT_US_2015_03_01:9631008 UMLS_CUI:C0038013 disease_ontology rheumatoid arthritis An arthritis that is an autoimmune disease which attacks healthy cells and tissue located_in joint. Arthritis or polyarthritis, rheumatic DOID:7148 EFO:0000685 ICD10CM:M06.9 ICD9CM:714.0 KEGG:05323 MSH:D001172 NCI:C27206 NCI:C2884 OMIM mapping confirmed by DO. [SN]. OMIM:180300 SNOMEDCT_US_2015_03_01:156471009 SNOMEDCT_US_2015_03_01:156481008 SNOMEDCT_US_2015_03_01:287010008 SNOMEDCT_US_2015_03_01:69896004 UMLS_CUI:C0003873 atrophic Arthritis disease_ontology lung disease A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide. DOID:11894 DOID:11895 DOID:29 DOID:766 DOID:850 ICD10CM:J98.4 MSH:D008171 NCI:C3198 Non-neoplastic pulmonary disorder SNOMEDCT_US_2015_03_01:196164004 SNOMEDCT_US_2015_03_01:19829001 SNOMEDCT_US_2015_03_01:266374002 UMLS_CUI:C0024115 Updating out dated CUI and removing lung abscess as a synonym. disease_ontology non-neoplastic lung disorder impetigo A pyoderma consisting of three forms of skin lesions having either a thick, adherent, recurrent, dirty yellow crust with an erythematous margin (common or superficial impetigo) or lessions which are superficial, thin-walled, and bullous as found in bullous impetigo. The lesions in bullous (staphylococcal) impetigo, which are always caused by S aureus, are superficial, thin-walled, and bullous. DOID:8504 ICD10CM:L01 ICD10CM:L01.0 ICD10CM:L01.00 ICD9CM:684 MSH:D007169 NCI:C99088 SNOMEDCT_US_2015_03_01:156319000 SNOMEDCT_US_2015_03_01:200710001 SNOMEDCT_US_2015_03_01:267836006 SNOMEDCT_US_2015_03_01:48277006 UMLS_CUI:C0021099 disease_ontology herpes zoster A viral infectious disease that results_in infection located_in nerve fiber, has_material_basis_in Human herpesvirus 3, which reactivates after appearing as chickenpox in childhood. The virus is transmitted_by direct contact with the rash, which can develop into chickenpox in newly-infected individuals. The infection has_symptom rash which is followed by blisters, has_symptom headache, has_symptom fever, has_symptom malaise, has_symptom itching, has_symptom burning pain, and has_symptom paresthesia. DOID:8536 DOID:8554 DOID:8555 DOID:8772 DOID:8801 DOID:9085 ICD10CM:B02 ICD10CM:B02.9 ICD9CM:053 MSH:D006562 NCI:C71079 SNOMEDCT_US_2015_03_01:154326002 SNOMEDCT_US_2015_03_01:186514003 SNOMEDCT_US_2015_03_01:186533008 SNOMEDCT_US_2015_03_01:4740000 Shingles UMLS_CUI:C0019360 disease_ontology herpes zona chickenpox A viral infectious disease that results_in infection located_in skin, has_material_basis_in Human herpesvirus 3, which is transmitted_by direct contact with secretions from the rash, or transmitted_by droplet spread of respiratory secretions. The infection has_symptom anorexia, has_symptom myalgia, has_symptom nausea, has_symptom fever, has_symptom headache, has_symptom sore throat, and has_symptom blisters. DOID:8658 DOID:8659 DOID:8693 DOID:9243 ICD10CM:B01 ICD10CM:B01.9 ICD9CM:052 MSH:D002644 NCI:C97132 SNOMEDCT_US_2015_03_01:154325003 SNOMEDCT_US_2015_03_01:186508005 SNOMEDCT_US_2015_03_01:38907003 UMLS_CUI:C0008049 disease_ontology varicella Crohn's disease An intestinal disease that involves inflammation located_in intestine. Crohn disease Crohn's disease of colon (disorder) Crohn's disease of large bowel DOID:8778 DOID:8784 DOID:8855 DOID:8942 EFO:0000384 Granulomatous Colitis ICD10CM:K50.0 ICD9CM:555.0 MSH:C536215 added from NeuroDevNet [WAK]. NCI:C35210 Pediatric Crohn's disease SNOMEDCT_US_2015_03_01:155761004 SNOMEDCT_US_2015_03_01:196980005 SNOMEDCT_US_2015_03_01:56689002 UMLS_CUI:C0156146 disease_ontology regional Ileitis regional colitis regional enteritis regional enteritis of small intestine with large intestine regional enteritis of the large bowel regional ileocolitis intermediate coronary syndrome (Angina: [crescendo] or [unstable] or [at rest]) or (preinfarction syndrome) or (impending infarction) Angina at rest Anginal chest pain at rest DOID:8805 ICD10CM:I20.0 ICD9CM:411.1 Impending infarction (disorder) MSH:D000789 NCI:C66911 Preinfarction angina Preinfarction angina (disorder) SNOMEDCT_US_2015_03_01:155308009 SNOMEDCT_US_2015_03_01:155313008 SNOMEDCT_US_2015_03_01:155314002 SNOMEDCT_US_2015_03_01:194814006 SNOMEDCT_US_2015_03_01:194816008 SNOMEDCT_US_2015_03_01:194817004 SNOMEDCT_US_2015_03_01:194819001 SNOMEDCT_US_2015_03_01:233818002 SNOMEDCT_US_2015_03_01:233820004 SNOMEDCT_US_2015_03_01:25106000 SNOMEDCT_US_2015_03_01:4557003 SNOMEDCT_US_2015_03_01:59021001 SNOMEDCT_US_2015_03_01:64333001 UMLS_CUI:C0002965 Unstable angina Worsening angina disease_ontology psoriasis DOID:8893 EFO:0000676 ICD10CM:L40 ICD10CM:L40.9 MSH:D011565 NCI:C3346 OMIM:177900 OMIM:601454 OMIM:602723 OMIM:603935 OMIM:604316 OMIM:605364 OMIM:605606 OMIM:607857 OMIM:610707 OMIM:612410 OMIM:612599 OMIM:612950 OMIM:614070 SNOMEDCT_US_2015_03_01:156369008 SNOMEDCT_US_2015_03_01:156371008 SNOMEDCT_US_2015_03_01:200961000 SNOMEDCT_US_2015_03_01:200978009 SNOMEDCT_US_2015_03_01:267851002 SNOMEDCT_US_2015_03_01:9014002 UMLS_CUI:C0033860 disease_ontology systemic lupus erythematosus A lupus erythematosus that is an inflammation of connective tissue marked by skin rashes, joint pain and swelling, inflammation of the kidneys and inflammation of the tissue surrounding the heart. DOID:9074 EFO:0002690 ICD10CM:M32 ICD10CM:M32.9 ICD9CM:710.0 KEGG:05322 Lupus Erythematosus, systemic MSH:D008180 NCI:C3201 OMIM:152700 OMIM:300809 OMIM:601744 OMIM:605218 OMIM:605480 OMIM:608437 OMIM:609903 OMIM:609939 OMIM:610065 OMIM:610066 OMIM:610927 OMIM:612251 OMIM:612253 OMIM:612254 OMIM:612378 OMIM:613145 OMIM:614420 ORDO:536 SLE - Lupus Erythematosus, systemic SNOMEDCT_US_2015_03_01:156450004 SNOMEDCT_US_2015_03_01:201435004 SNOMEDCT_US_2015_03_01:201439005 SNOMEDCT_US_2015_03_01:55464009 UMLS_CUI:C0024141 Xref MGI. disease_ontology disseminated lupus erythematosus diabetes mellitus A glucose metabolism disease characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both. DOID:9351 ICD10CM:E08-E13 ICD10CM:E11 ICD9CM:250 MSH:D003920 NCI:C2985 SNOMEDCT_US_2015_03_01:154671004 SNOMEDCT_US_2015_03_01:191044006 SNOMEDCT_US_2015_03_01:267467004 SNOMEDCT_US_2015_03_01:73211009 UMLS_CUI:C0011849 disease_ontology geographic location A reference to a place on the Earth, by its name or by its geographical location. GAZ GAZ:00000448 GAZ:00000467 geographic region {alternative name} United States of America A federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, DC, the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The State of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait, and the State of Hawaii is in the mid-Pacific. The United States also possesses several territories, or insular areas, that are scattered around the Caribbean and Pacific. The states are divided into smaller administrative regions, called counties in most states, exceptions being Alaska (parts of the state are organized into subdivisions called boroughs; the rest of the state's territory that is not included in any borough is divided into "census areas"), and Louisiana (which is divided into county-equivalents that are called parishes). There are also independent cities which are within particular states but not part of any particular county or consolidated city-counties. Another type of organization is where the city and county are unified and function as an independent city. There are thirty-nine independent cities in Virginia and other independent cities or city-counties are San Francisco, California, Baltimore, Maryland, St. Louis, Missouri, Denver, Colorado and Carson City, Nevada. Counties can include a number of cities, towns, villages, or hamlets, or sometimes just a part of a city. Counties have varying degrees of political and legal significance, but they are always administrative divisions of the state. Counties in many states are further subdivided into townships, which, by definition, are administrative divisions of a county. In some states, such as Michigan, a township can file a charter with the state government, making itself into a "charter township", which is a type of mixed municipal and township status (giving the township some of the rights of a city without all of the responsibilities), much in the way a metropolitan municipality is a mixed municipality and county. GAZ GAZ:00002459 ISO3166-1:840 ISO3166-1:US ISO3166-1:USA ISO3166-2:US U.S.A USA Territory of Guam An unincorporated territory of the United States. GAZ GAZ:00003706 GNISID:01802705 GU INCITS38:66 ISO3166-1:316 ISO3166-1:GU ISO3166-1:GUM ISO3166-2:US-GU lat_lon: 13deg27minN, 144deg47minE. Unincorporated Territory (USA) An area of the United States of America under United States jurisdiction, to which Congress has determined that only select parts of the United States of America Constitution apply. GAZ GAZ:00003956 American Samoa AS An unincorporated territory of the United States located in the South Pacific Ocean, southeast of the sovereign State of Samoa. The main (largest and most populous) island is Tutuila, with the Manu'a Islands, Rose Atoll, and Swains Island also included in the territory. GAZ GAZ:00003957 GNISID:01802701 INCITS38:60 ISO3166-1:016 ISO3166-1:AS ISO3166-1:ASM ISO3166-2:AS ISO3166-2:US-AS United States Virgin Islands A group of islands in the Caribbean that are an insular area of the United States. The islands are geographically part of the Virgin Islands archipelago and are located in the Leeward Islands of the Lesser Antilles. The US Virgin Islands are an organized, unincorporated United States territory. The US Virgin Islands are administratively divided into two districts and subdivided into 20 sub-districts. GAZ GAZ:00003959 GNISID:01802710 INCITS38:78 ISO3166-1:850 ISO3166-1:VI ISO3166-1:VIR ISO3166-2:US-VI US Virgin Islands VI Republic of the Marshall Islands A Micronesian island nation in the western Pacific Ocean, located north of Nauru and Kiribati, east of the Federated States of Micronesia and south of the United States territory of Wake Island, to which it lays claim. GAZ GAZ:00006470 ISO3166-1:584 ISO3166-1:MH ISO3166-1:MHL ISO3166-2:MH Commonwealth of Puerto Rico A semi-autonomous territory composed of an archipelago in the northeastern Caribbean, east of the Dominican Republic and west of the Virgin Islands, approximately 2,000 km off the coast of Florida (the nearest of the mainland United States). Estado Libre Asociado de Puerto Rico GAZ GAZ:00006935 GNISID:01779808 INCITS38:72 ISO3166-1:630 ISO3166-1:PR ISO3166-1:PRI ISO3166-2:US-PR Northern Marianas A commonwealth in political union with the United States. Commonwealth of the Northern Mariana Islands GAZ GAZ:00007109 GNISID:01779809 INCITS38:69 ISO3166-1:580 ISO3166-1:MNP ISO3166-1:MP ISO3166-2:US-MP MP Sankattan Siha Na Islas Marianas Territory of Wake Island An unorganized, unincorporated territory of the United States, administered by the Office of Insular Affairs, US Department of the Interior. GAZ GAZ:00007110 ISO3166-2:UM-79 United States Minor Outlying Islands A statistical designation defined by ISO3166-1, consists of nine insular United States possessions. Palmyra Atoll is the only incorporated territory of the United States. Currently, none of the islands have any permanent residents. GAZ GAZ:00007113 GNISID:01878752 INCITS38:74 ISO3166-1:581 ISO3166-1:UM ISO3166-1:UMI ISO3166-2:US-UM objective specification 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. OBI Plan and Planned Process/Roles Branch OBI_0000217 PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel 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. goal specification objective specification purpose of a study; support of hypothesis, discovery of new information action specification Alan Ruttenberg OBI Plan and Planned Process branch Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take action specification data item 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. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ 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. Data items include counts of things, analyte concentrations, and statistical summaries. PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees 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. data data item symbol 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://code.google.com/p/information-artifact-ontology/issues/detail?id=154). An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. PERSON: James A. Overton PERSON: Jonathan Rees a serial number such as "12324X" a stop sign a written proper name such as "OBI" based on Oxford English Dictionary symbol information content entity 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). A generically dependent continuant that is about some thing. Examples of information content entites include journal articles, data, graphical layouts, and graphs. OBI_0000142 PERSON: Chris Stoeckert information content entity directive information entity 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO An information content entity whose concretizations indicate to their bearer how to realize them in a process. PERSON: Alan Ruttenberg PERSON: Bjoern Peters 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 directive information entity curation status specification Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 PERSON:Bill Bug 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. curation status specification data about an ontology part Person:Alan Ruttenberg data about an ontology part data about an ontology part is a data item about a part of an ontology, for example a term plan specification 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. Alan Ruttenberg Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved OBI Plan and Planned Process branch OBI_0000344 PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. plan specification textual entity 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 Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities text textual entity document A collection of information content entities intended to be understood together as a whole A journal article, patent application, laboratory notebook, or a book PERSON: Lawrence Hunter document documenting 11609 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape Bjoern Peters C1548385 Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. a planned process in which a document is created or added to by including the specified input in it. documenting wikipedia http://en.wikipedia.org/wiki/Documenting informed consent form NCIt C16468 AK, FM, YH, YL, MH, EE The term definition is adapted from NCIt definition of 'consent form' (C16468) with modification. Compared to the NCIt definition, the ICO definition does not restrict the form to a clinical trial. A document that explains all relevant study information to assist a human subject in understanding the expectations and requirements of participation in a research study. This form document is presented to and signed by the study subject. C0009797 C16468 informed consent form design AK, FM, YH a planned process that involves the design of an informed consent form. informed consent regulatory body AK, FM, YH an organization that approves the clinical study protocol, and ensures the applicable governing rules and laws are upheld. study requiring informed consent YH a planned process that is a study requiring an official informed consent process. consenter