A biomedical ontology in the area of vaccine adverse events.
Erica Marcos
Jiangan Xie
OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE).
OVAE: Ontology of Vaccine Adverse Events
OWL-DL
Vision Release: 1.0.34
Yongqun "Oliver" He (YH)
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
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
PERSON:Daniel Schober
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
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
example
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
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.
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
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
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 note
An administrative note of use for a curator but of no use for a user
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
expand assertion to
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
person:Alan Ruttenberg
has associated axiom(nl)
An axiom associated with a term expressed using natural language
Person:Alan Ruttenberg
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
Chinese translation
a chinese translation represents a chinese translation of the existing term.
adverse event outcome
The AE 'cough AE' has the 'label of AE outcome' of 'cough'; 'infection AE' has the 'label of AE outcom' of 'infection'.
an annotation property that represents the label of an adverse event
organism NCBITaxon ID
The NCBITaxon ontology ID of an organism.
temporal interpretation
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.
x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
Chris Mungall
tooth SubClassOf 'never in taxon' value 'Aves'
taxonomic class assertion
An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost
S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
logical macro assertion
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 class
A logical macro assertion whose domain is an IRI for a class
The domain for this class can be considered to be owl:Class, but we cannot assert this in 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
logical macro assertion on an annotation property
relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
A textual description of an axiom loss in this ontology compared to an external ontology.
Notes on the homology status of this class.
An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info.
Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.
Notes on the how instances of this class vary across species.
Notes on the evolved function of instances of this class.
Notes on the structure, composition or histology of instances of this class.
Notes on the ontogenic development of instances of this class.
Notes on how similar or equivalent classes are represented in other ontologies.
Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy.
A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates)
Most land mammals including humans have a 2-3-3-3-3 formula in both the hands (or paws) and feet. Primitive reptiles typically had the formula 2-3-4-4-5, and this pattern, with some modification, remained in many later reptiles and in the mammal-like reptiles. The phalangeal formula in the flippers of cetaceans (marine mammals) is 2-12-8-1
x phalanx_number N if and only if (i) x is a phalanx, and (ii) x is phalanx number N in a series of phalanges repeated along an prixomo-distal axis, with phalanx_number 1 being the proximalmost phalanx. Note that in humans, the distalmost phalanx has phlanax_number 3, except in ray_number 1, where the distalmost has phalanx_number 2
A metadata relation between a class and its taxonomic rank (eg species, family)
A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes.
derived from the union of EHDAA2 and EMAPA - still to be checked
Subset consisting of classes creating for grouping purposes
A grouping class that depends on an assumption of homology between subclasses
classes that have some inconsistency with FMA
somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads
abstract class brought in to group ontology classes but not informative
organs, excluding individual muscles and skeletal elements
Uberon slim - subset that excludes obscure terms and deep compositional terms
abstract upper-level terms not directly useful for analysis
core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO
Source
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.
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
is part of
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
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.
a core relation that holds between a whole and its 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
BFO2 Reference: independent continuant that is not a spatial region
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])
realized in
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
[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])
is realized by
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
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
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])
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.
[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)
preceded by
X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
occurs in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t [XXX-001
occurs_in
unfolds in
unfolds_in
contains process
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
site of
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
(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
(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
occupies spatial region at some time
(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]
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]
(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])
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])
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])
(iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]
[copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
[copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
has proper occurrent part
[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 spatial occupant at some time
[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 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.
[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
BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])
part of occurrent
(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])
(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
spatial projection of spatiotemporal at some time
projects onto temporal region
temporal projection of spatiotemporal
occupies temporal region
p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
has temporal occupant
[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])
during which exists
[copied from inverse property 'exists at'] BFO2 Reference: entity
[copied from inverse property 'exists at'] BFO2 Reference: temporal region
[copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
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)
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])
(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
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.
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]
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.
[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])
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.
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.
x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer
x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.
x proximal_to y iff x is closer to the point of attachment with the body than y.
x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
is evidence of
This represents a relation between two adverse events AE1 and AE2. However, AE1 may be an evidence of another adverse event AE3, and a dfferent adverse event AE4 may also be an evidence of the same AE2.
An electrocardiogram qt prolonged AE is_evidence_of arrhythmia AE; arrhythmia AE is_evidence_of cardiomyopathy AE; fever AE is_evidence_of inflammation AE; fever AE is_evidence_of viral infection AE; plural effusion AE is_evidence_of cardiac disorder AE.
has participant quality
an object property that represents a relation between a process and a quality, in which the process has a participant that has the quality.
An adverse event has a participant quality, such as a hyperkalemia AE has a participatn quality blood potassium increased.
adverse event occurs in
a 'occurs in' relation that is applied at the adverse event setting and indicates where an adverse event occurs in.
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
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
is_manufactured_by
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_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.
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
is genome of organism
a 'part of continuant at some time' relation that incides a genome belongs to a organism.
is gene of organism
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.
occurs in population
an vaccine adverse event 'occurs in population' human vaccinee population is equivalent to say: 'occurs in' human vaccinee 'part of' human vaccine population.
an 'occurs in' relation that is a shortcut relation combining the 'occurs in' relation in an specific term which is part of a population.
participates in
a relation between a continuant and a process, in which the continuant is somehow involved in the process
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
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).
has function
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
has_function
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
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
this person has role this investigator role (more colloquially: this person has this role of investigator)
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
my brain is located in my head
this rat is located in this cage
A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
before or simultaneous with
Primitive instance level timing relation between events
simultaneous with
Relation between occurrents, shares start and end boundaries.
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
ends after
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
immediately preceded by
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately precedes
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
starts during
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
happens during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
ends during
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
overlaps
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
x overlaps y if and only if there exists some z such that x has part z and z part of y
Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
x adjacent_to y iff: x and y share a boundary
temporally related to
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
Relation between occurrents, shares a start boundary with.
starts with
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
Relation between occurrents, shares an end boundary with.
ends with
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
mereotopologically related to
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
has potential to developmentally contribute to
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
x composed_primarily_of y iff: more than half of the mass of x is made from parts of y
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
Relation between continuant and occurrent, such that c comes into existence at the start of p.
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
This relation may be replaced by has_vaccine_allergen. We need to determine if any vaccine contraindicator is not a vaccine allergen.
has_vaccine_contraindication is a relation that specifies contraindication of a vaccine.
a object property that specifies a relation between a vaccine and a vaccine allergen
an object property that specifies a relation between a vaccine and a vaccinate route
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.
x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
x is a conduit for y iff y passes through the lumen of x.
x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.
X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides.
x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
a data property that indicates a vaccinee having an occurrence of a specific VAE of a particular data value that is in the range of 0 and 1.
has age in year
a data property that represents the age with the unit of year.
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
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
the Second World War
your body mass index
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]
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])
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
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
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])
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 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.
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])
independent continuant
(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.
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 leg
a molecule
an atom
an organism
a chair
a heart
a spatial region
an orchestra.
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])
the bottom right portion of a human torso
the interior of your mouth
dependent continuant
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
spatial region
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
(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])
temporal region
(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
(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
(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]
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
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.
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])
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]
(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
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.
an atom of element X has the disposition to decay to an atom of element Y
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])
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])
(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]
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])
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
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]
(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]
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 > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < 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])
of one-sided specifically dependent continuants: the mass of this tomato
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
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 relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
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 shape of this hole.
the smell of this portion of mozzarella
role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
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])
the priest role
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 stone in marking a property boundary
the role of subject in a clinical trial
the student role
three-dimensional spatial 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
(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
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
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.
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])
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.
function
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
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 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
(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.
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])
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])
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
zero-dimensional temporal region
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
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.
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.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
A (1->6)-alpha-D-glucan which has extra branching consisting of (1->2), (1->3) or (1->4) linkages.
A broad-spectrum highly toxic antibiotic or mixture of antibiotics produced by a streptomyces (Streptomyces fradiae) and used medically especially to treat local infections.
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
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
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.
PERSON: Chris Stoeckert
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.
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
negative-sense genome single-stranded RNA viruses
Cell-associated subacute sclerosing panencephalitis
Subacute sclerosing panencephalitis virus
subacute sclerosing panencephalitis virus, SSPEV
purple photosynthetic bacteria and relatives
ssRNA positive-strand viruses, no DNA stage
Diplokokkus intracellularis meningitidis
Micrococcus meningitidis cerebrospinalis
Bordetella Moreno-Lopez 1952 (Approved Lists 1980) emend. Von Wintzingerode et al. 2001
Enterobacteraceae (ex Lapage 1979) Lapage 1982, fam. nov., nom. rev.
Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980, fam. nov., nom. rev.
Salmonella cholerae-suis subsp. cholerae-suis
Salmonella choleraesuis subsp. choleraesuis
Burkholderia/Oxalobacter/Ralstonia group
Salmonella enterica subsp. enterica serovar Typhi
Bacillus/Lactobacillus/Streptococcus group
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'.
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
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.
medical intervention is a planned process that has the goal of diagnosing, preventing or relieving illness or injury.
WEB: http://wiki.answers.com/Q/What_is_medical_intervention
an adverse event that occurs after a vaccination.
an adverse event that has an outcome of abnormal sign in a musculoskeletal or connective tissue.
WEB: http://www.cdc.gov/niosh/programs/msd/
musculoskeletal and connective tissue disorder AE
A musculoskeletal disorder is an injury or disorder of the muscles, nerves, tendons, joints, cartilage, or supporting structures of the upper or lower limbs, neck, or lower back that are caused, precipitated, or exacerbated by sudden exertion or prolonged exposure to physical factors such as repetition, force, vibration, or awkward posture
MedDRA: 10016256 (fatigue); MedDRA: 10024264 (lethargy)
WEB: http://en.wikipedia.org/wiki/Fatigue_%28medical%29
a behavior and neurological AE that has an outcome of fatigue, which is a state of awareness describing a range of afflictions, usually associated with physical and/or mental weakness, though varying from a general state of lethargy to a specific work-induced burning sensation within one's muscles. Physical fatigue is the inability to continue functioning at the level of one's normal abilities.
Yongqun He, Sirarat Sarntivijai, Mathias Brochhausen, William Hogan, ‎Philip E. Empey
A contraindication is a disposition that increases the risk of harm involved in using a particular drug, carrying out a medical procedure, or engaging in a particular activity such that the risk of harm exceeds a threshold. An contraindication serves as a reason to withhold a certain medical treatment.
clinical laboratory test
WEB: http://labmed.ascpjournals.org/content/40/2/105.full
a planned process that is specifically a test conducted in a clinical laboratory.
a cardiovascular disorder AE that has a cardiac disorder outcome.
WEB: Primary Source: http://medical-dictionary.thefreedictionary.com/heart+disease Secondary Source: http://www.ncbi.nlm.nih.gov/pubmed/23091623
an adverse event that occurs in hair, skin, or nail.
a hair, skin, and nail AE that occurs in hair.
a hair, skin, and nail AE that occurs in nail.
inconsolable crying AE
a crying abnormal AE that has an outcome of abnormal inconsolable crying in a patient
unusual high-pitched crying AE
a crying abnormal AE that has an outcome of abnormal unusual high-pitched crying in a patient
prolonged crying AE
a crying abnormal AE that has an outcome of abnormal prolonged crying in a patient
medical intervention site AE
an adverse event that occurs in the site of a medical intervention (e.g., vaccination injection site).
medical intervention site
a site that is used for a medical intervention
convulsion AE is a muscle adverse event that results in a medical condition where body muscles contract and relax rapidly and repeatedly, resulting in an uncontrolled shaking of the body
WEB: http://en.wikipedia.org/wiki/Convulsion
WEB: http://wordnetweb.princeton.edu/perl/webwn?s=induration
injection-site induration AE is an skin AE that results in hardening or thickening of tissue at the physical injection site
WEB: http://medical-dictionary.thefreedictionary.com/pruritus
injection-site pruritus AE is an pruritus AE that results in an unpleasant sensation that evokes the desire or reflex to scratch at the physical area of injection
injection-site rash AE is a rash AE that results in a change of the skin which affects its color, appearance or texture at the physical injection site
injection-site warmth AE is a homeostasis AE that results in feeling of warmth at the physical injection site
A joint disorder AE that has an outcome of joint swelling, which is a joint disorder that results in a buildup of fluid in the soft tissue surrounding the joint
WEB: http://www.nlm.nih.gov/medlineplus/ency/article/003262.htm
WEB: http://en.wikipedia.org/wiki/Lymphadenopathy
A lymphadenopathy AE that results in swollen/enlarged lymph nodes
a muscle AE that has an outcome of muscular weakness AE (i.e., lack of muscle strength).
WEB: http://en.wikipedia.org/wiki/Muscular_weakness
a sensory capability AE that has an outcome of a sensation of stiffness in muscles and skeleton
WEB: http://en.wikipedia.org/wiki/Nasal_congestion
nasal congestion AE is a respiratory system AE that results in a blockage of the nasal passages usually due to membranes lining the nose becoming swollen from inflamed blood vessels
a respiratory system inflammation AE which has an outcome of nasopharyngitis, a respiratory system inflammation that results in common cold, a contagious, viral infectious disease of the upper respiratory system
WEB: http://en.wikipedia.org/wiki/Nasopharyngitis
an ear disorder AE which has an outcome of otitis media that results in inflammation of the middle ear, or middle ear infection
WEB: http://en.wikipedia.org/wiki/Otitis_media
WEB: http://en.wikipedia.org/wiki/Pharyngitis
pharyngitis AE is a digestive system AE that results in an inflammation of the throat or pharynx
a pain AE that shows a pain in sinus and throat
WEB: http://www.wordinfo.info/words/index/info/view_unit/1631/
WEB: http://en.wikipedia.org/wiki/Rhinitis
WEB: http://medical-dictionary.thefreedictionary.com/rhinitis
rhinitis AE is a respiratory system inflammation characterized by runny nose,irritation and inflammation of some internal areas of the nose
WEB: http://en.wikipedia.org/wiki/Rhinorrhoea
rhinorrhoea AE is a respiratory system AE that results in runny nose, an unusually significant amount of nasal fluid
an infection AE is a respiratory system AE that results in illnesses caused by an acute infection which involves the upper respiratory tract: nose, sinuses, pharynx or larynx
WEB: http://en.wikipedia.org/wiki/Upper_respiratory_tract_infection
Axelrod YK1, Diringer MN. Temperature management in acute neurologic disorders. Neurol Clin. 2008 May;26(2):585-603, xi. doi: 10.1016/j.ncl.2008.02.005. PMID: 18514828.
WEB: http://en.wikipedia.org/wiki/Pyrexia
an abnormal body temperature AE which has an outcome of fever
Fever is a frequent medical sign that describes an increase in internal body temperature to levels above normal. Fever is characterized as a temporary elevation in the body's thermoregulatory set-point, usually by about 1-2 °F).
Drug-induced rash is the most commonly reported drug reaction.
URL: http://www.webmd.com/skin-problems-and-treatments/guide/common-rashes
Wick JY. Drug-induced rash: nuisance or threat? Consult Pharm. 2013 Mar;28(3):160-6. PMID: 23462025.
a skin AE that shows the symptom of rash, i.e., an abnormal change in skin color, appearance, or texture. A rash may cause the skin to change color, itch, become warm, bumpy, dry, cracked or blistered, swell and may be painful.
change of name from 'infection adverse event' to 'infectious adverse event' on 09/23/13 for a better clinical relevance, move 'infection adverse event' as an alternative term - SS
an adverse event that has an outcome of a pathogen infection, i.e., an infection caused by a pathogen such as a virus, bacterium, or parasite.
WEB: http://medical-dictionary.thefreedictionary.com/infection
An AE that has an outcome of syndrome. Syndrome is the association of several clinically recognizable features, signs (observed by a physician), symptoms (reported by the patient), phenomena or characteristics that often occur together, so that the presence of one feature alerts the physician to the presence of the others.
injection-site AE is an AE that occurs in an injection site (e.g., during vaccination).
an edema AE which occurs at the injection site. In this case, a collection of fluid at the injection site is found.
WEB: http://www.uptodate.com/contents/edema-swelling-beyond-the-basics
a pain AE that occurs in an injection site of a medical intervention
an injection-site AE that display an injection-site mass
injection-site mass is a mass at physical injection site
WEB: http://www.ncbi.nlm.nih.gov/sites/entrez?db=mesh&cmd=DetailsSearch&term=pruritus+generalised&log$=activity
Pruritus is an itch (Latin: pruritus), i.e., an unpleasant sensation that evokes the desire or reflex to scratch.
a skin adverse event that has an outcome of pruritus
a sensory capability AE that has an outcome of pain in a patient
a pain AE that has outcome of myalgia. Myalgia means "muscle pain" and is a symptom of many diseases and disorders.
Urticaria AE is a rash AE notable for dark red, raised, itchy bumps.
a pain AE that has an outcome of headache
I created this term and make it to be an umbrella term for different disorder terms related to respiratory system. --Oliver He
an AE that occurs in respiratory system.
a cardiovascular disorder AE that has an outcome of abnormal blood pressure, representing altered tension of the blood within the systemic arteries
a muscle adverse event which has an outcome of asthenia, which is a medical term denoting symptoms of physical weakness and loss of strength.
a muscle pain AE that has an outcome of muscle ache.
An joint disorder AE that has an outcome of arthralgia. Arthralgia means joint pain. It is a symptom of injury, infection, illnesses (in particular arthritis) or an allergic reaction to medication. According to MeSH, the term "arthralgia" should only be used when the condition is non-inflammatory, and the term "arthritis" should be used when the condition is inflammatory.
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.
Malaise is a feeling of general discomfort or uneasiness, an "out of sorts" feeling. Malaise is often the first indication of an infection or other disease. Vaccination may induce malaise.
a sensory capability AE that has an outcome of malaise
a behavior and neurological AE that has an outcome of somnolence
Somnolence (or "drowsiness") is a state of near-sleep, a strong desire for sleep, or sleeping for unusually long periods (c.f. hypersomnia).
a behavior and neurological AE that has an outcome of abnormal crying in a patient
Chills refers to feeling cold after an exposure to a cold environment. The word can also refer to an episode of shivering, accompanied by paleness and feeling cold.
a sensory capability AE that has an outcome of chills
a gustatory system AE which demonstrates a decreased sensation of appetite.
MedDRA: 10002649 (anorexia nervosa); MedDRA: 10061428 (decreased appetite); MedDRA: 10002646 (anorexia).