role YL a role that inheres in a patient or the legal guadian when he/she participates the consenting process. review board approval number C2985863 For the review board approval, different countries or continents may have different responsible entities for approving the study. For example, in USA, the board is called "Institutional Review Board" (IRB). In many countries in Europe, it is called Ethics committee. This term definition is adapted from the definition of the NCIt term 'Review Board Approval Number Text'. A character string that is assigned by the review board upon approval of the study. C93662 YL, EE, YH, AK, MH vaccination informed consent form immunization consent form an informed consent form that is used for vaccination YH, YL question textual entity a textual entity that provides a question in text. YL, YH filled questionnaire A questionaire that is filled up with answers. YH, YL answer option text entity YL, YH, JZ a textual entity that answers a question with an option. yes answer text entity an answer option textual entity that answers a question with a yes. YL, YH, JZ no answer text entity YL, YH, JZ an answer option textual entity that answers a question with a no. filling informed consent form YH, YL a planned process that involves the filling of an informed consent form. filling questionnaire a planned process that involves the filling of a questionnaire form that includes a list of questions. YH, YL Viruses GC_ID:1 Vira Viridae Viruses ncbi_taxonomy viruses Variola virus GC_ID:1 NCBITaxon:12871 ncbi_taxonomy small pox virus smallpox smallpox virus variola virus VAR H5N1 subtype GC_ID:1 H5N1 ncbi_taxonomy Human herpesvirus 3 GC_ID:1 HHV-3 Human alphaherpesvirus 3 VZV Varicella Zoster Virus Varicella-zoster virus ncbi_taxonomy varicella zoster virus VZV varicella-zoster virus VZV Hepatitis B virus GC_ID:1 HBV Human hepatitis B virus hepatitis B virus (HBV) hepatitis B virus HBV hepatitis B virus, HBV human hepatitis B virus HBV ncbi_taxonomy Human papillomavirus GC_ID:1 Human Papilloma Virus human papillomavirus HPV ncbi_taxonomy Rotavirus GC_ID:1 Rotaviruses ncbi_taxonomy Rubella virus GC_ID:1 ncbi_taxonomy Flavivirus GC_ID:1 arboviruses group B ncbi_taxonomy Japanese encephalitis virus GC_ID:1 Japanese encephalitis Japanese encephalitis (JE) virus Japanese encephalitis virus JE Japanese encephalitis virus JEV ncbi_taxonomy Tick-borne encephalitis virus FSME virus GC_ID:1 TBEV ncbi_taxonomy tick-borne encephalitis virus TBE virus tick-borne encephalitis virus TBEV Yellow fever virus Flavivirus febricis GC_ID:1 YFV ncbi_taxonomy yellow fever virus YFV Mononegavirales GC_ID:1 ncbi_taxonomy negative-sense genome single-stranded RNA viruses Paramyxovirinae GC_ID:1 ncbi_taxonomy Mumps virus GC_ID:1 ncbi_taxonomy Measles virus Cell-associated subacute sclerosing panencephalitis GC_ID:1 NCBITaxon:11230 Subacute sclerosing panencephalitis virus measles virus MV ncbi_taxonomy rougeole virus rubeola virus subacute sclerose panencephalitis virus subacute sclerosing panencephalitis virus, SSPEV Rabies virus GC_ID:1 ncbi_taxonomy Orthomyxoviridae GC_ID:1 ncbi_taxonomy Influenza A virus FLUAV GC_ID:1 Influenza virus type A influenza A virus INF A ncbi_taxonomy H1N1 subtype GC_ID:1 H1N1 ncbi_taxonomy Euteleostomi Euteleostomi bony vertebrates Hepatitis A virus GC_ID:1 ncbi_taxonomy Proteobacteria GC_ID:11 PMID:11321122 PMID:11542017 PMID:11837318 PMID:16280474 ncbi_taxonomy proteobacteria purple bacteria purple bacteria and relatives purple non-sulfur bacteria purple photosynthetic bacteria purple photosynthetic bacteria and relatives Gammaproteobacteria GC_ID:11 Gammaproteobacteria Garrity et al. 2005 PMID:16280474 Proteobacteria gamma subdivision Purple bacteria, gamma subdivision g-proteobacteria gamma proteobacteria gamma subdivision gamma subgroup ncbi_taxonomy Firmicutes Bacillus/Clostridium group Clostridium group firmicutes Firmacutes GC_ID:11 Gram positive bacteria Gram-positive bacteria Low G+C firmicutes NCBITaxon:31968 PMID:10555317 PMID:11034484 PMID:11542017 PMID:15143038 clostridial firmicutes firmicutes low G+C Gram-positive bacteria low GC Gram+ ncbi_taxonomy Streptococcus pneumoniae Diplococcus pneumoniae GC_ID:11 Micrococcus pneumoniae ncbi_taxonomy Bacillus anthracis Bacillus cereus var. anthracis Bacteridium anthracis GC_ID:11 PMID:8123566 anthrax anthrax bacterium ncbi_taxonomy Clostridium tetani Bacillus tetani GC_ID:11 ncbi_taxonomy Corynebacterium diphtheriae Bacillus diphtheriae Bacterium diphtheriae GC_ID:11 Microsporon diphthericum Microsporon diphtheriticum Mycobacterium diphtheriae PMID:7729671 Pacinia loeffleri ncbi_taxonomy Mycobacterium tuberculosis Bacillus tuberculosis Bacterium tuberculosis GC_ID:11 Mycobacterium tuberculosis typus humanus Mycobacterium tuberculosis var. hominis ncbi_taxonomy Influenzavirus B GC_ID:1 ncbi_taxonomy Bacteria Bacteria GC_ID:11 Monera PMID:10425795 PMID:10425796 PMID:10425797 PMID:10490293 PMID:10843050 PMID:10939651 PMID:10939673 PMID:10939677 PMID:11211268 PMID:11321083 PMID:11321113 PMID:11411719 PMID:11540071 PMID:11542017 PMID:11542087 PMID:11760965 PMID:12054223 PMID:2112744 PMID:270744 PMID:8123559 PMID:8590690 PMID:9103655 PMID:9336922 Procaryotae Prokaryota Prokaryotae bacteria eubacteria eubacteria ncbi_taxonomy not Bacteria Haeckel 1894 prokaryote prokaryotes Archaea Archaea Eukaryota Eukaryota eucaryotes eukaryotes Betaproteobacteria 'Betaproteobacteria' GC_ID:11 Proteobacteria beta subdivision Purple bacteria, beta subdivision b-proteobacteria beta proteobacteria beta subdivision beta subgroup ncbi_taxonomy Euarchontoglires Euarchontoglires Tetrapoda Tetrapoda tetrapods Amniota Amniota amniotes Opisthokonta Opisthokonta Bilateria Bilateria GC_ID:1 ncbi_taxonomy dsDNA viruses, no RNA stage GC_ID:1 ncbi_taxonomy ssRNA positive-strand viruses, no DNA stage GC_ID:1 ncbi_taxonomy ssRNA negative-strand viruses GC_ID:1 ncbi_taxonomy Mammalia Mammalia mammals ssRNA viruses GC_ID:1 ncbi_taxonomy Neisseria meningitidis Diplokokkus intracellularis meningitidis GC_ID:11 Micrococcus intracellularis Micrococcus meningitidis Micrococcus meningitidis cerebrospinalis Neisseria meningitidis. Neisseria weichselbaumii ncbi_taxonomy Bordetella pertussis Bacterium tussis-convulsivae GC_ID:11 Haemophilus pertussis Hemophilus pertussis Microbe de la coqueluche PMID:8240949 ncbi_taxonomy Enterobacteriaceae Enterobacteraceae Enterobacteraceae (ex Lapage 1979) Lapage 1982, fam. nov., nom. rev. Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980, fam. nov., nom. rev. Enterobacteriaceae Rahn 1937 GC_ID:11 PMID:10555323 PMID:10555334 PMID:16166704 gamma-3 proteobacteria ncbi_taxonomy Dintheria GC_ID:1 ncbi_taxonomy Escherichia coli Bacillus coli Bacterium coli Bacterium coli commune Enterococcus coli Escherchia coli Eschericia coli GC_ID:11 NCBITaxon:662101 NCBITaxon:662104 PMID:10319482 bacterium E3 ncbi_taxonomy Yersinia pestis Bacillus pestis Bacterium pestis GC_ID:11 Pasteurella pestis Pestisella pestis Yersinia pseudotuberculosis subsp. pestis ncbi_taxonomy Vibrio cholerae Bacillo virgola del Koch Bacillus cholerae Bacillus cholerae-asiaticae GC_ID:11 Kommabacillus Liquidivibrio cholerae Microspira comma PMID:9272984 Pacinia cholerae-asiaticae Spirillum cholerae Spirillum cholerae-asiaticae Vibrio choleae Vibrio cholera Vibrio cholerae-asiaticae Vibrio comma ncbi_taxonomy Vertebrata <Metazoa> Vertebrata Vertebrata <Metazoa> vertebrates Corynebacterineae GC_ID:11 NCBITaxon:1761 PMID:11837321 PMID:1736962 PMID:19244447 ncbi_taxonomy Salmonella enterica subsp. enterica serovar Typhi Bacillus typhi Bacterium (subgen. Eberthella) typhi GC_ID:11 NCBITaxon:41530 NCBITaxon:601 NCBITaxon:72667 PMID:10319519 PMID:10758910 PMID:15653930 PMID:16558776 PMID:9336938 Salmonella choleraesuis serovar Typhi Salmonella choleraesuis typhi Salmonella enterica ser. typhi Salmonella enterica serotype Typhi Salmonella enterica serovar Typhi Salmonella typhi ncbi_taxonomy Bacilli Bacillus/Lactobacillus/Streptococcus group Firmibacteria GC_ID:11 PMID:20212322 ncbi_taxonomy Homo sapiens GC_ID:1 Homo sapiens human human human being man man ncbi_taxonomy adverse event Melanie 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'. AE 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'. a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event. 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. WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068 The OAE official website is: http://www.oae-ontology.org/. WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm adverse reaction 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. WEB: http://en.wikipedia.org/wiki/Adverse_event 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. Yongqun He vaccine adverse event an adverse event that occurs after a vaccination. YH dizziness AE HPO: HP_0002321 NCIt:C37943 SIDER: C0012833 MedDRA ID: 10013573 YH, SS, MW a sensory capability AE that has an outcome of dizziness Dizziness describes a number of subjective symptoms, which the patient may describe as feelings of lightheadedness, floating, wooziness, giddiness, confusion, disorientation or loss of balance. Medical terms include vertigo, disequilibrium, pre-syncope or syncoptic episode. Causes may stem from a variety of failures of equilibrioception, hypotension, cerebral hypoxia or a reaction to environmental chemicals or drugs. CTCAE:E12631 syncope AE SIDER: C0039070 MedDRA: 10024855 a sensory capability AE that has an outcome of loss of consciousness, fainting WEB: http://en.wikipedia.org/wiki/Unconsciousness fainting Syncope is the medical term for fainting, a sudden, usually temporary, loss of consciousness. MedDRA:10042772 NCIt:C35053 CTCAE:E12832 YH, SS, MW HPO: HP_0001279 WEB: http://en.wikipedia.org/wiki/Syncope_%28medicine%29 Guillain-Barre syndrome AE SIDER: C0018378 WEB: http://www.ncbi.nlm.nih.gov/pubmed/23299621 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. GBS AE YH, SS HPO: HP_0007131 MedDRA: 10018767 MedDRA ID: 10018767 serious adverse event serious adverse event WEB: http://www.google.ca/url?sa=t&source=web&ct=res&cd=1&ved=0CA4QFjAA&url=http%3A%2F%2Fwww.irrd.ca%2Fethics%2Fimages%2FAdverse-event-definition.doc&ei=eqFMS-yFNZSoswOt6siKAQ&usg=AFQjCNGnQcwI8OXH7dqxwo4RgZEEn8X6lg&sig2=UNngkCdO5ZTFvbIB1pKuaA WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm WEB: http://en.wikipedia.org/wiki/Serious_adverse_event YH, MC severe adverse event serious adverse event is an adverse event that requires in-patient hospitalization, or prolongation of existing hospitalization, or that causes congenital malformation, or that results in persistent or significant disability or incapacity, or that is life threatening or results in death. planned process '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.) 6/11/9: Edited at workshop. Used to include: is initiated by an agent Bjoern Peters Injecting mice with a vaccine in order to test its efficacy branch derived A processual entity that realizes a plan which is the concretization of a plan specification. 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 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 investigation Could add specific objective specification Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation study Bjoern Peters OBI branch derived a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). investigation investigation agent role Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. investigation agent role investigator study person role GROUP: Role Branch OBI Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009) Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. organization GROUP: OBI PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone An entity that can bear 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. 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. organization protocol study protocol A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. PlanAndPlannedProcess Branch protocol material to be added role 9 March 09 from discussion with PA branch OBI Role Branch drug added to a buffer contained in a tube; substance injected into an animal; material to be added role 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 drawing a conclusion based on data Bjoern Peters Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. PERSON: Bjoern Peters PERSON: Jennifer Fostel A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion drawing a conclusion based on data planning 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. Bjoern Peters Bjoern Peters Plans and Planned Processes Branch The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. a process of creating or modifying a plan specification planning target of material addition role 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 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 target of material addition role is a role realized by an entity into which a material is added in a material addition process study design execution 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. a planned process that realizes the concretization of a study design branch derived injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. study design execution informed consent process 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#informed informed consent process questionnaire Need to clarify if this is a document or a directive information entity (or what their connection is)) questionnaire A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. Merriam-Webster PERSON: Jessica Turner conclusion based on data In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group conclusion based on data An information content entity that is inferred from data. Group:2013 Philly Workshop group organism 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 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. WEB: http://en.wikipedia.org/wiki/Organism animal fungus organism plant virus study design A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design genome of Bacteria 2 The genome of an organism of Bacteria Yue Liu, Bin Zhao, Oliver He genome of Proteobacteria 1224 The genome of an organism of Proteobacteria Yue Liu, Bin Zhao, Oliver He gene of Bacteria 2 A gene of an organism of Bacteria Yue Liu, Bin Zhao, Oliver He gene of Proteobacteria 1224 A gene of an organism of Proteobacteria Yue Liu, Bin Zhao, Oliver He age A time quality inhering in a bearer by virtue of how long the bearer has existed. PATO:0000011 quality biological sex An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. PATO:0000047 quality female A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. PATO:0000383 quality male A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. PATO:0000384 quality quality of a single physical entity A physical object quality which inheres in a single-bearer. quality of a single physical entity seizure SYMP:0000124 seizure symptoms faint Faint is a alteration of consciousness characterized by a loss of consciousness because of a temporary decrease in the blood supply to the brain. SYMP:0000445 fainting symptoms syncope symptom A symptom is a perceived change in function, sensation, loss, disturbance or appearance reported by a patient indicative of a disease. SYMP:0000462 SyOID:14974 symptoms rash A skin and integumentary tissue symptom characterized as an eruption on the body typically with little or no elevation above the surface. ICD9CM_2005:782.1 SYMP:0000487 SyOID:13022 UMLS_CUI:C0015230 UMLS_ICD9CM_2005_AUI:A0243780 erythema rubor skin eruption skin rash skin redness symptoms respiratory system and chest symptom ICD9CM_2005:786 SYMP:0000514 SyOID:5868 UMLS_CUI:C0476271 UMLS_ICD9CM_2005_AUI:A0284200 symptoms chest pain ICD9CM_2005:786.5 ICD9CM_2005:786.50 SYMP:0000576 SyOID:4705 UMLS_CUI:C0008031 UMLS_ICD9CM_2005_AUI:A0243830 UMLS_ICD9CM_2005_AUI:A0400627 symptoms convulsion ICD9CM_2005:780.3 SYMP:0000596 SyOID:6961 UMLS_CUI:C0009951 UMLS_ICD9CM_2005_AUI:A0042665 symptoms wheezing ICD9CM_2005:786.07 SYMP:0000604 SyOID:7248 UMLS_CUI:C0043144 UMLS_ICD9CM_2005_AUI:A0133941 Wheezing is a respiratory abnormality characterized by breathing with difficulty usually with a whistling sound. symptoms dizziness Dizziness is a neurological and physiological symptom characterized by a sensation of unsteadiness accompanied by a feeling of movement within the head. ICD9CM_2005:780.4 SYMP:0000610 SyOID:7637 UMLS_CUI:C0476206 UMLS_ICD9CM_2005_AUI:A0243727 dizzy symptoms fever Fever is a neurological and physiological symptom characterized by a rise of body temperature above the normal whether a natural response (as to infection) or artificially induced for therapeutic reasons. ICD9CM_2005:780.6 SYMP:0000613 SyOID:776 UMLS_CUI:C0015967 UMLS_ICD9CM_2005_AUI:A0058972 pyrexia symptoms low-grade fever 2010-10-15T11:28:26Z Low-grade fever is a fever that does not exceed 38.5 degree centrigrade. SYMP:0000879 lschriml symptoms high fever 2010-10-15T11:28:26Z High fever is a fever that involved an elevated temperature. SYMP:0000882 lschriml symptoms vomiting SYMP:0019145 Vomiting is a digestive system symptom characterized by throwing up the stomach contents. emesis symptoms dyspnea Dyspnea is a respiratory abnormality characterized by difficult or labored respiration. SYMP:0019153 breathing difficulty breathlessness difficulty breathing labored respiration shortness of breath symptoms mouth AAO:0010355 BTO:0001090 EFO:0000825 FBbt:00003126 FMA:49184 First portion of the digestive tract[WP]. The portion of the digestive that develops from the stomodeum GAID:75 MA:0002474 MAT:0000038 MESH:A.01.456.505.631 MIAA:0000038 OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA TADS:0000040 TAO:0000547 TGMA:0000131 TODO - check fly mouthpart. note in uberon we distinguish between the mouth and the oral opening. the mouth is part of the digestive tract. TODO - check isa parent subdivision of head - is it a subdivision of the head or digestive tract UBERON:0000165 VHOG:0000812 XAO:0003029 ZFA:0000547 adult mouth cavitas oris cavum oris galen:Mouth http://upload.wikimedia.org/wikipedia/commons/thumb/d/d4/Illu01_head_neck.jpg/200px-Illu01_head_neck.jpg mouth cavity oral vestibule regio oralis rima oris stoma uberon vestibule of mouth vestibulum oris skeletal muscle tissue AAO:0011099 BTO:0001103 EFO:0000888 EHDAA2:0001842 EHDAA:2923 EHDAA:5035 EHDAA:5043 EHDAA:5978 EHDAA:5984 EHDAA:8277 EHDAA:8291 EHDAA:8326 EHDAA:9146 EV:0100377 FMA:14069 GAID:141 MA:0002439 MAT:0000302 MESH:A.02.633.567 MIAA:0000302 OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA SCTID:426215008 TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Consider FBbt:00005073 - somatic muscle. Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]. Striated muscle tissue under control of the somatic nervous system. It is one of three major muscle types, the others being cardiac and smooth muscle. As its name suggests, most skeletal muscle is attached to bones by bundles of collagen fibers known as tendons. Skeletal muscle is made up of individual components known as muscle fibers. These fibers are formed from the fusion of developmental myoblasts. The myofibers are long, cylindrical, multinucleated cells composed of actin and myosin myofibrils repeated as a sarcomere, the basic functional unit of the cell and responsible for skeletal muscle's striated appearance and forming the basic machinery necessary for muscle contraction. The term muscle refers to multiple bundles of muscle fibers held together by connective tissue[WP]. UBERON:0001134 UBERON:FMA_14069-MA_0002439 VHOG:0000319 XAO:0000174 ZFA:0005277 ncithesaurus:Skeletal_Muscle_Tissue skeletal muscle skeletal muscle organ skeletal muscle system somatic muscle uberon urinary bladder AAO:0000623 BTO:0001418 EFO:0000290 EHDAA2:0000174 EHDAA:9328 EMAPA:18321 EV:0100098 FMA:15900 GAID:0000004 MA:0000380 MAT:0000122 MESH:A.05.810.161 MIAA:0000122 OpenCyc:Mx4rvVjMmZwpEbGdrcN5Y29ycA Organ with organ cavity which is continuous proximally with the right and left ureters and distally with the urethra. SCTID:302512001 UBERON:0001255 UBERON:FMA_15900-FMA_7203-MA_0000368-MA_0000380-MIAA_0000118-MIAA_0000119-MIAA_0000122-WBbt_0005775-XAO_0000154-ZFA_0000529 VHOG:0000740 XAO:0000154 bladder editor note: consider adding a 'bladder' grouping class excretory canal galen:UrinaryBladder http://upload.wikimedia.org/wikipedia/commons/thumb/3/30/Urinary_system.svg/200px-Urinary_system.svg.png ncithesaurus:Bladder uberon hypodermis BTO:0004525 FMA:70544 FMA:9630 GAID:929 Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA]. MESH:A.10.165.887 Note that this class combines superficial fascia and hypodermis in FMA. Note also BTO has 'subcutis' TAO:0001136 UBERON:0002072 UBERON:FMA_70544-MIAA_0000418-ZFA_0000117-ZFA_0001136 ZFA:0001136 http://upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Skin.svg/200px-Skin.svg.png hypoderm ncithesaurus:Superficial_Fascia subcutaneous tissue subcutis superficial fascia tela subcutanea uberon vertebrate hypodermis skin of body BTO:0001253 EFO:0000962 EHDAA2:0001844 EMAPA:17525 FMA:7163 MESH:A.17.815 Nonparenchymatous organ that consists of the dermis and epidermis. Subdivisions of the skin surround various body parts; as a whole, the skin constitutes the external layer of the body. Examples: There is only one skin[FMA]. Surface structure that consists of the external membranous integument of the animal. Note that FMA uses 'skin' for the entire organ. XAO seems consistent. MA seems to use it analagously to zone of skin OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA SCTID:181469002 UBERON:0002097 UBERON:FMA_7163-MA_0000151-MIAA_0000284-XAO_0000023 XAO:0000023 entire skin galen:Skin http://upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Skin.svg/200px-Skin.svg.png integument ncithesaurus:Skin skin uberon Manitoba vaccination informed consent form A vaccination informed consent form that is provided by Manitoba government in Canada YL, YH questionnaire for Manitoba vaccination consent YH, YL We may also model the Minatoba Child Informed Consent form: http://www.gov.mb.ca/health/publichealth/cdc/div/docs/7707.pdf a questionnaire that is part of the Manitoba vaccination informed consent form. vaccination screening questionnaire A questionnaire that contains different questions of an intended vaccine reciepiant's health history, allergy history, and current condition, in order to assess the contraindication and precaution for administering a vaccine. YL,JZ,YH question whether allergic to vaccine component YL a question textual entity that asks whether the questionee is allergic to a vaccine component don't know answer text entity YL questionnaire for Rite Aid vaccination consent https://shop.riteaid.com/info/pharmacy/services/vaccine-central/consent-forms filled questionnaire for Costco vaccination consent YH, YL a questionnaire for Costco vaccination consent that is filled filled questionnaire for Walgreens vaccination consent YH, YL a questionnaire for Walgreens vaccination consent that is filled questionnaire for Rite Aid vaccination consent in California https://content.riteaid.com/pharmacy/immundest/20141016_CA_CAIR_Screening_Questionnaire_Consent.pdf vaccination patient with asthma questionnaire for Rite Aid injectable flu vaccination consent in South Carolina https://content.riteaid.com/pharmacy/immundest/20141015_SC_Screening_Questionnaire_Consent.pdf questionnaire for Rite Aid non-flu vaccination consent in South Carolina http://content.riteaid.com/pharmacy/20150726_ScreeningQuesConsent.pdf questionnaire for Rite Aid vaccination consent in other states than SC, NC and CA http://content.riteaid.com/pharmacy/20150726_ScreeningQuesConsent.pdf vaccination patient After the vaccination process, this vaccination patient will bear the role of human vaccinee, and become a human vaccinee. If the patient is a minor, his/her legal representative will answer the screening question for him/her. a human who is going to recieve an administration of a vaccine, who bears a vaccination patient role, which is realized when he/she sits in a vaccination provider's site and is the bject of screening questions for receiving a vaccine. legal representative of minor vaccination patient Costco vaccination informed consent form A vaccination informed consent form that is provided by Costco https://www.costco.com/wcsstore/CostcoUSBCCatalogAssetStore/rx/Immunization_consent_form_v2-2012.pdf YH, YL Walgreens vaccination informed consent form A vaccination informed consent form that is provided by Walgreens https://www.walgreens.com/images/pdfs/IN-2225/WAG_VAR_Form_EDIT_10172013_v1.pdf YH, YL questionnaire for Walgreens vaccination consent a questionnaire that is part of the Walgreens vaccination informed consent form. YH, YL https://www.walgreens.com/images/pdfs/IN-2225/WAG_VAR_Form_EDIT_10172013_v1.pdf questionnaire for Costco vaccination consent YH, YL a questionnaire that is part of the Costco vaccination informed consent form. http://www2.costco.com/Images/Content/misc/PDF/Immunization_consent_form_v2-2012.pdf minor vaccination patient a vaccination patient who is under the age of legal competence.According to US Civil Law, which described a person under a certain age as less than so many years. In most states, a person is no longer a minor after reaching the age of 18. https://en.wikipedia.org/wiki/Minor_(law) http://legal-dictionary.thefreedictionary.com/minor female vaccination patient flumist vaccination Rite Aid vaccination informed consent form https://shop.riteaid.com/info/pharmacy/services/vaccine-central/consent-forms pneumococcal vaccination shingles vaccination Zoster vaccination Tdap vaccination vaccination patient over 65 years old questionnaire for Rite Aid vaccination consent in North Carolina http://content.riteaid.com/pharmacy/20150726_ScreeningQuesConsent.pdf Td vaccination vaccination patient with COPD vaccination patient with smoking habit 2-4 year old vaccination patient parent of minor vaccination patient influenza vaccination injectable influenza vaccination intranasal influenza vaccination Rite Aid injectable flu vaccination informed consent form in South Carolina https://content.riteaid.com/pharmacy/immundest/20141015_SC_Screening_Questionnaire_Consent.pdf Rite Aid non-flu vaccination informed consent form in South Carolina http://content.riteaid.com/pharmacy/20150726_ScreeningQuesConsent.pdf Rite Aid vaccination informed consent form in California https://content.riteaid.com/pharmacy/immundest/20141016_CA_CAIR_Screening_Questionnaire_Consent.pdf Rite Aid vaccination informed consent form in North Carolina https://content.riteaid.com/pharmacy/immundest/20140924_NC_Screening_Questionnaire_Consent.pdf Rite Aid vaccination informed consent form in other states than SC, NC and CA http://content.riteaid.com/pharmacy/20150726_ScreeningQuesConsent.pdf Manitoba Seasonal Influenza and Pneumococcal vaccination informed consent form http://www.gov.mb.ca/health/flu/docs/flupneumo_consentform.pdf Manitoba child immunization consent form http://www.gov.mb.ca/health/publichealth/cdc/div/docs/7707.pdf questionnaire for Manitoba child immunization consent yellow fever vaccination MMR vaccination typhoid vaccination oral typhoid vaccination live vaccine vaccination University of Maryland College Park vaccination informed consent form questionnaire for University of Maryland College Park vaccination consent http://hr.gmu.edu/wellnessbymason/docs/ConsentFormF13.pdf UM College Park injectable influenza vaccination informed consent http://www.health.umd.edu/sites/default/files/InfluenzaVaccineform2015-2016.pdf UM College Park flumist vaccination informed consent http://www.health.umd.edu/sites/default/files/FluMistVaccineConsentform2015-2016.pdf UM College Park Smallpox vaccination informed consent form http://www.health.umd.edu/sites/default/files/Smallpox-History-WebForm_1.pdf questionnaire for UM College Park flumist vaccination consent http://www.health.umd.edu/sites/default/files/FluMistVaccineConsentform2015-2016.pdf questionnaire for UM College Park injectable influenza vaccination consent http://www.health.umd.edu/sites/default/files/InfluenzaVaccineform2015-2016.pdf screening questionnaire for UM College Park smallpox vaccination consent http://www.health.umd.edu/sites/default/files/Smallpox-History-WebForm_1.pdf smallpox vaccination household member of vaccination patient YL a person lives in the same house with vaccination patient close physical contact person of vaccination patient YL a person who has close physical contact with the vaccination patient, such as sex partner newborn infant A newborn infant, or neonate, is a child under 28 days of age. NCI: C16731 NCI: C16731 WHO (http://www.who.int/topics/infant_newborn/en/) YL https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=15.12d&ns=NCI_Thesaurus&code=C16731 vaccination informed consent process question whether currently sick 1. Are you sick today? There is no evidence that acute illness reduces vaccine efficacy or increases vaccine adverse events (1). However, as a precaution with moderate or severe acute illness, all vaccines should be delayed until the illness has improved. Mild illnesses (such as upper respiratory infections or diarrhea) are NOT contraindications to vaccination. Do not withhold vaccination if a person is taking antibiotics. (http://www.immunize.org/catg.d/p4065.pdf) Are you sick today a question textual entity that asks whether the questionee is currently sick. LOINC:66373-2 YL, YH allergy question a question textual entity that asks whether the questionee is allergic to some material. YL, YH 2. Do you have allergies to medications, food, a vaccine component, or latex? If a person has anaphylaxis after eating gelatin, do not administer MMR,varicella, standard trivalent Fluzone, Flumist, rabies (Rabavert), oral typhoid, or yellow fever vaccine. A local reaction to a prior vaccine dose or vaccine components (e.g., latex) is not a contraindication to a subsequent dose or vaccine containing that component. For a table of vaccines supplied in vials or syringes that contain latex, go to www.cdc.gov/vaccines/pubs/pinkbook/downloads/appendices/B/latex-table.pdf. For an extensive list of vaccine components, see reference 2. An egg-free recombinant influenza vaccine (RIV3) may be used in people age 18 years and older with egg allergy of any severity who have no other contraindications. People younger than age 18 years who have experienced a serious systemic or anaphylactic reaction (e.g., hives, swelling of the lips or tongue, acute respiratory distress, or collapse) after eating eggs can usually be vaccinated with inactivated influenza vaccine (IIV); consult ACIP recommendations (see reference 3). 