WEB: http://www.mayoclinic.org/diseases-conditions/anorexia/basics/definition/con-20033002
WEB: http://medical-dictionary.thefreedictionary.com/cough
WEB: http://www.nlm.nih.gov/medlineplus/cough.html
an abnormal respiration AE that shows a sudden and often repetitively occurring reflex to keep the throat and airways clear
a syndrome AE that has an outcome of a flu syndrome AE and occurs after a medical intervention.
a sensory capability AE that has an outcome of loss of consciousness, fainting
WEB: http://en.wikipedia.org/wiki/Unconsciousness
Syncope is the medical term for fainting, a sudden, usually temporary, loss of consciousness.
WEB: http://en.wikipedia.org/wiki/Syncope_%28medicine%29
WEB: http://en.wikipedia.org/wiki/Abdominal_pain
According to the Vaccine Adverse Event Reporting System (VAERS), 'abdominal pain' is an adverse event that was mentioned in 2,254 VAERS reports (1.8%) during1991-2001 (Reference: PMID: 12825543).
a pain AE that is observed in abdominal cavity
WEB: http://www.ncbi.nlm.nih.gov/pubmed/21722707
an abnormal blood pressure AE that has an outcome of sustained high blood pressure at a level that is likely to result in cardiovascular disease and/or other pathological states
According to the Vaccine Adverse Event Reporting System (VAERS), 'skin nodule' was mentioned in 1,134 VAERS reports (0.9%) during1991-2001 (Reference: PMID: 12825543).
a skin adverse event that has an outcome of skin nodule
WEB: http://medical-dictionary.thefreedictionary.com/hemorrhage
a cardiovascular disorder AE that has an outcome of hemorrhage
loss of blood from the vascular compartment to the exterior or into nonvascular body space as a result of rupture or severance of the blood vessels
a respiratory system AE which has an outcome of lung disorder
a musculoskeletal system AE that occurs in muscle.
a musculoskeletal system AE which has an outcome of joint disorder
According to the Vaccine Adverse Event Reporting System (VAERS), 'gastrointestinal disorder' is an adverse event that was mentioned in 449 VAERS reports (0.3%) during1991-2001 (Reference: PMID: 12825543).
a digestive system AE which has an outcome of a gastrointestinal disorder
According to the Vaccine Adverse Event Reporting System (VAERS), 'immune system disorder' was mentioned in 292 VAERS reports (0.2%) during1991-2001 (Reference: PMID: 12825543).
a syndrome AE that has an outcome of an acute brain syndrome AE and occurs after a medical intervention.
an AE that occurs in cardiovascular system.
a respiratory system AE which has an outcome of sore throat
WEB: http://www.thefreedictionary.com/skin+disorder
a hair, skin, and nail AE that occurs in skin.
a homeostasis AE which has an outcome of abnormal fluid regulation, which is any anomaly in the control of intracellular and/or extracellular fluid
blood pressure decreased, low blood pressure
an abnormal blood pressure AE that has an outcome of sustained low blood pressure at a level that is likely to result in cardiovascular disease and/or other pathological states
a digestive system AE which has an outcome of abnormal digestion, which is an altered ability of the mechanical, chemical, and enzymatic processes of the body to convert ingested food into material suitable for assimilation for synthesis of tissues or liberation of energy
an AE that occurs in the homeostasis system.
anomaly in the processes involved in the maintenance of an internal equilibrium of various functions and chemical or protein composition of the fluids and tissues
WEB: http://en.wikipedia.org/wiki/Oedema
an abnormal fluid regulation AE which has an outcome of edema, which is an accumulation of an excessive amount of watery fluid in cells or intercellular tissues
WEB: http://en.wikipedia.org/wiki/Swelling_(medical)
WEB: http://en.wikipedia.org/wiki/Inflammation
an immune system disorder AE that results in complex biological response of vascular tissues to harmful stimuli, such as pathogens, damaged cells, or irritants. Inflammation is a protective attempt by the organism to remove the injurious stimuli as well as initiate the healing process for the tissue greater than expected response to injury, infection, or insult.
an inflammation AE which has an outcome of respiratory system inflammation, the local accumulation of fluid, plasma proteins, and leukocytes in the respiratory system
an inflammation AE that has an outcome of vasculitis, which is an inflammation of a blood or lymph vessel
Not sure if it is same as respiratory system disorder or abnormal respiration. --Oliver He
According to the Vaccine Adverse Event Reporting System (VAERS), 'respiratory disorder' is an adverse event that was mentioned in 556 VAERS reports (0.4%) during1991-2001 (Reference: PMID: 12825543).
a respiratory system AE which has an outcome of abnormal respiration, an anomaly in the movement of gases into and out of the lung
an adverse event that occurs in a gustatory system
WEB: http://www.psychguides.com/guides/behavioral-disorder-symptoms-causes-and-effects/
any anomaly in the actions, reactions, or performance of an organism in response to external or internal stimuli compared to controls
an adverse event that has an outcome of an abnormal behavior and neurological phenotype.
a behavior and neurological AE that has an outcome of altered ability to coordinate voluntary movement or repetitive, compulsive movements
a behavior and neurological AE that has an outcome of inability or altered ability to respond to a sensory stimulus
Hypersensitivity AE is a immune system AE that is a set of undesirable reactions produced by the normal immune system, including allergies and autoimmunity. These reactions may be damaging, uncomfortable, or occasionally fatal.
WEB: http://en.wikipedia.org/wiki/Hypersensitivity
an abnormal digestion AE which has an outcome of nausea, a gastric discomfort associated with the inclination to vomit
an abnormal digestion AE which has an outcome of vomiting, the retrograde expulsion of gastric contents through the oral cavity
a digestive system AE that has an outcome of abnormal defecation, an anomaly in the production and excretion of feces
WEB: http://medical-dictionary.thefreedictionary.com/diarrhea
an abnormal defecation AE that has an outcome of diarrhea, which is abnormally frequent discharge of semi-solid or fluid fecal matter from the bowel
a homeostasis AE whic has an outcome of abnomal body temperature, which is a deviation in the level of heat natural to a living being
a hemorrhage AE that has an outcome of ecchymosis
an ecchymosis is a spot caused by loss of blood from a vessel; it implies a larger size than a petechiae, and has a more diffuse border than purpura; an ecchymosis can be caused by a bruise (which implies trauma), but can also be caused by bleeding diathesis
WEB: http://www.toyourhealth.com/mpacms/tyh/article.php?id=1521
The low-grade level of fever is beneficial. With most microbes/"bugs" that a child will be exposed to, this fever will assist the body in repelling the invader.
low-grade fever AE is a fever adverse event with a temperature between 100° F and 102.2° F (37.8° C and 39° C).
Musculoskeletal pain is pain that affects the muscles, ligaments and tendons, along with the bones.
WEB: http://www.webmd.com/pain-management/guide/musculoskeletal-pain
a pain AE that has an outcome of musculoskeletal pain
injection-site erythema AE is an erythema AE that results in redness of skin, caused by hyperermia of the capillaries in the lower layers of the skin at the physical area of injection
WEB: http://en.wikipedia.org/wiki/Erythema
WEB: http://medical-dictionary.thefreedictionary.com/erythema
Erythema AE is a skin adverse event that showns redness of the skin caused by hyperemia of the capillaries in the lower layers of the skin.
an cardiovascular adverse event that is a collection of blood outside the blood vessels, generally the result of hemorrhage, or more specifically, internal bleeding. It is commonly called a bruise.
YH: MedDRA ID: 10018852 is for "haematoma"; MedDRA ID: 10019428 is for "hematoma".
WEB: http://en.wikipedia.org/wiki/Hematoma
a cardiovascular disorder AE which has an outcome of vasodilatation, which refers to the widening of blood vessels resulting from relaxation of smooth muscle cells within the vessel walls, particularly in the large arteries, smaller arterioles and large veins.
WEB: http://en.wikipedia.org/wiki/Vasodilation
a lung disorder AE that has an outcome of a sudden constriction of the muscles in the walls of the bronchioles
WEB: http://medical-dictionary.thefreedictionary.com/bronchospasm
a cardiovascular disorder AE that results in the inability of the heart to provide sufficient pump action to distribute blood flow to meet the needs of the body
WEB: http://medical-dictionary.thefreedictionary.com/cardiac+failure
WEB: https://en.wikipedia.org/wiki/Cardiomyopathy
a cardiovascular disorder AE that has an outcome of deterioration of the function of the myocardium, usually leads to heart failure
WEB: http://medical-dictionary.thefreedictionary.com/cardiomyopathy
Behavior and Neurological AE that results in the patient being easily annoyed/irritated
WEB: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1115975/
an edema AE occuring in a specific region
WEB: http://medical-dictionary.thefreedictionary.com/lymphadenopathy
an immune system disorder AE that has an outcome of lymphadenopathy, which is a term meaning "disease of the lymph nodes" . It is generally a disease or inflammation of the lymph nodes, could be due to infection, auto-immune disease or malignancy
a behavior and neurological AE that results in irregular sleep patterns
WEB: http://medical-dictionary.thefreedictionary.com/sleep+disorder
injection-site redness AE
an injection-site AE that display an redness in the injection-site
injection-site tenderness AE
a sensory capability AE that shows up skin tenderness and occurs in an injection site of a medical intervention
arm motion limitation AE
a movement disorder AE that has an outcome of arm motion limitation
injection-site muscular soreness AE
a sensory capability AE that shows up muscular soreness at the injection site of a medical intervention
sleepiness AE
a sleep disorder AE that shows up sleepiness (Sluggish from sleep, inactive, quiet).
mild hypersensitivity AE
injection-site arm edema AE
an injection-site edema AE that occurs in the arm.
restlessness AE
a psychiatric disorder AE that shows restlessness
WEB: http://dictionary.reference.com/browse/restlessness
induration with tenderness AE
a sensory capability AE that results in a sensation of induration with tenderness.
fussiness AE
a sensory capability AE that results in a sensation of fussiness
decreased sleep AE
a sleep disorder AE that shows decreased sleep
increased sleep AE
a sleep disorder AE that shows increased sleep
joint pain AE
This term appears to be a synonym to the 'fatigue AE'.
Tiredness AE is a sensory capability AE that results in a sensation of tiredness.
severity of adverse event
a process quality that represents the level of severity of an adverse event.
WEB: http://en.wikipedia.org/wiki/Mental_disorder
a behavior and neurological AE that has an outcome of a mental illness or psychiatiric disorder. The mental illness is a mental or behavioral pattern or anomaly that causes either suffering or an impaired ability to function in ordinary life (disability), and which is not developmentally or socially normative.
mental disorder AE
AE severity G1
a severity of AE that shows asymptomatic, or involves mild or minor symptoms, or is of marginal clinical relevance, or consists of clinical or diagnostic observations alone, or where intervention is not indicated, or where only non-prescription intervention is indicated.
Note the AE severity Grade 1 equals to CTCAE G1 AE severity.
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_1_Adverse_Event
AE severity G2
a severity of AE for which only minimal, local, or noninvasive intervention (e.g. packing, cautery) is indicated, or that limits instrumental activities of daily living (ADLs, e.g., shopping, laundry, transportation, or ability to conduct finances).
Note the AE severity Grade 2 equals to CTCAE G2 AE severity.
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_2_Adverse_Event
AE severity G3
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_3_Adverse_Event
Note the AE severity Grade 3 equals to CTCAE G3 AE severity.
a severity of AE that shows an outcome which is medically significant but not life-threatening; or for which inpatient care or prolongation of hospitalization are indicated; or that is an important medical event that does not result in hospitalization, but may jeopardize the patient or may require intervention either to prevent hospitalization, to prevent the AE from becoming life-threatening or causing death; or that is disabling; or that results in persistent or significant disability, incapacity, or limitation of self care activities of daily living (ADLs, getting in and out of bed, dressing, eating, getting around inside, bathing, or using the toilet).
AE severity G4
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_4_Adverse_Event
a severity of AE that has life-threatening consequences, for which urgent intervention is indicated, that puts the patient is at risk of death at the time of the event if immediate intervention is not undertaken, or that causes blindness or deafness (need to decide if unilateral or bilateral).
Note the AE severity Grade 4 equals to CTCAE G4 AE severity.
AE severity G5
Note the AE severity Grade 5 equals to CTCAE G5 AE severity.
Web: http://ncicb.nci.nih.gov/xml/owl/EVS/ctcae.owl#Grade_5_Adverse_Event
local AE
an adverse event that occurs locally in a certain location. This is different from the systematci adverse event that occurs throughout the systemtic circulation.
URL: https://en.wikipedia.org/wiki/Adverse_drug_reaction
behavior abnormal quality
a behavioral quality where the behavior in an organism is abnormal.
WEB: https://en.wikipedia.org/wiki/Abnormality_(behavior)
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
Injecting mice with a vaccine in order to test its efficacy
A processual entity that realizes a plan which is the concretization of a plan specification.
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)
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.
organization
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.
material to be added role
9 March 09 from discussion with PA branch
drug added to a buffer contained in a tube; substance injected into an animal;
material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
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.
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
target of material addition role is a role realized by an entity into which a material is added in a material addition process
30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition
In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09
host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role
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')
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
plant
virus
administering substance in vivo
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178
A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance.
Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
Bjoern Peters
Different routes and means of administration should go as children underneath this
IEDB
injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor.
genome
Book: Eugene Nester, Denise Anderson, C. Evans Roberts, Jr., Microbiology (Companion Site): A Human Perspective, 7th Edition. Mcgraw Hill, October 18, 2011. ISBN-13: 978-0073375311
A genome is a material entity that represents the entirety of an organism's hereditary information. The genome includes both the genes and the non-coding sequences of the DNA and RNA.
WEB: http://en.wikipedia.org/wiki/Genome
gene
A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule.
WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/
In addition to the coding regions (exons), a gene includes transcription-control regions and sometimes introns. Although the majority of genes encode proteins, some encode tRNAs, rRNAs, and other types of RNA.
The genome of an organism of Proteobacteria
A bodily process that is clinically abnormal.
a vaccine adverse event that is associated with administration of a bacterial vaccine
a vaccine adverse event that is associated with administration of a virus vaccine
a vaccine adverse event that is associated with administration of a parasite vaccine
a vaccine adverse event that is associated with administration of a fungal vaccine
a vaccine adverse event that is associated with administration of a cancer vaccine
bacterial and viral combination vaccine adverse event
a vaccine adverse event that is associated with administration of a bacterial and viral combination vaccine
adverse event associated with Diphtheria & Tetanus Toxoids Absorbed
An influenza vaccine adverse event that is associated with the administration of Flublok.
An influenza vaccine adverse event that is associated with the administration of Fluarix.
Fluarix Quadrivalent vaccine adverse event
An influenza vaccine adverse event that is associated with the administration of Fluarix Quadrivalent vaccine.
An influenza vaccine adverse event that is associated with the administration of Flucelvax.
An influenza vaccine adverse event that is associated with the administration of Flulaval.
FluMist Quadrivalent vaccine adverse event
An influenza vaccine adverse event that is associated with the administration of FluMist Quadrivalent vaccine.
An influenza vaccine adverse event that is associated with the administration of Fluvirin.
An influenza vaccine adverse event that is associated with the administration of Fluzone.
An influenza vaccine adverse event that is associated with the administration of Fluzone High-dose vaccine.
Fluzone Intradermal vaccine adverse event
An influenza vaccine adverse event that is associated with the administration of Fluzone intradermal vaccine.
Influenza Virus Vaccine H5N1 vaccine adverse event
An influenza vaccine adverse event that is associated with the administration of Influenza virus vaccine H5N1 vaccine.
Menomune-A/C/Y/W-135 vaccine adverse event
adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological
Tetanus Toxoid (boost only) vaccine adverse event
Tetanus Toxoid Absorbed vaccine adverse event
An influenza vaccine adverse event that is associated with the administration of Agriflu.