2. Table of Vaccine Components: www.cdc.gov/vaccines/pubs/pinkbook/downloads/appendices/B/excipient-table-2.pdf. 3. CDC. Prevention and control of influenza with vaccines:Recommendations of the Advisory Committee on Immunization Practices (ACIP), United States, 2015–16 Influenza Season at www.cdc.gov/mmwr/pdf/wk/mm6430.pdf, pages 818–825 http://www.immunize.org/catg.d/p4065.pdf question whether allergic to latex a question textual entity that asks whether the questionee is allergic to latex. YL, YH question whether allergic to food YL, YH a question textual entity that asks whether the questionee is allergic to food question whether allergic to egg a question textual entity that asks whether the questionee is allergic to food YL, YH question whether allergic to medication a question textual entity that asks whether the questionee is allergic to a medication YL, YH question whether allergic to vaccine YL, YH a question textual entity that asks whether the questionee is allergic to a vaccine question on reaction after immunization YL, YH a question textual entity that asks whether the questionee had any reaction after a vaccination (i.e., immunization) in the past. seizure disorder question a question textual entity that asks whether the questionee has experienced any seizure disorder YL, YH immunocompromisation question a question textual entity that asks whether the vaccination patient is immunocomprised YL, YH question on woman pregnancy a question textual entity that asks whether a woman is pregnant now YL, YH current treatment question a question textual entity that asks whether the questionee is currently under any treatment YL, YH cortisone treatment question YL, YH a current treatment question that asks whether the questionee is currently under any cortisone treatment X-ray treatment question a current treatment question that asks whether the questionee is currently under any X-ray treatment YL, YH question on vaccination in past 4 weeks YL, YH a question textual entity that asks whether the questionee has been vaccinated in the past four weeks question on TB skin test in past 4 weeks YL, YH a question textual entity that asks whether the questionee has conducted a TB skin test in the past four weeks question on blood transfusion in past year a question textual entity that asks whether the questionee has conducted a blood transfusion in the past year YL, YH question on high-dose steroid therapy for longer than 2 weeks YL, YH a current treatment question that asks whether the questionee has been under a high-dose steroid therapy ((prednisone > 20mg/day or equivalent)) for longer than two weeks question on thymus disease a question textual entity that asks whether the questionee has a thymus disease This question is needed for yellow fever vaccination YL, YH question on current antibiotics usage YL, YH a question textual entity that asks whether the questionee is currently taking some antibiotics This question is needed for oral typhoid vaccination question on thrombocytopenia history a question textual entity that asks whether the questionee has a history of thrombocytopenia YL, YH question on current aspirin medication This question is needed for oral typhoid vaccination YL, YH a question textual entity that asks whether the questionee is currently taking aspirin question on asthma or wheezing history a question textual entity that asks whether the questionee has a history of asthma or wheezing YL, YH question on serious nasal condition YL, YH a question textual entity that asks whether the questionee has a serious nasal condition, which makes breathing difficult, such as a very stuffy nose. question on long-term health problem a question textual entity that asks whether the questionee has a a long-term health problem with heart disease, lung disease, asthma, kidney disease, metabolic disease (e.g., diabetes), anemia or other blood disorder. YL, YH question on long-term heart disease YL, YH a question on long-term health problem that asks whether the questionee has a long-term heart disease question on cancer YL, YH a question on long-term health problem that asks whether the questionee has cancer question on leukemia a question on long-term health problem that asks whether the questionee has leukemia YL, YH question on long-term lung disease YL, YH a question on long-term health problem that asks whether the questionee has a long-term lung disease filled questionnaire for Manitoba Seasonal Influenza and Pheumococcal vaccination consent a questionnaire that is part of the Manitoba vaccination informed consent form. YL,YH question on long-term metabolic disease a question on long-term health problem that asks whether the questionee has a long-term metabolic disease question on long-term diabetes YL,YH a question on long-term health problem that asks whether the questionee has diabetes question on anemia YL,YH a question on long-term health problem that asks whether the questionee has anemia question on AIDS YL,YH a question on long-term health problem that asks whether the questionee has AIDS prednisone treatment question YL,YH a current treatment question that asks whether the questionee is currently under prednisone treatment steroids treatment question YL,YH a current treatment question that asks whether the questionee is currently under any steroid treatment question on current anti-cancer drug usage YL,YH a question textual entity that asks whether the questionee is currently taking any anti-cancer drugs question on whether fainted or felt dizzy after immunization Walgreens immunization informed consent: https://www.walgreens.com/images/pdfs/IN-2225/WAG_VAR_Form_EDIT_10172013_v1.pdf YL,YH a question textual entity that asks whether the questionee hasfainted or felt dizzy after a vaccination (i.e., immunization) question on transfusion of blood products in past year a question textual entity that asks whether the questionee has been given transfusion of blood products in the past year question on given immune (gamma) globulin in last year YL,YH a question textual entity that asks whether the questionee has been given immune (gamma) globulin in the past year question on history of thymoma YL,YH a question textual entity that asks whether the questionee has a history of thymoma question on previous thymectomy procedure YL, YH a question textual entity that asks whether the questionee has his/her thymus removed previously question on current antimalarial medication YL,YH a question textual entity that asks whether the questionee is currently under antimalarial medication asked in prior for using Oral thyphoid vaccine only question on seizure, brain, or nerve problem a question textual entity that asks whether the questionee has experienced any seizure disorder, brain or nerve problem. YL, YH Have you had a seizure, brain, or other nervous system problem? LOINC:66379-9 question on blood or blood product transfusion, or immune (gamma) globulin in past year Cosco Pharmacy vaccine informed consent form: http://www2.costco.com/Images/Content/misc/PDF/Immunization_consent_form_v2-2012.pdf During the past year, have you received a transfusion of blood or blood products, including antibodies? YL, YH a question textual entity that asks whether the questionee has conducted a blood or blood product transfusion, or given a medicine called immune (gamma) globulin, in the past year question on woman pregnancy now or during the next month YL, YH LOINC:66381-5 a question textual entity that asks whether a woman is pregnant now or could become pregrant during the next month question on cancer, leukemia, AIDS or any other immune system problem Cosco Pharmacy vaccine informed consent form: http://www2.costco.com/Images/Content/misc/PDF/Immunization_consent_form_v2-2012.pdf YL, YH a question textual entity that asks whether the questionee has cancer, leukemia, AIDS or any other immune system problem question whether currently sick with a moderate to high fever, vomiting/diarrhea YL, YH a question textual entity that asks whether the questionee is currently sick with a moderate to high fever, vomiting/diarrhea Walgreens immunization informed consent: https://www.walgreens.com/images/pdfs/IN-2225/WAG_VAR_Form_EDIT_10172013_v1.pdf question on any medication affecting blood clotting YL, YH a question textual entity that asks whether the questionee has taken any medication that affects blood clotting question on history of thrombocytopenia or thrombocytopenic purpura Walgreens immunization informed consent: https://www.walgreens.com/images/pdfs/IN-2225/WAG_VAR_Form_EDIT_10172013_v1.pdf YL,YH a question textual entity that asks whether the questionee has a history of thrombocytopenia or thrombocytopenic purpura. questionare for Manitoba Seasonal Influenza and Pneumococcal vaccination consent http://www.gov.mb.ca/health/flu/docs/flupneumo_consentform.pdf a questionnaire that is part of the vaccination informed consent form used for Seasonal Influenza and Phenumococcal vaccination in Manitoba, Canada. question on long-term kidney disease a question on long-term health problem that asks whether the questionee has a long-term kidney disease question whether allergic to gentamicin question whether allergic to neomycin question whether allergic to formaldehyde question whether allergic to thimerosal question whether allergic to bovine protein question whether allergic to phenol question whether allergic to polymyxin question whether allergic to gelatin question whether allergic to yeast question whether allergic to baker’s yeast question on vaccination caused disorder question on vaccination caused Guillain-Barre syndrome question on neurological disorder question whether relate to new born infant Are you a parent, family member, or caregiver to a new born infant? YL a question asks the questionee if he or she is taking care of a new born infant or close family member of a new born infant. question on asthma history question on wheezing history question on serious reaction after immunization question whether a parent of a new born infant question whether a family member of a new born infant question whether a care giver of a new born infant question whether smoke Do you smoke? question on past vaccination information YL questions that related to patient's vaccination history, warnings received from health provider about a certain vaccination, and adverse event related with a vaccination. question whether had Pneumococcal vaccination question whether had Shingles vaccination question whether had Tdap vaccination question on antiviral drug usage question on whether having cut, injury, puncture or open wound Do you have a cut, injury, puncture or open wound that prompted you to get a tetanus shot? question on COPD question whether react to triple antibiotic ointment question on health provider precaution or warning of specific vaccination Has any physician or other healthcare professional ever cautioned or warned you about receiving certain vaccines or receiving vaccines outside of a medical setting? * YL a question asks if the vaccination patient received warning or precaution information from his/her health provider in the past. question about vaccination patient age question on long-term liver disease question on faintig after vaccination question on long-term aspirin therapy question whether patient is older than 18 years old Are you 18 years of age or older? question on whether having atopic dermatitis question whether diagnosed with rheumatoid arthritis question whether diagnosed with ankylosing spondylitis question whether diagnosed with Crohn’s disease question whether diagnosed with Guillain-Barre syndrome Have you ever been diagnosed as having Guillain-Barre syndrome? question on health condition requires doctor visit question whether had chickenpox a question textual entity that asks the patient whether he/she had diagnosed, treated and recovered from chickenpox, or varicella-zoster virus (VZV) infection. question on dizzy after vaccination question whether bring imunization record card Did you bring your Immunization Record Card with you? question on asplenia question on CSF leak question on cochlear implant 01/25/2016 The United States Food and Drug Administration reports that cochlear implant recipients may be at higher risk for meningitis.[76] A study of 4,265 American children who received implants between 1997 and 2002 concluded that recipient children had a risk of pneumococcal meningitis more than 30 times greater than that for children in the general population.A later, UK-based, study found that while the incidence of meningitis in implanted adults was significantly higher than the general population, the incidence in children was no different from the general population. As a result, the Centers for Disease Control and Prevention and the Food and Drug Administration both recommend that would-be implant recipients be vaccinated against meningitis prior to surgery.(https://en.wikipedia.org/wiki/Cochlear_implant) YL question on weekly injection question on weekly injection of adalmumab question on weekly injection of infliximab question on weekly injection of etanercept question on home infusion question on high-dose methotrexate usage question on azathioprine or 6-mercaptopurine usage question on current anti-malarial medication question whether recieving aspirin-containing therapy 5 year and younger vaccination patient a minor vaccination patient whose age is younger thatn 5 or equal to 5. question on fever Do you have a fever? question whether allergic to egg products question on stroke leading brain or nerve damage question on convulsion leading brain or nerve damage question on brain or nerve damage question on respiratory illness YL question that is about the patient's repiratory system or chest symptoms. question whether in contact with severely immunocompromised person question on woman's possibility of geting pregnant Is there a possibility of pregnancy? <used in UM College Park injectable influenza vaccination consent questionnaire> [VICO_0000065] Pregnancy tests prior to vaccination are not routinely recommended. However, females of childbearing age should be asked about the possibility of their being pregnant prior to being given any vaccine for which pregnancy is a contraindication or precaution. The patient's answer should be documented in the medical record. If the patient is uncertain if she is pregnant, a test should be performed before administering live virus vaccines (measles-mumps-rubella, varicella, live attenuated influenza, yellow fever). (http://www.immunize.org/askexperts/precautions-contraindications.asp) question on agammaglobulinemia question on lymphoma question on severe autoimmune disease question on SLE question on immunosuppressive drug usage question on drug usage after organ transplant question on autoimmune disease drug usage question on cancer treatment question on autoimmune disease question on current condition leads to skin break question onwhether having skin rash question on whethere having severe burn question on whether having impetigo question whether having chickenpox question on whether having shingles question on whether having herpes question on whether having psoriasis question on whether having severe acne question on Darier's disease question on whether using steroid eye drop question on whether diagnosed with