Flublok-associated muscle pain AE
A Flublok vaccine adverse event that is associated with an administration of Flublok and displays a muscle pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM336020.pdf
a virus vaccine adverse event that is associated with administration of an influenza virus vaccine
a bacterial adverse event that is associated with administration of a Haemophilus vaccine
adenovirus vaccine adverse event
a virus vaccine adverse event that is associated with administration of an adenovirus vaccine
adverse event associated with Adenovirus Type 4 and Type 7 Vaccine, Live, Oral
an adenovirus vaccine adverse event that is associated with administration of an adenovirus vaccine Adenovirus Type 4 and Type 7 Vaccine, Live, Oral
human papillomavirus vaccine adverse event
a virus vaccine adverse event that is associated with administration of a human papillomavirus vaccine
Bacillus anthracis vaccine adverse event
a bacterial adverse event that is associated with administration of a Bacillus anthracis vaccine
Streptococcus pneumoniae vaccine adverse event
Neisseria meningitidis vaccine adverse event
a bacterial vaccine adverse event that is associated with administration of diphtheria vaccine
Diphtheria-Tetanus vaccine adverse event
a bacterial vaccine adverse event that is associated with administration of Diphtheria-Tetanus vaccine
Diphtheria-Tetanus-Pertussis vaccine adverse event
a bacterial vaccine adverse event that is associated with administration of Diphtheria-Tetanus-Pertussis vaccine
Diphtheria-Tetanus-Poliovirus vaccine adverse event
a bacterial vaccine adverse event that is associated with administration of Diphtheria-Tetanus-Poliovirus vaccine
Diphtheria-Tetanus-Pertussis-Poliovirus vaccine adverse event
a bacterial vaccine adverse event that is associated with administration of Diphtheria-Tetanus-Pertussis-Poliovirus vaccine
Diphtheria-Tetanus-Pertussis-Poliovirus-Haemophilus b vaccine adverse event
a bacterial vaccine adverse event that is associated with administration of Diphtheria-Tetanus-Pertussis-Poliovirus-Haemophilus b vaccine
Diphtheria-Tetanus-Pertussis-Poliovirus-Hepatitis B vaccine adverse event
a bacterial vaccine adverse event that is associated with administration of Diphtheria-Tetanus-Pertussis-Poliovirus-Hepatitis B vaccine
a bacterial vaccine adverse event that is associated with administration of Salmonella vaccine
Haemophilus b and Hepatitis B vaccine adverse event
a viral vaccine adverse event that is associated with administration of Haemophilus b and Hepatitis B vaccine
a viral vaccine adverse event that is associated with administration of Hepatitis A virus vaccine
a viral vaccine adverse event that is associated with administration of Hepatitis A&B vaccine
a viral vaccine adverse event that is associated with administration of Hepatitis B virus vaccine
a viral vaccine adverse event that is associated with administration of Herpesvirus vaccine
Japanese encephalitis virus vaccine adverse event
a viral vaccine adverse event that is associated with administration of Japanese encephalitis virus vaccine
a viral vaccine adverse event that is associated with administration of Measles virus vaccine
Measles-Mumps-Rubella-Vericella vaccine adverse event
a viral vaccine adverse event that is associated with administration of Measles-Mumps-Rubella-Vericella vaccine
a viral vaccine adverse event that is associated with administration of Poliovirus vaccine
a viral vaccine adverse event that is associated with administration of smallpox vaccine
a viral vaccine adverse event that is associated with administration of Rabies vaccine
a viral vaccine adverse event that is associated with administration of Rotavirus vaccine
a viral vaccine adverse event that is associated with administration of Rubella vaccine
a viral vaccine adverse event that is associated with administration of Yellow fever vaccine
Afluria-associated injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM263239.pdf
A Afluria vaccine adverse event that is associated with an administration of Afluria and displays an injection-site pain AE
Afluria-associated injection-site redness AE
A Afluria vaccine adverse event that is associated with an administration of Afluria and displays an injection-site redness AE
A Afluria vaccine adverse event that is associated with an administration of Afluria and displays an local swelling AE
A Afluria vaccine adverse event that is associated with an administration of Afluria and displays an headache AE
A Afluria vaccine adverse event that is associated with an administration of Afluria and displays an myalgia AE
A Afluria vaccine adverse event that is associated with an administration of Afluria and displays an malaise AE
A Afluria vaccine adverse event that is associated with an administration of Afluria and displays an fever AE
Afluria-associated injection-site tenderness AE
A Afluria vaccine adverse event that is associated with an administration of Afluria and displays an injection-site tenderness AE
A Afluria vaccine adverse event that is associated with an administration of Afluria and displays an muscle ache AE
Agriflu-associated injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM192127.pdf
A Afluria vaccine adverse event that is associated with an administration of Agriflu and displays an injection-site pain AE
A Afluria vaccine adverse event that is associated with an administration of Agriflu and displays an headache AE
A Afluria vaccine adverse event that is associated with an administration of Agriflu and displays an myalgia AE
A Afluria vaccine adverse event that is associated with an administration of Agriflu and displays an malaise AE
Flulaval-associated injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM112904.pdf
A Flulaval vaccine adverse event that is associated with an administration of Flulaval and displays an injection-site pain AE
Flulaval-associated injection-site redness AE
A Flulaval vaccine adverse event that is associated with an administration of Flulaval and displays an injection-site redness AE
A Flulaval vaccine adverse event that is associated with an administration of Flulaval and displays an local swelling AE
A Flulaval vaccine adverse event that is associated with an administration of Flulaval and displays an fatigue AE
A Flulaval vaccine adverse event that is associated with an administration of Flulaval and displays an headache AE
A Flulaval vaccine adverse event that is associated with an administration of Flulaval and displays an myalgia AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM335392.pdf
A Flulaval vaccine adverse event that is associated with an administration of Fluarix and displays an drowsiness
A Flulaval vaccine adverse event that is associated with an administration of Fluarix and displays an irritability AE
Fluarix-associated decreased appetite AE
A Flulaval vaccine adverse event that is associated with an administration of Fluarix and displays an decreased appetite AE
A Flulaval vaccine adverse event that is associated with an administration of Fluarix and displays an arthralgia AE
Fluarix-associated gastrointestinal disorder AE
A Flulaval vaccine adverse event that is associated with an administration of Fluarix and displays an gastrointestinal disorder AE
Fluarix-associated injection-site redness AE
A Flulaval vaccine adverse event that is associated with an administration of Fluarix and displays an injection-site redness AE
A Flulaval vaccine adverse event that is associated with an administration of Fluarix and displays an local swelling AE
Fluarix-associated injection-site pain AE
A Flulaval vaccine adverse event that is associated with an administration of Fluarix and displays an injection-site pain AE
A Flulaval vaccine adverse event that is associated with an administration of Fluarix and displays an muscle ache AE
A Flulaval vaccine adverse event that is associated with an administration of Fluarix and displays an headache AE
A Flulaval vaccine adverse event that is associated with an administration of Fluarix and displays an fatigue AE
Flublok-associated injection-site pain AE
A Flublok vaccine adverse event that is associated with an administration of Flublok and displays an injection-site pain AE
A Flublok vaccine adverse event that is associated with an administration of Flublok and displays a headache AE
A Flublok vaccine adverse event that is associated with an administration of Flublok and displays a fatigue AE
A Flublok vaccine adverse event that is associated with an administration of Flublok and displays a myalgia AE
Flucelvax-associated injection-site pain AE
A Flucelvax vaccine adverse event that is associated with an administration of Flucelvax and displays an injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM329134.pdf
A Flucelvax vaccine adverse event that is associated with an administration of Flucelvax and displays an myalgia AE
Flucelvax-associated injection-site erythema AE
A Flucelvax vaccine adverse event that is associated with an administration of Flucelvax and displays an injection-site erythema AE
A Flucelvax vaccine adverse event that is associated with an administration of Flucelvax and displays an fatigue AE
A Flucelvax vaccine adverse event that is associated with an administration of Flucelvax and displays an headache AE
A Flucelvax vaccine adverse event that is associated with an administration of Flucelvax and displays an malaise AE
Fluvirin-associated mild hypersensitity AE
A Fluvirin vaccine adverse event that is associated with an administration of Fluvirin and displays an mild hypersensitity AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM123694.pdf
Fluvirin-associated flu-like syndrome AE
A Fluvirin vaccine adverse event that is associated with an administration of Fluvirin and displays an flu-like syndrome AE
Fluzone-associated injection-site tenderness AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM305089.pdf
A Fluzone vaccine adverse event that is associated with an administration of Fluzone and displays an injection-site tenderness AE
Fluzone-associated injection-site redness AE
A Fluzone vaccine adverse event that is associated with an administration of Fluzone and displays an injection-site redness AE
A Fluzone vaccine adverse event that is associated with an administration of Fluzone and displays an irritability AE
A Fluzone vaccine adverse event that is associated with an administration of Fluzone and displays an drowsiness
A Fluzone vaccine adverse event that is associated with an administration of Fluzone and displays an myalgia AE
Fluzone-associated injection-site pain AE
A Fluzone vaccine adverse event that is associated with an administration of Fluzone and displays an injection-site pain AE
A Fluzone vaccine adverse event that is associated with an administration of Fluzone and displays an headache AE
A Fluzone vaccine adverse event that is associated with an administration of Fluzone and displays an malaise AE
Fluzone High-Dose-associated injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM305079.pdf
A Fluzone High-Dose vaccine adverse event that is associated with an administration of Fluzone High-Dose and displays an injection-site pain AE
Fluzone High-Dose-associated headache AE
A Fluzone High-Dose vaccine adverse event that is associated with an administration of Fluzone High-Dose and displays an headache AE
A Fluzone High-Dose vaccine adverse event that is associated with an administration of Fluzone High-Dose and displays an myalgia AE
Fluzone High-Dose-associated erythema AE
A Fluzone High-Dose vaccine adverse event that is associated with an administration of Fluzone High-Dose and displays an erythema AE
A Fluzone High-Dose vaccine adverse event that is associated with an administration of Fluzone High-Dose and displays an malaise AE
Fluzone Intradermal-associated injection-site erythema AE
A Fluzone Intradermal vaccine adverse event that is associated with an administration of Fluzone Intradermal and displays an injection-site erythema AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM305080.pdf
Fluzone Intradermal-associated injection-site induration AE
A Fluzone Intradermal vaccine adverse event that is associated with an administration of Fluzone Intradermal and displays an injection-site induration AE
Fluzone Intradermal-associated local swelling AE
A Fluzone Intradermal vaccine adverse event that is associated with an administration of Fluzone Intradermal and displays an local swelling AE
Fluzone Intradermal-associated injection-site pain AE
A Fluzone Intradermal vaccine adverse event that is associated with an administration of Fluzone Intradermal and displays an injection-site pain AE
Fluzone Intradermal-associated OAE_0000373
A Fluzone Intradermal vaccine adverse event that is associated with an administration of Fluzone Intradermal and displays an OAE_0000373
Fluzone Intradermal-associated headache AE
A Fluzone Intradermal vaccine adverse event that is associated with an administration of Fluzone Intradermal and displays an headache AE
Fluzone Intradermal-associated myalgia AE
A Fluzone Intradermal vaccine adverse event that is associated with an administration of Fluzone Intradermal and displays an myalgia AE
Fluzone Intradermal-associated malaise AE
A Fluzone Intradermal vaccine adverse event that is associated with an administration of Fluzone Intradermal and displays an malaise AE
A FluMist vaccine adverse event that is associated with an administration of FluMist and displays an fever AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM123743.pdf
A FluMist vaccine adverse event that is associated with an administration of FluMist and displays an nasal congestion AE
A FluMist vaccine adverse event that is associated with an administration of FluMist and displays an sore throat AE
FluMist Quadrivalent-associated nasal congestion AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM294307.pdf
A FluMist Quadrivalent vaccine adverse event that is associated with an administration of FluMist Quadrivalent and displays an nasal congestion AE
FluMist Quadrivalent-associated fever AE
A FluMist Quadrivalent vaccine adverse event that is associated with an administration of FluMist Quadrivalent and displays an fever AE
FluMist Quadrivalent-associated sore throat AE
A FluMist Quadrivalent vaccine adverse event that is associated with an administration of FluMist Quadrivalent and displays an sore throat AE
Fluarix Quadrivalent-associated injection-site pain AE
A FluMist Quadrivalent vaccine adverse event that is associated with an administration of Fluarix Quadrivalent and displays an injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM220624.pdf
Fluarix Quadrivalent-associated injection-site redness AE
A FluMist Quadrivalent vaccine adverse event that is associated with an administration of Fluarix Quadrivalent and displays an injection-site redness AE
Fluarix Quadrivalent-associated local swelling AE
A FluMist Quadrivalent vaccine adverse event that is associated with an administration of Fluarix Quadrivalent and displays an local swelling AE
Fluarix Quadrivalent-associated drowsiness
A FluMist Quadrivalent vaccine adverse event that is associated with an administration of Fluarix Quadrivalent and displays an drowsiness
Fluarix Quadrivalent-associated irritability AE
A FluMist Quadrivalent vaccine adverse event that is associated with an administration of Fluarix Quadrivalent and displays an irritability AE
Fluarix Quadrivalent-associated decreased appetite AE
A FluMist Quadrivalent vaccine adverse event that is associated with an administration of Fluarix Quadrivalent and displays an decreased appetite AE
Fluarix Quadrivalent-associated fatigue AE
A FluMist Quadrivalent vaccine adverse event that is associated with an administration of Fluarix Quadrivalent and displays an fatigue AE
Fluarix Quadrivalent-associated muscle ache AE
A FluMist Quadrivalent vaccine adverse event that is associated with an administration of Fluarix Quadrivalent and displays an muscle ache AE
Fluarix Quadrivalent-associated headache AE
A FluMist Quadrivalent vaccine adverse event that is associated with an administration of Fluarix Quadrivalent and displays an headache AE
Fluarix Quadrivalent-associated arthralgia AE
A FluMist Quadrivalent vaccine adverse event that is associated with an administration of Fluarix Quadrivalent and displays an arthralgia AE
Fluarix Quadrivalent-associated gastrointestinal disorder AE
A FluMist Quadrivalent vaccine adverse event that is associated with an administration of Fluarix Quadrivalent and displays an gastrointestinal disorder AE
Influenza Virus Vaccine H5N1-associated injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM112836.pdf
A Influenza Virus Vaccine H5N1 vaccine adverse event that is associated with an administration of Influenza Virus Vaccine H5N1 and displays an injection-site pain AE
Influenza Virus Vaccine H5N1-associated headache AE
A Influenza Virus Vaccine H5N1 vaccine adverse event that is associated with an administration of Influenza Virus Vaccine H5N1 and displays an headache AE
Influenza Virus Vaccine H5N1-associated malaise AE
A Influenza Virus Vaccine H5N1 vaccine adverse event that is associated with an administration of Influenza Virus Vaccine H5N1 and displays an malaise AE
Influenza Virus Vaccine H5N1-associated myalgia AE
A Influenza Virus Vaccine H5N1 vaccine adverse event that is associated with an administration of Influenza Virus Vaccine H5N1 and displays an myalgia AE
Adenovirus Type 4 and Type 7 Vaccine, Live, Oral-associated upper respiratory tract infection AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM247515.pdf
A adverse event associated with Adenovirus Type 4 and Type 7 Vaccine, Live, Oral that is associated with an administration of Adenovirus Type 4 and Type 7 Vaccine, Live, Oral and displays an upper respiratory tract infection AE
Adenovirus Type 4 and Type 7 Vaccine, Live, Oral-associated headache AE
A adverse event associated with Adenovirus Type 4 and Type 7 Vaccine, Live, Oral that is associated with an administration of Adenovirus Type 4 and Type 7 Vaccine, Live, Oral and displays an headache AE
Adenovirus Type 4 and Type 7 Vaccine, Live, Oral-associated nasal congestion AE
A adverse event associated with Adenovirus Type 4 and Type 7 Vaccine, Live, Oral that is associated with an administration of Adenovirus Type 4 and Type 7 Vaccine, Live, Oral and displays an nasal congestion AE
Adenovirus Type 4 and Type 7 Vaccine, Live, Oral-associated pharyngolaryngeal pain AE
A adverse event associated with Adenovirus Type 4 and Type 7 Vaccine, Live, Oral that is associated with an administration of Adenovirus Type 4 and Type 7 Vaccine, Live, Oral and displays an pharyngolaryngeal pain AE
Adenovirus Type 4 and Type 7 Vaccine, Live, Oral-associated cough
A adverse event associated with Adenovirus Type 4 and Type 7 Vaccine, Live, Oral that is associated with an administration of Adenovirus Type 4 and Type 7 Vaccine, Live, Oral and displays an cough
Adenovirus Type 4 and Type 7 Vaccine, Live, Oral-associated arthralgia AE
A adverse event associated with Adenovirus Type 4 and Type 7 Vaccine, Live, Oral that is associated with an administration of Adenovirus Type 4 and Type 7 Vaccine, Live, Oral and displays an arthralgia AE
Adenovirus Type 4 and Type 7 Vaccine, Live, Oral-associated nausea AE
A adverse event associated with Adenovirus Type 4 and Type 7 Vaccine, Live, Oral that is associated with an administration of Adenovirus Type 4 and Type 7 Vaccine, Live, Oral and displays an nausea AE
Adenovirus Type 4 and Type 7 Vaccine, Live, Oral-associated abdominal pain AE
A adverse event associated with Adenovirus Type 4 and Type 7 Vaccine, Live, Oral that is associated with an administration of Adenovirus Type 4 and Type 7 Vaccine, Live, Oral and displays an abdominal pain AE
Adenovirus Type 4 and Type 7 Vaccine, Live, Oral-associated diarrhea AE
A adverse event associated with Adenovirus Type 4 and Type 7 Vaccine, Live, Oral that is associated with an administration of Adenovirus Type 4 and Type 7 Vaccine, Live, Oral and displays an diarrhea AE
Adenovirus Type 4 and Type 7 Vaccine, Live, Oral-associated vomiting AE
A adverse event associated with Adenovirus Type 4 and Type 7 Vaccine, Live, Oral that is associated with an administration of Adenovirus Type 4 and Type 7 Vaccine, Live, Oral and displays an vomiting AE
Biothrax-associated injection-site tenderness AE
A Biothrax vaccine adverse event that is associated with an administration of Biothrax and displays an injection-site tenderness AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/BloodBloodProducts/ApprovedProducts/LicensedProductsBLAs/UCM074923.pdf
Biothrax-associated injection-site pain AE
A Biothrax vaccine adverse event that is associated with an administration of Biothrax and displays an injection-site pain AE
Biothrax-associated injection-site erythema AE
A Biothrax vaccine adverse event that is associated with an administration of Biothrax and displays an injection-site erythema AE
Biothrax-associated injection-site edema AE
A Biothrax vaccine adverse event that is associated with an administration of Biothrax and displays an injection-site edema AE
Biothrax-associated arm motion limitation AE
A Biothrax vaccine adverse event that is associated with an administration of Biothrax and displays an arm motion limitation AE
A Biothrax vaccine adverse event that is associated with an administration of Biothrax and displays an muscle ache AE
A Biothrax vaccine adverse event that is associated with an administration of Biothrax and displays an fatigue AE
A Biothrax vaccine adverse event that is associated with an administration of Biothrax and displays an headache AE
Diphtheria & Tetanus Toxoids Absorbed (for pediatric use)-associated injection-site redness AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM101500.pdf
A adverse event associated with Diphtheria & Tetanus Toxoids Absorbed that is associated with an administration of Diphtheria & Tetanus Toxoids Absorbed and displays an injection-site redness AE
Diphtheria & Tetanus Toxoids Absorbed (for pediatric use)-associated injection-site warmth AE
A adverse event associated with Diphtheria & Tetanus Toxoids Absorbed that is associated with an administration of Diphtheria & Tetanus Toxoids Absorbed and displays an injection-site warmth AE
Diphtheria & Tetanus Toxoids Absorbed (for pediatric use)-associated injection-site edema AE
A adverse event associated with Diphtheria & Tetanus Toxoids Absorbed that is associated with an administration of Diphtheria & Tetanus Toxoids Absorbed and displays an injection-site edema AE
Diphtheria & Tetanus Toxoids Absorbed (for pediatric use)-associated injection-site induration AE
A adverse event associated with Diphtheria & Tetanus Toxoids Absorbed that is associated with an administration of Diphtheria & Tetanus Toxoids Absorbed and displays an injection-site induration AE
Diphtheria & Tetanus Toxoids Absorbed (for pediatric use)-associated local swelling AE
A adverse event associated with Diphtheria & Tetanus Toxoids Absorbed that is associated with an administration of Diphtheria & Tetanus Toxoids Absorbed and displays an local swelling AE
Diphtheria & Tetanus Toxoids Absorbed (for pediatric use)-associated urticaria AE
A adverse event associated with Diphtheria & Tetanus Toxoids Absorbed that is associated with an administration of Diphtheria & Tetanus Toxoids Absorbed and displays an urticaria AE
Diphtheria & Tetanus Toxoids Absorbed (for pediatric use)-associated injection-site rash AE
A adverse event associated with Diphtheria & Tetanus Toxoids Absorbed that is associated with an administration of Diphtheria & Tetanus Toxoids Absorbed and displays an injection-site rash AE
Diphtheria & Tetanus Toxoids Absorbed (for pediatric use)-associated malaise AE
A adverse event associated with Diphtheria & Tetanus Toxoids Absorbed that is associated with an administration of Diphtheria & Tetanus Toxoids Absorbed and displays an malaise AE
Diphtheria & Tetanus Toxoids Absorbed (for pediatric use)-associated fever AE
A adverse event associated with Diphtheria & Tetanus Toxoids Absorbed that is associated with an administration of Diphtheria & Tetanus Toxoids Absorbed and displays an fever AE
Diphtheria & Tetanus Toxoids Absorbed (for pediatric use)-associated pain AE
A adverse event associated with Diphtheria & Tetanus Toxoids Absorbed that is associated with an administration of Diphtheria & Tetanus Toxoids Absorbed and displays an pain AE
Diphtheria & Tetanus Toxoids Absorbed (for pediatric use)-associated hypotension AE
A adverse event associated with Diphtheria & Tetanus Toxoids Absorbed that is associated with an administration of Diphtheria & Tetanus Toxoids Absorbed and displays an hypotension AE
Diphtheria & Tetanus Toxoids Absorbed (for pediatric use)-associated nausea AE
A adverse event associated with Diphtheria & Tetanus Toxoids Absorbed that is associated with an administration of Diphtheria & Tetanus Toxoids Absorbed and displays an nausea AE
Diphtheria & Tetanus Toxoids Absorbed (for pediatric use)-associated arthralgia AE
A adverse event associated with Diphtheria & Tetanus Toxoids Absorbed that is associated with an administration of Diphtheria & Tetanus Toxoids Absorbed and displays an arthralgia AE
Tripedia-associated injection-site redness AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM101580.pdf
A Tripedia vaccine adverse event that is associated with an administration of Tripedia and displays an injection-site redness AE
A Tripedia vaccine adverse event that is associated with an administration of Tripedia and displays an local swelling AE
Tripedia-associated injection-site pain AE
A Tripedia vaccine adverse event that is associated with an administration of Tripedia and displays an injection-site pain AE
A Tripedia vaccine adverse event that is associated with an administration of Tripedia and displays an fever AE
A Tripedia vaccine adverse event that is associated with an administration of Tripedia and displays an anorexia AE
A Tripedia vaccine adverse event that is associated with an administration of Tripedia and displays an vomiting AE
A Tripedia vaccine adverse event that is associated with an administration of Tripedia and displays an drowsiness
A Tripedia vaccine adverse event that is associated with an administration of Tripedia and displays an irritability AE
Infanrix-associated injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM124514.pdf
A Infanrix vaccine adverse event that is associated with an administration of Infanrix and displays an injection-site pain AE
Infanrix-associated injection-site redness AE
A Infanrix vaccine adverse event that is associated with an administration of Infanrix and displays an injection-site redness AE
A Infanrix vaccine adverse event that is associated with an administration of Infanrix and displays an local swelling AE
A Infanrix vaccine adverse event that is associated with an administration of Infanrix and displays an fever AE
A Infanrix vaccine adverse event that is associated with an administration of Infanrix and displays an drowsiness
A Infanrix vaccine adverse event that is associated with an administration of Infanrix and displays an irritability AE
Infanrix-associated decreased appetite AE
A Infanrix vaccine adverse event that is associated with an administration of Infanrix and displays an decreased appetite AE
Daptacel-associated injection-site tenderness AE
A Daptacel vaccine adverse event that is associated with an administration of Daptacel and displays an injection-site tenderness AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM103037.pdf
Daptacel-associated injection-site redness AE
A Daptacel vaccine adverse event that is associated with an administration of Daptacel and displays an injection-site redness AE
Daptacel-associated injection-site edema AE
A Daptacel vaccine adverse event that is associated with an administration of Daptacel and displays an injection-site edema AE
A Daptacel vaccine adverse event that is associated with an administration of Daptacel and displays an irritability AE
Daptacel-associated inconsolable crying AE
A Daptacel vaccine adverse event that is associated with an administration of Daptacel and displays an inconsolable crying AE
A Daptacel vaccine adverse event that is associated with an administration of Daptacel and displays an lethargy AE
A Daptacel vaccine adverse event that is associated with an administration of Daptacel and displays an fever AE
Pediarix-associated injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM241874.pdf
A Pediarix vaccine adverse event that is associated with an administration of Pediarix and displays an injection-site pain AE
Pediarix-associated injection-site redness AE
A Pediarix vaccine adverse event that is associated with an administration of Pediarix and displays an injection-site redness AE
A Pediarix vaccine adverse event that is associated with an administration of Pediarix and displays an local swelling AE
A Pediarix vaccine adverse event that is associated with an administration of Pediarix and displays an fever AE
A Pediarix vaccine adverse event that is associated with an administration of Pediarix and displays an drowsiness
A Pediarix vaccine adverse event that is associated with an administration of Pediarix and displays an irritability AE
Pediarix-associated decreased appetite AE
A Pediarix vaccine adverse event that is associated with an administration of Pediarix and displays an decreased appetite AE
Kinrix-associated injection-site pain AE
A Kinrix vaccine adverse event that is associated with an administration of Kinrix and displays an injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM241453.pdf
Kinrix-associated injection-site redness AE
A Kinrix vaccine adverse event that is associated with an administration of Kinrix and displays an injection-site redness AE
Kinrix-associated injection-site edema AE
A Kinrix vaccine adverse event that is associated with an administration of Kinrix and displays an injection-site edema AE
A Kinrix vaccine adverse event that is associated with an administration of Kinrix and displays an local swelling AE
A Kinrix vaccine adverse event that is associated with an administration of Kinrix and displays an drowsiness
A Kinrix vaccine adverse event that is associated with an administration of Kinrix and displays an fever AE
A Kinrix vaccine adverse event that is associated with an administration of Kinrix and displays an decreased appetite AE
A Pentacel vaccine adverse event that is associated with an administration of Pentacel and displays an irritability AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM109810.pdf
Pentacel-associated inconsolable crying AE
A Pentacel vaccine adverse event that is associated with an administration of Pentacel and displays an inconsolable crying AE
A Pentacel vaccine adverse event that is associated with an administration of Pentacel and displays an fever AE
Pentacel-associated injection-site tenderness AE
A Pentacel vaccine adverse event that is associated with an administration of Pentacel and displays an injection-site tenderness AE
Pentacel-associated injection-site edema AE
A Pentacel vaccine adverse event that is associated with an administration of Pentacel and displays an injection-site edema AE
ActHIB-associated injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM109841.pdf
A ActHIB vaccine adverse event that is associated with an administration of ActHIB and displays an injection-site pain AE
ActHIB-associated injection-site redness AE
A ActHIB vaccine adverse event that is associated with an administration of ActHIB and displays an injection-site redness AE
A ActHIB vaccine adverse event that is associated with an administration of ActHIB and displays an local swelling AE
A ActHIB vaccine adverse event that is associated with an administration of ActHIB and displays an fever AE
A ActHIB vaccine adverse event that is associated with an administration of ActHIB and displays an irritability AE
A ActHIB vaccine adverse event that is associated with an administration of ActHIB and displays an lethargy AE
Hiberix-associated injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM179530.pdf
A Hiberix vaccine adverse event that is associated with an administration of Hiberix and displays an injection-site pain AE
Hiberix-associated injection-site redness AE
A Hiberix vaccine adverse event that is associated with an administration of Hiberix and displays an injection-site redness AE
A Hiberix vaccine adverse event that is associated with an administration of Hiberix and displays an fever AE
A Hiberix vaccine adverse event that is associated with an administration of Hiberix and displays an fussiness AE
Hiberix-associated decreased appetite AE
A Hiberix vaccine adverse event that is associated with an administration of Hiberix and displays an decreased appetite AE
A Hiberix vaccine adverse event that is associated with an administration of Hiberix and displays an restlessness AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM253652.pdf
A PedvaxHIB vaccine adverse event that is associated with an administration of PedvaxHIB and displays an irritability AE
A PedvaxHIB vaccine adverse event that is associated with an administration of PedvaxHIB and displays an sleepiness AE
PedvaxHIB-associated injection-site pain AE
A PedvaxHIB vaccine adverse event that is associated with an administration of PedvaxHIB and displays an injection-site pain AE
PedvaxHIB-associated injection-site erythema AE
A PedvaxHIB vaccine adverse event that is associated with an administration of PedvaxHIB and displays an injection-site erythema AE
A PedvaxHIB vaccine adverse event that is associated with an administration of PedvaxHIB and displays an local swelling AE
PedvaxHIB-associated injection-site induration AE
A PedvaxHIB vaccine adverse event that is associated with an administration of PedvaxHIB and displays an injection-site induration AE
PedvaxHIB-associated unusual high-patched crying AE
A PedvaxHIB vaccine adverse event that is associated with an administration of PedvaxHIB and displays an unusual high-patched crying AE
PedvaxHIB-associated prolonged crying AE
A PedvaxHIB vaccine adverse event that is associated with an administration of PedvaxHIB and displays an prolonged crying AE
A PedvaxHIB vaccine adverse event that is associated with an administration of PedvaxHIB and displays an diarrhea AE
A PedvaxHIB vaccine adverse event that is associated with an administration of PedvaxHIB and displays an vomiting AE
A PedvaxHIB vaccine adverse event that is associated with an administration of PedvaxHIB and displays an crying abnormal AE
A PedvaxHIB vaccine adverse event that is associated with an administration of PedvaxHIB and displays an pain AE
A PedvaxHIB vaccine adverse event that is associated with an administration of PedvaxHIB and displays an otitis media AE
A PedvaxHIB vaccine adverse event that is associated with an administration of PedvaxHIB and displays an rash AE
PedvaxHIB-associated upper respiratory tract infection AE
A PedvaxHIB vaccine adverse event that is associated with an administration of PedvaxHIB and displays an upper respiratory tract infection AE
Comvax-associated injection-site pain AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM109869.pdf
Comvax-associated injection-site tenderness AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an injection-site tenderness AE
Comvax-associated injection-site soreness AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an injection-site soreness AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an local swelling AE
Comvax-associated injection-site induration AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an injection-site induration AE
Comvax-associated injection-site erythema AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an injection-site erythema AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an fever AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an anorexia AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an diarrhea AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an vomiting AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an irritability AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an somnolence AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an crying abnormal AE
Comvax-associated upper respiratory tract infection AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an upper respiratory tract infection AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an rhinorrhea AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an cough
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an rhinitis AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an rash AE
A Comvax vaccine adverse event that is associated with an administration of Comvax and displays an otitis media AE
Havrix-associated injection-site muscular soreness AE
A Havrix vaccine adverse event that is associated with an administration of Havrix and displays an injection-site muscular soreness AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM224555.pdf
A Havrix vaccine adverse event that is associated with an administration of Havrix and displays an headache AE
Havrix-associated injection-site pain AE
A Havrix vaccine adverse event that is associated with an administration of Havrix and displays an injection-site pain AE
Havrix-associated injection-site redness AE
A Havrix vaccine adverse event that is associated with an administration of Havrix and displays an injection-site redness AE
A Havrix vaccine adverse event that is associated with an administration of Havrix and displays an irritability AE
A Havrix vaccine adverse event that is associated with an administration of Havrix and displays an drowsiness
A Havrix vaccine adverse event that is associated with an administration of Havrix and displays an decreased appetite AE
Vaqta-associated injection-site erythema AE
A Vaqta vaccine adverse event that is associated with an administration of Vaqta and displays an injection-site erythema AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM110049.pdf
A Vaqta vaccine adverse event that is associated with an administration of Vaqta and displays an fever AE
A Vaqta vaccine adverse event that is associated with an administration of Vaqta and displays an injection-site pain AE
Vaqta-associated injection-site tenderness AE
A Vaqta vaccine adverse event that is associated with an administration of Vaqta and displays an injection-site tenderness AE
Vaqta-associated injection-site muscular soreness AE
A Vaqta vaccine adverse event that is associated with an administration of Vaqta and displays an injection-site muscular soreness AE
Vaqta-associated injection-site warmth AE
A Vaqta vaccine adverse event that is associated with an administration of Vaqta and displays an injection-site warmth AE
A Vaqta vaccine adverse event that is associated with an administration of Vaqta and displays an headache AE
Twinrix-associated injection-site muscular soreness AE
A Twinrix vaccine adverse event that is associated with an administration of Twinrix and displays an injection-site muscular soreness AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM110079.pdf
Twinrix-associated injection-site redness AE
A Twinrix vaccine adverse event that is associated with an administration of Twinrix and displays an injection-site redness AE
A Twinrix vaccine adverse event that is associated with an administration of Twinrix and displays an headache AE
A Twinrix vaccine adverse event that is associated with an administration of Twinrix and displays an fatigue AE
Engerix-B-associated injection-site muscular soreness AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM224503.pdf
A Engerix-B vaccine adverse event that is associated with an administration of Engerix-B and displays an injection-site muscular soreness AE
A Engerix-B vaccine adverse event that is associated with an administration of Engerix-B and displays an fatigue AE
Recombivax HB-associated irritability AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an irritability AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM110114.pdf
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an fever AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an diarrhea AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an fatigue AE
Recombivax HB-associated decreased appetite AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an decreased appetite AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an rhinitis AE
Recombivax HB-associated injection-site muscular soreness AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an injection-site muscular soreness AE
Recombivax HB-associated injection-site pain AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an injection-site pain AE
Recombivax HB-associated injection-site tenderness AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an injection-site tenderness AE
Recombivax HB-associated injection-site pruritus AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an injection-site pruritus AE
Recombivax HB-associated injection-site erythema AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an injection-site erythema AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an ecchymosis AE
Recombivax HB-associated local swelling AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an local swelling AE
Recombivax HB-associated injection-site warmth AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an injection-site warmth AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an skin nodule AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an headache AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an malaise AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an nausea AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an pharyngitis AE
Recombivax HB-associated upper respiratory tract infection AE
A Recombivax HB vaccine adverse event that is associated with an administration of Recombivax HB and displays an upper respiratory tract infection AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM111263.pdf
A Gardasil vaccine adverse event that is associated with an administration of Gardasil and displays an headache AE
A Gardasil vaccine adverse event that is associated with an administration of Gardasil and displays an fever AE
A Gardasil vaccine adverse event that is associated with an administration of Gardasil and displays an nausea AE
A Gardasil vaccine adverse event that is associated with an administration of Gardasil and displays an dizziness AE
Gardasil-associated injection-site pain AE
A Gardasil vaccine adverse event that is associated with an administration of Gardasil and displays an injection-site pain AE
A Gardasil vaccine adverse event that is associated with an administration of Gardasil and displays an local swelling AE
Gardasil-associated injection-site erythema AE
A Gardasil vaccine adverse event that is associated with an administration of Gardasil and displays an injection-site erythema AE
Gardasil-associated injection-site pruritus AE
A Gardasil vaccine adverse event that is associated with an administration of Gardasil and displays an injection-site pruritus AE
Gardasil-associated hematoma, bruise, ecchymoses AE
A Gardasil vaccine adverse event that is associated with an administration of Gardasil and displays an hematoma, bruise, ecchymoses AE
Cervarix-associated injection-site pain AE
A Cervarix vaccine adverse event that is associated with an administration of Cervarix and displays an injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM186981.pdf
Cervarix-associated injection-site redness AE
A Cervarix vaccine adverse event that is associated with an administration of Cervarix and displays an injection-site redness AE
A Cervarix vaccine adverse event that is associated with an administration of Cervarix and displays an local swelling AE
A Cervarix vaccine adverse event that is associated with an administration of Cervarix and displays an fatigue AE
A Cervarix vaccine adverse event that is associated with an administration of Cervarix and displays an headache AE
A Cervarix vaccine adverse event that is associated with an administration of Cervarix and displays an myalgia AE
Cervarix-associated gastrointestinal disorder AE
A Cervarix vaccine adverse event that is associated with an administration of Cervarix and displays an gastrointestinal disorder AE
A Cervarix vaccine adverse event that is associated with an administration of Cervarix and displays an arthralgia AE
Ixiaro-associated injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142570.pdf
A Ixiaro vaccine adverse event that is associated with an administration of Ixiaro and displays an injection-site pain AE
Ixiaro-associated injection-site tenderness AE
A Ixiaro vaccine adverse event that is associated with an administration of Ixiaro and displays an injection-site tenderness AE
A Ixiaro vaccine adverse event that is associated with an administration of Ixiaro and displays an headache AE
A Ixiaro vaccine adverse event that is associated with an administration of Ixiaro and displays an myalgia AE
JE-Vax-associated injection-site tenderness AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM123761.pdf
A JE-Vax vaccine adverse event that is associated with an administration of JE-Vax and displays an injection-site tenderness AE
JE-Vax-associated injection-site redness AE
A JE-Vax vaccine adverse event that is associated with an administration of JE-Vax and displays an injection-site redness AE
A JE-Vax vaccine adverse event that is associated with an administration of JE-Vax and displays an local swelling AE
A JE-Vax vaccine adverse event that is associated with an administration of JE-Vax and displays an fever AE
A JE-Vax vaccine adverse event that is associated with an administration of JE-Vax and displays an headache AE
A JE-Vax vaccine adverse event that is associated with an administration of JE-Vax and displays an malaise AE
A JE-Vax vaccine adverse event that is associated with an administration of JE-Vax and displays an rash AE
A JE-Vax vaccine adverse event that is associated with an administration of JE-Vax and displays an chills AE
A JE-Vax vaccine adverse event that is associated with an administration of JE-Vax and displays an dizziness AE
A JE-Vax vaccine adverse event that is associated with an administration of JE-Vax and displays an myalgia AE
A JE-Vax vaccine adverse event that is associated with an administration of JE-Vax and displays an nausea AE
A JE-Vax vaccine adverse event that is associated with an administration of JE-Vax and displays an vomiting AE
A JE-Vax vaccine adverse event that is associated with an administration of JE-Vax and displays an abdominal pain AE
ProQuad-associated injection-site pain AE
A ProQuad vaccine adverse event that is associated with an administration of ProQuad and displays an injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM123793.pdf
ProQuad-associated injection-site tenderness AE
A ProQuad vaccine adverse event that is associated with an administration of ProQuad and displays an injection-site tenderness AE
ProQuad-associated injection-site muscular soreness AE
A ProQuad vaccine adverse event that is associated with an administration of ProQuad and displays an injection-site muscular soreness AE
ProQuad-associated injection-site erythema AE
A ProQuad vaccine adverse event that is associated with an administration of ProQuad and displays an injection-site erythema AE
A ProQuad vaccine adverse event that is associated with an administration of ProQuad and displays an local swelling AE
A ProQuad vaccine adverse event that is associated with an administration of ProQuad and displays an fever AE
A ProQuad vaccine adverse event that is associated with an administration of ProQuad and displays an irritability AE
A ProQuad vaccine adverse event that is associated with an administration of ProQuad and displays an rash AE
Menveo-associated injection-site erythema AE
A Menveo vaccine adverse event that is associated with an administration of Menveo and displays an injection-site erythema AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM201349.pdf
A Menveo vaccine adverse event that is associated with an administration of Menveo and displays an irritability AE
Menveo-associated injection-site induration AE
A Menveo vaccine adverse event that is associated with an administration of Menveo and displays an injection-site induration AE
A Menveo vaccine adverse event that is associated with an administration of Menveo and displays an sleepiness AE
Menveo-associated injection-site pain AE
A Menveo vaccine adverse event that is associated with an administration of Menveo and displays an injection-site pain AE
A Menveo vaccine adverse event that is associated with an administration of Menveo and displays an headache AE
A Menveo vaccine adverse event that is associated with an administration of Menveo and displays an myalgia AE
A Menveo vaccine adverse event that is associated with an administration of Menveo and displays an malaise AE