myocardial infarction question on whether diagnosed with angina question on whether diagnosed with congestive heart failure question on whether diagnosed with cardiomyopathy question on whether had transient ischemic attack question on chest pain question on shortness of breath when exert question whether allergic to smallpox vaccine question whether allergic to polymixin B question whether allergic to streptomycin question whethere allergic to chlortetracycline question whethere allergic to neomycin question on last month's sexual intercourse without effecctive birth control question on sexual intercourse without effecctive birth control after the vaccination question whether live with a child less than one year old question whether current breast-feeding question for woman CDC guidance for pregnancy vaccination http://www.cdc.gov/vaccines/acip/committee/downloads/preg-principles-2008.pdf question for household memeber of vaccination patient question for close physical contact person of vaccination patient question on current medication usage YL question asks vaccination patient about current drug usage. question whether had organ transplant question whether had chickenpox vaccination current health condition question YL a question asks if the patient currently has any disease that requies regular doctor's vsisit, long tem disease that impacts current well-being, any symptoms, or feeling ill at the time when he/she is being accessed by vaccination providers. previous medical precedure question question whether live with immunocompromise person sickness 01/17/2016 YL A disposition of ill health, bodily malfunction, or discomfort. NCI:C107499 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C107499 immunocompromised condition 01/17/2016 A condition or state in which the immune system doesn't have ability to fight infectious disease or medical challenges. A person who has an immunodeficiency of any kind is said to be immunocompromised. An immunocompromised person may be particularly vulnerable to opportunistic infections, in addition to normal infections that could affect everyone. Immunodeficiency may also decrease cancer immunosurveillance. Most cases of immunodeficiency are acquired ("secondary") but some people are born with defects in their immune system, or primary immunodeficiency. Transplant patients take medications to suppress their immune system as an anti-rejection measure, as do some patients suffering from an over-active immune system. YL functional asplenia The organism's spleen doesn't work, or anatomical asplenia The organsim is lacking of the spleen as a part of its body. asplenia 01/17/2016 Asplenia refers to the absence of normal spleen function and is associated with some serious infection risks. Vaccinations It is suggested that splenectomized persons receive the following vaccinations, and ideally prior to planned splenectomy surgery: Pneumococcal polysaccharide vaccine (not before 2 years of age). Children may first need one or more boosters of pneumococcal conjugate vaccine if they did not complete the full childhood series. Haemophilus influenzae type b vaccine, especially if not received in childhood. For adults who have not been previously vaccinated, two doses given two months apart was advised in the new 2006 UK vaccination guidelines (in the UK may be given as a combined Hib/MenC vaccine). Meningococcal conjugate vaccine, especially if not received in adolescence. Previously vaccinated adults require a single booster and non-immunised adults advised, in UK since 2006, to have two doses given two months apart. Children too young for the conjugate vaccine should receive meningococcal polysaccharide vaccine in the interim. Influenza vaccine, every winter, to help prevent getting secondary bacterial infection. (https://en.wikipedia.org/wiki/Asplenia) Asplenia refers to the absence of normal spleen function and is associated with some serious infection risks.Asplenia is a form of immunodeficiency, increasing the risk of sepsis from polysaccharide encapsulated bacteria,and can result in overwhelming post splenectomy infection (OPSI), often fatal within a few hours. In particular, patients are at risk from Streptococcus pneumoniae, Haemophilus influenzae, and meningococcus.The risk is elevated as much as 350–fold. (https://en.wikipedia.org/wiki/Asplenia) YL YL acquired immunocompromised condition due to transplant 01/17/2016 The immunocomproised condition accquired by transplant patients taking medications to suppress their immune system as an anti-rejection measure. YL cerebrospinal fluid leak A health condition where the fluid surrounding the brain and spinal cord escapes. CSF leak YL http://www.adultvaccination.org/professional-resources/pneumo/adult-pneumo-guide-hcp.pdf cochlear implant The United States Food and Drug Administration reports that cochlear implant recipients may be at higher risk for meningitis.[76] A study of 4,265 American children who received implants between 1997 and 2002 concluded that recipient children had a risk of pneumococcal meningitis more than 30 times greater than that for children in the general population.[77] A later, UK-based, study found that while the incidence of meningitis in implanted adults was significantly higher than the general population, the incidence in children was no different from the general population.[78] As a result, the Centers for Disease Control and Prevention and the Food and Drug Administration both recommend that would-be implant recipients be vaccinated against meningitis prior to surgery.[79] YL a condition of person who has been surgically implanted an electronic device under the skin behind the ear to provide hearing. http://www.adultvaccination.org/professional-resources/pneumo/adult-pneumo-guide-hcp.pdf serious vaccine adverse event pregancy http://www.ebi.ac.uk/efo/EFO_0002950 01/25/2016 NCI:C25742 YL UMLS CUI:C0032961 https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=15.12d&ns=NCI_Thesaurus&code=C25742 NCI:C25742 The state or condition of having a developing embryo or fetus in the body (uterus), after union of an ovum and spermatozoon, during the period from conception to birth. burns A burn is an injury to the skin or other organic tissue primarily caused by heat or due to radiation, radioactivity, electricity, friction or contact with chemicals. Skin injuries due to ultraviolet radiation, radioactivity, electricity or chemicals, as well as respiratory damage resulting from smoke inhalation, are also considered to be burns. NCI:C34441 NCI:C34441 WHO (http://www.who.int/violence_injury_prevention/other_injury/burns/en/) YL https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=15.12d&ns=NCI_Thesaurus&code=C34441 breastfeeding The feeding of babies and young children with milk from a woman's breast. YL https://en.wikipedia.org/wiki/Breastfeeding smoking behaviour UMLS CUI:C1519386 https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=15.12d&ns=NCI_Thesaurus&code=C19796 01/25/2016 A person's current tobacco and nicotine consumption as well as his/her smoking history. http://www.ebi.ac.uk/efo/EFO_0004318 NCI:C19796 NCI:C19796 YL unprotected sexual intercourse NCI thesaurus NCI:C88146 Sexual intercourse without the use of precautions to prevent conception or the transmission of sexually transmitted diseases. YL part of pathogen organism in vaccine YH 'part of organism in vaccine' is a pathogen component in vaccine that contains only a part of the pathogen organism instead of the whole organism. 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 MeSH: D014612 a role that inheres in a prepared material entity that is designed to induce protection or treament for a diease or infection in vivo. 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. vaccination 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. vaccine administration YH, BP ACAM2000 Smallpox (Vaccinia) Vaccine, Live YH CVX: 75 Trade Name: ACAM2000 ActHIB Product Name: Haemophilus b Conjugate Vaccine (Tetanus Toxoid Conjugate) YH PMID: PMID: 1735812 PMID: 1517908 Trade Name: ActHIB CVX: 48 Adacel Product Name: Tetanus Toxoid, Reduced Diphtheria Toxoid and Acellular Pertussis Vaccine, Adsorbed CVX: 20 Trade Name: Adacel CVX: 115 YH Afluria Product Name: Influenza Virus Vaccine CVX: 141 Trade Name: Afluria CVX: 140 WEB: http://www.cdc.gov/vaccines/pubs/pinkbook/downloads/appendices/B/excipient-table-2.pdf YH Attenuvax Product Name: Measles Virus Vaccine, Live Trade Name: Attenuvax YH Bacillus anthracis vaccine YH A vaccine that protects against Bacillus anthrax that causes anthrax. anthrax vaccine MeSH: D022122 Biothrax Product Name: Anthrax Vaccine Adsorbed YH CVX: 24 Trade Name: Biothrax Boostrix Product Name: Tetanus Toxoid, Reduced Diphtheria Toxoid and Acellular Pertussis Vaccine, Adsorbed CVX: 115 YH CVX: 20 Trade Name: Boostrix Comvax Product Name: Haemophilus b Conjugate Vaccine (Meningococcal Protein Conjugate) & Hepatitis B Vaccine (Recombinant) Trade Name: Comvax YH PMID: CVX: 51 Daptacel Product Name: Diphtheria & Tetanus Toxoids & Acellular Pertussis Vaccine Adsorbed YH Trade Name: DAPTACEL CVX: 106 Vaccine components see http://www.vaccinesafety.edu/components-DTaP.htm CVX: 20 DECAVAC Product Name: Tetanus & Diphtheria Toxoids Adsorbed for Adult Use YH Trade Name: DECAVAC CVX: 113 Diphtheria and Tetanus Toxoids Adsorbed USP by Sanofi Pasteur Inc Product Name: Diphtheria & Tetanus Toxoids Adsorbed YH CVX: 28 Diphtheria and Tetanus Toxoids Adsorbed by Sanofi Pasteur Ltd Product Name: Diphtheria & Tetanus Toxoids Adsorbed YH Dryvax Product Name: Smallpox Vaccine, Dried, Calf Lymph Type Dryvax is a freeze-dried calf lymph smallpox vaccine. It is the world's oldest smallpox vaccine, created in the late 19th century by American Home Products, a predecessor of Wyeth. By the 1940s, Wyeth was the leading US manufacturer of the vaccine and the only manufacturer by the 1960s. After world health authorities declared smallpox had been eradicated from nature in 1980, Wyeth stopped making the vaccine. Trade Name: Dryvax YH CVX: 75 http://en.wikipedia.org/wiki/Dryvax a vaccinia virus vaccine that is a freeze-dried calf lymph smallpox vaccine, specifically, Dryvax is a live-virus preparation of vaccinia prepared from calf lymph. FluLaval Product Name: Influenza Virus Vaccine, Trivalent, Types A and B YH Trade Name: FluLaval CVX: 141 FluMist Product Name: Influenza Virus Vaccine, Live, Intranasal CVX: 111 YH WEB: http://www.cdc.gov/vaccines/pubs/pinkbook/downloads/appendices/B/excipient-table-2.pdf Trade Name: FluMist Fluarix Product Name: Influenza Virus Vaccine, Trivalent, Types A and B Trade Name: Fluarix YH CVX: 140 Fluvirin Product Name: Influenza Virus Vaccine, Trivalent, Types A and B Trade Name: Fluvirin CVX: 140 CVX: 141 YH Fluzone Product Name: Influenza Virus Vaccine, Trivalent, Types A and B CVX: 141 YH CVX: 140 CVX: 144 Trade Name: Fluzone Gardasil Product Name: Human Papillomavirus (Types 6, 11, 16, 18) Recombinant Vaccine CVX: 62 Trade Name: Gardasil YH Havrix Product Name: Hepatitis A Vaccine, Inactivated Trade Name: Havrix YH CVX: 83 CVX: 52 Neisseria meningitidis vaccine A bacterial vaccine that prevents Neisseria meningitidis infection. Meningococcal vaccine MeSH: D022401 YH IPOL Product Name: Poliovirus Vaccine Inactivated (Monkey Kidney Cell) PMID: YH Trade Name: IPOL CVX: 10 Imovax Rabies (USA) Product Name: Rabies Vaccine YH CVX: 18 Trade Name: Imovax Infanrix Product Name: Diphtheria & Tetanus Toxoids & Acellular Pertussis Vaccine Adsorbed YH CVX: 20 Trade Name: Infanrix Influenza Virus Vaccine H5N1 (Sanofi Pasteur Inc) Product Name: Influenza Virus Vaccine, H5N1 (for National Stockpile) YH WEB: http://atomicnewsreview.org/2009/10/22/approval-for-the-arepanrix%E2%84%A2-gsk-vaccine-in-canada/ JE-Vax Product Name: Japanese Encephalitis Virus Vaccine Inactivated YH CVX: 39 Trade Name: JE-Vax Kinrix Product Name: Diphtheria and Tetanus Toxoids and Acellular Pertussis Adsorbed and Inactivated Poliovirus Vaccine Trade Name: KINRIX CVX: 130 YH M-M-R II Product Name: Measles, Mumps, and Rubella Virus Vaccine, Live Trade Name: M-M-R II YH A Measles-Mumps-Rubella vaccine that is live attenuated and manufactured by Merck & Co, Inc. CVX: 03 M-M-Vax Product Name: Measles and Mumps Virus Vaccine, Live A Measles-Mumps vaccine that is manufactured by Merck and used for human. YH Trade Name: M-M-Vax Menactra Product Name: Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugate Vaccine YH WEB: http://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm176044.htm Trade Name: Menactra Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugate Vaccine CVX: 114 Menomune A C Y W135 Product Name: Meningococcal Polysaccharide Vaccine, Groups A, C, Y and W-135 Combined YH Trade Name: Menomune-A/C/Y/W-135 CVX: 32 Meruvax II Product Name: Rubella Virus Vaccine Live CVX: 06 Trade Name: Meruvax II YH Mumpsvax Product Name: Mumps Virus Vaccine Live Trade Name: Mumpsvax YH CVX: 07 Mycobax Product Name: BCG Vaccine Trade Name: Mycobax YH CVX: 19 Fluzone High-dose Product Name: Influenza Virus Vaccine, Trivalent, Types A and B an influenza vaccine that is similar to Fluzone but has high dose. YH WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM305079.pdf CVX: 140 CVX: 141 Trade Name: Fluzone CVX: 144 Influenza A (H1N1) 2009 Monovalent Vaccine (Novartis) Pediarix Product Name: Diphtheria & Tetanus Toxoids & Acellular Pertussis Vaccine Adsorbed, Hepatitis B (recombinant) and Inactivated Poliovirus Vaccine Combined CVX: 110 Trade Name: Pediarix YH PedvaxHIB Product Name: Haemophilus b Conjugate Vaccine (Meningococcal Protein Conjugate) PMID: CVX: 49 YH Trade Name: PedvaxHIB PMID: 2791073 Pentacel Product Name: Diphtheria and Tetanus Toxoids and Acellular Pertussis Adsorbed, Inactivated Poliovirus and Haemophilus b Conjugate (Tetanus Toxoid Conjugate) Vaccine YH CVX: 120 Trade Name: Pentacel Plague Vaccine by Greer Laboratories Inc Product Name: Plague Vaccine CVX: 23 YH Pneumovax 23 (USA) Product Name: Pneumococcal Vaccine, Polyvalent CVX: 33 Trade Name: Pneumovax 23 YH Poliovax Product Name: Poliovirus Vaccine Inactivated (Human Diploid Cell) Trade Name: Poliovax YH Prevnar (USA) Product Name: Pneumococcal 7-valent Conjugate Vaccine (Diphtheria CRM197 Protein) YH Trade Name: Prevnar CVX: 100 ProQuad Product Name: Measles, Mumps, Rubella and Varicella Virus Vaccine Live YH A Measles-Mumps-Rubella-Vericella vaccine that is live and manufactured by Merck & Co, Inc. Trade Name: ProQuad WEB: http://www.merck.com/product/usa/pi_circulars/p/proquad/proquad_pi.pdf CVX: 94 Fluzone intradermal Trade Name: Fluzone intradermal WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM305080.pdf YH RabAvert Product Name: Rabies Vaccine WEB: http://www.cdc.gov/vaccines/pubs/pinkbook/downloads/appendices/B/excipient-table-2.pdf CVX: 18 Trade Name: RabAvert YH Rabies Vaccine Adsorbed by BioPort Corp Product Name: Rabies Vaccine Adsorbed YH RotaTeq Product Name: Rotavirus Vaccine, Live, Oral, Pentavalent Trade Name: RotaTeq YH CVX: 116 TENIVAC Product Name: Tetanus & Diphtheria Toxoids Adsorbed for Adult Use YH Trade Name: TENIVAC TICE BCG Intravesical TICE BCG has been used as a therapy for, and to prevent recurrence of, tumors in patients with carcinoma in situ (CIS) of the urinary bladder, and to prevent recurrence of Stage Ta T1 papillary tumors of the bladder at high risk of