A Menveo vaccine adverse event that is associated with an administration of Menveo and displays an nausea AE
MenHibrix-associated injection-site pain AE
A MenHibrix vaccine adverse event that is associated with an administration of MenHibrix and displays an injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM308577.pdf
MenHibrix-associated injection-site redness AE
A MenHibrix vaccine adverse event that is associated with an administration of MenHibrix and displays an injection-site redness AE
A MenHibrix vaccine adverse event that is associated with an administration of MenHibrix and displays an local swelling AE
A MenHibrix vaccine adverse event that is associated with an administration of MenHibrix and displays an irritability AE
A MenHibrix vaccine adverse event that is associated with an administration of MenHibrix and displays an drowsiness
MenHibrix-associated decreased appetite AE
A MenHibrix vaccine adverse event that is associated with an administration of MenHibrix and displays an decreased appetite AE
A MenHibrix vaccine adverse event that is associated with an administration of MenHibrix and displays an fever AE
Menactra-associated injection-site tenderness AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an injection-site tenderness AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM131170.pdf
Menactra-associated injection-site erythema AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an injection-site erythema AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an local swelling AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an irritability AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an crying abnormal AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an drowsiness
Menactra-associated decreased appetite AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an decreased appetite AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an vomiting AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an fever AE
Menactra-associated injection-site pain AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an injection-site pain AE
Menactra-associated injection-site redness AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an injection-site redness AE
Menactra-associated injection-site induration AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an injection-site induration AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an anorexia AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an diarrhea AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an headache AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an fatigue AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an malaise AE
A Menactra vaccine adverse event that is associated with an administration of Menactra and displays an arthralgia AE
Menomune-A/C/Y/W-135-associated injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM308370.pdf
A Menomune-A/C/Y/W-135 vaccine adverse event that is associated with an administration of Menomune-A/C/Y/W-135 and displays an injection-site pain AE
Menomune-A/C/Y/W-135-associated drowsiness
A Menomune-A/C/Y/W-135 vaccine adverse event that is associated with an administration of Menomune-A/C/Y/W-135 and displays an drowsiness
Menomune-A/C/Y/W-135-associated irritability AE
A Menomune-A/C/Y/W-135 vaccine adverse event that is associated with an administration of Menomune-A/C/Y/W-135 and displays an irritability AE
Menomune-A/C/Y/W-135-associated diarrhea AE
A Menomune-A/C/Y/W-135 vaccine adverse event that is associated with an administration of Menomune-A/C/Y/W-135 and displays an diarrhea AE
Menomune-A/C/Y/W-135-associated injection-site redness AE
A Menomune-A/C/Y/W-135 vaccine adverse event that is associated with an administration of Menomune-A/C/Y/W-135 and displays an injection-site redness AE
Menomune-A/C/Y/W-135-associated injection-site induration AE
A Menomune-A/C/Y/W-135 vaccine adverse event that is associated with an administration of Menomune-A/C/Y/W-135 and displays an injection-site induration AE
Menomune-A/C/Y/W-135-associated headache AE
A Menomune-A/C/Y/W-135 vaccine adverse event that is associated with an administration of Menomune-A/C/Y/W-135 and displays an headache AE
Menomune-A/C/Y/W-135-associated fatigue AE
A Menomune-A/C/Y/W-135 vaccine adverse event that is associated with an administration of Menomune-A/C/Y/W-135 and displays an fatigue AE
Menomune-A/C/Y/W-135-associated malaise AE
A Menomune-A/C/Y/W-135 vaccine adverse event that is associated with an administration of Menomune-A/C/Y/W-135 and displays an malaise AE
Menomune-A/C/Y/W-135-associated arthralgia AE
A Menomune-A/C/Y/W-135 vaccine adverse event that is associated with an administration of Menomune-A/C/Y/W-135 and displays an arthralgia AE
Pneumovax 23-associated injection-site pain AE
A Pneumovax 23 vaccine adverse event that is associated with an administration of Pneumovax 23 and displays an injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM257088.pdf
Pneumovax 23-associated injection-site muscular soreness AE
A Pneumovax 23 vaccine adverse event that is associated with an administration of Pneumovax 23 and displays an injection-site muscular soreness AE
Pneumovax 23-associated injection-site tenderness AE
A Pneumovax 23 vaccine adverse event that is associated with an administration of Pneumovax 23 and displays an injection-site tenderness AE
Pneumovax 23-associated local swelling AE
A Pneumovax 23 vaccine adverse event that is associated with an administration of Pneumovax 23 and displays an local swelling AE
Pneumovax 23-associated injection-site induration AE
A Pneumovax 23 vaccine adverse event that is associated with an administration of Pneumovax 23 and displays an injection-site induration AE
Pneumovax 23-associated injection-site erythema AE
A Pneumovax 23 vaccine adverse event that is associated with an administration of Pneumovax 23 and displays an injection-site erythema AE
A Pneumovax 23 vaccine adverse event that is associated with an administration of Pneumovax 23 and displays an headache AE
A Pneumovax 23 vaccine adverse event that is associated with an administration of Pneumovax 23 and displays an asthenia AE
A Pneumovax 23 vaccine adverse event that is associated with an administration of Pneumovax 23 and displays an fatigue AE
A Pneumovax 23 vaccine adverse event that is associated with an administration of Pneumovax 23 and displays an myalgia AE
Prevnar-associated injection-site erythema AE
A Prevnar vaccine adverse event that is associated with an administration of Prevnar and displays an injection-site erythema AE
Prevnar-associated injection-site induration AE
A Prevnar vaccine adverse event that is associated with an administration of Prevnar and displays an injection-site induration AE
Prevnar-associated injection-site tenderness AE
A Prevnar vaccine adverse event that is associated with an administration of Prevnar and displays an injection-site tenderness AE
Prevnar 13-associated injection-site tenderness AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM201669.pdf
A Prevnar 13 vaccine adverse event that is associated with an administration of Prevnar 13 and displays an injection-site tenderness AE
Prevnar 13-associated injection-site redness AE
A Prevnar 13 vaccine adverse event that is associated with an administration of Prevnar 13 and displays an injection-site redness AE
A Prevnar 13 vaccine adverse event that is associated with an administration of Prevnar 13 and displays an local swelling AE
Prevnar 13-associated decreased appetite AE
A Prevnar 13 vaccine adverse event that is associated with an administration of Prevnar 13 and displays an decreased appetite AE
Prevnar 13-associated decreased sleep AE
A Prevnar 13 vaccine adverse event that is associated with an administration of Prevnar 13 and displays an decreased sleep AE
Prevnar 13-associated increased sleep AE
A Prevnar 13 vaccine adverse event that is associated with an administration of Prevnar 13 and displays an increased sleep AE
A Prevnar 13 vaccine adverse event that is associated with an administration of Prevnar 13 and displays an fever AE
A Prevnar 13 vaccine adverse event that is associated with an administration of Prevnar 13 and displays an irritability AE
Prevnar 13-associated injection-site pain AE
A Prevnar 13 vaccine adverse event that is associated with an administration of Prevnar 13 and displays an injection-site pain AE
A Prevnar 13 vaccine adverse event that is associated with an administration of Prevnar 13 and displays an fatigue AE
A Prevnar 13 vaccine adverse event that is associated with an administration of Prevnar 13 and displays an headache AE
A Prevnar 13 vaccine adverse event that is associated with an administration of Prevnar 13 and displays an muscle pain AE
A Prevnar 13 vaccine adverse event that is associated with an administration of Prevnar 13 and displays an joint pain AE
Prevnar 13-associated arm motion limitation AE
A Prevnar 13 vaccine adverse event that is associated with an administration of Prevnar 13 and displays an arm motion limitation AE
A Prevnar 13 vaccine adverse event that is associated with an administration of Prevnar 13 and displays an chills AE
A Prevnar 13 vaccine adverse event that is associated with an administration of Prevnar 13 and displays an rash AE
IPOL-associated injection-site erythema AE
A IPOL vaccine adverse event that is associated with an administration of IPOL and displays an injection-site erythema AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM133479.pdf
IPOL-associated injection-site induration AE
A IPOL vaccine adverse event that is associated with an administration of IPOL and displays an injection-site induration AE
A IPOL vaccine adverse event that is associated with an administration of IPOL and displays an injection-site pain AE
A IPOL vaccine adverse event that is associated with an administration of IPOL and displays an fever AE
A IPOL vaccine adverse event that is associated with an administration of IPOL and displays an irritability AE
A IPOL vaccine adverse event that is associated with an administration of IPOL and displays an sleepiness AE
A IPOL vaccine adverse event that is associated with an administration of IPOL and displays an fussiness AE
A IPOL vaccine adverse event that is associated with an administration of IPOL and displays an crying abnormal AE
Imovax Rabies-associated injection-site pain AE
A Imovax Rabies vaccine adverse event that is associated with an administration of Imovax Rabies and displays an injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM133484.pdf
Imovax Rabies-associated injection-site erythema AE
A Imovax Rabies vaccine adverse event that is associated with an administration of Imovax Rabies and displays an injection-site erythema AE
Imovax Rabies-associated local swelling AE
A Imovax Rabies vaccine adverse event that is associated with an administration of Imovax Rabies and displays an local swelling AE
A Imovax Rabies vaccine adverse event that is associated with an administration of Imovax Rabies and displays an itching
A Imovax Rabies vaccine adverse event that is associated with an administration of Imovax Rabies and displays an headache AE
A Imovax Rabies vaccine adverse event that is associated with an administration of Imovax Rabies and displays an nausea AE
Imovax Rabies-associated abdominal pain AE
A Imovax Rabies vaccine adverse event that is associated with an administration of Imovax Rabies and displays an abdominal pain AE
A Imovax Rabies vaccine adverse event that is associated with an administration of Imovax Rabies and displays an muscle ache AE
A Imovax Rabies vaccine adverse event that is associated with an administration of Imovax Rabies and displays an dizziness AE
RabAvert-associated injection-site erythema AE
A RabAvert vaccine adverse event that is associated with an administration of RabAvert and displays an injection-site erythema AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM312931.pdf
RabAvert-associated injection-site induration AE
A RabAvert vaccine adverse event that is associated with an administration of RabAvert and displays an injection-site induration AE
RabAvert-associated injection-site pain AE
A RabAvert vaccine adverse event that is associated with an administration of RabAvert and displays an injection-site pain AE
A RabAvert vaccine adverse event that is associated with an administration of RabAvert and displays an asthenia AE
A RabAvert vaccine adverse event that is associated with an administration of RabAvert and displays an fatigue AE
A RabAvert vaccine adverse event that is associated with an administration of RabAvert and displays an fever AE
A RabAvert vaccine adverse event that is associated with an administration of RabAvert and displays an headache AE
A RabAvert vaccine adverse event that is associated with an administration of RabAvert and displays an myalgia AE
A RabAvert vaccine adverse event that is associated with an administration of RabAvert and displays an malaise AE
A RabAvert vaccine adverse event that is associated with an administration of RabAvert and displays an arthralgia AE
A RabAvert vaccine adverse event that is associated with an administration of RabAvert and displays an dizziness AE
A RabAvert vaccine adverse event that is associated with an administration of RabAvert and displays an lymphadenopathy AE
A RabAvert vaccine adverse event that is associated with an administration of RabAvert and displays an nausea AE
A RabAvert vaccine adverse event that is associated with an administration of RabAvert and displays an rash AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM133539.pdf
A Rotarix vaccine adverse event that is associated with an administration of Rotarix and displays an irritability AE
A Rotarix vaccine adverse event that is associated with an administration of Rotarix and displays an cough
A Rotarix vaccine adverse event that is associated with an administration of Rotarix and displays an runny nose
A Rotarix vaccine adverse event that is associated with an administration of Rotarix and displays an fever AE
Rotarix-associated decreased appetite AE
A Rotarix vaccine adverse event that is associated with an administration of Rotarix and displays an decreased appetite AE
A Rotarix vaccine adverse event that is associated with an administration of Rotarix and displays an vomiting AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142288.pdf
A RotaTeq vaccine adverse event that is associated with an administration of RotaTeq and displays an diarrhea AE
A RotaTeq vaccine adverse event that is associated with an administration of RotaTeq and displays an vomiting AE
A RotaTeq vaccine adverse event that is associated with an administration of RotaTeq and displays an irritability AE
A RotaTeq vaccine adverse event that is associated with an administration of RotaTeq and displays an otitis media AE
A RotaTeq vaccine adverse event that is associated with an administration of RotaTeq and displays an nasopharyngitis AE
A RotaTeq vaccine adverse event that is associated with an administration of RotaTeq and displays an bronchospasm AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142553.pdf
A Meruvax II vaccine adverse event that is associated with an administration of Meruvax II and displays an fever AE
A Meruvax II vaccine adverse event that is associated with an administration of Meruvax II and displays an syncope AE
A Meruvax II vaccine adverse event that is associated with an administration of Meruvax II and displays an headache AE
A Meruvax II vaccine adverse event that is associated with an administration of Meruvax II and displays an dizziness AE
A Meruvax II vaccine adverse event that is associated with an administration of Meruvax II and displays an malaise AE
A Meruvax II vaccine adverse event that is associated with an administration of Meruvax II and displays an irritability AE
A Meruvax II vaccine adverse event that is associated with an administration of Meruvax II and displays an vasculitis AE
A Meruvax II vaccine adverse event that is associated with an administration of Meruvax II and displays an diarrhea AE
A Meruvax II vaccine adverse event that is associated with an administration of Meruvax II and displays an vomiting AE
A Meruvax II vaccine adverse event that is associated with an administration of Meruvax II and displays an nausea AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142572.pdf
A ACAM2000 vaccine adverse event that is associated with an administration of ACAM2000 and displays an lymphadenitis AE
A ACAM2000 vaccine adverse event that is associated with an administration of ACAM2000 and displays an malaise AE
A ACAM2000 vaccine adverse event that is associated with an administration of ACAM2000 and displays an fatigue AE
A ACAM2000 vaccine adverse event that is associated with an administration of ACAM2000 and displays an fever AE
A ACAM2000 vaccine adverse event that is associated with an administration of ACAM2000 and displays an myalgia AE
A ACAM2000 vaccine adverse event that is associated with an administration of ACAM2000 and displays an headache AE
Tetanus and Diptheria Toxoids Absorbed-associated injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM164127.pdf
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an injection-site pain AE
Tetanus and Diptheria Toxoids Absorbed-associated injection-site tenderness AE
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an injection-site tenderness AE
Tetanus and Diptheria Toxoids Absorbed-associated injection-site erythema AE
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an injection-site erythema AE
Tetanus and Diptheria Toxoids Absorbed-associated injection-site induration AE
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an injection-site induration AE
Tetanus and Diptheria Toxoids Absorbed-associated injection-site pruritus AE
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an injection-site pruritus AE
Tetanus and Diptheria Toxoids Absorbed-associated local swelling AE
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an local swelling AE
Tetanus and Diptheria Toxoids Absorbed-associated oedema, swelling dropsy
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an oedema, swelling dropsy
Tetanus and Diptheria Toxoids Absorbed-associated pyrexia AE
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an pyrexia AE
Tetanus and Diptheria Toxoids Absorbed-associated malaise AE
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an malaise AE
Tetanus and Diptheria Toxoids Absorbed-associated dizziness AE
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an dizziness AE
Tetanus and Diptheria Toxoids Absorbed-associated headache AE
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an headache AE
Tetanus and Diptheria Toxoids Absorbed-associated convulsion AE
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an convulsion AE
Tetanus and Diptheria Toxoids Absorbed-associated myalgia AE
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an myalgia AE
Tetanus and Diptheria Toxoids Absorbed-associated musculoskeletal stiffness AE
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an musculoskeletal stiffness AE
Tetanus and Diptheria Toxoids Absorbed-associated musculoskeletal pain AE
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an musculoskeletal pain AE
Tetanus and Diptheria Toxoids Absorbed-associated arthralgia AE
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an arthralgia AE
Tetanus and Diptheria Toxoids Absorbed-associated rash AE
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an rash AE
Tetanus and Diptheria Toxoids Absorbed-associated nausea AE
A adverse event associated with Tetanus and Diptheria Toxoids Absorbed by MA Biological that is associated with an administration of Tetanus and Diptheria Toxoids Absorbed and displays an nausea AE
Decavac-associated injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM246215.pdf
A Decavac vaccine adverse event that is associated with an administration of Decavac and displays an injection-site pain AE
A Decavac vaccine adverse event that is associated with an administration of Decavac and displays an headache AE
A Decavac vaccine adverse event that is associated with an administration of Decavac and displays an local swelling AE
Decavac-associated injection-site erythema AE
A Decavac vaccine adverse event that is associated with an administration of Decavac and displays an injection-site erythema AE
A Decavac vaccine adverse event that is associated with an administration of Decavac and displays an pain AE
A Decavac vaccine adverse event that is associated with an administration of Decavac and displays an muscular weakness AE
A Decavac vaccine adverse event that is associated with an administration of Decavac and displays an tiredness AE
A Decavac vaccine adverse event that is associated with an administration of Decavac and displays an diarrhea AE
A Decavac vaccine adverse event that is associated with an administration of Decavac and displays an chills AE
A Decavac vaccine adverse event that is associated with an administration of Decavac and displays an nausea AE
A Decavac vaccine adverse event that is associated with an administration of Decavac and displays an joint swelling AE
Tenivac-associated injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/UCM152826.pdf
A Tenivac vaccine adverse event that is associated with an administration of Tenivac and displays an injection-site pain AE
A Tenivac vaccine adverse event that is associated with an administration of Tenivac and displays an headache AE
Tenivac-associated injection-site redness AE
A Tenivac vaccine adverse event that is associated with an administration of Tenivac and displays an injection-site redness AE
A Tenivac vaccine adverse event that is associated with an administration of Tenivac and displays an local swelling AE
A Tenivac vaccine adverse event that is associated with an administration of Tenivac and displays an malaise AE
A Tenivac vaccine adverse event that is associated with an administration of Tenivac and displays an muscular weakness AE
A Tenivac vaccine adverse event that is associated with an administration of Tenivac and displays an joint pain AE
Tetanus Toxoid-associated injection-site redness AE
A Tetanus Toxoid (boost only) vaccine adverse event that is associated with an administration of Tetanus Toxoid and displays an injection-site redness AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM166873.pdf
Tetanus Toxoid-associated injection-site warmth AE
A Tetanus Toxoid (boost only) vaccine adverse event that is associated with an administration of Tetanus Toxoid and displays an injection-site warmth AE
Tetanus Toxoid-associated injection-site edema AE
A Tetanus Toxoid (boost only) vaccine adverse event that is associated with an administration of Tetanus Toxoid and displays an injection-site edema AE
Tetanus Toxoid-associated injection-site induration AE
A Tetanus Toxoid (boost only) vaccine adverse event that is associated with an administration of Tetanus Toxoid and displays an injection-site induration AE
Tetanus Toxoid-associated induration with tenderness AE
A Tetanus Toxoid (boost only) vaccine adverse event that is associated with an administration of Tetanus Toxoid and displays an induration with tenderness AE
A Tetanus Toxoid (boost only) vaccine adverse event that is associated with an administration of Tetanus Toxoid and displays an urticaria AE
A Tetanus Toxoid (boost only) vaccine adverse event that is associated with an administration of Tetanus Toxoid and displays an rash AE
A Tetanus Toxoid (boost only) vaccine adverse event that is associated with an administration of Tetanus Toxoid and displays an malaise AE
A Tetanus Toxoid (boost only) vaccine adverse event that is associated with an administration of Tetanus Toxoid and displays an fever AE
A Tetanus Toxoid (boost only) vaccine adverse event that is associated with an administration of Tetanus Toxoid and displays an pain AE
Tetanus Toxoid-associated hypotension AE
A Tetanus Toxoid (boost only) vaccine adverse event that is associated with an administration of Tetanus Toxoid and displays an hypotension AE
A Tetanus Toxoid (boost only) vaccine adverse event that is associated with an administration of Tetanus Toxoid and displays an nausea AE
A Tetanus Toxoid (boost only) vaccine adverse event that is associated with an administration of Tetanus Toxoid and displays an arthralgia AE
Tetanus Toxoid Absorbed-associated injection-site redness AE