recurrence. Refernce URL: http://www.ticebcg.com/Consumer/aboutTice/index.asp Product Name: BCG Vaccine CVX: 19 Trade Name: TICE BCG YH TYPHIM Vi Product Name: Typhoid Vi Polysaccharide Vaccine CVX: 101 Trade Name: TYPHIM Vi YH Tetanus Toxoid Adsorbed by Aventis Pasteur Inc Product Name: Tetanus Toxoid Adsorbed YH CVX: 35 Tetanus and Diphtheria Toxoids Adsorbed by MA Biologic Lab Product Name: Tetanus & Diphtheria Toxoids Adsorbed for Adult Use YH Tripedia Product Name: Diphtheria & Tetanus Toxoids & Acellular Pertussis Vaccine Adsorbed Trade Name: Tripedia CVX: 20 YH Twinrix Product Name: Hepatitis A Inactivated and Hepatitis B (Recombinant) Vaccine CVX: 104 YH Trade Name: Twinrix Varivax Product Name: Varicella Virus Vaccine Live Trade Name: Varivax YH CVX: 21 Vivotif (USA) Product Name: Typhoid Vaccine Live Oral Ty21a CVX: 25 Trade Name: Vivotif YH YF-Vax Product Name: Yellow Fever Vaccine Trade Name: YF-Vax YH http://www.cdc.gov/vaccines/pubs/pinkbook/downloads/appendices/B/excipient-table-2.pdf CVX: 37 Yellow fever virus vaccine A viral vaccine that protects against infection with Yellow fever virus. MeSH: D022341 YH Zostavax Product Name: Zoster Vaccine, Live, (Oka/Merck) CVX: 121 YH Trade Name: Zostavax vaccine adjuvant role an adjuvant role that inheres in a vaccine component which is added as part of a vaccine and induces enhanced adaptive immune response to the vaccine antigen. YH Influenza A (H1N1) 2009 Monovalent Vaccine (Sanofi Pasteur) bacterial vaccine A vaccine that targets against a bacterial disease. MeSH: D001428 YH vaccine organism live attenuated a virulence of vaccine organism that shows an attenuated pheontype of the organism as the major component of a vaccine. YH cancer vaccine neoplasm vaccine MeSH: D019496 YH A vaccine that prevents or treats cancer. It is produced using the patient's own whole tumor cells as the source of antigens, or using tumor-specific antigens, often recombinantly produced. tumor vaccine vaccine component YH a processed material that is output of the vaccine preparation and part of a vaccine. vaccine ingredient cardinal part of vaccine vaccine organism inactivated an organismal quality of a whole organism vaccine where the whole organism is inactivated/killed and lacks the capability of replication. vaccine organism killed YH hypersensitivity to chicken egg YH vaccine function YH, MC, XZ, and AR 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. 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. company YH intramuscular route a route of administration that inject the material(such as vaccines, allergens) directly into a muscle. I.M. YH,YL intramuscular injection route intranasal route YH rounte of administration that located in nose. I.N. intranasal route by spray YH Influenza A (H1N1) 2009 Monovalent Vaccine (CSL Limited) vaccine additive role 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. YL,YH Menactra injection 0.5mL vial Product Name: Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugate Vaccine injection 0.5mL vial YH Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugate Vaccine injection 0.5mL vial WEB: http://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm176044.htm SNOMEDCT: 416532007; UMLS_CUI:C1563043 Trade Name: Menactra Varicella-zoster virus live vaccine SNOMEDCT: 412530002; ULMS_CUI: C0770687 a Varicella-zoster virus vaccine that is live attenuated. YH polyvalent pneumococcal vaccine YH WEB: http://www.who.int/vaccines/en/pneumococcus.shtml a pneumococcal vaccine that is formed using polyvalent polysaccharides The most common form of the polyvalent pneumococcal vaccine is called the protein-polysaccharide combinations which is known as conjugate vaccines and contain 7–11 selected polysaccharides bound to a protein carrier. The protein-polysaccharide combinations are able to induce a T-cell dependent immune response. These vaccines are likely to be protective even in children under two years of age, and may reduce pneumococcal transmission through a herd effect. vaccinia virus vaccine WEB: http://en.wikipedia.org/wiki/Vaccinia a Smallpox virus vaccine that uses vaccinia virus YH Vaccinia virus is well known for its role as a vaccine that helped eradicate the smallpox disease, making it the first human disease to be successfully eradicated by science. preventive vaccine function 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. prophylactic vaccine function YH protein of pathogen organism as vaccine component YH chicken ovalbumin egg protein allergen WEB: http://en.wikipedia.org/wiki/Ovalbumin a chicken egg protein allergen where the protein allergen is ovalbumin, the main protein found in egg write, making up 60-65% of the total protein. YH typhoid live oral vaccine YH a S. typhi vaccine that is live and orally administerred UMLS_CUI: C0359940; SNOMEDCT: 346696005 active immunization YH, XZ WEB: http://en.wikipedia.org/wiki/Immunization 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. vaccine immunization artificial active immunization is an active immunization that occurs when a person or animal is vaccinated with a specific vaccine. artificial active immunization WEB: http://en.wikipedia.org/wiki/Immunization YH, XZ induction of adaptive immune response to antigen YH, XZ 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. disorder prevention disorder prevention is a processual entity that prevents a disorder that is the physical basis of a disease. YH, XZ disorder treatment disorder treatment is a processual entity that leads to treat a disorder that is the physical basis of a disease. YH, XZ modification of adaptive immune response to antigen 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 subcutaneous route YH YL S.C. a route of administration that is loacted in the hypodermis (subcutaneous tissue) region. human vaccinee a human who has been administrated a vaccine a vaccinee that is a human being therapeutic vaccine function YH 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. route of administration http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C38114 YH,YL CDISC has a codelist: Rout of Administration. Desription from CDISC: The course by which a substance was administered in order to reach the site of action in the body. CDISC_SDTM_Route_of_Administration_Terminology http://en.wikipedia.org/wiki/Route_of_administration a path that is located in gross anatomical part of an organism (e.g., human) and is used for administering a vaccine, a drug, fluid, poison, or other substance into the body. http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C66729 thimerosal vaccine preservative vaccine preservative that has thimerosal as part. YH H1N1 Influenza vaccine H1N1 Influenza vaccine is an Influenza virus vaccine that is used to vaccinate against H1N1 Influenza subtype vaccine. YH vaccine adjuvant 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 immunization objective WEB: http://en.wikipedia.org/wiki/Immunization YH, XZ immunization objective is the specification of an objective to achieve immunization. vaccine preparation vaccine production vaccine generation vaccine preparation is a manufacturing process to produce a vaccine. YH, BP viral vaccine A vaccine that targets against a viral disease. MeSH: D014765 YH vaccine role YH a role that inheres in a prepared material entity that is designed to induce protection or treatment for a disease or infection. vaccine component role a role that inheres in a material entity that becomes an ingredient of a vaccine. YH conjugate vaccine role a vaccine role that indicates the vaccine being a conjugate vaccine. YH licensed vaccine role YH licensed vaccine role is a regulation-assigned role that indicates that a vaccine obtains official approval for commercial production and selling on the market. Clostridium vaccine YH A bacterial vaccine that protects against infection with Clostridium spp. Clostridium tetani vaccine tetanus vaccine YH a Clostridium vaccine that protects against infection with Clostridium tetani that causes tenanus. Influenza virus vaccine MeSH: D007252; UMLS_CUI: C0021403; SNOMEDCT: 46233009 A viral vaccine that protects against infection with influenza virus. YH Influenza vaccine Hepatitis B virus vaccine MeSH: D017325 A viral vaccine that protects against infection with Hepatitis B virus. YH Hepatitis A virus vaccine YH MeSH: D022362 A viral vaccine that protects against infection with Hepatitis A virus. Yersinia pestis vaccine YH A bacteria vaccine that prevents against Yersinia pestis infection that causes plague. Plague vaccine MeSH: D010931; SNOMEDCT: 11866009; UMLS_CUI:C0032066 Rabies virus vaccine YH MeSH: D011819; SNOMEDCT: 333606008; UMLS_CUI:C0034496 A viral vaccine that protects against infection with Rabies virus. Smallpox virus vaccine A viral vaccine that protects against infection with Smallpox virus. YH MeSH: D012900 Measles virus vaccine MeSH: D008458 YH A viral vaccine that protects against infection with Measles virus. Measles vaccine Rotavirus vaccine A viral vaccine that protects against infection with Rotavirus. YH MeSH: D022243; UMLS_CUI: C0597418; SNOMEDCT: 116077000 Haemophilus vaccine A bacterial vaccine that protects against infection with Haemophilus. YH MeSH: D018073 Haemophilus influenzae serotype b vaccine Haemophilus b vaccine YH Poliovirus vaccine MeSH: D023321 YH A viral vaccine that protects against infection with Poliovirus. Japanese encephalitis virus vaccine Japanese encephalitis vaccine MeSH: D022321 A viral vaccine that protects against infection with Japanese encephalitis virus. YH human papillomavirus vaccine UMLS_CUI: C1512511; SNOMEDCT: 424519000 a vaccine against human papillomavirus infection YH Varicella-zoster virus vaccine UMLS_CUI: C0078048; SNOMEDCT: 108729007 a Herpesvirus vaccine that is used against Varicella-zoster virus infection. YH chickenpox virus vaccine Salmonella typhi vaccine typhoid vaccine a Salmonella vaccine against typhoid fever (or called typoid), caused by Salmonella enterica enterica, serovar Typhi. YH Streptococcus pneumoniae vaccine YH a Streptococcal vaccine that is used against S. pneumoniae infection, which causes pneumococcal diseases. WEB: http://www.who.int/vaccines/en/pneumococcus.shtml pneumococcal vaccine vaccine allergen disposition YH Measles-Mumps-Rubella vaccine MMR A Measles-Mumps vaccine that also protects against infection with Rubella virus. MMR is usually live attenuated. YH Diphtheria-Tetanus vaccine YH A Corynebacterium diphtheriae vaccine that also protect against infection with Clostridium tetani. Corynebacterium diphtheriae vaccine diphtheria vaccine YH A bacterial vaccine that protects against infection with Corynebacterium diphtheriae that causes Diphtheria. Measles-Mumps vaccine YH A Measles virus vaccine that also protects against infection with Mumps virus. Measles-Mumps-Rubella-Vericella vaccine YH A Measles-Mumps-Rubella vaccine that also protects against Vericella. Diphtheria-Tetanus-Pertussis vaccine DTP vaccine YH UMLS_CUI: C0012559; SNOMEDCT: 421245007 DTaP vaccine Haemophilus influenzae serotype b YH Diphtheria-Tetanus-Pertussis-Poliovirus vaccine YH Diphtheria-Tetanus-Pertussis-Poliovirus-Hepatitis B vaccine YH Diphtheria-Tetanus-Pertussis-Poliovirus-Haemophilus b vaccine YH Hepatitis A&B vaccine YH Haemophilus b and Hepatitis B vaccine a viral vaccine against Hepatitis B virus and at the same time against bacterial H. influenzae serotype b. YH Vibrio cholerae vaccine YH cholera vaccine MeSH: D022121 A bacterial vaccine that prevents infection with Vibrio cholera. BCG vaccine Bacillus Calmette Guerin BCG Vaccine is a Mycobacterium tuberculosis vaccine that is a live attenuated strain of Mycobacterium bovis (Bacillus Calmette Guerin; BCG). CVX: 19 YH USA licensed vaccine role YH a licensed vaccine role that indicates the vaccine occurs in USA. vaccine preservative antimicrobial agent in vaccine YH vaccine stabilizer 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. Finn TM and Egan W, in Vaccines fifth edition, 2008. Page 75. YH cell culture residual in vaccine a vaccine residual that is generatead from cell culture for vaccine preparation. Examples include: antibiotics, sensitizing substances, bacterial and cellular residuals, and adventitious agents. YH Finn TM and Egan W, in Vaccines fifth edition, 2008. Page 78-81. Canada licensed vaccine role YH a licensed status that occurs in Canada. Fluviral S/F YH Influvac YH Influvac is an Influenza virus vaccine that is manufactured by Solvay Pharma. Vaxigrip YH, Melanie Vaxigrip is an Influenza virus vaccine that is manufactured by 'Sanofi Pasteur Limited. aluminum vaccine adjuvant YH 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. vaccine preservative role 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.) YH,YL 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. oral route YH a route of administration that located in the mouth intradermal route intradermal injection route YH,YL a route of administration that inject the material(such as vaccines, allergens) into the skin itself. I.D. phenol vaccine preservative YH phenoxy ethanol vaccine preservative YH vaccine allergen WEB: http://www.cdc.gov/vaccines/pubs/pinkbook/downloads/appendices/B/excipient-table-2.pdf vaccine allergen is a material entity that is capable of stimulating a type-I hypersensitivity reaction in atopic individuals who has been vaccinated with a vaccine. YH, ZX latex vaccine allergen YH, ZX gelatin vaccine allergen YH, ZX protamine sulfate vaccine allergen YH, ZX bovine albumin cell culture residual in vaccine a cell culture residual in vaccine that is bovine albumin. YH, ZX bovine serum cell culture residual in vaccine a cell culture residual in vaccine that is bovine serum. YH monosodium glutamate stabliizer a vaccine stablizer that is based on monosodium glutamate. C5H8NNaO4 http://www.novaccine.com/vaccine-ingredients/results.asp?sc=13 YL,YH glutaraldehyde vaccine additive human albumin cell culture residual in vaccine a cell culture residual in vaccine that is human albumin. YH human serum cell culture residual in vaccine YH a cell culture residual in vaccine that is human serum. polysorbate 20 vaccine stabilizer a vaccine stabilizer that is a polysorbate 20. It encourages the suspension of one liquid in another and has mild toxicity. YH, YL http://www.novaccine.com/vaccine-ingredients/results.asp?sc=95 Potential Acute Health Effects: Slightly hazardous in case of skin contact (irritant), of eye contact (irritant), of ingestion, of inhalation. Reference: http://www.sciencelab.com/msds.php?msdsId=9926640 polysorbate 80 vaccine emulsifier YH,YL a vaccine emulsifier that uses polysorbate 80, also known as polyoxyethylene sorbitan monooleate or Tween™ 80. Tween 80 vaccine emulsifier Tween 80 is an amber-colored, viscous liquid with a slightly bitter taste. The product is a derivative of sorbitol and oleic acid. WEB: http://www.wisegeek.org/what-is-polysorbate-80.htm vaccine residual protein from cell culture YH a cell culture residual in vaccine that is residual protein from cell culture. sorbitol vaccine stabilizer YH, YL glucitol Sorbitol, also known as glucitol, is a sugar alcohol that the human body metabolizes slowly. It can be obtained by reduction of glucose, changing the aldehyde group to a hydroxyl group. Sorbitol is found in apples, pears, peaches, and prunes. It is synthesized by sorbitol-6-phosphate