A Tetanus Toxoid Absorbed vaccine adverse event that is associated with an administration of Tetanus Toxoid Absorbed and displays an injection-site redness AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142732.pdf
Tetanus Toxoid Absorbed-associated injection-site warmth AE
A Tetanus Toxoid Absorbed vaccine adverse event that is associated with an administration of Tetanus Toxoid Absorbed and displays an injection-site warmth AE
Tetanus Toxoid Absorbed-associated injection-site edema AE
A Tetanus Toxoid Absorbed vaccine adverse event that is associated with an administration of Tetanus Toxoid Absorbed and displays an injection-site edema AE
Tetanus Toxoid Absorbed-associated injection-site induration AE
A Tetanus Toxoid Absorbed vaccine adverse event that is associated with an administration of Tetanus Toxoid Absorbed and displays an injection-site induration AE
Tetanus Toxoid Absorbed-associated induration with tenderness AE
A Tetanus Toxoid Absorbed vaccine adverse event that is associated with an administration of Tetanus Toxoid Absorbed and displays an induration with tenderness AE
Tetanus Toxoid Absorbed-associated urticaria AE
A Tetanus Toxoid Absorbed vaccine adverse event that is associated with an administration of Tetanus Toxoid Absorbed and displays an urticaria AE
Tetanus Toxoid Absorbed-associated rash AE
A Tetanus Toxoid Absorbed vaccine adverse event that is associated with an administration of Tetanus Toxoid Absorbed and displays an rash AE
Tetanus Toxoid Absorbed-associated malaise AE
A Tetanus Toxoid Absorbed vaccine adverse event that is associated with an administration of Tetanus Toxoid Absorbed and displays an malaise AE
Tetanus Toxoid Absorbed-associated fever AE
A Tetanus Toxoid Absorbed vaccine adverse event that is associated with an administration of Tetanus Toxoid Absorbed and displays an fever AE
Tetanus Toxoid Absorbed-associated pain AE
A Tetanus Toxoid Absorbed vaccine adverse event that is associated with an administration of Tetanus Toxoid Absorbed and displays an pain AE
Tetanus Toxoid Absorbed-associated hypotension AE
A Tetanus Toxoid Absorbed vaccine adverse event that is associated with an administration of Tetanus Toxoid Absorbed and displays an hypotension AE
Tetanus Toxoid Absorbed-associated nausea AE
A Tetanus Toxoid Absorbed vaccine adverse event that is associated with an administration of Tetanus Toxoid Absorbed and displays an nausea AE
Tetanus Toxoid Absorbed-associated arthralgia AE
A Tetanus Toxoid Absorbed vaccine adverse event that is associated with an administration of Tetanus Toxoid Absorbed and displays an arthralgia AE
Adacel-associated injection-site pain AE
A Adacel vaccine adverse event that is associated with an administration of Adacel and displays an injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142764.pdf
A Adacel vaccine adverse event that is associated with an administration of Adacel and displays an local swelling AE
Adacel-associated injection-site erythema AE
A Adacel vaccine adverse event that is associated with an administration of Adacel and displays an injection-site erythema AE
A Adacel vaccine adverse event that is associated with an administration of Adacel and displays an fatigue AE
A Adacel vaccine adverse event that is associated with an administration of Adacel and displays an headache AE
A Adacel vaccine adverse event that is associated with an administration of Adacel and displays an muscular weakness AE
Boostrix-associated injection-site pain AE
A Boostrix vaccine adverse event that is associated with an administration of Boostrix and displays an injection-site pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/UCM152842.pdf
Boostrix-associated injection-site redness AE
A Boostrix vaccine adverse event that is associated with an administration of Boostrix and displays an injection-site redness AE
A Boostrix vaccine adverse event that is associated with an administration of Boostrix and displays an local swelling AE
Boostrix-associated injection-site edema AE
A Boostrix vaccine adverse event that is associated with an administration of Boostrix and displays an injection-site edema AE
A Boostrix vaccine adverse event that is associated with an administration of Boostrix and displays an headache AE
A Boostrix vaccine adverse event that is associated with an administration of Boostrix and displays an fatigue AE
Boostrix-associated gastrointestinal disorder AE
A Boostrix vaccine adverse event that is associated with an administration of Boostrix and displays an gastrointestinal disorder AE
A Vivotif vaccine adverse event that is associated with an administration of Vivotif and displays an abdominal pain AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142807.pdf
A Vivotif vaccine adverse event that is associated with an administration of Vivotif and displays an nausea AE
A Vivotif vaccine adverse event that is associated with an administration of Vivotif and displays an headache AE
A Vivotif vaccine adverse event that is associated with an administration of Vivotif and displays an fever AE
A Vivotif vaccine adverse event that is associated with an administration of Vivotif and displays an diarrhea AE
A Vivotif vaccine adverse event that is associated with an administration of Vivotif and displays an vomiting AE
A Vivotif vaccine adverse event that is associated with an administration of Vivotif and displays an rash AE
Typhim Vi-associated injection-site tenderness AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142811.pdf
A Typhim Vi vaccine adverse event that is associated with an administration of Typhim Vi and displays an injection-site tenderness AE
Typhim Vi-associated injection-site pain AE
A Typhim Vi vaccine adverse event that is associated with an administration of Typhim Vi and displays an injection-site pain AE
Typhim Vi-associated injection-site induration AE
A Typhim Vi vaccine adverse event that is associated with an administration of Typhim Vi and displays an injection-site induration AE
Typhim Vi-associated injection-site erythema AE
A Typhim Vi vaccine adverse event that is associated with an administration of Typhim Vi and displays an injection-site erythema AE
A Typhim Vi vaccine adverse event that is associated with an administration of Typhim Vi and displays an malaise AE
A Typhim Vi vaccine adverse event that is associated with an administration of Typhim Vi and displays an headache AE
A Typhim Vi vaccine adverse event that is associated with an administration of Typhim Vi and displays an myalgia AE
A Typhim Vi vaccine adverse event that is associated with an administration of Typhim Vi and displays an nausea AE
A Typhim Vi vaccine adverse event that is associated with an administration of Typhim Vi and displays an diarrhea AE
A Typhim Vi vaccine adverse event that is associated with an administration of Typhim Vi and displays an irritability AE
A Typhim Vi vaccine adverse event that is associated with an administration of Typhim Vi and displays an fever AE
A Typhim Vi vaccine adverse event that is associated with an administration of Typhim Vi and displays an vomiting AE
A Varivax vaccine adverse event that is associated with an administration of Varivax and displays an fever AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142813.pdf
Varivax-associated injection-site adverse event
A Varivax vaccine adverse event that is associated with an administration of Varivax and displays an injection-site adverse event
A YF-Vax vaccine adverse event that is associated with an administration of YF-Vax and displays an headache AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM142831.pdf
A YF-Vax vaccine adverse event that is associated with an administration of YF-Vax and displays an myalgia AE
A YF-Vax vaccine adverse event that is associated with an administration of YF-Vax and displays an low grade fever AE
YF-Vax-associated injection-site edema AE
A YF-Vax vaccine adverse event that is associated with an administration of YF-Vax and displays an injection-site edema AE
A YF-Vax vaccine adverse event that is associated with an administration of YF-Vax and displays an hypersensitivity AE
YF-Vax-associated injection-site pain AE
A YF-Vax vaccine adverse event that is associated with an administration of YF-Vax and displays an injection-site pain AE
YF-Vax-associated injection-site mass AE
A YF-Vax vaccine adverse event that is associated with an administration of YF-Vax and displays an injection-site mass AE
WEB: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM132831.pdf
A Zostavax vaccine adverse event that is associated with an administration of Zostavax and displays an headache AE
Zostavax-associated injection-site reaction
A Zostavax vaccine adverse event that is associated with an administration of Zostavax and displays an injection-site reaction
An influenza vaccine adverse event that is associated with the administration of Afluria.
An influenza vaccine adverse event that is associated with the administration of FluMist.
A smallpox vaccine adverse event that is associated with the administration of ACAM2000.
time
A quality in which events occur in sequence.
viability
An organismal quality inhering in a bearer or a population by virtue of the bearer's ability or inability to survive and develop normally or the number of surviving individuals in a given population.
An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation.
physical quality
A quality of a single physical entity that exists through action of continuants at the physical level of organisation.
See comments of relational quality of a physical entity.
quality of a single physical entity
A physical object quality which inheres in a single-bearer.
physical object quality
A quality which inheres in a continuant.
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
multiply inhering quality of a physical entity
organismal quality
A quality that inheres in an entire organism or part of an organism.
virulence
A quality inhering in a bearer by virtue of the bearer's pathogenicity.
Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047].
The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity.
a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose].
the organ that is specialized for smell and is part of the respiratory system
the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359]
(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
lateral part of the basal amygdalar nucleus
nucleus amygdalae basalis, pars lateralis
nucleus amygdaloideus basalis, pars lateralis magnocellularis
pars peripherica; systema nervosum periphericum
(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms.
An organ that is capable of transducing sensory stimulus to the nervous system.
Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)
An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018].
Major subdivision of an organism that protrudes from the body[DOS, CARO].
Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736].
this is currently a subtype of organism subdivision - which would exclude feathers
Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]
Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]
The head is the anterior-most division of the body [GO].
Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
Dense regular connective tissue that connects muscle to bone.[VSAO]
Dense regular connective tissue that connects muscle to bone[VSAO].
Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]
in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis
A biological tissue mass, most commonly a mass of nerve cell bodies.
A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures
Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG]
Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO]
Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NIFSTD:nlx_anat_100302].
TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.
A tubular structure that contains, conveys body fluid, such as blood or lymph.
A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].
A tubular structure that transports secreted or excreted substances.
Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here.
Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
Anatomical structure that performs a specific function or group of functions [WP].
CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.
FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction
Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball.
Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal.
A multicellular structure that is a part of an organ.
currently defined in a very broad sense, may be replaced by more specific classes in the future
Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
A stage that is part of the embryo stage.
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
proximo-distal subdivision of respiratory tract
MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole
Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis
The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
stage succeeding embryo, including mature structure
Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
A spatiotemporal region encompassing some part of the life cycle of an organism.
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
consider adding a preceding stage 'morula stage' as part of cleavage
A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
Structure derived from foregut that becomes a lung[GO].
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
First portion of the digestive tract[WP]. The portion of the digestive that develops from the stomodeum
Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
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
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
The pair of anatomical structures comprised of a left lung and right lung.
Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
A fluid that is composed of blood plasma and erythrocytes.
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula
In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted].
The hyoid bone and the clavicle are the only bones located in the throat of mammals.
Anatomical system that consists of the muscles of the body.[VSAO]
The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].
consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77
we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA
A gland in which the principal secretory cells are serous secreting cells.
glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
A portion of organism substance that is produced by exocrine glands.
BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
Anatomical structure that is an individual member of a species and consists of more than one cell.
TODO - split body and mc organism? body continues after death stage
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
Anatomical group that has its parts adjacent to one another.
Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
changed label and definition to reflect CARO2
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]
Epithelium that consists of more than one layer of epithelial cells.[CARO]
Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]
Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]
Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]
Compound organ that contains one or more macroscopic anatomical spaces.
this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
Epithelium that consists of a single layer of epithelial cells.[CARO]
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]
consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable
Subdivision of trunk that lies between the head and the abdomen.
note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest
The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.
Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
Primary germ layer that is the middle of the embryonic germ layers.[AAO]
The middle germ layer of the embryo, between the endoderm and ectoderm.
sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates
Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]
Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.
This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity.
consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence
the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]
Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" http://dx.doi.org/10.1101/gad.1485706
relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
requires review for applicability to invertebrate structures, e.g. synganglion
An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck.
Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]
A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]
The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]
The outer epithelial layer of the skin that is superficial to the dermis.
Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes).
relationship loss: subclass external integument structures (AAO:0000961)[AAO]
Functional system which consists of structures involved in respiration.
The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
An airway through which respiratory air passes in organisms.
This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class
Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]
We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]
organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
the cardiovascular system and the lymphatic system are parts of the circulatory system
Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]
Connective tissue in which fat is stored.[TAO]
In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]
in FMA this is dense irregular connective tissue
relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
A subdivision of the muscular system corresponding to a subdisivision of an organism.
In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here.
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
Part of the nervous system which includes the brain and spinal cord.[AAO]
The brain and spinal cord. Kimmel et al, 1995.[TAO]
The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
A portion of tissue which is a fasiculated group of axons.[TAO]
An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures.
An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
The sensory system for the sense of taste.
The sensory system for the sense of taste[NIFSTD:nlx_anat_090803].
The sensory system used for the sense of taste.[AAO]
in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes
Anterior subdivision of a digestive tract.
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure
The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder.
The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]
In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]
The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
Transudate contained in the synovial cavity of joints, and in the cavity of tendon sheaths and bursae.
Muscle tissue that consists primarily of skeletal muscle fibers.
Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]
TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Consider FBbt:00005073 - somatic muscle.
TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.
This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]
Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]
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].
Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. http://en.wikipedia.org/wiki/ The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column..
In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body
Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]
By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]
GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates
System that provides physical support to the organism.[AAO]
A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc).
Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face.
The area that extends from the median ocellus to the oral foramen[HAO].
The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)
Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]
Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
Skeletal element that is composed of bone tissue.
Skeletal element that is composed of bone tissue.[VSAO]
The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]
An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
A tube extending from the mouth to the anus.
FMA also has a term 'gastrointestinal tract', but this includes the liver.
The alimentary or digestive tract, and associated organs.[TAO]
we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this
we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509
Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage. The FMA includes nose, nasopharynx, oropharynx and larynx[WP]
The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea.
The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]
It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]
Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].
Portion of tissue composed of contractile fibers.[TAO]
Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG]
Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.
The organ of hearing and of equilibrium. [TFD][VHOG]
A horn-like keratin structure covering the dorsal aspect of the terminal phalanges of fingers and toes[WP].
A primate's nail consists of the unguis alone; the subunguis has disappeared
The nails of humans and the claws are moth are highly similar. Both species have a proximal nail fold, cuticle, nail matrix, nail bed, nail plate, and hyponychium. Distinguishing features are the shape of the nail and the presence of an extended hyponychium in the mouse [PMC3579226]
Use this class for both the nails of primates and the homologous claws of mammals such as mouse.
Ganglion which is located in the head.[TAO]
cranial ganglion part of peripheral nervous system
the groups of nerve cell bodies associated with the twelve cranial nerves
Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG]
the any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified]
Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord.
See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6
Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG]
classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN.
In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG]
Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO]
The most anterior region the brain including both the telencephalon and diencephalon.
The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO]
relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO]
Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]
Middle part of the brain composed of the optic tectum and penducular region.[AAO]
The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]
The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO].
developmental relationships need revised
part of brainstem in ABA - we reject this in favor of ISBN10:0471888893 which has an implicit overlaps relationships
From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG]
In mammals the cortex covers almost the whole of the cerebral hemispheres.
In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles.
In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum.
In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb.
Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000].
Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.
Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO]
The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO]
The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure.
dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight.
relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO]
Anterior part of the hindbrain ventral to the cerebellum[NIFSTD:birnlex_965].
Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified].
The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG]
The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]
the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA].
Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]
Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].
Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]
The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
'tegmentum' is used generically for the ventral part of the brainstem (ISBN10:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum
Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]
Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN10:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].