dehydrogenase, and converted to fructose by succinate dehydrogenase and sorbitol dehydrogenase. Succinate dehydrogenase is an enzyme complex that participates in the citric acid cycle. (wikipedia) a vaccine stabilizer that is specifically made by sorbitol. sucrose albumin cell culture residual in vaccine a cell culture residual in vaccine that is sucrose albumin. YH xanthan gum vaccine ajuvant PMID: 19608270 YL yeast extract cell culture residual in vaccine YH a cell culture residual in vaccine that is from yeast extract. yeast protein cell culture residual in vaccine YH a cell culture residual in vaccine that is yeast protein. Diphtheria-Tetanus-Pertussis-Haemophilus b vaccine Diphtheria-Tetanus-Poliovirus vaccine V. cholerae and E. coli vaccine Measles-Rubella vaccine A Measles virus vaccine that is also used against Rubella virus infection. YH Diphtheria-Tetanus-Pertussis-Poliovirus-Haemophilus b-Hepatitis B vaccine Salmonella typhi-Hepatitis A vaccine Flublok Yongqun He Trade Name: Flublok Flucelvax Yongqun He Trade Name: Flucelvax FluMist Quadrivalent YH Fluarix Quadrivalent YH Tetanus Toxoid (for Boost use Only) by Sanofi Pasteur Inc WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142732.pdf YH a tetanus vaccine manusfactured by Sanofi Pasteur Inc. that is only for booster use (not recommended for primary immunization) bacterial vaccine organism live attenuated YH a live attenuated quality of a bacterial vaccine strain. viral vaccine organism live attenuated YH a live attenuated quality of a virus vaccine strain. Agriflu CVX: 140 YH intramuscular vaccination a vaccination that occurs in the intramuscular route. YH, YL Prevnar 13 ZX VIOLIN Vaccine ID: 1114 CVX: 133 Menveo VIOLIN Vaccine ID: 1113 CVX: 136 capsular polysaccharide of pathogen organism as vaccine component YH vaccine host role 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 target specification The objective that intends to produce vaccine via the vaccine preparation process. YH Influenza A (H1N1) 2009 Monovalent Vaccine (IDB) intradermal vaccination vaccination process that occurs in intradermal route. YL intranasal vaccination vaccination process that occurs in intranasal route YL oral vaccination YL vaccination process that occurs in oral route. subcutaneous vaccination YL vaccination process that occurs in the subcutaneous route vaccine emulsifier role YL a role inheres in the vaccine component when it is added into vaccine's formulation, it tends to stabilizes an emulsion by increasing its kinetic stablity. vaccine stabilizer role YL 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. vaccine conjugate protein The conjugate protein is a part of a conjugate vaccine and acts as a carrier protein that is covalently attached to a vaccine antigen with poor antigenicity (e.g., a polysaccharide). A conjugate protein is able to induce T-cell-dependent immune responses and stimulate the production of immune memory. YL,YH vaccine conjugate role YL role inheres in a material eneitity that union itself chemically with a relative weak vaccine antigen to form a new whole that can create an effective miinuogen. The percutaneous route YL epicutaneous (application onto the skin), e percutaneous vaccination Administration of a drug by the way of absorption through the skin, usually for systemic action. The route allows sustained therapeutic plasma drug levels and avoids first pass effect. Simplicity of administration tends to result in high patient compliance. YL intravesical route intravesical vaccination The injection of a given substance directly into the bladder via a urethral catheter instead of being injected under the skin. YL Actacel todo: Proteins + Conjugate Trade Name: Actacel YH, ZX Avaxim todo: Killed virus YH, ZX Trade Name: Avaxim Avaxim - Pediatric todo: Killed virus Trade Name: Avaxim - Pediatric YH, ZX BCG Vaccine (Freeze-Dried) (by Sanofi Pasteur) todo: Live bacteria Trade Name: BCG Vaccine (Freeze-Dried) YH, ZX DT Polio Adsorbed todo: Proteins + killed virus YH, ZX Trade Name: DT Polio Adsorbed Dukoral todo: Proteins + killed bacteria YH, ZX Trade Name: Dukoral Engerix-B CVX: 08 YH, ZX CVX: 44 Product Name: Hepatitis B Vaccine (Recombinant) Trade Name: Engerix-B Eolarix YH, ZX Trade Name: Eolarix A Measles-Rubella vaccine that is live attenuated and manufactured by GlaxoSmithKline Biologicals. Epaxal todo: Killed virus YH, ZX Trade Name: Epaxal FSME - IMMUN todo: Inactivated whole virus Trade Name: FSME - IMMUN YH, ZX Hiberix CVX: 48 YH, ZX Trade Name: Hiberix Imovax Polio todo: Killed virus YH, ZX Trade Name: Imovax Polio Imovax Rabies (Canada) YH, ZX Trade Name: Imovax Rabies Inactivated Poliomyelitis Vaccine - IPV todo: Killed virus Trade Name: Inactived Poliomyelitis Vaccine - IPV YH, ZX Infanrix-hexa todo: Proteins + killed viruses + conjugate Trade Name: Infanrix-hexa YH, ZX Infanrix/Hib todo: Proteins + conjugate Trade Name: Infanrix/Hib YH, ZX Infanrix-IPV todo: Proteins + killed virus Trade Name: Infanrix-IPV YH, ZX Infanrix -IPV/Hib todo: Proteins + killed virus + conjugate Trade Name: Infanrix -IPV/Hib YH, ZX CVX: 120 Liquid Pedvax HIB YH, ZX Trade Name: Liquid Pedvax HIB Meningitec todo: Conjugate Trade Name: Meningitec YH, ZX Meningococcal Polysaccharide Vaccine, Groups A & C, Menomune A/C todo: Polysaccharide YH, ZX Trade Name: Meningococcal Polysaccharide Vaccine, Groups A & C, Menomune A/C Menjugate todo: Conjugate Trade Name: Menjugate YH, ZX Menomune A/C/Y/W-135 todo: Polysaccharide YH, ZX Trade Name: Menomune A/C/Y/W-135 Mutacol todo: Live bacteria YH, ZX A live attenuated V. cholerae vaccine that is manufactured by Berna Biotech, Ltd. This vaccine uses the V. Cholera strain CVD 103-HGR. Trade Name: Mutacol Neisvac-C todo: Conjugate Trade Name: Neisvac-C YH, ZX Pediacel todo: Proteins, killed virus + conjugate Trade Name: Pediacel YH, ZX Pneumo 23 todo: Polysaccharide YH, ZX Trade Name: Pneumo 23 Pneumovax 23 (Canada) YH, ZX Trade Name: Pneumovax 23 Prevnar (Canada) todo: Conjugate YH, ZX Trade Name: Prevnar Priorix YH, ZX A MMR vaccine that is manufactured by GlaxoSmithKline Biologicals. Trade Name: Priorix Priorix-Tetra A Measles-Mumps-Rubella-Vericella vaccine that is live attenuated and manufactured by GlaxoSmithKline Biologicals. YH, ZX Trade Name: Priorix-Tetra Quadracel todo: Proteins + killed virus Trade Name: Quadracel YH, ZX Recombivax HB todo: Recombinant protein CVX: 08 CVX: 44 CVX: 43 YH, ZX Trade Name: Recombivax HB Rotarix todo: Live virus YH, ZX ROTARIX Trade Name: Rotarix Td Adsorbed todo: Proteins Trade Name: Td Adsorbed YH, ZX Tripacel todo: Proteins YH, ZX Trade Name: Tripacel Twinrix Junior todo: Recombinant protein + killed virus YH, ZX Trade Name: Twinrix Junior Typherix todo: Polysaccharide YH, ZX Trade Name: Typherix Vaqta todo: Killed virus Trade Name: Vaqta VAQTA YH, ZX Varilrix todo: Live virus YH, ZX Trade Name: Varilrix Varivax III todo: Live virus Trade Name: Varivax III YH, ZX ViVaxim todo: Polysaccharide + killed virus todo: assign parent immunogen: Typh-I + (HA) YH, ZX Trade Name: ViVaxim Vivotif (Canada) todo: Live virus Trade Name: Vivotif YH, ZX Ixiaro YH, ZX VIOLIN Vaccine ID: 741 CVX: 134 Cervarix CVX: 118 YH, ZX VIOLIN Vaccine ID: 740 Haemophilus influenzae vaccine Haemophilus influenzae A vaccine that protects against Haemophilus influenzae. YH, ZX Tick-borne Encephalitis Virus (TBEV) vaccine A vaccine that protects against Tick-borne Encephalitis Virus (TBEV). Tick-borne Encephalitis Virus (TBEV) YH, ZX nose structure *Subdivision of face which consists of the nasal skeleton, nasal septum and nasal cavity. 1a: The part of the face that bears the nostrils and covers the anterior part of the nasal cavity; broadly: this part together with the nasal cavity.n1b: The anterior part of the head at the top or end of the muzzle: snout, proboscis.n2: The vertebrate olfactory organ. 1a: The part of the face that bears the nostrils and covers the anterior part of the nasal cavity; broadly: this part together with the nasal cavity.n1b: The anterior part of the head at the top or end of the muzzle: snout, proboscis.n2: The vertebrate olfactory organ.[accessedResource: BTO:0000840][accessDate: 05-04-2011] 1a: The part of the face that bears the nostrils and covers the anterior part of the nasal cavity; broadly: this part together with the nasal cavity.nb: The anterior part of the head at the top or end of the muzzle: snout, proboscis.n2. The vertebrate olfactory organ. AAO:0000334 Any sense organ (FBbt:00005155) that functions in (some) detection of chemical stimulus involved in sensory perception (GO:0050907). Any sense organ (FBbt:00005155) that functions in (some) detection of chemical stimulus involved in sensory perception (GO:0050907).[accessedResource: FBbt:00005157][accessDate: 05-04-2011] Any sense organ (FBbt:00005155) that has function 'detection of chemical stimulus involved in sensory perception (GO:0050907)'. BTO:0000840 EHDAA:1502 EMAPA:16542 EV:0100037 FBbt:00005157 FMAID:46472 James Malone MA:0000281 MFO:0003640 Nose[accessedResource: FMAID:46472][accessDate: 05-04-2011] SAEL:72 TAO:0001149 XAO:0000201 XAO:0003033 ZFA:0001149 chemosensory sensory organ chemosensory sensory organ[accessedResource: FBbt:00005157][accessDate: 05-04-2011] nose olfactory system olfactory system[accessedResource: TAO:0001149][accessDate: 05-04-2011] State of California A state on the West Coast of the United States, along the Pacific Ocean. It is bordered by Oregon to the north, Nevada to the east, Arizona to the southeast, and to the south the Mexican state of Baja California. CA Califor-nia California GAZ GAZ:00002461 GNISID:01779778 INCITS38:06 ISO3166-2:US-CA Hawaiian Islands State of New York GAZ GAZ:00002514 GNISID:01779796 INCITS38:36 ISO3166-2:US-NY NY State of Oregon A state in the Pacific Northwest region of the United States. Oregon is located on the Pacific coast between Washington to the north, California to the south, Nevada on the southeast and Idaho to the east. The Columbia and Snake rivers delineate much of Oregon's northern and eastern boundaries respectively. GAZ GAZ:00002515 INCITS38:41 ISO3166-2:US-OR OR Oregon State of Arizona A state located in the southwestern region of the United States. It borders New Mexico, Utah, Nevada, California, touches Colorado, and has a 626 km international border with the States of Sonora and Baja California in Mexico. AZ GAZ GAZ:00002518 GNISID:01779777 INCITS38:04 ISO3166-2:US-AZ State of Maryland A state located in the Mid Atlantic region of the United States, bordering Virginia, West Virginia and the District of Columbia to the south and west, Pennsylvania to the north, and Delaware to the east. GAZ GAZ:00002519 GNISID:01714934 INCITS38:24 ISO3166-2:US-MD MD State of North Carolina A state located on the Atlantic Seaboard in the southeastern United States. The state borders South Carolina and Georgia to the south, Tennessee to the west and Virginia to the north. GAZ GAZ:00002520 GNISID:01027616 INCITS38:37 ISO3166-2:US-NC NC North Carolina State of Alaska A state in the United States of America, in the extreme northwest portion of the North American continent. The state is bordered by Yukon Territory and British Columbia, Canada to the east, the Gulf of Alaska and the Pacific Ocean to the south, the Bering Sea, Bering Strait, and Chukchi Sea to the west, and the Beaufort Sea and the Arctic Ocean. AK GAZ GAZ:00002521 GNISID:01785533 INCITS38:02 ISO3166-2:US-AK State of South Carolina A state in the southern region (Deep South) of the United States. It borders Georgia to the south and North Carolina to the north. GAZ GAZ:00002524 GNISID:01779799 INCITS38:45 ISO3166-2:US-SC SC South Carolina State of Rhode Island A state in the New England region of the United States. By land Rhode Island borders Connecticut to the west and Massachusetts to the north and east. Rhode Island also shares a water border with New York to the southwest. GAZ GAZ:00002531 GNISID:01219835 INCITS38:44 ISO3166-2:US-RI RI State of Rhode Island and Providence Plantations State of Wyoming A state in the northwestern region of the United States. Wyoming is bordered on the north by Montana, on the east by South Dakota and Nebraska, on the south by Colorado, on the southwest by Utah, and on the west by Idaho. GAZ GAZ:00002533 GNISID:01779807 INCITS38:56 ISO3166-2:US-WY WY Commonwealth of Massachusetts A state located in the New England region of the northeastern United States. It borders Rhode Island and Connecticut to the south, New York to the west, and Vermont and New Hampshire to the north. To the east, it borders the Atlantic Ocean. GAZ GAZ:00002537 ISO3166-2:US-MA MA State of Minnesota A state in the Midwestern region of the United States. The state shares a Lake Superior water border with Michigan and Wisconsin on the northeast; the remainder of the eastern border is with Wisconsin. Iowa is to the south, North Dakota and South Dakota to the west, and the Canadian provinces of Ontario and Manitoba to the north. GAZ GAZ:00002539 GNISID:00662849 INCITS38:27 ISO3166-2:US-MN MN Commonwealth of Pennsylvania A state located in the Northeastern and Middle Atlantic regions of the United States. The state borders Delaware and Maryland to the south, West Virginia to the southwest, Ohio to the west, New York and Canada to the north, and New Jersey to the east. GAZ GAZ:00002542 GNISID:01779798 INCITS38:42 ISO3166-2:US-PA PA Pennsylvania State of Pennsylvania State of Oklahoma A state located in the South Central region and Southern Region of the United States of America. It is bounded on the east by Arkansas and Missouri, on the north by Kansas, on the northwest by Colorado, on the far west by New Mexico, and on the south and near-west by Texas. GAZ GAZ:00002546 GNISID:01102857 INCITS38:40 ISO3166-2:US-OK OK State of Washington GAZ GAZ:00002553 GNISID:01779804 INCITS38:53 ISO3166-2:US-WA The Northwestern-most state of the contiguous United States. Its northern border lies mostly along the 49th parallel, and then via marine boundaries through the Strait of Georgia, Haro Strait and Strait of Juan de Fuca, with the Canadian province of British Columbia to the north. Washington borders Oregon to the south, with the Columbia River forming most of the boundary and the 46th parallel forming the eastern part of the southern boundary. To the east Washington borders Idaho, bounded mostly by the meridian running north from the confluence of the Snake River and Clearwater River, except for the southernmost section where the border follows the Snake River. To the west of Washington lies the Pacific Ocean. WA Washington State of New Jersey A state in the Mid-Atlantic and Northeastern regions of the United States. It is bordered on the north by New York, on the east by the Atlantic Ocean, on the southwest by Delaware, and on the west by Pennsylvania. New Jersey lies within the sprawling metropolitan areas of New York and Philadelphia. GAZ GAZ:00002557 GNISID:01779795 INCITS38:34 ISO3166-2:US-NJ NJ State of Texas A state located in the South Central United States. The Rio Grande, Red River and Sabine River form natural state borders, Oklahoma on the north, Louisiana and Arkansas on the east, and the Mexican states of Chihuahua, Coahuila, Nuevo Leon, and Tamaulipas to the south. GAZ GAZ:00002580 GNISID:01779801 INCITS38:48 ISO3166-2:US-TX TX State of Wisconsin A State located in the north-central part of the