The liquid component of blood, in which erythrocytes are suspended.
A vessel through which blood circulates in the body.
Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
Any of the vessels through which blood circulates in the body.[AAO]
FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
annelids have blood vessels, but this class is not applicable to annelids.
consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons.
Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]
Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]
The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]
The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA].
in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps
relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]
Muscle tissue that contains fibers that are divided by transverse bands into striations.
Voluntary muscle tissue arranged in bundles of fibers.[AAO]
Dorsal part of the hindbrain that coordinates muscle movement, posture, and balance.[AAO]
However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor.[well established][VHOG]
Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA].
Specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period. Kimmel et al, 1995.[TAO]
The absence of a cerebellum in hagfishes and lampreys appears to be the only exception [to the rule that vertebrates possess the same number of brain divisions]. Both hagfishes and lampreys do possess a thin band of cells located medial to the lateral line centers of the medulla (Ronan and Northcutt, 1998), which has been interpreted as a primitive cerebellum (Larsell, 1967), but more recent experimental studies (Kishida et al., 1987; Weigle and Northcutt, 1998) fail to support Larsell's claim[http://icb.oxfordjournals.org/content/42/4/743.full]
almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem
Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]
Respiration organ that develops as an oupocketing of the esophagus.
Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi
An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.
see also: vascular system. Consider merging?
Anatomical structure that is part of an embryo.
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]
Consider adding a layer-of-skin grouping class for all skin layers
The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]
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. Le Guellec et al, 2004.[TAO]
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:70544].
BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument.
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].
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].
Note that this class combines superficial fascia and hypodermis in FMA. Note also BTO has 'subcutis'
Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]
The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]
The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]
The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]
The post-cranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].
previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed.
Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO]
Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO]
Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm].
The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO]
ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved.
MA uses the term skin to refer to what is called here: zone of skin
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
The organ covering the body that consists of the dermis and epidermis.
consider 'integumentary system' for invertebrates
Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]
Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.
Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]
A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts.
Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO]
Sensory system responsible for the perception of spatial orientation and auditory stimuli.
The sensory system used for balance and hearing.[AAO]
Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
Lung which consists of the left upper lobe and left lower lobe.[FMA]
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]
Surface structure that is the outer protective covering of the body.[VSAO]
The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]
in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition.
Anatomical system that consists of the muscular and skeletal systems.
Anatomical system that provides locomotion and physical support to the organism.[AAO]
There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]
Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]
Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]
In many species, the diaphragm separates thoracic and abdominal cavities
The part of the coelemic cavity lumen that is enclosed by the walls of the thorax.
Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO)
Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]
TODO - add superclass to unify with VNC?
An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ.
fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN10:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions).
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707].
Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized].
the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]
Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA].
In mammals it forms the peritoneal, pleural, and pericardial cavities
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO].
check the FMA placement here; ncit placement of body cavity here probably not correct
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]
A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube.
Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]
In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord.
Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]
Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]
The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]
relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]
(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]
Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]
Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.
Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]
When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]
currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk
relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]
relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]
relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]
Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia].
A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]
A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP].
A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]
Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells.
Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]
We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]
consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams).
(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]
Embryonic ectoderm that gives rise to nervous tissue.
epithelium tubi neuralis; neuroectoderma
we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas
Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses
One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]
Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]
Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.
Anatomical system that consists of the blood and blood forming tissues.[AAO]
Anatomical system that is involved in the production of hematopoietic cells.
In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes
Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.
The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]
(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]
Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO]
Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG]
Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO]
Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO]
A bone that is part of a limb [Automatically generated definition].
NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle
the formal definition is very inclusive, and includes sesamoids
Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton.
Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot
The middle free limb segment, between the autopod and stylopod segments. Includes as parts the zeugopodial skeleton. Examples: There are two types of zeugopod: forelimb zeugopod (aka forearm), hindlimb zeugopod (aka crus).
There exists some controversy about which podial segments are present in some fishes, e.g. if the autopod is not newly evolved in tetrapods, there is a question as to which segments are actually present in basal vertebrate taxa.[PHENOSCAPE:curators]
Naming conventions for pod terms under discussion within phenoscape group
The proximal free limb segment. Includes as parts the stylopod skeleton.
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]
see https://github.com/obophenotype/uberon/issues/27
Endochondral_ossification is an essential process during the rudimentary formation of long bones, with the exception of the clavicle[Wikipedia:Endochondral_ossification]. The medial and and lateral ends undergo EO, the mid-portion is formed by a process with features of EO & IO (the process is shared by the mandible)[ISBN:9780397517251]
Long bone is a limb bone that is subcylindrical and has a shaft with periosteum separating the ends of the bones. Long bones are present only in the limbs[VSAO:wd].
Replacement bone that forms within cartilage.
Replacement bone that forms within cartilage.[VSAO]
some structures, e.g. in ZFA are both intramembrane and endochondral
A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles.
FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z
TODO - align this with the CARO2 class 'appendage segment'; note the FMA class does not appear to require repetition
an organ that functions as a secretory or excretory organ
An outgrowth on the lateral trunk of the embryo that develops into a paired fin. The fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
Embryonic surface structure that develops into a paired fin.[ZFA]
In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]
In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]
MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class
Fin that is one of a pair located ventrally on the organism.
A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans).
Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG]
digit (phalangeal portion) plus soft tissue
this class represents the entire organism subdivision encompassing soft tissue as well as the underlying skeletal framework. The class represents the phalangeal part only - historically the term 'digit' has also been used to represent the unit consisting of a series of phalanges together with a metapodial bone. We may in future relabel this class to avoid confusion with this concept, but the class will continue to represent the phalangeal portion
Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons
Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.
The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this.
to avoid confusion, we include neurogenic placode as a subclass. Do not merge.
Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.
Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia.
A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity.
Olfactory placodes are the only ectodermal placodes to produce glia, a cell type typically derived from neural crest // Note that NBK53171 classifies this as non-neurogenic
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG]
Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]
The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate.
consider adding class for organizer. Consider adding separate class for isthmus as a structure
A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis.
In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]
In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis
Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)
The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]
relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]
The portion of neural plate anterior to the mid-hindbrain junction.
The portion of neural plate posterior to the mid-hindbrain junction.
It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]
Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].
EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac
Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]
Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]
Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]
relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]
The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.
The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]
The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]
Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]
Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]
note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)
TODO - add grouping class for the anterior end of the neural tube at all stages
A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]
Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]
Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].
The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.
In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]
Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]
The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere.
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone.
The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]
relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]
should probably be merged with heart rudiment.
The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]
Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].
Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]
Neural crest that is part of the head.[TAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage.
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]
Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs
A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO].
the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense
Endochondral bones that are often elongate and arranged in rows of articulating elements, and form the visible part of the digits.
In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three
An endoderm that is part of a foregut [Automatically generated definition].
A long bone that is part of a limb [Automatically generated definition].
Any joint that is part of a (free) limb.
Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses
One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
A limb joint that is part of an autopod [Automatically generated definition].
joint of limb of distal free limb segment
An anatomical space that surrounded_by a neural tube.
A neural crest that has_potential_to_developmentally_contribute_to a midbrain.
A neural crest that has_potential_to_developmentally_contribute_to a telencephalon.
Cranial neural crest that is part of the telencephalon.[TAO]
A neural crest that has_potential_to_developmentally_contribute_to a hindbrain.
Cranial neural crest that is part of the hindbrain.[TAO]
A neural crest that has_potential_to_developmentally_contribute_to a spinal cord.
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]
A presumptive structure that has the potential to develop into a ganglion.
An anatomical cavity that has the potential to develop into a coelemic cavity lumen.
(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]
The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom
consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults
Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers
An epithelium that lines the lumen of the digestive tract.
Epithelium lining the lumen of the gut.[TAO]
A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.
Not to be confused with 'dermatome segment of skin'.
As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]
The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells
The layer of undifferentiated, proliferating cells that line the neural tube lumen
The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium
consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure
The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer.
The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter
Any tube, opening or passage that connects two distinct anatomical spaces.
FMA has both conduit and conduit space. In EHDAA2 this is a surface feature
An anatomical structure that develops (entirely or partially) from the endoderm.
An anatomical structure that develops (entirely or partially) from the mesoderm.
An anatomical structure that develops (entirely or partially) from the ectoderm.
(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]
TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO
The first recognizable structure derived from the heart field
A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.
this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]
An epithelial tube that will give rise to the mature heart.
the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube.
A cardiac chamber surrounds an enclosed cavity within the heart
generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768].
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]
Portion of somites that gives rise to dermis and muscles.[AAO]
The bilaminar epithelium formed from the myotome and dermatome.
Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]
all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis.
A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.
The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]
In human anatomy, the distal phalanges of the four fingers and toes articulate proximally with the intermediate phalanges at the distal interphalangeal joints (DIP); in the thumb and big toe, with only two phalanges, the distal phalanges articulate proximally with the proximal phalanges. The distal phalanges carry and shape nails and claws and are therefore occasionally referred to as the ungual phalanges. The distal phalanges are cone-shaped in most mammals, including most primates, but relatively wide and flat in humans.
A phalanx located between proximal and distal phalanges.
Intermediate phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones of the finger and toe which lie in the middle, between the two wrinkly joints. The thumb and big toe do not have intermediate phalanges. In most other vertebrates, they have a corresponding place in their limbs, whether they be paw, wing, hoof or fin
consider using numbering system, and axioms to the effect that there is a single middle phalanx per finger in humans. This should perhaps be renamed 'intermediate phalanx', leaving the term middle phalanx open for the specific intermediate phalanx of a 3-phalanx digit
in some groups such as whales, there are multiple intermediate phalanges
Proximal phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones at the base of a toe or finger, the prominent, knobby ends of which are often called the knuckles. In other vertebrates, proximal phalanges have a similar placement in the corresponding limbs, be they paw, wing or fin. In many species, they are the longest and thickest phalanx ('finger' bone)
An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
Early outgrowth of presumptive limb.[AAO]
developmentally_induced_by Fgf10, capable of initiating limb forming interactions between endoderm and mesoderm
Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO]
Proliferative region that is part of the developing fin fold or fin.[TAO]
The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold
maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop
multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP].
note that media, dorsal fins etc have AERs.
relationship loss: subclass proliferative region (TAO:0000098)[TAO]
An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056]
The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG]
A bone that is part of an appendage [Automatically generated definition].
bone of free segment of appendicular skeleton
EHDAA2 considers hip and shoulder joints part of limb skeleton.
Skeletal subdivision that is part of the limb.[VSAO]
The collection of all skeletal elements in an individual limb.
Sum of all sensory systems in an organism.
A projection or outgrowth of tissue from a larger body or organ.
Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO]
Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO]
Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO]
should be declared disjoint from organ, but in some ontologies (e.g. ZFA), structures such as neural spines are classified as bones (and hence organs)
Anatomical system that has as its parts the heart and blood vessels.
The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]
we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.
A vascular network consisting of blood vessels.
An appendage that is part of a appendage girdle complex.
this class is the union of the classes limb, pectoral fin and pelvic fin.
EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus
The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].
Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres.
revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)
An organ subunit that is part of a hindbrain [Automatically generated definition].
We explicitly merge the NCITA terms here
A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]
Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
Anatomical system that consists of all the joints of the body.
splanchnic layer of lateral plate mesoderm
Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].
We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors
Notochord rudiment[ZFIN:ZDB-PUB-961014-576].
The central region of trunk mesoderm. This tissue forms the notochord
WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord.
Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts.
A proximal-distal subdivision of the digestive tract.
intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
A part of a wall of an organ that forms a layer.
The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.
The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove].
In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold].
One of the two elevated edges of the neural groove[GO,MP].
A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].
An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]
An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]
With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates.
consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness
in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous.
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila
A bud is a protrusion that forms from an epithelial sheet by localized folding.
An epithelial sheet bent on a linear axis.
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'
An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.
An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
Mesenchyme that is part of a developing trunk.
The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]
The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP].
the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes
A portion of tissue that is part of an embryo.
alimentary part of gastrointestinal system
All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG]
The part of the digestive system that excludes the hepatobiliary system.
The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System].
that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla.
the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system
After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm.
Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998). Editor note: todo - epidermis? todo - track down EHDAA2 class in new release
In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG]
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum.
A sensory system that is capable of olfacttion (the sensory perception of smell).
In mammals, the main olfactory system detects odorants that are inhaled through the nose, where they contact the main olfactory epithelium, which contains various olfactory receptors. These olfactory receptors are membrane proteins of bipolar olfactory receptor neurons in the olfactory epithelium. Rather than binding specific ligands like most receptors, olfactory receptors display affinity for a range of odor molecules. Olfactory neurons transduce receptor activation into electrical signals in neurons. The signals travel along the olfactory nerve, which belongs to the peripheral nervous system. This nerve terminates in the olfactory bulb, which belongs to the central nervous system. The complex set of olfactory receptors on different olfactory neurons can distinguish a new odor from the background environmental odors and determine the concentration of the odor[WP].
The olfactory system is the sensory system used for olfaction, or the sense of smell. Most mammals and reptiles have two distinct parts to their olfactory system: a main olfactory system and an accessory olfactory system. The main olfactory system detects volatile, airborne substances, while the accessory olfactory system senses fluid-phase stimuli. Behavioral evidence indicates that most often, the stimuli detected by the accessory olfactory system are pheromones. The olfactory system is often spoken of along with the gustatory system as the chemosensory senses because both transduce chemical signals into perception[WP][Wikipedia:Olfactory_system].
The sensory system used for olfaction (the sense of smell).[AAO]
consider splitting into main and accessory. See also: vomeronasal organ
we make the relationship to nervous system 'overlaps', as the olfactory system includes e.g. apertures in the cranium that are not part of the nervous system
A limb/fin field that has_potential_to_developmentally_contribute_to a paired fin bud.
A ring of cells capable of forming a limb or paired fin[Gilbert,modified].
limb/fin field of lateral plate mesoderm
we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this.
A ring of cells capable of forming a limb.
the central portion of the limb field gives rise to the limb proper. mesenchyme cells proliferate from from the somatic layer of limb field lateral plate mesoderm (limb skeletal precursors) and from the somites (limb muscle precursors) . these mesenchymal cells accumulate under the ectedermal tissue to make a limb bud. // The lateral plate mesoderm in the limb field is also special in that it will induce myoblasts to migrate out from the somites and enter the limb bud. No other region of the lateral plate mesoderm will do that (Hayashi and Ozawa 1995)
A acellular anatomical structure that is the bounding layer of a anatomical structure.
An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.
this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell.
A delimited region of dense mesenchyme within looser mesenchyme.
Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes.
isa cell condensation in VSAO; has_part chondroblast in AEO
A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage.
A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts.
A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis.
encompasses digits and prepollex. requires review
Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]
Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]
Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers.
add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis.
the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678]
The interface between the dorsal neuroepithelium and the roofplate of the fourth ventricle. The source of a number of migratory neuron populations of the hindbrain.[TAO]
dorsal part of alar plate of metencephalon
the posterior section of the developing metencephalon recognized transiently within the vertebrate embryo; the rhombic lip extends posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cell and can be divided into eight structural units based on rhombomeres 1-8 (r1-r8), recognized at early stages of hindbrain development; producing granule cells and five brainstem nuclei, the rhombic lip plays an important role in developing a complex cerebellar neural system
The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)
A presumptive structure that has the potential to develop into a forebrain.
TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate)
TODO - check ordering; awaiting confirmation from JB
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]
A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot
The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus.
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
currently this is an extremely generic class, encompassing both protostomes and deuterostomes.
Presumptive structure of the blastula that will develop into endoderm.
Portion of embryonic tissue determined by fate mapping to become a structure.
Presumptive structure of the blastula that will develop into ectoderm.
Presumptive structure of the blastula that will develop into mesoderm.
A joint that connects one phalanx to another along a proximodistal axis.
Hinge joints between the phalanges of the hand or foot[ncithesaurus:Interphalangeal_Joint].
The third segment of the limb, including either the wrist segment (carpus) or the ankle segment (tarsus)
Distal section of the limb skeleton, consisting of the anterior autopodium or posterior autopodium.[VSAO]
The collection of all skeletal elements in an autopodium region.
An epithelium characterised by its most superficial layer consisting of squamous epithelial cells.
FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium
The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA].
A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n
Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism.
The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO].
consider FBbt:00005541 ! cardiogenic mesoderm
The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]
The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR].
The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure.
Embryonic structure that gives rise to the midbrain hindbrain boundary.
A presumptive structure that has the potential to develop into a presomitic mesoderm.
A presumptive structure that has the potential to develop into a neural plate.
Region of the gastrula which gives rise to the neural plate.[TAO]
A presumptive structure that has the potential to develop into a paraxial mesoderm.
The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO].
this grouping class exists primarily to align with GO - see GO:0008544.
Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network.
Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Le Guellec et al, 2004.[TAO]
connective tissue in the skin is usually diffuse and irregular, although in some species collagen bundles are arranged in a distinct ordered layer in the dermis
relationship loss: develops_from collagenous dermal stroma (TAO:0001186)[TAO]
Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm.
Outermost layer of cells surrounding the embryo.
Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]
relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]
An epithelial tube open at both ends that allows fluid flow.
Mesenchyme with little extracellular matrix.
this class will be an important part of the NC reorganization
A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO].
An anatomical cavity that surrounded_by a synovial joint.
cavitas articularis (junctura synovialis)
An anatomical structure that connects two structures
Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.
the FMA def is Transudate contained in a serous sac
Anatomical system that consists of all blood and lymph vessels.
The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System].
in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system
The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]
Skeletal element that is composed of cartilage tissue and may be permanent or transient.
Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue.
the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification).
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]
Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]
dense regular collagenous connective tissue
typus regularis (textus connectivus collagenosus compactus)
An external projection of an aquatic animal as a fish used in propelling or guiding the body[BTO].
Surface structure involved in locomotion.[TAO]
Surface structure involved in locomotion.[VSAO]
This class groups together various structures that may have arisen through convergent evolution, including, for example, the dorsal fin of a cetacean
consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)
A segment of a digit containing the distal phalanx, and overlapping the distal interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium).
Newborn and adult mice are able to regrow forelimb (finger) and hindlimb (toe) digit tips after their amputation through the distal interphalangeal joint. Regeneration of the digit tip involves the integrated regrowth of multiple tissues within 2-3 months, reaching an external morphology that is cosmetically and functionally similar to normal digits. Most importantly, regeneration of the mouse distal digit shares morphological similarities with clinical cases documenting regrowth of missing distal portions of fingers in both children and adults
midbrain hindbrain boundary neural plate
TODO - developmental relationships for lines
midbrain-hindbrain boundary neural plate
A presumptive structure that has the potential to develop into a midbrain.
The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells.
An inter-phalangeal joint that connects a distal phalanx to either a medial or proximal phalanx.
The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form.
Intermediate segment of the autopod, between the mesopodial region and and acropodial region. Examples: metacarpal region, metatarsal region
Limb skeleton subdivision consisting of endochondral bones increasing the freedom of movement of the autopodia, and located between zeugopodia and autopodia.[VSAO]
The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia.
Includes: trigeminal, otic, lateral line and epibranchial placodes.
While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000)
An anatomical structure that has more than one cell as a part.
A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function.
Mesenchyme that has the potential to develop into a dermis.
A developing anatomical structure that has the potential to develop into a metencephalon.
A developing anatomical structure that has the potential to develop into a myelencephalon.
The distal elements of the developing limb of vertebrates that will give rise to the pedal appendages (e.g. manus, pes, paw)
Portion of tissue that is dorsolateral to the floor plate and part of the midbrain.
Portion of neural tube that gives rise to the midbrain.
we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed
structure with developmental contribution from neural crest
An anatomical structure that has some part that develops from the neural crest.
A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification.
Epithelium composed of cells that develops from the ectoderm[FMA,modified].
An appendage segment that is part of a limb/fin.
The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the autopodium - i.e. the bones of the digits or their cartilaginous precursors[VSAO,modified].
Endochondral bone complex located between the mesopodium and the acropodium and consisting of the metacarpals or metatarsals.[VSAO]
Subdivision of skeleton that corresponds to metapodium region, between acropodial skeleton and mesopdoial skeleton.
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
An organism subdivision that includes both an appendage and its accociated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]
It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]
note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region)
Skeletal subdivision that is a segment of the limb skeleton.
note the distinction between this and skeleton of limb
Skeletal system that consists of the paired fins (pectoral or pelvic fins).[VSAO]
The collection of all skeletal elements in a single paired fin.
Skeletal subdivision that is part of the appendage girdle region.[VSAO]
The subdivision of the skeleton of either the pectoral or pelvic girdle.
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle).
subdivision of organism along appendicular axis
A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg.
A skeletal element that is part of a limb and composed of cartilage tissue.
A skeletal element that is part of a limb and composed of pre-cartilage tissue.
Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints.
Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]
Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis.
Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.
Subdivision of the skeletal system which consists of the post-cranial axial skeleton plus associated joints.
Any synovial joint that is part of a (free) limb.
central nervous system cell part cluster
A multi cell part structure that is part of a central nervous system.
Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]
Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints.
A bone that is part of a autopod region. Note that this incudes the carpal and tarsal bones.
compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm'
Skeletal subdivision that is part of the paired limb/fin.[VSAO]
The collection of all skeletal elements in an individual limb or fin.
Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified].
Proximal element of the limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively.[VSAO]
Section of the forelimb skeleton located between the stylopodium and the autopodium.
Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).
consider obsoleting, coordinate with VSAO
subdivision of organism along main body axis
A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.
Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem
A cardiovascular system that is part of a conceptus.
Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium.
Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium.
Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]
typus irregularis (textus connectivus collagenosus compactus)
Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]
Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets
our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid.
Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue.
An acinus that is part of a exocrine gland.
the FMA class specifically refers to ureter
Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous.
The Epimysium also protects muscles from friction against other muscles and bones
EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining.
The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.
A segment of the autopod consisting of both acropodial region and metapodial region, but excluding the mesopodial/basopodial region.
some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod
A subdivision of the autopod skeleton consisting of both acropodial skeleon and metapodial skeleton, but excluding the mesopodial/basopodial skeleton.
Epithelium that derives from the mesoderm. [Automatically generated definition].
Skeletal subdivision consisting of all the skeletal elements in a single fin.
The segment of the autopod that is distal to the metapodial region and consists of the digits.
class refers to an entire limb segment, not just the bones
A bone that is part of a the digitopodium skeleton - i.e. the acropodial skeleton or the metapodial skeleton.
The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells.
An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].
A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424].
The region of the organism associated with the visceral organs.
Anatomical projection that is part of the integumentl system.
A organ component layer that is part of a integumental system.
Embryonic structure that gives rise to the telencephalon.
paired anteriolateral division of the embryonic prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived[MP]
Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.
A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles).
A portion of tissue that will develop into vasculature.
A phalanx bone or its cartilage or pre-cartilage precursor.
A limb bone or its cartilage or pre-cartilage precursor.
A endochondral element that is part of a autopod region.
A autopod endochondral element that is composed primarily of a cartilage tissue.
Any structure that is placed on one side of the left-right axis of a bilaterian.
This class is primarily to implement taxon constraints. It may be removed in the future.
A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
Primordium that develops into the central nervous system
Primordium that develops into the nervous system
The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.
An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development.
A mesenchyme-derived anatomical entity undergoing a transtion to become another structure.
Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104
An embryonic or larval epithelium that is committed to form part of the nervous system.
An epithelium that is undergoing proliferation to provide large numbers of neuronal cells.
A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.
Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain
A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology.
Any substance in the body or expelled from the body that is in a gaseous state.
Any portion of gas located in a part of the respiratory system that is composed primarily of air.
An multicellular anatomical structure that has subparts of multiple organs as a part.
A cluster of cells, largely surrounded by a morphological boundary.
A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected
A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures.
organ region with floating fiat boundary
Any portion of gas located in a part of the respiratory system.
The primordial mouth region of the developing head.
Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes.
This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument.
This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
A subdivision of the autopod consisting of digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis.
digit ( phalanges plus metapodial) plus soft tissue
this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit.
individual digit of digitopodial skeleton
A subdivision of the skeleton of the autopod consisting of the phalanges of a single digit plus the associated metapodial element.
this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials.
'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.
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.
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.
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.
a medical intervention that involves in adding vaccine into a host (e.g., human, mouse) in vivo with the intent to invoke an adaptive immune response.
Product Name: Haemophilus b Conjugate Vaccine (Tetanus Toxoid Conjugate)
Product Name: Tetanus Toxoid, Reduced Diphtheria Toxoid and Acellular Pertussis Vaccine, Adsorbed
WEB: http://www.cdc.gov/vaccines/pubs/pinkbook/downloads/appendices/B/excipient-table-2.pdf
A vaccine that protects against Bacillus anthrax that causes anthrax.
Product Name: Haemophilus b Conjugate Vaccine (Meningococcal Protein Conjugate) & Hepatitis B Vaccine (Recombinant)
Product Name: Diphtheria & Tetanus Toxoids & Acellular Pertussis Vaccine Adsorbed
Vaccine components see http://www.vaccinesafety.edu/components-DTaP.htm
Product Name: Tetanus & Diphtheria Toxoids Adsorbed for Adult Use
MenHibrix
a vaccine for active immunization to prevent invasive disease caused by Neisseria meningitidis serogroups C and Y and Haemophilus influenzae type b. MENHIBRIX is approved for use in children 6 weeks of age through 18 months of age.
Diphtheria and Tetanus Toxoids Adsorbed USP by Sanofi Pasteur Inc
Product Name: Diphtheria & Tetanus Toxoids Adsorbed
Diphtheria and Tetanus Toxoids Adsorbed by Sanofi Pasteur Ltd
A viral vaccine that protects against infection of an adenovirus.
Product Name: Influenza Virus Vaccine, Trivalent, Types A and B
Product Name: Influenza Virus Vaccine, Live, Intranasal
Product Name: Human Papillomavirus (Types 6, 11, 16, 18) Recombinant Vaccine
Product Name: Hepatitis A Vaccine, Inactivated
A bacterial vaccine that prevents Neisseria meningitidis infection.
Product Name: Poliovirus Vaccine Inactivated (Monkey Kidney Cell)
Influenza Virus Vaccine H5N1 (Sanofi Pasteur Inc)
Product Name: Influenza Virus Vaccine, H5N1 (for National Stockpile)
WEB: http://atomicnewsreview.org/2009/10/22/approval-for-the-arepanrix%E2%84%A2-gsk-vaccine-in-canada/
Product Name: Japanese Encephalitis Virus Vaccine Inactivated
Product Name: Diphtheria and Tetanus Toxoids and Acellular Pertussis Adsorbed and Inactivated Poliovirus Vaccine
Product Name: Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugate Vaccine
WEB: http://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm176044.htm
Meningococcal Polysaccharide (Serogroups A, C, Y and W-135) Diphtheria Toxoid Conjugate Vaccine
Product Name: Rubella Virus Vaccine Live
Fluzone High-dose
an influenza vaccine that is similar to Fluzone but has high dose.
Product Name: Diphtheria & Tetanus Toxoids & Acellular Pertussis Vaccine Adsorbed, Hepatitis B (recombinant) and Inactivated Poliovirus Vaccine Combined
Product Name: Haemophilus b Conjugate Vaccine (Meningococcal Protein Conjugate)
Product Name: Diphtheria and Tetanus Toxoids and Acellular Pertussis Adsorbed, Inactivated Poliovirus and Haemophilus b Conjugate (Tetanus Toxoid Conjugate) Vaccine
Product Name: Pneumococcal Vaccine, Polyvalent
Product Name: Pneumococcal 7-valent Conjugate Vaccine (Diphtheria CRM197 Protein)
Product Name: Measles, Mumps, Rubella and Varicella Virus Vaccine Live
A Measles-Mumps-Rubella-Vericella vaccine that is live and manufactured by Merck & Co, Inc.
WEB: http://www.merck.com/product/usa/pi_circulars/p/proquad/proquad_pi.pdf
Fluzone intradermal
a vaccine adjuvant that is formed as a mineral salt.
Adenovirus Type 4 and Type 7 Vaccine, Live, Oral
Product Name: Rotavirus Vaccine, Live, Oral, Pentavalent
Product Name: Typhoid Vi Polysaccharide Vaccine
Tetanus and Diphtheria Toxoids Adsorbed by MA Biologic Lab
Product Name: Hepatitis A Inactivated and Hepatitis B (Recombinant) Vaccine
Product Name: Varicella Virus Vaccine Live
Product Name: Typhoid Vaccine Live Oral Ty21a
A viral vaccine that protects against infection with Yellow fever virus.
Product Name: Zoster Vaccine, Live, (Oka/Merck)
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.
A vaccine that targets against a bacterial disease.
a virulence of vaccine organism that shows an attenuated pheontype of the organism as the major component of a vaccine.
a processed material that is output of the vaccine preparation and part of a vaccine.
USA licensed human vaccine role
a USA licensed vaccine role that inheres ina vaccine approven to be by the US FDA to be used for humans in the USA.
A vaccine contraindication is a contraindication that increases the risks of a vaccination.
an organismal quality of a whole organism vaccine where the whole organism is inactivated/killed and lacks the capability of replication.
pgp.LAMP-1 DNA vaccine plasmid
A DNA vaccine plasmid vector that has the plasmid label pgp.LAMP-1. This plasmid has a CMV promoter and contains the human lysosomal-associated membrane protein-1 signal sequence.
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.
a medical intervention site that is used for injection of a substance.
a route of administration that inject the material(such as vaccines, allergens) directly into a muscle.
rounte of administration that located in nose.
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.
a Varicella-zoster virus vaccine that is live attenuated.
a vaccine component that originates from an organism such as a pathogen or a modified organism.
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.
WEB: http://en.wikipedia.org/wiki/Vaccinia
a Smallpox virus vaccine that uses vaccinia virus
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.
a vaccine component that is composed of a plasmid and used in the generation of a DNA vaccine.
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.
protein of pathogen organism as vaccine component
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.
licensed human vaccine role
a licensed vaccine role that is bears in a licensed human vaccine.
WEB: http://en.wikipedia.org/wiki/Immunization
immunization is a processual entity that primes or modifies an adaptivie immune response to some antigens.
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.
artificial active immunization is an active immunization that occurs when a person or animal is vaccinated with a specific vaccine.
induction of adaptive immune response to antigen
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 is a processual entity that prevents a disorder that is the physical basis of a disease.
disorder treatment is a processual entity that leads to treat a disorder that is the physical basis of a disease.
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.
Pox vaccine
a viral vaccine against a disease caused by a virus belong to Poxviridae.
a route of administration that is loacted in the hypodermis (subcutaneous tissue) region.
a population of human beings who are vaccinated.
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.
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
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.
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.
immunization objective is the specification of an objective to achieve immunization.
vaccine preparation is a manufacturing process to produce a vaccine.
Canada licensed human vaccine role
a Canada licensed vaccine role that indicates the vaccine is used for human
A vaccine that targets against a viral disease.
vaccine role
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.
conjugate vaccine role
a vaccine role that indicates the vaccine being a conjugate vaccine.
licensed vaccine role is a regulation-assigned role that indicates that a vaccine obtains official approval for commercial production and selling on the market.
A bacterial vaccine that protects against infection with Clostridium spp.
a Clostridium vaccine that protects against infection with Clostridium tetani that causes tenanus.
A viral vaccine that protects against infection with influenza virus.
A viral vaccine that protects against infection with Hepatitis B virus.
A viral vaccine that protects against infection with Hepatitis A virus.
A viral vaccine that protects against infection with Rabies virus.
A viral vaccine that protects against infection with Smallpox virus.
A viral vaccine that protects against infection with Measles virus.
A viral vaccine that protects against infection with Rotavirus.
A bacterial vaccine that protects against infection with Haemophilus.
Haemophilus influenzae serotype b vaccine
A viral vaccine that protects against infection with Poliovirus.
A viral vaccine that protects against infection with Japanese encephalitis virus.
a vaccine against human papillomavirus infection
a Herpesvirus vaccine that is used against Varicella-zoster virus infection.
a Salmonella vaccine against typhoid fever (or called typoid), caused by Salmonella enterica enterica, serovar Typhi.
a Streptococcal vaccine that is used against S. pneumoniae infection, which causes pneumococcal diseases.
A viral vaccine that protects against infection with Herpesvirus.
A Measles-Mumps vaccine that also protects against infection with Rubella virus.
A Corynebacterium diphtheriae vaccine that also protect against infection with Clostridium tetani.
A bacterial vaccine that protects against infection with Corynebacterium diphtheriae that causes Diphtheria.
A Measles virus vaccine that also protects against infection with Mumps virus.
A Measles-Mumps-Rubella vaccine that also protects against Vericella.
Diphtheria-Tetanus-Pertussis-Poliovirus vaccine
Diphtheria-Tetanus-Pertussis-Poliovirus-Hepatitis B vaccine
Diphtheria-Tetanus-Pertussis-Poliovirus-Haemophilus b vaccine
a viral vaccine against Hepatitis B virus and at the same time against bacterial H. influenzae serotype b.
A viral vaccine that protects against infection with Papillomavirus.
A bacterial vaccine that protects against infections by various Salmonella species.
A bacterial vaccine that prevents streptococcal infections.
a licensed vaccine role that indicates the vaccine occurs in USA.
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.
Finn TM and Egan W, in Vaccines fifth edition, 2008. Page 73.
Although no all manufacturing residuals may be identified and quantified, their presence and quantity is assumed to be constant because of the constancy of the manufacturing process.
a vaccine component that remains from the vaccine manufacturing process.
a vaccine residual that is generatead from cell culture for vaccine preparation. Examples include: antibiotics, sensitizing substances, bacterial and cellular residuals, and adventitious agents.
Finn TM and Egan W, in Vaccines fifth edition, 2008. Page 78-81.
a licensed status that occurs in Canada.
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.
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.)
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.
a route of administration that located in the mouth
a route of administration that inject the material(such as vaccines, allergens) into the skin itself.
Age at vaccination is the age of an experiment animal at the time of vaccination.
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.
chicken egg protein allergen is a vaccine allergen that is composed of chicken egg protein.
bovine albumin cell culture residual in vaccine
a cell culture residual in vaccine that is bovine albumin.
vaccine residual protein from cell culture
a cell culture residual in vaccine that is residual protein from cell culture.
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.
yeast protein cell culture residual in vaccine
a cell culture residual in vaccine that is yeast protein.
pBLUESCRIPT DNA vaccine plasmid
Davidson College - pBLUESCRIPT: Plasmids and Phages Combine For pBluescript [http://www.bio.davidson.edu/Courses/Molbio/MolStudents/spring2003/Keogh/plasmids.html]
Derived from pUC vectors; cross between phages and plasmids and therefore in a special category called "phagemids" (Davidson College - pBLUESCRIPT)
A DNA vaccine plasmid vector that has the plasmid label pBLUESCRIPT.
nkCMVint DNA vaccine plasmid
A DNA vaccine plasmid vector that has the plasmid label nkCMVint.
A pUC-18-based plasmid; also contains intron A and an SV40 polyadenylation termination signal sequence. It has a CMV promoter.
Flublok
Flucelvax
FluMist Quadrivalent
Tetanus Toxoid (for Boost use Only) by Sanofi Pasteur Inc
a tetanus vaccine manusfactured by Sanofi Pasteur Inc. that is only for booster use (not recommended for primary immunization)
viral vaccine organism live attenuated
a live attenuated quality of a virus vaccine strain.
vaccine viability is a viability of a vaccine organism.
a vaccination that occurs in the intramuscular route.
capsular polysaccharide of pathogen organism as vaccine component
polysaccharide of pathogen organism as vaccine component
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).
A vaccine aduvant that contains synthetic material.
an organism that is vaccinated with a vaccine
The objective that intends to produce vaccine via the vaccine preparation process.
vaccination process that occurs in intradermal route.
vaccination process that occurs in oral route.
vaccination process that occurs in the subcutaneous route
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.
a vaccine stabilizer that is specifically made by a sugar.
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.
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
epicutaneous (application onto the skin), e
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.
A viral vaccine that protects against infection with Rubella virus.
Product Name: Hepatitis B Vaccine (Recombinant)
A vaccine that protects against Haemophilus influenzae.
*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.
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)'.
Nose[accessedResource: FMAID:46472][accessDate: 05-04-2011]
chemosensory sensory organ[accessedResource: FBbt:00005157][accessDate: 05-04-2011]
olfactory system[accessedResource: TAO:0001149][accessDate: 05-04-2011]
ready for release
pending final vetting
axiom holds for all times
GlaxoSmithKline Biologicals
Massachusetts Public Health Biologic Lab
Research Foundation for Microbial Diseases of Osaka University
Vical, Inc.
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.
see is_input_of example_of_usage
has_specified_output