United States. Wisconsin is bordered by the Montreal River; Lake Superior and Michigan to the north; by Lake Michigan to the east; by Illinois to the south; and by Iowa and Minnesota to the west. The state's boundaries include the Mississippi River and Saint Croix River in the west, and the Menominee River in the northeast Wisconsin's capital is Madison, and its largest city is Milwaukee. GAZ GAZ:00002586 GNISID:01779806 INCITS38:55 ISO3166-2:US-WI WI Wisconsin State of Connecticut A state located in the New England region of the northeastern United States of America. The state borders New York to the west and south (Long Island by sea), Massachusetts to the north, and Rhode Island to the east. Portions of southwestern Connecticut are considered part of the New York metropolitan area. CT GAZ GAZ:00002591 GNISID:01779780 INCITS38:09 ISO3166-2:US-CT State of Maine A state in the New England region of the northeastern United States of America, bordering the Atlantic Ocean to the southeast, New Hampshire to the southwest, the Canadian provinces of Quebec to the northwest and New Brunswick to the northeast. GAZ GAZ:00002602 GNISID:01779787 INCITS38:23 ISO3166-2:US-ME ME Main State of Montana A state in the Western United States. To the north, Montana and Canada share a 877 km border. The state borders the Canadian provinces of British Columbia, Alberta, and Saskatchewan. To the east, the state borders North Dakota and South Dakota. To the south is Wyoming and to the west and southwest is Idaho. GAZ GAZ:00002606 GNISID:00767982 INCITS38:30 ISO3166-2:US-MT MT State of Georgia GA GAZ GAZ:00002611 GNISID:01705317 Georgia Georgia is bordered on the south by Florida; on the east by the Atlantic Ocean and South Carolina; on the west by Alabama and by Florida in the extreme southwest; and on the north by Tennessee and North Carolina. The northern part of the state is in the Blue Ridge Mountains, a mountain range in the vast mountain system of the Appalachians. The central piedmont extends from the foothills to the fall line, where the rivers cascade down in elevation to the continental coastal plain of the southern part of the state. INCITS38:13 ISO3166-2:US-GA State of Delaware A state located on the Atlantic Coast in the Mid-Atlantic region of the United States. Delaware is located in the eastern section of the Delmarva Peninsula, between Delaware Bay and Chesapeake Bay. Delaware is bounded to the north by Pennsylvania; to the east by the Delaware River, Delaware Bay, New Jersey and the Atlantic Ocean; and to the west and south by Maryland. DE GAZ GAZ:00002878 GNISID:01779781 INCITS38:10 ISO3166-2:US-DE State of Florida A state located in the southeastern region of the United States, bordering Alabama to the northwest and Georgia to the northeast. Much of the land mass of the state is a large peninsula with the Gulf of Mexico to the west and south, and the Atlantic Ocean to the east. Florida F{language: Bulgarian} GAZ GAZ:00002888 GNISID:00294478 INCITS38:12 ISO3166-2:US-FL Middle Atlantic Division East North Central Division State of Illinois A midwestern state of the United States of America. The Northeastern border of Illinois is Lake Michigan. Its eastern border with Indiana is all of the land west of the Wabash River, and a north-south line above Post Vincennes, or 87deg31min30secW. Its northern border with Wisconsin is fixed at 42deg30minN. Its western border with Missouri and Iowa is the Mississippi River. Its southern border with Kentucky is the Ohio River. Illinois also borders Michigan, but only via a water boundary in Lake Michigan. GAZ GAZ:00003142 GNISID:01779784 INCITS38:17 ISO3166-2:US-IL Illinois I{language: Bulgarian} State of Michigan A Midwestern state of the United States of America. Michigan consists of two peninsulas that lie between 82deg30minW to about 90deg30minW longitude, and are separated by the Straits of Mackinac. With the exception of two small areas that are drained by the Mississippi River by way of the Wisconsin River in the Upper Peninsula and by way of the Kankakee-Illinois River in the Lower Peninsula, Michigan is drained by the Great Lakes-Saint Lawrence watershed. The Great Lakes that border Michigan from east to west are Lake Erie, Lake Huron, Lake Michigan and Lake Superior. The state is bounded on the south by the states of Ohio and Indiana, sharing land and water boundaries with both. GAZ GAZ:00003152 GNISID:01779789 INCITS38:26 ISO3166-2:US-MI MI Michigan Commonwealth of Virginia A state on the Atlantic Coast of the Southern United States. Virginia is bordered by Maryland and the District of Columbia to the north and east; the Atlantic Ocean to the east; by North Carolina and Tennessee to the south; by Kentucky to the west and by West Virginia to the north and west. Due to a peculiarity of Virginia's original charter, its boundary with Maryland does not extend past the low-water mark of the southern shore of the Potomac River, so Maryland and the District of Columbia contain the whole width of the river rather than splitting it between them and Virginia. The southern border is defined as the 36deg30min parallel north. GAZ GAZ:00003171 GNISID:01779803 INCITS38:51 ISO3166-2:UA-VA VA Virginia Pacific Division West North Central Division Greater Antilles West South Central Division East South Central Division South Atlantic Division Mountain Division State of Hawaii A state in the United States, located on an archipelago in the central Pacific Ocean southwest of the continental United States, southeast of Japan, and northeast of Australia. GAZ GAZ:00003939 GNISID:01779782 HI INCITS38:15 ISO3166-2:US-HI Northern Mariana Islands Virgin Islands Archipelago State of Tennessee A state located in the Southern United States. The capital city is Nashville, and the largest city is Memphis. Tennessee borders eight other states: Kentucky and Virginia to the north; North Carolina to the east; Georgia, Alabama and Mississippi on the south; Arkansas and Missouri on the Mississippi River to the west. GAZ GAZ:00004411 GNISID:01325873 INCITS38:47 ISO3166-2:US-TN TN Tennessee State of Utah A western state of the United States. Utah has three distinct geological regions: the Rocky Mountains, the Great Basin, and the Colorado Plateau. GAZ GAZ:00004413 GNISID:01455989 INCITS38:49 ISO3166-2:US-UT UT State of West Virginia A state in the Appalachian, Upland South, and Mid-Atlantic regions of the United States, bordered by Virginia on the southeast, Kentucky on the southwest, Ohio on the northwest, and Pennsylvania and Maryland on the northeast. The capital and largest city is Charleston. GAZ GAZ:00004414 GNISID:01779805 INCITS38:54 ISO3166-2:US-WV WV West Virginia State of Ohio A Midwestern state of the United States. Ohio's southern border is defined by the Ohio River (with the border being at the 1793 low-water mark on the north side of the river), and much of the northern border is defined by Lake Erie. Ohio's neighbors are Pennsylvania to the east, Michigan to the northwest, Ontario Canada, to the north, Indiana to the west, Kentucky on the south, and West Virginia on the southeast. GAZ GAZ:00004421 GNISID:01085497 INCITS38:39 ISO3166-2:US-OH OH Ohio State of New Mexico A state located in the southwestern region of the United States. GAZ GAZ:00004427 GNISID:00897535 INCITS38:35 ISO3166-2:US-NM NM State of New Hampshire A state in the New England region of the northeastern United States of America. It borders Massachusetts to the south, Vermont to the west, Maine to the east, and the Canadian province of Quebec to the north. GAZ GAZ:00004428 GNISID:01779794 INCITS38:33 ISO3166-2:US-NH NH State of Vermont A state in the New England region of the northeastern United States of America. It is bordered by Massachusetts to the south, New Hampshire to the east, New York to the west, and the Canadian province of Quebec to the north. GAZ GAZ:00004429 GNISID:01779802 INCITS38:50 ISO3166-2:US-VT VT State of Mississippi A state located in the Deep South of the United States. Jackson is the state capital and largest city. Mississippi is bordered on the north by Tennessee, on the east by Alabama, on the south by Louisiana and a narrow coast on the Gulf of Mexico, and on the west, across the Mississippi River, by Louisiana and Arkansas. GAZ GAZ:00004430 GNISID:01779790 INCITS38:28 ISO3166-2:US-MS MS Mississippi State of Missouri A state in the Midwest region of the United States. Missouri is bounded on the north by Iowa; on the east, across the Mississippi River, by Illinois, Kentucky, and Tennessee; on the south by Arkansas; and on the west by Oklahoma, Kansas, and Nebraska (the last across the Missouri River). GAZ GAZ:00004431 GNISID:01779791 INCITS38:29 ISO3166-2:US-MO MO State of Louisiana A state located in the southern region of the United States of America. Louisiana is bordered to the west by the State of Texas; to the north by Arkansas; to the east by the State of Mississippi; and to the south by the Gulf of Mexico. GAZ GAZ:00004432 GNISID:01629543 INCITS38:22 ISO3166-2:US-LA LA State of Kansas A state in the central region of the United States of America. Kansas is bordered by Nebraska on the north; Missouri on the east; Oklahoma on the south; and Colorado on the west. GAZ GAZ:00004435 GNISID:00481813 INCITS38:20 ISO3166-2:US-KS KS State of Iowa A state located in the Midwestern region of the United States of America. Iowa is bordered by the Mississippi River on the east; the Missouri River and the Big Sioux River on the west; the northern boundary is a line along 43 degrees, 30 minutes north latitude. The southern border is the Des Moines River and a line along approximately 40 degrees 35 minutes north. GAZ GAZ:00004438 GNISID:01779785 IA INCITS38:19 ISO3166-2:US-IA State of Indiana A midwestern state of the United States of America. Indiana is bounded on the north by Lake Michigan and the state of Michigan; on the east by Ohio; on the south by Kentucky, with which it shares the Ohio River as a border; and on the west by Illinois. Indiana is one of the Great Lakes states. GAZ GAZ:00004439 GNISID:00448508 IN INCITS38:18 ISO3166-2:US-IN Indiana Commonwealth of Kentucky A state located in the East Central United States of America. Kentucky borders on seven states, from both the Midwest and the Southeast. West Virginia lies to the east, Virginia to the southeast, Tennessee to the south, Missouri to the west, Illinois and Indiana to the northwest, and Ohio to the north and northeast. GAZ GAZ:00004440 ISO3166-2:US-KY KY Kentucky State of Kentucky {alternative name} State of Arkansas A state located in the southern region of the United States. Arkansas shares a border with six states, with its eastern border largely defined by the Mississippi River. Arkansas shares its southern border with Louisiana, its northern border with Missouri, its eastern border with Tennessee and Mississippi, and its western border with Texas and Oklahoma. AR GAZ GAZ:00004441 GNISID:00068085 INCITS38:05 ISO3166-2:US-AR State of North Dakota A state located in the Midwestern and Western regions of the United States of America. GAZ GAZ:00004442 INCITS38:38 ISO3166-2:US-ND ND State of South Dakota A state located in the Midwestern region of the United States of America. GAZ GAZ:00004443 GNISID:01785534 INCITS38:46 ISO3166-2:US-SD SD State of Nevada A state located in the western region of the United States of America. Nevada is almost entirely within the Basin and Range Province, and is broken up by many north-south mountain ranges. Most of these ranges have endorheic valleys between them, which belies the image portrayed by the term Great Basin. The southern third of the state, where the Las Vegas area is situated, is within the Mojave Desert. GAZ GAZ:00004444 GNISID:01779793 INCITS38:32 ISO3166-2:US-NV NV State of Nebraska A state located on the Great Plains of the Midwestern United States and Western United States. GAZ GAZ:00005070 GNISID:01779792 INCITS38:31 ISO3166-2:US-NE NE Polynesia Micronesia State of Colorado A state located in the Rocky Mountain region of the United States of America. CO GAZ GAZ:00006254 GNISID:01779779 INCITS38:08 ISO3166-2:US-CO State of Idaho A state in the Pacific Northwest region of the United States of America. Idaho borders six states and one Canadian province, but does not border the Pacific Ocean at any point and is not, as such, a coastal state. The states of Washington and Oregon are to the west, Nevada and Utah are to the south, and Montana and Wyoming are to the east. The province of British Columbia, to the north, also shares a small (77 km) border with Idaho. GAZ GAZ:00006291 GNISID:01779783 ID INCITS38:16 ISO3166-2:US-ID New England Division State of Alabama A state located in the southern region of the United States of America. It is bordered by Tennessee to the north, Georgia to the east, Florida and the Gulf of Mexico to the south, and Mississippi to the west. Alabama A{language: Bulgarian} GAZ GAZ:00006881 GNISID:01779775 INCITS38:01 ISO3166-2:US-AL Samoan Archipelago Wake Island Marshall Islands Delmarva Peninsula Southern Marianas Islands University of Maryland, College Park A public research university located in the city of College Park in Prince George's County, Maryland. GAZ GAZ:00157006 example to be eventually removed example to be eventually removed metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term PERSON:Alan Ruttenberg organizational term term created to ease viewing/sort terms for development purpose, and will not be included in a release ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting to be replaced with external ontology term Alan Ruttenberg Terms with this status should eventually replaced with a term from another ontology. group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion axiom holds for all times axiom holds for all times Minatoba government Public Health division Rite Aid Costco Walgreens Have you had a disorder in the last month that caused brain or nerve damage such as stroke or convulsion? Intercell Biomedical Acambis, Inc YH http://www.acambis.com/ Berna Biotech, Ltd http://www.crucell.com/ YH BioPort Corp YH http://www.bioport.com/ CSL Limited http://www.csl.com.au/ YH GlaxoSmithKline Biologicals YH http://www.gsk-bio.com/english/index.html Greer Laboratories Inc http://www.greerlabs.com/ YH ID Biomedical Corp of Quebec YH http://www.ctidirectory.com/search/company.cfm?company=129584 Massachusetts Public Health Biologic Lab YH MedImmune Vaccines, Inc http://www.medimmune.com/ YH Merck & Co, Inc http://www.merck.com/ YH Merck Sharp & Dohme Corp. Novartis Vaccines and Diagnostics http://www.novartis.com/about-novartis/our-businesses/vaccines-diagnostic.shtml YH Organon Teknika Corp LLC YH Research Foundation for Microbial Diseases of Osaka University http://read.jst.go.jp/public/cs_kkn_004EventAction.do?action5=event&lang_act5=E&kcd1_act5=9535000000&judge_act5=2 YH Sanofi Pasteur Limited YH http://www.sanofipasteur.com Sanofi Pasteur, Inc YH http://www.sanofipasteur.us Aventis Pasteur Inc. Wyeth Pharmaceuticals Inc YH http://www.wyeth.com/ Sanofi Pasteur, SA YH http://www.sanofipasteur.co.za/ Solvay Pharmaceuticals YH Baxter Healthcare Corporation YH, ZX http://www.baxter.com/ Merck Frosst YH, ZX http://www.merckfrosst.ca/ SBL Vaccine YH, ZX Wyeth Canada http://www.wyeth.ca/ YH, ZX Novartis YH Aqua Health http://www.novartis.com/ ID Biomedical Corporation of Quebec YL